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Alterations of the Primary Cilia Gene SPAG17 and SOX9 Locus Noncoding RNAs Identified by RNA-Sequencing Analysis in Patients With Systemic Sclerosis

dc.contributor.authorRoberson, Elisha D. O.
dc.contributor.authorCarns, Mary
dc.contributor.authorCao, Li
dc.contributor.authorAren, Kathleen
dc.contributor.authorGoldberg, Isaac A.
dc.contributor.authorMorales-Heil, David J.
dc.contributor.authorKorman, Benjamin D.
dc.contributor.authorAtkinson, John P.
dc.contributor.authorVarga, John
dc.date.accessioned2023-01-11T16:23:54Z
dc.date.available2024-02-11 11:23:51en
dc.date.available2023-01-11T16:23:54Z
dc.date.issued2023-01
dc.identifier.citationRoberson, Elisha D. O.; Carns, Mary; Cao, Li; Aren, Kathleen; Goldberg, Isaac A.; Morales-Heil, David J. ; Korman, Benjamin D.; Atkinson, John P.; Varga, John (2023). "Alterations of the Primary Cilia Gene SPAG17 and SOX9 Locus Noncoding RNAs Identified by RNA- Sequencing Analysis in Patients With Systemic Sclerosis." Arthritis & Rheumatology 75(1): 108-119.
dc.identifier.issn2326-5191
dc.identifier.issn2326-5205
dc.identifier.urihttps://hdl.handle.net/2027.42/175447
dc.publisherWiley Periodicals, Inc.
dc.titleAlterations of the Primary Cilia Gene SPAG17 and SOX9 Locus Noncoding RNAs Identified by RNA-Sequencing Analysis in Patients With Systemic Sclerosis
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelRheumatology
dc.subject.hlbtoplevelHealth Sciences
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175447/1/art42281-sup-0001-Disclosureform.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175447/2/art42281.pdf
dc.description.bitstreamurlhttp://deepblue.lib.umich.edu/bitstream/2027.42/175447/3/art42281_am.pdf
dc.identifier.doi10.1002/art.42281
dc.identifier.sourceArthritis & Rheumatology
dc.identifier.citedreferenceCordova-Fletes C, Becerra-Solano LE, Rangel-Sosa MM, et al. Uncommon runs of homozygosity disclose homozygous missense mutations in two ciliopathy-related genes (SPAG17 and WDR35) in a patient with multiple brain and skeletal anomalies. Eur J Med Genet 2018; 61: 161 – 7.
dc.identifier.citedreferenceRice LM, Ziemek J, Stratton EA, et al. A longitudinal biomarker for the extent of skin disease in patients with diffuse cutaneous systemic sclerosis. Arthritis Rheumatol 2015; 67: 3004 – 15.
dc.identifier.citedreferenceKim YH, Lee JR, Hahn MJ. Regulation of inflammatory gene expression in macrophages by epithelial-stromal interaction 1 (Epsti1). Biochem Biophys Res Commun 2018; 496: 778 – 83.
dc.identifier.citedreferenceTrombetta AC, Soldano S, Contini P, et al. A circulating cell population showing both M1 and M2 monocyte/macrophage surface markers characterizes systemic sclerosis patients with lung involvement. Respir Res 2018; 19: 186.
dc.identifier.citedreferenceTeves ME, Zhang Z, Costanzo RM, et al. Sperm-associated antigen-17 gene is essential for motile cilia function and neonatal survival. Am J Respir Cell Mol Biol 2013; 48: 765 – 72.
dc.identifier.citedreferenceXu X, Sha YW, Mei LB, et al. A familial study of twins with severe asthenozoospermia identified a homozygous SPAG17 mutation by whole-exome sequencing. Clin Genet 2018; 93: 345 – 9.
dc.identifier.citedreferenceVan der Valk RJ, Kreiner-Moller E, Kooijman MN, et al. A novel common variant in DCST2 is associated with length in early life and height in adulthood. Hum Mol Genet 2015; 24: 1155 – 68.
dc.identifier.citedreferenceKim JJ, Lee HI, Park T, et al. Identification of 15 loci influencing height in a Korean population. J Hum Genet 2010; 55: 27 – 31.
dc.identifier.citedreferenceAbdelhamed Z, Lukacs M, Cindric S, et al. A novel hypomorphic allele of Spag17 causes primary ciliary dyskinesia phenotypes in mice. Dis Model Mech 2020; 13: dmm045344.
dc.identifier.citedreferenceAndjelkovic M, Minic P, Vreca M, et al. Genomic profiling supports the diagnosis of primary ciliary dyskinesia and reveals novel candidate genes and genetic variants. PloS One 2018; 13: e0205422.
dc.identifier.citedreferenceRusu MC, Mirancea N, Manoiu VS, et al. Skin telocytes. Ann Anat 2012; 194: 359 – 67.
dc.identifier.citedreferenceCorallo C, Cutolo M, Volpi N, et al. Histopathological findings in systemic sclerosis-related myopathy: fibrosis and microangiopathy with lack of cellular inflammation. Ther Adv Musculoskelet Dis 2017; 9: 3 – 10.
dc.identifier.citedreferenceOkroj M, Johansson M, Saxne T, et al. Analysis of complement biomarkers in systemic sclerosis indicates a distinct pattern in scleroderma renal crisis. Arthritis Res Ther 2016; 18: 267.
dc.identifier.citedreferencePerez NA, Morales ML, Sanchez RS, et al. Endothelial lesion and complement activation in patients with Scleroderma Renal Crisis. J Bras Nefrol 2019; 41: 580 – 4.
dc.identifier.citedreferenceNoris M, Caprioli J, Bresin E, et al. Relative role of genetic complement abnormalities in sporadic and familial aHUS and their impact on clinical phenotype. Clin J Am Soc Nephrol 2010; 5: 1844 – 59.
dc.identifier.citedreferenceCofiell R, Kukreja A, Bedard K, et al. Eculizumab reduces complement activation, inflammation, endothelial damage, thrombosis, and renal injury markers in aHUS. Blood 2015; 125: 3253 – 62.
dc.identifier.citedreferenceDevresse A, Aydin S, Le Quintrec M, et al. Complement activation and effect of eculizumab in scleroderma renal crisis. Medicine (Baltimore) 2016; 95: e4459.
dc.identifier.citedreferenceUriarte MH, Larrarte C, Rey LB. Scleroderma renal crisis debute with thrombotic microangiopathy: a successful case treated with eculizumab. Case Rep Nephrol 2018; 2018: 6051083.
dc.identifier.citedreferenceZhang W, Wu Y, Hou B, et al. A SOX9-AS1/miR-5590-3p/SOX9 positive feedback loop drives tumor growth and metastasis in hepatocellular carcinoma through the Wnt/β-catenin pathway. Mol Oncol 2019; 13: 2194 – 210.
dc.identifier.citedreferenceBarter MJ, Gomez R, Hyatt S, et al. The long non-coding RNA ROCR contributes to SOX9 expression and chondrogenic differentiation of human mesenchymal stem cells. Development 2017; 144: 4510 – 21.
dc.identifier.citedreferenceLafyatis R, Mantero JC, Gordon J, et al. Inhibition of β-catenin signaling in the skin rescues cutaneous adipogenesis in systemic sclerosis: a randomized, double-blind, placebo-controlled trial of C-82. J Invest Dermatol 2017; 137: 2473 – 83.
dc.identifier.citedreferenceTsai MC, Manor O, Wan Y, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329: 689 – 93.
dc.identifier.citedreferenceRinn JL, Kertesz M, Wang JK, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129: 1311 – 23.
dc.identifier.citedreferenceAssassi S, Mayes MD, Arnett FC, et al. Systemic sclerosis and lupus: points in an interferon-mediated continuum. Arthritis Rheum 2010; 62: 589 – 98.
dc.identifier.citedreferenceVan den Hoogen F, Khanna D, Fransen J, et al. 2013 classification criteria for systemic sclerosis: an American College of Rheumatology/European League against Rheumatism collaborative initiative. Arthritis Rheum 2013; 65: 2737 – 47.
dc.identifier.citedreferenceAllanore Y, Simms R, Distler O, et al. Systemic sclerosis [review]. Nat Rev Dis Primers 2015; 1: 15002.
dc.identifier.citedreferenceVarga J, Roberson ED. Genomic advances in systemic sclerosis: it’s time for precision. Arthritis Rheumatol 2015; 67: 2801 – 5.
dc.identifier.citedreferenceDerrett-Smith EC, Martyanov V, Chighizola CB, et al. Limited cutaneous systemic sclerosis skin demonstrates distinct molecular subsets separated by a cardiovascular development gene expression signature. Arthritis Res Ther 2017; 19: 156.
dc.identifier.citedreferenceAssassi S, Wang X, Chen G, et al. Myeloablation followed by autologous stem cell transplantation normalises systemic sclerosis molecular signatures. Ann Rheum Dis 2019; 78: 1371 – 8.
dc.identifier.citedreferenceBeretta L, Barturen G, Vigone B, et al. Genome-wide whole blood transcriptome profiling in a large European cohort of systemic sclerosis patients. Annals Rheum Dis 2020; 79: 1218 – 26.
dc.identifier.citedreferenceBrkic Z, van Bon L, Cossu M, et al. The interferon type I signature is present in systemic sclerosis before overt fibrosis and might contribute to its pathogenesis through high BAFF gene expression and high collagen synthesis. Ann Rheum Dis 2016; 75: 1567 – 73.
dc.identifier.citedreferenceHiggs BW, Liu Z, White B, et al. Patients with systemic lupus erythematosus, myositis, rheumatoid arthritis and scleroderma share activation of a common type I interferon pathway. Ann Rheum Dis 2011; 70: 2029 – 36.
dc.identifier.citedreferencePendergrass SA, Lemaire R, Francis IP, et al. Intrinsic gene expression subsets of diffuse cutaneous systemic sclerosis are stable in serial skin biopsies. J Invest Dermatol 2012; 132: 1363 – 73.
dc.identifier.citedreferenceSkaug B, Khanna D, Swindell WR, et al. Global skin gene expression analysis of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive inflammatory profile. Ann Rheum Dis 2020; 79: 379 – 86.
dc.identifier.citedreferenceAssassi S, Swindell WR, Wu M, et al. Dissecting the heterogeneity of skin gene expression patterns in systemic sclerosis. Arthritis Rheumatol 2015; 67: 3016 – 26.
dc.identifier.citedreferenceApostolidis SA, Stifano G, Tabib T, et al. Single cell RNA sequencing identifies HSPG2 and APLNR as markers of endothelial cell injury in systemic sclerosis skin. Front Immunol 2018; 9: 2191.
dc.identifier.citedreferenceKarimizadeh E, Sharifi-Zarchi A, Nikaein H, et al. Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis. BMC Med Genomics 2019; 12: 199.
dc.identifier.citedreferenceHinchcliff M, Huang CC, Wood TA, et al. Molecular signatures in skin associated with clinical improvement during mycophenolate treatment in systemic sclerosis. J Invest Dermat 2013; 133: 1979 – 89.
dc.identifier.citedreferenceJohnson ME, Mahoney JM, Taroni J, et al. Experimentally-derived fibroblast gene signatures identify molecular pathways associated with distinct subsets of systemic sclerosis patients in three independent cohorts. PloS One 2015; 10: e0114017.
dc.identifier.citedreferenceRichardson C, Agrawal R, Lee J, et al. Esophageal dilatation and interstitial lung disease in systemic sclerosis: a cross-sectional study. Semin Arthritis Rheum 2016; 46: 109 – 14.
dc.identifier.citedreferenceMartin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 2011; 17: 10 – 2.
dc.identifier.citedreferenceDobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013; 29: 15 – 21.
dc.identifier.citedreferenceLiao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014; 30: 923 – 30.
dc.identifier.citedreferenceLangfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 2008; 9: 559.
dc.identifier.citedreferenceLove MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 2014; 15: 550.
dc.identifier.citedreferenceRaudvere U, Kolberg L, Kuzmin I, et al. g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic Acids Res 2019; 47: W191 – 8.
dc.identifier.citedreferenceFingerlin TE, Murphy E, Zhang W, et al. Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nat Genet 2013; 45: 613 – 20.
dc.identifier.citedreferenceZhang Y, Wang S, Wang C, et al. High expression of FAM13A was associated with increasing the liver cirrhosis risk. Mol Genet Genomic Med 2019; 7: e543.
dc.identifier.citedreferenceKrausgruber T, Blazek K, Smallie T, et al. IRF5 promotes inflammatory macrophage polarization and TH1-TH17 responses. Nat Immunol 2011; 12: 231 – 8.
dc.identifier.citedreferenceDuan H, Fleming J, Pritchard DK, et al. Combined analysis of monocyte and lymphocyte messenger RNA expression with serum protein profiles in patients with scleroderma. Arthritis Rheum 2008; 58: 1465 – 74.
dc.identifier.citedreferenceKazarian E, Son H, Sapao P, et al. SPAG17 is required for male germ cell differentiation and fertility. Int J Mol Sci 2018; 19: 1252.
dc.identifier.citedreferenceTeves ME, Sundaresan G, Cohen DJ, et al. Spag17 deficiency results in skeletal malformations and bone abnormalities. PloS One 2015; 10: e0125936.
dc.identifier.citedreferenceBahar Halpern K, Massalha H, Zwick RK, et al. Lgr5+ telocytes are a signaling source at the intestinal villus tip. Nat Commun 2020; 11: 1936.
dc.identifier.citedreferenceManetti M, Rosa I, Messerini L, et al. A loss of telocytes accompanies fibrosis of multiple organs in systemic sclerosis. J Cell Mol Med 2014; 18: 253 – 62.
dc.identifier.citedreferenceManetti M, Guiducci S, Ruffo M, et al. Evidence for progressive reduction and loss of telocytes in the dermal cellular network of systemic sclerosis. J Cell Mol Med 2013; 17: 482 – 96.
dc.identifier.citedreferenceScambi C, Ugolini S, Jokiranta TS, et al. The local complement activation on vascular bed of patients with systemic sclerosis: a hypothesis-generating study. PloS One 2015; 10: e0114856.
dc.identifier.citedreferenceFarina G, Lafyatis D, Lemaire R, et al. A four-gene biomarker predicts skin disease in patients with diffuse cutaneous systemic sclerosis. Arthritis Rheum 2010; 62: 580 – 8.
dc.identifier.citedreferenceChristmann RB, Sampaio-Barros P, Stifano G, et al. Association of interferon- and transforming growth factor β–regulated genes and macrophage activation with systemic sclerosis–related progressive lung fibrosis. Arthritis Rheumatol 2014; 66: 714 – 25.
dc.working.doiNOen
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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