Materials. Dulbecco’s Modified Eagle’s Medium (DMEM) (Cat No. C11995500BT), trypsin–ethylenediaminetetraacetic acid (EDTA) (Cat No. 25200072), fetal bovine serum (FBS) (Cat No. 10091148), and bicinchoninic acid (BCA) (Cat No. 23227) protein assay were obtained from Thermo Fisher Scientific (Waltham, MA, USA). TUNEL Apoptosis Detection Kit I POD (Cat No. MK1025) was purchased from Boster Biological Technology Co., Ltd. (Pleasanton, CA, USA). Antigen repair solution (Cat No. MVS-0066) and UltraSensitive™ SP (mouse/rabbit) immunohistochemistry (IHC) (Cat No. KIT-9720) and DAB (Cat No. DAB-0031) kits were purchased from Maixin Biotechnology (Fuzhou, Fujian, China). Annexin V- AbFluorTM647 Apoptosis Detection Kit (Cat No. KTA0004), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Cat No. Abp57259) antibody, and Cell Counting Kit-8 (CCK8) (Cat No. KTA1020) were purchased from Abbkine (Wuhan, Hubei, China). Polyvinylidene fluoride (PVDF) membranes (Cat No. IPVH00010) was obtained Millipore (Billireca, MA, USA). Antibodies against p53 (Cat No. 10442-1-AP) and Bcl-2 (Cat No. 12789-1-AP) were acquired Proteintech (Rosemont, IL, USA). Antibodies against BaX (Cat No. 2772), cleaved-caspase-3 (Cat No. 9662), and cleaved-caspase-9 (Cat No. 9508) and secondary antibodies anti-mouse (Cat No. 7076) and anti-rabbit (Cat No. 7074) were obtained from Cell Signaling Technology (CST; Danvers, MA, USA). Angiotensin II (Ang II) (Cat No. ab120183) was acquired Abcam (Cambridge Science Park, Cambridge, UK). Quercetin (Cat No. Q4951-10G) was purchased from Sigma (St. Louis, MO, USA) with > 95% purity (HPLC).
Retrieval of quercetin and hypertensive renal injury targets. Hypertensive renal injury related targets were collected from the Genecards (https://www.GeneCards.org/) database33. Further, DisGeNET (https://www.disgenet.org/) database34 was employed for the extraction of targets via “kidney injury (KI) terms”. Quercetin targets were collected using Traditional Chinese Medicine Systems Pharmacology database (TCMSP, https://old.tcmsp-e.com/tcmsp.php)35 and Traditional Chinese Medicine database (TCMIP, http://www.tcmip.cn/TCMIP/index.php/)36.
Construction and analysis Protein-Protein Interactions (PPIs). To identify the potential hub targets of common genes between quercetin and hypertensive renal injury, the selected targets were introduced into the search tool for the retrieval of interacting genes (STRING) network platform (https://cn.string-db.org/, Version 11.5), followed by construction the PPI network. The interaction network of “quercetin- hypertensive renal injury -target” was further processed to realize visualization and screen out the core targets by using the software of Cytoscape (Version 3.8.2).
Functional annotation and pathways enrichment analyses. Based on the common genes, database of Database for Annotation Visualization and Integration Discovery (DAVID) was used to identify the enriched functional processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways37–38.
Molecular docking. As one of the most enriched apoptosis-associated target, TP53 was selected as candidate potential target of quercetin, which was performed by molecular docking. The 3D protein structures of TP53 (PDB: 8F2I)39 was retrieved from the protein databank (PDB)40. Moreover, pocket sites of TP53 was identified by implementing Prankweb online server. The 2D structures of quercetin was retrieved from the PubChem database41. Then, the energy of quercetin structures was minimized by using the Chem3D program (Version 20.0.0.41). Quercetin and protein structure were optimized and converted into PDBQT format for docking using AutoDockTools (Version 1.5.7), and the interaction between proteins and quercetin were visualized by PyMOL program (Version 2.5.4). The 2D- interacting residues of proteins to quercetin molecule were obtain by using Proteins Plus online server.
Animal experiments. Animal welfare and experimental protocols were performed in accordance with the ARRIVE guidelines and were applied in strict accordance with the Guide for the Care and Use of Laboratory Animals of the US National Institutes of Health. The animal experimental protocol of this research was approved by the Animal Use Committee of the Fujian University of Traditional Chinese Medicine (Fuzhou, Fujian, China; Ethical code: FJTCM IACUC 2022112). Male C57BL/6 mice (weight, 28 ± 1 g; age, 8 weeks) were obtained from SLAC Laboratory Animal Technology Co., Ltd. (Shanghai, China). All animals were subjected to a 12 h light dark cycle under specific pathogen free conditions at constant temperature (24 ± 2°C) and relative humidity (50–60%). The mice were randomly divided into four groups (n = 6 each group): Control, Ang II, Ang II + Quercetin-L, and Ang II + Quercetin-H groups. The mice in the Ang II, Ang II + Quercetin-L, and Ang II + Quercetin-H groups were infused with Ang II (500 ng/kg/min), and those in the control group were infused with saline for 4 weeks by subcutaneously implanting micro osmotic pumps. The mice in the Ang II + Quercetin-L and Ang II + Quercetin-H groups intragastrically administrated with quercetin daily (2.5 mg/kg/day and 5 mg/kg/day, respectively; 200 µL for each mouse), and those in the control and Ang II groups were intragastrically administrated with equal volumes of double distilled water for 4 weeks.
hmatoxylin-eosin (H&E) staining. The collected renal tissues were fixed at room temperature for 48 h using a 4% paraformaldehyde solution, followed by dehydrated via an alcohol gradient and embedded into paraffin. Then tissues were sectioned into 4-µm thick slices and stained with hematoxylin for 1 min and eosin for 2 sec at room temperature. The stained sliced tissues were imaged with optical microscope using 400x magnification (Leica DM4000B, Wetzlar, Germany).
RNA sequencing. The collected renal tissues were stored in RNA later® (Takara, Beijing, China) for 1 h at room temperature and then was stored at -20°C for prolonged time. RNA sequencing was performed by the Capital Bio Technology (Beijing, China). Briefly, the NEBNext Ultra RNA Library Prep Kit for Illumina was used to prepare a sequencing library (NEB, Ipswich, MA, USA) as per the guidelines of according to the manufacturer, and oligo(dT) beads were used to purify mRNA from total RNA. Total RNA concentration and quality were determined using the Qubit 3.0 and Agilent 2100. Bioanalyzers were used for the determination of quantity and quality of extracted total RNA. Then, library was appropriately quantified using the KAPA quantitative kit (KAPA Biosystem, Wilmington, MA, USA). As stated in earlier studies, raw data were processed and differential expressed transcripts were identified42. Moreover, analyses of gene ontology (GO) processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were performed to identify enriched functional processes and pathways.
Immunohistochemical (IHC) analysis. IHC was used to detect the protein expression of p53, BaX, Bcl-2, cleaved-caspase-3, and cleaved-caspase-9 in renal tissues of mice from each group. Briefly, the renal tissues were cut into 4-µm sections. After rehydration with gradient ethanol, the tissues were treated with a 0.01-M citrate-based antigen retrieval solution for 10 min at a high temperature, and then incubated with the primary antibodies for p53 (1:200), BaX (1:100), Bcl-2 (1:200), cleaved caspase-3 (1:200), or cleaved caspase-9 (1:200) at 4°C overnight. After washed with PBS, slides were incubated with secondary antibody coated with biotinylated beads, and the conjugated with streptavidin (horseradish peroxidase-labeled). These slides were stained with diaminobenzidine as chromogen and suspended with diluted Harris hematoxylin. The images were taken using optical microscope (Leica DM4000B, Wetzlar, Germany) at a magnification of 400x.
Terminal deoxynucleotidyl transferase (TdT) dUTP nick-end labeling (TUNEL) assay. The renal tissues were sliced into 4-µm thick sections and staining was performed via TUNEL kit, as directed by the producer. Briefly, after that sections were deparaffinized and were incubated with Proteinase K for 15 min at 37°C, and then washed with 1× Tris-buffered saline (TBS) for three times. Slides were coated with Labeling Reaction Mix at 37°C for 2 h, then rinsed thrice with 1× TBS and incubated with block solution, followed by incubation of diaminobenzidine at room temperature for 30 min and diluted Harris hematoxylin. The images were taken under an optical microscope (Leica, Wetzlar, Germany) at 400x magnification. Image J was used to identify the percentage of positive area relative to the total area.
Cell culture and quercetin treatment. NRK-52E cells were obtained from BeNa (Beijing, China). And was seeded into DMEM contains 10% FBS, 100-µg/mL streptomycin, and 100-units/mL penicillin at 37°C with 5% CO2 (humified air). NRK-52E cells was stimulated with Ang II (1µM) and were treated with or without quercetin (20 µM and 40 µM) for 48 h. The cells in the control group were treated with an equal volume of dimethyl sulfoxide for 48 h.
Cell viability analysis. The NRK-52E cells were seeded in 96-well plates in suspension (100 µL) at a density of 2 × 104 cells/mL overnight at 37°C and 5% CO2, they were incubated with indicated concentrations of quercetin for 48 h. At the end of treatment, CCK-8 reagent (10 µL) was supplemented into each well and incubated in dark for additional 2 h at 37°C. A microplate reader (Multiskan FC; Thermo Fisher Scientific) was used to observe absorbance at 450 nm. The viability of untreated cells was considered at 100%.
Annexin V staining. Annexin V apoptosis kit with propidium iodide (PI) was used to identify cellular apoptosis. The NRK-52E cells (8 × 104 cells/well) were seeded into six-well plates and incubated for 24 h, and then starved with DMEM serum free media for 12 h and were then treated with Ang II (1 µM) and without or with quercetin (20 µM or 40 µM) in minimal medium (0.5% FBS) for 24 h. After treatment, cells were washed using PBS and collected with trypsin (without EDTA). The centrifuged supernatant was discarded and pellet propagated in 1x binding buffer (5 µL annexin V-fluorescein isothiocyanate and 2 µL PI) and then incubated for 15 min. Fluorescence-activated cell sorting (BD, Franklin Lakes, NJ, USA) analysis was used to identify and quantify cell apoptosis.
Western blotting. The collected cells were lysed with cell lysis buffer contains protease inhibitor and phenylmethylsulfonyl fluoride (PMSF) on ice for 30 min. The lysed cells were centrifuged at 14,000 g for 20 min at 4°C.The protein concentration was determined using BCA kit. The total 50 µg of protein from each group was separated on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene fluoride (PVDF) membranes, and were blocked using 5% non-fat milk in TBST (TBS + 0.1% Tween) at 37ºC for 2 h. Furthermore, the membranes were incubated with primary antibodies, including rabbit anti-BaX (1:1000), Bcl-2 (1:1000), p53 (1:1000), cleaved-caspase-3 (1:1000), GAPDH (1:5000), or mouse anti- cleaved-caspase-9 (1:1000) 4ºC overnight, followed by incubation of secondary anti-mouse/rabbit IgG (1:5000) for 2 h at room temperature and determination of protein expression by advanced chemiluminescence detection ChemiDoc XRS and Imaging System (Bio-Rad Laboratories, Inc., Hercules, CA, USA). Image J was used to calculate the optical density of each protein band.
Statistical analysis. The results were presented as the mean value ± standard deviation (SD). One-way analysis of variance was used to compare the differences among three or more groups when the data were normally distributed, followed by Bonferroni analysis when the variance was chi-square, or Games Howell analysis when the variance was not chi-square. Statistical significance was assigned to differences with p values < 0.05. The Statistical Package for the Social Sciences, version 25.0 (IBM Corp., Chicago, IL, USA) was used for all statistical analyses.