T Cell Global Intron Retention Describes patient subtypes in Systemic lupus erythematousus
Creators: name: Xiaoqian Sun
Publisher: name: Zenodo
Year: 2019
Subjects: T cell
SLE
Lupus
Intron Retention
Lupus Suppressor
Lupus Activator

description: <br>
Abstract: SLE is a complex autoimmune disease and its cause is unclear. Given the autoimmune nature of SLE and the newly-recognizedrole of intron retention (IR) played in global gene regulation, we studied the global gene expression and intron retention pattern of lupus patients.
description: {"references": ["Tsokos GC. Systemic lupus erythematosus. N Engl J Med. 2011;365(22):2110-21. doi: 10.1056/NEJMra1100359. PubMed PMID: 22129255", "Bradley SJ, Suarez-Fueyo A, Moss DR, Kyttaris VC, Tsokos GC. T Cell Transcriptomes Describe Patient Subtypes in Systemic Lupus Erythematosus. PLoS One. 2015;10(11):e0141171. doi: 10.1371/journal.pone.0141171. PubMed PMID: 26544975; PubMed Central PMCID: PMCPMC4636226", "Koga T, Hedrich CM, Mizui M, Yoshida N, Otomo K, Lieberman LA, et al. CaMK4-dependent activation of AKT/mTOR and CREM-alpha underlies autoimmunity-associated Th17 imbalance. J Clin Invest. 2014;124(5):2234-45. doi: 10.1172/JCI73411. PubMed PMID: 24667640; PubMed Central PMCID: PMCPMC4001553.", "Kis-Toth K, Tsokos GC. Engagement of SLAMF2/CD48 prolongs the time frame of effective T cell activation by supporting mature dendritic cell survival. J Immunol. 2014;192(9):4436-42. doi: 10.4049/jimmunol.1302909. 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PubMed PMID: WOS:000357021700001.", "Yap K, Lim ZQ, Khandelia P, Friedman B, Makeyev EV. Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Gene Dev. 2012;26(11):1209-23. doi: 10.1101/gad.188037.112. PubMed PMID: WOS:000304767000008.", "Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 2016;44(2):838-51. doi: 10.1093/nar/gkv1168. PubMed PMID: 26531823; PubMed Central PMCID: PMCPMC4737145.", "Ni T, Yang W, Han M, Zhang Y, Shen T, Nie H, et al. Global intron retention mediated gene regulation during CD4+ T cell activation. Nucleic Acids Res. 2016;44(14):6817-29. doi: 10.1093/nar/gkw591. PubMed PMID: 27369383; PubMed Central PMCID: PMCPMC5001615.", "Chen W, Moore MJ. The spliceosome: disorder and dynamics defined. Curr Opin Struct Biol. 2014;24:141-9. doi: 10.1016/j.sbi.2014.01.009. PubMed PMID: 24530854; PubMed Central PMCID: PMCPMC3987960.", "Scotti MM, Swanson MS. RNA mis-splicing in disease. Nat Rev Genet. 2016;17(1):19-32. doi: 10.1038/nrg.2015.3. PubMed PMID: 26593421; PubMed Central PMCID: PMCPMC5993438.", "Evsyukova I, Somarelli JA, Gregory SG, Garcia-Blanco MA. Alternative splicing in multiple sclerosis and other autoimmune diseases. RNA Biol. 2010;7(4):462-73. PubMed PMID: 20639696; PubMed Central PMCID: PMCPMC3070910.", "Bombardier C, Gladman DD, Urowitz MB, Caron D, Chang CH. Derivation of the SLEDAI. A disease activity index for lupus patients. The Committee on Prognosis Studies in SLE. Arthritis Rheum. 1992;35(6):630-40. PubMed PMID: 1599520.", "Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. PubMed PMID: 19289445; PubMed Central PMCID: PMCPMC2672628.", "Shi X, Ran L, Liu Y, Zhong SH, Zhou PP, Liao MX, et al. Knockdown of hnRNP A2/B1 inhibits cell proliferation, invasion and cell cycle triggering apoptosis in cervical cancer via PI3K/AKT signaling pathway. Oncol Rep. 2018;39(3):939-50. doi: 10.3892/or.2018.6195. PubMed PMID: 29328485; PubMed Central PMCID: PMCPMC5802035.", "Li D, Tang Q, Tan L, Zhao M, Liang GP, Yang Y, et al. Ten-Eleven Translocation 2 Protein Down-Regulates DNA Methylation of Interleukin-17A Promoter and Induces Its Expression in CD4(+)t Cells of Patients with Systemic Lupus Erythematosus. Arthritis Rheumatol. 2014;66:S1175-S. PubMed PMID: WOS:000344384905362.", "1.\tTsokos GC. Systemic lupus erythematosus. N Engl J Med. 2011;365(22):2110-21. doi: 10.1056/NEJMra1100359. PubMed PMID: 22129255. 2.\tBradley SJ, Suarez-Fueyo A, Moss DR, Kyttaris VC, Tsokos GC. T Cell Transcriptomes Describe Patient Subtypes in Systemic Lupus Erythematosus. PLoS One. 2015;10(11):e0141171. doi: 10.1371/journal.pone.0141171. PubMed PMID: 26544975; PubMed Central PMCID: PMCPMC4636226. 3.\tKoga T, Hedrich CM, Mizui M, Yoshida N, Otomo K, Lieberman LA, et al. CaMK4-dependent activation of AKT/mTOR and CREM-alpha underlies autoimmunity-associated Th17 imbalance. J Clin Invest. 2014;124(5):2234-45. doi: 10.1172/JCI73411. PubMed PMID: 24667640; PubMed Central PMCID: PMCPMC4001553. 4.\tKis-Toth K, Tsokos GC. Engagement of SLAMF2/CD48 prolongs the time frame of effective T cell activation by supporting mature dendritic cell survival. J Immunol. 2014;192(9):4436-42. doi: 10.4049/jimmunol.1302909. PubMed PMID: 24670806; PubMed Central PMCID: PMCPMC4017928. 5.\tMizui M, Koga T, Lieberman LA, Beltran J, Yoshida N, Johnson MC, et al. IL-2 protects lupus-prone mice from multiple end-organ damage by limiting CD4-CD8- IL-17-producing T cells. J Immunol. 2014;193(5):2168-77. doi: 10.4049/jimmunol.1400977. PubMed PMID: 25063876; PubMed Central PMCID: PMCPMC4135016. 6.\tAlmlof JC, Alexsson A, Imgenberg-Kreuz J, Sylwan L, Backlin C, Leonard D, et al. Novel risk genes for systemic lupus erythematosus predicted by random forest classification. Sci Rep. 2017;7(1):6236. doi: 10.1038/s41598-017-06516-1. PubMed PMID: 28740209; PubMed Central PMCID: PMCPMC5524838. 7.\tTan EM, Cohen AS, Fries JF, Masi AT, McShane DJ, Rothfield NF, et al. The 1982 revised criteria for the classification of systemic lupus erythematosus. Arthritis Rheum. 1982;25(11):1271-7. PubMed PMID: 7138600. 8.\tLawrence JS, Martins CL, Drake GL. A family survey of lupus erythematosus. 1. Heritability. J Rheumatol. 1987;14(5):913-21. PubMed PMID: 3430520. 9.\tMorris DL, Sheng Y, Zhang Y, Wang YF, Zhu Z, Tombleson P, et al. Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus. Nat Genet. 2016;48(8):940-6. doi: 10.1038/ng.3603. PubMed PMID: 27399966; PubMed Central PMCID: PMCPMC4966635. 10.\tMoser KL, Kelly JA, Lessard CJ, Harley JB. Recent insights into the genetic basis of systemic lupus erythematosus. Genes and Immunity. 2009;10(5):373-9. doi: 10.1038/gene.2009.39. PubMed PMID: WOS:000268168800001. 11.\tDai C, Deng Y, Quinlan A, Gaskin F, Tsao BP, Fu SM. Genetics of systemic lupus erythematosus: immune responses and end organ resistance to damage. Curr Opin Immunol. 2014;31:87-96. doi: 10.1016/j.coi.2014.10.004. PubMed PMID: 25458999; PubMed Central PMCID: PMCPMC4274270. 12.\tKariuki SN, Ghodke-Puranik Y, Dorschner JM, Chrabot BS, Kelly JA, Tsao BP, et al. Genetic analysis of the pathogenic molecular sub-phenotype interferon-alpha identifies multiple novel loci involved in systemic lupus erythematosus. Genes Immun. 2015;16(1):15-23. doi: 10.1038/gene.2014.57. PubMed PMID: 25338677; PubMed Central PMCID: PMCPMC4305028. 13.\tTsokos GC, Lo MS, Reis PC, Sullivan KE. New insights into the immunopathogenesis of systemic lupus erythematosus. Nat Rev Rheumatol. 2016;12(12):716-30. doi: 10.1038/nrrheum.2016.186. PubMed PMID: WOS:000389219600006. 14.\tHarley JB, Moser KL, Gaffney PM, Behrens TW. The genetics of human systemic lupus erythematosus. Curr Opin Immunol. 1998;10(6):690-6. PubMed PMID: 9914226. 15.\tGalante PAF, Sakabe NJ, Kirschbaum-Slager N, De Souza SJ. Detection and evaluation of intron retention events in the human transcriptome. Rna. 2004;10(5):757-65. doi: 10.1261/rna.5123504. PubMed PMID: WOS:000221072500001. 16.\tWang ET, Sandberg R, Luo SJ, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature. 2008;456(7221):470-6. doi: 10.1038/nature07509. PubMed PMID: WOS:000261170500031. 17.\tNilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature. 2010;463(7280):457-63. doi: 10.1038/nature08909. PubMed PMID: WOS:000273981100037. 18.\tBoutz PL, Bhutkar A, Sharp PA. Detained introns are a novel, widespread class of post-transcriptionally spliced introns. Gene Dev. 2015;29(1):63-80. doi: 10.1101/gad.247361.114. PubMed PMID: WOS:000347372100006. 19.\tWong JJL, Ritchie W, Ebner OA, Selbach M, Wong JWH, Huang YZ, et al. Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation. Cell. 2013;154(3):583-95. doi: 10.1016/j.cell.2013.06.052. PubMed PMID: WOS:000322629900012. 20.\tDvinge H, Bradley RK. Widespread intron retention diversifies most cancer transcriptomes. Genome Med. 2015;7. doi: ARTN 45 10.1186/s13073-015-0168-9. PubMed PMID: WOS:000357021700001. 21.\tYap K, Lim ZQ, Khandelia P, Friedman B, Makeyev EV. Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention. Gene Dev. 2012;26(11):1209-23. doi: 10.1101/gad.188037.112. PubMed PMID: WOS:000304767000008. 22.\tPimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 2016;44(2):838-51. doi: 10.1093/nar/gkv1168. PubMed PMID: 26531823; PubMed Central PMCID: PMCPMC4737145. 23.\tNi T, Yang W, Han M, Zhang Y, Shen T, Nie H, et al. Global intron retention mediated gene regulation during CD4+ T cell activation. Nucleic Acids Res. 2016;44(14):6817-29. doi: 10.1093/nar/gkw591. PubMed PMID: 27369383; PubMed Central PMCID: PMCPMC5001615. 24.\tChen W, Moore MJ. The spliceosome: disorder and dynamics defined. Curr Opin Struct Biol. 2014;24:141-9. doi: 10.1016/j.sbi.2014.01.009. PubMed PMID: 24530854; PubMed Central PMCID: PMCPMC3987960. 25.\tScotti MM, Swanson MS. RNA mis-splicing in disease. Nat Rev Genet. 2016;17(1):19-32. doi: 10.1038/nrg.2015.3. PubMed PMID: 26593421; PubMed Central PMCID: PMCPMC5993438. 26.\tEvsyukova I, Somarelli JA, Gregory SG, Garcia-Blanco MA. Alternative splicing in multiple sclerosis and other autoimmune diseases. RNA Biol. 2010;7(4):462-73. PubMed PMID: 20639696; PubMed Central PMCID: PMCPMC3070910. 27.\tBombardier C, Gladman DD, Urowitz MB, Caron D, Chang CH. Derivation of the SLEDAI. A disease activity index for lupus patients. The Committee on Prognosis Studies in SLE. Arthritis Rheum. 1992;35(6):630-40. PubMed PMID: 1599520. 28.\tTrapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25(9):1105-11. doi: 10.1093/bioinformatics/btp120. PubMed PMID: 19289445; PubMed Central PMCID: PMCPMC2672628. 29.\tShi X, Ran L, Liu Y, Zhong SH, Zhou PP, Liao MX, et al. Knockdown of hnRNP A2/B1 inhibits cell proliferation, invasion and cell cycle triggering apoptosis in cervical cancer via PI3K/AKT signaling pathway. Oncol Rep. 2018;39(3):939-50. doi: 10.3892/or.2018.6195. PubMed PMID: 29328485; PubMed Central PMCID: PMCPMC5802035. 30.\tLi D, Tang Q, Tan L, Zhao M, Liang GP, Yang Y, et al. Ten-Eleven Translocation 2 Protein Down-Regulates DNA Methylation of Interleukin-17A Promoter and Induces Its Expression in CD4(+)t Cells of Patients with Systemic Lupus Erythematosus. Arthritis Rheumatol. 2014;66:S1175-S. PubMed PMID: WOS:000344384905362. 31.\tWu H, Huang X, Qiu H, Zhao M, Lu Q. 16 High salt promotes systemic lupus erythematosus by TET2-induced dna demethylation and driving the differentiation of TFH cells. Archives of Disease in childhood; 2017."]}