Identification of RNA-binding protein genes associated with renal rejection and graft survival

References

• Port FK, Wolfe RA, Mauger EA, et al. Comparison of survival probabilities for dialysis patients vs cadaveric renal transplant recipients. JAMA. 1993;270(11):1–15. doi: 10.1001/jama.1993.03510110079036.
   Web of Science ®Google Scholar
• Russell JD, Beecroft ML, Ludwin D, et al. The quality of life in renal transplantation – a prospective study. Transplantation. 1992;54(4):656–660. doi: 10.1097/00007890-199210000-00018.
   PubMed Web of Science ®Google Scholar
• Wekerle T, Segev D, Lechler R, et al. Strategies for long-term preservation of kidney graft function. Lancet. 2017;389(10084):2152–2162. doi: 10.1016/S0140-6736(17)31283-7.
   PubMed Web of Science ®Google Scholar
• Lamb KE, Lodhi S, Meier-Kriesche HU. Long-term renal allograft survival in the United States: a critical reappraisal. Am J Transplant. 2011;11(3):450–462. doi: 10.1111/j.1600-6143.2010.03283.x.
   PubMed Web of Science ®Google Scholar
• Bloom RD, Augustine JJ. Beyond the biopsy: monitoring immune status in kidney recipients. CJASN. 2021;16(9):1413–1422. doi: 10.2215/CJN.14840920.
   PubMed Web of Science ®Google Scholar
• Zhao BS, Roundtree IA, He C. Post-transcriptional gene regulation by mRNA modifications. Nat Rev Mol Cell Biol. 2017;18(1):31–42. doi: 10.1038/nrm.2016.132.
   PubMed Web of Science ®Google Scholar
• Corbett AH. Post-transcriptional regulation of gene expression and human disease. Curr Opin Cell Biol. 2018;52:96–104. doi: 10.1016/j.ceb.2018.02.011.
   PubMed Web of Science ®Google Scholar
• Corley M, Burns MC, Yeo GW. How RNA-binding proteins interact with RNA: molecules and mechanisms. Mol Cell. 2020;78(1):9–29. doi: 10.1016/j.molcel.2020.03.011.
   PubMed Web of Science ®Google Scholar
• Duan Y, Du A, Gu J, et al. PARylation regulates stress granule dynamics, phase separation, and neurotoxicity of disease-related RNA-binding proteins. Cell Res. 2019;29(3):233–247. doi: 10.1038/s41422-019-0141-z.
   PubMed Web of Science ®Google Scholar
• Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol. 2022;86(Pt 2):664–677. doi: 10.1016/j.semcancer.2022.03.025.
   PubMedGoogle Scholar
• Gerstberger S, Hafner M, Tuschl T. A census of human RNA-binding proteins. Nat Rev Genet. 2014;15(12):829–845. doi: 10.1038/nrg3813.
   PubMed Web of Science ®Google Scholar
• Yang Y-C, Lin Y-W, Lee W-J, et al. The RNA-binding protein KSRP aggravates malignant progression of clear cell renal cell carcinoma through transcriptional inhibition and post-transcriptional destabilization of the NEDD4L ubiquitin ligase. J Biomed Sci. 2023;30(1):68. doi: 10.1186/s12929-023-00949-9.
   PubMed Web of Science ®Google Scholar
• Guo J, Lei M, Cheng F, et al. RNA-binding proteins tristetraprolin and human antigen R are novel modulators of podocyte injury in diabetic kidney disease. Cell Death Dis. 2020;11(6):413. doi: 10.1038/s41419-020-2630-x.
   PubMed Web of Science ®Google Scholar
• Shi Q, Lee D-Y, Féliers D, et al. Interplay between RNA-binding protein HuR and Nox4 as a novel therapeutic target in diabetic kidney disease. Mol Metab. 2020;36:100968. doi: 10.1016/j.molmet.2020.02.011.
   PubMed Web of Science ®Google Scholar
• Wang J-N, Wang F, Ke J, et al. Inhibition of METTL3 attenuates renal injury and inflammation by alleviating TAB3 m6A modifications via IGF2BP2-dependent mechanisms. Sci Transl Med. 2022;14(640):eabk2709. doi: 10.1126/scitranslmed.abk2709.
   PubMed Web of Science ®Google Scholar
• Pullmann R, Rabb H. HuR and other turnover- and translation-regulatory RNA-binding proteins: implications for the kidney. Am J Physiol Renal Physiol. 2014;306(6):F569–F576.
   PubMed Web of Science ®Google Scholar
• Hart A, Lentine KL, Smith JM, et al. OPTN/SRTR 2019 annual data report: kidney. Am J Transplant. 2021;21(Suppl. 2):21–137.
   PubMedGoogle Scholar
• Mayrdorfer M, Liefeldt L, Wu K, et al. Exploring the complexity of death-censored kidney allograft failure. JASN. 2021;32(6):1513–1526. doi: 10.1681/ASN.2020081215.
   Web of Science ®Google Scholar
• Reynolds N, Cooke HJ. Role of the DAZ genes in male fertility. Reprod Biomed Online. 2005;10(1):72–80. doi: 10.1016/s1472-6483(10)60806-1.
   PubMed Web of Science ®Google Scholar
• Wang T, Bray SM, Warren ST. New perspectives on the biology of fragile X syndrome. Curr Opin Genet Dev. 2012;22(3):256–263. doi: 10.1016/j.gde.2012.02.002.
   PubMed Web of Science ®Google Scholar
• Randhawa PS, Finkelstein S, Scantlebury V, et al. Human polyoma virus-associated interstitial nephritis in the allograft kidney. Transplantation. 1999;67(1):103–109. doi: 10.1097/00007890-199901150-00018.
   PubMed Web of Science ®Google Scholar
• Sawinski D, Goral S. BK virus infection: an update on diagnosis and treatment. Nephrol Dial Transplant. 2015;30(2):209–217.
   PubMed Web of Science ®Google Scholar
• Finan JM, Sutton TL, Dixon DA, et al. Targeting the RNA-binding protein HuR in cancer. Cancer Res. 2023;83(21):3507–3516. doi: 10.1158/0008-5472.CAN-23-0972.
   PubMed Web of Science ®Google Scholar
• Hutchins EJ, Gandhi S, Chacon J, et al. RNA-binding protein Elavl1/HuR is required for maintenance of cranial neural crest specification. Elife. 2022;11:e63600. doi: 10.7554/eLife.63600.
   PubMed Web of Science ®Google Scholar
• Paz S, Ritchie A, Mauer C, et al. The RNA binding protein SRSF1 is a master switch of gene expression and regulation in the immune system. Cytokine Growth Factor Rev. 2021;57:19–26. doi: 10.1016/j.cytogfr.2020.10.008.
   PubMed Web of Science ®Google Scholar
• Medzhitov R, Janeway C. Innate immunity. N Engl J Med. 2000;343(5):338–344. doi: 10.1056/NEJM200008033430506.
   PubMed Web of Science ®Google Scholar
• Wu H, Chen G, Wyburn KR, et al. TLR4 activation mediates kidney ischemia/reperfusion injury. J Clin Invest. 2007;117(10):2847–2859. doi: 10.1172/JCI31008.
   PubMed Web of Science ®Google Scholar
• Leventhal JS, Schröppel B. Toll-like receptors in transplantation: sensing and reacting to injury. Kidney Int. 2012;81(9):826–832. doi: 10.1038/ki.2011.498.
   PubMed Web of Science ®Google Scholar
• Kaczorowski DJ, Nakao A, Vallabhaneni R, et al. Mechanisms of toll-like receptor 4 (TLR4)-mediated inflammation after cold ischemia/reperfusion in the heart. Transplantation. 2009;87(10):1455–1463. doi: 10.1097/TP.0b013e3181a36e5e.
   PubMed Web of Science ®Google Scholar
• Tsung A, Klune JR, Zhang X, et al. HMGB1 release induced by liver ischemia involves toll-like receptor 4 dependent reactive oxygen species production and calcium-mediated signaling. J Exp Med. 2007;204(12):2913–2923. doi: 10.1084/jem.20070247.
   PubMed Web of Science ®Google Scholar
• Braza F, Brouard S, Chadban S, et al. Role of TLRs and DAMPs in allograft inflammation and transplant outcomes. Nat Rev Nephrol. 2016;12(5):281–290. doi: 10.1038/nrneph.2016.41.
   PubMed Web of Science ®Google Scholar
• El-Zoghby ZM, Stegall MD, Lager DJ, et al. Identifying specific causes of kidney allograft loss. Am J Transplant. 2009;9(3):527–535.
   PubMed Web of Science ®Google Scholar
• Sellarés J, de Freitas DG, Mengel M, et al. Understanding the causes of kidney transplant failure: the dominant role of antibody-mediated rejection and nonadherence. Am J Transplant. 2012;12(2):388–399.
   PubMed Web of Science ®Google Scholar
• Halloran PF. T cell-mediated rejection of kidney transplants: a personal viewpoint. Am J Transplant. 2010;10(5):1126–1134. doi: 10.1111/j.1600-6143.2010.03053.x.
   PubMed Web of Science ®Google Scholar
• Halloran PF, Famulski KS, Reeve J. Molecular assessment of disease states in kidney transplant biopsy samples. Nat Rev Nephrol. 2016;12(9):534–548. doi: 10.1038/nrneph.2016.85.
   PubMed Web of Science ®Google Scholar
• Halloran PF, Pereira AB, Chang J, et al. Potential impact of microarray diagnosis of T cell-mediated rejection in kidney transplants: the INTERCOM study. Am J Transplant. 2013;13(9):2352–2363.
   PubMed Web of Science ®Google Scholar
• Pang Q, Chen H, Wu H, et al. N6-methyladenosine regulators-related immune genes enable predict graft loss and discriminate T-cell mediate rejection in kidney transplantation biopsies for cause. Front Immunol. 2022;13:1039013. doi: 10.3389/fimmu.2022.1039013.
   PubMed Web of Science ®Google Scholar
• Bi Q, Wu JY, Qiu XM, et al. Identification of potential necroinflammation-associated necroptosis-related biomarkers for delayed graft function and renal allograft failure: a machine learning-based exploration in the framework of predictive, preventive, and personalized medicine. EPMA J. 2023;14(2):307–328. doi: 10.1007/s13167-023-00320-w.
   PubMed Web of Science ®Google Scholar
• Rice GI, Bond J, Asipu A, et al. Mutations involved in Aicardi-Goutières syndrome implicate SAMHD1 as regulator of the innate immune response. Nat Genet. 2009;41(7):829–832. doi: 10.1038/ng.373.
   PubMed Web of Science ®Google Scholar
• Szaniawski MA, Spivak AM, Cox JE, et al. SAMHD1 phosphorylation coordinates the anti-HIV-1 response by diverse interferons and tyrosine kinase inhibition. mBio. 2018;9(3):e00819-18. doi: 10.1128/mBio.00819-18.
   PubMed Web of Science ®Google Scholar
• Goldstone DC, Ennis-Adeniran V, Hedden JJ, et al. HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature. 2011;480(7377):379–382. doi: 10.1038/nature10623.
   PubMed Web of Science ®Google Scholar
• Kim ET, Roche KL, Kulej K, et al. SAMHD1 modulates early steps during human cytomegalovirus infection by limiting NF-κB activation. Cell Rep. 2019;28(2):434–448.e6.
   PubMed Web of Science ®Google Scholar
• Chen S, Bonifati S, Qin Z, et al. SAMHD1 suppression of antiviral immune responses. Trends Microbiol. 2019;27(3):254–267. doi: 10.1016/j.tim.2018.09.009.
   PubMed Web of Science ®Google Scholar
• Li M, Zhang D, Zhu M, et al. Roles of SAMHD1 in antiviral defense, autoimmunity and cancer. Rev Med Virol. 2017;27(4):e1931.
   Web of Science ®Google Scholar
• Maharana S, Kretschmer S, Hunger S, et al. SAMHD1 controls innate immunity by regulating condensation of immunogenic self RNA. Mol Cell. 2022;82(19):3712–3728.e10.
   PubMed Web of Science ®Google Scholar
• Brandariz-Nuñez A, Valle-Casuso JC, White TE, et al. Role of SAMHD1 nuclear localization in restriction of HIV-1 and SIVmac. Retrovirology. 2012;9(1):49. doi: 10.1186/1742-4690-9-49.
   PubMedGoogle Scholar
• Coquel F, Silva M-J, Técher H, et al. SAMHD1 acts at stalled replication forks to prevent interferon induction. Nature. 2018;557(7703):57–61. doi: 10.1038/s41586-018-0050-1.
   PubMed Web of Science ®Google Scholar
• Mauney CH, Rogers LC, Harris RS, et al. The SAMHD1 dNTP triphosphohydrolase is controlled by a redox switch. Antioxid Redox Signal. 2017;27(16):1317–1331.
   PubMed Web of Science ®Google Scholar
• Du J, Peng Y, Wang S, et al. Nucleocytoplasmic shuttling of SAMHD1 is important for LINE-1 suppression. Biochem Biophys Res Commun. 2019;510(4):551–557.
   PubMed Web of Science ®Google Scholar
• Tzima E, Reader JS, Irani-Tehrani M, et al. Biologically active fragment of a human tRNA synthetase inhibits fluid shear stress-activated responses of endothelial cells. Proc Natl Acad Sci U S A. 2003;100(25):14903–14907. doi: 10.1073/pnas.2436330100.
   PubMed Web of Science ®Google Scholar
• Wakasugi K, Slike BM, Hood J, et al. A human aminoacyl-tRNA synthetase as a regulator of angiogenesis. Proc Natl Acad Sci U S A. 2002;99(1):173–177. doi: 10.1073/pnas.012602099.
   PubMed Web of Science ®Google Scholar
• Halloran PF, Venner JM, Madill-Thomsen KS, et al. Review: the transcripts associated with organ allograft rejection. Am J Transplant. 2018;18(4):785–795.
   PubMed Web of Science ®Google Scholar
• Chauveau B, Garric A, Di Tommaso S, et al. WARS1, TYMP and GBP1 display a distinctive microcirculation pattern by immunohistochemistry during antibody-mediated rejection in kidney transplantation. Sci Rep. 2022;12(1):19094. doi: 10.1038/s41598-022-23078-z.
   PubMed Web of Science ®Google Scholar
• Chauveau B, Raymond A-A, Di Tommaso S, et al. The proteome of antibody-mediated rejection: from glomerulitis to transplant glomerulopathy. Biomedicines. 2022;10(3):569. doi: 10.3390/biomedicines10030569.
   PubMed Web of Science ®Google Scholar