DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells

• Published in: Nature communications 2024-04, Vol.15 (1), p.3080-3080, Article 3080
• Main Authors: Ren, Xingxing, Liu, Qiuyuan, Zhou, Peirong, Zhou, Tingyue, Wang, Decai, Mei, Qiao, Flavell, Richard A., Liu, Zhanju, Li, Mingsong, Pan, Wen, Zhu, Shu
• Format: Article
• Language: English
• Subjects: 13/31; 13/51; 13/89; 14/1; 14/28; 14/32; 38/77; 45/23; 45/41; 45/91; 631/136/532/2437; 631/250/347; 64/60; 692/699/1503/257; 96/100; Accumulation; Animals; Cell self-renewal; Colitis; Crypts; DEAD-box RNA Helicases - metabolism; Epithelial cells; Epithelial Cells - metabolism; Epithelium; Genomic instability; Genomics; Homeostasis; Humanities and Social Sciences; Humans; Inflammatory bowel disease; Inflammatory bowel diseases; Inflammatory Bowel Diseases - pathology; Inflammatory response; Intestinal Mucosa - metabolism; Intestine; Mice; multidisciplinary; Neoplasm Proteins - metabolism; Paneth cells; Paneth Cells - metabolism; Pathogenesis; R-Loop Structures; R-loops; Risk factors; Science; Science (multidisciplinary); Stability; Stem cells; Stem Cells - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-024-47235-2

Epithelial barrier dysfunction and crypt destruction are hallmarks of inflammatory bowel disease (IBD). Intestinal stem cells (ISCs) residing in the crypts play a crucial role in the continuous self-renewal and rapid recovery of intestinal epithelial cells (IECs). However, how ISCs are dysregulated in IBD remains poorly understood. Here, we observe reduced DHX9 protein levels in IBD patients, and mice with conditional DHX9 depletion in the intestinal epithelium ( Dhx9 ΔIEC ) exhibit an increased susceptibility to experimental colitis. Notably, Dhx9 ΔIEC mice display a significant reduction in the numbers of ISCs and Paneth cells. Further investigation using ISC-specific or Paneth cell-specific Dhx9 -deficient mice demonstrates the involvement of ISC-expressed DHX9 in maintaining epithelial homeostasis. Mechanistically, DHX9 deficiency leads to abnormal R-loop accumulation, resulting in genomic instability and the cGAS-STING-mediated inflammatory response, which together impair ISC function and contribute to the pathogenesis of IBD. Collectively, our findings highlight R-loop-mediated genomic instability in ISCs as a risk factor in IBD. Inflammatory bowel disease (IBD) is featured with epithelial barrier dysfunction, however, the underlying mechanism is less clear. Here, the authors show that DHX9 deficiency in intestinal stem cells (ISCs) induces accumulation of abnormal R-loops and subsequent genomic instability, leading to impairment of ISCs and development of IBD.