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95 protocols using scd14

1

Serum Biomarker Measurement Protocol

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Serum biomarkers were measured at the University of Washington, Seattle, WA. IL-6, MCP-1, TNF-α, MIP-1β, IP-10, eotaxin, MCP-4, MDC, TARC, IFN-γ, IL-10, IL-8, were measured using electrochemiluminescence immunoassays (Meso Scale Diagnostics, Rockville, MD). sCD14 and presepsin concentrations were measured using enzyme-linked immunosorbent assays (sCD14: R&D Systems, Minneapolis, MN and presepsin: MyBiosource, San Diego, CA). Immunoassay performance characteristics are summarized in Supplemental Table S1.
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Fecal and Serum Biomarker Assay

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Enzyme-linked immunsorbent assay (ELISA) was used to measure fecal calprotectin, serum diamine oxidase (DAO) (both: Immundiagnostik, Bensheim, Germany), lipopolysaccharide binding protein (LBP, Hycult Biotech, Uden, the Netherlands), and soluble CD14 (sCD14, R&D Systems, Minneapolis, MN).
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3

Immune Profiling of HIV-Infected Women

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Cellular activation was assessed by staining mononuclear cell suspensions with antibodies to CD3, CD4, CD8, CCR5, CD69, and Ki67 in all participants. Naïve, effector, and memory T cells were characterized by CD45RA and CCR7 in HIV-infected women. Samples were stained as described,30 acquired on a LSRII instrument and analyzed using FlowJo software (FlowJo, Ashland, OR).
Soluble mediators in CVL and EML were analyzed in all participants using the Human Cytokine and Chemokine Panel I Kit (Millipore, Billerica, MA) using a MagPix instrument, or by ELISA (sCD163: Trillenium Diagnostics, LLC, Brewer, ME; sCD14: and R&D Systems, Minneapolis, MN). CVL specimens contained predominantly sloughed dead epithelial cells, and therefore, no further cellular evaluation was performed.
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4

Gut Immune Profiling in HIV Infection

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At baseline and after 9 months of ART, rectal (10–15cm from the anal verge) and duodenal (second and third segments) biopsies were placed immediately in either liquid nitrogen, paraformaldehyde for paraffin-embedding or sterile media for single cell suspension by a single investigator (DMA). Peripheral blood mononuclear cells (PBMC) were isolated using Ficoll-Hypaque™ (Pfizer-Pharmacia, New York, NY). Single-cell suspensions generated by collagenase digestion were stained and analyzed by flow cytometry (Becton-Dickinson LSRII) as previously described[7 (link), 24 (link)] and with the gating strategy as demonstrated in Figure S1. Similarly, immunofluorescent antibody tissue analysis was performed as previously reported[7 (link), 24 (link)]. The numbers of positive cells were counted by a single observer (Z-MM) and presented as cells/mm2 of lamina propria.
Plasma Interleukin-6 (IL-6; high-sensitivity kit, R&D Systems), soluble CD14 (sCD14; R&D Systems), high-sensitivity C Reactive Protein (CRP; CardioPhase high-sensitivity kit,-CRP assay, Siemens), and zonulin-1 (ALPCO) levels were assessed according to manufactures’ recommendations. Lipoteichoic acid (LTA) was measured as previously published[25 (link)]. IL-4 was measured by ELISA using the Vascular Injury-II kit (MesoScale Discovery, Gaithersburg, MD)
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5

Biomarkers of Intestinal Injury and Inflammation

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CCR2 and CCR5 ligands (CCL2, CCL3, CCL4, CCL5) and proinflammatory cytokines (IL‐6, TNF‐α, IL‐1β, TGF‐β) were measured on the Luminex platform on plasma samples from Day 1 and during cenicriviroc treatment at Days 7 and 14 (HCYTOMAG‐60K MILLIPLEX (Merck Millipore, Darmstadt, Germany) was used for CCL2, CCL3, CCL4, IL‐1β, IL‐6; Human RANTES enzyme‐linked immunosorbent assay (ELISA) kit (PeproTech, London, UK) for CCL5; Human TGF‐β 1 DuoSet ELISA (R&D Systems, Minneapolis, MN) for TGF‐β). Markers of enterocyte death, intestinal fatty acid binding protein (I‐FABP) (R&D Systems), and bacterial translocation, flagellin (MyBioSource, San Diego, CA), lipopolysaccharide binding protein (LBP) (Hycult Biotech, Plymouth Meeting, Philadelphia, PA), and sCD14 (R&D Systems), were measured at the same timepoints by ELISA according to the manufacturers’ instructions. Correlation between flagellin and I‐FABP or ALT levels was evaluated in both cohorts.
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6

Serum Endotoxin Marker Quantification

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Serum lipopolysaccaride (LPS) activity was determined with a Limulus amoebocyte lysate assay (Hycult Biotechnology). Serum LBP (Hycult Biotechnology), IgG antibody to LPS core (EndoCAb) (Hycult Biotechnology) and sCD14 (R&D Systems, Abingdon, United Kingdom) levels were measured by ELISA. The detection limit for LPS, LBP, sCD14 and EndoCAb were 0.04 Endotoxin Units (EU) /ml, 4.4 ng/ml, 0.125ng/ml and 0.125 EndoCAb Median Unit (EMU)/ml respectively. One EU equals approximately 0.1 to 0.2ng endotoxin/mL.
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7

Lipid, Protein, and Immune Markers Quantitation

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Lipid markers were measured by electrospray ionization tandem mass spectrometry as described previously (Haughey, Cutler et al. 2004 (link)). Protein carbonyls were quantitated using the OxyBlot Protein Oxidation Detection Kit as described previously (Schifitto, Yiannoutsos et al. 2009 (link)). Enzyme-linked immunosorbent assays (ELISA) were used to measure plasma Neopterin (GenWay Biotech), sCD14 (R&D Systems), sCD163 (from Trillium Diagnostics) and CSF sCD14, sCD163, neurofilament protein light chain (NFL) (UmanDiagnostics), and neurofilament protein heavy chain (NFH) (BioVendor) levels according to manufacturer’s protocols.
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8

Genetic Markers and Inflammation Profiling

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Whole blood was collected in EDTA-vacutainers. Peripheral blood mononuclear cells (PBMCs), plasma and neutrophils were isolated as previously described [37 (link)]. DNA was extracted using the Qiagen Blood and Tissue kit (Qiagen, Germany) from neutrophils and genotyped for the CD14 (rs2569190) and TLR4 (rs4986790 and rs2569190) SNPs at the Australian Genome Research Facility (AGRF) using the Sequenom MassArray platform. Markers of monocyte activation including sCD14 (R&D Systems, McKinley Place, MN) and sCD163 (Trilium Diagnostics, Bangor, ME) were measured by ELISA in plasma according to the manufacturer’s instructions. The systemic inflammation marker, hsCRP was determined by immunochemiluminometric assay by the hospitals clinical diagnostic laboratory.
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9

Plasma Biomarker Quantification Protocol

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Stored plasma samples from all 4 timepoints were thawed and analyzed in batch. Commercially available ELISA kits were used to determine the plasma concentrations of soluble CD14 (sCD14; R&D, Minneapolis, MN), soluble CD163 (sCD163; R&D), interleukin 6 (IL-6; R&D), interferon gamma-induced protein 10 (IP-10; R&D), and C-reactive protein (CRP; R&D) according to manufacturer’s instructions. Duplicates of 20% of the samples were included in each ELISA plate. Results were analyzed using an ELX808 ELISA reader (Biotek, Vinooski, VT) using Gen5 software v2.06.
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10

Evaluation of Plasma Immune Markers

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Presence of plasma IFNα (PBL Assay Science), IP-10 (R&D systems), sCD14 (R&D systems), TNFα (R&D systems), D-Dimer (Abcam), and C-Reactive Protein (CRP) (Abcam) was evaluated by ELISA per manufacturers protocol.
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