Integrated Analysis of Ferroptosis and Immunity-Related Genes Associated with Diabetic Kidney Disease

References

• Shlisky J, Bloom DE, Beaudreault AR, et al. Nutritional considerations for healthy aging and reduction in age-related chronic disease. Adv Nutr. 2017;8(1):17–26. doi:10.3945/an.116.013474
   PubMed Web of Science ®Google Scholar
• Zhang L, Long J, Jiang W, et al. Trends in chronic kidney disease in China. N Engl J Med. 2016;375(9):905–906. doi:10.1056/NEJMc1602469
   PubMed Web of Science ®Google Scholar
• Selby NM, Taal MW. An updated overview of diabetic nephropathy: diagnosis, prognosis, treatment goals and latest guidelines. Diabetes Obes Metab. 2020;22(Suppl 1):3–15. doi:10.1111/dom.14007
   PubMed Web of Science ®Google Scholar
• Yu Y, Yan Y, Niu F, et al. Ferroptosis: a cell death connecting oxidative stress, inflammation and cardiovascular diseases. Cell Death Discov. 2021;7(1):193. doi:10.1038/s41420-021-00579-w
   PubMed Web of Science ®Google Scholar
• Feng X, Wang S, Sun Z, et al. Ferroptosis enhanced diabetic renal tubular injury via HIF-1alpha/HO-1 pathway in db/db Mice. Front Endocrinol. 2021;12:626390. doi:10.3389/fendo.2021.626390
   PubMed Web of Science ®Google Scholar
• Kim S, Kang SW, Joo J, et al. Characterization of ferroptosis in kidney tubular cell death under diabetic conditions. Cell Death Dis. 2021;12(2):160. doi:10.1038/s41419-021-03452-x
   PubMed Web of Science ®Google Scholar
• Luo X, Gong HB, Gao HY, et al. Oxygenated phosphatidylethanolamine navigates phagocytosis of ferroptotic cells by interacting with TLR2. Cell Death Differ. 2021;28(6):1971–1989. doi:10.1038/s41418-020-00719-2
   PubMed Web of Science ®Google Scholar
• Kao JK, Wang SC, Ho LW, et al. M2-like polarization of THP-1 monocyte-derived macrophages under chronic iron overload. Ann Hematol. 2020;99(3):431–441. doi:10.1007/s00277-020-03916-8
   PubMed Web of Science ®Google Scholar
• Lu K, Dong S, Xia T, Mao L. Kupffer cells degrade (14)C-labeled few-layer graphene to (14)CO(2) in liver through erythrophagocytosis. ACS Nano. 2021;15(1):396–409. doi:10.1021/acsnano.0c07452
   PubMed Web of Science ®Google Scholar
• West AP, Brodsky IE, Rahner C, et al. TLR signalling augments macrophage bactericidal activity through mitochondrial ROS. Nature. 2011;472(7344):476–480. doi:10.1038/nature09973
   PubMed Web of Science ®Google Scholar
• Ni L, Cao J, Yuan C, Zhou LT, Wu X. Expression of ferroptosis-related genes is correlated with immune microenvironment in diabetic kidney disease. Diabetes Metab Syndr Obes. 2022;15:4049–4064. doi:10.2147/DMSO.S388724
   PubMed Web of Science ®Google Scholar
• Ma J, Li C, Liu T, et al. Identification of markers for diagnosis and treatment of diabetic kidney disease based on the ferroptosis and immune. Oxid Med Cell Longev. 2022;2022:9957172. doi:10.1155/2022/9957172
   PubMed Web of Science ®Google Scholar
• Jiang P, Yang F, Zou C, et al. The construction and analysis of a ferroptosis-related gene prognostic signature for pancreatic cancer. Aging. 2021;13(7):10396–10414. doi:10.18632/aging.202801
   PubMedGoogle Scholar
• Hsieh CH, Hsieh HC, Shih FS, et al. An innovative NRF2 nano-modulator induces lung cancer ferroptosis and elicits an immunostimulatory tumor microenvironment. Theranostics. 2021;11(14):7072–7091. doi:10.7150/thno.57803
   PubMed Web of Science ®Google Scholar
• Li Z, Rong L. Cascade reaction-mediated efficient ferroptosis synergizes with immunomodulation for high-performance cancer therapy. Biomater Sci. 2020;8(22):6272–6285. doi:10.1039/d0bm01168a
   PubMed Web of Science ®Google Scholar
• Gu Z, Liu T, Liu C, et al. Ferroptosis-strengthened metabolic and inflammatory regulation of tumor-associated macrophages provokes potent tumoricidal activities. Nano Lett. 2021;21(15):6471–6479. doi:10.1021/acs.nanolett.1c01401
   PubMed Web of Science ®Google Scholar
• Woroniecka KI, Park AS, Mohtat D, Thomas DB, Pullman JM, Susztak K. Transcriptome analysis of human diabetic kidney disease. Diabetes. 2011;60(9):2354–2369. doi:10.2337/db10-1181
   PubMed Web of Science ®Google Scholar
• Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013;41(Database issue):D991–D995. doi:10.1093/nar/gks1193
   PubMed Web of Science ®Google Scholar
• Chodary Khameneh S, Razi S, Shamdani S, Uzan G, Naserian S. Weighted correlation network analysis revealed novel long non-coding RNAs for colorectal cancer. Sci Rep. 2022;12(1):2990. doi:10.1038/s41598-022-06934-w
   PubMed Web of Science ®Google Scholar
• Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–425. doi:10.1016/j.cels.2015.12.004
   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. doi:10.1093/database/baaa021
   Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
   PubMed Web of Science ®Google Scholar
• Zhou M, Hu L, Zhang Z, Wu N, Sun J, Su J. Recurrence-associated long non-coding RNA signature for determining the risk of recurrence in patients with colon cancer. Mol Ther Nucleic Acids. 2018;12:518–529. doi:10.1016/j.omtn.2018.06.007
   PubMedGoogle Scholar
• Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287. doi:10.1089/omi.2011.0118
   PubMed Web of Science ®Google Scholar
• Wakonig B, Auersperg AMI, O’Hara M. String-pulling in the Goffin’s cockatoo (Cacatua goffiniana). Learn Behav. 2021;49(1):124–136. doi:10.3758/s13420-020-00454-1
   PubMed Web of Science ®Google Scholar
• Chin CH, Chen SH, Wu HH, Ho CW, Ko MT, Lin CY. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol. 2014;8(Suppl 4):S11. doi:10.1186/1752-0509-8-S4-S11
   PubMed Web of Science ®Google Scholar
• Wang W, Zhang J, Wang Y, Xu Y, Zhang S. Identifies microtubule-binding protein CSPP1 as a novel cancer biomarker associated with ferroptosis and tumor microenvironment. Comput Struct Biotechnol J. 2022;20:3322–3335. doi:10.1016/j.csbj.2022.06.046
   PubMed Web of Science ®Google Scholar
• Chen Y, Wang X. miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48(D1):D127–D131. doi:10.1093/nar/gkz757
   PubMed Web of Science ®Google Scholar
• Zhou KR, Liu S, Sun WJ, et al. ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. Nucleic Acids Res. 2017;45(D1):D43–D50. doi:10.1093/nar/gkw965
   PubMed Web of Science ®Google Scholar
• Zhang Q, Liu W, Zhang HM, et al. hTFtarget: a comprehensive database for regulations of human transcription factors and their targets. Genomics Proteomics Bioinformatics. 2020;18(2):120–128. doi:10.1016/j.gpb.2019.09.006
   PubMed Web of Science ®Google Scholar
• Cotto KC, Wagner AH, Feng YY, et al. DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. Nucleic Acids Res. 2018;46(D1):D1068–D1073. doi:10.1093/nar/gkx1143
   PubMedGoogle Scholar
• Steen CB, Liu CL, Alizadeh AA, Newman AM. Profiling cell type abundance and expression in bulk tissues with CIBERSORTx. Methods Mol Biol. 2020;2117:135–157. doi:10.1007/978-1-0716-0301-7_7
   PubMedGoogle Scholar
• Liu XQ, Jiang L, Li YY, et al. Wogonin protects glomerular podocytes by targeting Bcl-2-mediated autophagy and apoptosis in diabetic kidney disease. Acta Pharmacol Sin. 2022;43(1):96–110. doi:10.1038/s41401-021-00721-5
   PubMed Web of Science ®Google Scholar
• Schmid H, Boucherot A, Yasuda Y, et al. Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy. Diabetes. 2006;55(11):2993–3003. doi:10.2337/db06-0477
   PubMed Web of Science ®Google Scholar
• Ju W, Greene CS, Eichinger F, et al. Defining cell-type specificity at the transcriptional level in human disease. Genome Res. 2013;23(11):1862–1873. doi:10.1101/gr.155697.113
   PubMed Web of Science ®Google Scholar
• Ju W, Nair V, Smith S, et al. Tissue transcriptome-driven identification of epidermal growth factor as a chronic kidney disease biomarker. Sci Transl Med. 2015;7(316):316ra193. doi:10.1126/scitranslmed.aac7071
   PubMed Web of Science ®Google Scholar
• Liao CM, Wulfmeyer VC, Chen R, et al. Induction of ferroptosis selectively eliminates senescent tubular cells. Am J Transplant. 2022;22(9):2158–2168. doi:10.1111/ajt.17102
   PubMed Web of Science ®Google Scholar
• Wang YH, Chang DY, Zhao MH, Chen M. Glutathione peroxidase 4 is a predictor of diabetic kidney disease progression in type 2 diabetes mellitus. Oxid Med Cell Longev. 2022;2022:2948248. doi:10.1155/2022/2948248
   PubMed Web of Science ®Google Scholar
• Shaw J, Chakraborty A, Nag A, Chattopadyay A, Dasgupta AK, Bhattacharyya M. Intracellular iron overload leading to DNA damage of lymphocytes and immune dysfunction in thalassemia major patients. Eur J Haematol. 2017;99(5):399–408. doi:10.1111/ejh.12936
   PubMed Web of Science ®Google Scholar
• Li S, Huang Y. Ferroptosis: an iron-dependent cell death form linking metabolism, diseases, immune cell and targeted therapy. Clin Transl Oncol. 2022;24(1):1–12. doi:10.1007/s12094-021-02669-8
   PubMed Web of Science ®Google Scholar
• Feng ST, Yang Y, Yang JF, et al. Urinary sediment CCL5 messenger RNA as a potential prognostic biomarker of diabetic nephropathy. Clin Kidney J. 2022;15(3):534–544. doi:10.1093/ckj/sfab186
   PubMed Web of Science ®Google Scholar
• Ito S, Nakashima H, Ishikiriyama T, et al. Effects of a CCR2 antagonist on macrophages and Toll-like receptor 9 expression in a mouse model of diabetic nephropathy. Am J Physiol Renal Physiol. 2021;321(6):F757–F770. doi:10.1152/ajprenal.00191.2021
   PubMed Web of Science ®Google Scholar
• Seok SJ, Lee ES, Kim GT, et al. Blockade of CCL2/CCR2 signalling ameliorates diabetic nephropathy in db/db mice. Nephrol Dial Transplant. 2013;28(7):1700–1710. doi:10.1093/ndt/gfs555
   PubMed Web of Science ®Google Scholar
• Kim HR, Kim SY. Perilla frutescens sprout extract protect renal mesangial cell dysfunction against high glucose by modulating AMPK and NADPH oxidase signaling. Nutrients. 2019;11(2). doi:10.3390/nu11020356
   Web of Science ®Google Scholar
• Saisorn W, Saithong S, Phuengmaung P, et al. Acute kidney injury induced lupus exacerbation through the enhanced neutrophil extracellular traps (and apoptosis) in fcgr2b deficient lupus mice with renal ischemia reperfusion injury. Front Immunol. 2021;12:669162. doi:10.3389/fimmu.2021.669162
   PubMed Web of Science ®Google Scholar
• Zhou XJ, Cheng FJ, Qi YY, et al. FCGR2B and FCRLB gene polymorphisms associated with IgA nephropathy. PLoS One. 2013;8(4):e61208. doi:10.1371/journal.pone.0061208
   PubMed Web of Science ®Google Scholar
• Chen TK, Coca SG, Thiessen-Philbrook HR, et al. Urinary biomarkers of tubular health and risk for kidney function decline or mortality in diabetes. Am J Nephrol. 2022;53(11–12):775–785. doi:10.1159/000528918
   PubMed Web of Science ®Google Scholar
• Johnson NH, Keane RW, de Rivero Vaccari JP. Renal and inflammatory proteins as biomarkers of diabetic kidney disease and lupus nephritis. Oxid Med Cell Longev. 2022;2022:5631099. doi:10.1155/2022/5631099
   PubMed Web of Science ®Google Scholar
• Guo C, Zhang L, Nie L, et al. Association of polymorphisms in the MyD88, IRAK4 and TRAF6 genes and susceptibility to type 2 diabetes mellitus and diabetic nephropathy in a southern Han Chinese population. Mol Cell Endocrinol. 2016;429:114–119. doi:10.1016/j.mce.2016.04.003
   PubMed Web of Science ®Google Scholar
• Yuan Y, Li L, Zhu L, et al. Mesenchymal stem cells elicit macrophages into M2 phenotype via improving transcription factor EB-mediated autophagy to alleviate diabetic nephropathy. Stem Cells. 2020;38(5):639–652. doi:10.1002/stem.3144
   PubMed Web of Science ®Google Scholar
• Klessens CQF, Zandbergen M, Wolterbeek R, et al. Macrophages in diabetic nephropathy in patients with type 2 diabetes. Nephrol Dial Transplant. 2017;32(8):1322–1329. doi:10.1093/ndt/gfw260
   PubMed Web of Science ®Google Scholar
• Tang PM, Nikolic-Paterson DJ, Lan HY. Macrophages: versatile players in renal inflammation and fibrosis. Nat Rev Nephrol. 2019;15(3):144–158. doi:10.1038/s41581-019-0110-2
   PubMed Web of Science ®Google Scholar
• Tesch GH. Macrophages and diabetic nephropathy. Semin Nephrol. 2010;30(3):290–301. doi:10.1016/j.semnephrol.2010.03.007
   PubMed Web of Science ®Google Scholar
• Lampropoulou IT, Stangou M, Sarafidis P, et al. TNF-alpha pathway and T-cell immunity are activated early during the development of diabetic nephropathy in Type II Diabetes Mellitus. Clin Immunol. 2020;215:108423. doi:10.1016/j.clim.2020.108423
   PubMed Web of Science ®Google Scholar
• Ribot JC, Lopes N, Silva-Santos B. gammadelta T cells in tissue physiology and surveillance. Nat Rev Immunol. 2021;21(4):221–232. doi:10.1038/s41577-020-00452-4
   PubMed Web of Science ®Google Scholar
• Cortvrindt C, Speeckaert R, Moerman A, Delanghe JR, Speeckaert MM. The role of interleukin-17A in the pathogenesis of kidney diseases. Pathology. 2017;49(3):247–258. doi:10.1016/j.pathol.2017.01.003
   PubMed Web of Science ®Google Scholar
• Peng X, Xiao Z, Zhang J, Li Y, Dong Y, Du J. IL-17A produced by both gammadelta T and Th17 cells promotes renal fibrosis via RANTES-mediated leukocyte infiltration after renal obstruction. J Pathol. 2015;235(1):79–89. doi:10.1002/path.4430
   PubMed Web of Science ®Google Scholar