Inflammatory bowel disease (IBD) is associated with significant morbidity and mortality. Currently, the etiology of IBD is unknown. A new area of research is now focusing on aspects of gene regulation from previously uninvestigated portions of the genome, namely long noncoding RNAs (lncRNAs). These new players have been implicated in a variety of cell processes including cell-cycle control, embryonic development, and inflammation. However, their role in IBD has yet to be fully determined. To study their function, unbiased evaluations of the differentially expressed lncRNAs in IBD were performed.Methods:
RNA was extracted from IBD and control patients. A total of 8 ulcerative colitis (UC) patients, 7 Crohn's disease (CD) patients, and 7 control samples were profiled for lncRNA and protein-coding RNA expression using Arraystar lncRNA arrays. A validation cohort of 16 control and 15 UC patient colonic samples were used for qRT-PCR gene expression analysis. Gene pathway analysis was performed using Ingenuity Pathway Analysis software to determine molecular and cellular pathways associated with differentially expressed lncRNAs. Human NCM460 colonocytes were treated with TGF-beta and qRT-PCR was performed for gene expression analysis of lncRNAs.Results:
The lncRNA, CDKN2B-AS1, was found to be significantly downregulated by 12-fold (P-value = 0.0009) in UC patient samples and by 4.9-fold (P-value = 0.041) in CD patient samples when compared to controls. A separate validation cohort confirmed these results and showed significant downregulation in IBD colon samples. Analyzing the relationship with protein coding RNAs found that CDKN2B-AS1 was inversely correlated with TGF-beta1 expression. When TGF-beta was added to a normal human colonocyte cell line, CDKN2B-AS1 was significantly downregulated at 18 hours but not at 4 hours. Finally, gene pathway analysis revealed that differential expression of CDKN2B-AS1 is associated with molecular and cellular pathways associated with lipid metabolism and with cell-cell interactions.Conclusions:
The study of lncRNAs in IBD yields new and exciting targets for investigation. This analysis showed that CDKN2B-AS1 is a new lncRNA associated with IBD pathogenesis. Its expression is significantly downregulated in IBD patients and is regulated by TGF-beta signaling. Gene pathway analysis revealed that CDKN2B-AS1 is associated with gene pathways related to lipid metabolism and cell-cell interactions.