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19 protocols using podocin

1

Histological Assessment of Kidney Fibrosis

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Right kidney tissue was fixed in 4% paraformaldehyde and embedded in paraffin for histologic analysis. Tissue sections (∼2 μm thick) were deparaffinized and stained with periodic acid–Schiff and Masson staining. The interstitial fibrotic area stained blue with Masson staining was quantitatively estimated using a color image analyzer (Keyence, Osaka, Japan). Tissues were also processed for electron microscopy (Jem-1400; Jeol, Tokyo, Japan) to assess ultrastructural alterations in the tubular mitochondria (6 (link)).
Deparaffinized kidney sections (4 μm thick) were heated in a microwave at 500 W, 15 min for antigen retrieval and then incubated overnight with antibody against KIM-1 (R&D Systems, Minneapolis, MN, USA), F4/80 (Bio-Rad, Hercules, CA, USA), collagen IV (Abcam), and podocin (Abcam). The primary antibody was detected using the Histofine Simple Stain Max Peroxidase Kit (Nichirei, Tokyo, Japan) and 3,3′-diaminobenzidine (MilliporeSigma). The percentages of Masson blue–positive area and positive staining for KIM-1, F4/80, and collagen IV were quantified using a Color Image Analyzer (Keyence).
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2

Quantifying Podocyte Protein Levels

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Cell and tissue lysates were prepared using RIPA buffer and equal protein amounts resolved on 10% SDS-PAGE gels before transfer to PVDF membranes. The membranes were then blocked and incubated with primary antibodies against nephrin (catalog no. Ab216341, Abcam, UK), beclin1 (catalog no. NB500-249 Novus, USA), podocin (catalog no. Ab181143 Abcam, UK), synaptopodin (catalog no. sc-515842 Santa Cruz, USA), desmin (catalog no. Ab8592 Abcam, UK), LC3 (catalog no. NB100-2220 Novus, USA) and Atg16L1 (catalog no. A1871; ABdonal) overnight. Protein bands levels were detected and analyzed using Image-Pro plus software with β-actin used as the internal reference.
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3

Immunofluorescence Staining of Podocyte Markers

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Antibodies used in this study were as follows: Goat anti-synaptopodin (Santa Cruz), Rabbit anti-YB-1 (Abcam), Rabbit anti-PP2A (Abcam), Alexa Fluor 488 donkey anti-rabbit IgG (Life Technologies), Alexa Fluor 594 donkey anti-mouse IgG (Life Technologies), BMP7 (Abcam), a-SAM (Abcam), Desmin (Proteintech), ZO-1 (Proteintech), WT-1 (Abcam), Nephrin (R&D Systems), Podocin (Abcam).
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4

Immunostaining Analysis of Glomerular Proteins

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The protocol was previously described in detail.63 (link) The following antibodies were used: ZO-1 (Invitrogen, Carlsbad, CA, USA), Desmin, podocin, WT-1, α-tublin, H3-Ser10, goat anti-rabbit IgG H&L (Alexa Fluor 594 or 488), goat anti-mouse IgG H&L (Alexa Fluor 488; Abcam, Cambridge, MA, USA), synaptopodin, and p-cadherin (Proteintech, Rosemont, IL, USA). The level of WT-1 was measured in 5 glomeruli per mouse, and ImageJ 10.2 software was used to measure the intensity of immunostaining in the glomeruli.
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5

Western Blot Analysis of Renal Proteins

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Protein expression in cells and renal tissues was detected by Western blotting as described previously44 (link). An equal amount of protein (50 μg) from each sample was separated by SDS-PAGE and transferred to PVDF membranes. After blocking in blocking buffer containing 5% skim milk for 30 min, the membranes were incubated with primary antibodies for HDAC9 (Santa Cruz Biotechnology, Santa Cruz, CA, USA), p-STAT3 (ab76315, Abcam, Cambridge, MA, USA), STAT3 (Abcam), Bcl-2 (Santa Cruz Biotechnology), Bax (Santa Cruz Biotechnology), cleaved Caspase 3 (Abcam), Nephrin (Abcam), Podocin (Abcam) and GAPDH (Cell signaling Technology, Danvers, MA, USA) separately at 4 °C overnight. The membranes were incubated with appropriate HRP-conjugated secondary antibody at room temperature for 1 h and signals were detected by using enhanced chemiluminescence (BioRad, Richmond, CA, USA). The blotting bands were quantified by densitometric analysis using Image J software (National Institutes of Health, Bethesda, MD, USA).
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6

Immunofluorescence Staining of Kidney Tissues

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The frozen sections (3 μm) of the kidney tissues were fixed with 4% paraformaldehyde for 15 min at room temperature. Podocytes cultured on coverslips were fixed with cold methanol/acetone for 10 min at room temperature. Following blocking with 10% donkey serum for 60 min at room temperature, the slides were immunostained with primary antibodies against FN (cat. no. ab2413; Abcam), podocin (cat. no. SAB4200810; Sigma-Aldrich; Merck KGaA), synaptopodin (synap; cat. no. SAB3500585; Sigma-Aldrich; Merck KGaA), LC3 (cat. no. ab192890; Abcam), p62 (cat. no. MA5-27800; Invitrogen; Thermo Fisher Scientific, Inc.) at 4°C; subsequently, they were incubated with a secondary antibodies against Alexa Fluor 647-conjugated donkey anti-rabbit IgG H&L antibody (1:700; cat. no. ab150075; Abcam), Alexa Fluor 647-conjugated goat anti-mouse IgG H&L antibody (1:700; cat. no. ab150115; Abcam), Alexa Fluor® 488-conjugated goat anti-mouse IgG H&L antibody (1:500; cat. no. ab150113; Abcam) for 2 h at 37°C. The counterstaining of the cell nuclei was performed using 4′,6-diamidino-2-phenylindole (Sigma-Aldrich; Merck KGaA) for 10 min at room temperature. The images were obtained using a confocal microscope at a magnification of ×400.
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7

Investigating Renal Fibrosis and Oxidative Stress Mechanisms

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The primary antibodies used in this study targeted SDF-1α (Novus Biologicals, Littleton, CO, United States), DPP-4 (Abcam, Cambridge, MA, United States), p-PKA (clone EP2606Y, Abcam, Cambridge, MA, United States), PKA (Cell Signaling, Danvers, MA, United States), NOX2 (clone EPR6991, Abcam, Cambridge, MA, United States), p-ERK1/2 (clone D13.14.4E, Cell Signaling, Danvers, MA, United States), ERK1/2 (Cell Signaling, Danvers, MA, United States), transforming growth factor-β1 (TGF-β1) (clone EPR18163, Abcam, Cambridge, MA, United States), podocin (Abcam, Cambridge, MA, United States), desmin (Abcam, Cambridge, MA, United States), nephrin (clone B-12, Santa Cruz Biotechnology Inc., Dallas, TX, United States), fibronectin (Proteintech, Rosemont, IL, United States), Fsp1 (clone EPR14639(2), Abcam, Cambridge, MA, United States), and α-SMA (clone 1A4, Abcam, Cambridge, MA, United States). ROS levels in renal tissue were tested with a dihydroethidium (DHE) assay kit (Beyotime, Jiangsu, China), and ROS levels in cells were examined with a DCFH-DA assay kit (Beyotime, Jiangsu, China). DPP-4 enzyme activity was tested using a DPP-4 assay kit (Enzo Life Sciences, Farmingdale, NY, United States).
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8

Immunoprecipitation and Western Blotting Protocol

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For western blotting, the detailed protocol was previously described.63 (link) For IP, podocytes were lysed in IP lysis buffer before being briefly sonicated, and the supernatants were incubated with antibodies and protein A/G-Sepharose beads after centrifugation. Finally, the immunocomplexes were washed and immunoblotted with antibodies. The following antibodies were used: ZO-1 (Invitrogen, Calrsbad, CA, USA), Desmin, podocin, Sox4, p21cip1/waf1 (Abcam, Cambridge, MA, USA), β-actin, synaptopodin, cdc2, CyclinB, p53, GFP-tag, hemagglutinin (HA)-tag, Myc-tag, FLAG tag, and HRP-conjugated goat anti-rabbit/mouse IgG (Proteintech, Rosemont, IL, USA).
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9

Protein Expression Analysis in Podocytes

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MCP5 podocytes were lysed in RIPA lysis buffer (Beyotime), supplemented with protease inhibitor mixture (Beyotime). The protein samples were separated by SDS-PAGE, followed by transferring to PVDF membranes (Millipore, USA) and blocked with 5% non-fat milk at room temperature for 2 h. The membranes were incubated overnight with primary antibodies at 4°C then incubated with secondary antibodies at room temperature for 2 h. The primary antibodies used for Western blotting were as follows: KLF9 (Abcam, 1:1000), Bcl-2 (CST, 1:1000), Bax (CST, 1:1000), (cleaved) caspase 3 (Abcam, 1:1000), synaptopodin (Abcam, 1:1000), podocin (Abcam, 1:1000) and GAPDH (Abcam, 1:1000). After washing with TBST, the membrane was incubated with appropriate secondary antibodies (Abcam, 1:10,000). Blots were visualized by the enhanced chemiluminescence system (Santa Cruz Biotechnology Inc., CA, USA).
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10

Immunohistochemical Analysis of Kidney Tissue

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Kidney tissues were fixed in 4% paraformaldehyde in PBS at 4°C. Tissues were incubated in 30% sucrose in PBS overnight at 4°C and mounted in OCT (Tissue-Tek, Tokyo, Japan) for sectioning [34 (link)]. After blocking, tissue sections were stained with the indicated primary antibodies and affinity-purified secondary antibodies-conjugated HRP (DAKO, Glostrup, Denmark). Primary antibodies used included antibodies against αSMA (Sigma), desmin (DAKO, Glostrup, Denmark), podocin (Abcam, Cambridge, MA, USA), and 8-hydroxy-2′-deoxyguanosine (8OHdG) (JaICA, Shizuoka, Japan). Quantitative analysis of afferent arterioles was performed as previously described [16 (link)]. For afferent arterioles, vessels with internal elastic lamina adjacent to glomeruli were selected. Arcuate arteries were identified by the location at the border of renal cortex and medulla. Areas positive for αSMA in the cross section of these vessels were quantitated using NanoZoomer (Hamamatsu Photonics, Hamamatsu, Japan) and Aperio ImageScope (Leica, Buffalo Grove, IL, USA). For quantification of desmin, podocin, and 8OHdG in the glomeruli, the percentage of positive area was determined as positive pixels per total pixels in a glomerulus using Image Scope software. For each rat, 20 glomeruli were randomly analyzed.
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