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22 protocols using af1817

1

Comprehensive Kidney Protein Analysis

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Western blotting was performed as previously described (21 (link)). Mouse kidney and cultured cells were lysed in RIPA lysis buffer. Anti-GAPDH (1:2000 dilution, CW0100M, CWBio, China), anti-cleaved caspase 3 (1:1000 dilution, ab32503, Abcam, Cambridge, UK), anti-Bcl2 (1:1000 dilution, cst2870, Cell Signaling Technology, USA), anti-SIRT1 (1:1000 dilution, GT1189, Genetex, China),anti-KIM-1(0.25ug/ml, AF1817, RD systems, Canada), anti-PGC-1a(1:1000, # 2178, cell signaling technology, USA) and anti-Bax (1:1000 dilution, ab193349, Abcam Cambridge, UK) antibodies were used in this study. Experiments were repeated three times.
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2

Immunoblotting for Kidney Injury Markers

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The kidney sections were ground using a homogenizer or the cells were scratched and lysed in RIPA lysis buffer (Beyotime, Shanghai, China) with proteinase inhibitor (Roche, Switzerland) for 30 min on ice. Protein concentration was quantified using the Bicinchoninic acid assay (Beyotime, Shanghai, China). Protein samples (50 μg) were used to perform immunoblotting as described previously42 (link). The specific primary antibodies used were: anti-GSDME (ab215191, Abcam, 1:1000), anti-caspase-3 (9662, CST, 1:1000), anti-cleaved caspase-3 (9661, CST, 1:1000), phospho-NF-κB p65 (3033, CST, 1:1000), NGAL (ab63929, Abcam, 1:1000), KIM-1 (AF1817, R&D systems, 1:1000), and anti-GAPDH (5174, CST, 1:10000). Peroxidase-conjugated goat anti-rabbit secondary antibodies (A0277, Beyotime, Shanghai, China) were used for immunoblotting.
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3

Immunohistochemical Analysis of Kidney Markers

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Immunohistochemistry was performed on formalin-fixed, paraffin-embedded kidney sections from human and mouse using antibodies against RXRα (ET7108-99, Huabio, 1:200 dilution), α-SMA (ab5694, Abcam, 1:100 dilution), Collagne-1 (ab34710, Abcam, 1:800 dilution), and Fibronectin (F3648, Sigma, 1:1000 dilution). Briefly, deparaffinized and rehydrated sections were boiled in citrate antigen retrieval solution for antigen retrieval. After incubation with 10% goat serum, sections were incubated with primary antibodies overnight at 4 °C, followed by incubation with horseradish peroxidase-conjugated secondary antibodies (ZLI-9018, ZSGB-BIO, 1:20 dilution). DAB-positive staining was assessed by two experienced pathologists in a blinded manner and evaluated by H score as described previously40 (link). For immunofluorescence, deparaffinized and rehydrated sections were blocked and incubated with antibodies against KIM-1 (AF1817, R&D System, 1:200 dilution) overnight at 4 °C, followed by incubation with Alexa Fluor 555-conjugated secondary antibodies (Invitrogen, 2273776, 1:1000 dilution) and fluorescein-LTL (Vector Lab, FL-1321, 1:1000 dilution). The tissue slides were imaged with a fluorescence microscope (DMi8, Leica).
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4

Protein Expression Analysis in Kidney Cells

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Proteins from cultured cells or mice kidneys were extracted with TRI Reagent (Sigma–Aldrich) according to the manufacturer’s guidelines. Samples were separated by SDS-PAGE and transferred onto PVDF membranes (IPVH00010, Millipore). After blocking the membranes with 5% milk, we used primary antibodies to incubate the membranes overnight at 4 °C against the following proteins: KLF10 (1:1000, ab184182, Abcam), CCNB1 (1:1000, GTX100911, GeneTex), CCND1 (1:1000, GTX108624, GeneTex), PCNA (1:1000, 101239-T46, SinoBiological), KIM1 (1:1000, AF1817, R&D), Anti-FLAG (1:1000, 8146, CST), ACTIN (1:2000, GTX11003, GeneTex), ZBTB7A (1:1000, ab175918, Abcam), PTEN (1:1000, AB170941, Abcam), pAKT (1:1000, 4060 S, CST), AKT (1:1000, 4691 S, CST). The membranes were washed by TBST before incubated with secondary antibodies (1:2000, Jackson ImmunoResearch Inc). The bands of the target proteins were visualized by the LAS-3000 detection system and were quantitively analyzed by Fiji based on ACTIN and control groups respectively.
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5

Western Blot Protein Analysis Protocols

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Western blot was conducted and analysed as previously described.
9 (link) Proteins (50 μg) were separated by 8%, 10% and 12% SDS‐PAGE, respectively, according to molecular weight. The primary antibodies used were as following: GAPDH (1:1000, T0004, Affinity Biosciences, China), kidney injury molecule 1 (KIM‐1, 1:1000, AF1817, R&D Systems, USA), α‐SMA (1:1000, AF1032, Affinity Biosciences, China), FN (1:1000, ab2413, Abcam, UK), COL I (1:1000, ab138492, Abcam, UK), PAR4 (1:1000, AF5371, Affinity Biosciences, China). The secondary antibodies used were as following: goat anti‐mouse (1:2000, L3032, Signalway Antibody Co., China) and goat anti‐Rabbit (1:2000, L3012, Signalway Antibody Co., China).
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6

Immunofluorescence Staining of Kidney Cells

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Immunofluorescence protocols and antibodies are detailed below. Frozen sections were used for immunofluorescence staining. Primary cultured tubular epithelial cells on Matrigel-coated coverslips and kidney sections were permeabilized with 0.2% Triton X-100 and fixed with 4% (vol/vol) paraformaldehyde for 5 min. Samples were blocked with 5% (vol/vol) normal goat serum in PBS and incubated with primary antibodies including FITC-conjugated anti-lotus LTL (FL-1321; Vector Labs; 1:1,000), goat anti-α-smooth muscle actin (SMA) (1:1,000, Abcam, ab21027), goat anti-kidney injury molecule-1 (Kim-1) (AF1817; R&D Systems; 1:500), rabbit anti-Pax2 (ab92547; Abcam; 1:500), and rabbit anti-vimentin (#5741; CST; 1:500). Secondary antibodies were either FITC- or Cy3-conjugated (Jackson ImmunoResearch) and incubated for 1 h. Nuclear counterstaining was performed using DAPI (Invitrogen). Images were obtained by confocal (Nikon C1 Eclipse; Nikon) or standard (Nikon Eclipse 90i; Nikon) microscopy.
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7

Quantification of KIM-1 Protein Expression

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Antibodies specifically against human KIM-1 (hKIM-1: AF1750, less than 0.1% cross-reactivity with recombinant mouse or rat KIM-1), rat KIM-1 (rKIM-1: AF3689, less than 1%cross-reactivity with recombinant hKIM-1), and mouse KIM-1 (mKIM-1: AF1817, less than 5% cross-reactivity with recombinant hKIM-1) were purchased from the R&D Systems (Minneapolis, MN). Antibodies against clathrin heavy chain and caveolin-1 were from Abcam Inc. (Boston, MA). Anti-β-actin antibody, chlorpromazine, and bovine serum albumin (BSA) were from Sigma–Aldrich (St. Louis, MO). In addition to antibodies against tight junction protein zonula occludens (ZO)-1, other reagents including CellLight Early Endosome Rab5a-GFP, Late Endosome Rab7a-red fluorescent protein (RFP), and lysosomal associated protein 1 (LAMP1)-GFP BacMam 2.0, BSA conjugated with fluorescein isothiocyanate (FITC-BSA, green) or Alexa Fluor 594 (AF594-BSA, red), Dextran (10kDa) conjugated with Alexa Fluor 594 (AF594-dextran, red), Lysotracker, and all tissue culture reagents were from Life Technologies (Carlsbad, CA).
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8

Immunofluorescence Analysis of Kidney Injury

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The kidneys were fixed for 24 h in 4% paraformaldehyde at 4 °C, incubated for 2 h in a 30% sucrose solution and embedded in optimal cutting temperature compound. Each embedded kidney was cut into 5-µm-thick sections and permeabilized with 0.4% Triton X-100 buffer. After being washed with PBS, the sections were blocked with 5% bovine serum albumin and incubated with primary antibodies overnight. The primary antibodies used were as follows: KIM-1 (AF1817, R&D), PCNA (ab92552, Abcam), α-SMA (ab7817, Abcam), fibronectin (ab2413, Abcam), and CD73 (AF 7638, Beyotime Biotechnology). To visualize the primary antibodies, the slides were stained with cyanine FITC- or Cy3-conjugated secondary antibodies (Beyotime Biotechnology, China) for 2 h at room temperature. Fluorescein labeled Lotus Tetragonolobus Lectin (LTL; marker of proximal tubule) were obtained from Vector labs (FLe1321, Vector Laboratories). Finally, 4′,6-diamidino-2-phenylindole (DAPI) was added (ab104139, Abcam). The stained slides were viewed under a Leica TCS-SL confocal microscope.
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9

Immunohistochemical Analysis of Kidney Proteins

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For immunohistochemistry, kidneys were embedded in paraffin and 5 μm thick sections prepared. After deparaffinization, tissue sections were quenched in 3% H2O2 (10 min, room temperature). Tissue sections were then blocked with an avidin/biotin blocking kit (Vector Laboratories, Burlingame, CA) followed by 5% goat or donkey serum. After 2 h of blocking at room temperature, tissues sections were incubated with primary antibodies to calbindin (ab49899, 1:500; abcam) or Kim-1 (AF1817, 1:500, R&D Systems) for 16 h at 4°C. Then, tissue sections were washed and incubated with biotinylated anti-rabbit (for calbindin staining) and anti-goat (for Kim-1 staining) secondary antibodies for 60 min at room temperature (Vector Laboratories, Burlingame, CA). Tissue sections were then stained using a 3,3′-diaminobenzidine peroxidase substrate kit (Vector Laboratories, Burlingame, CA). After counterstaining with hematoxylin, tissue sections were dehydrated and imaged by light microscopy (VS120-S5, Olympus, Center Valley, PA).
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10

Immunofluorescence Analysis of Oxidative Stress

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After fixation (4% paraformaldehyde for 10 min), permeabilization (0.3% Triton X-100 for 10 min), and blocking (1% BSA for 1 h), cells or sections were incubated with mouse anti-8-OHdG (sc-393871, Santa Cruz Biotechnology, Dallas, TX, USA), anti-mouse KIM-1 (AF1817, R&D Systems, Minneapolis, MN, USA), anti-mouse CD68 (ab201340, Abcam) and anti-human ACE2 (266699–1-Ig, Proteintech) overnight at 4 °C. After washing with PBS, slides were incubated with fluorescein isothiocyanate (FITC)-conjugated secondary antibody (A11017, Life Technologies, CA, USA) at 37 °C for 1 h. Nuclei were visualized by staining with DAPI. Digital images were captured using a confocal laser scanning microscope (Nikon).
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