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10 protocols using adam9

1

Peptide Substrate Cleavage Assay for ADAM-17

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ADAM-17 peptide substrate (sequence: LAQAVRSSSARLVFF) and its two cleavage fragments (sequences: LAQAV and RSSSARLVFF) were synthesized by WatsonBio (Houston, TX). ADAM-17 and ADAM-9 were ordered from R&D Systems (Minneapolis, MN), while MMP-9 was obtained from Sigma-Aldrich (St. Louis, MO). All the other chemicals, including sodium chloride, zinc chloride, Trizma base, hydrochloric acid, pentane, hexadecane, HPLC-grade water, and DNase, RNase free water, were purchased from Sigma-Aldrich (St. Louis, MO). 1,2-diphytanoylphosphatidylcholine was bought from Avanti Polar Lipids (Alabaster, AL). The stock solution of ADAM-17 was prepared in DNase, RNase free water at a concentration of 100 μg/mL and stored at −80 °C before and immediately after use. A stock solution of 10 mM for each peptide was also prepared with DNase, RNase free water and kept at −20 °C before and immediately after use.
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2

Identifying ADAM9 Cleavage Site in ELP

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To confirm that ADAM9 can cleave ELP, 18 μg of recombinant mouse ADAM9 (R&D Systems) was added to 50 μL of a 50 mg/ml solution of ELP dissolved in ADAM9 activity assay buffer. The mixture was allowed to incubate a room temperature for 2 days with constant agitation. ELP dissolved in ADAM9 activity assay buffer without addition of rmADAM9 was included as a control. After 2 days, the ELP solutions were separated by SDS-PAGE, transferred to a PVDF membrane, and stained by Coomassie blue to visualize protein bands. The band corresponding to the lowest molecular weight degradation product was cut out and submitted to the Stanford Protein and Nucleic Acid Facility for N-terminal Edman sequencing to identify the ADAM9 cleavage site in ELP.
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3

ADAM9 Peptide Cleavage Assay

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A Dabcyl- and FAM-modified linker peptide containing the ADAM9 cleavage site Ser-Pro-Leu-Ala-Gln-Ala-Val-Arg-Ser-Ser-Lys (SPLAQAVRSSK; ADAM9-peptide linker, cleavage sequence shown in bold [22 (link)]) was purchased from GL Biochem (Shanghai, China). The peptide (1 μM) was incubated in assay buffer (50 mM Tris-HCl, 20 mM NaCl, 2 mM CuCl2, 10 μM ZnCl2 in PBS) supplemented with thrombin (0.5, 1, or 2 units/mL; Sigma-Aldrich), ADAM9 (0.02, 0.01, or 0.005 units/mL; R&D Systems, Minneapolis, MN, USA) or CM from PANC-1, MIA PaCa-2, Panc02, KP, THP-1, RAW264.7, U-937, HL-60, or MH-S cells. Additional peptide cleavage assays were performed with CM from HuTu-80, MDST8, OE19, OE33, FLO-1, T24, RT-112, AMC-EAC-081R, and AMC-EAC-289B. Fluorescence was measured every 15 min at Ex/Em 485/528 nm wavelengths using a Biotek Synergy HT plate reader (Biotek Instruments, Winooski, VT, USA).
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4

Comprehensive Western Blot and RT-qPCR Analysis

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Western blotting was performed as described previously (15 (link)). All the types of cells were lysed by RIPA buffer with cocktail protease and phosphatase inhibitors (Thermo Fisher Scientific). Total protein extracts (40 μg) were subjected to western blotting analysis with antibodies against the following proteins: ADAM9 (R&D system); p-EGFR (Tyr1068), EGFR, p-MAPK (Tyr202/204), MAPK, GAPDH, p-AKT (Ser473), AKT, p-IKKα/β (Ser176/180), IKKβ, p-NF-κBp65 (Ser536), NF-κBp65, p-IκBα (Ser32), IκBα, and β-actin (Cell Signaling, Massachusetts, USA).
Total RNA was extracted from all the types of cells by using TRIzol Reagent (Thermo Fisher Scientific) according to the vendor's instruction. The cDNA synthesis was achieved by using PrimeScript reverse transcription reagent Kit with gDNA Eraser (TaKaRa, Shiga, Japan). Quantitative PCR was performed with ADAM9 and GAPDH primers by using SYBR Green PCR Master Mix (Roche, Baden-Württemberg, Germany) in a real-time PCR System (Applied Biosystems 7500, Thermo Fisher Scientific). Primer sequences were as follows: ADAM9, 5′-CCTCGGGGACCCTTCGTGT-3′ and 5′-ATCCCATAACTCGCATTCTCTAAA-3′; GAPDH, 5′-CCACCCATGGCAAATTCCATGGCA-3′ and 5′-TCTAGACGGCAGGTCAGGTCCACC-3′. Quantitative analysis of RT-qPCR was achieved by the 2−ΔΔCt method.
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5

ADAM9 Expression in Tissue Samples

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Sections (5 μm) were cut from formalin-fixed paraffin-embedded specimens and mounted on Superfrost slides (Menzel Glaser, Lower Saxony, Germany) and gradually rehydrated after deparaffinization by xylene. Antigen retrieval was achieved by super heating in microwave oven with pH 6 citrate buffer for 15 min after boiling. The primary antibody ADAM9 (R&D System, Minnesota, USA) was diluted to 1:50 in Antibody Diluent (Dako, Denmark). After incubation at room temperature for 30 min, antigen-antibody reaction was detected by using anti-goat HRP-DAB tissue staining kit (R&D System). The slides were then counterstained with haematoxylin. For the negative control, the primary antibody was omitted. The immunohistochemistry staining results were evaluated by two experienced pathologists. The ADAM9 IHC intensity was classified into 5 grades (0 = negative, 1 = weak, 2 = moderate, 3 = strong, and 4 = prominent staining). The ADAM9 staining percentage was calculated by quantifying stained cells. ADAM9 expression level was calculated by applying the following formula: Expression level = ADAM9 staining intensity x ADAM9 staining percentage.
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6

Quantifying sANPEP in Mouse and Human Samples

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To determine the level of sANPEP in the plasma of LPS-injected mice (sacrificed 72 h after intraperitoneal injection of 1 mg/kg LPS, male) and 5xFAD mice (8 months of age, male), blood samples were collected from the vena cava using EDTA tubes and shaken gently. To separate plasma from the blood, samples were centrifuged (1500g, 15 min, 4 °C), and then, the plasma was transferred into a new tube. Samples (1:100) were diluted and assessed using a Mouse ANPEP ELISA Kit (MyBioSource) according to the manufacturer’s instructions. To measure the levels of human sANPEP in the clinical samples, plasma (1:10,000) and CSF (1:10) were first diluted. ELISA kits for human ANPEP (R&D Systems), TNFAIP6 (MyBioSource), MXRA8 (Cusabio), PEDF (Cloud-Clone Corp), ADAM9 (R&D Systems), and C1NH (R&D Systems) were used for the assay according to the manufacturer’s instructions. The level of human IL-1β in the conditioned media was determined using a human IL-1β ELISA Kit (R&D Systems) following the manufacturer’s instructions. The absorbance was read at 450 and 540 nm using a microplate reader (Molecular Devices).
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7

Exosome Protein Analysis by Western Blotting

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Lysates of sucrose cushion-purified Du145 exosomes or whole cells, made using RIPA buffer (Santa Cruz), were boiled in SDS sample buffer containing 20 mm DTT as previously described (29 (link)) and prepared as matched protein doses (12.5 μg to 50 μg per lane). They were subjected to electrophoresis on NuPAGE precast 4–20% gradient gels (Invitrogen). Samples were transferred to PVDF membranes before blocking in PBS containing 0.5% (w/v) Tween-20 and 3% (w/v) nonfat powdered milk. Membranes were probed with antibodies including DAF (CD55) (Diaclone, Besancon Cedex, France), Notch 3, ADAM9 (R&D Systems), RAC1 (Becton Dickinson), Tissue Factor, TSG101, calnexin (Santa Cruz), or L1CAM (a gift from P. Altevolgt, Heidelberg, Germany). After incubation with goat anti-mouse-HRP conjugate (Santa Cruz), bands were detected using x-ray film (GE Healthcare) and a chemiluminescence reagent (Super Signal West Pico, Thermo/Pierce).
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8

TACE Activity in SLE Monocytes

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TACE activity was measured in SLE patient serum as well as from supernatants of stimulated monocytes with oxLDL and DNA-IC. Where indicated, anti-LOX-1 antibody (50 μg/mL) or TAPI-1 inhibitor (100 μM) were used to pre-treat cells for 30m. TACE activity was measured by using a synthetic peptide substrate containing the cleavage site (Mca-Pro-Leu-Ala-Gln-Ala-Val-Dpa-Arg-Ser-Ser-Ser-Arg-NH2) primarily for ADAM17 and related enzymes such as ADAM8, ADAM9 and ADAM10 (R&D Systems, Inc., MN, USA). The cleavage site by ADAM17 and ADAM10 is the peptide bond between Ala and Val. 10 μL of each sample (serum or supernatant) was added to 90 μL of 25 mM Tris buffer, pH 8.0. The substrate was then added at a final concentration of 10 μM in a total of 100 μL reaction mixture for 1h. Fluorescence units (FU) were measured using a fluorescent microplate reader, Spectramax (Molecular Devices, CA, USA), with an excitation wave length at 320 nm and an emission wavelength at 405 nm. TACE activity results were normalized to total protein concentration of serum samples or supernatant. Enzymatic activity of TACE is represented as FU/min/μg.
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9

ADAM17 Protease Kinetics Optimization

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ADAM9 and ADAM17 were purchased from R&D Systems (Minneapolis, MN), while the 5-FAM labeled ADAM17 protease substrate peptide (Pep-FAM) with a sequence of NH2-CALNNLAQAVRSSSARK(5-FAM) (95.22% pure) was ordered from WatsonBio Sciences (Houston, TX). Human serum and all the other chemicals, including graphene oxide and MMP-9, were obtained from Sigma-Aldrich (St. Louis, MO). ADAM17 and its substrate peptide were dissolved in HPLC-grade water (ChromAR, Mallinckrodt Baker). The stock solution of ADAM17 was prepared at 200 μg mL−1 and kept at −80 °C before and after immediate use, while that of the peptide substrate was prepared at a concentration of 1 mM and stored at −20 °C before and after use. Two buffer solutions were used in this study: (1) MES buffer (containing 100 mM 2-(N-morpholino)-ethanesulfonic acid, pH 6.0); and (2) Tris buffer, which was consisted of 50 mM Tris, 15 mM NaCl, and 5 μM ZnCl2 with the solution pH adjusted to 7.5 using HCl.
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10

Identifying ADAM9 Cleavage Site in ELP

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To confirm that ADAM9 can cleave ELP, 18 μg of recombinant mouse ADAM9 (R&D Systems) was added to 50 μL of a 50 mg/ml solution of ELP dissolved in ADAM9 activity assay buffer. The mixture was allowed to incubate a room temperature for 2 days with constant agitation. ELP dissolved in ADAM9 activity assay buffer without addition of rmADAM9 was included as a control. After 2 days, the ELP solutions were separated by SDS-PAGE, transferred to a PVDF membrane, and stained by Coomassie blue to visualize protein bands. The band corresponding to the lowest molecular weight degradation product was cut out and submitted to the Stanford Protein and Nucleic Acid Facility for N-terminal Edman sequencing to identify the ADAM9 cleavage site in ELP.
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