Volume 33, No 5, May 2023
EISSN: 1748-7838 2018
impact factor 17.848*
(Clarivate Analytics, 2019)
Volume 33 Issue 5, May 2023: 372-388 |
A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis
Hongdi Ma1,2,† , Taidou Hu1,2,† , Wanyin Tao1,2 , Jiyu Tong3 , Zili Han1,2 , Dietmar Herndler-Brandstetter3 , Zheng Wei3 , Ruize Liu4 , Tingyue Zhou1,2 , Qiuyuan Liu5 , Xuemei Xu1 , Kaiguang Zhang1 , Rongbin Zhou2 , Judy H. Cho6 , Hua-Bing Li7,* , Hailiang Huang4,* , Richard A. Flavell3,8,* , Shu Zhu1,2,9,10,*1Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
Inflammatory bowel diseases (IBD) are known to have complex, genetically influenced etiologies, involving dysfunctional interactions between the intestinal immune system and the microbiome. Here, we characterized how the RNA transcript from an IBD-associated long non-coding RNA locus (“CARINH-Colitis Associated IRF1 antisense Regulator of Intestinal Homeostasis”) protects against IBD. We show that CARINH and its neighboring gene coding for the transcription factor IRF1 together form a feedforward loop in host myeloid cells. The loop activation is sustained by microbial factors, and functions to maintain the intestinal host-commensal homeostasis via the induction of the anti-inflammatory factor IL-18BP and anti-microbial factors called guanylate-binding proteins (GBPs). Extending these mechanistic insights back to humans, we demonstrate that the function of the CARINH/IRF1 loop is conserved between mice and humans. Genetically, the T allele of rs2188962, the most probable causal variant of IBD within the CARINH locus from the human genetics study, impairs the inducible expression of the CARINH/IRF1 loop and thus increases genetic predisposition to IBD. Our study thus illustrates how an IBD-associated lncRNA maintains intestinal homeostasis and protects the host against colitis.