130
Views
0
CrossRef citations to date
0
Altmetric
Nephrology

Identification of Immune-Related Genes as Biomarkers for Uremia

, , , , , & show all
Pages 5633-5649 | Received 08 Sep 2023, Accepted 03 Nov 2023, Published online: 28 Nov 2023

References

  • Meyer TW, Hostetter TH. Uremia. N Engl J Med. 2007;357(13):1316–1325. doi:10.1056/NEJMra071313
  • Almeras C, Argilés À. Progress in uremic toxin research: the general picture of uremia. Semin Dial. 2009;22(4):329–333. doi:10.1111/j.1525-139X.2009.00575.x
  • Scherer A, Günther OP, Balshaw RF, et al. Alteration of human blood cell transcriptome in uremia. BMC Med Genomics. 2013;6(1):23. doi:10.1186/1755-8794-6-23
  • Ebert T, Pawelzik SC, Witasp A, et al. Inflammation and premature ageing in chronic kidney disease. Toxins. 2020;12:227.
  • Kooman JP, Kotanko P, Schols AMWJ, et al. Chronic kidney disease and premature ageing. Nat Rev Nephrol. 2014;10(12):732–742. doi:10.1038/nrneph.2014.185
  • Sato Y, Yanagita M. Immunology of the ageing kidney. Nat Rev Nephrol. 2019;15(10):625–640. doi:10.1038/s41581-019-0185-9
  • Meijers RW, Litjens NH, de Wit EA, et al. Uremia causes premature ageing of the T cell compartment in end-stage renal disease patients. Immun Ageing. 2012;9(1):19. doi:10.1186/1742-4933-9-19
  • 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
  • Xie L, Huang G, Gao M, et al. Identification of atrial fibrillation-related lncRNA based on bioinformatic analysis. Dis Markers. 2022;2022:8307975. doi:10.1155/2022/8307975
  • Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinf. 2008;9(1):559. doi:10.1186/1471-2105-9-559
  • Chen H, Boutros PC. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinf. 2011;12(1):35. doi:10.1186/1471-2105-12-35
  • Yu G, Wang LG, Han Y, et al. ClusterProfiler: an R package for comparing biological themes among gene clusters. Omics. 2012;16:284–287. doi:10.1089/omi.2011.0118
  • 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. doi:10.1101/gr.1239303
  • Lin Z, Xu Q, Miao D, et al. An inflammatory response-related gene signature can impact the immune status and predict the prognosis of Hepatocellular carcinoma. Front Oncol. 2021;11:644416. doi:10.3389/fonc.2021.644416
  • Núñez E, Steyerberg EW, Núñez J. Regression modeling strategies. Rev Esp Cardiol. 2011;64:501–507. doi:10.1016/j.recesp.2011.01.019
  • Yang Y, He W, Wang ZR, et al. Immune cell landscape in gastric cancer. Biomed Res Int. 2021;2021:1930706. doi:10.1155/2021/1930706
  • Xu M, Kong Y, Chen N, et al. Identification of immune-related gene signature and prediction of CeRNA network in active ulcerative colitis. Front Immunol. 2022;13:855645. doi:10.3389/fimmu.2022.855645
  • Liss MA, Chen Y, Rodriguez R, et al. Immunogenic heterogeneity of renal cell carcinoma with venous tumor thrombus. Urology. 2019;124:168–173. doi:10.1016/j.urology.2018.09.018
  • Chen L, Wang Y, Huang J, et al. Identification of immune-related hub genes in Parkinson’s disease. Front Genet. 2022;13:914645. doi:10.3389/fgene.2022.914645
  • Chang YC, Su CY, Chen MH, et al. Secretory RAB GTPase 3C modulates IL6-STAT3 pathway to promote colon cancer metastasis and is associated with poor prognosis. Mol Cancer. 2017;16:135. doi:10.1186/s12943-017-0687-7
  • Zemaitis MR, Foris LA, Katta S, et al. Uremia, in StatPearls. Treasure Island (FL): StatPearls Publishing Copyright © 2023, StatPearls Publishing LLC; 2023.
  • Ruiz-Ortega M, Rayego-Mateos S, Lamas S, et al. Targeting the progression of chronic kidney disease. Nat Rev Nephrol. 2020;16:269–288. doi:10.1038/s41581-019-0248-y
  • Stenvinkel P, Meyer CJ, Block GA, et al. Understanding the role of the cytoprotective transcription factor nuclear factor erythroid 2-related factor 2-lessons from evolution, the animal kingdom and rare progeroid syndromes. Nephrol Dial Transplant. 2020;35(12):2036–2045. doi:10.1093/ndt/gfz120
  • Stenvinkel P, Painer J, Kuro OM, et al. Novel treatment strategies for chronic kidney disease: insights from the animal kingdom. Nat Rev Nephrol. 2018;14:265–284. doi:10.1038/nrneph.2017.169
  • Cuadrado A, Manda G, Hassan A, et al. Transcription factor NRF2 as a therapeutic target for chronic diseases: a systems medicine approach. Pharmacol Rev. 2018;70(2):348–383. doi:10.1124/pr.117.014753
  • Kooman JP, Dekker MJ, Usvyat LA, et al. Inflammation and premature aging in advanced chronic kidney disease. Am J Physiol Renal Physiol. 2017;313(4):F938–F950. doi:10.1152/ajprenal.00256.2017
  • Cobo G, Lindholm B, Stenvinkel P. Chronic inflammation in end-stage renal disease and dialysis. Nephrol Dial Transplant. 2018;33(suppl_3):iii35–iii40. doi:10.1093/ndt/gfy175
  • Zoccali C, Mallamaci F. Innate immunity system in patients with cardiovascular and kidney disease. Circ Res. 2023;132(8):915–932. doi:10.1161/CIRCRESAHA.122.321749
  • Meng XM, Nikolic-Paterson DJ, Lan HY. Inflammatory processes in renal fibrosis. Nat Rev Nephrol. 2014;10:493–503. doi:10.1038/nrneph.2014.114
  • Kitching AR. Dendritic cells in progressive renal disease: some answers, many questions. Nephrol Dial Transplant. 2014;29(12):2185–2193. doi:10.1093/ndt/gfu076
  • Tang PM, Nikolic-Paterson DJ, Lan HY. Macrophages: versatile players in renal inflammation and fibrosis. Nat Rev Nephrol. 2019;15:144–158. doi:10.1038/s41581-019-0110-2
  • Lim WH, Kireta S, Leedham E, et al. Uremia impairs monocyte and monocyte-derived dendritic cell function in hemodialysis patients. Kidney Int. 2007;72(9):1138–1148. doi:10.1038/sj.ki.5002425
  • Lisowska KA, Pindel M, Pietruczuk K, et al. The influence of a single hemodialysis procedure on human T lymphocytes. Sci Rep. 2019;9(1):5041. doi:10.1038/s41598-019-41619-x
  • Li SS, Sheng MJ, Sun ZY, et al. Upstream and downstream regulators of Klotho expression in chronic kidney disease. Metabolism. 2023;142:155530. doi:10.1016/j.metabol.2023.155530
  • Schlosser P, Grams ME, Rhee EP. Proteomics: progress and promise of high-throughput proteomics in chronic kidney disease. Mol Cell Proteomics. 2023;22(6):100550. doi:10.1016/j.mcpro.2023.100550
  • Zhang H, Watanabe R, Berry GJ, et al. Immunoinhibitory checkpoint deficiency in medium and large vessel vasculitis. Proc Natl Acad Sci U S A. 2017;114(6):E970–E979. doi:10.1073/pnas.1616848114
  • Kobayashi M, Numakura K, Hatakeyama S, et al. Severe immune-related adverse events in patients treated with nivolumab for metastatic renal cell carcinoma are associated with PDCD1 polymorphism. Genes. 2022;13:1204.
  • Hakroush S, Tampe B. Association between loss of immune checkpoint programmed cell death protein 1 and active ANCA-associated renal vasculitis. Int J Mol Sci. 2023;24(3):2975. doi:10.3390/ijms24032975
  • Aqeel F, Monroy-Trujillo J, Geetha D. Immune checkpoint inhibitors as potential triggers for ANCA vasculitis. RMD Open. 2022;8(2):e002500. doi:10.1136/rmdopen-2022-002500
  • Xie S, Louis Sam Titus ASC, Mohan C. Elevated expression of receptors for EGF, PDGF, transferrin and folate within murine and human lupus nephritis kidneys. Clin Immunol. 2023;246:109188. doi:10.1016/j.clim.2022.109188
  • Nishimura H, Nose M, Hiai H, et al. Development of lupus-like autoimmune diseases by disruption of the PD-1 gene encoding an ITIM motif-carrying immunoreceptor. Immunity. 1999;11(2):141–151. doi:10.1016/S1074-7613(00)80089-8
  • Wang Y, Lin X, Wang C, et al. Identification of PDCD1 as a potential biomarker in acute rejection after kidney transplantation via comprehensive bioinformatic analysis. Front Immunol. 2022;13:1076546. doi:10.3389/fimmu.2022.1076546
  • Zhou H, Lu H, Sun L, et al. Diagnostic biomarkers and immune infiltration in patients with T cell-mediated rejection after kidney transplantation. Front Immunol. 2022;12:774321. doi:10.3389/fimmu.2021.774321
  • Thibult M-L, Mamessier E, Gertner-Dardenne J, et al. PD-1 is a novel regulator of human B-cell activation. Int Immunol. 2013;25(2):129–137. doi:10.1093/intimm/dxs098
  • Eddy AA, Neilson EG. Chronic kidney disease progression. J Am Soc Nephrol. 2006;17(11):2964–2966. doi:10.1681/ASN.2006070704
  • Vizza D, Perri A, Toteda G, et al. Nerve growth factor exposure promotes tubular epithelial-mesenchymal transition via TGF-β1 signaling activation. Growth Factors. 2015;33:169–180. doi:10.3109/08977194.2015.1054989
  • Triantafyllopoulou A, Franzke CW, Seshan SV, et al. Proliferative lesions and metalloproteinase activity in murine lupus nephritis mediated by type I interferons and macrophages. Proc Natl Acad Sci U S A. 2010;107:301s2–3017. doi:10.1073/pnas.0914902107
  • Jia T, Xu T, Smeets B, et al. The role of platelet-derived growth factor in focal segmental glomerulosclerosis. J Am Soc Nephrol. 2023;34(2):241–257. doi:10.1681/ASN.2022040491
  • Naghdibadi M, Momeni M, Yavari P, et al. Clear cell renal cell carcinoma: a comprehensive in silico study in searching for therapeutic targets. Kidney Blood Press Res. 2023;48(1):135–150. doi:10.1159/000529861
  • Chan AC, Iwashima M, Turck CW, et al. ZAP-70: a 70 kd protein-tyrosine kinase that associates with the TCR zeta chain. Cell. 1992;71(4):649–662. doi:10.1016/0092-8674(92)90598-7