2018
DOI: 10.1016/j.jid.2017.09.053
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Antisense Long Non-Coding RNAs Are Deregulated in Skin Tissue of Patients with Systemic Sclerosis

Abstract: Systemic sclerosis is an autoimmune disease characterized by fibrosis of skin and multiple organs of which the pathogenesis is poorly understood. We studied differentially expressed coding and non-coding genes in relation to systemic sclerosis pathogenesis with a specific focus on antisense non-coding RNAs. Skin biopsy-derived RNAs from 14 early systemic sclerosis patients and six healthy individuals were sequenced with ion-torrent and analyzed using DEseq2. Overall, 4,901 genes with a fold change >1.5 and a f… Show more

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Cited by 35 publications
(39 citation statements)
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“…5 6 8 The vast majority of gene expression studies in SSc are based on microarray technology, while NGS methods, namely RNA sequencing (RNA-seq), despite their advantages over existing approaches, have had limited applications. [9][10][11][12][13] RNA-seq yields an unlimited potential due to its resolution and deep-coverage, low sensitivity to background noise, high sensitivity at the extremes of gene expression ranges, high accuracy and concordance with quantitative PCR as well as high reproducibility. 14 High-quality RNA can be extracted from whole blood (WB) samples collected with RNA stabilisers, allowing the study of large populations 15…”
Section: Introductionmentioning
confidence: 99%
“…5 6 8 The vast majority of gene expression studies in SSc are based on microarray technology, while NGS methods, namely RNA sequencing (RNA-seq), despite their advantages over existing approaches, have had limited applications. [9][10][11][12][13] RNA-seq yields an unlimited potential due to its resolution and deep-coverage, low sensitivity to background noise, high sensitivity at the extremes of gene expression ranges, high accuracy and concordance with quantitative PCR as well as high reproducibility. 14 High-quality RNA can be extracted from whole blood (WB) samples collected with RNA stabilisers, allowing the study of large populations 15…”
Section: Introductionmentioning
confidence: 99%
“…Further studies revealed that TSIX siRNA significantly reduced type I collagen mRNA stability [ 119 ], implying a regulatory role of lncRNAs in the tissue fibrosis of SSc. RNA sequencing of skin biopsy samples found that 257 antisense lncRNAs are differentially expressed in early SSc patients compared to healthy individuals [ 120 ]. Recently, a comprehensive analysis of lncRNA expression in PBMCs from 20 SSc patients and 20 healthy donors revealed that the lncRNA ncRNA00201 is significantly downregulated in SSc.…”
Section: Important Roles Of Lncrnas In Autoimmune Diseasesmentioning
confidence: 99%
“… [ 113 ] IMMs lncRNA 7 ​S ​L Human Serum Autoantibody against lncRNA 7 ​S ​L is related to PM/DM. [ 115 ] ENST00000541196.1, uc011ihb.2, linc-DGCR6-1, Human Muscle Down-regulated [ 116 ] ENST00000551761.1, ENST00000583156.1 Human Muscle Down-regulated [ 116 ] H19, lncMyoD, MALAT1 Human Muscle Up-regulated [ 117 ] SSc TSIX Human Serum, skin fibroblast Up-regulated Increases type I collagen mRNA stability [ 119 ] CTBP1-AS2, AGAP2-AS1 Human Skin Up-regulated [ 120 ]. OTUD6B-AS1 Human Skin Down-regulated [ 120 ].…”
Section: Introductionmentioning
confidence: 99%
“…Previous RNA sequencing analysis of SSc and healthy control (HC) skin biopsies performed by our groups revealed 676 differentially expressed non-coding genes, 38% of these non-coding genes were classified as antisense genes. The differentially expressed antisense genes included ovarian tumor domain containing 6B (OTUD6B)-AS1 (22).…”
Section: Introductionmentioning
confidence: 99%
“…(A) OTUD6B-AS1 and OTUD6B are located on chromosome 8 and oriented head-to-head (GENCODE v27). (B) In the Leiden cohort, OTUD6B-AS1, and OTUD6B expression was analyzed in healthy control (HC), non-involved and involved skin of systemic sclerosis patients (SSc) using next generation sequencing [HC: n = 6, SSc (non-involved): n = 4, SSc (involved): n = 10, (22)]. (C) In the Zurich cohort, OTUD6B-AS1, and OTUD6B expression was measured in HC and non-involved SSc patients skin by qPCR (HC: n = 5, SSc (non-involved): n = 6).…”
Section: Introductionmentioning
confidence: 99%