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8 protocols using anti kim 1

1

Immunophenotyping Antibody Panel for Mice

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Cisplatin was purchased from Sigma-Aldrich (St. Louis, MO, USA). Anti-CD4 (RM4-5) APC/FITC/Pacific blue and anti-TCRβ (H57-597) FITC/BV421, CD45 (30-F11) APC-Cy7/BUV395, anti-CD8α (53 ± 6.7) PerCP-Cy5.5/APC-fire750, were purchased from BD Biosciences. Biotin-conjugated anti-CD16/32 (2.4G2) was purchased from BioLegend. Anti-AGTR2, anti-TIMP-1, and anti-KIM-1 antibodies were purchased from R&D systems (MN, USA). Anti-GAPDH and anti-Bcl-2 antibodies were from Santa Cruz Biotechnology, Inc. (CA, USA). Anti-calbindin antibody was purchased from Cell Signaling Technology, Inc. (MA, USA).
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2

Immunohistochemical Analysis of CD36, KIM-1, and SREBP

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The paraffin-embedded sections were deparaffinized before staining. Endogenous peroxidase activity was blocked by 3% hydrogen peroxide for 10 min before treatment with antibodies of anti-CD36 (Taiclone, Taipei, Taiwan), anti-KIM-1 (R&D Systems, Minneapolis, MN, USA) and anti-SREBP (Abcam, Cambridge, UK). Thereafter, horseradish peroxidase recombinant fusion protein anti-rabbit IgG (1:500) was applied. Finally, DAB chromogen (ScyTeck Laboratories, West Logan, UT, USA) was used and images were acquired using a fluorescent microscope (IX81, Olympus, Tokyo, Japan).
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3

Immunohistochemical Analysis of Kidney Injury

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Immunohistochemistry was performed in 1‐μm‐thick paraffin sections of methyl Carnoy's‐fixed specimens using the Vectastain Avidin/Biotin System (Vector Laboratories, Burlingame, CA), as described before 25. Renal tissues were stained using the following primary antibodies: anti‐human Col1A1 (Southern Biotech, Birmingham, AL), anti‐Kim1 (R&D systems, USA), anti‐mouse F4/80 (Serotec, Düsseldorf, Germany), anti‐proliferating cell nuclear antigen (PCNA) (Leinco Technologies, St. Louis, MO) and anti‐Ly6G (BD Biosciences, San Jose, CA). Negative controls for the immunohistochemical procedures consisted of substitution of the primary antibody with non‐immune IgG. Quantification of Ly6G was described before 4. Total number of PCNA‐stained nuclei in renal tubuli was counted in 25 randomly selected fields at ×200 magnification. For staining quantification of collagen and F4/80, 20 consecutive images of renal cortex were taken per section. The percentage of the positively stained area was extracted for intensity using ImageJ software (Wayne Rasband, NIH) and a mean area was calculated. Periodic acid–Schiff (PAS) staining was performed as described before 25, and the tubular injury was scored on a scale of 0–4: 0 = none; 1 = 0–25%; 2 = 25–50%; 3 = 50–75%; 4 = more than 75%. The total score is the calculated average of all tubular scores.
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4

Kidney Protein Isolation and Western Blotting

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Excised rat kidneys were washed with PBS, and homogenized 10 times in a Potter-Elvehjem glass homogenizer with a tight pestle containing 1× lysis buffer (Cell Signaling Technology) with protease inhibitor (Sigma) on ice before centrifugation (30 min, 14,000 × g). The resulting supernatants were mixed with Laemmli gel loading buffer containing 10% SDS and 200 mM DTT, followed by boiling. For western blotting urine samples, equal volume of urine samples were mixed with 6× Laemmli buffer containing 10% SDS and 200 mM DDT, followed by boiling. SDS-PAGE, unless otherwise stated, occurred in 10–12% gels that were blotted onto nitrocellulose membranes (Bio-Rad) and blocked with 5% nonfat dry milk (Bio-Rad). Detection used anti-CYP2E1 (Abcam, 1:2000), anti-myeloperoxidase (Abcam, 1:2000), anti-KIM-1 (R&D Systems, 1:2000), anti-NGAL (Abcam, 1:2000), or anti-albumin (Santa Cruz, 1:10000) antibodies (Abcam, 1:5000) incubated overnight at 4°C. The conjugates were then ligated by HRP-conjugated anti-rabbit (1:5000) or anti-mouse (1:10000) or anti-goat (1:20000) antibody before detection with Amersham Biosciences ECL Prime. Blots were reprobed with anti-β-actin (Santa Cruz Biotechnology).
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5

Cytokine Profiling in Immune Cell Activation

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Recombinant human IFN-γ, IL-17, IL-22, IL-23, TNF-α, IL-6 and IL-8 were purchased from R&D Systems (Minneapolis, MN). Anti-human IFN-γ, anti-IL-17, anti- IL-22, anti-IL-23, anti-IL-6, anti-IL-8 and anti-KIM-1 antibodies were purchased from R&D Systems. Anti-CD3 and anti-CD28 were obtained from BD Biosciences (San Diego, CA), and 1,25(OH)2D3 was obtained from Sigma (St. Louis, MO).
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6

Immunohistochemical Analysis of Renal Injury

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Paraffin-embedded renal sections (4 μm) were deparaffinized in xylene, rehydrated in graded alcohol and blocked with 10% goat serum for 30 min. Mouse monoclonal anti-GSDMD (1:50, Santa), mouse monoclonal anti-4-HNE (1:100, R&D), rabbit polyclonal anti-MLKL, goat polyclonal anti-KIM-1 (1:800, R&D), rabbit polyclonal anti-Ki67 (1:100, Abcam), rabbit polyclonal anti-ACSL4 (1:200, Abcam), rabbit polyclonal anti-CD3 (1:100, Dako), rabbit polyclonal anti-ly6G (1:100, Abcam), rat polyclonal anti-F4/80 (1:50, Abcam), and rabbit polyclonal anti-Sox9 (1:100, Abcam) primary antibodies were incubated at 4 °C overnight and subsequently visualized with HRP-conjugated secondary antibody for IHC and fluorescently labeled secondary antibodies for IF. Staining was carefully quantified in each slide by capturing 15 randomly chosen fields in a blind manner, and the data were analyzed using Image Pro Plus software (Media Cybernetics, USA).
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7

Urine Biomarker Quantification Protocol

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21 μL of urine from each patient were separated by acrylamide electrophoresis. Proteins were transferred to an Immobilon-P Transfer Membrane (Millipore, Madrid, Spain) and incubated with the following primary antibodies: (1) Anti KIM-1 (R&D Systems, Minneapolis, MN, USA); (2) TCP1-eta antibody (Novus Biologicals, Littleton, CO, USA); (3) Reg3A (R&D Systems, Minneapolis, MN, USA); (4) GM2AP [our polyclonal antibody, described in49 (link); (5) gelsolin (Santa Cruz Biotechnology, Dallas, TX, USA); and (6) FABP1 (SAB Signalway Antibody, College Park, MD, USA). Then, membranes were incubated with horseradish peroxidase-conjugated secondary antibodies and chemiluminescent detection (Immobilon Western Chemiluminescent HRP Substrate kit; Millipore, Madrid, Spain) with photographic films (Kodak, Madrid, Spain). Bands were quantified with the Scion Image software (Scion Corporation, Frederick, Maryland, USA), and normalized to the signal of a positive control (as arbitrary units), loaded in all gels. The positive control consisted of a urine sample from a designated AKI patient with increased biomarker excretion, used as trans normalization control in all experiments.
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8

Antibody Sources and Mitochondrial ROS

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The primary antibodies used in this study were purchased from the following sources: anti-Kim-1 (R&D Systems, USA); anti-TNF-α, anti-TOM20, anti-Bax (Cell Signaling Technology, Beverly, MA, USA); anti-8-OHdG, anti-dsDNA, anti-CD68 (Abcam, USA); anti-TFAM, anti-GAPDH, anti-Lon, anti-NGAL (ABclonal Biotech Co., Ltd., Cambridge, MA, USA); anti-p53, anti-ICAM, anti-ATP5a-1 (Proteintech, Rosemont, IL, USA). Mito-Tempo (MT, an mtROS scavenger) was purchased from Santa Cruz Biotechnology (CA, USA) and was dissolved in DMSO as a stock solution.
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