Bioinformatics analysis of potential key ferroptosis-related genes involved in tubulointerstitial injury in patients with diabetic nephropathy

References

• Alicic RZ, Rooney MT, Tuttle KR. Diabetic kidney disease: challenges, progress, and possibilities. Clin J Am Soc Nephrol. 2017;12(12):1–13.
   PubMed Web of Science ®Google Scholar
• Gilbert RE. Proximal tubulopathy: prime mover and key therapeutic target in diabetic kidney disease. Diabetes. 2017;66(4):791–800.
   PubMed Web of Science ®Google Scholar
• Bayır H, Anthonymuthu TS, Tyurina YY, et al. Achieving life through death: redox biology of lipid peroxidation in ferroptosis. Cell Chem Biol. 2020;27(4):387–408.
   PubMed Web of Science ®Google Scholar
• Xu F, Guan Y, Xue L, et al. The roles of ferroptosis regulatory gene SLC7A11 in renal cell carcinoma: a multi-omics study. Cancer Med. 2021;10(24):9078–9096.
   PubMed Web of Science ®Google Scholar
• Xu F, Wang H, Pei H, et al. SLC1A5 prefers to play as an accomplice rather than an opponent in pancreatic adenocarcinoma. Front Cell Dev Biol. 2022;10:800925.
   PubMed Web of Science ®Google Scholar
• Wang Y, Bi R, Quan F, et al. Ferroptosis involves in renal tubular cell death in diabetic nephropathy. Eur J Pharmacol. 2020;888:173574.
   PubMed Web of Science ®Google Scholar
• Kim S, Kang S-W, Joo J, et al. Characterization of ferroptosis in kidney tubular cell death under diabetic conditions. Cell Death Dis. 2021;12(2):160.
   PubMed Web of Science ®Google Scholar
• Feng X, Wang S, Sun Z, et al. Ferroptosis enhanced diabetic renal tubular injury via HIF-1α/HO-1 pathway in db/db mice. Front Endocrinol (Lausanne). 2021;12:626390.
   PubMed Web of Science ®Google Scholar
• Wang W-J, Jiang X, Gao C-C, et al. Salusin‑β participates in high glucose‑induced HK‑2 cell ferroptosis in a nrf‑2‑dependent manner. Mol Med Rep. 2021;24(3):674.
   PubMed Web of Science ®Google Scholar
• Li S, Zheng L, Zhang J, et al. Inhibition of ferroptosis by up-regulating Nrf2 delayed the progression of diabetic nephropathy. Free Radic Biol Med. 2021;162:435–449.
   PubMed Web of Science ®Google Scholar
• Chen X, et al. Ferroptosis in infection, inflammation, and immunity. J Exp Med. 2021;218(6):e20210518.
   PubMed Web of Science ®Google Scholar
• Woroniecka KI, Park ASD, Mohtat D, et al. Transcriptome analysis of human diabetic kidney disease. Diabetes. 2011;60(9):2354–2369.
   PubMed Web of Science ®Google Scholar
• Grayson PC, Eddy S, Taroni JN, et al. Metabolic pathways and immunometabolism in rare kidney diseases. Ann Rheum Dis. 2018;77(8):1226–1233.
   PubMed Web of Science ®Google Scholar
• Zhou N, Bao J. FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations. Database. 2020;2020:baaa021.
   PubMedGoogle Scholar
• Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
   PubMed Web of Science ®Google Scholar
• The gene ontology (GO) project in 2006. Nucleic Acids Res. 2006;34(Database issue):D322–6.
   PubMedGoogle Scholar
• Kanehisa M, Goto S, Sato Y, et al. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40(Database issue):D109–14.
   PubMed Web of Science ®Google Scholar
• Griss J, Viteri G, Sidiropoulos K, et al. ReactomeGSA - Efficient Multi-Omics comparative pathway analysis. Mol Cell Proteomics. 2020;19(12):2115–2125.
   PubMed Web of Science ®Google Scholar
• Szklarczyk D, Gable AL, Nastou KC, et al. The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res. 2021;49(D1):D605–d612.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–2504.
   PubMed Web of Science ®Google Scholar
• Chin C-H, Chen S-H, Wu H-H, et al. cytoHubba: identifying hub objects and Sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl 4):S11.
   PubMed Web of Science ®Google Scholar
• Ma H, He Z, Chen J, et al. Identifying of biomarkers associated with gastric cancer based on 11 topological analysis methods of CytoHubba. Sci Rep. 2021;11(1):1331.
   PubMed Web of Science ®Google Scholar
• Eddy S, Mariani LH, Kretzler M. Integrated multi-omics approaches to improve classification of chronic kidney disease. Nat Rev Nephrol. 2020;16(11):657–668.
   PubMed Web of Science ®Google Scholar
• Zeng D, Ye Z, Shen R, et al. IOBR: multi-Omics Immuno-Oncology biological research to decode tumor microenvironment and signatures. Front Immunol. 2021;12:687975.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, et al. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 2015;12(5):453–457.
   PubMed Web of Science ®Google Scholar
• Bardou P, Mariette J, Escudié F, et al. Jvenn: an interactive venn diagram viewer. BMC Bioinformatics. 2014;15(1):293.
   PubMed Web of Science ®Google Scholar
• Sharma K, Karl B, Mathew AV, et al. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol. 2013;24(11):1901–1912.
   PubMed Web of Science ®Google Scholar
• Nishi H, Nangaku M. Podocyte lipotoxicity in diabetic kidney disease. Kidney Int. 2019;96(4):809–812.
   PubMed Web of Science ®Google Scholar
• Duni A, et al. Oxidative stress in the pathogenesis and evolution of chronic kidney disease: untangling Ariadne’s thread. Int J Mol Sci. 2019;20(15):3711.
   PubMed Web of Science ®Google Scholar
• Zheng J, Conrad M. The metabolic underpinnings of ferroptosis. Cell Metab. 2020;32(6):920–937.
   PubMed Web of Science ®Google Scholar
• Chen P-H, Wu J, Ding C-KC, et al. Kinome screen of ferroptosis reveals a novel role of ATM in regulating iron metabolism. Cell Death Differ. 2020;27(3):1008–1022.
   PubMed Web of Science ®Google Scholar
• Yang WS, et al. Peroxidation of polyunsaturated fatty acids by lipoxygenases drives ferroptosis. Proc Natl Acad Sci U S A. 2016;113(34):E4966–75.
   PubMed Web of Science ®Google Scholar
• Ke Q, Costa M. Hypoxia-inducible factor-1 (HIF-1). Mol Pharmacol. 2006;70(5):1469–1480.
   PubMed Web of Science ®Google Scholar
• Yuan S, et al. Sorafenib attenuates liver fibrosis by triggering hepatic stellate cell ferroptosis via HIF-1α/SLC7A11 pathway. Cell Prolif. 2022;55(1):e13158.
   PubMed Web of Science ®Google Scholar
• Li A, Peng R, Sun Y, et al. LincRNA 1700020I14Rik alleviates cell proliferation and fibrosis in diabetic nephropathy via miR-34a-5p/Sirt1/HIF-1α signaling. Cell Death Dis. 2018;9(5):461.
   PubMedGoogle Scholar
• Ediriweera MK, Tennekoon KH, Samarakoon SR. Role of the PI3K/AKT/mTOR signaling pathway in ovarian cancer: biological and therapeutic significance. Semin Cancer Biol. 2019;59:147–160.
   PubMed Web of Science ®Google Scholar
• Su W-Y, Li Y, Chen X, et al. Ginsenoside Rh1 improves type 2 diabetic nephropathy through AMPK/PI3K/Akt-Mediated inflammation and apoptosis signaling pathway. Am J Chin Med. 2021;49(5):1215–1233.
   PubMedGoogle Scholar
• Sun L, Wang H, Xu D, et al. Lapatinib induces mitochondrial dysfunction to enhance oxidative stress and ferroptosis in doxorubicin-induced cardiomyocytes via inhibition of PI3K/AKT signaling pathway. Bioengineered. 2022;13(1):48–60.
   PubMed Web of Science ®Google Scholar
• Sun QY, Zhou HH, Mao XY. Emerging roles of 5-Lipoxygenase phosphorylation in inflammation and cell death. Oxid Med Cell Longev. 2019;2019:2749173.
   PubMed Web of Science ®Google Scholar
• Gaschler MM, Stockwell BR. Lipid peroxidation in cell death. Biochem Biophys Res Commun. 2017;482(3):419–425.
   PubMed Web of Science ®Google Scholar
• Dixon SJ, Lemberg KM, Lamprecht MR, et al. Ferroptosis: an iron-dependent form of nonapoptotic cell death. Cell. 2012;149(5):1060–1072.
   PubMed Web of Science ®Google Scholar
• Liu Y, Wang W, Li Y, et al. The 5-Lipoxygenase inhibitor zileuton confers neuroprotection against glutamate oxidative damage by inhibiting ferroptosis. Biol Pharm Bull. 2015;38(8):1234–1239.
   PubMed Web of Science ®Google Scholar
• Karuppagounder SS, Alin L, Chen Y, et al. N-acetylcysteine targets 5 lipoxygenase-derived, toxic lipids and can synergize with prostaglandin E(2) to inhibit ferroptosis and improve outcomes following hemorrhagic stroke in mice. Ann Neurol. 2018;84(6):854–872.
   PubMed Web of Science ®Google Scholar
• Proneth B, Conrad M. Ferroptosis and necroinflammation, a yet poorly explored link. Cell Death Differ. 2019;26(1):14–24.
   PubMed Web of Science ®Google Scholar
• Chen X, Xie H, Liu Y, et al. Interference of ALOX5 alleviates inflammation and fibrosis in high glucose‑induced renal mesangial cells. Exp Ther Med. 2023;25(1):34.
   PubMed Web of Science ®Google Scholar
• Galkina E, Ley K. Leukocyte recruitment and vascular injury in diabetic nephropathy. J Am Soc Nephrol. 2006;17(2):368–377.
   PubMed Web of Science ®Google Scholar
• Banerjee M, Vats P. Reactive metabolites and antioxidant gene polymorphisms in type 2 diabetes mellitus. Redox Biol. 2014;2:170–177.
   PubMed Web of Science ®Google Scholar
• Yi J, Zhu J, Wu J, et al. Oncogenic activation of PI3K-AKT-mTOR signaling suppresses ferroptosis via SREBP-mediated lipogenesis. Proc Natl Acad Sci U S A. 2020;117(49):31189–31197.
   PubMed Web of Science ®Google Scholar
• Yang WS, SriRamaratnam R, Welsch ME, et al. Regulation of ferroptotic cancer cell death by GPX4. Cell. 2014;156(1-2):317–331.
   PubMed Web of Science ®Google Scholar
• Zhao Y, Fu B, Chen P, et al. Activated mesangial cells induce glomerular endothelial cells proliferation in rat anti-Thy-1 nephritis through VEGFA/VEGFR2 and Angpt2/Tie2 pathway. Cell Prolif. 2021;54(6):e13055.
   PubMed Web of Science ®Google Scholar
• Kim I, Moon SO, Kim SH, et al. Vascular endothelial growth factor expression of intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), and E-selectin through nuclear factor-kappa B activation in endothelial cells. J Biol Chem. 2001;276(10):7614–7620.
   PubMed Web of Science ®Google Scholar
• Dixon SJ, Patel DN, Welsch M, et al. Pharmacological inhibition of cystine-glutamate exchange induces endoplasmic reticulum stress and ferroptosis. Elife. 2014;3:e02523.
   PubMed Web of Science ®Google Scholar
• Kapralov AA, Yang Q, Dar HH, et al. Redox lipid reprogramming commands susceptibility of macrophages and microglia to ferroptotic death. Nat Chem Biol. 2020;16(3):278–290.
   PubMed Web of Science ®Google Scholar
• Muri J, Thut H, Bornkamm GW, et al. B1 and marginal zone B cells but not follicular B2 cells require Gpx4 to prevent lipid peroxidation and ferroptosis. Cell Rep. 2019;29(9):2731–2744.e4.
   PubMed Web of Science ®Google Scholar
• Drijvers JM, Gillis JE, Muijlwijk T, et al. Pharmacologic screening identifies metabolic vulnerabilities of CD8(+) T cells. Cancer Immunol Res. 2021;9(2):184–199.
   PubMed Web of Science ®Google Scholar
• Matsushita M, Freigang S, Schneider C, et al. T cell lipid peroxidation induces ferroptosis and prevents immunity to infection. J Exp Med. 2015;212(4):555–568.
   PubMed Web of Science ®Google Scholar