Deregulation of Long Intergenic Non-coding RNAs in CD4+ T Cells of Lamina Propria in Crohn’s Disease Through Transcriptome Profiling

Abstract

Background The aetiology of Crohn’s disease [CD] involves immune dysregulation in a genetically susceptible individual. Genome-wide association studies [GWAS] have identified 200 loci associated with CD, ulcerative colitis, or both, most of which fall within non-coding DNA regions. Long non-coding RNAs [lncRNAs] regulate gene expression by diverse mechanisms and have been associated with disease activity in inflammatory bowel disease. However, disease-associated lncRNAs have not been characterised in pathogenic immune cell populations. Methods Terminal ileal samples were obtained from 22 CD patients and 13 controls. RNA from lamina propria CD4+ T cells was sequenced and long intergenic non-coding RNAs [lincRNAs] were detected. Overall expression patterns, differential expression [DE], and pathway and gene enrichment analyses were performed. Knockdown of novel lincRNAs XLOC_000261 and XLOC_000014 was performed. Expression of Th1 or Th17-associated transcription factors, T-bet and RORγt, respectively, was assessed by flow cytometry. Results A total of 6402 lincRNAs were expressed, 960 of which were novel. Unsupervised clustering and principal component analysis showed that the lincRNA expression discriminated patients from controls. A total of 1792 lincRNAs were DE, and 295 [79 novel; 216 known] mapped to 267 of 5727 DE protein-coding genes. The novel lincRNAs were enriched in inflammatory and Notch signalling pathways [p <0.05]. Furthermore, DE lincRNAs in CD patients were more frequently found in DNA regions with known inflammatory bowel disease [IBD]-associated loci. The novel lincRNA XLOC_000261 negatively regulated RORγt expression in Th17 cells. Conclusions We describe a novel set of DE lincRNAs in CD-associated CD4+ cells and demonstrate that novel lincRNA XLOC_000261 appears to negatively regulate RORγt protein expression in Th17 cells.

lncRNA STAT4-AS1 Inhibited TH17 Cell Differentiation by Targeting RORγt Protein

“…lncRNAs can also regulate the development and activation of TH17 cells by regulating the expression of ROR γ t protein. lncRNA XLOC_000261 negatively regulates the ROR γ t protein of TH17 cells in Crohn's disease [ 4 ].…”

Profiling non-coding RNA levels with clinical classifiers in pediatric Crohn’s disease

“…While changes in ncRNA during CD have been documented [6,10,11,28,29], little is known about the role of ncRNAs in different location of the intestine. At diagnosis, the location of the diseased mucosal biopsy obtained through colonoscopy often determines diagnosis of IBD subtypes.…”

LncRNA-BG Inhibited Th17 Cells Differentiation By Targeting RORγt Protein.

“…LncRNAs are involved in cell development, differentiation, and growth by regulating all aspects of gene expression. For example, lncRNA XLOC _000261 negatively regulates the RORγt protein of Th17 cells in Crohn's disease [34]. LncRNA-MEG3 binds microRNA-17 as a ceRNA to regulate RORγt, ultimately affecting Treg/Th17 balance in asthma [35].…”