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Tropomyosin-related kinase-B, human

Tropomyosin-related kinase B (TrkB) is a receptor tyrosine kinase that binds to the neurotrophic factor brain-derived neurotrophic factor (BDNF).
TrkB plays a crucial role in neuronal survival, differentiation, and synaptic plasticity.
It is expressed in the central and peripheral nervous systems and is involved in processes such as learning, memory, and neurogenesis.
Dysregulation of the TrkB signaling pathway has been implicated in various neurological and psychiatric disorders, including Alzheimer's disease, Parkinson's disease, depression, and anxiety.
Understanding the complex mechanisms of TrkB function is essential for developing targeted therapies for these conditions.

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A formal proposal to form a working group that would create a resource for undergraduate medical education was approved by the Association of Pathology Chairs Undergraduate Medical Education Section (UMEDS) Council. One goal of the project was to help medical students understand basic principles of laboratory testing to improve decision making and patient safety. Another goal was to create a useful resource that would allow medical educators to readily incorporate basic laboratory test information into their curricula. The project planned to link common laboratory tests to the third competency of the PCME, and to highlight pathophysiology and clinical pearls of those common laboratory tests.
A question regarding the teaching of laboratory values was posed on the UMEDS listserv July 7, 2020. As the question generated much discussion on this topic, a formal working group was presented to and approved by the UMEDS Council on August 24, 2020. A template for pathophysiology and clinical pearls was created with examples, and the initial laboratory list included approximately 250 laboratory tests generated from a survey of the Mayo Clinic Laboratory testing website.5 Follow up emails were sent to UMEDS members who had expressed interest in participating in the project in October 2020. Additional tests were added to the list based on the recommendations from UMEDS members. Once working group members had submitted their contributions for each laboratory test, clinical pathology editors and clinical colleagues were identified to review the submissions and recommend changes. Laboratory tests were correlated with the PCME, and revisions condensed the current laboratory test list to 181 common laboratory tests. The table was edited to create a uniform product with similar style and content depth for all entries. Table 1 includes the laboratory tests of the ELTME.

Essential laboratory tests.

Table 1
TestPCMEReference valuesPathophysiologyClinical PearlsReferences 5 , 6 , 7 , 8 , 9 , 10 are used when not otherwise specified.Organ system/Panel
25-Hydroxyvitamin D2 and D3, serumCHEM 1.420–50 ng/mL (optimal)When UVB strikes the epidermis, 7-dehydrocholesterol is converted into previtamin D3, which is next converted into vitamin D3 (cholecalciferol). In the liver, vitamin D3 is hydroxylated to form 25-hydroxyvitamin-D3. In the kidney, it is finally converted into the biologically active form: 1,25-dihydroxyvitamin-D3. Initial laboratory assessment for vitamin D status analyzes levels of 25-hydroxyvitamin-D3, not the biologically active form; testing for 1,25-dihydroxyvitamin D may be indicated in the setting of renal disease. Vitamin D promotes calcium absorption in the gut and helps maintain normal serum calcium and phosphate. Vitamin D can be obtained by sunlight, diet, or supplements.In children, vitamin D deficiency is associated with rickets, osteomalacia, muscle pain/weakness and tetany (due to hypocalcemia). In adults with vitamin D deficiency, risk of osteoporosis, osteomalacia and fracture is increased. Vitamin D deficiency is common, particularly with decreasing sun exposure. Clinical interpretation of vitamin D nutritional status typically uses total 25-hydroxyvitamin D levels, although some analytical methods can separately determine 25-hydroxyvitamin D2 and D3.Skeletal
ABO type, bloodTM1.1A, B, AB, OThe ABO system is essential in transfusion medicine and encompasses the four common blood types: A, B, AB, and O. The A and B codominant alleles encode homologous enzymes forming their respective defining terminal sugar after the first few months of life. Absence of A and B antigens leads to O blood type, the precursor antigen for which is the H system.The majority of the world's population are of blood type O. “universal donor” O red blood cells (RBCs) lacking A and B antigens are used in emergent transfusions when the blood type is unknown. Antibodies to A antigen (anti-A) and/or B antigen (anti-B) are naturally occurring and cause severe acute hemolytic transfusion reactions: Anti-A will lyse type A or AB cells, while anti-B will lyse type B or AB cells. Subgroups of B and especially A antigen are evaluated prior to solid organ transplantation.Transfusion
Acetaminophen, serumCHEM 1.710-25 μg/mLaAcetaminophen (N-acetyl-p-aminophenol or APAP) is used to relieve pain and reduce fever. It is processed in the liver, predominantly to sulfate and glucuronide. A smaller portion is metabolized by several cytochrome P-450 isoforms (most notably CYP2E1), which convert APAP to the reactive, toxic metabolite N-acetyl-p-benzoquinone imine (NAPQI). Normally, NAPQI is detoxified through glutathione conjugation and subsequently excreted in urine. When supratherapeutic doses are ingested, glutathione becomes depleted and excess NAPQI forms protein adducts, which initiate oxidative stress pathways, ultimately resulting in mitochondrial dysfunction and hepatocellular damage.Acetaminophen is rapidly absorbed from the gastrointestinal tract; the utility of serum measurements is dependent on the pharmacokinetics of immediate versus extended-release formulations. Peak serum concentrations are detectable as early as 1–2 h after ingestion (immediate release) or greater than 4 h after ingestion (extended release). Management of acetaminophen overdoses includes oral or IV N-acetylcysteine (NAC), which functions as a glutathione substitute and binds directly to NAPQI. Acetaminophen is a component of many medications which contributes to the risk of accidental overdose. In the United States, acetaminophen toxicity accounts for about 50% of cases of acute liver failure. Serum acetaminophen concentrations and estimated time of ingestion are used in decisions on antidote treatment.11 Toxicology
Acetylcholine (ACh) receptor antibodies, serumIMM 1.4≤0.02 nmol/L (binding antibodies)Negative (modulating antibodies)The ACh receptor (AChR) is found on the surface of muscle cells at the neuromuscular junction. AChR autoantibodies are found in ˜85% of patients with generalized and ˜50% with ocular myasthenia gravis (MG). MG is an autoimmune disorder characterized by skeletal muscle weakness and increased fatigability. Autoantibodies to AChR are classified as binding, blocking, or modulating. Binding antibodies cause complement activation that destroys the AChR. Blocking antibodies prevent the binding of ACh. Modulating antibodies crosslink the receptor subunits, resulting in internalization.AChR binding antibody titer does not necessarily correlate with disease severity, but changes in titer can be useful in monitoring response to treatment in individual patients. A negative result does not rule out the diagnosis of MG: 30 to 40% of patients with MG who are negative for AChR antibodies express a muscle-specific kinase (MuSK) autoantibody. False positives may occur in the setting of thymoma (without MG), Lambert-Eaton myasthenic syndrome, small cell lung carcinoma and penicillamine treatment.12 (link)Nervous
Activated partial thromboplastin time (aPTT), plasmaH 2.125–37 saPTT assesses the coagulation factors of the intrinsic (factors XII, XI, IX, and VIII) and the common (factors X, V, II, and fibrinogen) pathway. The test is performed by measuring time to clot formation when a surface activator, phospholipids, and calcium are added to the patient's platelet-poor plasma.Deficiency of any of the assessed factors can cause elevations of aPTT. When both PT and aPTT are elevated, the deficiency is in the common pathway. A prolonged aPTT should be interpreted in the context of a concurrent PT to determine whether the deficiency is in the intrinsic pathway or in the common pathway. A mixing study may be performed to distinguish a factor deficiency from inhibition. Heparin and antiphospholipid antibodies (lupus anticoagulant) cause isolated aPTT elevation. For most aPTT reagents, the factor VIII activity must be below 35–45% before changes in aPTT are noted. Since aPTT is a clot-based assay, anticoagulation therapy can result in elevated aPTT.Coagulation
Activated protein C (aPC) resistance, plasmaH 2.1Ratio ≥2.3Protein C is a vitamin K-dependent clotting factor synthesized in the liver that is activated by thrombin. Activated PC inhibits coagulation by cleaving factors Va and VIIIa and by inactivating plasminogen activator inhibitor, leading to fibrinolysis. aPC also cleaves FV, which increases its anticoagulant activity. Resistance to aPC is most commonly seen in the context of the factor V Leiden (FVL) mutation in which an amino acid substitution removes the aPC cleavage site in both FV and FVa. The consequence is a prothrombotic state since the coagulant activity of FVa is not impeded and the anticoagulant activity of FV is not enhanced.The FVL mutation increases the risk of venous thromboembolism in both heterozygotes and homozygotes. This assay reports the ratio of the aPTT with and without additional of exogenous aPC and is highly sensitive and specific. Diagnosis can also be made by genetic testing which may be indicated in suspected familial thrombophilia or when the patient is anticoagulated.Coagulation
ADAMTS13 activity, plasmaH 2.1≥70%ADAMTS13 is a circulating metalloproteinase protease synthesized primarily by the liver. It cleaves ultra-large multimers of von Willebrand factor (vWF), thereby disrupting platelet aggregation. An IgG autoantibody to ADAMTS13 inhibits enzyme activity, preventing vWF cleavage and resulting in a prothrombotic state in thrombotic thrombocytopenic purpura (TTP). This assay reports ADAMTS13 activity as a percentage of the activity seen in wildtype individuals.TTP is characterized by thrombocytopenia, microangiopathic hemolytic anemia (intravascular hemolysis with schistocyte formation), fever, renal dysfunction and neurological deficits. It can be inherited or, more commonly, acquired. In the latter, ADAMTS13 activity is typically <10%. Decreased ADAMTS13 activity can also be seen in liver disease, sepsis, disseminated intravascular coagulation and pregnancy.Coagulation
Adrenocorticotropic hormone (ACTH), plasmaCHEM 1.37.2–63 pg/mL a.m. drawsCorticotropin releasing hormone (CRH) from the hypothalamus induces ACTH synthesis in the adenohypophysis. The main function of ACTH is to stimulate cortisol secretion by the adrenal gland. CRH release is circadian resulting in an ACTH peak between 6 and 8 a.m. and a trough around 11 p.m. CRH may also be released in response to stress and hypoglycemia. There is tight feedback control between the adrenal glands, pituitary gland, and hypothalamus to regulate the secretion of ACTH, arginine vasopressin and CRH. Measuring levels based on ACTH's diurnal secretory pattern may aid in determining ACTH-dependent Cushing disease.Elevated cortisol levels can be seen in Cushing disease (pituitary ACTH-secreting tumor), Cushing syndrome, ectopic ACTH-secreting tumor and adrenal hyperplasia. A dexamethasone suppression test can help distinguish Cushing disease from other causes of hypercortisolism. Important causes of hypocortisolism include primary and secondary adrenal insufficiency and congenital adrenal hyperplasia.Endocrine
Alanine aminotransferase (ALT; aka serum glutamate pyruvate transaminase), serumCHEM 1.4Males: 7–55 U/LFemales: 7–45 U/LALT is an enzyme normally present in the cytoplasm of hepatocytes. With plasma membrane injury, it is released and enters the blood. Low levels of ALT may be released with damage to the kidney and skeletal and cardiac muscle. ALT is more specific for the liver than aspartate aminotransferase (AST).Both ALT and AST levels increase in liver disease; however, ALT is more specific for liver injury and remains elevated longer than AST. Increases in ALT may precede symptom onset. In inflammatory conditions of the liver (e.g., acute viral hepatitis, autoimmune hepatitis), ALT levels are usually equal to or higher than the increase seen in AST, resulting in an ALT:AST ratio of more than 1. In the setting of excess alcohol use, AST is elevated to a greater extent than ALT, leading to an AST:ALT ratio of >2. In end-stage liver disease, both enzymes may be low due to massive tissue destruction.Hepatic/Comprehensive Medical Panel (CMP)
Albumin, serumCHEM 1.43.5–5 g/dLAlbumin is the predominant serum protein and is made in the liver. It is the main protein for maintaining whole blood oncotic pressure and can be decreased in liver disease, malabsorption, burns or due to loss in nephrotic syndrome.A low albumin may be indicative of poor prognosis in renal disease as it reflects a loss of renal filtering capability.CMP
Aldosterone, serumCHEM 1.3Adults: ≤21 ng/dLAldosterone is the main mineralocorticoid produced by the adrenal cortex. Aldosterone production and secretion are controlled through the renin-angiotensin-aldosterone system. Aldosterone stimulates sodium transport in the distal renal tubules and is a key regulator of blood pressure and blood volume.Conditions that increase aldosterone include adrenal adenoma, adrenal hyperplasia and excessive activation of the renin-angiotensin-aldosterone system (e.g., renin-producing tumor, renal artery stenosis). Aldosterone deficiency can be seen with low renin (such as in renal disease) or with high renin (from primary adrenal insufficiency).Endocrine
Alkaline phosphatase (AP), serumCHEM 1.4Varies with age and sex.Adult males: 40–129 U/LAdult females: 35–104 U/LAlkaline phosphatase is an enzyme from the cellular membrane. The major isoenzymes are liver, bone, and placental. The liver isoenzyme remains constant throughout life, the bone isoenzyme (from osteoblasts) is predominant in the growing years, and the placental isoenzyme rises during pregnancy, then falls off quickly after parturition. In non-pregnant adults, the liver isoenzyme is the predominant isoenzyme.Alkaline phosphatase is a sensitive marker for biliary disease or metastasis to the liver. The intestinal isoenzyme is usually a smaller fraction of the total, but in patients with blood types O or B, the level may be elevated after meals and account for up to 25% of the alkaline phosphatase level. The most common causes of elevated alkaline phosphatase are related to the liver (e.g., biliary obstruction, metastases, primary sclerosing cholangitis) and bone (e.g., Paget disease, hyperparathyroidism, metastases). Other causes of increased alkaline phosphatase include malignancies, chronic inflammatory conditions (e.g., sarcoidosis, ulcerative colitis) and sepsis.Hepatic, Skeletal, CMP
Alpha 1 antitrypsin (AAT), serumGE 2.1100–190 mg/dLThe alpha-1 antitrypsin (AAT) protein is produced by hepatocytes and inhibits neutrophil serine proteases, most notably neutrophil elastase. AAT deficiency is caused by AAT mutations that result in protein misfolding and accumulation in the liver, resulting in hepatocyte damage. Consequent low AAT levels in lung alveolar cells renders them vulnerable to destructive proteases, increasing risk for emphysema (panacinar), especially at an early age.Inherited forms (autosomal recessive, co-dominant) of AAT deficiency are thought to be underdiagnosed, with the most common clinically relevant form (PiZZ type, with loss of up to 90% serum AAT) estimated to affect 1 in 2500 to 1 in 5000 individuals in the US and Europe. AAT serum measurements and protease inhibitor (Pi) phenotyping are important parts of the diagnostic work-up for symptomatic patients. In addition, both gene-targeted testing (single and multigene panel) as well as comprehensive genomic testing are available for genotyping of S and Z alleles and rare pathogenic variants. Liver dysfunction can be seen in patients with certain allele combinations (e.g., PiMZ), and rare patients present with necrotizing panniculitis.13 (link),14 (link)Hepatic
Alpha-fetoprotein (AFP), serumCHEM 1.4, 1.8<8.4 ng/mLAFP is a glycoprotein synthesized during development by embryonic hepatocytes and fetal yolk sac cells. In the fetus, its function is analogous to that of albumin and it is the most abundant serum protein. Production drops after birth; however, it is produced by some tumors, especially germ cell tumors.AFP is elevated in acute liver injury and hepatocellular carcinoma (HCC). In acute liver injury modest increases (100–200 ng/dL) reflect regenerating hepatocytes. Serum AFP levels are increased in 70% of patients with HCC and can be used to monitor therapeutic response and recurrences; however, the test lacks sensitivity and specificity for diagnosis of early disease. AFP is also increased in germ cell tumors of the ovary and testis (e.g., yolk sac tumor, embryonal carcinoma), but is negative in pure seminoma and choriocarcinoma. AFP is elevated in maternal serum in the setting of open neural tube defects (e.g., anencephaly, spina bifida). Pregnant people are typically screened at 15–20 weeks gestation.Tumor marker, Neuro
Amylase, serumCHEM 1.428–100 U/LAmylase hydrolyzes complex carbohydrates and is primarily secreted by the salivary glands and the pancreas. Amylase is increased with gland inflammation or duct obstruction.Amylase is increased in acute pancreatitis, pancreatic pseudocyst, pancreatic duct obstruction (e.g., choledocholithiasis, pancreatic cancer). In acute pancreatitis, amylase levels increase rapidly (3–6 h of symptom onset) and remain elevated for about 5 days; lipase is currently the preferred test for the diagnosis of acute pancreatitis due to higher specificity. Amylase levels are decreased in pancreatic insufficiency and chronic pancreatitis. Other rarer sources of increased amylase include anorexia (due to salivary gland hyperplasia), small bowel injury, salpingitis or hepatitis among others.Pancreatic
Androstenedione, serumCHEM 1.3Varies with age, sex and sexual developmentAdult males: 40–150 ng/dLAdult females: 30–200 ng/dLAndrostenedione is a steroid hormone produced from cholesterol in the testes, adrenal cortex, and ovaries. Androstenedione production in the adrenal glands is controlled by the adrenocorticotropic hormone (ATCH), whereas in the gonad it is controlled by luteinizing hormone and follicle-stimulating hormone. Androstenedione is a precursor of testosterone.Androstenedione is increased in hirsutism, polycystic ovary syndrome (PCOS), virilizing adrenal tumors, precocious puberty, Cushing disease, ectopic ACTH-producing tumors and congenital adrenal hyperplasia. Androstenedione can be decreased in hyperlipidemia, psychosis, psoriasis, hypopituitarism, glucocorticoid treatment, and with increasing age.Endocrine
Anti-centromere antibody, serumIMM 1.2<1.0 UAnti-centromere antibodies arise when nuclear fragments, typically from apoptotic cells, are not effectively cleared, thereby eliciting autoantibodies. These antigens are not typically accessible to the immune system and, therefore, are recognized as non-self. Anti-centromere antibodies are associated with a speckled antinuclear antibody (ANA) pattern.Anti-centromere antibodies are present in approximately 80% of cases of limited cutaneous scleroderma/CREST syndrome (calcinosis, Reynaud phenomenon, esophageal dysmotility, sclerodactyly, and telangiectasia). These antibodies are not specific and can also be present in systemic sclerosis and systemic lupus erythematosus.Autoimmunity
Anti-citrullinated peptide antibody, serumIMM 1.2<20 UCitrullinated proteins represent post-translational modifications that can be associated with inflammation, particularly in synovial tissues. In rheumatoid arthritis (RA), autoantibodies are induced against a number of citrullinated antigens. These anti-citrullinated peptide antibodies (ACPA) have been identified in synovial fluid of some RA patients, and may play a pathogenic role by triggering proinflammatory cytokines and bone destruction via osteoclastogenesis.ACPA can be found in 60–80% of patients with RA. ELISA-based serum tests show specificity ranging from 85 to 99%, which is higher than rheumatoid factor. ACPA may precede RA symptoms by several years. ACPA levels may correlate with disease progression and response to anti–tumor necrosis factor-alpha antibody treatment.15 (link)Autoimmunity, Skeletal
Anti-DNA topoisomerase I (Scl-70) antibody, serumIMM 1.2<1.0 UDNA topoisomerase I is present in the nucleolus and nucleoplasm and its function is to cleave and relax supercoiled DNA. Anti-DNA topoisomerase I antibodies arise when nuclear fragments, typically from apoptotic cells, are not effectively cleared, thereby eliciting autoantibodies. Anti-DNA topoisomerase antibodies produce a fine-speckled nuclear or nucleolar ANA pattern.Anti-DNA topoisomerase antibodies are found in 20–60% of patients with systemic sclerosis/scleroderma. They are associated with the diffuse variant of the disease, pulmonary fibrosis and poor prognosis.Autoimmunity
Anti-double-stranded (ds) DNA antibody, serumIMM 1.2<30 IU/mLAnti-ds DNA antibodies arise when nuclear fragments, typically from apoptotic cells, are not effectively cleared, thereby eliciting autoantibodies. These antibodies form immune complexes that fix complement and cause damage to kidneys, skin, and other tissues. Anti-ds DNA antibodies produce a peripheral or diffuse staining pattern.Anti-ds DNA antibodies are seen in systemic lupus erythematosus (fairly sensitive and specific for SLE) and in Sjögrens yndrome or mixed connective tissue disease. Anti-dsDNA IgG levels appear to correlate with disease activity and renal involvement in SLE. Anti-ds DNA antibodies are rare in other rheumatologic diseases but may be seen.Autoimmunity
Anti-histone antibody, serumIMM 1.2<100 AU/mLaAnti-histone antibodies arise when nuclear fragments, typically from apoptotic cells, are not effectively cleared, thereby eliciting autoantibodies. Histones are the nuclear proteins that bind to DNA and help condense it into chromatin. Anti-histone antibodies produce a homogenous (diffuse) nuclear staining pattern.Anti-histone antibodies are positive in drug-induced lupus, but they are not specific. Patients with low levels of the acetyltransferase that acetylates and detoxifies some drugs (e.g., hydralazine, procainamide) appear to be more likely to develop a positive antinuclear antibody after exposure to these drugs.Autoimmunity
Anti-mitochondrial antibody (AMA), serumIMM 1.2<0.1 UAMAs are seen in 95% of patients with primary biliary cholangitis (PBC) with high specificity (98%). An infectious etiology with molecular mimicry to mitochondrial antigens has been hypothesized. The most common autoantigen is the E2 subunit of pyruvate dehydrogenase (PDC-E2). The role of AMAs in the pathogenesis of PBC is unclear; disease severity and rate of progression do not correlate with antibody titer. B and T cells autoreactive for PDC-E2 are seen in PBC.On indirect immunofluorescence, AMAs have a coarse, granular cytoplasmic pattern. AMAs are both sensitive and specific for PBC, though they are rarely positive in CREST (calcinosis, Raynaud phenomenon, esophageal hypomotility, sclerodactyly, and telangiectasia) syndrome.Autoimmunity
Anti-neutrophil cytoplasmic antibody (ANCA) – myeloperoxidase (MPO), serumIMM 1.2NegativeANCAs are predominantly IgG that bind Fcγ receptors in neutrophils. MPO is found in the granules of neutrophils and the lysosomes of monocytes; MPO-ANCA activates both cell types. MPO-ANCA was formerly known as pANCA (perinuclear-ANCA) based on indirect immunofluorescent staining. Positive indirect immunofluorescence results should be followed by ELISA testing for the specific antibody target.The ANCA-associated vasculitides are a group of small-vessel necrotizing vasculitis syndromes that include granulomatosis with polyangiitis (GPA); microscopic polyangiitis (MPA); and eosinophilic granulomatosis with polyangiitis (EGPA). EGPA is typically associated with MPO-ANCA. Both MPO-ANCA and PR3-ANCA may be seen in MPA, though MPO-ANCA is more common.Autoimmunity, Vascular
Anti-neutrophil cytoplasmic antibody (ANCA) – proteinase 3 (PR3), serumIMM 1.2NegativeANCA are predominantly IgG that bind Fcγ receptors in neutrophils. PR3-ANCA was formerly known as cANCA (cytoplasmic-ANCA) based on indirect immunofluorescent staining. The primary target of these antibodies is proteinase 3 (PR3) in the cytoplasm of neutrophils. Positive indirect immunofluorescence results should be followed by ELISA testing for the specific antibody target.The ANCA-associated vasculitides are a group of small vessels necrotizing vasculitis syndromes that include granulomatosis with polyangiitis (GPA); microscopic polyangiitis (MPA); and eosinophilic granulomatosis with polyangiitis (EGPA). PR3-ANCA is positive in the majority of cases of GPA.Autoimmunity, Vascular
Anti-nuclear antibody (ANA), serumIMM 1.2≤1.0 UANAs arise when nuclear fragments, typically from apoptotic cells, are not effectively cleared, thereby eliciting autoantibodies. This test detects serum levels of antibodies against multiple nuclear and cytoplasmic cellular structures. ELISA is more specific but is less sensitive. ANAs are present in many autoimmune diseases but are not specific; they can be seen in other conditions (e.g., infection, malignancy) or in otherwise healthy individuals. Different autoantibodies produce different ANA patterns on immunofluorescence (e.g., homogeneous, speckled, centromere, nucleolar).Further testing to refine the diagnosis is based on the pattern of ANA staining and the patient's clinical symptoms. The clinical setting should guide selection of further autoantibody testing. The American College of Rheumatology generally recommends against testing for ANA subserologies if ANA is negative.Autoimmunity
Anti-nucleosome antibody (anti-chromatin), serumIMM 1.2<1.0 Negative AIAntinucleosome antibodies arise when nuclear fragments, typically from apoptotic cells, are not effectively cleared, thereby eliciting autoantibodies. These antigens are not typically accessible to the immune system and, therefore, are recognized as non-self. Nucleosomes are subunits of the histone-DNA complex.Antinucleosome antibodies are positive in up to 75% of patients with systemic lupus erythematosus (SLE) and up to 100% of drug-induced lupus patients; in the former, they are associated with renal disease. Antibody titer correlates with disease severity.Autoimmunity
Anti-phospholipid antibody (aPL; also known as lupus anticoagulant antibody), serumIMM 1.4NegativeaPLs are acquired, heterogeneous autoantibodies that bind negatively charged phospholipid proteins. They are frequently seen in patients with systemic lupus erythematosus. aPLs prolong the aPTT by binding phospholipids, a necessary cofactor in this test. In vivo, however, aPLs may cause arterial and venous thrombosis and are associated with antiphospholipid syndrome (multiple thrombi and multiple late spontaneous abortions).aPL testing is complex and incorporated in the workup of patients with suspected antiphospholipid syndrome. aPTT (>PT) is typically prolonged in the presence of aPL due to prolonged time to form a clot in vitro due to binding of aPL to the antiphospholipid surface. Although the in vitro test suggests anticoagulation, aPL are prothrombotic in vivo and the term lupus anticoagulant is misleading.16 (link)Autoimmunity, Coagulation
Anti-Ro (anti-SS-A) antibody, serumIMM 1.2<1.0 UThese antibodies are a type of anti-nuclear autoantibody against cellular proteins. Depending on the technique used for detection, these antibodies are present in 40–80% of patients with primary Sjögren syndrome. They can be found in 50% of patients with SLE as well as subacute cutaneous lupus erythematosus (SCLE), neonatal lupus and primary biliary cholangitis.In recent years, there has been increasing literature regarding the significance of serum anti-52-kD Ro and anti-60-kD Ro; the former has a reported association with congenital heart block and the latter is more often present in autoimmune disease.17 (link), 18 (link), 19 (link)Autoimmunity
Anti-Smith (Sm) antigen antibody, serumIMM 1.2<1.0 USm antigens are part of a group of nuclear proteins called extractable nuclear antigens (ENAs). Other ENAs include SSA, SSB, and ribonuclear protein. Anti-Sm antibodies arise when nuclear fragments, typically from apoptotic cells, are not effectively cleared, thereby eliciting autoantibodies. Anti-Sm antibodies are associated with a speckled ANA pattern.Anti-Sm antibodies are fairly specific for lupus; they are positive in 20–30% of SLE patients and tend to remain constant as the disease progresses.Autoimmunity
Anti-smooth muscle antibody (ASMA), serumIMM 1.2NegativeASMAs are associated with autoimmune hepatitis (AIH), though their role in pathogenesis is unknown. They are typically directed against filamentous actin (F-actin) in AIH.ASMA are positive in approximately 50% of patients with type I autoimmune hepatitis. ASMA is more specific than ANA for AIH, particularly when titers are greater than 1:80. ASMA may be the only marker present in AIH. ASMA (and ANA) levels may fluctuate during treatment and may disappear with corticosteroid therapy. Antibody titer does not predict outcome.Autoimmunity, Hepatic
Antibody screen, bloodTM1.1NegativeAntibodies can be made against self-red blood cell (RBC) antigens (autoantibodies) and against foreign RBC antigens (alloantibodies) after exposure (e.g., blood transfusion, pregnancy, transplantation). In an antibody screen, a patient serum sample is mixed with reagent RBCs with known antigen profiles. When the antibody screen is positive, the blood bank identifies these antibodies. This process may also be performed for platelets.The most clinically significant natural alloantibodies target A and/or B antigens, depending on the recipient's blood type. An ABO-incompatible RBC transfusion can result in an acute hemolytic transfusion reaction. A screen is valid for no more than 3 days.20 Transfusion
Antithrombin (AT) activity, plasmaH 2.1Adults: 80–130%AT is an anticoagulant produced by hepatocytes that inactivates factors IIa, IXa and Xa. It also inhibits other serine proteases in the coagulation cascade to a lesser degree.AT deficiency is a risk factor for venous thromboembolism and may be inherited or acquired (e.g., nephrotic syndrome, fulminant hepatic failure, disseminated intravascular coagulation). Since heparin acts as an anticoagulant by potentiating the activity of AT, AT deficiency leads to heparin resistance. When inherited thrombophilia is under consideration, a panel of tests is usually performed and typically includes AT activity, factor V Leiden mutation, prothrombin G20210A mutation, protein C activity/resistance, protein S activity, and free protein S antigen.Coagulation
Arsenic, blood/hairCHEM 1.7Blood: <13 ng/mLHair: <1.0 μg/g of hairArsenic is rapidly cleared from the circulation into the phosphate pool; therefore, blood levels are only useful for acute toxicity. However, arsenic has a high affinity for the sulfhydryl groups of the amino acid cysteine, which is highly prevalent in keratin-rich tissues such as hair and nails. Testing of hair samples or toenail clippings can document exposure and correlates with time of exposure.Acute arsenic toxicity presents as arrhythmias and non-specific gastrointestinal symptoms such as diarrhea, nausea and vomiting. Chronic exposure typically manifests as hyperkeratosis, peripheral neuropathies, renal failure, anemia, liver dysfunction or cardiac arrhythmias. Chronic exposure is associated with an increased risk of cancers of the urinary bladder, liver, skin and lung. Hair from the nape of the neck is used to assess recent exposure; pubic or axillary hair is evaluated for long-term exposure.21 (link)Toxicology
Aspartate aminotransferase (AST; aka serum glutamate oxaloacetate transaminase), serumCHEM 1.4Males: 8–48 U/LFemales: 8–43 U/LAST is an enzyme normally present in the cytoplasm and mitochondria of hepatocytes. With hepatocyte membrane injury, it is released and enters the blood. In addition to the liver, AST can also be released from the kidney, skeletal muscle, and the heart. Alanine aminotransferase (ALT) is more specific for the liver than AST.AST is increased in liver disease, toxic injury, or viral infections of the liver. In the setting of excess alcohol use, AST is elevated to a greater extent than ALT, leading to an AST:ALT ratio of >2. Both ALT and AST require vitamin B6 for activity, but ALT is more dependent on vitamin B6, which is often deficient in individuals who chronically drink excessively.Hepatic, CMP
Basophil count, bloodH 4.20.01–0.08 × 109/LA basophil count is part of a complete blood count (CBC) with a differential. Basophils are the least common white blood cells (WBC) in the peripheral blood. They arise from myeloid precursor cells in the bone marrow. Basophils release histamine, cytokines, and other compounds to assist with immune responses.Basophils are increased in myeloproliferative neoplasms (especially chronic myeloid leukemia), hypothyroidism, chronic inflammation and autoimmune diseases. Basopenia can occur in hyperthyroidism, infection and severe allergies.CBC
Beta-2-microglobulin (B2M), serumCHEM 1.81.21–2.70 μg/mLB2M is the constant light chain of HLA Class I expressed on the surfaces of most nucleated cells. It is filtered in the glomerulus.B2M is elevated in diseases such as B-cell non-Hodgkin lymphomas and plasma cell neoplasms. B2M levels are used for staging and monitoring treatment in myeloma though serum free light chain levels are more effective for the latter. Elevated B2M is a poor prognostic indicator in this disease. Serum B2M may also be elevated in patients on long-term hemodialysis, in whom B2M may deposit as amyloid. Risk of this complication has been decreased, but not eliminated, by improved hemodialysis protocols.22 Immunologic, Tumor Marker
Bicarbonate, serumCHEM 1.6Males ≥18 years; Females ≥10 years: 22–29 mEq/LBicarbonate (HCO3) is an important buffer in the body to prevent acid-base disorders and to maintain the proper pH of epithelial secretions. Luminal concentration is regulated by the cystic fibrosis transmembrane conductance regulator (CFTR). Bicarbonate is an important component of gastrointestinal mucus secretions, such as in the stomach, where it helps prevent gastritis and gastric ulcers. Renal bicarbonate excretion increases in alkalemia.Serum bicarbonate concentration is used to calculate pH in the Henderson-Hasselbalch equation when evaluating an acid-base disorder. Bicarbonate levels are low in metabolic acidosis and respiratory alkalosis and elevated in metabolic alkalosis and respiratory acidosis. If serum levels are sufficiently high, metabolic alkalosis will result. Causes of increased serum bicarbonate include gastric HCl loss (e.g., vomiting) and K+ loss. CFTR mutations seen in cystic fibrosis lead to decreased bicarbonate levels in luminal secretions.23 BMP/Chem 7
Bilirubin (total, direct and indirect),serumCHEM 1.4Total bilirubin, varies with ageAdults: ≤ 1.2 mg/dLDirect bilirubin: 0.0–0.3 mg/dLBilirubin is the principal pigment in bile. 80% is derived from breakdown of aged red blood cells (RBCs); the remaining 20% is derived from destruction of heme-containing proteins (e.g., myoglobin, cytochromes, catalase) and from catabolism of heme. Total bilirubin is the sum of direct (conjugated) bilirubin, which is water soluble and excreted in urine, and indirect (unconjugated) bilirubin, which is not water soluble. There is a minor, generally clinically insignificant discrepancy when the total and direct bilirubin values are subtracted to obtain a value for indirect bilirubin.Neonates are at risk for kernicterus (unconjugated hyperbilirubinemia) due to immature uridine diphosphoglucuronate glucuronosyltransferase (UGT), as well as increased erythrocyte destruction. Breast-fed infants are also at higher risk of kernicterus. Elevated total bilirubin in older children and adults can result from increased RBC destruction or decreased liver function.24 Hepatic
Blood urea nitrogen (BUN), serumCHEM 1.5Males ≥18 years: 8–24 mg/dLFemales ≥18 years: 6–21 mg/dLAmmonia is generated when proteins are catabolized. The liver metabolizes this ammonia to urea, which is released into the blood and then eliminated by the kidneys, thereby removing nitrogen from the body.BUN may be elevated due to liver damage or conditions affecting the urinary tract (e.g., acute glomerulonephritis, polycystic kidney disease, urinary obstruction due to benign prostatic hyperplasia [BPH]). Dehydration and congestive heart failure can lead to increased BUN, the latter due to decreased renal perfusion. BUN alone is not tremendously informative; these data are usually compared with creatinine to give a BUN/creatinine ratio which is more useful in monitoring renal health.BMP/Chem 7, Hepatic, Renal
Brain natriuretic peptide or B-type natriuretic peptide (BNP), plasmaN-terminal (NT)-pro hormone BNP (NT-proBNP), serumCHEM 1.2Varies with sex and ageIn response to ventricular wall stretch and volume overload, cardiac myocytes cleave an N-terminal section from the BNP prohormone (NT-proBNP) to release active BNP and the inactive N-terminal fragment, NT-proBNP. BNP downregulates the renin-angiotensin-aldosterone system, decreases sympathetic tone in the heart and kidney, and increases renal blood flow and sodium excretion. NT-proBNP has a longer half-life than BNP.NT-proBNP and BNP levels are useful in distinguishing acute onset dyspnea secondary to congestive heart failure (CHF) versus lung disease since it is elevated in the former, but not the latter. However, NT-proBNP should not be used in isolation to establish the diagnosis of CHF.Cardiac
C-reactive protein (CRP), serumIMM 1.1≤8 mg/LCRP is an acute phase reactant that acts as an opsonin. In acute inflammation, IL-6 stimulates production of CRP from hepatocytes. CRP is a sensitive but non-specific marker of inflammation. It has a short half-life (hours).CRP is increased in a variety of acute illnesses and inflammatory conditions (e.g., bacterial infection, myocardial infarction). Higher baseline levels of plasma CRP are associated with increased risk of chronic heart disease and stroke, possibly through the inflammatory response associated with atherosclerosis. Assays to measure the low baseline levels of CRP are often referred to as ‘high-sensitivity’ or ‘cardiac’ CRP assays to distinguish from regular CRP assays that measure the much higher levels seen inflammation or infection.Inflammatory
C3 complement, serumIMM 1.175–175 mg/dLComplement proteins are plasma proteins that are activated directly by microbes or by antibodies bound to antigens, and mediate important functions (opsonization, inflammation, lysis of some cells). Most are made by the liver and are decreased in severe liver disease or when widespread complement activation consumes these proteins. They are acute phase reactants and are increased in multiple disease states. The 3 complement activation pathways converge with the activation of the C3 protein. The C3b fragment coats the surface of the target cell, attracting phagocytes and continuing the complement cascade to cell lysis.C3 complement is measured by immunoassay, which does not address its function, and is evaluated in the workup of autoimmune diseases (e.g., SLE). Levels often correlate with disease activity. Low levels of both C3 and C4 indicate classical pathway activation while low serum level of C3 with normal C4 level indicates alternative pathway activation. The C3a fragment is an anaphylatoxin that stimulates mast cell and basophil degranulation leading to increased vascular permeability and vasodilation. C3 deficiency leads to increased risk of pyogenic infections.25 Inflammatory
C4 complement, serumIMM 1.114–40 mg/dLComplement proteins are plasma proteins that are activated directly by microbes or by antibodies bound to antigens, and mediate important functions (opsonization, inflammation, lysis of some cells). Most are made by the liver and are decreased in severe liver disease or when widespread complement activation consumes these proteins. They are acute phase reactants and are increased in multiple disease states. There are 3 complement activation pathways; C4 is part of the classical pathway and levels are low when this pathway is activated.C4 complement is measured by immunoassay, which does not address its function. C4 evaluation is part of the workup of autoimmune diseases (e.g., SLE). Levels may help determine disease activity. The C4a fragment is an anaphylatoxin that stimulates mast cell and basophil degranulation leading to increased vascular permeability and vasodilation. C4 deficiency is associated with an increased risk of developing autoimmune diseases.25 Inflammatory
Cadmium, urine/bloodCHEM 1.3Urine: <3 mg/g creatinineBlood: <4.9 μg/LCadmium forms adducts with proteins, followed by protein denaturation and cell cycle disruption through indirect oxidative damage.Chronic exposure to cadmium can be nephrotoxic, accumulating in the medulla and the proximal tubule and leading to tubulointerstitial nephritis and proteinuria. Common sources of cadmium exposure include tobacco smoke and prolonged spray painting without respiratory protection (e.g., auto body repair).26 (link)Toxicology
Calcitonin, serumCHEM 1.3Adult males ≤14.3 pg/mLAdult females ≤7.6 pg/mLCalcitonin is secreted by parafollicular cells (C cells) of the thyroid gland in response to elevated ionized calcium concentration. Calcitonin inhibits the action of parathyroid hormone and also inhibits bone resorption by directly binding to osteoclasts. Calcitonin lowers serum calcium and phosphorus levels.Calcitonin can be elevated in patients with medullary thyroid carcinoma, which may be seen in the setting of multiple endocrine neoplasia (MEN) syndrome type 2.Endocrine
Calcium, serumCHEM 1.3Ionized (free) calcium:Adults: 4.57–5.43 mg/dLTotal calcium:Adults: 8.6–10.0 mg/dLCalcium binds to negatively charged sites on proteins and is affected by pH. Alkalosis leads to an increase in negative charge and binding and thus a decrease in free calcium. Acidosis leads to a decrease in negative charge and binding and thus an increase in free calcium. Decreased ionized calcium levels stimulate the parathyroid glands to secrete parathyroid hormone (PTH), which leads renal tubular cells to increase calcium absorption and drives osteoclasts to release calcium from bone. It also induces renal conversion of calcidiol to calcitriol, which increases intestinal absorption of calcium.Serum calcium is 50% ionized (“free” or “active”), 40% bound to albumin, and 10% bound to other ions. “Total” calcium is a sum of these 3 components. Total calcium measures are affected by serum albumin levels; direct measurement of ionized calcium is more precise. Hypercalcemia can be seen in primary hyperparathyroidism (increased PTH secretion) or in malignancy (secretion of PTH-related proteins or by bone destruction from metastases). Other causes of hypercalcemia include drugs/supplements, endocrine disorders, granulomatous diseases. Common causes of hypocalcemia include chronic renal failure and hypomagnesemia due to impaired PTH secretion and PTH end-organ resistance. Hypoalbuminemia is the most common cause of pseudohypocalcemia.27 Endocrine, Metabolic
Cancer antigen 125 (CA-125), serumCHEM 1.8<46 U/mLCA-125 is a glycoprotein that is normally expressed on cells derived from coelomic epithelium (e.g., fallopian tube, ovary, colon).Serum CA-125 is increased in advanced epithelial ovarian cancer and can be used to assess the presence of residual disease following debulking surgery or to monitor for recurrence. It should not be used as a screening test for ovarian cancer. CA-125 can also be elevated with pregnancy, non-malignant pathology such as endometriosis and pelvic inflammatory disease, and other non-gynecologic cancers.Tumor marker
Cancer antigen 19-9 (CA19-9), serumCHEM 1.8<35 U/mLCA 19-9 is an FDA-approved serum tumor marker for pancreatic ductal adenocarcinoma. It is the sialylated form of the Lewis (a) blood group antigen found on red blood cells (RBCs). It is shed from neoplastic pancreatic ductal cells into blood in ∼70–90% of patients with pancreatic ductal adenocarcinoma. CA 19-9 can be elevated in other malignancies (e.g., cholangiocarcinoma, colon cancer, gastric cancer, ovarian cancer).In patients who are Lewis negative, tumor cells cannot produce CA 19-9, due to lack of the enzyme fucosyltransferase. CA 19-9 is not useful as a screening test as it can be elevated in benign liver disease and patients with cholestasis. In the setting of malignancy, high levels correlate with unresectable disease and a worse prognosis. It can be used to assess tumor response to treatment and presence of recurrence/metastasis if pre-treatment CA 19-9 levels are known.Tumor marker
Carcinoembryonic antigen (CEA), serumCHEM 1.8Nonsmokers: ≤ 3.0 ng/mLSmokers: <5.0 ng/mLCEA is an oncofetal antigen normally expressed during fetal development, but not in the tissue of healthy children or adults. It is expressed by certain epithelial malignancies (e.g., colorectal, pancreatic, and lung cancer).Serum CEA elevations of >20 ng/mL are generally associated with malignancy; however, this should not be used as a screening test due to low sensitivity and specificity. It is useful for monitoring recurrence of colon cancer after resection.Tumor marker
CD4 count, bloodM 3.4Adults: 400–1400 CD4+ T cells/μLaPediatric ranges vary by ageCD4+ T-cell counts are considered the best indicator of the current state of immune competence in patients with HIV. CD4 counts may be directly measured by flow cytometry, or a percentage of CD4+ T-cells can be measured by flow cytometry and the absolute count calculated (CD4+ T-cell % x WBC count).CD4 counts are not used for the initial diagnosis of HIV infection. They are used in patients with known HIV infection for disease staging, to assess risk for certain HIV-associated complications and the need for prophylaxis, and to evaluate response to antiretroviral therapy. Key clinical indicators include CD4 counts <200 cells/μL (Pneumocystisjirovecii prophylaxis indicated) and <50/μL (Mycobacteriumavium complex prophylaxis indicated). CD4 counts are typically performed at diagnosis and subsequently every 3–6 months; more frequently if counts are trending down. CD4 counts may also be performed as part of evaluation of other immune deficiency syndromes, typically as part of a more extensive panel to evaluate T-cell and/or B-cell populations.28 (link)Hematologic
Ceruloplasmin, serumCHEM 1.4Varies with age and sexAdult males: 19.0–31.0 mg/dLAdult females: 20.0–51.0 mg/dLCeruloplasmin is an acute-phase reactant synthesized by the liver and is the primary copper-carrying protein in the blood. It carries 95% of total copper in human plasma. In Wilson disease, a mutation in the ATP7B gene results in decreased copper transport into bile, decreased incorporation into ceruloplasmin and decreased ceruloplasmin secretion into blood. Copper accumulates in hepatocytes, which can cause injury by 1) the Fenton reaction; 2) binding to protein sulfhydryl groups; and 3) displacement of other metals from hepatic metalloenzymes.Low ceruloplasmin levels can be seen in the setting of Wilson disease, Menkes disease, zinc toxicity, or malnutrition (trace mineral deficiency). Pathologic effects of excess copper include cirrhosis, neuropsychiatric symptoms, hematuria/proteinuria and Kayser-Fleischer rings.Hepatic
Chloride, serumCHEM 1.5≥18 years: 98–107 mmol/LChloride is part of the basic metabolic panel (BMP: Cl, Na+, glucose, BUN, K+, CO2, creatinine) and reflects the body's ability to maintain fluid homeostasis and acid-base balance. It is the primary anion in the extracellular fluid and is necessary for transmitting action potentials in neurons. Dietary salt intake is the main source of chloride for humans. Serum levels are partially regulated by the kidney, and reabsorption occurs by both passive and active processes.When chloride levels are the only abnormality in the BMP, a metabolic disorder is most likely. Alkalosis is seen with low chloride levels while acidosis is associated with high chloride levels. Causes of decreased chloride include vomiting, diarrhea, diabetic ketoacidosis, syndrome of inappropriate antidiuretic hormone secretion (SIADH), metabolic alkalosis and heart failure. Low levels in patients with heart failure indicate advanced disease and decreased left ventricular ejection fraction. Causes of increased chloride include renal failure, dehydration, diabetes insipidus and respiratory alkalosis.23 ,29 (link)BMP/Chem 7
Cold agglutinin titer, serumIMM 1.4<1:64Cold agglutinin syndrome is caused by IgM antibodies that bind red blood cells (RBCs) in peripheral parts of the body in which the temperature is < 37 °C. They may produce hemolysis or blood stasis, leading to cyanosis of the ears, fingers, and toes.Blood specimen must be kept at 37-38 °C before testing. Autoimmune hemolytic anemia (AIHA) is caused by warm, cold or mixed-reactive antibody types. Cold antibody AIHA includes cold agglutinin disease (CAD) and paroxysmal cold hemoglobinuria (PCH). When cold antibody AIHA is suspected, a Coombs test for C3d antibodies should be performed; if this is positive, cold agglutinin titer and thermal activity should be performed. Titer does not correspond to disease activity. High titers can be seen in other conditions such as mycoplasma pneumonia, infectious mononucleosis and hematologic malignancies.30 (link)Coagulation
Complete blood count (CBC), bloodH 4.2See individual testsThe CBC includes red blood cell (RBC), white blood cell (WBC) and platelet counts as well as all the RBC indices (mean corpuscular volume [MCV], mean corpuscular hemoglobin [MCH], mean corpuscular hemoglobin concentration [MCHC], RBC distribution width [RDW]). A CBC with differential includes all the above tests, plus a white blood cell differential count.The CBC is a general screening test to evaluate overall health, to assess a wide range of hematologic disorders and to determine eligibility for medications and/or chemotherapy. See individual tests for further information.CBC
Copeptin proAVP (arginine vasopressin), plasmaCHEM 1.3Non-water deprived, non-fasting adults: <13.1 pmol/LWater deprived, fasting adults: <15.2 pmol/LNeurosecretory cells in the hypothalamus secrete a pre-prohormone that is composed of AVP (also known as antidiuretic hormone, ADH), copeptin and neurophysin II; these three components are transported to the posterior pituitary. In response to decreased intravascular volume and increased plasma osmolarity/sodium concentration, AVP stimulates water reabsorption in the distal renal tubules.When there is inadequate ADH, most commonly due to damage to the hypothalamus or pituitary stalk, diabetes insipidus results with consequent polyuria, polydipsia and hypernatremia. Syndrome of inappropriate antidiuretic hormone (SIADH) is when there is an inappropriate release of ADH leading to hyponatremia. This can occur in CNS disorders, lung disease or from a paraneoplastic syndrome caused by ectopic ADH secretion (e.g., small cell carcinoma of the lung). AVP has a short half-life in plasma, which makes analysis challenging; however, copeptin, which is secreted in equimolar amounts as AVP, has a longer half-life and, therefore, is used as a surrogate marker for AVP.23 ,31 (link)Endocrine
Copper, serumCHEM 1.7≥11 years old: 0.75–1.45 mg/mLCopper is a component of multiple metalloproteins. About 90% of serum copper is complexed to ceruloplasmin with a smaller amount bound to transcuprein, metallothionein or albumin. Serum copper can be measured with mass spectrometry as free (non-ceruloplasmin-bound) serum copper or total (free and ceruloplasmin-bound) copper.Low serum copper may be due to excess dietary iron or zinc or, less commonly, dietary deficiency (often in the setting of remote GI surgery such as gastric bypass) or Wilson disease. In Wilson disease, serum copper and ceruloplasmin may be normal due to hepatic injury, which releases these intracellular components into the blood. Free serum copper is a better means of diagnosing Wilson disease than is total serum copper due to variability in ceruloplasmin levels (e.g., pregnancy, inflammation).Hepatic
Cortisol (free), serumCHEM 1.35-25 μg/dL (morning collection)2-14 μg/dL (afternoon collection)Cortisol is the major endogenous glucocorticoid and is a key regulator of the stress response and glucose metabolism. Cortisol levels are regulated by adrenocorticotropic hormone (ACTH) from the pituitary gland in response to cyclic release of corticotropin releasing hormone (CRH) from the hypothalamus. Levels of ACTH and cortisol peak in the morning and trough in the late evening. In the serum, the majority of cortisol is bound to corticosteroid-binding globulin (CBG) and albumin.Conditions that increase cortisol are known as hypercortisolism (Cushing syndrome); common causes include adrenal adenoma, pituitary adenoma (Cushing disease), ectopic ACTH production (e.g., from a tumor) and exogenous steroids. Symptoms associated with hypercortisolism include obesity, glucose intolerance and high blood pressure. Hypocortisolism (Addison disease) can be due to damage/disease of the adrenal glands or pituitary glands. Use of glucocorticoid medications will cause adrenal atrophy with reduction in endogenous cortisol production until medications are withdrawn.Endocrine
Creatine kinase (CK; AKA creatine phosphokinase/CPK), serumCHEM 1.2Male: 39–308 U/LFemale: 26–192 U/LCK is the enzyme that phosphorylates creatine, generating phosphocreatine, an energy source abundant in the metabolically demanding tissues such as the brain, myocardium and skeletal muscle. There are several different CK isotypes with specialized subcellular and tissue distributions. The low CK level normally measurable in the blood reflects baseline leakage from skeletal muscle; abnormally elevated levels are due to the enzyme release from necrotic/injured myocardium or skeletal muscle.CK elevation is one of the oldest markers of acute myocardial infarction, but it lacks specificity; currently, the more specific troponin test is used instead. Elevated CK remains a clinically useful marker of skeletal myonecrosis (e.g., due to muscular dystrophies, drug-induced/toxic myopathies, and autoimmune myopathies). In addition, CK levels can be elevated following infections, strenuous exercise, and crush injuries. Rhabdomyolysis (acute severe myonecrosis) is accompanied by markedly elevated CK levels (generally above 2000 U/L, although there is no absolute cutoff value).Musculoskeletal
Creatinine, serumCHEM 1.5Males ≥15 years: 0.7–1.3 mg/dL Females ≥18 years: 0.6–1.0 mg/dLCreatinine is derived from creatine (primarily synthesized in kidney and liver) and phosphocreatine (a quickly accessible energy source for brain and muscle). A relatively constant proportion of creatinine (related to skeletal muscle mass and metabolism) is released into blood, and creatinine is freely filtered by the glomerulus (with a minor contribution from renal tubular secretion). Serum creatinine has a nonlinear, inversely proportional relationship to glomerular filtration rate (GFR).In addition to its role in GFR estimation, serum creatinine values can be used to evaluate kidney function in pathological states such as acute kidney injury. Both serum BUN and creatinine levels vary in inverse proportion to GFR, both increasing as GFR falls with the normal ratio being 10–15:1. When there is a disproportionate rise in BUN (higher ratio), it suggests pre-renal failure (e.g., dehydration, congestive heart failure). When the relative ratio is tilted toward creatinine, it is indicative of renal failure caused by intrinsic diseases of the kidney that affect GFR. Loss of muscle mass can lead to falsely low serum creatinine levels. Angiotensin-converting enzyme (ACE) inhibitors and angiotensin II receptor blockers (ARBs) can elevate serum creatinine.24 ,32 (link)Renal, BMP/Chem 7
Crossmatch, bloodTM1.1Not applicableIf antibodies are identified in the antibody screen, donor red blood cells (RBCs) that are negative for the corresponding antigens reduce the risk of hemolysis. This test assesses donor red blood cell compatibility with recipient plasma by mixing patient serum with a sample of donor RBCs and is the final check prior to issuing a unit of RBCs from the blood bank for a patient. The process may also be performed for platelets.Crossmatch reduces the general blood bank inventory by allocating specific units of blood (or platelets) to an intended recipient of a transfusion. This order is recommended for patients expecting a blood transfusion imminently or in some surgical cases. In an emergency, uncrossmatched RBCs may be used.20 Transfusion
Cryoglobulins, serumIMM 1.4NegativeCryoglobulins are immunoglobulins that precipitate at temperatures below 37°. There are three subtypes: Type I, monoclonal IgG or IgM; type II, a mixture of polyclonal and monoclonal immunoglobulins; and type III, polyclonal.Type I cryoglobulins are associated with lymphoplasmacytic lymphoma and multiple myeloma. Type II cryoglobulins are seen in the setting of chronic hepatitis C and autoimmune disorders such as SLE. Type III cryoglobulins are seen in some autoimmune diseases and infections. At low temperatures, cryoglobulins can precipitate in the extremities or skin and occlude blood vessels, leading to purpura, skin necrosis, Raynaud phenomenon, arthralgias and neuropathy.Coagulation
D-dimer, plasmaH 2.4≤500 ng/mL fibrinogen equivalent units (FEU)Thrombin cleaves fibrinogen to yield a fibrin monomer with a D domain on each end. The monomers polymerize to form a fibrin clot. D-dimers are a proteolytic byproduct of plasmin degradation of this clot and indicate 1) a fibrin clot was formed and 2) the clot was crosslinked by FXIIIa, followed by plasmin-mediated cleavage of the insoluble crosslinked fibrin clot.Elevated D-dimer levels are seen in disorders marked by procoagulant and fibrinolytic activity (e.g., disseminated intravascular coagulation [DIC], deep venous thrombosis [DVT], pulmonary embolism [PE], recent surgery and trauma) and hypercoagulable states (e.g., pregnancy, liver disease, inflammation). A negative D-dimer result helps exclude DVT and PE; however a positive D-dimer is not specific. The extent of clotting/fibrinolysis does not correlate with the amount of D-dimers.Coagulation
Deamidated gliadin IgG and IgA antibody, serumIMM 1.4Negative: <20.0 UWeak positive: 20.0–30.0 UPositive: > 30.0 UDeamidated gliadin antibody is a serum test for celiac disease in patients with IgA deficiency (approximately 2% of patients with celiac disease) who therefore lack IgA antibodies against tissue transglutaminase (TTG), which is the first line serologic test for celiac disease. Celiac disease is an immune-mediated enteropathy of the small intestine triggered by gluten exposure in genetically susceptible individuals. Gliadin peptides are deamidated by tissue transglutaminase (tTG) and the deamidated fragments are presented to CD4+ T-cells, leading to activation/expansion of B-cells that secrete the deamidated gliadin antibody.This test is used in IgA-deficient patients in whom anti-TTG (IgA) testing is not informative. While patients with celiac disease and IgA deficiency also make an IgG anti-tTG, IgG antibodies to deamidated gliadin are more sensitive/specific. The sensitivity of this test is reduced if patients are on a gluten-free diet prior to testing.33 (link)Gastrointestinal
Dehydroepiandrosterone sulfate (DHEAS), serumCHEM 1.3Varies with ageDHEA is the major adrenal androgen and is a precursor for sex steroids; the majority is secreted as a conjugate to sulfate, DHEAS. DHEA and DHEAS test results can be used interchangeably in most clinical situations.DHEAS is secreted by the adrenal glands and is therefore a good marker for adrenal androgen production. Elevated DHEAS levels can cause symptoms or signs of hyperandrogenism in women though men are typically asymptomatic. DHEA/DHEAS are usually assessed in investigations of adrenal androgen production, such as the assessment of (1) hyperplasia, (2) adrenal tumors, (3) delayed puberty, and (4) hirsutism.Endocrine
Desmoglein 1/3 antibody, serumIMM 1.4<20 RU/mLDesmoglein 1 (DSG1) and desmoglein 3 (DSG3) are adhesion molecules on cell surface desmosomes. DSG1 is distributed from the stratum corneum to the basement membrane whereas DSG3 is limited to the lower portion of the epidermis. Autoantibodies to these proteins are seen in pemphigus foliaceous (DSG1) and pemphigus vulgaris (DSG3 and/or DSG1); binding activates complement, leading to disruption of intercellular adhesionsand blistering.Pemphigus foliaceous is characterized by superficial blistering and rarely affects mucosal membranes. Pemphigus vulgaris is more common and shows more extensive blistering; the mucosa is frequently involved.Skin
Direct antiglobulin test (DAT, direct Coombs test)Indirect antiglobulin test (indirect Coombs test), bloodTM 1.2NegativeThe DAT assesses in vivo coating of red blood cells (RBCs) by IgG and complement C3d, which can cause hemolysis resulting in anemia. IgG-bound RBCs are usually removed by the spleen, while complement-bound RBCs are destroyed by the membrane-attack complex. The direct Coombs test uses antihuman globulin to detect antibodies/complement that are bound to a patient's RBCs; the indirect Coombs test uses antihuman globulin to detect antibodies and/or complement present in a patient's plasma.In the DAT, the patient's RBCs are washed and then incubated with antihuman globulin (AHG, Coombs reagent), which causes the RBCs to agglutinate if antibodies/complement are present. In the indirect antiglobulin test (indirect Coombs test), the patient's serum is incubated with RBCs with defined antigens; AHG is added, which causes agglutination if antibodies/complement are present. The DAT is useful in assessing patients with hemolytic anemia to exclude transfusion reactions and autoimmune and drug-related etiologies.33 (link)Coagulation
Endomysial antibody , IgA, serumIMM 1.4NegativeCeliac disease is an immune-mediated enteropathy of the small intestine triggered by gluten exposure in genetically susceptible individuals. IgA autoantibodies to the endomysium (connective tissue surrounding muscle cells) are elevated in 70–80% of patients with celiac disease or dermatitis herpetiformis. By comparison, anti-tissue transglutaminase autoantibodies have a sensitivity and specificity of 90–98% and 95 to 97%, respectively; therefore, this test is often the first-line test in celiac disease assessment.This test is highly specific and can obviate the need for small bowel biopsies. Since this is an IgA antibody, the test cannot be used in individuals with IgA deficiency (about 2% of patients with celiac disease); in such patients, an IgG test can be performed. Titer generally correlates with disease severity and declines with strict adherence to a gluten-free diet.33 (link)Gastrointestinal
Eosinophil countH 4.20.03–0.48 × 109/LEosinophils arise from precursor cells in the bone marrow and are relatively infrequent in the peripheral blood in health. Eosinophil granules contain cytotoxic compounds, including major basic protein and eosinophil cationic protein. Eosinophils are capable of antigen presentation and are important in defense against parasitic infections.Eosinophils are increased in parasitic infections, allergic conditions, asthma, drug hypersensitivity, autoimmune and connective tissue disorders, eosinophilic granulomatosis with polyangiitis, myeloproliferative neoplasms, and some types of lymphoma. Eosinophils are typically decreased in Cushing syndrome and corticosteroid therapy.CBC
Erythrocyte sedimentation rate (ESR) aka Sed rate, sed, Westergren test, bloodIMM 1.1Male 0–22 mm/h Female 0–29 mm/hIn health, the negatively charged red blood cell (RBC) membrane prevents aggregation. In the setting of inflammation, positively charged immunoglobulins and acute phase proteins (e.g., prothrombin, plasminogen, fibrin, C-reactive protein) bind to the RBC membrane, neutralizing the negative charge and causing RBCs to clump into stacks referred to as rouleaux. These large aggregates sediment more rapidly than individual RBCs, thereby increasing the ESR.ESR can be elevated in infections, most anemias, inflammation (e.g., rheumatoid arthritis, SLE), pregnancy, malignancy (e.g., multiple myeloma, Waldenström macroglobulinemia, colorectal carcinoma, renal cell carcinoma); end-stage renal disease (uremia) and nephrotic syndrome (hypoalbuminemia). ESR is typically decreased in polycythemia vera (increased blood viscosity), sickle cell disease and hereditary spherocytosis.Inflammatory
Erythropoietin (EPO), serumCHEM 1.52.6–18.5 mIU/mLEPO is a glycoprotein that is mainly produced by peritubular cells in the kidney after birth. This hormone stimulates red blood cell (RBC) production in the bone marrow.Hypoxia stimulates EPO production. Decreased EPO production can be seen in renal failure while increased production is seen in hypoxemia (e.g., chronic obstructive pulmonary disease); the former can result in anemia and the latter in erythrocytosis. EPO levels are normal or decreased in polycythemia vera. Some neoplasms such as hepatocellular carcinoma, renal cell carcinoma, and adrenal adenoma may secrete erythropoietin.34 (link)Renal, Hematologic
Estradiol (E2), serumCHEM 1.3Varies with age, sex and sexual development (i.e., Tanner stage)Adult males: 10–40 pg/mLAdult females (premenopausal): 15–350 pg/mLAdult females (postmenopausal): <10 pg/mLEstrone (E1), estradiol (E2), and estriol (E3) are three endogenously produced estrogens that are responsible for the development and regulation of the female reproductive system and secondary sex characteristics. Estrogens are produced from androgens such as testosterone through aromatization, an enzymatic step that may be blocked by aromatase inhibitor drugs. Estradiol is the dominant estrogen hormone present in nonpregnant, premenopausal females. It is produced in the ovarian follicles and regulates the menstrual cycle. It is produced in smaller amounts in the testes, adrenal glands and adipose tissue. After menopause, estradiol levels decrease dramatically. Increased estrogens, including estradiol are implicated as a driving factor in some malignancies including type 1 endometrial carcinomas and certain breast cancers.Levels of estradiol and other estrogens vary depending on age, sex, menopausal status and stage of the menstrual cycle; therefore, clinical correlation is necessary. Evaluation of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) levels can be useful. Levels rise during the follicular phase and peak during ovulation, falling again during the luteal phase. Estradiol levels are used to evaluate fertility, monitor ovulation and to evaluate oligomenorrhea and menopausal status.35 (link)Endocrine
Estrone (E1), serumCHEM 1.3Varies with age, sex and sexual development (i.e., Tanner stage)Adult males: 10–60 pg/mLAdult females (premenopausal): 17–200 pg/mLEstrone (E1) is the dominant form of estrogen during menopause and is principally derived from peripheral aromatization of androstenedione in adipose tissue and the adrenal gland. Estrone acts as a precursor to estradiol, which is more potent than estrone, and conversion back and forth occurs.Levels of estrone and other estrogens vary depending on age, sex, menopausal status and stage of the menstrual cycle; therefore, clinical correlation is necessary. E1 levels are used in conjunction with other steroid hormones to evaluate delayed/ precocious puberty (females > males), evaluation of sex steroid disorders (e.g., 17 alpha-hydroxylase deficiency) and in fracture risk assessment and monitoring hormone replacement therapy in postmenopausal women. Levels may be increased in the setting of hyperthyroidism, cirrhosis, Turner syndrome, estrogen- or androgen-producing tumors and polycystic ovary syndrome (PCOS).Endocrine
Ethanol, bloodCHEM 1.7Legal limit of intoxication in most of the United States: > 80 mg/dL Potentially lethal: ≥ 400 mg/dLEthanol is metabolized in the liver, primarily through an oxidative pathway in which alcohol dehydrogenase converts ethanol into acetaldehyde, which is further metabolized to acetic acid by aldehyde dehydrogenase. With increasing blood alcohol levels or chronic ethanol consumption, micro-somal cytochrome P450 metabolism of ethanol becomes increasingly significant, particularly the CYP2E1 isoform. CYP2E1 levels increase with chronic alcohol consumption, which contributes to increased tolerance.Serum, plasma, and whole blood are appropriate samples for laboratory ethanol testing. When interpreting results, both serum and plasma ethanol levels are generally higher than whole blood due to its solubility in water (ratio of serum or plasma to whole blood ranges from 1.08 to 1.18). The blood ethanol test is most reliable < 8–12 h after ingestion. Whole blood ethanol concentrations used in the legal setting (e.g., driving under the influence) often uses % ethanol by volume where, for example, 80 g/dL is the same as 0.08%.Toxicology
Factor IX (FIX) activity assay, plasmaH 2.165–140%FIX is a protease that is part of the intrinsic coagulation pathway. It is activated by Factor XIa or Factor VIIa/tissue factor. In the presence of calcium, phospholipids and Factor VIIIa, FIXa activates Factor X, which generates thrombin from prothrombin. FIX is inhibited by anti-thrombin. The gene for FIX is on chromosome X.Hemophilia B, also called Christmas disease, is an inherited deficiency of FIX and is an X-linked recessive disorder. It is much less common than hemophilia A (factor VIII deficiency). About one third of cases arise from spontaneous mutations and two thirds are inherited.36 (link)Coagulation
Factor V Leiden (FVL) mutation, bloodH 2.1NegativeFactor V (FV) is a vitamin K-independent coagulation factor that is an essential cofactor in the conversion of prothrombin to thrombin. In FVL, a point mutation substitutes arginine for glutamine (R506Q) preventing cleavage by activated protein C (aPC); persistent Factor Va produces a hyper-coagulable state. This PCR-based test detects FV R506Q mutation.FVL is the most common cause of inherited venous thromboembolism in individuals of European ancestry, though it can be seen in other groups due to population admixture. FVL increases the risk of thrombosis 25 to 50- fold in homozygotes and five-fold in heterozygotes; however, most heterozygotes do not develop blood clots. Compound heterozygotes with the prothrombin G20210A allele are not uncommon.Coagulation
Factor VIII (FVIII) activity assay, plasmaH 2.155–200%FVIII is a coagulation cofactor that is bound to and stabilized by von Willebrand factor (vWF) in the plasma. It is an essential cofactor in Factor X activation by Factor IX. This test measures the activity of FVIII in patient plasma and is reported as a percentage relative to reference normal plasma.The FVIII gene is located on chromosome X. Hemophilia A is an X-linked recessive disorder due to an inherited deficiency of FVIII; it presents with hemarthroses and prolonged bleeding. Rare patients with homozygous von Willebrand disease may present with low FVIII levels and hemophilia-like bleeding. Autoantibodies to FVIII can inhibit its function, resulting in acquired hemophilia.Coagulation
Ferritin, serumH 3.2Male: 24–336 μg/L Female: 11–307 μg/LFerritin is found in serum and in the cytoplasm of tissue macrophages; it is the major storage protein for iron. Ferritin concentration varies with age and sex and correlates with total iron stores; therefore, ferritin levels are low in iron-deficiency anemia and high in iron overload (e.g., hemo-chromatosis). Ferritin is an acute phase reactant and can be increased in acute and chronic inflammation as well as in chronic kidney disease and some malignancies.Ferritin is often measured in combination with serum iron, transferrin saturation and total iron binding capacity; these tests may be less precise and do not distinguish depleted iron stores from impaired iron release (e.g., anemia of chronic inflammation). Low serum ferritin is highly specific for iron deficiency anemia. However, acute phase reaction can sometimes mask the low ferritin that would otherwise be seen in iron deficiency anemia.37 (link),38 Hepatic, Hematology
Fibrinogen, plasmaH 2.1200–393 mg/dLFibrinogen (Factor I) is essential for formation of stable clots and thus hemostasis. Fibrinogen links activated platelets via the GpIIb-IIIa receptor and is cleaved by thrombin to form insoluble fibrin polymers. These polymers are further cross-linked by factor XIIIa to form a stable clot that is eventually broken down by plasmin.Fibrinogen is an acute phase reactant synthesized by the liver and may be elevated in inflammatory conditions. Decreased levels may be due to underproduction (e.g., intrinsic liver disease, protein malnutrition, rare genetic disorders) or over “consumption” (e.g., disseminated intravascular coagulation).Coagulation, Inflammatory
Folate, serumHB 3.2≥4.0 μg/LFolate (vitamin B9) is an essential water-soluble vitamin that is a coenzyme for one carbon metabolism. Biochemically, a carbon unit from serine or glycine is transferred to tetrahydrofolate (THF) to form methylene-THF, which then is 1) used in the synthesis of thymidine (and incorporation into DNA); 2) oxidized to formyl-THF for use in the synthesis of purines (precursors of RNA and DNA); or 3) reduced to methyl-THF, which is necessary for the methylation of homocysteine to methionine.Megaloblastic anemia (characterized by large, abnormally nucleated erythrocytes in the bone marrow) is the major clinical manifestation of folate deficiency. Low serum folate concentrations in pregnancy are associated with neural tube defects. Folate deficiency may be due to poor absorption (e.g., celiac disease), insufficient intake (e.g., chronic excess alcohol use) and medications (e.g., methotrexate). Folate deficiency in the United States has become less common with widespread supplementation of breads, grains, and other foods with folate.Hematologic
Follicle-stimulating hormone (FSH), serumCHEM 1.3Varies with age, sex, menstrual cycle and sexual development (i.e., Tanner stage) Adult males: 1.2–15.8 IU/LAdult females:Premenopausal:Follicular: 2.9–14.6 IU/LMidcycle: 4.7–23.2 IU/LLuteal: 1.4–8.9 IU/LPostmenopausal: 16.0–157.0 IU/LFSH is a gonadotropin released by the anterior pituitary in response to gonadotropin releasing hormone (GnRH). It is most specifically associated with initiating follicular growth in ovaries. The mid-menstrual cycle surge in FSH and luteinizing hormone (LH) culminates in ovulation.FSH assays can be useful in assessing fertility, in the evaluation of menstrual irregularities, predicting ovulation and investigating pituitary disorders. FSH and LH may be elevated in primary gonadal failure, precocious puberty and menopause. FSH may be normal or decreased in polycystic ovary syndrome. Both FSH and LH are decreased with pituitary or hypothalamic dysfunction.Endocrine
Gamma-glutamyltranspeptidase (GGT), serumCHEM 1.4Adult males: 8–61 U/LAdult females: 5–36 U/LGGT is a membrane protein that transfers gamma glutamyl groups from substrates such as glutathione to other peptides and amino acids. It is central to the synthesis and degradation of glutathione, an antioxidant that also plays a role in the detoxification of xenobiotics. GGT is present in multiple tissues including liver, kidney and pancreas.The highest levels of GGT elevations are seen in intra- and posthepatic biliary obstruction; moderate levels are less specific and can be seen in all types of liver disease (e.g., alcohol-related hepatitis) and with some medications (e.g., anticonvulsants, oral contraceptives). Combined elevations of alkaline phosphatase and GGT suggest biliary tract disease.39 (link)Hepatic
Glucose, serumCHEM 1.3≥1 year old: 70–140 mg/dLPhysiologic glucose levels are primarily maintained by insulin and glucagon. Hyperglycemia may be due to either insufficient insulin (e.g., type I diabetes) or peripheral insulin resistance (e.g., type II diabetes). Measurement of serum glucose is useful in the diagnosis and management of diabetes.Glucose levels vary depending on whether or not an individual is fasting. For the diagnosis of diabetes, a repeat test on a different day is necessary. Hemoglobin A1c provides a longer-term assessment of glucose control and is thus complementary to day-to-day glucose levels. Hypoglycemia, usually in the setting of excess insulin dose, can be life threatening.BMP/Chem 7, Endocrine
Growth hormone (GH; somatotropin), serumCHEM 1.3Adult males: 0.01–0.97 ng/mLAdult females: 0.01–3.61 ng/mLGH secretion from the somatotroph cells in the anterior pituitary is stimulated by ghrelin (stomach) and GH releasing factor (GHRH) (hypothalamus) and inhibited by somatostatin (hypothalamus). GH and insulin-like growth factor 1 (IGF-1) inhibit GH secretion. GH induces growth in most tissues and organs, but its effect is most pronounced on cartilage and bone. GH levels increase in childhood, are at their peak during puberty and decrease with increasing age.Low levels of GH in infancy or early childhood can cause dwarfism and elevated levels causes gigantism in children (before physis closure) or acromegaly once the growth plate has closed. GH is released in a pulsatile fashion such that random GH levels are of little diagnostic value. GH stimulation tests use drugs (e.g., l-dopa, clonidine) to prompt GH secretion. IGF-1 levels are also informative. Since GH counteracts the effect of insulin, type 2 diabetes and hyperlipidemia are associated with acromegaly.Endocrine
Growth hormone releasing hormone (GHRH), serumCHEM 1.3Baseline ranges: 5–18 pg/mLGHRH stimulates synthesis and secretion of growth hormone (GH) by the anterior pituitary. GHRH is secreted in a pulsatile fashion, with a bolus at the onset of sleep. Hypothalamic somatostatin suppresses release of both GH and GHRH. GHRH synthesis is inhibited by GH and IGF-1. GHRH elaboration is modulated by a number of proteins including thyroid hormones, glucocorticoids, leptin, ghrelin and testosterone and estrogen.Excess GHRH may be due to hypothalamic tumors or as a paraneoplastic syndrome (e.g., well differentiated neuroendocrine tumors). Excess GHRH can cause gigantism or acromegaly, sporadically or as part of multiple endocrine neoplasia syndrome. Decreased GHRH can result in dwarfism.Endocrine
Haptoglobin, serumH 4.130–200 mg/dLHaptoglobin is a serum protein produced by the liver that binds to hemoglobin released by lysed red blood cells (RBCs). Hemoglobin-haptoglobin complexes are rapidly removed from the circulation by the reticuloendothelial system. If the rate of hemolysis overwhelms the binding capacity of serum haptoglobin, free hemoglobin passes through the kidneys (hemoglobinuria). Haptoglobin is an acute-phase reactant and its levels may increase in certain conditions (e.g., extensive burns).Haptoglobin levels are useful in the evaluation of hemolysis. Haptoglobin levels decrease in extensive hemolysis (e.g., autoimmune hemolytic anemia, transfusion reaction) and may be persistently low with chronic intravascular hemolysis. Significant liver disease (e.g., cirrhosis) can also cause reduced haptoglobin levels. Haptoglobin elevations can be seen during stress or inflammation; comparison with additional acute-phase reactants (e.g., CRP) may be indicated.Hematologic
Helicobacter pylori breath testM 1.3NegativeH. pylori causes chronic gastritis, peptic ulcer disease, gastric adenocarcinoma and lymphoma. The organism produces urease, which neutralizes gastric acid and provides ammonia for bacterial protein synthesis. Patients with suspected H. pylori infection ingest a small amount of urea labeled with a rare isotope (e.g., nonradioactive carbon-13); when H. pylori organisms are present, they split the urea, releasing isotope-labeled carbon dioxide in the patient's breath. The carbon isotope can be quantified and is proportional to the urease activity.This high sensitivity, high specificity test may be used for initial diagnosis of H. pylori infection and for confirming H. pylori eradication. By comparison, since infection may be localized, gastric biopsy may provide a false negative. Antibiotics and drugs that suppress gastric acid production may also cause false negative results. False positive results may be seen in the setting of achlorhydria and infection with other urease-positive organisms. This test should not be used for screening asymptomatic patients.24 Gastrointestinal
Helicobacter pylori stool testM 1.3NegativeH. pylori causes chronic gastritis, peptic ulcer disease, gastric adenocarcinoma and lymphoma. H. pylori is shed in the stool of infected patients. Two types of tests evaluate the presence of H. pylori in the stool: 1) enzyme immunoassay or immunochromatography for bacterial antigens and 2) PCR for H. pylori bacterial sequences. These tests are noninvasive, in contrast to gastric biopsy.These high sensitivity, high specificity tests may be used for initial diagnosis of H. pylori infection and for confirming H. pylori eradication. Effective treatment results in loss of stool antigen within 4+ weeks. Antibiotics and drugs that suppress gastric acid production may cause false negative results.24 Gastrointestinal
Hematocrit (Hct), bloodH 4.2Males: 38–49%Females: 35%–45%Spun hematocrit (packed cell volume) is the percentage of blood volume that is taken up by packed red blood cells (RBCs) in a centrifuged sample. Hematology analyzers calculate hematocrit from the mean corpuscular volume (MCV) and the red blood cell count (Hct = (MCV x red blood cell count/10)) or derive it by measuring the cumulative volume of red blood cells in the sample.The hematocrit is decreased in anemia and increased in polycythemia. It may be falsely elevated in the setting of sickled RBCs, dehydration and severe hypertriglyceridemia and may be falsely decreased following volume resuscitation. The hematocrit is approximately three times the hemoglobin (assuming the RBCs are normal in size and shape).40 Hematologic
Hemoglobin A1c (HbA1c), bloodCHEM 1.34.0–5.6%When glucose attaches nonezymatically to hemoglobin, a glycated hemoglobin (HbA1c) is formed. This process occurs continually and therefore reflects mean plasma glucose levels over the course of red blood cell's life span of 8–12 weeks. Patients with high average blood concentrations of glucose (e.g., diabetes) will have higher HbA1c levels than those with unimpaired glucose metabolism.HbA1c is the key laboratory test for monitoring long-term glucose control. HbA1c is also a diagnostic test for diabetes: HbA1c of 6.5% or higher on two different days is diagnostic of diabetes. HbA1c can also identify patients who may become diabetic: values of 5.7–6.4% are associated with increased risk of diabetes. HbA1c may be falsely low in conditions associated with shortened red blood cell lifespan (e.g., hemolysis, blood loss, hemoglobinopathies).Endocrine
Hemoglobin S (HbS), bloodH 4.4AbsentHbS has a valine residue instead of the normal glutamate residue at position 6 of beta-globin. The protein tends to aggregate and polymerize in the deoxygenated state. Homozygosity for HbS results in sickle cell anemia (SCA), while heterozygosity for this allele results in sickle cell trait, which is typically asymptomatic. The HbS allele confers a heterozygote advantage in the setting of falciparum malaria and proliferated in ancestral populations affected by this parasite (e.g., sub-Saharan Africa, parts of Southern Europe, the Middle East and India).Recent transfusions can lower HbS concentration and complicate diagnosis of sickle cell disease. Measurement of HbS pre- and post-transfusion by serum electrophoresis is frequently used to monitor patients with SCA on regular transfusion protocols. In sickle cell trait, HbS should be between 35% and 45%; higher values suggest concurrent beta thalassemia trait, while lower values suggest concurrent alpha thalassemia trait. The presence of HbS may artifactually alter hemoglobin A1c levels.Hematologic
Hemoglobin, bloodH 4.2Males: 13.2–16.6 g/dLFemales: 11.6–15.0 g/dLHemoglobin is the oxygen-carrying molecule in red blood cells (RBCs). The hemoglobin molecule is a tetramer that, after the first year of life, consists of two alpha globin chains and two beta globin chains. Each subunit contains a heme molecule composed of an iron molecule in a porphyrin ring. Each heme molecule can bind one oxygen molecule. Automated hematology analyzers calculate hemoglobin by lysing the RBCs and measuring the hemoglobin concentration by optical density.Hemoglobin is decreased in anemia and increased in polycythemia. It can be falsely elevated in hyperlipidemia due to increased plasma turbidity. Hemoglobin is approximately one third the hematocrit (assuming the RBCs are normal size and shape).40 ,41 (link)Hematologic, CBC
Heparin-PF4 IgG antibody, serumH 2.1AbsentAntibodies to heparin-platelet factor 4 (PF4) complexes form in a subset of patients following heparin administration and cause heparin-induced thrombocytopenia (HIT), which is characterized by a decrease in platelet count of 50% or more from baseline, generally beginning 5–10 days after heparin administration. These patients are at risk for venous and arterial thromboembolism.While the test is sensitive (98–100%), specificity is limited since not all anti-PF4 antibodies activate or deplete platelets. Assays that specifically measure heparin-PF4 IgG antibodies are more sensitive and specific than those that also measure IgA and IgM antibodies. In most laboratories, measurement is by ELISA. The serotonin release assay is more sensitive and is recommended for confirmation of a positive result.42 (link)Coagulation
Hepatitis A virus (HAV) IgG antibody, serumM 3.1NegativeHAV is a picornavirus that is spread by the fecal-oral route. IgG antibodies directed against HAV (IgG anti-HAV) are produced at the onset of clinical symptoms. These antibodies persist and provide immunity for the patient's lifetime.IgG anti-HAV are produced by either acute infection with hepatitis A or through immunization. A positive test indicates immunity to HAV but does not indicate acute infection.43 Hepatic
Hepatitis A virus (HAV) IgM antibody, serumM 3.1NegativeHAV is a picornavirus that is spread by the fecal-oral route. IgM antibodies directed against HAV (IgM anti-HAV) are produced 5–10 days before the onset of clinical symptoms; levels decline after 3–6 months and become undetectable.The presence of IgM anti-HAV is used to diagnose acute infection with HAV. The total anti-HAV test assesses both IgG and IgM antibodies. HAV infection is associated with acute, self-limited illness and does not lead to a carrier state or to chronic disease.43 ,44 Hepatic
Hepatitis A virus (HAV) polymerase chain reaction (PCR), serumM 3.1NegativePCR can be used to detect HAV RNA during the viremic period, shortly after infection, until alanine aminotransferase (ALT) levels decline.Detection of viral RNA can be used to confirm acute infection and is particularly useful in assessing outbreaks or response to therapy. It can also be used to confirm that blood products are free of virus prior to transfusion. This test is not as commonly used as serologic tests for diagnosis in clinical practice.43 ,44 Hepatic
Hepatitis B virus core (HBc) antibody, IgM, serumM 3.1NegativeHBc is a nucleocapsid protein necessary for virion assembly. IgM antibodies to HBc can be detected after symptom onset and remain in the serum for about 6 months after initial infection. A positive test for IgM indicates recent infection. HBc IgM may be the only serologic test that is positive once HBV surface antigen declines and before the appearance of hepatitis B virus (HBV) surface antibody (“serologic window period”).Anti-HBc IgM is produced during acute infection and decreases after a few months, regardless of whether the infection is acute and resolves or remains chronic. Anti-HBc antibodies are produced only when the patient has been naturally infected with hepatitis B and are not seen in individuals who have been vaccinated against HBV.Hepatic
Hepatitis B virus e-antibody (HBeAb), serumM 3.1NegativeHBeAb is seen in patients recovering from acute hepatitis and is typically present before HBsAg to HBsAb conversion. As HBeAb increases, HBeAg decreases.HBeAb is a sign of resolving acute hepatitis. HBeAb is produced in patients who have been naturally infected with hepatitis B and is absent in individuals who have been vaccinated.Hepatic
Hepatitis B virus surface antibody (HBsAb), serumM 3.1NegativeHBsAb are antibodies to the 3 related viral envelope proteins encompassed by HBsAg. Levels typically increase with resolution of acute hepatitis and falling HBsAg. However, in some patients, HBsAb is not detectable for months after HBsAg disappears; in such patients, diagnosis can be confirmed by IgM for hepatitis B virus core protein.HBsAb will be present after vaccination or after clearance of active infection, but may be delayed for months. Once present, it persists for life. HBsAb can be seen in vaccinated individuals (since HBsAg is the basis for the vaccine) or in individuals who have been naturally exposed to HBV.Hepatic
Hepatitis B virus surface antigen (HBsAg), serumM 3.1NegativeHBsAg encompasses 3 related envelope glycoproteins (large, medium and small). Large HBsAg is seen in complete, infective virions whereas small HBsAg are noninfective. HBsAg is the first serologic marker to be detectable, even before a patient is symptomatic, typically 6–16 weeks after HBV infection. With resolution of acute hepatitis, HBsAg disappears about 12 weeks after symptom onset.Persistence of HBsAg 6 months or more is seen in chronic carrier states and chronic HBV infection. Recombinant HBsAg is the basis for the HBV vaccine. Therefore, HBsAg may be seen transiently in individuals (particularly neonates and children) who have recently received the HBV vaccine; typically, HBsAg is only seen in patients who have been naturally infected with hepatitis B.Hepatic
Hepatitis B virus core (HBc) total antibodies, serumM 3.1NegativeHBc is a nucleocapsid protein necessary for virion assembly. Antibodies to HBc can be detected soon after symptom onset and after antibodies to HBV surface antigen are present. Initial antibodies are IgM, followed by IgG. Total Anti-HBc antibody is a measure of IgM and IgG.Total HBc antibody persists for life; therefore, a positive test does not indicate recent or chronic infection. Neonates with a positive test result should be evaluated for anti-HBc IgM to exclude transplacental antibody transfer from the mother. Anti-HBc antibodies are produced only when the patient has been naturally infected with hepatitis B and are not seen in individuals who have been vaccinated against HBV.Hepatic
Hepatitis B virus DNA PCR, serumM 3.1NegativeHBV DNA is detectable by 30 days after infection, about 3 weeks before HBsAg appears, peaks with acute hepatitis, and slowly declines with resolution of infection. Although serologic methods are the primary means of diagnosis in acute HBV infection, HBV DNA PCR is useful for the diagnosis of early infection, prior to appearance of HBsAg; differentiating between active and inactive HBV infection; and monitoring response to anti-HBV treatment.HBV DNA levels can be useful in the further classification of patients with chronic HBV infection as chronic active (high levels of HBV DNA, positive for HBeAg) and chronic inactive (low or no HBV DNA, negative for HBeAg). With reactivation of inactive chronic HBV, HBeAg may be negative, leaving HBV DNA as the only indication of active viral replication.Hepatic
Hepatitis B virus e-antigen (HBe–Ag), serumM 3.1NegativeThe hepatitis B virus e-antigen (HBeAg) is a secretory protein that is seen in active viral replication. HBeAg can be detected soon after HBV surface antigen appears.While HBeAg is detectable, active infection is ongoing. It can be seen in both acute and chronic hepatitis. Some strains of hepatitis B do not produce HBe antigen, however. High HBeAg levels in the absence of HBe antibody (HBeAb) are associated with active viral replication and high infectivity; as HBeAb levels rise, infectivity decreases. HBeAg may be used to monitor disease activity in individuals who are carriers for HBV and individuals with chronic hepatitis B infection.Hepatic
Hepatitis C virus (HCV) antibody screen, serumM 3.1NegativeIgG antibodies to HCV are generally not detectable for the first two months after infection, but are typically seen by 6 months. Delay is more common in individuals who are immunocompromised. Antibodies do not confer protection from the virus. Though typically persistent, they can be lost over time.The majority of patients infected with HCV are asymptomatic. Screening for HCV is recommended at least once in adults and during each pregnancy. Additional testing may be needed with certain medical conditions, exposures, or risk factors. A negative antibody screen is seen in truly negative individuals but can also be seen in very early infection (in the window period before antibodies are detectable). Since IgG antibodies typically persist, a positive test requires RNA testing to confirm active disease.43 Hepatic
Hepatitis C virus RNA detection by reverse transcription polymerase chain reaction (RT-PCR), serumM 3.1UndetectedHepatitis C virus (HCV) is a small, enveloped RNA virus; its RNA is detectable 1–3 weeks after infection (1–1.5 months before HCV antibodies are seen) and can be reported either qualitatively or quantitatively (via real time RT-PCR).The majority of patients infected with HCV are asymptomatic. Serologic testing is the usual modality for determining HCV infection. In chronic HCV infection, circulating HCV RNA persists in 90% of patients despite the presence of neutralizing antibodies. Viral load (quantitative HCV RNA) and genotype are used to guide treatment decisions; viral load is useful in following response to treatment. A positive antibody screen with no detectable HCV RNA indicates clearance of the infection.43 Hepatic
Hepatitis D virus total antibodies, serumM 3.1NegativeHepatitis D virus (HDV) is a defective RNA virus that cannot replicate without HBV, which provides HBsAg. Infection can either by simultaneous with HBV (coinfection) or acutely in the context of chronic HBV infection (superinfection). IgM anti-HDV appears 2–3 weeks after infection and is a reliable indicator of recent HDV exposure, but is frequently short-lived. Acute coinfection by HDV and HBV is associated with the presence of IgM against HDAg and HBcAg (denoting new infection with hepatitis B). When chronic hepatitis arises from HDV superinfection, HBsAg is present in serum, and anti-HDV antibodies (IgG and IgM) persist for months or longer.Patients with HDV antibodies should be evaluated for IgM HBc; their presence indicates HBV-HDV coinfection, which has a higher risk for progression to cirrhosis. A negative IgM HBc indicates superinfection in a patient with chronic HBV.Hepatic
Hepatitis E Virus IgM and IgG antibodies, serumM 3.1NegativeHepatitis E virus (HEV) is an unenveloped RNA virus that is primarily transmitted by the fecal-oral route. Like HAV, HEV causes acute, self-limited illness; however chronic hepatitis can occur in patients who are immunocompromised. Symptoms typically become apparent 2 weeks to 2 months after exposure. IgM antibodies are detectable early and disappear within 4–5 months. IgG antibodies appear almost immediately after the IgM response; it is not clear how long they persist.Acute HEV infection in the third trimester of pregnancy has a high mortality rate (15–25%). Patients who are immunocompromised may have prolonged viral shedding. Tests for IgM and IgG antibodies may be negative, even in patients with HEV infection, but infection can be confirmed by PCR and stool culture.43 Hepatic
Hexoasaminidase A activity, leukocytesACD 3.2≥16 years old: 56–80% of total hexosaminidase activityHexosaminidase A levels are decreased in the lysosomal storage disorder, Tay-Sachs disease, a GM2 gangliosidosis caused by deficiency of the ∝ subunit of hexosaminidase A. Loss of this enzyme causes GM2 ganglioside to accumulate in cells. Hexosaminidase A and hexosaminidase B are isoenzymes. This test measures activity of total hexosaminidase (A and B) using an artificial substrate, followed by heat inactivation of hexosaminidase A and a repeat activity test to calculate the percentage activity of hexosaminidase A.False positive results can be seen due to pseudodeficiency alleles that produce enzymes that are active in vivo but that have decreased activity with the artificial substrate used in the enzyme assay. This test can also be used to detect carrier status.45 ,46 (link)Nervous
High-risk HPV (hrHPV) test, site variesGE 3.1Not detectedMost invasive cervical cancers are squamous cell carcinoma; persistent infection with high-risk human papillomavirus (HPV) is usually necessary but not sufficient for the development of squamous cell carcinoma. HrHPV DNA integrates into the host genome and disrupts the viral DNA in the E1/E2 open reading frame, leading to loss of the E2 viral repressor and over-expression of E6 and E7 oncoproteins. E6 and E7 normally inactivate tumor suppressors, activate cyclins and inhibit apoptosis; therefore, overexpression of E6 and E7 extends the lifespan of epithelial cells. E6 and E7 bind to and increase the degradation of p53 and Rb tumor suppressor proteins respectively, and E7 inactivates the cyclin-dependent kinase (CDK) inhibitor p21.The goal of HPV screening is to identify HPV types likely to progress to cervical carcinoma. Pap test and hrHPV tests may be used alone or in combination; many countries and professional organizations recommend testing for hrHPV types first, followed by a Pap test in some situations.47 (link)Gynecologic
High density lipoprotein (HDL), serumCHEM 1.2Males: ≥ 40 mg/dLFemales: ≥ 50 mg/dLOf the lipoproteins (HDL, low density lipoprotein [LDL], very low density lipoprotein [ VLDL]), HDL is the smallest and has the highest ratio of proteins to lipids (about 50% protein). HDL transports cholesterol from the periphery to the liver where it is catabolized and excreted.Low levels of HDL are a risk factor for atherosclerosis. HDL levels may be increased due to exercise, alcohol consumption and some medications (e.g., hormone replacement therapy).Vascular
HIV antibody/antigen, plasmaM 3.4NegativeThird generation IgM and IgG tests can detect the presence of antibodies 20–30 days after human immunodeficiency virus (HIV) exposure and are often the initial screening test used for HIV infection. Combination HIV antigen/antibody tests detect IgG and IgM antibodies as well as the HIV p24 antigen and can become positive 15–20 days after exposure. By comparison, HIV RNA tests can be positive 10–15 days after exposure.First-time positive tests should be confirmed by another method (e.g., HIV RNA, HIV-1/HIV-2 differentiation assay). Combination tests can detect p24 antigen before seroconversion (the “window period”). Detection occurs earlier for both antibody tests and combination tests with blood taken by venipuncture rather than from a finger stick (18–45 days vs 18–90 days). Rapid antibody tests have > 99% specificity and sensitivity in chronic infection, but are less sensitive in acute infection.Immunologic
HIV DNA, plasmaM 3.4UndetectedDiagnosis of HIV infection is primarily serologic (i.e., detection of HIV-specific antibodies). However, in neonates (who have immature immune systems and who may have maternal anti-HIV antibodies), in early HIV infection (< 30 days from exposure) or in individuals with equivocal serologic results, assays for HIV pro-viral DNA and HIV RNA are useful adjuncts. These tests are typically informative 10–14 days after infection.Although antiretroviral therapy can decrease viral load in plasma to undetected levels, disease is not eradicated. Viral rebound is linked to the persistence and transcriptional activation of HIV proviral DNA, which can be assessed by this test. Neonates born to mothers who are HIV positive should have DNA/RNA tests at multiple intervals (e.g., 0–2 days, 2 weeks, 1–2 months, and 4–6 months after birth). For accurate diagnosis in children under two years, two consecutive positive nucleic acid tests are necessary.Immunologic
HIV NAT (nucleic acid test), plasmaM 3.4UndetectedNAT is used to detect a particular nucleic acid sequence for a specific organism (e.g., HIV, Neisseria gonorrhoeae). Quantitative assays can be used to guide antiretroviral therapy, while qualitative assays are used for HIV diagnosis. NAT can detect infection 10–33 days after exposure, compared to antigen/antibody tests (18–45 days after exposure) and antibody tests (23–90 days). NAT is based on DNA or RNA detection using RT-PCR, nucleic acid sequence-based amplification (NASBA) and technologies based on branched chain DNA methods (b-DNA), transcription-mediated amplification (TMA) and real time PCR.The NAT qualitative test is mainly used at donor centers to confirm safety of blood products and for early diagnosis in infants born to mothers who are HIV positive.48 (link)Immunologic
HIV RNA (HIV viral load), plasmaM 3.4UndetectedMore than 99% of HIV cases worldwide are due to HIV-1. Therefore, this is the viral type most commonly assessed. HIV viral load (number of HIV-1 RNA copies/mL of plasma) correlates with disease stage and, combined with CD4+ T cell numbers, is useful in monitoring response to treatment. This test determines how actively virus is replicating in a person with HIV infection. US Health and Human Services defines > 200 copies/mL as virologic failure.When 2 tests performed at least 2–4 weeks apart show virologic failure, drug-drug interactions and patient adherence to the regimen should be evaluated. At determined levels (e.g., 500 copies/mL), testing for drug resistant genotypes may be warranted.Immunologic
Human chorionic gonadotropin (hCG), serumCHEM 1.3Males and non-pregnant females: < 5 mIU/mLVaries during pregnancyhCG is a hormone comprised of α and β subunits. The α subunit is the same as that of follicle stimulating hormone (FSH), luteinizing hormone (LH) and thyroid stimulating hormone (TSH); therefore, most tests assess levels of the β subunit to increase sensitivity. During the first trimester, hCG synthesized by placental syncytiotrophoblastic cells stimulates the corpus luteum to secrete progesterone; subsequently, the placenta secretes progesterone and hCG levels fall. hCG may also be secreted by neoplasms derived from germ cell, placental, or embryonic origins.hCG is commonly measured in pregnancy tests and is usually significantly above baseline levels by 4–5 weeks gestation in a healthy uterine pregnancy. hCG rises more slowly in ectopic pregnancy. hCG levels may be extremely elevated in choriocarcinoma and molar pregnancies. In males, elevated hCG raises the possibility of seminomatous and nonseminomatous testicular tumors. hCG is clinically useful as a tumor marker for diagnosis and disease monitoring.Endocrine
Human herpesvirus 8 (HHV8), bloodM 3.3Quantitative real-time PCR: <1000 copies/mLHHV8 (also known as Kaposi sarcoma-associated herpesvirus, KSHV) is a DNA virus that is associated with Kaposi sarcoma (KS), primary effusion lymphoma and Castleman disease. HHV8 seroprevalence varies geographically and is common, underscoring the importance of host factors (e.g., immune status, proinflammatory cytokines) in development of disease. HHV8 infects multiple cell types, including B cells and endothelial cells, in which it can remain latent, thereby escaping immune surveillance and resulting in lifelong infection. When HHV8 enters the lytic phase, intact, infectious virions are produced.HHV8 is associated with all four types of KS (i.e., classic, endemic, organ transplant-associated, epidemic/AIDS related). KS will often regress with reduction of immunosuppressive medication in transplant patients; however, this raises the risk of transplant rejection. Primary effusion lymphoma arises in the pericardial, pleural and peritoneal cavities. HHV8 positivity can be seen in all variants of Castleman disease in patients who are HIV-positive and patients who are HIV-negative.Vascular
International normalized ratio (INR), plasmaH 2.10.9–1.1The prothrombin time (PT), which is used as a screening test for coagulopathies, shows intra- and interlaboratory variation due to differences in instruments used and variable tissue factor activity. To correct for these differences, the INR is calculated by dividing the patient's PT by a control PT with a standardized thromboplastin reagent.INR is most commonly used as a means to monitor response in patients who are being anticoagulated with vitamin K antagonists (e.g., warfarin). It is also used to assess patients with bleeding diatheses secondary to defects in the extrinsic pathway, in disseminated intravascular coagulation and to monitor patients with end-stage liver disease.Coagulation
Intrinsic factor (IF) antibodies, serumIMM 1.4 and H 4.1NegativeIntrinsic factor is secreted by gastric parietal cells and binds to vitamin B12, facilitating its absorption in the terminal ileum. In pernicious anemia, autoantibodies to IF prevent vitamin B12 binding, leading to vitamin B12 deficiency. Vitamin B12 deficiency can manifest as megaloblastic anemia and neurologic symptoms.Although anti-IF antibodies are very specific, they are positive in only about 50% of patients with pernicious anemia. False positives can occur when patients have received intramuscular or subcutaneous vitamin B12.Gastrointestinal
Iron, serumH 3.2Males: 50–150 mg/dLFemales: 35–145 mg/dLMost of the body's iron is incorporated into hemoglobin. Iron can also be stored in tissues (complexed with ferritin) or transported in the serum (bound to transferrin). When iron stores in the body are depleted (e.g., iron deficiency anemia), transferrin levels increase in the blood, which increases the total iron binding capacity (TIBC). Percent saturation is calculated using serum iron and TIBC. Iron stores can also be evaluated via bone marrow aspirate.In iron deficiency, TIBC is increased, since transferrin levels are relatively high compared to iron content; in iron overload, TIBC decreases since the free transferrin diminishes. TIBC, serum iron and percent saturation are often assessed in the setting of iron deficiency anemia; however, serum ferritin is more sensitive and more accurately reflects the body's iron stores.Hematologic
Lactate dehydrogenase (LDH), serumCHEM 1.4≥ 18 years: 122–222 U/LLactate dehydrogenase is an enzyme that is present in almost all cells. Five different isomers of LDH are expressed at different levels in different tissues. High concentrations of LDH are present in liver, muscle, and kidney; moderate concentrations are present in red blood cells.Serum LDH levels are increased in conditions associated with cell damage/death, including myocardial infarction, liver disease, hemolytic anemia, megaloblastic anemia, pulmonary embolus, and tumors such as metastatic melanoma and lymphoma. Falsely elevated serum LDH levels may occur if the blood specimen becomes hemolyzed in vitro.Hepatic
Lead, bloodCHEM 1.7Children <5 mg/dLAdults:≤ 40 mg/dL (occupational)Most lead is absorbed via the gastrointestinal tract and can be distributed throughout the body, with some preference to bone, erythrocytes and keratin-rich tissues. Adults typically absorb 1–10% of the ingested amount; this increases to up to 50% in children, particularly if they have coexistent nutritional deficiencies. Lead forms covalent bonds with protein cysteine sulfhydryl groups; this contributes to renal toxicity and accumulation in keratin-rich hair. Lead decreases heme biosynthesis and acts as a mitochondrial toxin.Clinical manifestations vary by age. Children may show decreased nerve conduction velocity, decreased vitamin D metabolism, abdominal pain, anemia, nephropathy and encephalopathy. Lead incorporated into the physes can be seen radiographically as “lead lines”. In adults, initial presentation is typically elevations of systolic pressure and decreased hearing, progressing to peripheral neuropathies and nephropathy, and finally to anemia and encephalopathy at later stages.26 (link)Toxicology
Lipase, serumCHEM 1.213–60 U/LLipase is a digestive enzyme produced in pancreatic acinar cells and secreted into the duodenum to digest lipids. With acinar cell injury (e.g., acute pancreatitis), lipase can be released into the pancreas itself where it contributes to local tissue damage, including acute inflammation, autodigestion of pancreatic parenchyma, fat necrosis and vascular damage.Serum lipase is elevated in acute pancreatitis and is a more sensitive and specific test than serum amylase. In this setting, serum lipase is typically elevated > three times the upper limit of normal. The degree of lipase elevation does not correlate with the severity of pancreatitis. Serum lipase increases within 4–8 h in acute pancreatitis and may remain elevated for up to 14 days. Lipase has limited utility for the diagnosis of chronic pancreatitis due to destruction of pancreatic parenchyma.Pancreatic
Lipoprotein (a) (Lp[a]), serumCHEM 1.2<5 mg/dLLp(a) is composed of apolipoprotein(a) bound to the apo(b) moiety of LDL via a disulfide bridge. Lp(a) is atherogenic and prothrombotic. Proposed mechanisms include interference with fibrinolysis, macrophage binding and recruitment in atherosclerotic plaques, and disruption of normal endothelial function.Increased lipoprotein (a) is an independent risk factor for cardiovascular diseaseVascular
Low density lipoprotein (LDL), serumCHEM 1.2Adults: <100 mg/dL, desirableFifty percent of the total lipoprotein mass is LDL which is the product of VLDL metabolism. It is composed of cholesterol (50%), protein (25%), phospholipid (20%) and a trace amount of triglycerides (TG). LDL delivers cholesterol to peripheral tissues: ApoB located on the LDL surface binds to LDL receptors on the cell surface. LDL in serum can be measured directly but more commonly is estimated by the Friedewald equation: [LDL] = [Total cholesterol] - [HDL] - ([TG]/5), with concentrations in mg/dL. The calculated value may be inaccurate in the setting of markedly elevated triglycerides.LDL is a major component of atheromatous plaques and elevated LDL is a risk factor in cardiovascular disease. Serum levels are affected by lifestyle factors (e.g., diet, exercise) and some diseases. Conditions in which LDL levels are elevated include familial hypercholesterolemia, hypothyroidism, uncontrolled diabetes, nephrotic syndrome, Cushing syndrome, and corticosteroid use. LDL levels are typically decreased in severe liver disease, hyperthyroidism and in the setting of severe acute or chronic illness, malnutrition, malabsorption or extensive burns.Vascular
Luteinizing hormone, serumCHEM 1.3Males: > 18 years: 1.3–9.6 IU/LFemales: Premenopausal:Follicular: 1.9–14.6 IU/LMidcycle: 12.2–118.0 IU/LLuteal: 0.7–12.9 IU/LPostmenopausal: 5.3–65.4 IU/LLuteinizing hormone (LH) is a hormone co-secreted with follicle stimulating hormone (FSH) by the anterior pituitary gland in response to gonadotropin-releasing hormone (GnRH) from the hypothalamus. It is composed of α and β subunits. The α subunit is identical with the α subunit of follicle stimulating hormone (FSH), thyroid stimulating hormone, and human chorionic gonadotropin. LH is essential for reproduction in both sexes.LH is measured in the workup of hypogonadism and will be low if failure is central (pituitary gland or hypothalamus) and elevated if failure is primary due to the ovaries or testes. LH is measured to predict ovulation and in the workup of menstrual irregularities and infertility.Endocrine
Lymphocyte count, bloodH 4.20.95–3.07 × 109/LLymphocytes are a subset of white blood cells (WBC) that includes T cells, B cells, and NK cells. Lymphocytes are the most plentiful circulating WBC type in young children, and the second most plentiful WBC type (after neutrophils) in healthy adults.The most important causes of significant lymphocytosis include viral infections, autoimmune diseases and lymphoproliferative disorders (e.g., chronic lymphocytic leukemia). Lymphocytopenia may be due to infections (especially HIV), immunosuppressive therapy, medications (e.g., corticosteroids) and inherited immunodeficiency syndromes. Lymphocyte subsets (e.g., CD4, CD8) can be determined by flow cytometry.Hematologic, CBC
Mean corpuscular hemoglobin (MCH), bloodH 4.226.5–34.0 pgaMCH is a measure of the average quantity of hemoglobin (Hgb) per red blood cell (RBC). It is calculated by dividing hemoglobin by the RBC count (MCH = Hgb x 10/RBC count). MCH and mean corpuscular volume (MCV) are related such that when MCV is low, MCH is also low. When MCH is low, the oxygen-carrying capacity of the blood is reduced.The most common cause of low MCH is iron deficiency. Elevated MCH may be seen in megaloblastic anemia due to folate or vitamin B12 deficiency.40 CBC
Mean corpuscular hemoglobin concentration (MCHC), bloodH 4.2Males: 31.5–36.3%aFemales: 31.4–36.0%aMCHC is the average concentration of hemoglobin (Hgb) per red blood cell. It is calculated by dividing hemoglobin by hematocrit (Hct) (MCHC = Hgb x 10/Hct).MCHC is increased in spherocytosis and homozygous hemoglobin C and sickle cell anemia. Since the MCHC is calculated from the Hgb and Hct, inaccuracies in their measurement (e.g., due to hyperlipidemia or hyperbilirubinemia), will result in artificially high MCHC. Free plasma hemoglobin due to hemolysis can also cause a falsely high MCHC. Though MCHC is decreased in iron deficiency anemia, it is not a sensitive test for this condition.40 CBC
Mean corpuscular volume (MCV), bloodH 4.278.2–97.9 fLMCV is directly measured by many automated hematology analyzers or can be calculated from hematocrit (Hct) and red blood cell (RBC) count (MCV = Hct x 10/red blood cells). When MCV is increased, RBCs are called macrocytic; when MCV is low, they are microcytic.MCV is elevated in reticulocytosis (e.g., hemolytic anemia), megaloblastic anemia (e.g., vitamin B12 or folate deficiency) and myelodysplasia. MCV may be falsely elevated in red blood cell agglutination. MCV is decreased in a variety of anemias including iron deficiency anemia, anemia of chronic disease, thalassemia/thalassemia trait and sideroblastic anemia.40 CBC
Mercury, bloodCHEM 1.7<10 ng/mLMercury is primarily absorbed from the GI tract. It can bind to sulfhydryl groups on proteins. It is lipophilic, which enables it to cross the placenta and to concentrate in lipid-rich tissues such as the central nervous system. Because it is cleared by the kidney, renal damage may result.Mercury affects the motor, sensory, cognitive and behavioral functions of the brain. Acute toxicity is associated with renal tubular injury and oliguria or anuria. Mercury exposure in utero can cause major CNS pathology, cerebral palsy and blindness. Vomiting and abdominal pain may develop upon acute ingestion.26 (link)Toxicology
Metanephrines (free), plasma or 24 h urineCHEM 1.3Plasma: <0.50 nmol/L.Urine:Normotensive adult males: 44–261 μg/24 hNormotensive adult females: 30–180 μg/24 hHypertensive adults:< 400 μg/24 hMetanephrines are two of the main metabolites of norepinephrine and epinephrine, two hormones that are secreted by pheochromocytomas and other tumors of neural crest origin. Measurement of metanephrines is more accurate than directly measuring epinephrine or norepinephrine. Symptoms associated with catecholamine-secreting tumors include hypertensive episodes, sweating, palpitations and headaches.Measurement of plasma free metanephrines has very high sensitivity for pheochromocytoma and paraganglioma. Elevated metanephrine levels are suggestive of neural crest tumors but should be confirmed by a second test (24-hour urine metanephrines).Neurologic
Monocyte count, bloodH 4.20.26–0.81 × 109/LMonocytes are a component of the innate immune system. They circulate in the blood before differentiating into macrophages and dendritic cells.Monocyte numbers increase in chronic infection (e.g., tuberculosis), chronic inflammation (e.g., autoimmune disease) and myeloid neoplasms (e.g., chronic myeloid leukemia). Monocyte levels may be decreased in inherited immune disorders, corticosteroid therapy, chemotherapy, some infections and hairy cell leukemia.CBC
N-type and P/Q-type calcium channel antibodies, serumCHEM 1.6N-type: ≤ 0.03 nmol/LP/Q type: ≤ 0.02 nmol/LN-type or P/Q type voltage-gated calcium channels (VGCCs) are expressed on presynaptic axon terminals and regulate presynaptic neurotransmitter release. Antibodies against these proteins mediate cross-linking of channel subunits, reducing channel cell surface expression and thereby attenuating channel activity. Of the two anti-VGCC antibody subtypes, anti-P/Q antibodies are more common.Anti-VGCC antibodies are seen in Lambert-Eaton myasthenic syndrome (LEMS), an autoimmune disease of presynaptic terminals; the majority of cases (50–60%) occur in association with small cell lung cancer. Impaired neurotransmitter release from the lower motor neurons, sympathetic neurons, and parasympathetic neurons in LEMS results in weakness, reduced tendon reflexes and autonomic dysfunction.49 (link)Nervous
Neutrophil count, bloodH 4.21.56–6.45 × 109/LNeutrophils are phagocytic white blood cells that are important in acute inflammation. They are the most plentiful WBC in the peripheral blood of adult patients. Mature neutrophils have segmented nuclei; immature neutrophils have unsegmented, S- or U- shaped nuclei (“band forms”). Neutrophils contain granules with antimicrobial compounds, such as myeloperoxidase, elastase and lysozyme. Neutrophils generate antimicrobial reactive oxygen species via a respiratory burst.Absolute neutrophilia is seen in acute infections (especially bacterial and fungal), tissue necrosis, growth factor (granulocyte colony stimulating factor, G-CSF) effect, corticosteroid therapy and chronic myeloid neoplasms. “Left shift” refers to the presence of an increased proportion of band neutrophils and is characteristic of acute infection. Neutropenia is primarily due to destruction or decreased production of neutrophils. Causes include medications (e.g., chemotherapy), radiation, certain infections, autoimmune disease and bone marrow failure (e.g., myelodysplastic syndromes).CBC
Nontreponemal syphilis tests (rapid plasma reagin [RPR], venereal disease research laboratory [VDRL], serum/cerebrospinal fluid (CSF)M 2.13Non-reactiveVDRL and RPR are non-treponemal serologic tests that measure antibodies to lipoprotein/cardiolipin antigens that are released from cells damaged by Treponema pallidum, the etiologic agent of syphilis. Titers decrease with time and following treatment, so these tests are most useful in the diagnosis of primary and secondary syphilis infection and in following response to therapy. Antibodies are detectable with both tests within a few weeks of development of the primary chancre, about 4–6 weeks after infection.Titers between different non-treponemal tests and are not comparable, so the same test should be used to monitor response to treatment. Because the antibodies are not specific for syphilis, a treponemal test (e.g., T. pallidum IgG/IgM antibody test) is required for confirmation. Nontreponemal serologic tests use cardiolipin antigens in the analysis, which can lead to false positive in patients with systemic lupus erythematosus (SLE) who have antiphospholipid antibodies.Genitourologic/Gynecologic
Oligoclonal bands, cerebrospinal fluid (CSF)CHEM 1.8<2 unique bandsIgG in the CSF is indicative of central nervous system (CNS) inflammation. Electrophoresis of the patient's CSF and serum normally yields no or at most one band. When two or more bands are seen in the CSF that are not in the serum, it is likely there is an autoimmune or infectious response within the CNS.Oligoclonal bands are seen in the setting of CNS inflammation such as in multiple sclerosis (MS), CNS syphilis, progressive multifocal leukoencephalopathy and Guillain-Barre syndrome. Up to 95% of patients with MS are positive for oligoclonal bands, though additional clinical and imaging studies are necessary for diagnosis.Central nervous
Oral glucose tolerarance test, bloodCHEM 1.3Fasting: <95 mg/dL1 h glucose level: < 180 mg/dL2 h glucose level: < 155 mg/dL3 h glucose level: <140 mg/dLGlucose metabolism is impaired in diabetes, including gestational diabetes. For an oral glucose tolerance test, the patient ingests a standard amount of glucose and blood glucose levels are measured at defined time points. There are separate reference ranges for the various time points.This testing is used most commonly in evaluation of gestational diabetes but can also play a role in the diagnosis of type 2 diabetes.Endocrine
Parathyroid hormone, serumCHEM 1.3Adults:15–65 pg/mLPTH is synthesized and secreted by the chief cells of parathyroid glands. It plays a crucial role in maintaining calcium homeostasis by acting directly on bone and kidney, and indirectly on the intestines through 1,25-dihydroxyvitamin D. PTH promotes osteoclastic bone resorption and calcium and phosphate release. In the kidney, PTH stimulates calcium reabsorption and inhibition of phosphate reabsorption. These actions increase the plasma concentration of free calcium and decrease plasma phosphate concentration. The primary regulators of PTH secretion are calcium, 1,25-dihydroxyvitamin D, and phosphate.Determination of PTH is useful in the differential diagnosis of both hypercalcemia and hypocalcemia. In hypercalcemia due to primary hyperparathyroidism (adenoma, hyperplasia), patients have increased PTH levels. In hypercalcemia due to other causes (e.g., PTHrP in malignancy), PTH is typically low. Secondary hyperparathyroidism is compensatory oversecretion of PTH due to abnormally low serum calcium (e.g., renal failure, gastrointestinal malabsorption, vitamin D deficiency). The most common causes of hypoparathyroidism are parathyroidectomy or thyroidectomy with accidental removal of parathyroids. The short half-life of PTH makes it possible to measure PTH levels intraoperatively during surgeries for primary hyperparathyroidism to assess effectiveness of resection of the parathyroids.50 (link)Endocrine
Parathyroid hormone- related peptide (PTHrP), plasmaCHEM 1.3≤4.2 pmol/LParathyroid hormone related peptide (PTHrP) is secreted in low levels by most tissues and binds to the same receptor as parathyroid hormone. Elevation of PTHrP is often part of a paraneoplastic syndrome and causes humoral hypercalcemia of malignancy by stimulating calcium resorption in bone and calcium reabsorption in the kidney. Elevated PTHrP is most commonly produced by breast carcinoma, squamous cell carcinoma of lung and squamous cell carcinoma of the head and neck.In humoral hypercalcemia of malignancy, parathyroid hormone levels are generally low or undetectable due to feedback inhibition. PTHrP can be elevated in benign conditions such as pregnancy and systemic lupus erythematosus (SLE) and others. Successful treatment of the underlying malignancy usually results in decreased levels of PTHrP and calcium and subsequent increases in parathyroid hormone levels.Skeletal
Parietal cell antibodies, serumIMM 1.4Negative: ≤20.0 UEquivocal: 20.1–24.9 UPositive: ≥ 25.0 UParietal cell antibodies are IgG that bind to the H+/K+ ATPase pump on gastric parietal cells. They are seen in autoimmune gastritis, a T-cell mediated inflammatory condition that leads to loss of parietal cells, atrophy and metaplasia of the oxyntic mucosa, and, if chronic, pernicious anemia, caused by loss of intrinsic factor and decreased vitamin B12 absorption.Parietal cell antibodies are found in more than 90% of patients with pernicious anemia, but are less specific than intrinsic factor antibodies since they may be positive in patients with other forms of chronic gastritis and in patients with thyroid disorders. False positives can occur when patients have received intramuscular or subcutaneous vitamin B12.Gastrointestinal
Peripheral smear, bloodH4.3Not applicableA peripheral blood smear is made by spreading a drop of blood on a glass slide and staining the slide with Wright or Wright-Giemsa stain. This test is useful for investigating abnormal results from automated testing.Review is used to evaluate red blood cell morphology (e.g., sickle cells, poikilocytosis) and atypical white blood cells (e.g., blasts), to confirm low platelet counts, and occasionally to identify microbial pathogens (e.g., malaria and babesia).CBC
Phospholipase A2 receptor (PLA2R) antibody, serumCHEM 1.5NegativeMembranous nephropathy (MN) is a renal disease in which immune complexes deposit along the subepithelial surface of the glomerular basement membrane. In about 70% of cases of primary MN, the immune complexes are directed against the podocyte PLA2R protein.The PLA2R antibody test can be used to differentiate primary from secondary MN and, with eGFR and proteinuria, correlates with risk of disease progression. PLA2R levels can also be used to monitor response to treatment.Renal
Platelet count, bloodH 4.2Males: 135–317 × 109/LFemales: 157–371 × 109/LPlatelets are central to primary hemostasis. They interact with von Willebrand factor and exposed collagen to form a platelet plug at sites of endothelial injury. They also have receptors for fibrinogen, allowing for fibrin formation/crosslinking. A part of the platelet pool is normally sequestered in the spleen. Platelet counts may be falsely reported as low due to specimen clotting, platelet clumping and platelet satellitosis in which platelets adhere to neutrophils. Hematology analyzers count platelets based on size and do not recognize these aggregates as platelets.Causes of thrombocytopenia are sequestration (e.g., hypersplenism), increased consumption (e.g., heparin-induced thrombocytopenia, immune thrombocytopenic purpura, disseminated intravascular coagulation, thrombotic thrombocytopenic purpura) or decreased production (infiltration of bone marrow, leukemias, viral infections). Causes of thrombocytosis include inflammation, hyposplenism/splenectomy, iron deficiency and myeloproliferative neoplasms. Even if counts are normal, platelets may be dysfunctional due to drugs (e.g., aspirin), uremia and genetic diseases (e.g., Bernard-Soulier syndrome, Glanzmann thrombasthenia).CBC
Porphobilinogen and aminolevulinic acid, plasmaH 4.4Porphobilinogen: ≤ 0.5 nmol/mLAminolevulinic Acid: ≤ 0.5 nmol/mLThe porphyrias are a group of diseases caused by abnormalities in the enzymes involved in heme synthesis. Intermediates accumulate or are deficient, depending on the enzyme affected. The first step of the heme biosynthetic pathway involves synthesis of aminolevulinic acid (ALA) from succinyl CoA and glycine through the action of ALA synthase. ALA dehydratase, the next enzyme in the pathway, converts ALA to porphobilinogen (PBG).The porphyrias are subclassified based on their clinical presentation (acute versus cutaneous). Acute porphyrias can present with attacks of neuropsychiatric symptoms, discolored urine and abdominal pain. Cutaneous porphyrias are associated with skin manifestations and photosensitivity related to accumulation of porphyrins in the skin. Serum ALA and porphobilinogen testing are part of the initial evaluation of porphyria. Both are elevated during acute attacks of acute intermittent porphyria, hereditary coproporphyria and variegate porphyria. Elevation of ALA without PBG can be seen in aminolevulinic acid dehydratase deficiency porphyria, tyrosinemia and heavy metal exposure. ALA dehydratase is inhibited by lead.Hematologic
Potassium, serumCHEM 1.2 and CHEM 1.43.6–5.2 mmol/LPotassium, K+, is the main intracellular cation, while sodium is the main extracellular cation. The Na+/K+ ATPase membrane pump maintains the concentrations of these 2 cations in their respective compartments. Plasma level is regulated by the kidney. Abnormally high or low potassium concentrations interfere with muscle contraction including the myocardium, and nerve conduction; low levels increase the cell membrane potential while high levels decrease the membrane potential.Potassium is part of a basic metabolic panel. Both hypo- and hyperkalemia can lead to cardiac arrhythmias. Important causes of hypokalemia include medications (e.g., diuretics), vomiting, diarrhea and diabetic ketoacidosis. Hyperkalemia may be due to medications (e.g., angiotensin coverting enzyme [ACE] inhibitors), Addison disease, renal failure (decreased excretion) and extracellular potassium shift (e.g., secondary to diabetic ketoacidosis). Extensive cellular destruction (e.g., trauma, burns, hemolysis) can also lead to hyperkalemia. Potassium may appear falsely elevated in hemolyzed blood samples.23 BMP/Chem 7
Progesterone, serumCHEM 1.3Adult females (non-pregnant):Follicular phase: ≤ 0.89 ng/mLOvulation: ≤12 ng/mLLuteal phase: 1.8–24 ng/mLPregnancy: 1st trimester: 11–44 ng/mL2nd trimester: 25–83 ng/mL3rd trimester: 58–214 ng/mLProgesterone is produced by the corpus luteum, placenta, and the adrenal cortex. During the luteal phase of the menstrual cycle, progesterone helps prepare the endometrium for embryo implantation by promoting endometrial gland secretions and the development of spiral arteries.Measurement of a midluteal progesterone level can be used to determine whether ovulation has occurred. In the absence of fertilization, the corpus luteum regresses, which causes progesterone levels to drop, and menses will occur as the uterine lining sheds.Endocrine
Prolactin, serumCHEM 1.3Adult males: 4.0–15.2 ng/mLAdult females: 4.8–23.3 ng/mLProlactin is produced by lactotrophs of the anterior pituitary gland and is responsible for lactation. Its secretion is circadian and pulsatile with highest levels during sleep and is under the inhibitory control of dopamine produced by the hypothalamus. Prolactin levels rise during pregnancy and are highest in the third trimester; in the absence of breastfeeding, they return to baseline about three weeks after delivery. Prolactinomas are the most common adenomas of the pituitary (40% of total).Common causes of elevated prolactin levels are prolactinoma, diseases of the hypothalamus, primary hypothyroidism and polycystic ovary syndrome. Hyperprolactinemia may cause galactorrhea (nipple discharge), menstrual cycle disruption, infertility, and loss of libido.Endocrine
Prostate specific antigen (PSA), serumCHEM 1.8Total PSA 0–4 ng/mLPSA is a protease secreted by the epithelial cells of the acini and ducts of the prostate gland that is found in the blood in protein-bound and free forms.Total PSA (bound + unbound) is a marker for prostate cancer and is useful in diagnosis, staging and monitoring treatment, though it is not specific for malignancy. PSA elevations can also be seen in prostatitis, benign prostatic hyperplasia and after procedures and ejaculation. Definitive diagnosis of prostate cancer requires biopsy and pathologist examination. Higher rates of change in PSA levels (> 0.75 μg/L/yr) are seen in patients with prostate cancer.Urologic
Protein C activity, plasmaH 2.470–150%Protein C is a vitamin K-dependent anticoagulant synthesized by hepatocytes. Binding of thrombin to the endothelial cell receptor thrombomodulin activates protein C. Activated protein C (APC), combined with protein S, inactivates factors Va and VIIIa, which are needed for thrombin generation.Protein C deficiency is a rare cause of inherited thrombophilia and may also be secondary to vitamin K deficiency, severe liver disease, medications and disseminated intravascular coagulation. Protein C deficiency can lead to skin necrosis when warfarin treatment is initiated and neonatal purpura fulminans in neonates.Coagulation
Protein S activity, plasmaH 2.4Males: 65–160%Females<50 years: 50–160%≥ 50 years: 65–160%Protein S is a vitamin K-dependent anticoagulant synthesized by hepatocytes. It enhances the effect of activated protein C to accelerate the degradation of factors Va and VIIIa.Protein S deficiency is a rare cause of inherited thrombophilia and may also be secondary to vitamin K deficiency, severe liver disease, medications and the nephrotic syndrome. Like protein C, protein S deficiency can lead to skin necrosis when warfarin treatment is initiated and, less commonly than protein C deficiency, can cause neonatal purpura fulminans in neonates.Coagulation
Protein (total), serumCHEM 1.46–8.5 g/dLSerum total protein measures all circulating protein, which is primarily albumin (made in the liver) and globulins. Protein electrophoresis can be performed to differentiate the different contributions of these proteins.Since total protein consists primarily of albumin, it is most informative to combine this test with an albumin level. When albumin is low and total protein is high, protein electrophoresis can identify which proteins are elevated.Hepatic
Prothrombin G20210A mutation, bloodH 2.7NegativeThe prothrombin G20210A mutation confers an increased risk of venous thromboembolism (VTE). It is the second most common thrombophilic mutation (factor V Leiden is more common). The mutation is in the 3′ untranslated region and results in increased prothrombin function, perhaps due to increased prothrombin synthesis or stability.The primary effect of this mutation is increased risk of VTE and a slight increase in risk of arterial thromboembolism. Heterozygote individuals have a 3- to 4-fold risk of VTE over baseline; due to the rarity of homozygote individuals, absolute risk cannot be calculated. This test is typically part of a panel in patients who are thrombophilic and includes factor V Leiden mutation, activated protein C resistance, antithrombin activity, protein C activity and protein S. Compound heterozygotes of factor V Leiden and the prothrombin G20210A mutation can be seen.51 Coagulation
Prothrombin time (PT), plasmaH 2.4PT: 9.4–12.5 s International normalized ratio (INR): 0.9–1.1PT assesses the extrinsic pathway of the coagulation cascade. The test is performed by adding phospholipids, tissue factor, and calcium to the patient's plasma and measuring time to clot. Since tissue factor activity may vary in different batches and from different sources, PT results are typically standardized by converting the value into an International Normalized Ratio (INR) (see INR entry).Prothrombin time is elevated in patients with a deficiency in or inhibition of factors VII, X, II (thrombin), or I (fibrinogen) due to a genetic deficiency or as a secondary effect (e.g., liver failure, warfarin therapy). A prolonged PT should be interpreted in the context of a concurrent PTT to determine whether the deficiency is in the extrinsic pathway or in the common pathway. A mixing study may be performed to distinguish a factor deficiency from inhibition. PT/INR is commonly used as a screening test or to monitor patients on warfarin therapy.Coagulation
Quadruple marker test: Alpha-fetoprotein (AFP), unconjugated estriol (uE3), human chorionic gonadotropin (hCG), dimeric inhibin A (DIA), maternal serumFDP 1.3Down Syndrome: Calculated screen risks <1/270: screen negative Calculated screen risks ≥1/270: screen positive Trisomy 18: Calculated screen risks <1/100: screen negative Calculated screen risks ≥1/100: screen positive Neural Tube Defects: AFP multiple of the median (MoM) < 2.5: screen negative. AFP multiple of the median (MoM) < 2.5: screen negative. AFP MoMs ≥2.5: screen positiveThe quadruple marker test, or quad screen, is a 2nd trimester prenatal screening test, which uses the levels of four biomarkers produced during pregnancy by the mother, the placenta, or the fetus (AFP, uE3, hCG, DIA) to estimate the risk of fetal chromosomal abnormalities, including trisomy 18 and 21, as well as neural tube and abdominal wall defects.The Quad test is a screening test. Negative tests do not exclude an abnormality. Positive tests may indicate the need for further testing. Since the substrate is maternal blood, there is no risk to the fetus. Several factors may affect results including calculated gestational age, diabetes, multiple gestations (i.e., twins, triplets), maternal weight and maternal smoking.Gynecologic
Rapid plasma reagin (RPR), serumM 2.13Non-reactiveThe RPR test is a non-treponemal serologic test for syphilis that measures antibodies to lipoprotein/cardiolipin antigens that are released from cells damaged by T. pallidum; these antibodies are not specific for syphilis. RPR titers decrease with time; therefore this test is less sensitive for detection of tertiary and latent syphilis than for detection of primary and secondary syphilis. Antibodies are detectable with RPR within 1–4 weeks of development of the primary chancre.RPR is often used for syphilis screening due to its low cost and ease of use; however both false positives and false negatives are possible. A treponemal antibody test should be used for confirmation or in the setting of a negative test if suspicion is high. RPR is semiquantitative and can be used to monitor therapy since titer decreases with successful treatment. Titers between different non-treponemal tests cannot be compared; therefore, the patient must be monitored with the same test over time. Nontreponemal serologic tests use cardiolipin antigens in the analysis, which can lead to false positive in patients with systemic lupus erythematosus (SLE) who have antiphospholipid antibodies.Genitourinary/Gynecologic
Red blood cell (RBC) count, bloodH 4.2Male: 4.35–5.65 × 1012/L Female: 3.92–5.13 × 1012/LRed blood cell count is reported as the number of RBCs per L of blood, but gives no information about the size or functional status of the RBCs. RBC production is stimulated by erythropoietin (EPO), which is produced by the kidneys.The RBC count is increased in polycythemia and decreased in anemia. In thalassemia trait, the RBC count is often higher than expected for the degree of anemia. Polycythemia is due to increased production (e.g., polycythemia vera, EPO administration, EPO-producing tumors), whereas anemia may be due to decreased production (e.g., iron deficiency, infiltrative marrow processes) or increased destruction (e.g., sickle cell anemia, hereditary spherocytosis). Inaccurate RBC counts may be due to agglutination. Microcytic RBCs and RBC fragments (e.g., schistocytes) may be erroneously counted as platelets by the automated analyzer.40 CBC
Red blood cell distribution width (RDW), bloodH 4.2Males: 11.8–14.5%Females: 12.2–16.1%RDW is a measure of the variability in red blood cell (RBC) size. Increased RDW is seen when there is anisocytosis or when there is a dimorphic RBC population (i.e., two populations of differing size as is the case in recent transfusion in a patient with a microcytic anemia). The presence of reticulocytes also increases the RDW.In the setting of microcytic anemia, increased RDW suggests iron deficiency anemia rather than thalassemia trait, which typically has more uniform cell sizes. An increased RDW in the setting of macrocytosis is more suggestive of vitamin B12 or folic acid deficiency than other causes of macrocytosis. Sideroblastic anemia is another cause of dimorphic RBC populations.40 CBC
Renin activity, plasmaCHEM 1.5Adults, normal sodium diet:0.6–4.3 ng/mL/hrThe renal juxtaglomerular apparatus produces renin, an enzyme that converts angiotensinogen to angiotensin I, which is then further converted to angiotensin II. Angiotensin II stimulates the zona glomerulosa of the adrenal cortex to release aldosterone, which increases sodium reabsorption. Consequent water reabsorption causes a rise in systemic (and therefore renal) blood pressure. Renin secretion by the kidney is stimulated by a fall in glomerular blood pressure, by decreased sodium concentration at the macula and by stimulation of sympathetic outflow to the kidney.Plasma renin activity (PRA) is measured as part of the diagnosis and treatment of hypertension. Interpretation is dependent on salt intake, posture, time of day, and certain medications. Increased PRA may indicate Addison disease, cirrhosis, essential hypertension, hemorrhage, hypokalemia, renin-producing renal tumors, and renovascular hypertension. Decreased PRA may can be seen in primary hyperaldosteronism, salt-retaining steroid therapy, and salt-sensitive essential hypertension. Renal disease, especially unilateral renal artery stenosis, results in elevated aldosterone and renin. A high ratio of serum aldosterone to renin activity suggests primary aldosteronism.Renal
Reticulocyte count, bloodH 4.20.60–2.71%Reticulocytes are immature red blood cells (RBCs) released from the bone marrow that are anucleate but still contain some organelles, such as ribosomes. They are slightly larger and more basophilic than mature RBCs due to retained RNA. The reticulocyte count reports reticulocytes as a percentage of total number of RBCs.Reticulocyte count reflects recent bone marrow erythropoetic function. Elevated reticulocyte count is a normal physiologic response to anemia of any cause; the reticulocyte index may be calculated in a patient with anemia to determine if the bone marrow is responding appropriately to compensate for the anemia. However, in these patients, the reticulocyte count may be falsely elevated since it is reported as a percentage of RBCs (which are low in anemia).CBC
Rh(D) type, serumTM1.1, TM1.6Positive or negative, varies by populationThe Rh system demonstrates >50 antigens, the most important of which is the D antigen. Antibody to D antigen (anti-D) is acquired after Rh(D)negative individuals are exposed to the D antigen (transfusion, pregnancy, transplant).Women who are Rh(D) negative and have a fetus who is Rh(D) positive can have a healthy pregnancy; however, in subsequent pregnancies, an Rh(D) positive fetus is at risk of hemolytic disease of the fetus and newborn (HDFN). Therefore, Rh(D) negative women who are carrying an Rh(D) positive fetus are treated prophylactically with Rh(D) immunoglobulin at 28 weeks' gestation and within 72 hours of delivery. Anti-D can also cause a mild to severe immediate or delayed hemolytic transfusion reaction.52 Transfusion
Rheumatoid factor (RF), serumIMM 1.4<15 IU/mLRF is an antibody that reacts with the Fc portion of other immunoglobulin G antibodies. Despite its name, RF lacks specificity for rheumatoid arthritis (RA) and can be seen in other inflammatory conditions and autoimmune diseases, particularly Sjögren syndrome.RF can be a prognostic indicator in RA as its presence correlates with increased severity of disease. RF has a sensitivity and specificity of about 70% and 85% for RA, respectively. Combination of RF and anti-citrullinated peptide antibodies have a higher diagnostic yield than RF alone.Skeletal, Autoimmunity
Salicylate, serumCHEM 1.7Therapeutic:< 30 mg/dLAspirin has a short half-life (15 min) and is rapidly metabolized to salicylate. In aspirin overdose, cyclooxygenase inhibition leads to platelet dysfunction and gastric mucosal injury; stimulation of the medulla resulting in hyperventilation, respiratory alkalosis, nausea and vomiting; and disruption of cellular metabolism (e.g., oxidative phosphorylation) which can cause metabolic acidosis.Serum salicylate levels above 40 mg/dL typically result in toxicity. Symptom onset is usually within 3–8 h, but absorption rates are not uniform. Timing and concentration of peak serum levels can vary depending on the amount and form of aspirin ingested; therefore, serial measurements every two hours are recommended until two consecutive tests show decreasing concentration. Acetaminophen levels should also be ordered since some formulations have both compounds.Toxicology
Sodium, serumCHEM 1.5 and CHEM 1.3135–145 mmol/LSodium, Na+, is the main extracellular cation while potassium, K+, is the main intracellular cation. The Na+/K+ ATPase membrane pump maintains the concentrations of these two cations in their respective locations. When extracellular Na+ levels decrease, water shifts into cells and vice versa. With chronically low levels of Na+, cells adapt and patients may be asymptomatic, but acute hyponatremia can result in seizures or brain herniation due to cerebral edema. There are two main hormones that are important in Na+ regulation: arginine vasopressin (antidiuretic hormone [ADH]) and aldosterone. Abnormal Na+ concentrations are usually due to renal dysfunction or changes in intake.Na+ is the electrolyte that is most commonly abnormal. Hyponatremia is usually due to excess hydration, not insufficient intake, and can be seen in renal failure, primary polydipsia, thiazide diuretics, SIADH, and adrenal insufficiency. Rapid correction of hyponatremia can lead to osmotic demyelination syndrome. Hypernatremia is often due to fluid depletion (e.g., vomiting, diarrhea, dehydration, osmotic diuresis in uncontrolled diabetes) though it can also be due to excess intake (e.g., saline emetic, hypertonic sodium bicarbonate to treat metabolic acidosis). Symptoms include signs of dehydration such as thirst, headache, lethargy, and weakness. When untreated, severe hypernatremia can cause spasms, seizure, and coma.BMP/Chem 7
T3 (triiodothyronine), total, serumCHEM 1.180–200 ng/dLT3 (triiodothyronine) is the most physiologically active form of thyroid hormone. Only a small percentage of thyroid hormone is released as T3; the rest is thyroxine or T4. T4 is slowly deiodinated to T3 once in circulation. Several tests may be used to evaluate T3 including total T3 and free T3 (measures unbound T3).T3 levels are assessed in conjunction with thyroid stimulating hormone (TSH), total and free T4 to evaluate thyroid function and to assess treatment for thyroid disease. T3 and free T3 are not routinely used for this purpose, since total and free T4 are sufficient in most cases. T3 is used to evaluate thyrotoxicosis.53 (link)Endocrine
T4 (thyroxine), free, serumCHEM 1.1Adults:0.9–1.7 ng/dLThyroxine (T4) is synthesized in the thyroid gland and metabolized peripherally to triiodothyronine (T3). The majority of T4 is bound to thyroid binding globulin; free T4 is the active form. Measurement of total T4 was once routine for thyroid assessment; however, interpretation is complicated by variation in binding proteins across individuals and physiologic conditions. Although only about 0.05% of circulating T4 is unbound to binding proteins (“free”), measurement of free T4 provides an accurate assessment of thyroid status in most patient populations. Total T4, free T4 and thyroid stimulating hormone (TSH) are often used together to evaluate thyroid function.Low free T4 is seen in hypothyroidism; high free T4 is seen in hyperthyroidism. Free T4 should be assessed in conjunction with TSH, the pituitary hormone that regulates thyroid hormone production. A common algorithm is TSH measurement, which reflexes to free T4 if TSH concentration is abnormal.Endocrine
Testosterone, serumCHEM 1.3Varies with age and sexTestosterone is the main endogenous androgen. In males, testosterone controls development of external genitalia and secondary sexual characteristics. The testicular Leydig cells are the main source of testosterone, with the adrenal cortex producing lesser amounts. In females, testosterone is primarily a precursor to estrogens, with the ovaries as the main source of production. Testosterone production in testes and ovaries is regulated via pituitary-gonadal feedback involving luteinizing hormone (LH) and, to a lesser degree, inhibins and activins.Excess testosterone can manifest as precocious puberty in boys, masculinization in girls and virilization in women. Polycystic ovarian syndrome is a relatively common condition characterized by elevated testosterone in females. Elevated testosterone may also be due to testicular or adrenal tumors, anabolic steroid use and congenital adrenal hyperplasia (in babies and children). Testosterone levels may be assessed in adult males and females with reduced libido.Endocrine
Thyroid-stimulating hormone (TSH), serumCHEM 1.1Adults:0.3–4.2 mIU/LTSH (thyrotropin; thyroid stimulating hormone) is produced by the anterior pituitary with feedback inhibition by thyroid hormones. It interacts with cell receptors on the thyroid follicular cells to stimulate cell division, cell hypertrophy and increased synthesis of thyroid hormones (thyroxine and triiodothyronine).TSH is the primary screen for primary hypothyroidism and primary hyperthyroidism. When TSH is low, free T4 and T3 are added to determine the extent and etiology of thyroid dysfunction. When TSH is high, free T4 is performed to assess the degree of hypothyroidism. For patients with primary hypothyroidism who are treated with levothyroxine, TSH alone is a sufficient monitoring test. For patients with central hypothyroidism (hypothyroidism caused by hypothalamic or pituitary disease), free T4 is low or low-normal and the TSH may be low or normal.53 (link),54 (link)Endocrine
Thyroid peroxidase antibody, serumCHEM 1.1<9.0 IU/mLThyroid peroxidase (TPO) catalyzes iodination of thyroglobulin to form monoiodotyrosine and diiodotyrosine, precursors of thyroid hormone.Antibodies against TPO are common in autoimmune thyroid disease, though they are also present in 5–20% of the general population. They are polyclonal, which suggests they are secondary phenomena to thyroid injury. Anti-TPO antibodies can activate complement and likely play a key role in the pathogenesis of autoimmune-mediated hypothyroidism.Anti-TPO antibodies are sensitive tests for autoimmune thyroid disease (e.g., Hashimoto thyroiditis, Graves disease) but are not specific within this class of disorders. The highest anti-TPO levels are generally seen with Hashimoto thyroiditis.53 (link)Endocrine, Autoimmunity
Thyrotropin (thyroid stimulating hormone, TSH) receptor antibody, serumCHEM 1.1≤1.75 IU/LIn Graves disease, TSH receptor antibodies (also called thyroid-stimulating immunoglobulin) bind to and activate the TSH receptor without feedback inhibition, causing thyrotoxicosis. TSH receptor antibodies that block the receptor may also be seen and it is thought that the balance between blocking vs activating antibodies may contribute to disease severity in Graves disease.TSH receptor antibody testing is useful when Graves disease is suspected clinically, but thyroid function tests are normal and in patients for whom radioisotope testing is contraindicated (e.g., during pregnancy). TSH receptor antibodies may persist even with successful surgical or ablation therapy; since these are IgG antibodies, they can cross the placenta and cause neonatal thyrotoxicosis.Endocrine, Autoimmunity
Tissue transglutaminase antibody, IgA, serumIMM 1.4Negative: <4.0 U/mL Weak positive: 4.0–10.0 U/mLPositive > 10.0 U/mLTissue transglutaminase (tTG) deamidates gliadin, which is bound with increased affinity by HLA-DQ2 and DQ8 molecules on antigen presenting cells, leading to a CD4+ T cell response. Injured or inflamed endothelial cells and fibroblasts release tTG. tTG autoantibodies are elevated in patients with celiac disease; therefore, this is the first-line screening test, in conjunction with biopsy, to confirm the diagnosis.The test queries IgA tTG antibodies and will be negative in patients with IgA deficiency (about 2% of patients with celiac disease). Patients who have been on a gluten-free diet may have a negative result and the test is therefore useful in monitoring adherence to a gluten-free diet in patients with celiac disease. When combined with an endomysial antibody test, it is useful for screening for dermatitis herpetiformis.33 (link)Gastrointestinal, Autoimmunity
ToRCH Antibody, serumM 3.3Toxoplasmosis gondii antibody: Negative Rubella antibody: Vaccinated, Positive; Unvaccinated, Negative Cytomegalovirus (CMV) antibody: NegativeHerpes simplex Virus (HSV) type 1 and 2 antibodies: NegativePerinatal infections are responsible for 2–3% of congenital anomalies. Toxoplasma gondii, CMV, Rubella and HSV type 1/2 are assessed in pregnancy since while the patient may be asymptomatic, the fetus can be severely affected due to transplacental spread. “Other” entities (e.g., syphilis, human immunodeficiency virus, parvovirus B19) may be tested for separately. Positive results to the IgG test indicate past exposure or immunization. A positive result for IgM antibodies indicates current or recent infection.In utero ToRCH infections are associated with growth retardation, fetal demise, hepatosplenomegaly, jaundice and lethargy. Additional findings such as distinctive rashes or chorioretinitis may suggest a specific diagnosis.Gynecologic
Total cholesterol, serumCHEM 1.2Desirable: <200 mg/dLBorderline high: 200–239 mg/dLHigh risk: ≥ 240 mg/dLTotal cholesterol includes high-density lipoprotein (20–30%), low-density lipoprotein (60–70%) and very-low-density lipoprotein (10–15%). Low-density lipoprotein (LDL) is usually calculated from total cholesterol, high-density lipoprotein (HDL) and triglycerides. About 75% of the total cholesterol is synthesized by the liver and 25% comes from the diet.Total cholesterol is elevated in a number of conditions including familial hypercholesterolemia (deficiency of LDL receptors), uncontrolled diabetes, hypothyroidism, nephrotic syndrome and biliary obstruction. Corticosteroids also increase total cholesterol. Total cholesterol may be decreased in severe liver disease, hyperthyroidism, severe acute or chronic illness, malnutrition, malabsorption and extensive burns.Vascular
Total iron binding capacity (TIBC), serumH 4.1 and CHEM 1.7250–400 μg/dLIn the serum, iron is bound to transferrin, which is typically about one third saturated with iron. When iron stores in the body are depleted (e.g., iron deficiency anemia), transferrin levels increase in the blood, which increases the total iron binding capacity (TIBC).In iron deficiency, TIBC is increased, since transferrin levels are relatively high compared to iron content; in iron overload, TIBC decreases since the free transferrin diminishes. TIBC, serum iron and percent saturation are often assessed in the setting of iron deficiency anemia; however, serum ferritin is more sensitive and more accurately reflects the body's iron stores.Hematologic
Treponema pallidum IgG/IgM antibody, serumM 2.13 and M 1.3Non-reactiveA test for IgG and IgM antibodies to T. pallidum is a specific test for the causative agent of syphilis. This test is particularly useful in diagnosing tertiary and latent syphilis. However, these antibodies persist after infection and can be seen in treated individuals. Therefore, a second method such as the non-treponemal RPR or VDRL tests can help establish how recent the infection is and whether or not the patient has received adequate treatment.This test is particularly useful in diagnosing tertiary and latent syphilis.Genitourinary/Gynecologic
Triglycerides, serumCHEM 1.2Normal: <150 mg/dLBorderline high: 150–199 mg/dLHigh: 200–499 mg/dLVery high: ≥ 500 mg/dLTriglycerides (TGs), low-density lipoprotein (LDL) and high-density lipoprotein (HDL) are the primary lipids found in plasma. Triglycerides are transported from the small bowel inside chylomicrons and as very low-density lipoprotein (VLDL) particles. TGs are directly measured in the laboratory. This value, along with total cholesterol and HDL, is used to calculate LDL. Patients with extremely elevated TGs may have inaccurate LDL results.Elevated triglycerides are an independent risk factor for coronary artery disease as well as a risk factor for acute pancreatitis. Triglycerides are increased in wide range of conditions including diabetes, nephrotic syndrome, biliary tract obstruction, obesity, cirrhosis and some glycogen storage diseases. Many medications increase triglycerides: β-blockers, cholestyramine, corticosteroids, diazepam, diuretics and estrogens.Vascular
Troponin T, high sensitivity (hs-cTnT), plasmaCHEM 1.2Males: ≤ 20 ng/LFemales: ≤ 15 ng/LTroponin is a regulatory protein of striated muscle composed of three subunits: T, C, and I. The T, or tropomyosin-binding subunit, binds to muscle fibers. cTnT is specific for cardiac muscle and is released in myocardial cell death, about 2–3 hours after acute myocardial infarction. Because cTnT is bound to muscle fibers, it is released slowly into the peripheral blood following myocardial infarction. Its concentration peaks at 24 hours but it can persist 2 weeks or longer in the blood.Hs-cTnT assays are preferred over conventional tests, which are relatively insensitive; for example, the former are reported as ng/L while the latter are reported as ng/mL. With hs-cTnT tests, low levels of troponin are detectable in healthy individuals. In addition to myocardial infarction, elevated cTnT can be seen in cardiac contusion, congestive heart failure, renal failure, pulmonary embolism and myocarditis. Biotin (vitamin B7), which is found in many multivitamins, interferes with the assay and can cause inaccurate results.55 (link),56 (link)Cardiac
Uric acid, serumCHEM 1.5Males: < 8.0 mg/dL Females: < 6.1 mg/dLUric acid is generated by purine metabolism. Purines are synthesized by the body or are ingested, particularly in foods with abundant nucleic material (e.g., liver). About 75% of the body's uric acid is excreted in the urine.Hyperuricemia can be seen in patients on cytotoxic drug regimens (e.g., cancer chemotherapy) and in the context of gout, leukemia, chronic renal failure (decreased excretion) and psoriasis. Most patients with hyperuricemia do not develop gout.Skeletal, Renal
Venereal disease research laboratory (VDRL) test, spinal fluidM 2.13Non-reactiveThe VDRL test is a non-treponemal serologic test for syphilis that measures antibodies to lipoprotein/cardiolipin antigens that are released from cells damaged by T. pallidum; these antibodies are not specific for syphilis.The VDRL test is often used for syphilis screening due to its low cost and ease of use; however both false positives and false negatives are possible. A treponemal test (such as an antibody test) should be used for confirmation or in the setting of a negative test if suspicion is high. A spinal fluid sample that is positive by the VDRL test is very specific for neurosyphilis; however, false negatives are common. Non-treponemal serologic tests use cardiolipin antigens in the analysis, which can lead to false positives in patients with systemic lupus erythematosus (SLE) who have antiphospholipid antibodies.Genitourinary/Gynecologic
Vitamin B12 (cobalamin), serumH 3.2180–914 ng/LVitamin B12 (cobalamin) is a water-soluble vitamin. Uptake requires binding to intrinsic factor (IF) produced by parietal cells in the stomach and absorption in the terminal ileum. Vitamin B12 is required for the conversion of homocysteine to methionine in a process that yields tetrahydrofolic acid (TH4), which is required for the synthesis of deoxythymidine monophosphate (dTMP), a building block for DNA.The most common cause of vitamin B12 deficiency is chronic atrophic gastritis (pernicious anemia), an autoimmune disease in which autoantibodies attack gastric parietal cells and IF. Vitamin B12 deficiency leads to megaloblastic anemia and subacute combined degeneration of the spinal cord. Subacute combined degeneration is characterized by degeneration of the dorsal and lateral columns of the spinal cord due to demyelination. It commonly presents with sensory deficits, paresthesia, weakness, ataxia, and gait disturbances. Neurologic symptoms may occur without any discernible hematologic changes in the blood.Hematologic
Von Willebrand factor (vWF) antigen, plasmaH 2.155–200%vWF is synthesized by endothelial cells and megakaryocytes. vWF participates in primary hemostasis by binding to platelet receptor GPIb-IX and by binding to subendothelial collagen. vWF binds and stabilizes factor VIII in circulation. The vWF antigen test measures the quantity of vWF.This test is generally used in combination with a test evaluating the function/activity of vWF such as the vWF:ristocetin cofactor assay. Decreased levels of vWF can be seen in association with inherited or acquired forms of von Willebrand disease. The ratio of vWF antigen to activity level can help determine if there is a deficiency in production or in function of vWF.Coagulation
White blood cell (WBC) count, bloodH 4.23.4–9.6 × 109/LWBCs are counted using an automatic analyzer. The WBC count may or may not include a differential count (a separate count of each type of WBC). Most labs perform an automated differential count as part of the WBC count. When abnormal cells are detected, a manual review of the blood smear is performed.Increased WBCs are most often due to infection (i.e., neutrophils) or hematologic malignancies (often lymphocytes or myeloid cells). A low WBC count is usually a reflection of impaired marrow production due to medication, hematologic or metastatic malignancies or marrow infiltration (e.g., fibrosis, granulomas). In severe sepsis, there may be a paradoxical drop in the WBC count due to consumption in “neutrophil extracellular traps” (NETs).CBC

Duke University Hospital System (DUHS) reference value.

As laboratory tests have varying, population-dependent reference ranges, a uniform reference range that could be used for all included tests was sought. The Mayo Clinic graciously permitted the use of their normal reference ranges for all laboratory tests within ELTME. Common references cited for creation of the table include the Test Catalog from Mayo Clinic Laboratories,5
Henry's Clinical Diagnosis and Management by Laboratory Methods,6
Tietz Textbook of Clinical Chemistry and Molecular Diagnostics7 , Guide to Diagnostic Tests8 , Robbins and Cotran Pathologic Basis of Disease9 , and Blood Cells: A Practical Guide.10 Specific additional references are noted in the table as appropriate.
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Publication 2022
The surface expression of two BDNF receptors-neurotrophic receptor tyrosine kinase 2 (NTRK2; also named tropomyosin-related kinase B, TrkB ) and nerve growth factor receptor 2 (NGFR, also named neurotrophin receptor, p75NTR) was determined by stained phycoerythrin-conjugated mouse monoclonal antibody against human NTRK2 (BioLegend, San Diego, California, U.S.), rabbit polyclonal antibodies against NGFR followed by fluorescein isothiocyanate conjugate polyclonal goat-anti-rabbit antibodies (BD Biosciences, Franklin Lakes, NJ, USA) or isotype control (BD Biosciences) analyzing by flow cytometry (FACSMelody, Becton Dickinson, Franklin Lakes, NJ, USA) using FACSChorus software.
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Publication 2021
Anti-Antibodies Antibodies Flow Cytometry Fluorescein Goat Homo sapiens Immunoglobulin Isotypes Isothiocyanates Monoclonal Antibodies Mus NGFR Protein NGFR protein, human Phycoerythrin Rabbits Receptor Protein-Tyrosine Kinases Receptors, Nerve Growth Factor tropomyosin-related kinase-B, human

Example 1

Results

The development of a compound screening platform with RTT KCC2-2A-luciferase reporter neurons to identify KCC2 expression enhancing compounds are outlined in FIGS. 1A to 1D. The compounds screened were selected from LINCS (Library of Integrated Network-based Cellular Signatures) kinase inhibitor library and IRSF (International Rett Syndrome Foundation) SMART (Selected Molecular Agents for Rett Therapy) compound library. The compounds within both libraries include compounds that belong to one or more of the following compound classes: Feline McDonough sarcoma-like tyrosine kinase 3 (FLT3) inhibitors, glycogen synthase kinase 3 (GSK3) inhibitors, gamma-aminobutyric acid (GABA) inhibitors, GABA reuptake inhibitors, monoamine oxidase inhibitors (MAOI), norepinephrine reuptake inhibitor (NRI), dopamine antagonist, Sirtuin 1 (SIRT1) activators, transient receptor potential cation channel subfamily V member 1 (TRPV1) activators, monoamine transporter activators, tropomyosin receptor kinase B (TrkB) agonists, or ampakines.

The RTT KCC2-2A-luciferase reporter neurons were treated with the test compounds from the LINCS kinase inhibitor library and IRSF SMART compound library and incubated before being lysed. The cell lysate was divided into two parts to measure luciferase signal (KCC2 translation) and Cell-Titer Glow (CTG, amount of ATP). The luciferase signal was normalized to CTG for each well, and the Luc/CTG ratio was normalized to the in-plate DMSO negative control to calculate fold change ratio.

The list of hit compounds identified from the compound screening with RTT KCC2 reporter neurons are given in Table 1.

TABLE 1
List of hit compounds identified from compound screening
with RTT KCC2 reporter neurons.
Compound NameCellular Effect
KW-2449FLT3 inhibitor
KIN 001-043GSK3 inhibitor
AR-A014418GSK3 inhibitor
Nipecotic acidGABA reuptake inhibitor
MethysticinNeuroprotective, MAOI, NRI
Trifluoperazine dihydrochlorideDopamine Antagonist
ResveratrolSIRT1 activator
PiperineTRPV1 activator
Luteolin, FlacitranMonoamine transporter activator
7,8-DihydroxyflavoneTrkB agonist
CX-614, BDP37Ampakine, Antidepressant
The measure of KCC2 levels in cultured female ESC-derived human RTT neurons after Western blot analysis are shown in FIGS. 2A to 2D. Treatment with KW-2449, KIN 001-043, resveratrol, and piperine is shown to increase KCC2 expression in RTT neurons at varying concentrations. Further, FIGS. 3A to 3F show the molecular pathways through which hit compounds regulate KCC2 expression with cultured human RTT neurons derived from gene-targeted ESC.

In addition, CRISPR/Cas9 genome editing technology was utilized to insert a 2A-luciferase reporter gene directly before the stop codon of the endogenous KCC2 locus in human ES cells, thus creating wild type (WT) cells isogenic to the MECP2-null RTT human KCC2 reporter neurons. KCC2 expression reporter human neurons were differentiated from the gene-targeted ES cells and utilized as the substrate for unbiased compound screening (FIG. 6A; see also FIG. 1A). Sanger sequencing and Southern blot analyses were used to confirm correct editing (FIG. 7A), and assay development experiments were conducted to optimize the parameters for screening (FIG. 7B, 7C, 7D).

Gene-targeted KCC2 reporter cells were used in a HTS pipeline to screen for small molecule compounds that enhance KCC2 gene expression (FIG. 1B; note that reporter neurons were adapted to 384 well format for some screens, and the same workflow was used both for WT KCC2 reporter neurons and RTT KCC2 reporter neurons). Six replicate screens were performed in WT KCC2 reporter neurons using the LINCS and SMART libraries as well as the ICCB known bioactive library (FIG. 6B). From these screens, a total of 14 compounds were identified as hit KCC2 expression-enhancing compounds (KEECs, B score >3), including KW-2449, BIO (6-bromoindirubin-3′-oxime) and Resveratrol (FIG. 6C). Most KEECs that enhanced KCC2 expression in WT neurons, including KW-2449, BIO, and Resveratrol, were among the hits that had been found to induce a significant increase of KCC2 reporter activity in RTT neurons. A list of the top 14 hit compounds identified in the screens using WT human KCC2 reporter neurons is provided in Table 2.

TABLE 2
List of hit compounds identified from compound screening with wild type KCC2
reporter neurons (and certain analogs).
BMajor
NameIUPAC NameScoreClasstargets
7,8-Dihydroxy-7,8-Dihydroxyflavone4.01TrkBTrkB
flavoneagonist
8-methoxy-8-(Methoxymethyl)-1-methyl-3-(2-4.8PhosphodiesterasePDE1
methyl-IBMXmethylpropyl)-7H-purine-2,6-dioneinhibitor
BIO2H-Indol-2-one, 6-bromo-3-[(3E)-1,3-3.42GSK-3α/βGSK3
dihydro-3-(hydroxyimino)-2H-indol-2-inhibitor
ylidene]-1,3-dihydro-, (3Z)-
Dovitinib1-amino-5-fluoro-3-(6-(4-4.44RTKFLT3/c-
methylpiperazin-1-yl)-1H-inhibitorKit,
benzo[d]imidazol-2-yl)quinolin-2(1H)-FGFR1/3,
oneVEGFR1,
VEGFR4
ForetinibN1′-[3-fluoro-4-[[6-methoxy-7-(3-4.05Kinasec-Met,
morpholinopropoxy)-4-inhibitorVEGFR2; F
quinolyl]oxy]phenyl]-N1-(4-FLT3 is
fluorophenyl)cyclopropane-1,1-also a
dicarboxamidetarget
Indirubin(3Z)-3-(3-Oxo-1,3-dihydro-2H-indol-2-3.73N.A.PLK1,
ylidene)-1,3-dihydro-2H-indol-2-onePIN1,
CDC25B
KW-2449(E)-(4-(2-(1H-indazol-3-5.45Multi-FLT3,
yl)vinyl)phenyl)(piperazin-1-targetABL,
yl)methanoneinhibitorABL-
T315I,
Aurora
kinase
Methysticin(2R)-2-[(E)-2-(1,3-Benzodioxol-5-7.17MAOI,CYP1A1
yl)ethenyl]-4-methoxy-2,3-NRI
dihydropyran-6-one
Paliperidone9-Hydroxyrisperidone11.03D2 andDopamine
5HT2Areceptor,
receptor5-HT2A,
antagonistα 1/2
adrenergic
receptors,
H1
histaminergic
receptors
Paxilline(2R,4bS,6aS,12bS,12cR,14aS)-4.1PotassiumPotassium
5,6,6a,7,12,12b,12c,13,14,channelchannels
14a-Decahydro-4b-hydroxy-2-(1-blocker
hydroxy-1-methylethyl)-12b,12c-
dimethyl-2H-
pyrano[2″,3″:5″,6′]benz[1′,2′:6,7]indeno
[1,2-b]indol-3(4bH)-one
Resveratrol3,5,4′-trihydroxy-trans-stilbene12.65MAOI,Sirtuin1,
Anti-PGC-1α
oxidant
Safinamide(2S)-2[[4-[(3-4.82MAOIMAO,
fluorophenyl)methoxy]phenyl]Sigma
methylamino]propanamidereceptor
SB-4152863-[(3-Chloro-4-hydroxyphenyl)amino]-5.58GSK-3GSK-3
4-(2-nitrophenyl)-1H-pyrrol-2,5-dioneinhibitor
SU-43123-(4-Dimethyl3.55KinaseFLT1,
aminobenzylidenyl)-2-indolinone, 3-inhibitorVEGF,
[[(4-Dimethyl-PDGF,
amino)phenyl]methylene]-1,3-dihydro-neuronal
2H-indol-2-oneNOS
Crenolanib1-(2-{5-[(3-Methyloxetan-3-N/AKinaseFLT3,
yl)methoxy]-1H-benzimidazol-1-inhibitorPDGFRα/β
yl}quinolin-8-yl)piperidin-4-amine
SunitinibN-[2-(Diethylamino)ethyl]-5-[(Z)-(5-N/ARTKPDGFRs,
fluor-1,2-dihydro-2-oxo-3H-indol-3-inhibitorVEGFRs,
yliden)-methyl]-2,4-dimethyl-1H-c-KIT
pyrrol-3-carboxamid
XL184N-(4-((6,7-Dimethoxyquinolin-4-N/AKinasec-Met,
(Cabozantinib)yl)oxy)phenyl)-N′-(4-inhibitorVEGFR2,
fluorophenyl)cyclopropane-1,1-AXL, RET
dicarboxamide
TWS-1193-[6-(3-Amino-phenyl)-7H-N/AGSK3GSK3β
pyrrolo[2,3,-d]pyrimidin-4-yloxy]-inhibitor
phenol
Indirubin-3-[1,3-dihydro-3-(hydroxyimino)-2H-N/AGSK3GSK3,
monoxiomeindol-2-ylidene]-1,3-dihydro-2H-indol-inhibitorCDK1/5
2-one
Note:
The compounds with the description ‘N/A’ in the B-score field are analog compounds of primary hit compounds identified from screening.

To validate the KEECs, human neurons derived from WT ES cells (WIBR1 male ES cell line) were treated with KEECs, and conducted Western blot experiments were conducted to measure changes in KCC2 expression. Treatment of cultured WT human neurons with KW-2449, a potent inhibitor of fms-like tyrosine kinase-3 (FLT3) (41), induced a significant increase in KCC2 expression in a dose-dependent manner (FIG. 6D; see also FIG. 4A). BIO, an inhibitor of the glycogen synthase kinase 3 β (GSK3β) pathway (42), significantly increased KCC2 expression, while the inactive analog compound MeBIO failed to activate KCC2 expression (FIG. 6E). To elucidate the molecular mechanisms through which hit KEECs regulate KCC2 expression, additional chemical compounds that are structurally different, but functionally analogous to the primary hit compounds KW-2449 and BIO were tested. The results demonstrated significant enhancement of KCC2 expression in human neurons treated with a number of structurally diverse FLT3 kinase inhibitors including Crenolanib, XL-184, and Sunitinib (FIGS. 6F to 6H; see also FIGS. 4D, 4C, and 4B). TWS-119 is a GSK3β inhibitor that is structurally unrelated to the primary hit compound BIO. The results show that treatment of WT neurons with TWS-119 robustly increased KCC2 expression by more than two-fold even at the relatively low concentration of 0.03 μM (FIG. 6I; see also FIG. 4E).

Example 3

Additional screens for reporter activation in the MECP2-null RTT human KCC2 reporter neurons (isogenic to the WT reporter cells used above) were performed with the LINCS and SMART libraries as well as the ICCB known bioactive library and identified hits as compounds with B score >3. Most KEECs that enhanced KCC2 expression in WT neurons, including KW-2449, BIO, Resveratrol, also induced a significant increase of KCC2 reporter activity in RTT neurons, as described in Example 1 (FIGS. 10A and 10B). A list of the top 30 hits identified in these additional rounds of screens with RTT KCC2 reporter neurons is given in Table 3.

TABLE 3
List of hit compounds identified from expanded compound screening with RTT
KCC2 reporter neurons (and certain analogs)
Class/
BCellularMajor
NameIUPAC NameScoreEffecttargets
(R)-BaclofenBenzenepropanoic acid6.65GABABGABAB
agonistreceptor
7,8-7,8-Dihydroxyflavone4.01TrkB agonistTrkB
Dihydroxy-
flavone
8-8-(Methoxymethyl)-1-methyl-3-(2-4.8Phospho-PDE1
methoxymethyl-methylpropyl)-7H-purine-2,6-diesterase
IBMXdioneinhibitor
AR-A014418N-(4-Methoxybenzyl)-N′-(5-nitro-8.69GSK3GSK3
1,3-thiazol-2-yl)ureainhibitor
Ataluren3-[5-(2-Fluorophenyl)-1,2,4-7.43nonsense-CTFR
oxadiazol-3-yl]benzoic acidsuppressingmutation
agentcausal for CF
BIO(2′Z,3′E)-6-Bromoindirubin-3′-3.42GSK-3α/βGSK3α/β
oximeinhibitor
BMS 777607N-(4-(2-amino-3-chloropyridin-4-11.97Met-relatedc-Met,
yloxy)-3-fluorophenyl)-4-ethoxy-protein kinaseAxl, Ron,
1-(4-fluorophenyl)-2-oxo-1,2-inhibitorTyro3
dihydropyridine-3-carboxamide
XL-184N-(4-(6,7-dimethoxyquinolin-4-3.25KinaseFLT3, MET,
(Cabozantinib)yloxy)phenyl)-N-(4-fluorophenyl)inhibitorVEGFR,
cyclopropane-1,1-dicarboxamideRET,
GAS6
receptor
(AXL),
KIT
Daidzein7-hydroxy-3-(4-hydroxyphenyl)-4.64AntioxidantGPER
4H-chromen-4-one
Dovitinib1-amino-5-fluoro-3-(6-(4-4.44Multi-targetFLT3/c-Kit,
methylpiperazin-1-yl)-1H-RTK inhibitorFGFR1/3,
benzo[d]imidazol-2-yl)quinolin-VEGFR1-4
2(1H)-one
ForetinibN1′-[3-fluoro-4-[[6-methoxy-7-(3-4.05Kinasec-Met,
morpholinopropoxy)-4-inhibitorVEGFR-2;
quinolyl]oxy]phenyl]-N1-(4-FLT3 is also
fluorophenyl)cyclopropane-1,1-a target
dicarboxamide
Genistein4′,5,7-Trihydroxyisoflavone5.11Nrf2 + PPARERβ, GPER,
activator,PPARs,
EGFRtyrosine
inhibitorkinases, topo-
isomerase,
AAADs
Indirubin(3Z)-3-(3-Oxo-1,3-dihydro-2H-3.73KinaseGSK3
indol-2-ylidene)-1,3-dihydro-2H-inhibitorPLK1,
indol-2-onePIN1,
CDC25B
Kaempferol3,5,7-Trihydroxy-2-(4-3.92SIRT1Sirtuin1,
hydroxyphenyl)-4H-chromen-4-activator, Anti-MAO,
onedepressantPGC-1α,
ERRα/β
KW-2449(E)-(4-(2-(1H-indazol-3-5.45KinaseFLT3, ABL,
yl)vinyl)phenyl)(piperazin-1-inhibitorABL-T315I,
yl)methanoneAurora
kinase
Luteolin2-(3,4-Dihydroxyphenyl)-5,7-11.34MonoNFκB
dihydroxy-4-chromenoneamine
transporter
activator
Methysticin(2R)-2-[(E)-2-(1,3-Benzodioxol-5-7.17Neuro-CYP1A1
yl)ethenyl]-4-methoxy-2,3-protective,
dihydropyran-6-oneMAOI, NRI
OSI-9303-[(4-quinolinylmethyl) amino]-5.55KinaseKit, KDR,
N-[4-(trifluoromethoxy) phenyl]-inhibitorCSF-1R, Flt-
2-thiophenecarboxamide1, c-Raf Lck.
PDGFRα/β,
Flt-3, Abl
Paxilline(2R,4bS,6aS,12bS,12cR,14aS)-4b-4.1PotassiumPotassium
hydroxy-2-(1-hydroxy-1-channelchannels
methylethyl)-12b,12c-dimethyl-5,blocker
6,6a,7,12,12b,12c,13,14,14a-
decahydro-2H-chromeno[5′,6′:6,7]
indeno[1,2-b]indol-3(4bH)-one
PepstatinIsovalery-Val-Val-Sta-Ala-Sta8.64AspartylAcidic
[Sta = statine = (3S,4S)-4-amino-3-peptidasesproteases e.g.
hydroxy-6-methylheptanoic acid]pepsin, renin,
cathepsin D,
bovine
chymosin,
protease B
Piperine(2E,4E)-5-(Benzo[d][1,3]dioxol-5-4.69TRPV1TRPV1,
yl)-1-(piperidin-1-yl)penta-2,4-activator,TRPA1,
dien-1-onetyrosineP-Glyco-
protein kinasesprotein,
inhibitorCYP450,
CYP3A4
Quercetin•2H2O2-(3,4-dihydroxyphenyl)-3,5,7-7.76Polar auxinER a/b,
trihydroxy-4H-chromen-4-onetransport inhibitor,GPER,
phospho-PI3-kinase,
di-esterasemitochondrial
inhibitorATPase
Resveratrol3,5,4′-12.65MAOI, Anti-Sirtuin1,
trihydroxy-oxidantPGC-1α
trans-
stilbene
Ro 31-82202-{1-[3-(Amidinothio)propyl]-1H-10.11KinaseGRK-5,
indol-3-yl}-3-(1-methylindol-3-inhibitorPKC,
yl)maleimide methanesulfonateMAPKAP
saltkinase
Safinamide(2S)-2-[[4-[(3-4.82MAO inhibitorMAO,
fluorophenyl)methoxy]phenyl]σ receptor
methylamino]propanamide
SB-4152863-[(3-Chloro-4-hydroxyphenyl)-5.58GSK-3GSK-3
amino]-4-(2-nitrophenyl)-1H-inhibitor
pyrrol-2,5-dione
Splitomycin1,2-Dihydro-3H-naphtho[2,1-9.79N.ASir2p,
b]pyran-3-oneHDAC,
SIRT1
TWS1193-[6-(3-Amino-phenyl)-7H-3.64GSK-3βGSK-3β
pyrrolo[2,3,-d]pyrimidin-4-yloxy]-inhibitor
phenol
ValinomycinCyclo-4.49Cyclo-dodeca-Biological,
(L-Val-D-HyIva-D-Val-L-Lac-)3depsipeptideartificial lipid
[Hylva = a-Hydroxyionophore 1membranes
isovaleric acid,antibiotic
lac = Lactic acid]
Valnoctamide2-ethyl-3-methyl-pentanamide14.99Anti-GABA trans-
convulsan, indirectamination
GABA
agonist
Crenolanib1-(2-{5-[(3-Methyloxetan-3-N/AKinaseFLT3,
yl)methoxy]-1H-benzimidazol-1-inhibitorPDGFRα/β
yl}quinolin-8-yl)piperidin-4-amine
SunitinibN-[2-(Diethylamino)ethyl]-5-[(Z)-N/ARTK inhibitorPDGFRs,
(5-fluor-1,2-dihydro-2-oxo-3H-VEGFRs, c-
indol-3-yliden)-methyl]-2,4-KIT; FLT3 is
dimethyl-1H-pyrrol-3-carboxamidalso a target
XL-184N-(4-((6,7-Dimethoxyquinolin-4-N/AKinasec-Met,
(Cabozantinib)yl)oxy)phenyl)-N′-(4-inhibitorVEGFR2,
fluorophenyl)cyclopropane-1,1-AXL, RET
dicarboxamide
TWS-1193-[6-(3-Amino-phenyl)-7H-N/AGSK3GSK3β
pyrrolo[2,3,-d]pyrimidin-4-yloxy]-inhibitor
phenol
Indirubin3-[1,3-dihydro-3-(hydroxyimino)-N/AGSK3GSK3,
monoxiome2H-indol-2-ylidene]-1,3-dihydro-inhibitorCDK1/5
2H-indol-2-one
FLT inhibitor-2-(3,4-dimethoxybenzamido)-5,6-N/AFLT3 inhibitorFLT3
1 (Calbiochemdihydro-4H-
343020)cyclopenta[b]thiophene-3-
carboxamide
Note:
The compounds with the description ‘N/A’ in the B-score field are analog compounds of primary hit compounds identified from screening.

Almost all of the compounds identified in the screens described in Example 1 were also identified as hits in these screens. A number of additional compounds were also identified. As described in Example 1, a significant enhancement of KCC2 expression was detected in human RTT neurons treated with FLT3 kinase inhibitors, including KW-2449 (FIG. 10C), Crenolanib (FIG. 10E; see also FIG. 3A), XL-184 (FIG. 10G; see also FIG. 3B), and FLT3 Inhibitor-1 (FIG. 10H). The GSK3β inhibitor BIO (FIG. 10D), and a structural analog of BIO, indirubin monoxiome (FIG. 10F; see also FIG. 3C), also increased KCC2 expression levels significantly. The increases in KCC2 signal induced by KEECs are higher in RTT neurons than in WT neurons, which is consistent with the previous report that the baseline KCC2 expression level is lower in RTT neurons (7, 48).

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Patent 2022
Not available on PMC !

Example 4

Mitogen-activated protein kinases (MAPKs) provide a wide-ranging signaling cascade that allow cells to quickly respond to biotic and abiotic stimuli. The objective of this project was to determine if HE extracts from Fungi Perfecti (FP) impact MAPKs (e.g., influence the expression and phosphorylation of various MAPKs—notably JNK, c-Jun, and c-fos—to promote nerve growth factor (NGF) expression). Here, four FP extracts were tested at three concentrations each (Table 1). These extracts were tested against five MAPKs: c-Jun N-terminal kinase 1-3 (JNIK1, JNK2, JNK3), Rho Associated Coiled-Coil Containing Protein Kinases 1 and 2 (ROCK1, ROCK2), and tropomyosin receptor kinase B (TRKB). Collectively, these MAPKs are major players in neural health, influencing neurogenesis, neural growth and differentiation, and neurodegenerative diseases.

TABLE 11
Concentrations of FP HE extracts tested for binding to MAPK targets
ExtractConcentrations Tested (μg/mL)
HD HE Extract62.5125250
HE EtOAc62.5125250
HE Water Wash62.5125250
HD Powder31.2562.5125
HD: Host Defense ® Lion's Mane (Hericium erinaceus) product (Fungi Perfecti)

While several potential MAPK hits were identified for all extracts, the Host Defense® (Fungi Perfecti; “HD”) HE EtOH and HE EtOAc extracts elicited the most pronounced impacts, particularly the latter extract (FIG. 12). (Note: based on the % Control kinase binding calculation, stronger hits are represented by lower values.)

Interestingly, the top two hits included the HE EtOAc extract on JNK3 and the HD HE EtOH extract with ROCK1 (Table 12). This suggests that the extraction method may play a significant role in the ways in which neural health is impacted. While the strongest MAPK impact was found on JNK3 with the EtOAc extract, the EtOH extract did not produce a strong impact on this specific kinase. This may be due to the EtOAc extraction method producing the strongest detectable erinacine content.

TABLE 12
Top ten hits identified in the MAPK binding assay
DiscoveRxEntrez Compound
Compound GeneGenePercentConc.
NameSymbolSymbolControl(μg/mL)
HE EtOAcJNK3MAPK1054250
HD ExtractROCK1ROCK165250
HE EtOAcJNK2MAPK970250
HE EtOAcROCK1ROCK173250
HD ExtractROCK2ROCK274250
HE EtOAcJNK3MAPK1074125
HE EtOAcJNK1MAPK874250
HE EtOAcROCK2ROCK276250
HE Water WashJNK1MAPK876250
HE EtOAcJNK2MAPK97862.5
HD: Host Defense ® Lion′s Mane (Hericium erinaceus) product (Fungi Perfecti)

Collectively, MARK binding data suggest that FP HE extracts impact neural health on several broad levels. Of the top MARKs impacted by HE extracts, the JNKs play a role in cell degeneration, while the ROCKs play a role in cell survival. Accordingly, FP HE extracts may play an immunomodulatory role in influencing immune system homeostasis (FIG. 13).

Contrary to results from neurite outgrowth cellular assays, higher extract concentrations in MARK binding assays tended to elicit a stronger response. At 250 μg/mL, the EtOAc had a strong impact on the binding of TRKB, a well-characterized, high affinity receptor of brain-derived neurotrophic factor (BDNF), further broadening the scope at which FP HE extracts modulate neural activity.

Ultimately, findings from the MARK binding assays strengthen the mechanisms by which FP HE extracts influence neurogenic activity. In addition to morphology-based cellular assays in several cell lines, there is now evidence that FR extracts are driving neurite growth through diverse, classical neurogenic pathways related to neurotrophic factors including both NGF and BDNF.

The ability of psilocybin analogs to stimulate neurite outgrowth is demonstrated in several cell models. Accordingly, preliminary research has started to reveal the mechanisms by which psilocybin analogs may confer neurotrophic benefits that facilitate neurite outgrowth. Human 1321N1 brain cells treated with norbaeocystin have increased expression of NGF protein when compared to a vehicle control (FIG. 16).

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Patent 2023

Example 4

Mitogen-activated protein kinases (MAPKs) provide a wide-ranging signaling cascade that allow cells to quickly respond to biotic and abiotic stimuli. The objective of this project was to determine if HE extracts from Fungi Perfecti (FP) impact MAPKs (e.g., influence the expression and phosphorylation of various MAPKs—notably JNK, c-Jun, and c-fos—to promote nerve growth factor (NGF) expression). Here, four FP extracts were tested at three concentrations each (Table 11). These extracts were tested against five MAPKs: c-Jun N-terminal kinase 1-3 (JNK, JNK2, JNK3), Rho Associated Coiled-Coil Containing Protein Kinases T and 2 (ROCK, ROCK2), and tropomyosin receptor kinase B (TRKB). Collectively, these MAPKs are major players in neural health, influencing neurogenesis, neural growth and differentiation, and neurodegenerative diseases.

TABLE 11
Concentrations of FP HE extracts tested for binding to MAPK targets
ExtractConcentrations Tested (μg/mL)
HD HE Extract62.5125250
HE EtOAc62.5125250
HE Water Wash62.5125250
HD Powder31.2562.5125
HD: Host Defense ® Lion's Mane (Hericium erinaceus) product (Fungi Perfecti)

While several potential MAPK hits were identified for all extracts, the Host Defense (Fungi Perfecti; “HO”) HE EtGH and HE EtOAc extracts elicited the most pronounced impacts, particularly the latter extract (FIG. 12). (Note: based on the % Control kinase binding calculation, stronger hits are represented by lower values.)

Interestingly, the top two hits included the HE EtOAc extract on JNK3 and the HO HE EtOH extract with ROCK1 (Table 12). This suggests that the extraction method may play a significant role in the ways in which neural health is impacted. While the strongest MAPK impact was found on JNK3 with the EtOAc extract, the EtOH extract did not produce a strong impact on this specific kinase. This may be due to the EtOAc extraction method producing the strongest detectable erinacine content.

TABLE 12
Top ten hits identified in the MAPK binding assay
DiscoveRx Entrez Compound
Compound GeneGenePercentConc.
NameSymbolSymbolControl(μg/mL)
HE EtOAcJNK3MAPK1054250
HD ExtractROCK1ROCK165250
HE EtOAcJNK2MAPK970250
HE EtOAcROCK1ROCK173250
HD ExtractROCK2ROCK274250
HE EtOAcJNK3MAPK1074125
HE EtOAcJNK1MAPK874250
HE EtOAcROCK2ROCK276250
HE Water WashJNK1MAPK876250
HE EtOAcJNK2MAPK97862.5
HD: Host Defense ® Lion's Mane (Hericium erinaceus) product (Fungi Perfecti)

Collectively, MAPK binding data suggest that FP HE extracts impact neural health on several broad levels. Of the top MAPKs impacted by HE extracts, the JNKs play a role in cell degeneration, while the ROCKs play a role in cell survival. Accordingly, FP HE extracts may play an immunomodulatory role in influencing immune system homeostasis (FIG. 13).

Contrary to results from neurite outgrowth cellular assays, higher extract concentrations in MAPK binding assays tended to elicit a stronger response. At 250 μg/mL, the EtOAc had a strong impact on the binding of TRKB, a well-characterized, high affinity receptor of brain-derived neurotrophic factor (BDNF), further broadening the scope at which FP HE extracts modulate neural activity.

Ultimately, findings from the MAPK binding assays strengthen the mechanisms by which FP HE extracts influence neurogenic activity. In addition to morphology-based cellular assays in several cell lines, there is now evidence that FP extracts are driving neurite growth through diverse, classical neurogenic pathways related to neurotrophic factors including both NGF and BDNF.

The ability of psilocybin analogs to stimulate neurite outgrowth is demonstrated in several cell models. Accordingly, preliminary research has started to reveal the mechanisms by which psilocybin analogs may confer neurotrophic benefits that facilitate neurite outgrowth. Human 1321N1 brain cells treated with norbaeocystin have increased expression of NGF protein when compared to a vehicle control (FIG. 16).

Full text: Click here
Patent 2023

Most recents protocols related to «Tropomyosin-related kinase-B, human»

Example 8

In a second screening with 6088 antigens, the antigens which differentiate between healthy controls and donors with rheumatoid arthritis were tested on patients with early rheumatoid arthritis, SSc and SPA., This is of importance in particular since patients with collagenoses and mixed collagenoses have an overlapping autoantibody profile and therefore are difficult to diagnose, particularly in the early phase

FIG. 3 shows a volcano plot of the antigen reactivities of SLE patients against a combined group of patients with various autoimmune diseases, such as SSc, SPA, early rheumatoid arthritis, and SPA.

Following univariate statistical evaluation, a threshold value of p<0.05 and a 1.5 times modified reactivity compared with the control group were applied. A final list of antigen reactivities over both screens was established (Table 2).

In order to analyse the frequency of the newly identified antigens in comparison with, known antigens, a threshold value of 3 standard deviations (SD) above the mean value of the healthy samples was defined.

Astonishingly, at least 4 additional antigens were identified of which the frequency in SLE patients lies above 15%. These include TMPO (19%) (SEQ ID No. 13), HNRNPA1 (26%) (SEQ ID No. 5), XRCC5 (15%) (SEQ ID No. 22) and MVP (15%) (SEQ ID No. 7).

FIG. 4 shows the frequency of 23 antigens in comparison to the healthy controls.

Table 2 summarises the identified antigen reactivities and different group comparisons.

TABLE 2
List of all antigen reactivities
Statistical Test
SEQGeneGeneGenePanelSLEENA-4 negL. Nephr.SLE
ID No.IDSymbolNameGroupSLEL. Nephr.Clustervs HVvs SLEvs control
11629DBTdihydrolipoamide1xxSLE
branched chainvs
transacylase E2AID
21737DLATdihydrolipoamide S-1xSLE
acetyltransferasevs
AID
37430EZRezrin1xxxSLE
vs
AID
43017HIST1H2BDhistone cluster 1,1xxSLE
H2bdvs
AID
53178HNRNPA1heterogeneous1xxSLE
nuclearvs
ribonucleoprotein A1AID
63181HNRNPA2B1heterogeneous1xxSLE
nuclearvs
ribonucleoproteinAID
A2/B1
79961MVPmajor vault protein1xxxxSLE
vs
AID
86175RPLP0ribosomal protein,1xxxSLE
large, P0vs
AID
96176RPLP1ribosomal protein,1xxxxSLE
large, P1vs
AID
106181RPLP2ribosomal protein,1xxxSLE
large, P2vs
AID
1130011SH3KBP1SH3-domain kinase1xxSLE
binding protein 1vs
AID
126625SNRNP70small nuclear1xSLE
ribonucleoproteinvs
70 kDa (U1)AID
136628SNRPBsmall nuclear1xxxSLE
ribonucleoproteinvs
polypeptides B andAID
B1
146638SNRPNsmall nuclear1xSLE
ribonucleoproteinvs
polypeptide NAID
156672SP100SP100 nuclear1xxSLE
antigenvs
AID
166710SPTBspectrin, beta,1xxSLE
erythrocyticvs
AID
176741SSBSjogren syndrome1xxSLE
antigen Bvs
(autoantigen La)AID
187112TMPOthymopoietin1xxxSLE
vs
AID
196737TRIM21tripartite motif-1xxxSLE
containing 21vs
AID
206738TROVE2TROVE domain family,1xxSLE
member 2vs
RA
217431VIMvimentin1xxSLE
vs
AID
227520XRCC5X-ray repair1xxSLE
complementingvs
defective repair inAID
Chinese hamster
cells 5 (double-
strand-break
re joining)
237764ZNF217zinc finger protein1xxSLE
217vs
AID
2464763ZNF574zinc finger protein1xxSLE
574vs
AID
25148741ANKRD35ankyrin repeat2xxSLE
domain 35vs
HV
2684779ARD1BARD1 homolog B2xxSLE
(S. cerevisiae)vs
AID
27672BRCA1breast cancer 1,2xxSLE
early onsetvs
HV
28134359C5orf37chromosome 5 open2xxxSLE
reading frame 37vs
HV
299478CABP1calcium binding2xxSLE
protein 1vs
HV
3090557CCDC74Acoiled-coil domain2xxSLE
containing 74Avs
HV
319973CCScopper chaperone for2xxxxSLE
superoxide dismutasevs
AID
321410CRYABcrystallin, alpha B2xxSLE
vs
HV
3355802DCP1ADCP1 decapping2xxSLE
enzyme homolog Avs
(S. cerevisiae)HV
3479147FKRPfukutin related2xSLE
proteinvs
HV
3526128KIAA1279KIAA12792xxSLE
vs
HV
3657608KIAA1462KIAA14622xxSLE
vs
HV
371939LGTNligatin2xxSLE
vs
HV
3884298LLPHLLP homolog, long-2xxSLE
term synapticvs
facilitationHV
(Aplysia)
3911253MAN1B1mannosidase, alpha,2xxSLE
class 1B, member 1vs
HV
4084930MASTLmicrotubule2xxSLE
associatedvs
serine/threonineHV
kinase-like
4154531MIER2mesorm induction2xxxxSLE
early response 1,vs
family member 2RA
424594MUTmethylmalonyl2xxSLE
Coenzyme A mutasevs
HV
43399687myO18Amyosin XVIIIA2xxSLE
vs
HV
448883NAE1NEDD8 activating2xxSLE
enzyme E1 andvs
subunit 1HV
4510458BAIAP2BAI1-associated2xxSLE
protein 2vs
HV
464869NPM1nucleophosim2xxSLE
(nucleolarvs
phosphoprotein B23,HV
numatrin)
475223PGAM1phosphoglycerate2xxSLE
mutase 1 (brain)vs
HV
4811040PIM2pim-2 oncogene2xxSLE
vs
HV
4954517PUS7pseudouridylate2xxSLE
synthase 7 homologvs
(S. cerevisiae)HV
506605SMARCE1SWI/snf related,2xxSLE
matrix associated,vs
actin dependentAID
regulator of
chromatin,
subfamily e, member
1
5123635SSBP2single-stranded DNA2xxxSLE
binding protein 2vs
HV
5283660TLN2talin 22xxSLE
vs
HV
5351673TPPP3tubulin2xxSLE
polymerization-vs
promoting proteinHV
family member 3
547265TTC1tetratricopeptide2xxSLE
repeat domain 1vs
HV
55124930ANKRD13Bankyrin repeat3xSLE
domain 13Bvs
HV
56160AP2A1adaptor-related3xSLE
protein complex 2,vs
alpha 1 subunitHV
5753335BCL11AB-cell CLL/lymphoma3xx
11A (zinc finger
protein)
5879959CEP76centrosomal protein3x
76 kDA
591153CIRBPcold inducible RNA3xSLE
binding proteinvs
HV
6051084CRYL1crystallin, lambda 13x
6155827DCAF6DDB1 and CUL43xxxSLE
associated factor 6vs
AID
626993DYNLT1dynein, light chain,3xSLE
Tctex-type 1vs
HV
63283991FAM100Bfamily with sequence3xSLE
similarity 100,vs
member BHV
649815GIT2G protein-coupled3xSLE
receptor kinasevs
interacting ArfGAP 2HV
6584706GPT2glutamic pyruvate3x
transaminase
(alanine
aminotransferase) 2
663059HCLS1hematopoieti cell-3xxSLE
specific Lynvs
substrate 1AID
673329HSPD1heat shock 60 kDa3x
protein 1
(chaperonin)
683490IGFBP7insulin-like growth3xSLE
factor bindingvs
protein 7HV
6923392KIAA0368KIAA03683x
7084695LOXL3lysyl oxidase-like3x
3
714133MAP2microtubule-3xSLE
associated proteinvs
2HV
726837MED22mediator complex3x
subunit 22
7329079MED4mediator complex3xx
subunit 4
7410933MORF4L1mortality factor 43x
like 1
7564963MRPS11mitochondrial3xxSLE
ribosomal proteinvs
HV
7681565NDEL1nudE nuclear3x
distribution gene E
homolog
(A. nidulans)-like 1
7757447NDRG2NDRG family member3xSLE
2vs
HV
784744NEFHneurofilament, heavy3x
polypeptide
79153478PLEKHG4Bpleckstrin homology3x
domain containing,
family G (with
RhoGef domain)
member 4B [homo
sapiena (human)]
8011054OGFRopioid growth factor3xxSLE
receptorvs
AID
8156122PCDHB14protocadherin beta3xSLE
14vs
HV
822923PDIA3protein disulfide3xSLE
isomerase family A,vs
member 3HV
8323646PLD3phospholipase D3xSLE
family, member 3vs
HV
8423759PPIL2peptdylprolyl3xx
isomerase
(cyclophilin)-like
2
855557PRIM1primase, DNA,3xSLE
polypeptide 1vs
(49 kDa)HV
865682PSMA1proteasome (prosome,3xSLE
macropain) subunit,vs
alpha type, 1HV
875802PTPRSprotein tyrosine3xSLE
phosphatase,vs
receptor type, SHV
8881890QTRT1queuine tRNA-3xSLE
ribosyltransferase 1vs
HV
89116362RBP7retinol binding3xSLE
protein 7, cellularvs
HV
9010287RGS19regulator of G-3xx
protein signaling 19
9183642RP3-402G11.5selenoprotein O3xSLE
vs
HV
926389SDHAsuccinate3xxSLE
dehydrogenasevs
complex, subunit A,AID
flavoprotein (Fp)
9354437SEMA5Bsema domain, seven3x
thrombospondin
repeats (type 1 and
type 1-like),
transmembrane
domain (TM) and
short cytoplasmic
domain,
(semaphorin) 5B
9459343SENP2SUMO1/sentrin/SMT33xSLE
specific peptidasevs
2HV
956629SNRPB2small nuclear3xSLE
ribonucleoproteinvs
polypeptide B″AID
9627131SNX5sorting nexin 53xSLE
vs
HV
979021SOCS3suppressor of3xxSLE
cytokine signalingvs
3HV
983925STMN1stathmin 13xSLE
vs
HV
9981551STMN4stathmin-like 43xSLE
vs
HV
10027097TAFSLTAF5-like RNA3xSLE
polymerase II,vs
p300/CBP-associatedHV
factor (PCAF)-
associated factor,
65 kDa
10179521TCEAL4transcription3xSLE
elongation factor Avs
(SII)-like 4HV
10210040TOM1L1target of mybl3xSLE
(chicken)-like 1vs
HV
10322974TPX2TPX2, microtubule-3xSLE
associated, homologvs
(Xenopus laevis)HV
10451567TTRAPTRAF and TNF3x
receptor associated
protein
1058615USO1US01 homolog,3xx
vescicle docking
protein (yeast)
10610869USP19ubiquitin specific3xSLE
peptidase 19vs
RA
10729761USP25ubiquitin specific3x
peptidase 25
108375690WASH5PWAS protein family3xxSLE
homolog 5vs
pseudogeneHV
10910413YAP1Yes-associated3x
protein 1, 65 kDa
110653121ZBTB8Azinc finger and BTB3xxSLE
domain containingvs
BAHV
11155311ZNF444zinc finger protein3x
444
11229ABRactive BCR-related4xSLE
genevs
AID
113118ADD1adducin 1 (alpha)4xSLE
vs
AID
11455256ADI1acireductone4xSLE
dioxygenase 1vs
HV
1159255AIMP1aminoacyl tRNA4x
synthetase complex-
interacting
multifunctional
protein 1
11654522ANKRD16ankyrin repeat4xSLE
domain 16vs
HV
117348APOEapolipoprotein E4xSLE
vs
HV
11864333ARHGAP9Rho GTPase4xSLE
activating proteinvs
9HV
11922994AZI15-azacytidine4SLE
induced 1vs
HV
12055971BAIAP2L1BAI1-associated4x
protein 2-like 1
1217919BAT1HLA-B associated4xSLE
transcript 1vs
RA
1226046BRD2bromodomain4x
containing 2
12356912C11orf60chromosome 11 open4x
reading frame 60
12479415C17orf62chromosome 17 open4x
reading frame 62
12551300C3orf1chromosome 3 open4xSLE
reading frame 1vs
RA
126128866CHMP4Bchromatin modifying4xSLE
protein 4Bvs
AID
12723122CICcapicua homolog4xSLE
(Drosophila)vs
AID
12810970CKAP4cytoskeleton-4xSLE
associated proteinvs
4HV
12923122CLASP2cytoplasmic linker4x
associated protein
2
1301311COMPcartilage4x
oligomeric matrix
protein
1317812CSDE1cold shock domain4xSLE
containing E1, RNA-vs
bindingHV
1328642DCHS1dachsous 14xSLE
(Drosophila)vs
AID
1339909DENND4BDENN/MADD domain4xx
containing 4B
1341743DLSTdihydrolipoamide S-4x
succinyltransferase
(E2 component of 2-
oxo-glutarate
complex)
13584444DOT1LDOT1-like, histone4x
H3 methyltransferase
(S. cerevisiae)
13651143DYNC1LI1dynein, cytoplasmic4xSLE
1, lightvs
intermediate chain 1HV
13751011FAHD2Afumarylacetoacetate4x
hydrolase domain
containing 2A
13892689FAM114A1family with sequence4x
similarity 114,
member A1
13954463FAM134Bfamily with sequence4x
similarity 134,
member B
140100129583FAM47Efamily with sequence4xSLE
similarity 47,vs
member EHV
14193611FBXO44F-box protein 444x
14260681FKBP10FK506 binding4xSLE
protein 10, 65 kDavs
AID
14323360FNBP4formin binding4x
protein 4
1442300FOXL1forkhead box L14xSLE
vs
HV
14564689GORASP1golgi reassembly4xSLE
stacking protein 1,vs
65 kDaAID
1462934GSNgelsolin4xSLE
(amyloidosis,vs
Finnish type)HV
1473039HBA1hemoglobin, alpha4x
1483040HBA2hemoglobin, alpha 24x
14938858HES5hairy and enhancer4x
of split 5
(Drosophilia)
15010525HYOU1hypoxia up-regulated4x
1
1513608ILF2interleukin enhancer4xSLE
binding factor 2,vs
45 kDaRA
15223135KDM6Blysine (K)-specific4xSLE
demethylasae 6Bvs
AID
15356243KIAA1217KIAA12174xSLE
vs
HV
15457662KIAA1543KIAA15434x
15557498KIDINS220kinase D-interacting4x
substrate, 220 kDA
1563855KRT7keratin 74xSLE
vs
HV
157729970LOC729970similar to4x
hCG2028352
1589935MAFBv-maf4x
musculoaponeurotic
fibrosarcoma
oncogene homolog B
(avian)
15923764MAFFv-maf4xSLE
musculoaponeuroticvs
fibrosarcomaHV
oncogene homolog F
(avian)
16022924MAPRE3microtubule-4x
associated protein,
RP/EB family, member
3
1618079MLF2myeloid leukemia4x
factor 2
1624676NAP1L4nucleosome assembly4x
protein 1-like 4
1634688NCF2neutrophil cytosolic4xSLE
factor 2vs
HV
1644780NFE2L2nuclear factor4x
(erythroid-derived
2)-like 2
16579840NHEJ1nonhomologous end-4xx
joining factor 1
16622861NLRP1NLR family, pyrin4xSLE
domain containing 1vs
HV
16765009NDRG4NDRG family member 44xSLE
vs
HV
1684841NONOnon-POU domain4xSLE
containing, octamer-vs
bindingAID
16929982NRBF2nuclear receptor4xSLE
binding factor 2vs
AID
1708439NSMAFneutral4xSLE
sphingomyelinase (N-vs
SMase)activationHV
associated factor
1714926NUMA1nuclear mitotic4xSLE
apparatus protein 1vs
RA
17284759PCGF1polycomb group ring4x
finger 1
17384306PDCD2Lprogrammed cell4xSLE
death 2-likevs
HV
1745195PEX14peroxisomal4xSLE
biogenesis factor 14vs
HV
1759091PIGQphosphatidylinositol4xSLE
glycan anchorvs
biosynthesis, classRA
Q
176100137049PLA2G4Bphospholipase A2,4xSLE
group IVBvs
(cytosolic)RA
17710226PLIN3perilipin 34x
1785373PMM2phosphomannomutase 24x
17910450PPIEpeptidylprolyl4x
isomerase E
(cyclophilin E)
1805694PSMB6proteasome (prosome,4x
macropain) subunit,
beta type, 6
18122913RALYRNA binding protein,4xSLE
autoantigenicvs
(hnRNP-associatedHV
with lethal yellow
homolog (mouse))
1828241RBM10RNA binding motif4x
protein 10
1839904RBM19RNA binding motif4xSLE
protein 19vs
HV
1849743RICSRho GTPase-4x
activating protein
1858780RIOK3RIO kinase 3 (yeast)4x
1868578SCARF1scavenger receptor4xSLE
class 4, member 1vs
AID
18723513SCRIBscribbled homolog4xSLE
(Drosophila)vs
HV
188644096SDHAF1succinate4xSLE
dehydrogenasevs
complex assemblyRA
factor 1
18957794SF4splicing factor 44xSLE
vs
RA
1909814SFI1Sfi1 homolog,4x
spindle assembly
associated (yeast)
1916421SFPQsplicing factor4xSLE
proline/glutamine-vs
rich (polypyrimidineAID
tract binding
protein associated)
19283442SH3BGRL3SH3 domain binding4x
glutamic acid-rich
protein like 3
1936461SHBSrc homology 24xSLE
domain containingvs
adaptor protein BAID
19423381SMG5Smg-5 homolog,4xSLE
nonsense mediatedvs
mRNA decay factorHV
(C. elegans)
195112574SNX18sorting nexin 184xSLE
vs
HV
19684501SPIRE2spire homolog 24xSLE
(Drosophila)vs
HV
19754961SSH3slingshot homolog 34xSLE
(Drosophila)vs
AID
1989263STK17Aserine/threonine4x
kinase 17a
19951111SUV420H1suppressor of4x
variegation 4-20
homolog 1
(Drosophila)
2006902TBCAtubulin folding4x
cofactor A
2017024TFCP2transcription factor4xSLE
CP2vs
HV
2027030TFE3transcription factor4xSLE
binding to IGHMvs
enhancer 3HV
20390326THAP3THAP domain4xSLE
containing,vs
apoptosis associatedAID
protein 3
20410043TOM1target of myb14x
(chicken)
2057168TPM1tropomyosin 14xSLE
(alpha)vs
HV
20654952TRNAU1APtRNA selenocysteine4x
1 associated protein
1
20726140TTLL3tubulin tyrosine4x
ligase-like family,
member 3
2087371UCK2uridine-cytidine4xSLE
kinase 2vs
HV
2099277WDR46WD repeat domain 464xSLE
vs
HV
21055100WDR70WD repeat domain 704xSLE
vs
AID
21123038WDTC1WD and4xSLE
tetratricopeptidevs
repeats 1HV
2129831ZNF623zinc finger protein4x
623
21379364ZXDCZXD family zinc4xxSLE
finger Cvs
AID
2147791ZYXzyxin4xSLE
vs
AID
21555964SEPT3septin 35X
2165413SEPT5septin 55x
21726574AATFapoptosis5x
antagonizing
transcription factor
21891703ACY3aspartoacylase5x
(aminocyclase) 3
2199509ADAMTS2ADAM6SLE
metallopeptidasevs
with thrombospondinRA
type 1 motif, 2
22010939AFG3L2AFG3 ATPase family6SLE
gene 3-like 2vs
(yeast)HV
2211646AKR1C2aldo-keto reductase6SLE
family 1, member C2vs
(dihydrodiolRA
dehydrogenase 2;
bile acid binding
protein; 3-alpha
hydroxysteroid
dehydrogenase, type
III)
222267AMFRautocrine motility6SLE
factor receptorvs
RA
22310777ARPP-21cyclic AMP-regulated6SLE
phosphoprotein, 21vs
kDRA
224421ARVCFarmadillo repeat6SLE
gene deletes invs
velocardiofacialRA
syndrome
22580150ASRGL1asparaginase like 16SLE
vs
RA
226539ATP50ATP synthase, H+6SLE
transporting,vs
mitochondrial F1RA
complex, O subunit
22779870BAALCbrain and acute6SLE
leukemia,vs
cytoplasmicRA
2289531BAG3BCL2-associated5x
athanogene 3
2299275BCL7BB-cell CLL/lymphoma6SLE
7Bvs
HV
23055108BSDC1BSD domain6SLE
containing 1vs
AID
23154934C12orf41chromosome 12 open6SLE
reading frame 41vs
RA
23255049C19orf60chromosome 19 open6SLE
reading frame 60vs
RA
233388799C20orf107chromosome 20 open5x
reading frame 107
234149840C20orf196chromosome 20 open6SLE
reading frame 196vs
RA
23551507C20orf43chromosome 20 open6SLE
reading frame 43vs
RA
23655684C9orf86chromosome 9 open6SLE
reading frame 86vs
HV
23723523CABIN1calcineurin binding6SLE
protein 1vs
RA
238157922CAMSAP1calmodulin regulated6SLE
spectrin-associatedvs
protein 1RA
23923624CBLCCas-Br-M (murine)6SLE
ecotropic retroviralvs
transformingHV
sequence c
240124808CCDC43coiled-coil domain6SLE
containing 43vs
RA
241100133941CD24CD24 molecule5x
24211140CDC37cell division cycle6SLE
37 homologvs
(S. cerevisiae)RA
24310153CEBPZCCAAT/enhancer6SLE
binding proteinvs
(C/EBP), zetaRA
24451510CHMP5chromatin modifying6SLE
protein 5vs
RA
24563922CHTF18CTF18, chromosome5x
transmission
fidelity factor 18
homolog
(S. cerevisiae)
24651727CMPK1cytidine6SLE
monophosphate (UMP-vs
CMP) kinase 1,AID
cytosolic
24764708COPS7BCOP9 constitutive5x
photomorphogenic
homolog subunit 7B
(Arabidopsis)
24851117COQ4coenzyme Q4 homolog6SLE
(S. cerevisiae)vs
RA
24927254CSDC2cold shock domain5x
containing C2, RNA
binding
250162989DEDD2death effector6SLE
domain containing 2vs
RA
2519704DHX34DEAH (Asp-Glu-Ala-6SLE
His) box polypeptidevs
34RA
25255837EAPPE2F-associated6SLE
phosphoproteinvs
RA
2531915EEF1A1eukaryotic6SLE
translationvs
elongation factor 1RA
alpha 1
2541936EEF1Deukaryotic6SLE
translationvs
elongation factor 1RA
delta (guanine
nucleotide exchange
protein)
2558669EIF3Jeukaryotic6SLE
translationvs
initiation factor 3,RA
subunit J
25655740ENAHenabled homolog6SLE
(Drosophila)vs
HV
2572023ENO1enolase 1, (alpha)6SLE
vs
HV
25811124FAF1Fas (TNFRSF6)5x
associated factor 1
25911170FAM107Afamily with sequence6SLE
similarity 107,vs
member AHV
26084908FAM136Afamily with sequence6SLE
similarity 136,vs
member ARA
26110144FAM13Afamily with sequence6SLE
similarity 13,vs
member ARA
26226017FAM32Afamily with sequence6SLE
similarity 32,vs
member AHV
26364762FAM59Afamily with sequence6SLE
similarity 59,vs
member ARA
264150946FAM59Bfamily with sequence6SLE
similarity 59,vs
member BHV
26583706FERMT3fermitin family6SLE
homolog 3vs
(Drosophila)RA
26623307FKBP15FK506 binding6SLE
protein 15, 133 kDavs
HV
2672670GFAPglial fibrillary6SLE
acidic proteinvs
RA
26851031GLOD4glyoxalase domain6SLE
containing 4vs
AID
26981488GRINL1Aglutamate receptor,6SLE
ionotropic, N-methylvs
D-aspartate-like 1ARA
2702922GRPgastrin-releasing6SLE
peptidevs
RA
2712935GSPT1G1 to S phase6SLE
transition 1vs
RA
27293323HAUS8HAUS augmin-like6SLE
complex, subunit 8vs
HV
2733054HCFC1host cell factor C16SLE
(VP16-accessoryvs
protein)AID
2743069HDLBPhigh density6SLE
lipoprotein bindingvs
proteinRA
2753184HNRNPDheterogenous nuclear6SLE
ribonucleoprotein Dvs
(AU-rich element RNAHV
binding protein 1,
37 kDa)
2763320HSP90AA1heat shock protein6SLE
90 kDa alphavs
(cytosolic), class ARA
member 1
2777184HSP90B1heat shock protein6SLE
90 kDa beta (Grp94),vs
member 1RA
2783304HSPA1Bheat shock 70 kDa6SLE
protein 1Bvs
RA
2793315HSPB1heat shock 27 kDa4xxSLE
protein 1vs
RA
2805654HTRA1HtrA serine6SLE
peptidase 1vs
RA
2813382ICA1islet cell6SLE
autoantigen 1, 69 kDavs
RA
2823550IKIK cytokine, down-6SLE
regulator of HLA IIvs
HV
28380895ILKAPintegrin-linked6SLE
kinase-associatedvs
serine/threonineRA
phosphatase 2C
28484162KIAA1109KIAA11096SLE
vs
AID
2853856KRT8keratin 86SLE
vs
RA
28623367LARP1La ribonucleoprotein6SLE
domain family,vs
member 1AID
2874001LMNB1lamin B16SLE
vs
RA
28879888LPCAT1lysophosphatidylcholine5xSLE
acyltransferasevs
1HV
28910916MAGED2melanoma antigen5x
family D, 2
29055700MAP7D1MAP7 domain6SLE
containing 1vs
RA
2915602MAPK10mitogen-activated6SLE
protein kinase 10vs
HV
29222919MAPRE1microtubule-6SLE
associated protein,vs
RP/EB family, memberAID
1
2934137MAPTmicrotubule-6SLE
associated protein,vs
tauRA
29423139MAST2microtubule6SLE
associatedvs
serine/threonineRA
kinase 2
29553615MBD3methyl-CpG binding6SLE
domain protein 3vs
RA
29656922MCCC1methylcrotonoyl-6SLE
Coenzyme Avs
carboxylase 1HV
(alpha)
2971953MEGF6multiple EGF-like-6SLE
domains 6vs
RA
2984302MLLT6myeloid/lymphoid or6SLE
mixed-lineagevs
leukemia (trithoraxRA
homolog,
Drosophila);
translocated to, 6
29910200MPHOSPH6M-phase6SLE
phosphoprotein 6vs
RA
30010240MRPS31mitochondrial6SLE
ribosomal proteinvs
S31HV
30184939MUM1melanoma associated5x
antigen (mutated) 1
3024599MX1myxovirus (influenza6SLE
virus) resistance 1,vs
interferon-inducibleRA
protein p78 (mouse)
3034716NDUFB10NADH dehydrogenase6SLE
(ubiquinone) 1 betavs
subcomplex, 10,RA
22 kDa
3044796NFKBIL2nuclear factor of6SLE
kappa lightvs
polypeptide geneHV
enhancer in B-cells
inhibitor-like 2
30511188NISCHnischarin6SLE
vs
RA
30610381TUBB3tubulin, beta 36SLE
class IIIvs
RA
3078602NOP14NOP14 nucleolar6SLE
protein homologvs
(yeast)RA
3089722NOS1APnitric oxice6
synthase 1
(neuronal) adaptor
protein
30929959NRBP1nuclear receptor5x
binding protein 1
310142PARP1poly (ADP-ribose)6SLE
polymerase 1vs
RA
3115091PCpyruvate6SLE
carboxylasevs
RA
31223024PDZRN3PDZ domain6SLE
containing ringvs
finger 3RA
3138682PEA15phosphoprotein6SLE
enriched invs
astrocytes 15RA
3145187PER1period homolog 16SLE
(Drosophila)vs
HV
31557649PHF12PHD finger protein5x
12
31626227PHGDHphosphoglycerate5x
dehydrogenase
3171263PLK3polo-like kinase 36SLE
(Drosophila)vs
RA
31823654PLXNB2plexin B26SLE
vs
RA
31956902PNO1partner of NOB16SLE
homologvs
(S. cerevisiae)RA
3205479PPIBpeptidylprolyl6SLE
isomerase Bvs
(cyclophilin B)HV
32156978PRDM8PR domain6SLE
containing 8vs
HV
32255119PRPF38BPRP38 pre-mRNA6SLE
processing factorvs
38 (yeast) domainRA
containing B
3235764PTNpleiotrophin6SLE
vs
HV
3245819PVRL2poliovirus5x
receptor-related 2
(herpesvirus entry
mediator B)
3255831PYCR1pyrroline-5-6SLE
carboxylatevs
reductase 1RA
32665997RASL11BRAS-like, family6SLE
11, member Bvs
RA
32755658RNF126ring finger protein6SLE
126vs
AID
328115992RNF166ring finger protein6SLE
166vs
HV
3299025RNF8ring finger protein6SLE
8vs
HV
3306092ROBO2roundabout, axon5x
guidance receptor,
homolog 2
(Drosophila)
33164221ROBO3roundabout, axonx
guidance receptor,
homolog 3
(Drosophila)
3324736RPL10Aribosomal protein6SLE
L10avs
RA
3336152RPL24robosomal protein6SLE
L24vs
RA
334148418SAMD13sterile alpha motif6SLE
domain containingvs
13HV
33557147SCYL3SCY1-like 36SLE
(S. cerevisiae)vs
AID
3366382SDC1syndecan 16SLE
vs
RA
33791461SGK493protein kinase-like5x
protein SgK493
3386449SGTAsmall glutamine-6SLE
richvs
tetratricopeptideHV
repeat (TPR)-
containing, alpha
3399627SNCAIPsynuclein, alpha5x
interacting protein
3409552SPAG7sperm associated6SLE
antigen 7vs
RA
34157522SRGAP1SLIT-ROBO Rho6SLE
GTPase activatingvs
protein 1RA
3426744SSFA2sperm specific6SLE
antigen 2vs
RA
3436487ST3GAL3ST3 beta-6SLE
galactoside alpa-vs
2,3-RA
sialyltransferase 3
34423345SYNE1spectrin repeat6SLE
containing, nuclearvs
envelope 1AID
3456879TAF7TAF7 RNA polymerase6SLE
II, TATA boxvs
binding proteinHV
(TBF)-associated
factor, 55 kDa
3466895TARBP2TAR (HIV-1) RNA6SLE
binding protein 2vs
RA
3476949TCOF1Treacher Collins-6SLE
Franceschettivs
syndrome 1RA
3487980TFPI2tissue factor5x
pathway inhibitor 2
34956674TMEM9BTMEM9 domain6SLE
family, member Bvs
RA
35011189TNRC4trinucleotide5x
repeat containing 4
35110155TRIM28tripartite motif-6SLE
containing 28vs
HV
3527204TRIOtriple functional6SLE
domain (PTPRFvs
interacting)RA
353203068TUBBtubulin, beta6SLE
vs
RA
3547280TUBB2Atubulin, beta 2ASLE
vs
RA
35527229TUBGCP4tubulin, gamma6SLE
complex associatedvs
protein 4RA
35610422UBAC1UBA domain6SLE
containing 1vs
RA
3577316UBCubiquitin C6SLE
vs
RA
35855585UBE2Q1ubiquitin-6SLE
conjugating enzymevs
E2Q familiy member 1HV
35965109UPF3BUPF3 regulator of5x
nonsense
transcripts homolog
B (yeast)
3607378UPP1uridine6SLE
phosphorylase 1vs
AID
36164856VWA1von Willebrand6SLE
factor A domainvs
containing 1RA
36255884WSB2WD repeat and SOCS5x
box-containing 2
3639877ZC3H11Azinc finger CCCH-5x
type containing 11A
36455854ZC3H15zinc finger CCCH-6SLE
type containing 15vs
HV
3657592ZNF41zinc finger protein6SLE
41vs
RA
366170959ZNF431zinc finger protein6SLE
431vs
RA
367146542ZNF688zinc finger protein6SLE
688vs
RA
3684670HNRNPMheterogeneous7SLE
nuclearvs
ribonucleoprotein MHV
36910540DCTN2dynactin 2 (p50)7SLE
vs
HV
37010938EHD1EH-domain7SLE
containing 1vs
HV
37138ACAT1Acetyl-Coenzyme A7SLE
acetyltransferase 1vs
(acetoacetylHV
Coenzyme A
thiolase)
372684BST2bone marrow stromal7SLE
cell antigen 2vs
HV
3731058CENPAcentromere protein A7SLE
vs
HV
3741665DHX15DEAH (Asp-Glu-Ala-7SLE
His) box polypeptidevs
15HV
3753092HIP1Huntingtin7SLE
interacting proteinvs
1HV
3763336HSPE1heating shock 10 kDa7SLE
protein 1vs
(chaperonin 10)HV
3775455POU3F3POU class 3 homeobox7SLE
3vs
HV
3785918RARRES1retinoic acid7SLE
receptor respondervs
(tazarotene induced)HV
1
3796136RPL12ribosomalprotein L127SLE
vs
HV
3806626SNRPAsmall nuclear7SLE
ribonucleoproteinvs
polypeptide AHV
3816631SNRPCsmall nuclear7SLE
ribonucleoproteinvs
polypeptide CHV
3826757SSX2synovial sarcoma, X7SLE
breakpoint 2vs
HV
3839788MTSS1metastasis7SLE
suppressor 1vs
HV
38410134BCAP31B-cell receptor-7SLE
associated proteinvs
31HV
38510522DEAFldeformed epidermal7SLE
autoregulatoryvs
factor 1HV
(Drosophila)
38610633RASLl0ARAS-like, family 10,7SLE
member Avs
HV
38754795TRPM4transient receptor7SLE
potential cationvs
channel, subfamilyHV
M, member 4
38854913RPP25ribonuclease P/MRP7SLE
25 kDa subunitvs
HV
38954994C20orf11chromosome 20 open7SLE
reading frame 11vs
HV
39055727BTBD7BTB (POZ) domain7SLE
containing 7vs
HV
39179140CCDC28Bcoiled-coil domain7SLE
containing 28Bvs
HV
39279613TMCO7transmembrane and7SLE
coiled-coil domainsvs
7HV
3935504PPP1R2protein phosphatase7SLE
1, regulatoryvs
(inhibitor subunit 2HV
3948349HIST2H2BEhistone cluster 2,7SLE
H2bevs
HV
39511168PSIPlPC4 and SFRS17SLE
interacting proteinvs
1HV
396149986LSM14BLSM14B, SCD6 homolog7SLE
B (S. cerevisiae)vs
HV
397655BMP7Bone morphogenetic7SLE
protein 7vs
(osteogenic proteinHV
1)
3981676DFFADNA fragmentation7SLE
factor, 45 kDa, alphavs
polypeptideHV
3993071NCKAPlLNCK-associated7SLE
protein 1-likevs
HV
4003727JUNDjun D proto-oncogene7SLE
vs
HV
4013960LGALS4lectin, galactoside-7SLE
binding, soluble, 4vs
HV
4024920ROR2Receptor tyrosine7SLE
kinase-like orphanvs
receptor 2HV
4037424VEGFCvascular endothelial7SLE
growth factor Cvs
HV
4048906AP1G2adaptor-related7SLE
protein complex 1,vs
gamma 2 subunitHV
40510297APC2adenomatosis7SLE
polyposis coli 2vs
HV
40610841FTCDFormiminotransferase7SLE
cyclodeaminasevs
HV
40711066SNRNP35small nuclear7SLE
ribonucleoproteinvs
35 kDa (Ull/U12)HV
40811345GABARAPL2GABA(A)receptor-7SLE
associated protein-vs
like 2HV
40925854FAM149Afamily with sequence7SLE
similarity 149,vs
member AHV
41026065LSM14ALSM14A, SCD6 homolog7SLE
A (S. cerevisiae)vs
HV
41128998MRPL13mitochondrial7SLE
ribosomal proteinvs
L13HV
41251520LARSleucyl-tRNA7SLE
systhetasevs
HV
41355747FAM21Bfamily with sequence7SLE
similarity 21,vs
member BHV
41464841GNPNAT1glucosamine-7SLE
phosphate N-vs
acetyltransferase 1HV
41583483PLVAPPlasmalemma vesicle7SLE
associated proteinvs
HV
41684968PNMA6Aparaneoplastic7SLE
antigen like 6Avs
HV
417118430MUCLlMucin-like 17SLE
vs
HV
418122830NAT12N-acetyltransferase7SLE
12vs
HV
419221092HNRNPUL2heterogeneous7SLE
nuclearvs
ribonucleoprotein U-HV
like 2
420388962BOLA3bolA homolog 37SLE
(E. coli)vs
HV
421729230FLJ78302Similar to c-c7SLE
chemokine receptorvs
type 2 (C-C CKR-2)HV
(CC-CKR-2) (CCR-2)
(CCR2) (Monocyte
chemoattractant
protein 1 receptor)
(MCP-1-R) (CD192
antigen)
422729447GAGE2AG antigen 2A7SLE
vs
HV
4231152CKBNo Gene Name;7SLE
creatine kinase,vs
brainHV
424972CD74CD74 molecule, major7SLE
histocompatibilityvs
complex, class IIHV
invariant chain
4251397CRIP2cysteine-rich7SLE
protein 2vs
HV
4262040STOMstomatin7SLE
vs
HV
4272316FLNAfilamin A, alpha7SLE
vs
HV
4284000LMNAlamin A/C7SLE
vs
HV
4294582MUClmucin 1, cell7SLE
surface associatedvs
HV
4305230PGKlPhosphoglycerate7SLE
kinase 1vs
HV
4315340PLGplasminogen7SLE
vs
HV
4326525SMTNsmoothelin7SLE
vs
HV
4338936WASFlWAS protein family,7SLE
member 1vs
HV
43423647ARFIP2ADP-ribosylation7SLE
factor interactingvs
protein 2HV
4356712SPTBN2spectrin, beta, non-7SLE
erythrocytic 2vs
HV
4366729SRP54signal recognition7SLE
particle 54 kDavs
HV
4379987HNRPDLheterogeneous7SLE
nuclearvs
ribonucleoprotein D-HV
like
438337APOA4Apolipoprotein A-IV7SLE
vs
HV
439950SCARB2scavenger receptor
class B, member 2
4403183HNRNPCheterogeneous7SLE
nuclearvs
ribonucleoprotein CHV
(Cl/C2)
4413185HNRPFHeterogeneous7SLE
nuclearvs
ribonucleoprotein FHV
4423313HSPA9heat shock 70 kDa7SLE
protein 9 (mortalin)vs
HV
4433467IFNWlInterferon, omega 17SLE
vs
HV
4443799KIF5Bkinesin family7SLE
member 5Bvs
HV
4457918BAT4HLA-B associated7SLE
transcript 4vs
HV
4468337HIST2H2AA3histone cluster 2,7SLE
H2aa3vs
HV
44710195ALG3asparagine-linked7SLE
glycosylation 3,vs
alpha-1,3-HV
mannosyltransferase
homolog
(S. cerevisiae)
44823299BICD2bicaudal D homolog 27SLE
(Drosophila)vs
HV
44980184CEP290centrosomal protein7SLE
290 kDavs
HV
45090861HNlLhematological and7SLE
neurologicalvs
expressed 1-likeHV
451349136WDR86WD repeat domain 867SLE
vs
HV
452no Gene IDdsDNAdsDNA7SLE
vs
HV
45360ACTBactin, beta8SLE
vs
HV
454498ATP4A1ATP synthase, H+8SLE
transporting,vs
mitochondrial FlHV
complex, alpha
subunit 1, cardiac
muscle
455506ATP5BATP synthase, H+8SLE
transporting,vs
mitochondrial FlHV
complex, beta
polypeptide
456563AZGPlalpha-2-8SLE
glycoprotein 1,vs
zinc-bindingHV
457602BCL3B-cell CLL/lymphoma8SLE
3vs
HV
4581729DIAPHldiaphanous-related8SLE
formin 1vs
HV
4591937EEFlGeukaryotic8SLE
translationvs
elongation factor 1HV
gamma
4601973EIF4Aleukaryotic8SLE
translationvs
initiation factorHV
4A1
4612280FKBPlAFK506 binding8SLE
protein lA, 12 kDavs
HV
4622495FTHlferritin, heavy8SLE
polypeptide 1vs
HV
4632597GAPDHglyceraldehyde-3-8SLE
phosphatevs
dehydrogenaseHV
4642819GPDlglycerol-3-8SLE
phosphatevs
dehydrogenase 1HV
(soluble)
4653295HSD17B4hydroxysteroid 17-8SLE
beta) dehydrogenasevs
4HV
4663305HSPAlLheat shock 70 kDa8SLE
protein 1-likevs
HV
4673312HSPA8heat shock 70 kDa8SLE
protein 8vs
HV
4684174MCM5minichromosome8SLE
maintenance complexvs
component 5HV
4694215MAP3K3mitogen-activated8SLE
protein kinasevs
kinase kinase 3HV
4704591TRIM37tripartite motif8SLE
containing 37vs
HV
4714691NCLnucleolin8SLE
vs
HV
4724898NRDlnardilysin (N-8SLE
arginine dibasicvs
convertase)HV
4734904YBXlY box binding8SLE
protein 1vs
HV
4745037PEBPlphosphatidylethanol8SLE
amine bindingvs
protein 1HV
4755315PKM2pyruvate kinase,8SLE
musclevs
HV
4765481PPIDpeptidylprolyl8SLE
isomerase Dvs
HV
4775684PSMA3proteasome8SLE
(prosome,vs
macropain)subunit,HV
alpha type, 3
4786128RPL6ribosomal protein L68SLE
vs
HV
4796129RPL7ribosomal protein L78SLE
vs
HV
4806130RPL7Aribosomal protein8SLE
L7avs
HV
4816132RPL8ribosomal protein LB8SLE
vs
HV
4826187RPS2ribosomal protein S28SLE
vs
HV
4836189RPS3Aribosomal protein8SLE
S3Avs
HV
4846249CLIPlCAP-GLY domain8SLE
containing linkervs
protein 1HV
4856793STKl0serine/threonine8SLE
kinase 10vs
HV
4866880TAF9TAF9 RNA polymerase8SLE
II, TATA box bindingvs
protein (TBP)-HV
associated factor,
32 kDa
4877001PRDX2peroxiredoxin 28SLE
vs
HV
4887552ZNF711zinc finger protein8SLE
711vs
HV
4898260ARDlAN(alpha)-8SLE
acetyltransferasevs
10, NatA catalyticHV
subunit
4908317CDC7cell division cycle8SLE
7vs
HV
4918667EIF3Heukaryotic8SLE
translationvs
initiation factorHV
subunit H
4929223MAGilmembrane associated8SLE
guanylate kinase, WWvs
and PDZ domainHV
containing 1
4939230RABllBRABllB, member RAS8SLE
oncogene familyvs
HV
4949425CDYLchromodomain8SLE
protein, Y-likevs
HV
4959694EMC2ER membrane protein8SLE
complex subunit 2vs
HV
49610075HUWElHECT, UBA and WWE8SLE
domain containing 1,vs
E3 ubiquitin proteinHV
ligase
49710109ARPC2actin related8SLE
protein 2/3 complex,vs
subunit 2, 34 kDaHV
49810180RBM6RNA binding motif8SLE
protein 6vs
HV
49910273STUBlSTIPl homology and8SLE
U-box containingvs
protein 1, E3HV
ubiquitin protein
ligase
50010432RBM14RNA binding motif8SLE
protein 14vs
HV
50110539GLRX3glutaredoxin 38SLE
vs
HV
50210806SDCCAG8serologically8SLE
defined colon cancervs
antigen 8HV
50311108PRDM4PR domain containing8SLE
4vs
HV
50423002DAAMldishevelled8SLE
associated activatorvs
of morphogenesis 1HV
50523351KHNYNKH and NYN domain8SLE
containingvs
HV
50623589CARHSP1calcium regulated8SLE
heat stable proteinvs
1, 24 kDaHV
50726986PABPClpoly (A) binding8SLE
protein, cytoplasmicvs
1HV
50827072VPS41vacuolar protein8SLE
sorting 41 homologvs
(S. cerevisiae)HV
50930836DNTTIP2deoxynucleotidyltransferase,8SLE
terminal,vs
interacting proteinHV
2
51051028VPS36vacuolar protein8SLE
sorting 36 homologvs
(S. cerevisiae)HV
51151082POLRlDpolymerase (RNA) I8SLE
polypeptide D, 16 kDavs
HV
51251138COPS4COP9 signalosome8SLE
subunit 4vs
HV
51351466EVLEnah/Vasp-like8SLE
vs
HV
51454869EPS8LlEPS8-like 18SLE
vs
HV
51554903MKSlMeckel syndrome,8SLE
type 1vs
HV
51657017COQ9coenzyme Q98SLE
vs
HV
51757026PDXPpyridoxal8SLE
(pyridoxine, vitaminvs
B6) phosphataseHV
51857221ARFGEF3ARFGEF family8SLE
member 3vs
HV
51964753CCDC136coiled-coil domain8SLE
containing 136vs
HV
52080208SPGllspastic paraplegia8SLE
11 (autosomalvs
recessive)HV
52183858ATAD3BATPase family, AAA8SLE
domain containing 3Bvs
HV
52284893FBXO18F-box protein,8SLE
helicase, 18vs
HV
523129563DIS3L2DIS3 like 3′-5′8SLE
exoribonuclease 2vs
HV
524144097Cllorf84chromosome 11 open8SLE
reading frame 84vs
HV
525256364EML3echinorm microtubule8SLE
associated proteinvs
like 3HV
526347733TUBB2Btubulin, beta 2B8SLE
class IIbvs
HV
5273303HSPAlAheat shock 70 kDa8SLE
protein 1Avs
HV
5285163PDKlpyruvate8SLE
dehydrogenasevs
kinase, isozyme 1HV
5291001CDH3cadherin 3, type 1,8SLE
P-cadherinvs
(placental)HV

Full text: Click here
Patent 2024
Not available on PMC !

Example 1

As a first proof of concept of obtaining rigid antigen-binding chimeric proteins, such as Megabodies, a Nanobody was grafted onto a large scaffold protein via two peptide bonds that connect Nanobody to scaffold according to FIG. 2 to build a rigid Megabody.

The 58 kDa Megabody described here is a chimeric polypeptide concatenated from parts of single-domain immunoglobulin and parts of a scaffold protein connected according to FIGS. 2 and 3. Here, the immunoglobulin domain used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The scaffold protein is an adhesin domain of Helicobacter pylori strain G27 (PDB: 5LP2, SEQ ID NO:19) called HopQ (Javaheri et al, 2016). The N- and C-terminus of HopQ was connected to allow the creation of a circularly permutated variant of HopQ, called cHopQ, wherein a cleavage of the sequence was made somewhere else in its sequence. To design the MbNb207cHopQ construct, all parts were connected to each other from the amino (N-) to the carboxy (C-)terminus in the next given order by peptide bonds (SEQ ID NO:20): β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO: 1), a C-terminal part of HopQ (residues 192-414 of SEQ ID NO:19), a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant cHopQ of the scaffold protein, an N-terminal part of HopQ (residues 14-186 of SEQ ID NO:19), β-strands B to G of the GFP-binding Nanobody (residues 16-126 of SEQ ID NO:1), 6×His tag and EPEA tag (U.S. Pat. No. 9,518,084 B2; SEQ ID NO:209).

To demonstrate that MbNb207cHopQ (SEQ ID NO:20) can be expressed as a well folded and functional protein, we displayed this protein on the surface of yeast (Boder, 1997) and examined the specific binding of the cognate antigen (GFP) to yeast cells displaying this Megabody by flow cytometry. In order to display the MbNb207cHopQ on yeast, we used standard methods to construct an open reading frame that encodes the Megabody in fusion to a number of accessory peptides and proteins (SEQ ID NO:22): the appS4 leader sequence that directs extracellular secretion in yeast (Rakestraw, 2009), MbNb207cHopQ, a flexible peptide linker, the Aga2p the adhesion subunit of the yeast agglutinin protein Aga2p which attaches to the yeast cell wall through disulfide bonds to Aga1p protein, an acyl carrier protein for the orthogonal fluorescent staining of the displayed fusion protein (Johnsson, 2005) followed by the cMyc Tag. This open reading frame was put under the transcriptional control of galactose-inducible GAL1/10 promotor into the pCTCON2 vector (Chao, 2006) and introduced into yeast strain EBY100.

EBY100 yeast cells, bearing this plasmid, were grown and induced overnight in a galactose-rich medium to trigger the expression and secretion of the MbNb207cHopQ-Aga2p-ACP fusion. For the orthogonal staining of ACP, cells were incubated for 1 h in the presence a fluorescently labelled CoA analogue (coA-647, 2 μM) and catalytic amounts of the SFP synthase (1 μM). We found that expression of MbNb207cHopQ on the surface of yeast is induced by changing growing conditions from glucose-rich to galactose-rich media (FIG. 4). The surface display level can be easily and quantitively analysed by flow cytometry. In these experiments, induced yeast cells were washed and subjected to flow-cytometry to measure the Mb display level of each cell by comparing the CoA647-fluorescence level to yeast cells that do not display the Megabody but were stained orthogonally in the same way. Distinguishable yeast cells with a high CoA647-fluorescence signal were only detected in cultures expressing the MbNb207cHopQ, indicating that the Megabody can efficiently be displayed and orthogonally stained on the surface of yeast (FIG. 4).

To analyse the functionality of the displayed Megabody, we examined its binding to the cognate antigen (GFP) by flow cytometry. EBY100 yeast cells were induced and fluorescently stained orthogonally with CoA647 to monitor for MbNb207cHopQ-Aga2p-ACP fusion display, as described above. These orthogonally stained yeast cells were next incubated 1h in the presence of 100 nM GFP (Scholz et al., 2000). After washing these cells, we observed detectable amounts of GFP bound to the displayed MbNb207cHopQ, which should be linearly correlated to expression level of MbNb207cHopQ on the surface of yeast. Indeed, a two-dimensional flow cytometric analysis confirmed that GFP (high GFP-fluorescence level) only binds to yeast cells with significant Megabody display levels (high CoA647-fluorescence level) (FIG. 5). In contrast, GFP does not bind to wild type yeast cells that have been stained in the same way but do not express the MbNb207cHopQ. We conclude from these experiments that MbNb207cHopQ can be expressed as a well folded and functional antigen-binding (GFP-binding) chimeric protein on the surface of yeast.

Example 2

Next, we set out to express this 58 kDa MbNb207cHopQ in the periplasm of E. coli, purified this to homogeneity and determined its properties. In order to express Megabodies like MbNb207cHopQ (SEQ ID NO:20) in the periplasm of E. coli, we used standard methods to construct a cloning vector (called pMESD2) that allows the expression of any desired Megabody that is built from (a circularly permutated variant of) HopQ inserted into the first β-turn connecting the very conserved β-strand A, and β-strand B of any Nanobody. This vector is a derivative of pMES4 (Pardon, 2014) and contains an open reading frame that encodes the following polypeptides: the DsbA leader sequence that directs the secretion of the Megabody to the periplasm of E. coli, β-strand A of NbGFP207, representing an extremely conserved FR1 part of Nanobodies, a circularly permutated variant of HopQ, called cHopQ, the 6×His tag and the EPEA tag followed by the Amber stop codon. The C-terminal part of any Nanobody (from β-strand B to β-strand G) can be cloned as a Sapl fragment in this vector.

In order to express MbNb207cHopQ in the periplasm of E. coli and purify this recombinant protein to homogeneity, a DNA fragment encoding NbGFP207 from β-strand B to G (nucleotides 52-378 of SEQ ID NO:121) was amplified by PCR (with primers SEQ ID NO:122 and SEQ ID NO:123) and cloned as a Sapl fragment in pMESD2 vector that directs the expression of His-tagged and EPEA-tagged MbNb207cHopQ in the periplasm of E. coli under the transcriptional control of the Plac promotor.

WK6 bacterial cells (WK6 is a su nonsuppressor strain) were grown in 6 L TB medium at 37° C. and induced by IPTG when cells reached log-growing phase. Periplasmic expression of the His-tagged and EPEA-tagged MbNb207cHopQ was continued overnight at 28° C. Cells were harvested by centrifugation and the recombinant MbNb207cHopQ was released from the periplasm using an osmotic shock (Pardon et al., 2014). Recombinant Megabody was then separated from the protoplasts by centrifugation and recovered from the clarified supernatant on a HisTrap FF 5 mL prepacked column. The protein was next eluted from the NiNTA resin by applying 500 mM imidazole and concentrated by centrifugation using NMWL filters (Nominal Molecular Weight Limit) with a cut-off of 3 kDa. Concentrated samples were next applied on a Superdex 200 PG 16/90 size exclusion column to recover 24 mg of the recombinant Megabody as a soluble protein with an apparent molecular weight of about 60 kDa.

The functional properties of the purified recombinant MbNb207cHopQ were next analysed by size exclusion chromatography (SEC). The Megabody was incubated with 4 fold-molar excess of GFP for 30 min at 4° C. and applied on a Superdex 75 PG 16/90 column. Purified GFP alone was applied on the same size exclusion column separately (FIG. 6). Elution of the different proteins was monitored by measuring the UV absorption at 280 nm (absorbed by any protein) and 488 nm (absorbed by GFP). The elution spectra shown in FIG. 6 illustrate that the mixture containing Megabody and excess GFP elutes in two symmetric peaks (blue and red absorbance profiles). The first eluting peak (highest molecular weight) absorbs at 488 nm, indicating that it contains GFP. The second peak elutes at the same elution volume of GFP alone (green absorbance profile) and also adsorbs at 488 nm. SDS-polyacrylamide electrophoreses of the corresponding elution fractions confirms that the first elution peak of the mixture containing Megabody and excess GFP contains Megabody and GFP, whereas the second peak contains GFP only. All these data indicate that the purified recombinant MbNb207cHopQmakes a complex with GFP that resists separation by size-exclusion chromatography. Furthermore, real-time kinetic analysis of the specific binding of MbNb207cHopQ to GFP was performed by bio-layer interferometry. Streptavidin-coated Octet® biosensors were used to capture biotinylated GFP and associated with MbNb207cHopQ at different concentrations. The data as shown in FIG. 24 demonstrate that the affinity for GFP using the MbNb207cHopQ was similar to the affinity when using the NbGFP207 alone (FIG. 24B).

Example 3

As we were able to express and purify the 58 kDa chimer MbNb207cHopQ described in Examples 1 and 2, we set out to crystallize this Megabody and solve its structure by X-ray crystallography.

MbNb207cHopQ was purified by SEC (FIG. 6) as complex as described in Example 2, concentrated to 48 mg/mL and subjected to a number of commercial sparse-matrix crystallization screens (JSCG/Proplex/PEGion/Wizard12/Morpheus) in 0.1 μL lying drops, supplemented with 0.1 uL of the mother liquor. Small crystals obtained in the JSCG screen A2 condition (0.1 M sodium citrate, pH 5.5, 20% w/v PEG3000) were used in the seeding optimization approach. Well-diffracting crystals were obtained in 0.2 M ammonium citrate, 17% PEG3350, 10% Glycerol 48 mg/mL Mb207, seeded from JSCG A2 crystal. Data were collected at the 13 source of Diamond (UK) and the structure was refined to 2.6 Å resolution (Table 1).

TABLE 1
Crystallization, Data Collection and Refinement Statistics
Data statistics
X-ray sourceDiamond (I03)
Wavelength (Å)0.976230
Space groupP1
Unit Cell parameters (Å, º)a = 71.84 b = 92.92 c = 245.41
α = 91.76 β = 97.12 γ = 112.58
Resolution range (Å)29.44-2.62 (2.78-2.62)
Observed reflections572599 (91662)
Unique reflections321638(51292)
Completeness (%)92.4 (91.6)
Rmerge (I)0.04 (0.61)
Redundancy1.78 (1.78)
Mean I/σ(I)9.63 (1.05)
Refinement statistics
Rwork/Rfree a0.2651/0.3329
No of protein atoms32769
No of water26
B factor (Å2)107.68
Rmsd bond (Å)0.011
Rmsd angle (º)1.433
Ramachandran favoured/outlier (%)81.98/4.83 
Values for the highest-resolution shell are given in parentheses.
ª 5% of the reflections are used for the Rfree calculation.

The Megabody crystallized in P1 with 10 molecules per asymmetric unit. The RMSD between the different molecules in the asymmetric unit range from 0.3 to 2.7 Å4, indicating that the Nanobodies are rigidly linked to the scaffold via two peptide bonds that connect Nanobody to scaffold (FIG. 7).

Example 4

As a second antigen-binding chimeric protein example, we set out to express and purify 58 kD antigen-binding chimeric proteins built from the cHopQ scaffold inserted into the first β-turn connecting β-strands A and B of Nb35 that binds at the interface of the Gβ and Gα subunits of the β2 adrenergic receptor-Gs protein complex (Rasmussen et al, 2011a).

The 58 kDa Megabody called MbNb35cHopQ is a chimeric polypeptide concatenated from parts of single-domain immunoglobulin and parts of a scaffold protein connected according to FIGS. 2 and 3. Here, the immunoglobulin domain used is a Nanobody that binds at the interface of the Gβ and Gα subunits of the β2 adrenergic receptor-Gs protein complex (Rasmussen et al, 2011 a), with the CDR1 interacting primarily with Gβ and a long CDR3 loop interacting with both Gβ and Gα subunits as depicted in SEQ ID NO:24. All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:25): β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO:1), a C-terminal part of HopQ (residues 192-414 of SEQ ID NO:19), a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein, an N-terminal part of HopQ (residues 14-186 of SEQ ID NO:19), strands B to G of the Nanobody (residues 16-128 of SEQ ID NO:24), 6×His/EPEA tag.

In order to express MbNb35cHopQ in the periplasm of E. coli and purify this recombinant protein to homogeneity, a DNA fragment encoding Nb35 from β-strand B to G was amplified by PCR (with primers SEQ ID NO:122 and SEQ ID NO:123) and cloned as a Sapl fragment in pMESD2 vector that directs the expression of His-tagged and EPEA-tagged cHopQNb35 Megabody (SEQ ID NO:25) in the periplasm of E. coli under the transcriptional control of the PLac promotor.

The MbNb35cHopQ was also expressed in and purified to homogeneity from the periplasm of E. coli as described in example 2. Moreover, purified cHopQNb35 selectively binds at the interface of the Gβ and Ga subunits of the β2 adrenergic receptor-Gs protein complex.

Example 5

As a further example, we set out to express and purify another 58 kD antigen-binding chimeric protein built from cHopQ inserted into the first β-turn connecting β-strands A and B of Nb80 that binds to the human P2 adrenergic receptor and exhibits G protein-like behaviour (Rasmussen et al, 2011b). Alternatives to such Nanobodies have been described in for instance WO2012/007593 (see Table 1,2), WO2012/175643 (see Table 2, 3), WO2014/122183 (see Table 1 and 2), and WO2015/110449 (see Table 2 and 3). The invention therefore also includes all antigen-binding chimeric proteins designed and produced as described herein, based on the sequence of said Nbs listed in these cited patent applications (listed in said Tables). Alternatively, the CDRs of said Nbs are sufficient to obtain specific stabilization of the targeted GPCR complex protein as described, and the invention therefore also includes the antigen-binding chimeric proteins designed and produced as described herein, wherein the CDRs from said cited GPCR-complex specific Nbs are the basis of the CDRs of the antigen-binding domain of said GPCR-complex binding antigen-binding chimeric proteins.

The 58 kDa Megabody called MbNb80cHopQ is a chimeric polypeptide concatenated from parts of single-domain immunoglobulin and parts of a scaffold protein connected according to FIGS. 2 and 3. Here, the immunoglobulin domain used is Nb80 (SEQ ID NO:26), a Nanobody that binds at the cytoplasmic side of the β32 adrenergic receptor. An eight-amino-acid sequence of its CDR3 penetrates into a hydrophobic pocket formed by amino acids from TM segments 3, 5, 6 and 7 of the receptor. A four-amino-acid sequence of its CDR1 provides additional stabilizing interactions with cytoplasmic ends of TM segments and 6 (Rasmussen et al, 2011 b). Its CDR3 occupies a position similar to the carboxyl-terminal peptide of Gs in the β2AR-Gs protein complex (Rasmussen et al, 2011 a). All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:27): β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO:1), a C-terminal part of HopQ (residues 192-414 of SEQ ID NO:19), a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein, an N-terminal part of HopQ (residues 14-186 of SEQ ID NO:19, β-strands B to G of Nb80 (residues 16-120 of SEQ ID NO:27), 6×His/EPEA tag. In order to express MbNb80cHopQ in the periplasm of E. coli and purify this recombinant protein to homogeneity, a DNA fragment encoding Nb80 from β-strand B to G was amplified by PCR (with primers SEQ ID NO:122 and SEQ ID NO:123) and cloned as a Sapl fragment in pMESD2 vector as described under Example 4. This plasmid directs the expression of His-tagged and EPEA-tagged MbNb80cHopQ (SEQ ID NO:27) in the periplasm of E. coli under the transcriptional control of the Plac promotor.

Similar to the Megabodies of previous examples, MbNb80cHopQ can also be expressed in and purified to homogeneity from the periplasm of E. coli as described in Example 2. Moreover, purified MbNb80cHopQ selectively binds and stabilizes the active state conformation of β2AR. Similar to examples described in WO2012/007593, we compared the pharmacological properties of the β2AR-wild type (wt) receptor in the presence of Nb80 or MbNb80cHopQ with the properties of the β2AR-wt alone and with the properties of the β2AR-wt in the presence of an irrelevant Megabody MbNb207cHopQ (FIG. 53). Nb80 is a Nanobody that selectively binds to agonist bound β2AR and exhibits G protein-like behaviour, thus stabilizing the active-state conformation of the receptor in the agonist·β2AR·Nb 80 complex (Rasmussen et al., 2011). We investigated whether the properties of Nb80 to bind to the human β2 adrenergic receptor and to exhibit G protein-like behaviour (Rasmussen et al, 2011 b) are retained in MbNb80cHopQ via a Radio-ligand assay. NbGFP207, a Nanobody that specifically binds to GFP and has no affinity for β2AR. likewise, MbNb207cHopQ, were used as negative controls, and showed no affinity for β2AR (FIG. 53).

To be able to compare pharmacological effects of Nb80 or MbNb80cHopQ on the β2AR, we performed a radioligand assay as follows. To express the β2AR wild type (wt) receptor, 1 μg of the pFastBac1-β2ARwt construct was transformed into the DH10Bac™ cells using the Bac-to-Bac® Baculovirus Expression system according to the manufacturer's instructions (Invitrogen, cat. Nr. 10359-016) and plated on a fresh LB agar plate supplemented with 50 μg/ml kanamycin, 7 μg/ml gentamicin, 10 μg/ml tetracycline, 100 μg/ml X-gal and 40 μg/ml IPTG. White colonies were picked, the bacmid was purified and the sequence of the open reading frame was confirmed by sequencing. Recombinant baculoviruses were produced by transfection of 2 μg bacmid DNA into Sf9 cells in a 6-well plate format together with 8 μl of Cellfectin as the transfection reagent. The cells were incubated at 27° C. and P1 viruses were collected after 3 days. Viruses were subsequently amplified by serial passaging and P3 viruses were collected. Sf9 cells at concentration of 2-3×106 cells/ml were infected with baculoviruses at an M.O.I. of 0.5 and cells were expressing the receptor at 27° C. for 72 hours. Expression and cell surface localization of the receptor was assessed via Flow Cytometry using a mouse anti-FLAG M2 antibody as primary (1:100) which recognizes the FLAG peptide sequence at the N-terminal extracellular part of the receptor, and an anti-mouse DyLight405 as secondary antibody (1:100). Membranes were prepared from these cells by spinning down the cells at 1000×g for 30 minutes and by resuspending the resulting pellet in TME binding buffer (75 mM Tris/HCl pH7.4, 12.5 mM MgCl2, 1 mM EDTA) supplemented with protease inhibitors (cOmplete™ EDTA-free protease inhibitor cocktail tablets, Roche). The cells were lysed by six 10-seconds bursts using the Ultra turrax homogenizer at maximum speed. The lysates containing the membranes were then centrifuged at 40.000×g for 40 minutes at 4° C., the supernatant was discarded, and the membrane pellet was resuspended in TME binding buffer supplemented with 10% saccharose. The membranes were stored at −80° C. until further use. The total membrane protein content was estimated using a Pierce BCA Protein Assay Kit (Thermo Scientific) following the manufacturer's instructions. In order to normalize the data according to the total membrane protein concentration for further analysis, all samples were diluted to a final concentration of 0.2 mg/ml. For the radioligand competition binding assays, 10 μg of membranes expressing P2AR-wt were incubated with increasing concentrations of either epinephrine (natural agonist, Sigma cat. Nr E4250) or (−)-isoproterenol hydrochloride (full agonist, Sigma cat. Nr 16504) ranging from 10−11 M to 104 M in presence of 2 nM [3H]-dihydroalprenolol and in the presence of 5 μM Nb80, MbNb80cHopQ, MbNb207cHopQ, or no nanobody. Non-specific binding was determined in presence of 10 μM alprenolol. Samples were incubated for 2 hours at room temperature on a shaking platform, and receptor-bound radioligand was separated from free radioligand by filtration over Whatman GF/C unifilters (Perkin Elmer, cat nr 6005174) using a 96-well FilterMate harvester (Perkin Elmer). After filtration, membranes retained on the filter plates were washed with ice-cold wash buffer (20 mM Tris-HCl pH7.4), and filters were dried for 1 hour at 50° C. After adding 35 μl of scintillation fluid (MicroScint™-O, Perkin Elmer), radioactivity (cpm) retained on the filters was measured in a Wallac MicroBeta TriLux scintillation counter. Data represent the mean±s.e. of each experiment performed in duplicate. The IC50 values were determined by nonlinear regression analysis using Prism (GraphPad Software, San Diego, CA).

As shown in FIG. 53, we found that the pharmacological properties of the β2AR-wt in the presence of MbNb80cHopQ are very similar to the pharmacological properties of the β2AR-wt in the presence of Nb80 and profoundly different from the properties of P2AR-wt alone or P2AR-wt in the presence of MbNb207cHopQ Compared to the β2AR-wt alone, the β2AR-wt receptor in the presence of MbNb80cHopQ with G protein-like behaviour (cfr Nb80) exhibits increased affinities for agonists (epinephrine, isoproterenol), showing that the receptor in the presence of MbNb80cHopQ adopts an active-state conformation (Rasmussen et al, 2011 b). The increased affinity of the β2AR-wt in the presence of MbNb80cHopQ, compared to control β2AR-wt for the natural agonist epinephrine can be calculated from the ratio of the IC50 values from the competitive binding experiments depicted in FIG. 53 (A) by dividing the IC50 of epinephrine for P2AR-wt alone by the IC50high of epinephrine for P2AR-wt in the presence of MbNb80cHopQ, resulting in an apparent potency shift of ˜ 2000. The increased affinity of P2AR-wt in the presence of MbNb80cHOPQ for the synthetic agonist isoprotenerol can be calculated from the ratio of the IC50 values from the competitive binding experiments depicted in FIG. 53 (B) by dividing the IC50 of isoprotenerol for P2AR-wt by the IC50high of isoprotenerol for P2AR-wt in the presence of MbNb80cHopQ, resulting in an apparent potency shift of ≈ 2000. In conclusion, we demonstrated that the functionality of Nb80 has been retained in the MbNb80cHopQ format, moreover, that due to its retained antigen-binding affinity for the β2AR target, in fact it stabilizes the β2AR active-state conformation, and likewise to Nb80 provides conformation selective antigen binding.

Example 6

As a further example, we set out to express and purify another 58 kD antigen-binding chimeric protein built from cHopQ inserted into the first β-turn connecting β-strands A and B of Nb25 that binds the pentameric ligand-gated ion channel GABAA (Miller et al, 2017).

The 58 kDa Megabody called MbNb25cHopQ is a chimeric polypeptide concatenated from parts of single-domain immunoglobulin and parts of a scaffold protein connected according to FIGS. 2 and 3. Here, the immunoglobulin domain used is Nb25 (SEQ ID NO:28), a Nanobody that binds to the extracellular domain of the GABAA β33 subunit (Miller et al, 2017). All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:29): β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO:1), a C-terminal part of HopQ (residues 192-414 of SEQ ID NO:19), a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein, an N-terminal part of HopQ (residues 14-186 of SEQ ID NO:19), β-strands B to G of Nb25 (residues 16-125 of SEQ ID NO:28), 6×His/EPEA tag.

In order to express MbNb25cHopQ in the periplasm of E. coli and purify this recombinant protein to homogeneity, a DNA fragment encoding Nb25 from β-strand B to G was amplified by PCR (with primers SEQ ID NO:122 and SEQ ID NO:123) and cloned as a Sapl fragment in pMESD2 vector as described under Example 4. This plasmid directs the expression of His-tagged and EPEA-tagged MbNb25cHopQ (SEQ ID NO:29) in the periplasm of E. coli under the transcriptional control of the Plac promotor.

Similar to the Megabodies of previous examples, MbNb25cHopQ can also be expressed in and purified to homogeneity from the periplasm of E. coli as described in example 2. Moreover, purified MbNb25cHopQ binds to the extracellular domain of the GABAA 133 subunit.

Example 7

As the capacity to fold, but also the stability and the rigidity of Megabodies may rely on the composition and the length of the polypeptide linkages that connect the immunoglobulin to the scaffold, we introduced in vitro evolution techniques for the fine-tuning of particular Megabody formats if required. Starting from the Megabody described in Example 1, we constructed libraries encoding Megabodies with a similar design in which two short peptides of variable length and mixed amino acid composition connect Nanobody to scaffold according to FIG. 2 that are amenable to in vitro selection.

The 58 kDa Megabodies described here are chimeric polypeptides concatenated from parts of a single-domain immunoglobulin and parts of a scaffold protein connected by short polypeptide linkages according to FIG. 2. Here, the immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:30-33): β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, a C-terminal part of HopQ (residues 193-414 of SEQ ID NO:19), a peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein, an N-terminal part of HopQ (residues 15-186 of SEQ ID NO:19), a peptide linker of one or two amino acids with random composition, β-strands B to G of the anti-GFP-Nanobody (residues 11-126 of SEQ ID NO:1), 6×His tag and EPEA tag.

To display and select functional variants of the Megabody described in Examples 1, 2 & 3 that differ in composition and length of the linkers connecting Nanobody to scaffold on yeast, we used standard methods to construct a library of open reading frame that encode the various Megabodies in fusion to a number of accessory peptides and proteins (SEQ ID NO:34-37) according to FIG. 8: the appS4 leader sequence that directs extracellular secretion in yeast (Rakestraw, 2009), β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, a C-terminal part of HopQ (residues 193-414 of SEQ ID NO:19), a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein, an N-terminal part of HopQ (residues 15-186 of SEQ ID NO:19), a peptide linker of one or two amino acids with random composition, β-strands B to G of the anti-GFP-Nanobody (residues 11-126 of SEQ ID NO:1), a flexible (GGSG)n peptide linker, the Aga2p adhesion subunit of the yeast agglutinin protein Aga2p which attaches to the yeast cell wall through disulfide bonds to Aga1p protein, followed by an acyl carrier protein for the orthogonal fluorescent staining of the displayed fusion protein (Johnsson, 2005) and the myctag. These open reading frames were put under the transcriptional control of galactose-inducible GAL1/10 promotor into the pCTCON2 vector (Chao, 2006) to construct a yeast display library encoding 184.000 different variants of the Megabody described in Examples 1, 2 and 3 (See FIG. 8). For in vitro selection, this library was introduced into yeast strain EBY100. Transformed cells were grown and induced overnight in a galactose-rich medium. Induced cells were orthogonally stained with coA-647 (2 μM) using the SFP synthase (1 μM) and incubated with 100 nM of GFP. Next, these cells were washed and subjected to 2-parameter FACS analysis to identify yeast cells that display high levels of a particular Megabody (high CoA-647 fluorescence) and bind the antigen GFP (high GFP fluorescence). Cells that display high levels of a GFP binding Nanobody were sorted and amplified in a glucose-rich medium to be subjected to following rounds of selection by yeast display and two-parameter FACS analysis.

After one round of selection, a representative number of highly fluorescent cells in the CoA-647 and GFP channels were grown as single colonies and subjected to DNA sequencing to determine the sequences of a representative number of peptide linkers connecting Nanobody to scaffold protein. Four representative clones of each type of linkers with 1-1, 1-2, 2-1 and 2-2 amino acid short linker variants (Table 2) were confirmed to bind to 100 nM GFP in FACS experiments (FIG. 30). This demonstrates that different short peptide connections between antigen-binding domain and scaffold protein can be selected from Megabody libraries by in vitro selections and displayed as functional antigen-binding chimeric proteins. As we were able to display the functional variants of Megabody on the surface of yeast (above), we set out to express the four 1-1 amino acid short linkers representative Megabody clones (MP1331_A5, MP1331_A12, MP1331_B7 and MP1331_G10 from Table 2) in the periplasm of E. coli, purified these chimer to homogeneity and determined its properties. The four variants of Megabody MbNb207c7HopQ (MbNb207c7HopQ A5, MbNb207c7HopQ A12, MbNb207c7HopQB7, MbNb207c7HopQG10) and wild type with short (c7; see Example 23) circular permutation (MbNb207c7HopQ), were essentially generated as described in Example 2:MbNb207cHopQ (SEQ ID NO:136): β-strand A of the conserved N-terminus of the anti-GFP-Nanobody (1-13 of SEQ ID NO:1), a C-terminal part of HopQ (residues 192-411 of SEQ ID NO:19), an N-terminal part of HopQ (residues 18-186 of SEQ ID NO:19), β-strands B to G of the anti-GFP-Nanobody (residues 16-126 of SEQ ID NO:1), 6×His tag and EPEA tag.

The four MbNb207cHopQ variants (SEQ ID NO:137-140): β-strand A of the conserved N-terminus of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), one amino acid linker (Table 2), a C-terminal part of HopQ (residues 193-411 of SEQ ID NO:19), an N-terminal part of HopQ (residues 18-185 of SEQ ID NO:19), one amino acid linker (Table 2), β-strands B to G of the anti-GFP-Nanobody (residues 17-126 of SEQ ID NO:1), 6×His/EPEA tag.

These Megabodies (SEQ ID NO:136-140) were expressed in E. coli and purified as described in Example 2. Concentrated samples were next applied on a Superdex 200 PG 10/300 size exclusion column and eluted as homogenous, soluble protein samples with an apparent molecular weight of about 60 kDa (FIG. 31). The functional properties of the purified recombinant Megabodies (SEQ ID NO:136-140) were analysed by enzyme-linked immunosorbent assay (ELISA). Purified GFP was immobilized in the wells of a maxisorp microtitre plate (Nunc) at a concentration of 0,1 μg/well in sodium bicarbonate buffer pH 8.2. Residual protein binding sites in the wells were blocked for two hours at room temperature with milk in PBS. Purified Megabody samples were incubated on GFP coated and on non-coated wells. After washing steps, the binding of Megabodies to GFP was examined by using the CaptureSelect biotinylated antibody (Life Technologies) that specifically recognizes the EPEA-tag, present only on the Megabody. Subsequent detection of Capture Select biotinylated antibody was done with Streptavidin-Alkaline phosphatase (Promega). The absorption at 405 nm was measured after adding the enzyme substrate p-nitrophenyl phosphate. Detected signals show at least 10-fold higher signals of each Megabody comparing a condition with immobilized GFP to no GFP. The ELISA and SEC data indicate that the purified recombinant Megabodies (SEQ ID NO:136-140) can be purified to homogeneity and form complex with GFP (FIGS. 31 and 32).

TABLE 2
The composition and length of the yeast-display optimized
linker peptides connecting scaffold protein HopQ Nanobody
Megabody cloneConnection #1Connection #2
MP1331_A5AM
MP1331_A12RP
MP1331_B7YR
MP1331_G10LS
MP1331_B9VNT
MP1331_C1RGP
MP1331_C9PPA
MP1331_G5RPR
MP1331_A9VWR
MP1331_F6TWS
MP1331_A2HDS
MP1331_F9GGM
MP1331_H9FLHQ
MP1331_C7FVQP
MP1331_C11YRPT
MP1331_D7GSKQ

Example 8

Alternatively, a Megabody was designed built from Nanobodies connected to larger scaffolds. Libraries encoding Megabody variants in which two short peptides connect the Nanobody to another scaffold according to FIGS. 2 and 9 were constructed for in vitro selection.

The designed 100 kDa Megabodies are chimeric polypeptides concatenated from parts of a single-domain immunoglobulin and parts of a scaffold protein linked by short polypeptide linkers according to FIG. 2. The immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The alternative scaffold protein used was YgjK, a 86 kDA periplasmic protein of E. coli (PDB 3W7S, SEQ ID NO: 38). All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:39-42): β-strand A of the anti-GFP-Nanobody (residues 1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, the C-terminal part of YgjK (residues 464-760 of SEQ ID NO:38), a short peptide linker (SEQ ID NO:43) connecting the C-terminus and the N-terminus of YgjK to produce a circular permutant of the scaffold protein, the N-terminal part of YgjK (residues 1-461 of SEQ ID NO:38), a peptide linker of one or two amino acids with random composition, β-strands B to G of the anti-GFP-Nanobody (residues 17-126 of SEQ ID NO:1).

To display and select functional variants of MbNb207cYgjkQ randomlinkers (SEQ ID NO:39-42) that differ in composition and length of the linkers connecting Nanobody to scaffold on yeast, we used standard methods to construct a library of open reading frame that encode the various Megabodies in fusion to a number of accessory peptides and proteins (SEQ ID NO:44-47): the appS4 leader sequence that directs extracellular secretion in yeast (Rakestraw, 2009), β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, C-terminal part of YgjK (residues 464-760 of SEQ ID NO:38), a short peptide linker (SEQ ID NO:43) connecting the C-terminus and the N-terminus of YgjK to produce a circular permutant of the scaffold protein, an N-terminal part of YgjK (residues 1-461 of SEQ ID NO:38), a peptide linker of one or two amino acids with random composition, β-strands B to G of the anti-GFP-Nanobody (residues 17-126 of SEQ ID NO:1), a flexible (GGSG)n peptide linker, the Aga2p adhesion subunit of the yeast agglutinin protein Aga2p which attaches to the yeast cell wall through disulfide bonds to Aga1p protein, followed by an acyl carrier protein for the orthogonal fluorescent staining of the displayed fusion protein (Johnsson, 2005) and the myc tag. These open reading frames were put under the transcriptional control of galactose-inducible GAL1/10 promotor into the pCTCON2 vector (Chao, 2006) to construct a yeast display library encoding 184.000 different variants of MbNb207cYgjkQ randomlinkers (SEQ ID NO:39-42).

For in vitro selection, this library was introduced into yeast strain EBY100. Transformed cells were grown and induced overnight in a galactose-rich medium. Induced cells were orthogonally stained with coA-647 (2 μM) using the SFP synthase (1 μM) and incubated with 100 nM of GFP. Next, these cells were washed and subjected to 2-parameter FACS analysis to identify yeast cells that display high levels of a particular Megabody (high CoA-647 fluorescence) and bind the antigen GFP (high GFP fluorescence). Cells that display high levels of a GFP binding Nanobody were sorted and amplified in a glucose-rich medium to be subjected to following rounds of selection by yeast display and two-parameter FACS analysis.

After two rounds of selection, a representative number of highly fluorescent cells in the CoA-647 and GFP channels were grown as single colonies and subjected to DNA sequencing to determine the sequences of a representative number of peptide linkers connecting Nanobody to scaffold protein. One or two representative clones of each linker type (length) 1-1, 1-2, 2-1 and 2-2 amino acid short linker variants (Table 3) were confirmed to bind to 100 nM GFP in FACS experiments (FIG. 33). This demonstrates that different short peptide connections between antigen-binding domain and scaffold protein can be selected from Megabody libraries by in vitro selections and displayed as functional antigen-binding chimeric proteins. As we were able to display the functional variants of MbNb207cYgjkQ on the surface of yeast (above), we set out to express one clone of each amino-acid short linkers representative Megabody clones (MP1333_E2, MP1333_A2, MP1333_C4 and MP1333_F5 from Table 3) in the periplasm of E. coli. Four variants of MbNb207cYgjkQ, selected by yeast display were generated as chimeric polypeptides with following amino acid sequences: MbNb207cYgjkE2 (SEQ ID NO:141): β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), Tyr one amino acid linker, C-terminal part of YgjK (residues 464-760 of SEQ ID NO:38), a short peptide linker (SEQ ID NO:43) connecting the C-terminus and the N-terminus of YgjK to produce a circular permutant of the scaffold protein, an N-terminal part of YgjK (residues 1-461 of SEQ ID NO:38), Asp one amino acid linker, β-strands B to G of the anti-GFP-Nanobody (residues 17-126 of SEQ ID NO:1), 6×His/EPEA tag.

Similar constructs were obtained for the other Megabodies, with the difference found in the linker identity: MbNb207cYgjkA2 (SEQ ID NO:142): Glu 1-amino acid linker, Gly-Asp 2-amino acids linker; MbNb207cYgjkC4 (SEQ ID NO:143): Met-Tyr2-amino acids linker, Asn 1-amino acid linker, MbNb207cYgjkF5 (SEQ ID NO:144): Trp-Thr 2-amino acids linker, Gly-Ala 2-amino acids linker.

The MbNb207cYgjk variants (SEQ ID NO: 141-144) were expressed in E. coli, as described in Example 2, applying a modified pMESD2 vector. This new vector (called pMESP3) contains an open reading frame that encodes the following polypeptides: the pelB leader sequence that directs the secretion of the Megabody to the periplasm of E. coli, β-strand A of NbGFP207, a circularly permutated variant of YgjK, C-terminal part of any Nanobody (from β-strand B to β-strand G), the 6×His tag and the EPEA tag followed by the Amber stop codon.

The functional properties of the expressed Megabodies were analysed by ELISA as described in Example 7, using periplasmic extracts of each of four MbNb207cYgjk variants. Comparison of detected signals for sample with and without immobilized GFP (FIG. 34) clearly confirmed the periplasmic expression of functional MbNb207cYgjk variants (SEQ ID NO:141-144).

The MbNb207cYgjkE2 (SEQ ID NO:141) representing 1-1 amino acid short linkers variant was further purified to homogeneity using IMAC followed by SEC as described in Example 2 (FIG. 35). Binding kinetics to GFP of purified MbNb207cYgjkE2 (SEQ ID NO:141) was measured by Octet® and compared to NbGFP207 Nanobody (SEQ ID NO:1) and MbNb207cHopQ (SEQ ID NO:20) (FIG. 24). Calculated binding affinities confirmed that antigen-binding chimeric proteins, built from a circularly permutated HopQ or YgjK scaffold proteins do not interfere with the binding properties of the original single-domain immunoglobulin.

TABLE 3
The composition and length of the yeast-display optimized
linker peptides connecting scaffold protein YgjK to Nanobody
Megabody cloneConnection #1Connection #2
MP1333_E2YD
MP1333_E6LAD
MP1333_C4MYN
MP1333_A2EGD
MP1333_D6FGA
MP1333_F5WTGA
MP1333_C2FMPA

Example 9

We further developed even more rigid antigen-binding chimeric proteins by engineering an extra disulphide bond that connects the antigen-binding domain, here immunoglobulin domain, to the scaffold according to FIG. 10. Accordingly, we used site-directed mutagenesis to produce mutants of MbNb207cHopQ in which two short peptides and a disulphide bond connect the Nanobody to the scaffold according to FIGS. 2 and 10.

The 58 kDa Megabodies described here are chimeric polypeptides concatenated from parts of a single-domain immunoglobulin and parts of a scaffold protein linked by short polypeptide linkages and a disulphide bond according to FIGS. 2 and 10. Here, the immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The scaffold protein is an adhesin domain of Helicobacter pylori strain G27 (PDB: 5LP2, SEQ ID NO:19) called HopQ. All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:48-50): β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO:1), a C-terminal part of HopQ (residues 192-414 of SEQ ID NO:19), a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein (cHopQ), an N-terminal part of HopQ (residues 14-186 of SEQ ID NO:19) in which one residue was replaced by cysteine, β-strands B to G of the Nanobody (residues 16-126 of SEQ ID NO:1) in which one residue was replaced by cysteine, 6×His/EPEA tag. SEQ ID NO:51 was built from β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO: 1), a C-terminal part of HopQ (residues 192-414 of SEQ ID NO:1) in which one residue was replaced by cysteine, a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein (cHopQ), an N-terminal part of HopQ (residues 14-186 of SEQ ID NO:19), β-strands B to G of the Nanobody (residues 16-126 of SEQ ID NO:1) in which one residue was replaced by cysteine, 6×His/EPEA tag.

Further constructs were designed applying the shorter cHopQ circular permutant (for cHopQ: see Example 23) as scaffold protein: SEQ ID NO: 146-150 were built from β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO:1), a C-terminal part of HopQ (residues 192-411 of SEQ ID NO:19), an N-terminal part of HopQ (residues 18-186 of SEQ ID NO:19) in which one residue was replaced by cysteine, β-strands B to G of the Nanobody (residues 16-126 of SEQ ID NO:1) in which one residue was replaced by cysteine, 6×His tag and EPEA tag. SEQ ID NO:145 was built from β-strand A of the anti-GFP-Nanobody (1-13 of SEQ ID NO: 1), a C-terminal part of HopQ (residues 192-411 of SEQ ID NO:1) in which one residue was replaced by cysteine, an N-terminal part of HopQ (residues 18-186 of SEQ ID NO:19), β-strands B to G of the Nanobody (residues 16-126 of SEQ ID NO:1) in which one residue was replaced by cysteine, 6×His tag and EPEA.

In total 10 Megabody variants (MbNb207cHopQ Cys1-4 (SEQ ID NO:48-51) and MbNb207c7HopQ Cys5-10 (SEQ ID NO:145-150) were expressed and purified from E. coli as described in Example 2. The functional properties of these purified recombinant Megabodies were analysed by ELISA as described in Example 7. Comparison of detected signals for samples with and without immobilized GFP (FIG. 36) clearly confirmed the functionality of MbNb207cHopQ Cys1-4 (SEQ ID NO:48-51) and MbNb207c7HopQ Cys5-10 (SEQ ID NO:145-150), purified from periplasm of E. coli.

To measure the contribution of an introduced additional disulphide on the thermostability of these engineered Megabody variants we performed thermal Shift Assays (TSA) and calculated the melting temperature (Tm) of each Megabody variant as described before (Hunynh et al., 2015). Accordingly, 0.2 mg/mL of each gel-filtration purified Megabody variant was mixed with SYPRO Orange dye (Sigma) in 140 mM NaCl and 10 mM Tris pH 7.3 buffer. Next, the fluorescence of 20 μL samples was measured in triplicates by Real-Time PCR on a Bio-Rad CFX96 machine over a temperature range from 25 to 100° C. Individual Tm values were calculated by GraphPad Prism software using the Boltzmnann equation (Table 4). The melting temperatures increased by 10.9° C., 3.43° C., 4.29° C. and 6.14° C. compared to the wild-type Megabody for MbNb207cHopQ C15-C534 (SEQ ID NO:51), MbNb207c7HopQ C14-C512 (SEQ ID NO:145), MbNb207c7HopQ C316-C472 (SEQ ID NO:147) and MbNb207c7HopQ C314-C472 (SEQ ID NO:148), respectively indicating that these disulphide bonds are formed and rigidify the Megabodies.

TABLE 4
Melting temperatures (Tm) for MbNb207c/c7HopQ Cysteine variants.
Megabody cloneTm [° C.]
MbNb207cHopQ 48.7
MbNb207cHopQ C357-C42549
MbNb207cHopQ C358-C488(43.8)* 49.5
MbNb207cHopQ C359-C490(44.2)* 49.7
MbNb207cHopQ C15-C534(49.4)* 59.6
MbNb207c7HopQ 49.74
MbNb207c7HopQ C14-C51253.17
MbNb207c7HopQ C402-C47447.01
MbNb207c7HopQ C316-C47254.02
MbNb207c7HopQ C314-C472(49.16)* 55.88
MbNb207c7HopQ C312-C45350.34
MbNb207c7HopQ C349-C45250.03
*First transition melting temperature (see FIG. 36)

Example 10

Another manner to generate rigid antigen-binding chimeric proteins is to connect the immunoglobulins to their scaffolds via alternative linking schemes. Accordingly, libraries encoding Megabodies built from a Nanobody grafted onto a scaffold protein via three polypeptide linkages that connect Nanobody to scaffold as illustrated in FIG. 11 were constructed and are amenable to in vitro selection.

The rigid antigen-binding chimeric proteins described here are chimeric polypeptides concatenated from parts of a single-domain immunoglobulin and parts of a scaffold protein linked by three short polypeptide linkages according to FIG. 11. The immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The scaffold protein used was Azurin, a small copper containing single domain protein of Pseudomonas aeruginosa (PDB 2TSA, SEQ ID NO: 52, a M121A mutation compared to the P. aeruginosa protein). All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:53-60): β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, N-terminal part of Azurin (Residue 3-22 of SEQ ID NO:52), a peptide linker of one or two amino acids with random composition, β-strands B to G of the anti-GFP-Nanobody (residues 17-126 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, C-terminal part of Azurin (residues 31-128 of SEQ ID NO:52), 6×His and EPEA tag.

To display and select functional representatives of these metal-binding Megabodies in which three short peptides connect the Nanobody to the scaffold (SEQ ID NO:53-60) on yeast, we used standard methods to construct a library of open reading frames that encode the various Megabodies in fusion to a number of accessory peptides and proteins (SEQ ID NO:61-68): the appS4 leader sequence that directs extracellular secretion in yeast (Rakestraw, 2009), β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, N-terminal part of Azurin (Residue 3-22 of SEQ ID NO:52), a peptide linker of one or two amino acids with random composition, strands B to G of the anti-GFP-Nanobody (residues 17-126 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, C-terminal part of Azurin (residues 31-128 of SEQ ID NO:52), a flexible (GGSG)n peptide linker, the Aga2p adhesion subunit of the yeast agglutinin protein Aga2p which attaches to the yeast cell wall through disulphide bonds to Aga1p protein, followed by an acyl carrier protein for the orthogonal fluorescent staining of the displayed fusion protein (Johnsson, 2005) and the myctag. These open reading frames were put under control of galactose-inducible GAL1/10 promotor into the pCTCON2 vector (Chao, 2006) to construct a yeast display library encoding 77.280.000 different variants of the Megabody in which three short peptides and connect the Nanobody to Azurin according to FIG. 12.

For in vitro selection by yeast display and FACS, this library was introduced into yeast strain EBY100. Transformed cells were grown and induced overnight in a galactose-rich medium in the presence of Cu++. Induced cells were orthogonally stained with coA-647 (2 μM) using the SFP synthase (1 μM) and incubated with 100n M of GFP. Next, these cells were washed and subjected to 2-parameter FACS analysis to identify yeast cells that display high levels of a particular Megabody (high CoA-647 fluorescence) and bind the antigen GFP (high GFP fluorescence). Cells that display high levels of a GFP binding Nanobody were sorted and amplified in a glucose-rich medium to be subjected to following rounds of selection by yeast display and two-parameter FACS analysis.

After two rounds of selection, a representative number of highly fluorescent cells in the CoA-647 and GFP channels were grown as single colonies and subjected to DNA sequencing to determine the sequences of a representative number of peptide linkers connecting Nanobody to scaffold protein. Two representative clones of linker types 1-2-1, 2-2-1, 1-2-2, and 2-2-2 amino-acid short linker variants (Table 5) were confirmed to bind to 100 nM GFP in FACS experiments (FIG. 37). This demonstrates that Megabodies concatenated from parts of a single-domain immunoglobulin and parts of a scaffold protein linked by three short polypeptide linkages can be selected from Megabody libraries by in vitro selections and display as functional antigen-binding chimeric proteins.

As we were able to display the functional variants of MbNb207Azurin on the surface of yeast (above), we set out to express these antigen-binding chimeric proteins in the periplasm of E. coli. Eight MbNb207Azurinvariants, selected by yeast display (Table 5) were generated as chimeric polypeptides with following amino acid sequences: MbNb207Azurin variant (SEQ ID NO:151-158) β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), amino acid linker (Table 5), N-terminal part of Azurin (Residue 3-22 of SEQ ID NO:52), amino acids linker (Table 5), strands B to G of the anti-GFP-Nanobody (residues 17-126 of SEQ ID NO:1), amino acid linker (Table 5), C-terminal part of Azurin (residues 31-128 of SEQ ID NO:52), 6×His/EPEA tag.

In order to express Megabodies like MbNb207Azurin variants (SEQ ID NO:151-158) in the periplasm of E. coli, we modified the pMESD2 vector, described in Example 2. This new vector (called pMESP5) contains an open reading frame that encodes the following polypeptides: the pelB leader sequence that directs the secretion of the Megabody to the periplasm of E. coli, β-strand A of NbGFP207, N-terminal part of Azurin, C-terminal part of any Nanobody (from β-strand B to β-strand G), C-terminal part of Azurin, the 6×His tag and the EPEA tag followed by the Amber stop codon. Eight MbNb207Azurin variants (SEQ ID NO: 151-158) were expressed in periplasm of E. coli as described in Example 2. The functional properties of the expressed Megabodies were analysed by ELISA as described in Example 7 using periplasmic extracts of each of eight MbNb207Azurin variants. Comparison of detected signals for sample with and without immobilized GFP (FIG. 38) clearly confirmed the periplasmic expression of functional MbNb207Azurinvariants (SEQ ID NO: 151-158). This demonstrates that Megabodies concatenated from parts of a single-domain immunoglobulin and parts of a scaffold protein linked by three short polypeptide linkages can be functionally express in periplasm of E. coli.

TABLE 5
The composition and the length of the yeast-display optimized
linker peptides connecting scaffold protein Azurin to a
Nanobody.
Megabody Connection Connection Connection SEQ
clone#1#2#3ID NO:
MP1305_A8NNGA151
MP1304_D9PNGP152
MP1304_D10GNGGK153
MP1305_D11GENGN154
MP1304_G6GSTDG155
MP1304_B8GSRTM156
MP1304_B2GGNGPP157
MP1305_C8RINGNY158

Example 12

Three-dimensional structure determination by cryo-EM involves averaging the information present in 2D projection images of multiple copies of individual particles, which are oriented variably with respect to the incident electron beam. In the case of icosahedral viruses, although each individual virion can be considered a particle, the symmetry of these structures is such that many identical copies of the asymmetrical unit are included in each particle, increasing by many fold the effective number of units averaged to determine the structure. Accordingly, icosahedral viruses that rigidly array Nanobodies following the symmetry imposed by the coat proteins would be the ultimate tool to solve the structures of small proteins and their complexes by Cryo-EM.

Here we designed Nanobody-displaying icosahedral virus-like particles by grafting Nbs onto the coat protein of icosahedral bacteriophages that self-assemble into virus-like particles (VLPs). It was shown that 90 copies of a concatenated dimer of the coat protein of PP7 of an icosahedral bacteriophage of P. Aeruginosa, or 180 coat proteins can self-assemble upon overexpression in E. coli to form icosahedral viral like particles (VLPs) (O'Rourke et al., 2015). In these VLPs, the coat proteins intertwine pairwise with the N-terminus of one monomer very close to the C-terminus of the interlaced monomer. It has also been demonstrated that peptides can be inserted in an exposed loop of this dimer to display this peptide on the surface of the corresponding VLP. Accordingly, we constructed random libraries encoding rigid antibody chimera that are built from a Nanobody that was grafted onto the concatenated dimer of the PP7 coat protein in which two short peptides connect Nanobody to scaffold according to FIG. 2. The 3.9 MDa icosahedral virus-like particles described here self-assemble from chimeric polypeptides built from parts of a single-domain immunoglobulin and parts of a scaffold protein directly linked according to FIG. 14. The immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The scaffold protein used is a circular permutated version of a covalent dimer of the coat protein of PP7 (PDB: 1 DWN, SEQ ID NO:2). PP7 is an icosahedral RNA bacteriophage of P. Aeruginosa. All parts were connected to each other from the amino to the carboxy terminus in the next given order (SEQ ID NO:3-6): methionine encoded by the startcodon, β-strand A of the anti-GFP-Nanobody (residues 1-13 of SEQ ID NO:1), the PP7 coat protein (residues 12-128 of SEQ ID NO:2), a peptide linker of one or two amino acids with random composition, a glycine, the PP7 coat protein (residues 2-128 of SEQ ID NO:2), a peptide linker of one or two amino acids with random composition, a glycine, PP7 coat protein (residue 2-8 of SEQ ID NO:2), β-strands B to G of the GFP-binding Nanobody (residues 16-126 of SEQ ID NO:1), 6×His/EPEA tag. This rigid antigen-binding chimeric protein self assembles into an icosahedral VLP (NanoVLP) that displays 90 copies of the Nanobody on its surface (FIG. 14).

To select functional representatives of these engineered GFP-binding coat proteins that self-assemble into NanoVLPs, we used standard methods to construct libraries of open reading frames (SEQ ID NO:3-6) comprising a methionine, the β-strand A of the anti GFP-Nanobody, the circular permutated dimeric PP7 coat protein, the β-strands B to G of the GFP-binding Nanobody, the 6×His/EPEA tag. These DNA fragments were cloned as Ndel-EcoRI fragments in the pMESP vector (ref CA12729, a derivative of pMES4, GenBank GQ907248 where the Lgul site was removed) to replace the pelB signal peptide, any Nb sequence, and all detection tags including gene3. This newly created library was called pcPP72NbGFP207L.

For selecting recombinant GFP-binding PP7 coat proteins that can be recombinantly expressed and assembled in vitro to form icosahedral virus-like particles, libraries of chimeric dimers are constructed at the plasmid level. These libraries are used to transform E. coli cells. Chimeric dimers that can assemble into NanoVLPs were expressed in E. coli and subjected to a chromatographic selection. An IMAC purification was performed on the library to select for these clones that express the chimeric dimer and can assemble into a VLP. Since each assembly-competent VLP encapsulated the nucleic acid encoding the Nanobody-coat protein in its shell, we amplified the clones by RT-PCR of the RNA derived from those NanoVLPs. Several clones that express an antigen-binding chimeric protein, were grown as single colonies and subjected to DNA sequencing to determine the sequences of the peptide linkers that connect the first PP7 coat protein to the next PP7 and to determine the sequences of the circular permutation peptide linkers. Individual clones that carry a full length construct were subjected to an ELISA as described in Example 7 to identify the clones that bind GFP (FIG. 39). This demonstrates that the antigen-binding chimeric proteins concatenated from parts of a single-domain immunoglobulin and parts of the (circular permutated) PP7 coat protein linked by polypeptide linkages can be selected from libraries as functional antigen-binding chimeric proteins. Representative clones of with different linker variants are given in Table 6.

TABLE 6
Direct connecting of the PP7 coat protein to a Nanobody
(no amino acids) and linkers between the PP7 coat proteins.
Megabody connection linker connection linker SEQ
Clone#1#1#2#2ID
MP1403_A3GLRG159
MP1403_D3RPG160
MP1403_G5GVLG161
MP1403_E6WPG162
MP1403_D7RGPG163
MP1403_A9CRRG164
MP1403_B9RVPLG165

Example 14

The dimers described here self-assemble from chimeric polypeptides build from parts of a single-domain immunoglobulin and parts of a scaffold protein linked by short polypeptide linkers according to FIG. 40. The immunoglobulin used is a GFP-binding Nanobody (SEQ ID NO:1). The scaffold protein used was a covalent dimer of the coat protein of AP205 (PDB: 5FS4, SEQ ID NO: 166). AP205 is an icosahedral RNA bacteriophage of Acinetobacter bacteria. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions (Shishovs et al., 2016).

All parts were connected to each other from the amino to the carboxy terminus in the next given order (SEQ ID NO:167): a methionine encoded by the start codon, Nanobody β-strand A (β-strand A of the anti-GFP-Nanobody, residues 1-11), a random linker of one amino acid, the AP205 coat protein dimer (residues 4-128 of SEQ ID NO:166; followed by residues 4-126 of SEQ ID NO:166), β-strands B to G of the GFP-binding Nanobody (residues 16-126 of SEQ ID NO:1), 6×His/EPEA tag. To select functional representatives of such antigen-binding chimeric proteins, we used standard methods to construct libraries of open reading frames comprising a methionine, the β-strand A of the anti GFP-Nanobody, the dimeric AP205 coat protein, the β-strands B to G of the GFP-binding Nanobody, the 6×His/EPEA tag. These DNA fragments are cloned as Ndel-EcoRI fragments in the pMESP vector (ref CA12729). This newly created plasmid was called pMESAP2052XXPNbGFP207. For selecting antigen-binding chimeric (AP205) proteins that can be recombinantly expressed and assembled correctly in vitro, libraries of antigen-binding chimeric proteins are constructed at the plasmid level. These libraries are used to transform E. coli cells. To identify chimeric proteins that assemble correctly as chimeric dimers, individual clones were expressed in E. coli and subjected to an ELISA as described in Example 7 to screen for clones that bind GFP (FIG. 41). Several clones that express a MbNb207AP205x2XX that binds GFP, were grown as single colonies and subjected to DNA sequencing to determine the sequences of the peptide linkers connecting Nanobody to scaffold protein. This demonstrates that the antigen-binding chimeric proteins concatenated from parts of a single-domain immunoglobulin and parts of the viral AP205 coat protein linked by two short polypeptide linkages can be selected from libraries as functional antigen-binding chimeric proteins. Representative clones of 1-1 amino-acid short linker variants are given in Table 7. We found that some of these antigen-binding chimeric proteins self assembles into icosahedral VLPs that display 90 copies of the Nanobody on the surface.

TABLE 7
The composition of the linker peptides connecting the AP205
coat protein to Nanobody.
cloneConnection #1Connection #2SEQ ID NO:
MP1444_C5YN168
MP1445_B7VP169
MP1443_B8SL170
MP1445_D3LG171
MP1445_A4RS172

Example 15

The dimers described here self-assemble from chimeric polypeptides built from parts of a single-domain immunoglobulin and parts of a scaffold protein linked by short polypeptide linkers according to FIG. 42.

The immunoglobulin used is a GFP-binding Nanobody (SEQ ID NO:1). The scaffold protein used was the AP205 (PDB: 5FS4, SEQ ID NO: 166). When the AP205 monomers assemble into dimers or a VLP, the N-terminus of one monomer comes in close proximity of the C-terminus of a second monomer and vice versa. To get functional antigen binding chimeras the β-strand A of a first monomer needs to combine with the β-strands B to G of the GFP-binding Nanobody of a second monomer and the β-strands B to G of the GFP-binding Nanobody of the second monomer needs to combine with β-strand A of the first monomer to assemble into a dimeric antigen-binding chimeric protein.

All parts were connected to each other from the amino to the carboxy terminus in the next given order (SEQ ID NO:173): a methionine encoded by the start codon, Nanobody β-strand A (β-strand A of the anti-GFP-Nanobody, residues 1-11), a random linker of one amino acid, the AP205 coat protein (residues 4-126 of SEQ ID NO:166), β-strands B to G of the GFP-binding Nanobody (residues 16-126 of SEQ ID NO:1), 6×His/EPEA.

To select functional representatives of such dimeric antigen-binding chimeric proteins, we used standard methods to construct libraries of open reading frames comprising a methionine, the β-strand A of the anti GFP-Nanobody, the monomeric AP205 coat protein, the β-strands B to G of the GFP-binding Nanobody, the 6×His/EPEA tag. These DNA fragments are cloned as Ndel-EcoRI fragments in the pMESP vector. This newly created plasmid was called pMESAP2051XXPNbGFP207.

For selecting dimeric antigen-binding chimeric proteins that can be recombinantly expressed and correctly assembled in vitro, these libraries of dimeric antigen-binding chimeric proteins are constructed at the plasmid level. These libraries are used to transform E. coli cells. To identify chimeric proteins that assemble correctly as dimers, individual clones were expressed in E. coli and subjected to ELISA as described in Example 7 to screen for clones that bind GFP (FIG. 43). Several clones that express a dimers of MbNb207AP205XX that binds GFP, were grown as single colonies and subjected to DNA sequencing to determine the sequences of the peptide linkers connecting Nanobody to scaffold protein. This demonstrates that the dimeric antigen-binding chimeric proteins concatenated from parts of a single-domain immunoglobulin and parts of the viral AP205 coat protein linked by two short polypeptide linkages can be selected from libraries as functional dimeric antigen-binding chimeric proteins. Representative clones of 1-1 amino-acid short linker variants are given in Table 8.

If 2 antigen-binding chimeric proteins with a different antigen binding domain, one for example a GFP-binding Nanobody and a FedF-binding Nanobody, are co-expressed in the cell, they can assemble as a heterodimeric chimeric protein.

TABLE 8
The composition of the linker peptides connecting the
AP205 coat protein to Nanobody.
cloneConnection #1Connection #2SEQ ID NO:
MP1450_C12WS174
MP1453_A4MG175
MP1450_E8RI176
MP1450_D10SH177

Example 16

Building on the successful design of our first Megabodies, we also tested if immunoglobulin domains can also by rigidly grafted onto scaffolds that can be labelled with a fluorophore, dye, ion or metal to be used in diagnosis, imaging or in other biophysical applications. Accordingly, we constructed random libraries encoding rigid antibody chimera that are built from a Nanobody that was grafted onto ACP in which two short peptides connect Nanobody to scaffold according to FIG. 2 (but without the need for a circular permutation in the scaffold) to produce rigid antigen-binding chimeric proteins that can be labelled orthogonally to a specific serine (FIG. 16) by use of fluorescent derivatives of CoA and SFP synthases (Yin et al, 2006).

The Nanotool described here are chimeric polypeptide concatenated from parts of single-domain immunoglobulin and parts of a scaffold protein connected by short polypeptide linkages according to FIG. 2. In this particular Megabody, no circular permutation of the scaffold protein was required because the N-terminus and the C-terminus of wild type ACP are close to each other and well positioned for engineering two short polypeptide linkages that connect Nanobody to ACP (FIG. 16). The immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The scaffold protein is the acyl carrier protein of Escherichia coli (PDB:1T8K, SEQ ID NO:86), abbreviated as ACP. All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:87-90): β-strand A of the anti-GFP-Nanobody (residues 1-11 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, ACP (residues 2-76 of SEQ ID NO:86), a peptide linker of one or two amino acids with random composition, β-strands B to G of the Nanobody (residues 17-126 of SEQ ID NO:1), 6×His/EPEA tag according to FIG. 2.

To display and select functional representatives of these NanoTools in which two short peptides connect the Nanobody to ACP (SEQ ID NO:87-90) on yeast, we used standard methods to construct a library of open reading frames that encode the various MbNb207ACP Toolbodies in fusion to a number of accessory peptides and proteins (SEQ ID NO:91-94): the appS4 leader sequence that directs extracellular secretion in yeast (Rakestraw, 2009), β-strand A of the anti-GFP-Nanobody (residues 1-11 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, ACP (residues 2-76 of SEQ ID NO:86), a peptide linker of one or two amino acids with random composition, β-strands B to G of the Nanobody (residues 17-126 of SEQ ID NO:1), a flexible (GGSG)n peptide linker, the Aga2p adhesion subunit of the yeast agglutinin protein Aga2p which attaches to the yeast cell wall through disulphide bonds to Aga1p protein, followed by the myc tag. These open reading frames were put under the transcriptional control of galactose-inducible GAL1/10 promotor into the pCTCON2 vector (Chao, 2006) to construct a yeast display library encoding 77.280.000 different variants of the Nanotool in which two short peptides connect the Nanobody to ACP scaffold according to FIG. 16.

For in vitro selection by yeast display and FACS, this library was introduced into yeast strain EBY100. Transformed cells were grown and induced overnight in a galactose-rich medium. Induced cells were orthogonally stained with coA-647 (2 μM) using the SFP synthase (1 μM) and incubated with 100 nM of GFP. Next, these cells were washed and subjected to 2-parameter FACS analysis to identify yeast cells that display high levels of a particular Nanotool (high CoA-647 fluorescence) and bind GFP (high GFP fluorescence). Cells that display high levels of a GFP binding were sorted and amplified in a glucose-rich medium to be subjected to following rounds of selection by yeast display and two-parameter FACS analysis.

After one round of selection, a representative number of highly fluorescent cells in the CoA-647 and GFP channels were grown as single colonies and subjected to DNA sequencing to determine the sequences of a representative number of peptide linkers connecting Nanobody to scaffold protein. Two representative clones of 1-1, 2-1 and 2-2 amino-acid short linker variants (Table 9) were confirmed to bind to 100 nM GFP in FACS experiments (FIG. 44). This demonstrates that NanoTools concatenated from parts of a single-domain immunoglobulin and parts of acyl carrier protein linked by two short polypeptide linkages can be selected from Megabody libraries and display as functional antigen-binding chimeric proteins. As we were able to display the functional variants of MbNb207ACP NanoTool on the surface of yeast (above), we set out to express these antigen-binding chimeric proteins in the periplasm of E. coli. Six MbNb207ACPNanoTool variants, selected by yeast display (Table 9) were generated as chimeric polypeptides with following amino acid sequences MbNb207ACP variants (SEQ ID NO:178-183): β-strand A of the anti-GFP-Nanobody (residues 1-11 of SEQ ID NO:1), amino acid linker (Connection #1 Table 9), ACP (residues 2-76 of SEQ ID NO:86), amino acid linker (Connection #2 Table 9), β-strands B to G of the Nanobody (residues 17-126 of SEQ ID NO:1), 6×His/EPEA tag.

In order to express those variants in E. coli, the pMESD2 vector was modified, described in Example 2. This new vector (called pMESP6) contains an open reading frame that encodes the following polypeptides: the pelB leader sequence that directs the secretion of the NanoTool to the periplasm of E. coli, β-strand A of NbGFP207, ACP, C-terminal part of any Nanobody (from β-strand B to β-strand G), the 6×His/EPEA tag followed by the Amber stop codon. Six MbNb207ACP NanoTool variants (SEQ ID NO:178-182) were expressed as described in Example 2. The functional properties of the expressed Nanotools were next analysed by ELISA as described in Example 7, using periplasmic extracts of each of six MbNb207ACPNanoTool variants. Comparison of detected signals for sample with and without immobilized GFP (FIG. 45) clearly confirmed the periplasmic expression of functional MbNb207ACP NanoTool variants. This demonstrates that NanoTools concatenated from parts of a single-domain immunoglobulin and parts of the Acyl carrier protein linked by two short polypeptide linkages can be functionally express in periplasm of E. coli.

TABLE 9
The composition and length of the yeast-display optimized
linker peptides connecting scaffold protein Acyl carrier
protein to Nanobody.
NanoTool cloneConnection #1Connection #2SEQ ID NO:
MP1288_A3GY178
MP1288_A10KR179
MP1302_D10RTP180
MP1302_D2IFS181
MP1302_C10LENL182
MP1302_F1WYNL183

Example 22

The application of the antigen-binding chimeric proteins as described herein, which specifically bind so called ‘intractable’ targets facilitate their refined structural analysis. As exemplified already in Examples 4-6, 58 kDa Megabodies were designed, produced and used in structural determination of GPCRs, G proteins, or ion channels. In Example 4, the Mb35 construct based on Nb35, which specifically binds the interface of the Gβ and Gα subunits of the β2 adrenergic receptor-Gs protein complex; in Example 5, the Mb80 construct based on Nb80, which specifically binds the human P2 adrenergic receptor; in Example 6, the Mb25 construct based on Nb25, which specifically binds the pentameric ligand-gated ion channel GABAA (Miller et al, 2017). In addition, MbNb38cHopQ, based on Nanobody Nb38 (SEQ ID NO:130) specifically binding the extracellular domain of the GABAA ion channel P1 subunit (Miller et al. 2018), was produced, and allowed to determine the high resolution structure of this membrane-bound protein. The MbNb38cHopQ was generated as described in Example 6. Here, the immunoglobulin domain of Nb38 (SEQ ID NO:130), was connected with the scaffold protein cHopQ. All parts were connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds (SEQ ID NO:131): β-strand A of the conserved N-terminus of the anti-GFP-Nanobody (1-13 of SEQ ID NO:1), a C-terminal part of HopQ (residues 192-414 of SEQ ID NO:19), a short peptide linker (SEQ ID NO:21) connecting the C-terminus and the N-terminus of HopQ to produce a circular permutant of the scaffold protein, an N-terminal part of HopQ (residues 14-186 of SEQ ID NO:19), β-strands B to G of Nb38 (residues 16-123 of SEQ ID NO:130), 6×His/EPEA tag.

Expression of the MbNb38cHopQ construct in the E. coli and purification to homogeneity was done using nickel affinity chromatography, and size-exclusion chromatography to finally store the samples at 15 mg/mL at −80° C. Purified MbNb38cHopQ (SEQ ID NO: 131) has been used to solve high-resolution cryo-EM structures of the full-length human α1β3γ2 GABAA receptor in lipid nanodiscs bound to the competitive antagonist bicuculline, the channel blocker picrotoxin, the agonist GABA and the classical benzodiazepines alprazolam (Xanax) and diazepam (Valium), respectively. lonotropic signalling through type A γ-aminobutyric acid receptors (GABAARs) drive fast inhibitory neurotransmission in the mammalian nervous system. Consequently, GABAARs are crucial for virtually all aspects of brain function and represent important drug targets.

Alternatively, 100 kDa antigen-binding chimeric proteins are designed and produced based on said Nanobodies and applying the cYgjK scaffold, to facilitate structural analysis of such intractable membrane-bound complexes. This was demonstrated herein by grafting of Nb35, Nb80, Nb25 and Nb38 onto the circularly permutated version of YgjK. These Megabody clones were essentially generated as described in Example 8: MbNb35cYgjkE2 (SEQ ID NO:194): β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), Tyr one amino acid linker, C-terminal part of YgjK (residues 464-760 of SEQ ID NO:38), a short peptide linker (SEQ ID NO:43) connecting the C-terminus and the N-terminus of YgjK to produce a circular permutant of the scaffold protein, an N-terminal part of YgjK (residues 1-461 of SEQ ID NO:38), Asp one amino acid linker, β-strands B to G of the Nb35 Nanobody (residues 17-128 of SEQ ID NO:24), 6×His/EPEA tag. A similar construction was followed to design and produce MbNb80cYgjkE2 (SEQ ID NO:195), but using β-strands B to G of the Nb80 Nanobody (residues 17-120 of SEQ ID NO:26); MbNb25cYgjkE2 (SEQ ID NO:196), but using β-strands B to G of the Nb25 Nanobody (residues 17-125 of SEQ ID NO:28); MbNb38cYgjkE2 (SEQ ID NO:197), but using β-strands B to G of the Nb38 Nanobody (residues 17-123 of SEQ ID NO:130).

In addition, MbNb22cYgjkE2 based on Nb22 Nanobody (SEQ ID NO:198) specifically binding to the tropomyosin-related kinase receptor B (TrkB) was produced to allow the determination of the high-resolution structure of this membrane-bound receptor. The MbNb22cY9kE2 was as well generated as described in Example 8: MbNb22cYgjkE2 (SEQ ID NO:199): β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), Tyr one amino acid linker, C-terminal part of YgjK (residues 464-760 of SEQ ID NO:38), a short peptide linker (SEQ ID NO:43) connecting the C-terminus and the N-terminus of YgjK to produce a circular permutant of the scaffold protein, an N-terminal part of YgjK (residues 1-461 of SEQ ID NO:38), Asp one amino acid linker, β-strands B to G of the Nb22 Nanobody (residues 17-124 of SEQ ID NO:198), 6×His/EPEA tag. Periplasmic expression and purification to homogeneity of these Megabodies (SEQ ID NO: 194-195-196-197-199) was performed essentially as described in Example 8.

As an example, MbNb22cYgjkE2 (SEQ ID NO:199) has been used as a crystallization chaperone to crystallize the human brain-derived neurotrophic factor (BDNF) bound to the tropomyosin-related kinase receptor B (TrkB) and solved the high-resolution structure of the TrkB-BDNF-cYgjkE2Nb22 ternary complex by X-ray crystallography. BDNF is a neurotrophic factor that is involved in the development and functional modulation of circuits by promoting neuronal survival, synaptogenesis, synaptic transmission and synaptic plasticity. BDNF acts by binding to TrkB (Yoshii and Constantine-Paton, 2010).

Example 23

As schematically presented in FIG. 26, another antigen-binding chimeric protein has been generated, which comprises the cHopQ-specific Nanobody (Nb60), which is grafted onto a scaffold protein, according to the fusions in FIG. 2. The resulting composition of antigen-binding chimeric protein, or ‘assembled antigen-binding chimeric proteins’, or ‘Polybody’ or ‘enlarged antigen-binding chimeric protein scaffold’ allows to further increase the size of the antigen-binding chimeric proteins of the invention using this specific ‘anti-Mb-scaffold Megabody’. Such ‘Polybodies’ may for instance comprise as a scaffold protein a mutated cHopQ protein, which does not bind the Nb60 cHopQ binding site, as to avoid self-interaction that would lead to aggregation. The scaffold used in the Polybody may also constitute a different scaffold, such as the cYgjK scaffold protein described herein, to avoid said self-binding. First, Nb60 (SEQ ID NO:132), which binds to the cHopQ, was generated and used for crystallization in the presence of MbNb207cHopQ (SEQ ID NO:20). Based on the resolved crystal structure, the three residues (T289, N296 and E197) of cHopQ in the MbNb207cHopQ were identified as main contributors for the Nb60-cHopQ interaction (FIG. 27). Moreover, a shorter version of the cHopQ-based Megabody design could be proposed, with a truncation of the circular permutation region (called cHopQ) which always appeared as a loop never fully visible in electron density of MbNb207cHopQ crystal structures.

The MbNb60c7HopQ is constituted of the following parts, connected to each other from the amino to the carboxy terminus in the next given order by peptide bonds: β-strand A of the anti-GFP Nanobody (1-13 of SEQ ID NO: 1), a C-terminal part of HopQ (residues 192-411 of SEQ ID NO:19), an N-terminal part of HopQ (residues 18-186 of SEQ ID NO:19), β-strands B to G of the cHopQ-binding Nanobody (residues 16-133 of SEQ ID NO:132), 6×His/EPEA tag. However, to generate a MbNb60c7H opQ Megabody that binds to c/cHopQ-containing Megabodies but not to itself (auto-polymerization), two different mutants of the MbNb60c7HopQ were used:

    • N277K, T270R (MbNb60c7HopQ mut2, SEQ ID NO:133)
    • N277K, T270R, E197R (MbNb60cHopQmut3, SEQ ID NO:134)

Those mutants of MbNb60c7HopQ were expressed in the periplasm of E. coli as described in the Example 2, and purified to homogeneity. Next, Octet measurements (FIG. 29) provided evidence that those two MbNb60c7HopQ mutant Megabodies can bind to Megabodies containing wild type cHopQ scaffold protein, using similar measurements as shown in FIG. 24. Biotinylated MbNb207cHopQ (SEQ ID NO:20) was immobilized on Streptavidin biosensors. Different concentrations of Nb60 (SEQ ID NO:132), MbNb60c7HopQmut 2 (SEQ ID NO:133) and MbNb60c7H opQ mut 3 (SEQ ID NO:134) were examined against binding to immobilized MbNb207cHopQ. For Nb60 and two MbNb60c7H opQ mutants binding to MbNb207cHopQ was confirmed. Similar to the cHopQ-mutant-based approach, other scaffold proteins can be used to generate Polybodies or a composition of antigen-binding chimeric proteins. Accordingly, an alternative scaffold protein YgjK, a 86 kDA periplasmic protein of E. coli (PDB 3W7S, SEQ ID NO: 38) was used (FIG. 26, B). The MbNb60cYgjkE2 was generated as described in Example 8: MbNb60cYgjkE2 (SEQ ID NO:135): β-strand A of the anti-GFP-Nanobody (1-12 of SEQ ID NO:1), Tyr one amino acid linker, C-terminal part of YgjK (residues 464-760 of SEQ ID NO:38), a short peptide linker (SEQ ID NO:43) connecting the C-terminus and the N-terminus of YgjK to produce a circular permutant of the scaffold protein, an N-terminal part of YgjK (residues 1-461 of SEQ ID NO:38), Asp one amino acid linker, β-strands B to G of the Nb60 Nanobody (residues 17-133 of SEQ ID NO:132), 6×His/EPEA tag.

This Megabody was expressed and purified as described in Example 8. Next, binding of MbNb60cYgjkE2 to MbNb207cHopQ was validated by Octet measurements as described above (FIG. 29).

Example 24

Herein we demonstrate how immunoglobulin domains can also by rigidly grafted onto Dodecin Rv1498A. This small flavoprotein from archaea Mycobacterium tuberculosis is an assemble of 12 monomers. It was shown that 12 copies of the monomer can self-assemble upon overexpression in E. coli to form highly thermostable Dodecin (Liu et al., 2011). In Dodecin, the N-terminus of each monomer is very close to the C-terminus of the same monomer. Accordingly, we constructed random libraries encoding rigid antigen-binding chimeric proteins that are built from a Nanobody that was grafted onto a Dodecin monomer in which two short peptides connect Nanobody to scaffold according to FIG. 2.

The 258 kDa MbNb207Dodecin molecules described here, self-assemble from chimeric polypeptides built from parts of a single-domain immunoglobulin and parts of a scaffold protein directly linked according to FIG. 50. The immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The scaffold protein used was the monomer of the Dodecin Rv1498A (GenBank Accession Number: 3205040, SEQ ID NO:192) of M. tuberculosis. All parts were connected to each other from the amino to the carboxy terminus in the next given order (SEQ ID NO:193): methionine encoded by the startcodon, β-strand A of the anti-GFP-Nanobody (residues 1-11 of SEQ ID NO:1), a peptide linker of one amino acids with random composition, the Dodecin Rv1498A protein (residues 5-66 of SEQ ID NO:192), a peptide linker of one or two amino acids with random composition, β-strands B to G of the GFP-binding Nanobody (residues 17-126 of SEQ ID NO:1), 6×His/EPEA tag. This antigen-binding chimeric protein self assembles into a Dodecin multimer that contains 12 copies of the Megabody (FIG. 50).

To select functional representatives of these antigen-binding chimeric proteins in which two short peptides connect the Nanobody to Dodecin (SEQ ID NO:193), we used standard methods to construct a library of open reading frames that encode the described above antigen-binding chimeric proteins (SEQ ID NO:193). These DNA fragments are cloned as HindIII-Spl fragments in the pMESP vector. This newly created plasmid was called pMESPDodecinXNbGFP207. For selecting antigen-binding chimeric MbNb207Dodecin proteins that can be recombinantly expressed and assembled correctly in vitro, libraries of antigen-binding chimeric proteins were constructed at the plasmid level. These libraries were used to transform E. coli cells. To identify chimeric proteins that assemble correctly as Dodecins, individual clones were expressed in E. coli and subjected to an ELISA as described in Example 7 to screen for clones that bind GFP (FIG. 51). Several clones that express an antigen-binding chimeric protein and bind GFP, were grown as single colonies and subjected to DNA sequencing to determine the sequences of the peptide linkers connecting Nanobody to a scaffold protein. This demonstrates that the antigen-binding chimeric proteins concatenated from parts of a single-domain immunoglobulin and the Dodecin linked by two short polypeptide linkages can be selected from libraries as functional antigen-binding chimeric proteins. Representative clones of 1-1 amino-acid short linker variants are given in Table 13. This indicates that these antigen-binding chimeric proteins built from Nanobody grafted onto monomer of the Dodecin Rv1498A can be functionally expressed in a E. coli.

TABLE 13
The composition of linker peptides connecting the Dodecin
Rv1498A protein to Nanobody.
Megabody cloneConnection #1Connection #2
MP1462_G1LP
MP1462_E2FP
MP1462_B2VP
MP1462_E3GL
MP1462_D3DT
MP1462_F1EG

Example 25

Herein it is described how an immunoglobulin domain can also by rigidly grafted onto a homodimer called 4QYB. This small protein of unknown function from Burkholderia cenocepacia J2315, is a homodimer where two monomers are connected by a single intermolecular disulfide bridge, as confirmed by the reported crystal structure of this protein (Halavaty et. al. Unpublished data, PDB code 4QYB). Additionally, the N-terminus of one monomer is very close to the C-terminus of the same monomer. Accordingly, we constructed random libraries encoding rigid antibody chimera that are built from a Nanobody that was grafted onto a 4QYB monomer in which two short peptides connect Nanobody to scaffold according to FIG. 2.

The 51 kDa homodimeric MbNb2074QYB described here, self-assembles from chimeric polypeptides build from parts of a single-domain immunoglobulin and parts of a scaffold protein directly linked according to FIG. 52. The immunoglobulin used is a GFP-binding Nanobody as depicted in SEQ ID NO:1. The scaffold protein used was the monomer of the 4QYB from B. cenocepacia J2315 (PDB 4QYB, SEQ ID NO:200). All parts were connected to each other from the amino to the carboxy terminus in the next given order (SEQ ID NO:201-204): β-strand A of the anti-GFP-Nanobody (residues 1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, the 4QYB protein (residues 8-121 of SEQ ID NO:200), a peptide linker of one or two amino acids with random composition, β-strands B to G of the GFP-binding Nanobody (residues 16-126 of SEQ ID NO:1), 6×His/EPEA tag. This rigid antigen-binding chimeric protein self assembles into disulfide-bridged homodimer that contains 2 copies of the Nanobody (FIG. 52).

To select functional representatives of these antigen-binding chimeric proteins in which two short peptides connect the Nanobody to scaffold (SEQ ID NO:201-204) and express them in periplasm of E. coli, we used standard methods to construct a library of open reading frames that encode the described above antigen-binding chimeric proteins (SEQ ID NO:205-208): the PeIB leader sequence that directs the secretion of the fusion protein to the periplasm of E. coli, β-strand A of the anti-GFP-Nanobody (residues 1-12 of SEQ ID NO:1), a peptide linker of one or two amino acids with random composition, the 4QYB protein (residues 8-121 of SEQ ID NO:200), a peptide linker of one or two amino acids with random composition, β-strands B to G of the GFP-binding Nanobody (residues 16-126 of SEQ ID NO:1), 6×His/EPEA tag. These DNA fragments are cloned as Hindlll-Spl fragments in the pMESP vector. This newly created plasmid was called pMESP4QYBXXNbGFP207.

For selecting MbNb2074QYB proteins that can be recombinantly expressed and assembled correctly in vitro, libraries of antigen-binding chimeric proteins are constructed at the plasmid level. These libraries are used to transform E. coli cells, for the identification of correctly assembled homodimers. Individual clones were expressed in E. coli and subjected to an ELISA as described in Example 7 to screen for clones that bind GFP. Several clones that express an antigen-binding chimeric protein and bind GFP were grown as single colonies and subjected to DNA sequencing to determine the sequences of the peptide linkers connecting Nanobody to a scaffold protein.

Sequence list
>SEQ ID NO: 1: NbGFP207 GFP-specific Nanobody = Nb207
>SEQ ID NO: 2: bacteriophage of P. Aeruginosa PP7 coat protein monomer
>SEQ ID NO: 3-6: MbNb207cPP7x2L dimer
(NbGFP207 sequences in bold, circular permutation linker in italics, PP7 sequences underlined, [Figure (not displayed)]  is
a short peptide linker of variable length (1 or 2 amino acids), tags in small letters)
MQVQLVESGGGLVQATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVV
DCSTSVCGELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR([Figure (not displayed)] GSK
TIVLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDCSTSVC
GELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGR([Figure (not displayed)] GSKTIVLSGSL
RLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMD
SLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 7: cAbLys3 hen egg-white lysozyme specific Nanobody (PDB 1MEL)
>SEQ ID NO: 8: bacteriophage of Escherichia coli coat protein monomer (PDB 2MS2)
>SEQ ID NO: 9: MbcAbLys3cMS2x2L dimer
(NbGFP207 strand A and cAbLys3, sequences in bold, circular permutation linker in italics, MS2
sequences underlined, tags in small letters)
MQVQLQESGGGLVXXGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKV
ATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIYASNFTQFVL
VDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGVEL
PVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIYASNFTQFVLVDNGXXSLRL
SCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGGGITYYADSVKGRFTISQDNAKNTVYLLMNSLE
PEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 10-13: MbcAbLys3cMS2x2L dimer
MQVQLQESGGGLV([Figure (not displayed)] GDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVP
KVATQTVGGVELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIYASNFTQF
VLVDNGGTGDVTVAPSNFANGVAEWISSNSRSQAYKVTCSVRQSSAQNRKYTIKVEVPKVATQTVGGV
ELPVAAWRSYLNMELTIPIFATNSDCELIVKAMQGLLKDGNPIPSAIAANSGIYASNFTQFVLVDNG([Figure (not displayed)]
SLRLSCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGGGITYYADSVKGRFTISQDNAKNTVYLLM
NSLEPEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 14: N2bNb207cAbLys3L Nano2body
(NbGFP207 β-strand A double underlined, NbGFP207 in bold, and cAbLys3 sequences are underlined)
QVQLVESGGGLVQAG(X)3GVQLVESGGGLVQAGGSLRLSCAASGRTFSTAAMGWFRQAPGKERDF
VAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYD
YWGQ(X)2GSLRLSCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGGGITYYADSVKGRFTISQDNAK
NTVYLLMNSLEPEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWGQGTQVTVSS(X)3GQGTQVTV
SShhhhhhepea
>SEQ ID NO: 15: PelB_N2bNb207cAbLys3L_tags, amberstopcodon(*)_protein3 Nano2body
(the PelB leader sequence, NbGFP207 β-strand A double underlinedNbGFP207 in bold, cAbLys3 sequences
are underlined, tags in small letters, amberstopcodon as *, protein3 in italic_)
MKYLLPTAAAGLLLLAAQPAMAQVQLVESGGGLVQAGXXXGVQLVESGGGLVQAGGSLRLSCAASGR
TFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVY
YCAARRRGFTLAPTRANEYDYWGQXXGSLRLSCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGG
GITYYADSVKGRFTISQDNAKNTVYLLMNSLEPEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWG
QGTQVTVSSXXXGQGTQVTVSShhhhhhepea*ypydvpdygSTVESCLAKPHTENSFTNVWKDDKTLDRYA
NYEGCLWNATGVVVCTGDETQCYGTWVPIGLAIPENEGGGSEGGGSEGGGSEGGGTKPPEYGDTPIP
GYTYINPLDGTYPPGTEQNPANPNPSLEESQPLNTFMFQNNRFRNRQGALTVYTGTVTQGTDPVKTYY
QYTPVSSKAMYDAYWNGKFRDCAFHSGFNEDPFVCEYQGQSSDLPQPPVNAGGGSGGGSGGGSEG
GGSEGGGSEGGGSEGGGSEGGGSGGGSGSGDFDYEKMANANKGAMTENADENALQSDAKGKLDS
VATDYGAAIDGFIGDVSGLANGNGATGDFAGSNSQMAQVGDGDNSPLMNNFRQYLPSLPQSVECRPY
VFGAGKPYEFSIDCDKINLFRGVFAFLLYVATFMYVFSTFANILRNKES
>SEQ ID NO: 16: DsbA_N2bNb207cAbLys3L_tags, amberstopcodon(*)_protein3 Nano2body
(the DsbA leader sequence, NbGFP207 β-strand A double underlinedNbGFP207 in bold, cAbLys3
sequences are underlined, tags in small letters, amberstopcodon as *, protein3 in italic_)
MKKIWLALAGLVLAFSASAQVQLVESGGGLVQAGXXXGVQLVESGGGLVQAGGSLRLSCAASGRTFS
TAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYC
AARRRGFTLAPTRANEYDYWGQXXGSLRLSCAASGYTIGPYCMGWFRQAPGKEREGVAAINMGGGIT
YYADSVKGRFTISQDNAKNTVYLLMNSLEPEDTAIYYCAADSTIYASYYECGHGLSTGGYGYDSWGQG
TQVTVSSXXXGQGTQVTVSShhhhhhepea*ypydvpdygSTVESCLAKPHTENSFTNVWKDDKTLDRYANY
EGCLWNATGVVVCTGDETQCYGTWPIGLAIPENEGGGSEGGGSEGGGSEGGGTKPPEYGDTPIPGY
TYINPLDGTYPPGTEQNPANPNPSLEESQPLNTFMFQNNRFRNRQGALTVYTGTVTQGTDPVKTYYQY
TPVSSKAMYDAYWNGKFRDCAFHSGFNEDPFVCEYQGQSSDLPQPPVNAGGGSGGGSGGGSEGGG
SEGGGSEGGGSEGGGSEGGGSGGGSGSGDFDYEKMANANKGAMTENADENALQSDAKGKLDSVAT
DYGAAIDGFIGDVSGLANGNGATGDFAGSNSQMAQVGDGDNSPLMNNFRQYLPSLPQSVECRPYVFG
AGKPYEFSIDCDKINLFRGVFAFLLYVATFMYVFSTFANILRNKES
>SEQ ID NO: 17: NbFEDF9 the lectin domain of the F18 fimbrial adhesin FedF specific Nanobody (PDB
4W6Y)
>SEQ ID NO: 18: N2bNb207NbFEDF9L Nano2body
(NbGFP207 β-strand A double underlined, NbGFP207 in bold, and NbFedF9 sequences are underlined)
QVQLVESGGGLVQAGXXXGVQLVESGGGLVQAGGSLRLSCAASGRTFSTAAMGWFRQAPGKERDF
VAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYD
YWGQXXGSLRLSCAASGYTYSSNCMAWFRQVPGKEREGVASINTRGGITYYADSVKGRFTISRDNAK
NTVSLQMNSLKPEDTATYYCAAVREATYSDNRCSVRSYTYDYWGQGTQVTVSSXXXGQGTQVTVSSh
hhhhhepea
>SEQ ID NO: 19: Helicobacter pylori strain G27 HopQ adhesin domain protein (PDB 5LP2)
>SEQ ID NO: 20: MbNb207cHopQ
(NbGFP207 sequences in bold, circular permutation linker in italics, HopQ sequences underlined)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKN
TVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 21: cHopQ circular permutation linker peptide
>SEQ ID NO: 22: MbNb207cHopQ_Aga2p_ACP protein sequence
(appS4 leader sequence, Megabody cHopQNbGFP207 depicted in bold, flexible (GGGS)n polypeptide
linker, Aga2p protein sequence underlined, ACP sequence double underlined, cMyc Tag)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEAQVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKS
SSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNL
NLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQK
NNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRASGGGSGGGGSGKLS
DTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMG
YAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKI
HEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGRTFSTAAMGWFRQAPGKERD
FVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEY
DYWGQGTQVTVSSlgggsggggsggggsggggsggggsggggsggggsQELTTICEQIPSPTLESTPYSLSTTTILA
NGKAMQGVFEYYKSVTFVSNCGSHPSTTSKGSPINTQYVFKdnsstsMSTIEERVKKIIGEQLGVKQEEVT
NNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQAseqkliseedl
>SEQ ID NO: 23: DsbA-MbNb207cHopQ
>SEQ ID NO: 24: Nb35 Gβ/Gα subunit of the β2 adrenergic receptor-Gs protein complex-specific
Nanobody
>SEQ ID NO: 25: MbNb35cHopQ
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, Nb35 β-strands
B to G in bold, 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISYTGSVKGRFTISRDNAKN
TLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQGTQVTVSShhhhhhepea
>SEQ ID NO: 26: Nb80 β2 adrenergic receptor-specific Nanobody
>SEQ ID NO: 27: MbNb80cHopQ
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, Nb80 β-strands
B to G in bold, 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGSIFSINTMGWYRQAPGKQRELVAAIHSGGSTNYANSVKGRFTISRDNAANTV
YLQMNSLKPEDTAVYYCNVKDYGAVLYEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 28: Nb25 GABAA-specific Nanobody
>SEQ ID NO: 29: MbNb25cHopQ
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, Nb25 β-strands
B to G in bold, 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGHTFNYPIMGWFRQAPGKEREFVGAISWSGGSTSYADSVKDRFTISRDNAKN
TVYLEMNNLKPEDTAVYYCAAKGRYSGGLYYPTNYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 30-33: MbNb207cHopQrandomlinkers
(NbGFP207 sequences in bold, [Figure (not displayed)]  is a short peptide linker of variable length (1 or 2 amino acids) and
mixed composition, circular permutation linker in italics, HopQ sequences underlined)
QVQLVESGGGLV[Figure (not displayed)] KTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQ
TAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNA
QSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTS
AADFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAIN
QAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDEN
GNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEA
HVTTSK[Figure (not displayed)] SLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRD
NAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 34-37: MbNb207cHopQrandomlinkers_Aga2p_ACP protein sequence
(appS4 leader sequence, Megabody chopQNbGFP207randomlinkers depicted in bold, [Figure (not displayed)]  is a short
peptide linker of variable length (1 or 2 amino acids) and mixed composition, flexible (GGGS)n
polypeptidelinker in italics, Aga2p protein sequence underlined,
ACP sequence double underlined, cMyc Tag)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEAQVQLVESGGGLV[Figure (not displayed)] KTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIA
KSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPH
NLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQN
QKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRASGGGSGGGGSG
KLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWN
SMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQ
YEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSK[Figure (not displayed)] SLRLSCAASGRTFSTAAMGWFRQAP
GKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPT
RANEYDYWGQGTQVTVSSlgggsggggsggggsggggsggggsggggsggggsQELTTICEQIPSPTLESTPYSLS
TTTILANGKAMQGVFEYYKSVTFVSNCGSHPSTTSKGSPINTQYVFKdnsstsMSTIEERVKKIIGEQLGVK
QEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQAseqkliseedl
>SEQ ID NO: 38: E. coli Ygjk protein (PDB 3WFS)
>SEQ ID NO: 39-42: MbNb207cYgjkQrandomlinkers
(NbGFP207 sequences in bold, circular permutation linker in italics, Ygik sequences underlined, [Figure (not displayed)]  is
a short peptide linker of variable length (1 or 2 amino acids) and mixed composition, 6xHis & EPEA tags)
QVQLVESGGGLV[Figure (not displayed)] KEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLD
KYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQ
LAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVK
VMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAK
GLTADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRKQasgggsggggsggggsgNADNYKNVINR
TGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQ
DGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEG
KPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHI
NGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIE
TLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQP
GDSVRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLV
AYHDWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKK[Figure (not displayed)] SLRLSCAASGRTFSTAAMGWF
RQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFT
LAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 43: cYgjk circular permutation linker peptide
>SEQ ID NO: 44-47: MbNb207cYgjkrandomlinkers_Aga2p_ACP protein sequence
(appS4 leader sequence, Megabody cYgjkQNbGFP207randomlinkers library depicted in bold, flexible
(GGGS)n polypeptide linker, Aga2p protein sequence underlined, ACP sequence double underlined, cMyc
Tag)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEAQVQLVESGGGLV(X)1-2KEETQSGLNNYARVVEKGQYDSLEIPAQVAASW
ESGRDDAAVFGFIDKEQLDKYVANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNH
YLAEMATILGKPEEAKRYRQLAQQLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPE
GWSPLFNGAATQANADAVVKVMLDPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKG
MERYGYRDDALKLADTFFRHAKGLTADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRKQ[Figure (not displayed)]
[Figure (not displayed)] NADNYKNVINRTGAPQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPN
TMGGFPGVALLTEEYINFMASNFDRLTVWQDGKKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATP
RTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPLSDKTIAGEYPDYQRKISATRDGLKVTFGKVRAT
WDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGSTTLYTTYSHLLTAQEVSKEQMQIRDILARPAF
YLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLNGNWRSPGGAVKFNTVTPSVTGRWFSGNQ
TWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDSVRPQDVGFVPDLIAWNLSPERGGDGGNW
NERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYHDWWLRNRDHNGNGVPEYGATRDKAHN
TESGEMLFTVKK(X)1-2SLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKG
RFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSSlgggsgggg
sggggsggggsggggsggggsggggsQELTTICEQIPSPTLESTPYSLSTTTILANGKAMQGVFEYYKSVTFVSN
CGSHPSTTSKGSPINTQYVFKdnsstsMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVM
ALEEEFDTEIPDEEAEKITTVQAAIDYINGHQAseqkliseedl
>SEQ ID NO: 48: MbNb207cHopQC357-C425
(NbGFP207 sequences in bold, circular permutation linker in italics, HopQ sequences underlined,
[Figure (not displayed)] )
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggaggggagKLSDTYEQLSRLLTNDNGTNSKTSAQINAQ
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTCSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSL[Figure (not displayed)] LSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKN
TVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 49: MbNb207cHopQC358-C488
(NbGFP207 sequences in bold, circular permutation linker in italics, HopQ sequences underlined,
[Figure (not displayed)] )
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasggggggggKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNCNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKN
TVYL[Figure (not displayed)] MDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 50: MbNb207cHopQC359-C490
(NbGFP207 sequences in bold, circular permutation linker in italics, HopQ sequences underlined,
[Figure (not displayed)] )
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSCGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKN
TVYLQM[Figure (not displayed)] SLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 51: MbNb207cHopQC15-C534
(NbGFP207 sequences in bold, circular permutation linker in italics, HopQ sequences underlined)
QVQLVESGGGLVQT[Figure (not displayed)] TTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKN
TVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSSG[Figure (not displayed)] hhhhhhepea
>SEQ ID NO: 52: P. aeruginosa Azurin (PDB 2TSA) M121A mutant protein
>SEQ ID NO: 53-60: MbNb207AzurinQrandomlinkers
(NbGFP207 sequences in bold, Azurin sequences underlined, [Figure (not displayed)]  is a short peptide linker of variable
length (1 or 2 amino acids) and mixed composition)
QVQLVESGGGLV([Figure (not displayed)] )1-2CSVDIQGNDQMQFNTNAITV([Figure (not displayed)] )1-2SLRLSCAASGRTFSTAAMGWFRQAPGK
ERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRA
NEYDYWGQGTQVTVSS([Figure (not displayed)] )1-2VNLSHPGNLPKNVMGHNWWLSTAADMQGVVTDGMASGLDKDYLKPD
DSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALAKGTLTLKhhhhhhepea
>SEQ ID NO: 61-68: MbNb207AzurinQconnection library_Aga2p_ACP protein sequence
(appS4 leader sequence, Megabody AzurinNbGFP207_randomlinkers library depicted in bold, flexible
(GGGS)n polypeptide linker, Aga2p protein sequence underlined, ACP sequence double underlined, cMyc
Tag)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEAQVQLVESGGGLV(X)1-2CSVDIQGNDQMQFNTNAITV([Figure (not displayed)] )1-2
SLRLSCAASGRTFS
TAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYC
AARRRGFTLAPTRANEYDYWGQGTQVTVSS([Figure (not displayed)] )1-2
VNLSHPGNLPKNVMGHNWVLSTAADMQGVVTDG
MASGLDKDYLKPDDSRVIAHTKLIGSGEKDSVTFDVSKLKEGEQYMFFCTFPGHSALAKGTLTLKslgg
gsggggsggggsggggsggggsggggsggggsQELTTICEQIPSPTLESTPYSLSTTTILANGKAMQGVFEYYKSVT
FVSNCGSHPSTTSKGSPINTQYVFKdnsstsMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTV
ELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQAseqkliseedl
>SEQ ID NO: 69: Bacteroides thetaiotaomicron SusB protein (PDB3wfa)
>SEQ ID NO: 70-77: MbNb207SusBrandomlinkers Megabody library protein sequences
(NbGFP207 sequences in bold, [Figure (not displayed)]  is a short peptide linker of variable length (1 or 2 amino acids) and
mixed composition, susB sequences underlined)
QVQLVESGGGLVQAs[Figure (not displayed)] MQQKLTSPDNNLVMTFQVDSKGAPTYELTYKNKVVIKPSTLGLELKKEDN
TRTDFDWDRRDLTKLDS[Figure (not displayed)] GGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGST
YYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTV
S[Figure (not displayed)] FEVKDTQTATFDETWQPVWGEEKEIRNHYNELAVTLYQPMNDRSIVIRFRLENDGLGFRYEFPQ
QKSLNYFVIKEEHSQFGMNGDHIAFWIPGDYDTQEYDYTISRLSEIRGLMKEAITPNSSQTPFSQTGVQT
ALMMKTDDGLYINLHEAALVDYSCMHLNLDDKNMVFESWLTPDAKGDKGYMQTPCNTPWRTIIVSDDA
RNILASRITLNLNEPCKIADAASWVKPVKYIGVWWDMITGKGSWAYTDELTSVKLGETDYSKTKPNGKH
SANTANVKRYIDFAAAHGFDAVLVEGWNEGWEDWFGNSKDYVFDFVTPYPDFDVKEIHRYAARKGIKM
MMHHETSASVRNYERHMDKAYQFMADNGYNSVKSGYVGNIIPRGEHHYGQWMNNHYLYAVKKAADY
KIMVNAHEATRPTGICRTYPNLIGNESARGTEYESFGGNKVYHTTILPFTRLVGGPMDYTPGIFETHCNK
MNPANNSQVRSTIARQLALYVTMYSPLQMAADIPENYERFMDAFQFIKDVALDWDETNYLEAEPGEYITI
ARKAKDTDDWYVGCTAGENGHTSKLVFDFLTPGKQYIATVYADAKDADWKENPQAYTIKKGILTNKSKL
NLHAANGGGYAISIKEVKDKSEAKGLKRLhhhhhhepea
>SEQ ID NO: 78-85: homo-dimeric Megabody MbNb207SusBrandomlinkers_Aga2p_ACP protein sequences
(appS4 leader sequence, susBNbGFP207randomlinkers Megabody library depicted in bold, flexible
(GGGS)n polypeptide linker, Aga2p protein sequence underlined, ACP sequence double underlined, cMyc
Tag)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEAQVQLVESGGGLVQAs(X)1-2MQQKLTSPDNNLVMTFQVDSKGAPTYELTY
KNKVVIKPSTLGLELKKEDNTRTDFDWVDRRDLTKLDS(X)1-2GGSLRLSCAASGRTFSTAAMGWFRQ
APGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLA
PTRANEYDYWGQGTQVTVS(X)1-2FEVKDTQTATFDETWQPVWGEEKEIRNHYNELAVTLYQPMNDR
SIVIRFRLFNDGLGFRYEFPQQKSLNYFVIKEEHSQFGMNGDHIAFWIPGDYDTQEYDYTISRLSEIRGL
MKEAITPNSSQTPFSQTGVQTALMMKTDDGLYINLHEAALVDYSCMHLNLDDKNMVFESWLTPDAKG
DKGYMQTPCNTPWRTIIVSDDARNILASRITLNLNEPCKIADAASWVKPVKYIGVWWDMITGKGSWAY
TDELTSVKLGETDYSKTKPNGKHSANTANVKRYIDFAAAHGFDAVLVEGWNEGWEDWFGNSKDYVF
DFVTPYPDFDVKEIHRYAARKGIKMMMHHETSASVRNYERHMDKAYQFMADNGYNSVKSGYVGNIIP
RGEHHYGQWMNNHYLYAVKKAADYKIMVNAHEATRPTGICRTYPNLIGNESARGTEYESFGGNKVYH
TTILPFTRLVGGPMDYTPGIFETHCNKMNPANNSQVRSTIARQLALYVTMYSPLQMAADIPENYERFM
DAFQFIKDVALDWDETNYLEAEPGEYITIARKAKDTDDWYVGCTAGENGHTSKLVFDFLTPGKQYIAT
VYADAKDADWKENPQAYTIKKGILTNKSKLNLHAANGGGYAISIKEVKDKSEAKGLKRLslgggsggggsg
gggsggggsggggsggggsggggsQELTTICEQIPSPTLESTPYSLSTTTILANGKAMQGVFEYYKSVTFVSNCG
SHPSTTSKGSPINTQYVFKdnsstsMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMAL
EEEFDTEIPDEEAEKITTVQAAIDYINGHQAseqkliseedl
>SEQ ID NO: 86: E. coli Acyl carrier protein (PDB1T8K)
>SEQ ID NO: 87-90: Nanotool MbNb207ACPrandomlinkers
(NbGFP207 sequences in bold, [Figure (not displayed)]  is a short peptide linker of variable length (1 or 2 amino acids) and
mixed composition, ACP sequences underlined)
QVQLVESGGGL(X)1-2TIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPD
EEAEKITTVQAAIDYINGHQ(X)1-2SLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYY
ADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSSh
hhhhhepea
>SEQ ID NO: 91-94: Nanotool MbNb207ACPrandomlinkers_Aga2p protein sequences
(appS4 leader sequence, Nanotool ACPNbGFP207 randomlinkers, [Figure (not displayed)]  is a short peptide linker of
variable length (1 or 2 amino acids) and mixed composition, flexible (GGGS)n polypeptide linker, Aga2p
protein sequence underlined, cMyc Tag double underlined)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEAQVQLVESGGGL(X)1-2TIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSL
DTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQ(X)1-2SLRLSCAASGRTFSTAAMGWFRQAPG
KERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTR
ANEYDYWGQGTQVTVSSlgggsggggsggggsggggsggggsggggsggggsQELTTICEQIPSPTLESTPYSLST
TTILANGKAMQGVFEYYKSVTFVSNCGSHPSTTSKGSPINTQYVFKdnsstseqkliseedl
>SEQ ID NO: 95: MbNb207cHopQMP1251_A7
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1251_A7)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGRTFSVSNMGWFRQAPGKERVFVAAIGWTTGSTYYADSVKGRFTISRDNTKN
TVYLQMNSLKPEDTAVYRCAARRRGYSRVPMTPDEYEYWGQGTQVTVSS
>SEQ ID NO: 96: MbNb207cHopQMP1252_D10
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1252_D10)
>SEQ ID NO: 97: MbNb207cHopQMP1251_D10
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1251_D10)
>SEQ ID NO: 98: MbNb207cHopQMP1251_A10
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1251_A10)
>SEQ ID NO: 99: MbNb207cHopQMP1251_D4
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1251_D4)
>SEQ ID NO: 100: MbNb207cHopQMP1252_C10
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1252_C10)
>SEQ ID NO: 101: MbNb207cHopQMP1251_H6
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1251_H6)
>SEQ ID NO: 102: MbNb207cHopQMP1251_A5
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1251_A5)
>SEQ ID NO: 103: MbNb207cHopQMP1263_C9
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, β-strands A to
G of Nanobody MP1263_C9)
>SEQ ID NO: 104-107: MbNb207cHopQ_βturnCC′_randomlinkers protein sequences
(NbGFP207 β-strands A to C, [Figure (not displayed)]  is a short peptide linker of variable length (1 or 2 amino acids) and
mixed composition, circular permutation linker in italics, HopQ sequences underlined, Nb207 β-strands
C′ to G in bold, 6xHis tag, EPEA tag)
QVQLVESGGGLVQAGGSLRLSCAASGRTFSTAAMGWFRQ(X)1-2KTTTSVIDTTNDAQNLLTQAQTIVN
TLKDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQ
PKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSAN
MTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsg
KLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSM
GYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKI
HEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKY(X)1-2DFVAGIYWTVGSTYYADSAKGRFTISRDNA
KNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 108-111: MbNb207cHopQ_βturnCC′_randomlinkers_Aga2p_ACP protein sequences
(appS4 leader sequence, Megabody cHopQNbGFP207_βturnCC′_randomlinkers library depicted in
bold, flexible (GGGS)n polypeptide linker, Aga2p protein sequence underlined, ACP sequence double
underlined, cMyc Tag)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEAQVQLVESGGGLVQAGGSLRLSCAASGRTFSTAAMGWFRQ(X)1-2KTTTSV
IDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAAS
DMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNK
LSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNL
ANTLIQELGNNPFR[Figure (not displayed)] KLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLA
GGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNS
NGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKY(X)1-2DF
VAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYD
YWGQGTQVTVSSlgggsggggsggggsggggsggggsggggsggggsQELTTICEQIPSPTLESTPYSLSTTTILAN
GKAMQGVFEYYKSVTFVSNCGSHPSTTSKGSPINTQYVFKdnsstsMSTIEERVKKIIGEQLGVKQEEVTN
NASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQAseqkliseedl
>SEQ ID NO: 112: Deinococcus radiodurans Monobody NS1 (from PDB5E59)
>SEQ ID NO: 113-116: MbNS1cHopQ_randomlinkers
(NS1 β-strand A, [Figure (not displayed)]  is a short peptide linker of variable length (1 or 2 amino acids) and mixed
composition, HopQ sequences underlined, circular permutation linker in italics, NS1 β-strands B to G in
bold, 6xHis tag, EPEA tag)
SSVPTKLEVVAAT(X)1-2KTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQ
TAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNA
QSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTS
AADFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLLTNDNGTNSKTSAQAIN
QAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDEN
GNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEA
HVTTSKY(X)1-2SLLISWDAPAVTVDYYVITYGETGGNSPVQKFEVPGSKSTATISGLKPGVDYTITVYA
WGWHGQVYYYMGSPISINYRThhhhhhepea
>SEQ ID NO: 117-120: MbNS1cHopQ_randomlinkers_Aga2p_ACP protein sequences
(appS4 leader sequence, cHopQNS1_randomlinkers Megabody library depicted in bold, flexible
(GGGS)n polypeptide linker, Aga2p protein sequence underlined, ACP sequence double underlined, cMyc
Tag)
MRFPSIFTAVVFAASSALAAPANTTAEDETAQIPAEAVIGYLGLEGDSDVAALPLSDSTNNGSLSTNTTIA
SIAAKEEGVQLDKREAEASSVPTKLEVVAAT(X)1-2KTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIA
KSSSSNGGTNNANTPSWQTAGGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPH
NLNLNSPSSLTALAQKMLKNAQSQAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQN
QKNNWGNGCAGVEETQSLLKTSAADFNNQTPQINQAQNLANTLIQELGNNPFRASGGGSGGGGSG
KLSDTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWN
SMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQ
YEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKY(X)1-2SLLISWDAPAVTVDYYVITYGETGGN
SPVQKFEVPGSKSTATISGLKPGVDYTITVYAWGWHGQVYYYMGSPISINYRTslgggsggggsggggsgggg
sggggsggggsggggsQELTTICEQIPSPTLESTPYSLSTTTILANGKAMQGVFEYYKSVTFVSNCGSHPSTTS
KGSPINTQYVFKdnsstsMSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEI
PDEEAEKITTVQAAIDYINGHQAseqkliseedl
>SEQ ID NO: 121: NbGFP207 (DNA) = Nb207
>SEQ ID NO: 122: TU89 Forward primer (Sapl digestion site) (DNA)
>SEQ ID NO: 123: EP230 Reverse primer (Sapl digestion site) (DNA)
>SEQ ID NO: 124: TU64 primer (DNA)
>SEQ ID NO: 125: TU65 primer (DNA)
>SEQ ID NO: 126: TU131 primer (DNA)
>SEQ ID NO: 127: TU132 primer (DNA)
>SEQ ID NO: 128: TU133 primer (DNA)
>SEQ ID NO: 129: TU134 primer (DNA)
>SEQ ID NO: 130: Nb38 GABAA-specific Nanobody
>SEQ ID NO: 131: MbNb38cHopQ
(NbGFP207 β-strand A, circular permutation linker in italics, HopQ sequences underlined, Nb38 β-strands
B to G in bold, 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNPFRasgggsggggsgKLSDTYEQLSRLTNDNGTNSKTSAQAINQA
VNNLNERAKTLAGGTTNSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGN
GTTINCGGSTNSNGTHSYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHV
TTSKYGSLRLSCAASGRTFTTYIMAWFRQAPGKEREFLAAMDQGRIQYYGDSVRGRFTISRDYAKNS
VDLQLDGLRPEDTAVYYCAAGAGFWGLRTASSYHYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 132: Nb60 HopQ-specific Nanobody
>SEQ ID NO: 133: MbNb60c7HopQ N277K T270R
(NbGFP207 β-strand A, HopQ sequences underlined,  [Figure (not displayed)]  mutations, Nb60 β-strands B to G in
bold, 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNEAK [Figure (not displayed)] LAGGTT
[Figure (not displayed)] SPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTH
SYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASG
FTFSRYAMSWVRQAPGKGPEWVSAINSPGGSTSYADSVKGRFTISRDNAKNTLYLQMNSLKPDDTAV
YYCAKYERATEWGHTIVAVTPLLDGVHDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 134: MbNb60c7HopQ N277K T270R E197R
(NbGFP207 β-strand A, HopQ sequences underlined,  [Figure (not displayed)]  mutations, Nb60 β-strands B
to G in bold, 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVE [Figure (not displayed)] TQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAK [Figure (not displayed)] LAGTT
[Figure (not displayed)] SPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTH
SYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASG
FTFSRYAMSWVRQAPGKGPEWVSAINSPGGSTSYADSVKGRFTISRDNAKNTLYLQMNSLKPDDTAV
YYCAKYERATEWGHTIVAVTPLLDGVHDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 135: MbNb60cYgjkQE2
(NbGFP207 sequences in bold, circular permutation linker in italics, Ygjk sequences underlined,  [Figure (not displayed)]
[Figure (not displayed)] , 6xHis & EPEA tags)
QVQLVESGGGLV[Figure (not displayed)] KEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYV
ANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQ
QLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVML
DPKEFNTFVPLGTAALTNPAFGADIYWRGRVWVDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLT
ADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRKQasgggsggggsggggsgNADNYKNVINRTGA
PQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDG
KKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPL
SDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGS
TTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLN
GNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDS
VRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYH
DWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKK [Figure (not displayed)] SLRLSCAASGFTFSRYAMSWVRQAPG
KGPEWVSAINSPGGSTSYADSVKGRFTISRDNAKNTLYLQMNSLKPDDTAVYYCAKYERATEWGHTI
VAVTPLLDGVHDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 136: MbNb207c7HopQ
(NbGFP207 β-strand A, HopQ sequences underlined, NbGFP207 β-strands B to G in bold, 6xHis tag,
EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTT
NSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTH
SYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASG
RTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAV
YYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 137-140: MbNb207c7HopQ A5, A12, B7, and G10, resp.
>SEQ ID NO: 141: MbNb207cYgjkE2
(NbGFP207 sequences in bold,  [Figure (not displayed)]  short peptide linker, YgiK sequences underlined, circular permutation
linker in italics, YgiK sequences underlined,  [Figure (not displayed)]  short peptide linker, 6xHis & EPEA tags)
QVQLVESGGGLV [Figure (not displayed)] KEETQSGLNNYARVVEKGQYDSLEIPAQVAASWESGRDDAAVFGFIDKEQLDKYV
ANGGKRSDWTVKFAENRSQDGTLLGYSLLQESVDQASYMYSDNHYLAEMATILGKPEEAKRYRQLAQ
QLADYINTCMFDPTTQFYYDVRIEDKPLANGCAGKPIVERGKGPEGWSPLFNGAATQANADAVVKVML
DPKEFNTFVPLGTAALTNPAFGADIYWRGRVWDQFWFGLKGMERYGYRDDALKLADTFFRHAKGLT
ADGPIQENYNPLTGAQQGAPNFSWSAAHLYMLYNDFFRKQasgggsggggsggggsgNADNYKNVINRTGA
PQYMKDYDYDDHQRFNPFFDLGAWHGHLLPDGPNTMGGFPGVALLTEEYINFMASNFDRLTVWQDG
KKVDFTLEAYSIPGALVQKLTAKDVQVEMTLRFATPRTSLLETKITSNKPLDLVWDGELLEKLEAKEGKPL
SDKTIAGEYPDYQRKISATRDGLKVTFGKVRATWDLLTSGESEYQVHKSLPVQTEINGNRFTSKAHINGS
TTLYTTYSHLLTAQEVSKEQMQIRDILARPAFYLTASQQRWEEYLKKGLTNPDATPEQTRVAVKAIETLN
GNWRSPGGAVKFNTVTPSVTGRWFSGNQTWPWDTWKQAFAMAHFNPDIAKENIRAVFSWQIQPGDS
VRPQDVGFVPDLIAWNLSPERGGDGGNWNERNTKPSLAAWSVMEVYNVTQDKTWVAEMYPKLVAYH
DWWLRNRDHNGNGVPEYGATRDKAHNTESGEMLFTVKK[Figure (not displayed)] SLRLSCAASGRTFSTAAMGWFRQAPG
KERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTR
ANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 142-144: MbNb207cYgikA2, C4 and F5, resp.
>SEQ ID NO: 145: MbNb207c7HopQ C14-C512
(NbGFP207 β-strand A, HopQ sequences underlined, NbGFP207 β-strands B to G in bold  [Figure (not displayed)]
[Figure (not displayed)] ) 6xHis tag, EPEA tag)
QVQLVESGGGLVQ[Figure (not displayed)] KTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVSDFNKLSSGHLKDYIGKCCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTT
NSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTH
SYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASG
RTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAV
YYCAARRRGFTLAPTRANEYDYWGQGTQVTV[Figure (not displayed)] Shhhhhhepea
>SEQ ID NO: 146: MbNb207c7HopQ C402-C474
(NbGFP207 β-strand A, HopQ sequences underlined, NbGFP207 β-strands B to G in bold  [Figure (not displayed)]
[Figure (not displayed)] ), 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTT
NSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTH
SYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSK[Figure (not displayed)] GSLRLSCAASG
RTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSL[Figure (not displayed)] PEDTAV
YYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 147: MbNb207c7HopQ C316-C472
(NbGFP207 β-strand A, HopQ sequences underlined, NbGFP207 β-strands B to G inbold  [Figure (not displayed)]
[Figure (not displayed)] ) 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTT
NSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNCKDFHYTDENGNGTTINCGGSTNSNGTHS
YNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGR
TFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDCLKPEDTAVY
YCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 148: MbNb207c7HopQ C314-C472
(NbGFP207 β-strand A, HopQ sequences underlined, NbGFP207 β-strands B to G in bold  [Figure (not displayed)]
[Figure (not displayed)] ) 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTT
NSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGECNQKDFHYTDENGNGTTINCGGSTNSNGTH
SYNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASG
RTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQM[Figure (not displayed)] SLKPEDTAV
YYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 149: MbNb207c7HopQ C312-C453
(NbGFP207 β-strand A, HopQ sequences underlined, NbGFP207 β-strands B to G in bold  [Figure (not displayed)]
[Figure (not displayed)] ) 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLANTLIQELGNNTYEQLSRLLTNDNGTNSKTSAQAINQAVNNLNERAKTLAGGTT
NSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPCENNQKDFHYTDENGNGTTINCGGSTNSNGTHS
YNGTNTLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASGR
TFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKCRFTISRDNAKNTVYLQMDSLKPEDTAVY
YCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 150: MbNb207c7HopQ C349-C452
(NbGFP207 β-strand A, HopQ sequences underlined, NbGFP207 β-strands B to G in bold  [Figure (not displayed)]
[Figure (not displayed)] ) 6xHis tag, EPEA tag)
QVQLVESGGGLVQTKTTTSVIDTTNDAQNLLTQAQTIVNTLKDYCPILIAKSSSSNGGTNNANTPSWQTA
GGGKNSCATFGAEFSAASDMINNAQKIVQETQQLSANQPKNITQPHNLNLNSPSSLTALAQKMLKNAQS
QAEILKLANQVESDFNKLSSGHLKDYIGKCDASAISSANMTMQNQKNNWGNGCAGVEETQSLLKTSAA
DFNNQTPQINQAQNLNTLIQELGNNTYEQLSRLLTNDNGTNSKTSQAINQAVNNLNERKTLAGGTT
NSPAYQATLLALRSVLGLWNSMGYAVICGGYTKSPGENNQKDFHYTDENGNGTTINCGGSTNSNGTH
SYNGT[Figure (not displayed)] TLKADKNVSLSIEQYEKIHEAYQILSKALKQAGLAPLNSKGEKLEAHVTTSKYGSLRLSCAASG
RTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSACGRFTISRDNAKNTVYLQMDSLKPEDTAV
YYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 151-158: MbNb207Azurin A8, D9, D10, D11, G6, B8, B2, and C8, resp.
>SEQ ID NO: 159: MbNb207cPP7x2A3 (MP1403_A3)
(NbGFP207 sequences in bold, linkers in italics, PP7 sequences underlined, tags in small letters)
MQVQLVESGGGLVQATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVV
DCSTSVCGELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGRGLGSKTI
VLSVGEATRTLTEIQSTADRQIFEEKVGPLVGRLRLTASLRQNGAKTAYRVNLKLDQADVVDCSTSVCG
ELPKVRYTQVWSHDVTIVANSTEASRKSLYDLTKSLVATSQVEDLVVNLVPLGRRGSKTIVLSGSLRLSC
AASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKP
EDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 160-165: MbNb207cPP7x2 D3, G5, E6, D7, A9, B9, resp. (MP1403)
>SEQ ID NO: 166: AP205 Acinetobacter phage coat protein NP_085472.1
>SEQ ID NO: 167: MbNb207AP205x2 XX
(NbGFP207 sequences in bold, random linker in italics, [Figure (not displayed)]  is a short peptide linker (of 1 amino acid),
AP205 sequences underlined, tags in small letters)
MQVQLVESGGGLXKPMQPITSTANKIVWSDPTRLSTTFSASLLRQRVKVGIAELNNVSGQYVSVYKRPA
PKPEGCADACVIMPNENQSIRTVISGSAENLATLKAEWETHKRNVDTLFASGNAGLGFLDPTAAIVSSDK
PMQPITSTANKIVWSDPTRLSTTFSASLLRQRVKVGIAELNNVSGQYVSVYKRPAPKPEGCADACVIMP
NENQSIRTVISGSAENLATLKAEWETHKRNVDTLFASGNAGLGFLDPTAAIVSXGSLRLSCAASGRTFST
AAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCA
ARRRGFTLAPTRANEYDYWGQGTQVTVSSHHHHHHEPEA
>SEQ ID NO: 168-172: MbNb207AP205x2C5, B7, B8, D3, A4, resp.
>SEQ ID NO: 173: MbNb207AP205 XX
(NbGFP207 sequences in bold, random linker in italics, [Figure (not displayed)]  is a short peptide linker (of 1 amino acid),
AP205 sequences underlined, tags in small letters)
MQVQLVESGGGLXKPMQPITSTANKIVWSDPTRLSTTFSASLLRQRVKVGIAELNNVSGQYVSVYKRPA
PKPEGCADACVIMPNENQSIRTVISGSAENLATLKAEWETHKRNVDTLFASGNAGLGFLDPTAAIVSXGS
LRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVYLQM
DSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSSHHHHHHEPEA
>SEQ ID NO: 174 -183: MbNb207AP205C12, A4, E8, D10, A3, A10, D10, D2, C10, F1, resp.
>SEQ ID NO: 184: N2bNb207NbFedF9E
(NbGFP207 β-strand A double underlined, NbGFP207 in bold, and NbFedF9 sequences are underlined),
linker sequences are in italic
QVQLVESGGGLVQTENHQLQESGGGLVQAGGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAG
IYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWX
XXXGSLRLSCAASGYTYSSNCMAWFRQVPGKEREGVASINTRGGITYYADSVKGRFTISRDNAKNTVS
LQMNSLKPEDTATYYCAAVREATYSDNRCSVRSYTYDYWGQGTQVTVSGQEGQGTQVTVSShhhhhhe
pea
>SEQ ID NO: 185: N2bNb207NbFedF9Q
(NbGFP207 β-strand A double underlined, NbGFP207 in bold, and NbFedF9 sequences are underlined),
linker sequences are in italic
QVQLVESGGGLVQTENHQLQESGGGLVQAGGSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAG
IYWTVGSTYYADSAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWX
XXXGSLRLSCAASGYTYSSNCMAWFRQVPGKEREGVASINTRGGITYYADSVKGRFTISRDNAKNTVS
LQMNSLKPEDTATYYCAAVREATYSDNRCSVRSYTYDYWGQGTQVTVSGQQGQGTQVTVSShhhhhh
epea
>SEQ ID NO: 186: N2bNb207NbFedF9 CA14543 (MP1411_B3)
>SEQ ID NO: 187: N2bNb207NbFedF9 CA14544 (MP1411_C6)
>SEQ ID NO: 188: N2bNb207NbFedF9 CA14546 (MP1438_A5)
>SEQ ID NO: 189: N2bNb207NbFedF9 CA14548 (MP1438_B11)
>SEQ ID NO: 190: N2bNb207NbFedF9 CA14550 (MP1438_D2)
>SEQ ID NO: 191: N2bNb207NbFedF9 CA14552 (MP1440_C5)
>SEQ ID NO: 192: Mycobacterium tuberculosis dodecin Rv1498A protein (GenBank Accession Number:
3205040)
>SEQ ID NO: 193: MbNb207Dodecinrandomlinkers Megabody
(NbGFP207 sequences in bold, X is a short peptide linker (1 amino acids) of mixed composition, dodecin
Rv1498A protein sequences underlined, 6xHis tag, EPEA tag)
QVQLVESGGGLXTYRVIEIVGTSPDGVDAAIQGGLARAAQTMRALDWFEVQSIRGHLVDGAVAHFQVT
MKVGFRXSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNA
KNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 194: MbNb35cYgjkE2
>SEQ ID NO: 195: MbNb80cYgjkE2
>SEQ ID NO: 196: MbNb25cYgjkE2
>SEQ ID NO: 197: MbNb38cYgjkE2
>SEQ ID NO: 198: Nb22 Tropomyosin-Related Kinase receptor B (TrkB)-specific Nanobody
>SEQ ID NO: 199: MbNb22cYgjkE2
>SEQ ID NO: 200: Burkholderia cenocepacia 4QYB protein (PDB 4QYB)
>SEQ ID NO: 201-204: MbNb2074QYBrandomlinkers
(NbGFP207 sequences in bold, (X)1-2 is a short peptide linker (1 or 2 amino acids) of mixed composition,
4QYB protein sequences underlined, 6xHis tag, EPEA tag)
QVQLVESGGGLV(X)1-2MQVQDLTGAALDYWATAEGHEVPRADASGCTSIREPGGVPTPFAPSSSW
ADGGPIVERLPFAGFERDGGRGAWRAVLHRAVPAAGERCTFNQSGPTLLIAAMRTLVASTFGDD(X)1-2
GSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYADSAKGRFTISRDNAKNTVY
LQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhhhhhepea
>SEQ ID NO: 205-208: PelB_MbNb2074QYBrandomlinkers
(the PelB leader sequence double underlined, NbGFP207 sequences in bold, (X)1-2 is a short peptide
linker (1 or 2 amino acids) of mixed composition, 4QYB protein sequences underlined, 6xHis tag, EPEA
tag)
MKYLLPTAAAGLLLLAAQPAMAQVQLVESGGGLV(X)1-2MQVQDLTGAALDYWATAEGHEVPRADASG
CTSIREPGGVPTPFAPSSSWADGGPIVERLPFAGFERDGGRGAWRAVLHRAVPAAGERCTFNQSGPT
LLIAAMRTLVASTFGDD(X)1-2GSLRLSCAASGRTFSTAAMGWFRQAPGKERDFVAGIYWTVGSTYYAD
SAKGRFTISRDNAKNTVYLQMDSLKPEDTAVYYCAARRRGFTLAPTRANEYDYWGQGTQVTVSShhh
hhhepea
>SEQ ID NO: 209: affinity tag (U.S. Pat. No. 9,518,084 B2)
EPEA
>SEQ ID NO: 210-213: sequences from FIG. 8C.

Full text: Click here
Patent 2024
Not available on PMC !

Example 4

Mitogen-activated protein kinases (MAPKs) provide a wide-ranging signaling cascade that allow cells to quickly respond to biotic and abiotic stimuli. The objective of this project was to determine if HE extracts from Fungi Perfecti (FP) impact MAPKs (e.g., influence the expression and phosphorylation of various MAPKs—notably JNK, c-Jun, and c-fos—to promote nerve growth factor (NGF) expression). Here, four FP extracts were tested at three concentrations each (Table 1). These extracts were tested against five MAPKs: c-Jun N-terminal kinase 1-3 (JNIK1, JNK2, JNK3), Rho Associated Coiled-Coil Containing Protein Kinases 1 and 2 (ROCK1, ROCK2), and tropomyosin receptor kinase B (TRKB). Collectively, these MAPKs are major players in neural health, influencing neurogenesis, neural growth and differentiation, and neurodegenerative diseases.

TABLE 11
Concentrations of FP HE extracts tested for binding to MAPK targets
ExtractConcentrations Tested (μg/mL)
HD HE Extract62.5125250
HE EtOAc62.5125250
HE Water Wash62.5125250
HD Powder31.2562.5125
HD: Host Defense ® Lion's Mane (Hericium erinaceus) product (Fungi Perfecti)

While several potential MAPK hits were identified for all extracts, the Host Defense® (Fungi Perfecti; “HD”) HE EtOH and HE EtOAc extracts elicited the most pronounced impacts, particularly the latter extract (FIG. 12). (Note: based on the % Control kinase binding calculation, stronger hits are represented by lower values.)

Interestingly, the top two hits included the HE EtOAc extract on JNK3 and the HD HE EtOH extract with ROCK1 (Table 12). This suggests that the extraction method may play a significant role in the ways in which neural health is impacted. While the strongest MAPK impact was found on JNK3 with the EtOAc extract, the EtOH extract did not produce a strong impact on this specific kinase. This may be due to the EtOAc extraction method producing the strongest detectable erinacine content.

TABLE 12
Top ten hits identified in the MAPK binding assay
DiscoveRxEntrez Compound
Compound GeneGenePercentConc.
NameSymbolSymbolControl(μg/mL)
HE EtOAcJNK3MAPK1054250
HD ExtractROCK1ROCK165250
HE EtOAcJNK2MAPK970250
HE EtOAcROCK1ROCK173250
HD ExtractROCK2ROCK274250
HE EtOAcJNK3MAPK1074125
HE EtOAcJNK1MAPK874250
HE EtOAcROCK2ROCK276250
HE Water WashJNK1MAPK876250
HE EtOAcJNK2MAPK97862.5
HD: Host Defense ® Lion′s Mane (Hericium erinaceus) product (Fungi Perfecti)

Collectively, MARK binding data suggest that FP HE extracts impact neural health on several broad levels. Of the top MARKs impacted by HE extracts, the JNKs play a role in cell degeneration, while the ROCKs play a role in cell survival. Accordingly, FP HE extracts may play an immunomodulatory role in influencing immune system homeostasis (FIG. 13).

Contrary to results from neurite outgrowth cellular assays, higher extract concentrations in MARK binding assays tended to elicit a stronger response. At 250 μg/mL, the EtOAc had a strong impact on the binding of TRKB, a well-characterized, high affinity receptor of brain-derived neurotrophic factor (BDNF), further broadening the scope at which FP HE extracts modulate neural activity.

Ultimately, findings from the MARK binding assays strengthen the mechanisms by which FP HE extracts influence neurogenic activity. In addition to morphology-based cellular assays in several cell lines, there is now evidence that FR extracts are driving neurite growth through diverse, classical neurogenic pathways related to neurotrophic factors including both NGF and BDNF.

The ability of psilocybin analogs to stimulate neurite outgrowth is demonstrated in several cell models. Accordingly, preliminary research has started to reveal the mechanisms by which psilocybin analogs may confer neurotrophic benefits that facilitate neurite outgrowth. Human 1321N1 brain cells treated with norbaeocystin have increased expression of NGF protein when compared to a vehicle control (FIG. 16).

Full text: Click here
Patent 2023

Example 4

Mitogen-activated protein kinases (MAPKs) provide a wide-ranging signaling cascade that allow cells to quickly respond to biotic and abiotic stimuli. The objective of this project was to determine if HE extracts from Fungi Perfecti (FP) impact MAPKs (e.g., influence the expression and phosphorylation of various MAPKs—notably JNK, c-Jun, and c-fos—to promote nerve growth factor (NGF) expression). Here, four FP extracts were tested at three concentrations each (Table 11). These extracts were tested against five MAPKs: c-Jun N-terminal kinase 1-3 (JNK, JNK2, JNK3), Rho Associated Coiled-Coil Containing Protein Kinases T and 2 (ROCK, ROCK2), and tropomyosin receptor kinase B (TRKB). Collectively, these MAPKs are major players in neural health, influencing neurogenesis, neural growth and differentiation, and neurodegenerative diseases.

TABLE 11
Concentrations of FP HE extracts tested for binding to MAPK targets
ExtractConcentrations Tested (μg/mL)
HD HE Extract62.5125250
HE EtOAc62.5125250
HE Water Wash62.5125250
HD Powder31.2562.5125
HD: Host Defense ® Lion's Mane (Hericium erinaceus) product (Fungi Perfecti)

While several potential MAPK hits were identified for all extracts, the Host Defense (Fungi Perfecti; “HO”) HE EtGH and HE EtOAc extracts elicited the most pronounced impacts, particularly the latter extract (FIG. 12). (Note: based on the % Control kinase binding calculation, stronger hits are represented by lower values.)

Interestingly, the top two hits included the HE EtOAc extract on JNK3 and the HO HE EtOH extract with ROCK1 (Table 12). This suggests that the extraction method may play a significant role in the ways in which neural health is impacted. While the strongest MAPK impact was found on JNK3 with the EtOAc extract, the EtOH extract did not produce a strong impact on this specific kinase. This may be due to the EtOAc extraction method producing the strongest detectable erinacine content.

TABLE 12
Top ten hits identified in the MAPK binding assay
DiscoveRx Entrez Compound
Compound GeneGenePercentConc.
NameSymbolSymbolControl(μg/mL)
HE EtOAcJNK3MAPK1054250
HD ExtractROCK1ROCK165250
HE EtOAcJNK2MAPK970250
HE EtOAcROCK1ROCK173250
HD ExtractROCK2ROCK274250
HE EtOAcJNK3MAPK1074125
HE EtOAcJNK1MAPK874250
HE EtOAcROCK2ROCK276250
HE Water WashJNK1MAPK876250
HE EtOAcJNK2MAPK97862.5
HD: Host Defense ® Lion's Mane (Hericium erinaceus) product (Fungi Perfecti)

Collectively, MAPK binding data suggest that FP HE extracts impact neural health on several broad levels. Of the top MAPKs impacted by HE extracts, the JNKs play a role in cell degeneration, while the ROCKs play a role in cell survival. Accordingly, FP HE extracts may play an immunomodulatory role in influencing immune system homeostasis (FIG. 13).

Contrary to results from neurite outgrowth cellular assays, higher extract concentrations in MAPK binding assays tended to elicit a stronger response. At 250 μg/mL, the EtOAc had a strong impact on the binding of TRKB, a well-characterized, high affinity receptor of brain-derived neurotrophic factor (BDNF), further broadening the scope at which FP HE extracts modulate neural activity.

Ultimately, findings from the MAPK binding assays strengthen the mechanisms by which FP HE extracts influence neurogenic activity. In addition to morphology-based cellular assays in several cell lines, there is now evidence that FP extracts are driving neurite growth through diverse, classical neurogenic pathways related to neurotrophic factors including both NGF and BDNF.

The ability of psilocybin analogs to stimulate neurite outgrowth is demonstrated in several cell models. Accordingly, preliminary research has started to reveal the mechanisms by which psilocybin analogs may confer neurotrophic benefits that facilitate neurite outgrowth. Human 1321N1 brain cells treated with norbaeocystin have increased expression of NGF protein when compared to a vehicle control (FIG. 16).

Full text: Click here
Patent 2023
Not available on PMC !

Example 4

Mitogen-activated protein kinases (MAPKs) provide a wide-ranging signaling cascade that allow cells to quickly respond to biotic and abiotic stimuli. The objective of this project was to determine if HE extracts from Fungi Perfecti (FP) impact MAPKs (e.g., influence the expression and phosphorylation of various MAPKs—notably JNK, c-Jun, and c-fos—to promote nerve growth factor (NGF) expression). Here, four FP extracts were tested at three concentrations each (Table 1). These extracts were tested against five MAPKs: c-Jun N-terminal kinase 1-3 (JNIK1, JNK2, JNK3), Rho Associated Coiled-Coil Containing Protein Kinases 1 and 2 (ROCK1, ROCK2), and tropomyosin receptor kinase B (TRKB). Collectively, these MAPKs are major players in neural health, influencing neurogenesis, neural growth and differentiation, and neurodegenerative diseases.

TABLE 11
Concentrations of FP HE extracts tested for binding to MAPK targets
ExtractConcentrations Tested (μg/mL)
HD HE Extract62.5125250
HE EtOAc62.5125250
HE Water Wash62.5125250
HD Powder31.2562.5125
HD: Host Defense ® Lion's Mane (Hericium erinaceus) product (Fungi Perfecti)

While several potential MAPK hits were identified for all extracts, the Host Defense® (Fungi Perfecti; “HD”) HE EtOH and HE EtOAc extracts elicited the most pronounced impacts, particularly the latter extract (FIG. 12). (Note: based on the % Control kinase binding calculation, stronger hits are represented by lower values.)

Interestingly, the top two hits included the HE EtOAc extract on JNK3 and the HD HE EtOH extract with ROCK1 (Table 12). This suggests that the extraction method may play a significant role in the ways in which neural health is impacted. While the strongest MAPK impact was found on JNK3 with the EtOAc extract, the EtOH extract did not produce a strong impact on this specific kinase. This may be due to the EtOAc extraction method producing the strongest detectable erinacine content.

TABLE 12
Top ten hits identified in the MAPK binding assay
DiscoveRxEntrez Compound
Compound GeneGenePercentConc.
NameSymbolSymbolControl(μg/mL)
HE EtOAcJNK3MAPK1054250
HD ExtractROCK1ROCK165250
HE EtOAcJNK2MAPK970250
HE EtOAcROCK1ROCK173250
HD ExtractROCK2ROCK274250
HE EtOAcJNK3MAPK1074125
HE EtOAcJNK1MAPK874250
HE EtOAcROCK2ROCK276250
HE Water WashJNK1MAPK876250
HE EtOAcJNK2MAPK97862.5
HD: Host Defense ® Lion′s Mane (Hericium erinaceus) product (Fungi Perfecti)

Collectively, MARK binding data suggest that FP HE extracts impact neural health on several broad levels. Of the top MARKs impacted by HE extracts, the JNKs play a role in cell degeneration, while the ROCKs play a role in cell survival. Accordingly, FP HE extracts may play an immunomodulatory role in influencing immune system homeostasis (FIG. 13).

Contrary to results from neurite outgrowth cellular assays, higher extract concentrations in MARK binding assays tended to elicit a stronger response. At 250 μg/mL, the EtOAc had a strong impact on the binding of TRKB, a well-characterized, high affinity receptor of brain-derived neurotrophic factor (BDNF), further broadening the scope at which FP HE extracts modulate neural activity.

Ultimately, findings from the MARK binding assays strengthen the mechanisms by which FP HE extracts influence neurogenic activity. In addition to morphology-based cellular assays in several cell lines, there is now evidence that FR extracts are driving neurite growth through diverse, classical neurogenic pathways related to neurotrophic factors including both NGF and BDNF.

The ability of psilocybin analogs to stimulate neurite outgrowth is demonstrated in several cell models. Accordingly, preliminary research has started to reveal the mechanisms by which psilocybin analogs may confer neurotrophic benefits that facilitate neurite outgrowth. Human 1321N1 brain cells treated with norbaeocystin have increased expression of NGF protein when compared to a vehicle control (FIG. 16).

Full text: Click here
Patent 2023

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The BD FACSMelody is a cell sorter designed for high-speed and gentle cell sorting. It is capable of sorting up to four-way purification of cells from complex samples, with the ability to handle a wide range of sample types and cell sizes. The BD FACSMelody provides accurate and reliable cell sorting performance for a variety of applications.

More about "Tropomyosin-related kinase-B, human"

Tropomyosin-related kinase B (TrkB) is a critical receptor tyrosine kinase that binds to the neurotrophic factor brain-derived neurotrophic factor (BDNF).
This receptor plays a pivotal role in neuronal survival, differentiation, and synaptic plasticity, and is expressed throughout the central and peripheral nervous systems.
TrkB is involved in vital processes such as learning, memory, and neurogenesis.
Dysregulation of the TrkB signaling pathway has been implicated in various neurological and psychiatric disorders, including Alzheimer's disease, Parkinson's disease, depression, and anxiety.
Understanding the complex mechanisms of TrkB function is essential for developing targeted therapies for these conditions.
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Synonyms for TrkB include NTRK2, NYK, and TRK-B.
Related terms include neurotrophins, receptor tyrosine kinases, and neuroplasticity.
The abbreviation for Tropomyosin-related kinase B is TrkB.
Key subtopics include BDNF signaling, neuronal development, synaptic function, and neurological disorders.
Information from BD FACSMelody, a flow cytometry system, can also be utilized to study TrkB expression and function in various cell types.