Excessive nucleic acid R-loops induce mitochondria-dependent epithelial cell necroptosis and drive spontaneous intestinal inflammation

Abstract

Oxidative stress, which can be activated by a variety of environmental risk factors, has been implicated as an important pathogenic factor for inflammatory bowel disease (IBD). However, how oxidative stress drives IBD onset remains elusive. Here, we found that oxidative stress was strongly activated in inflamed tissues from both ulcerative colitis patients and Crohn’s disease patients, and it caused nuclear-to-cytosolic TDP-43 transport and a reduction in the TDP-43 protein level. To investigate the function of TDP-43 in IBD, we inducibly deleted exons 2 to 3 of Tardbp (encoding Tdp-43) in mouse intestinal epithelium, which disrupted its nuclear localization and RNA-processing function. The deletion gave rise to spontaneous intestinal inflammation by inducing epithelial cell necroptosis. Suppression of the necroptotic pathway with deletion of Mlkl or the RIP1 inhibitor Nec-1 rescued colitis phenotypes. Mechanistically, disruption of nuclear TDP-43 caused excessive R-loop accumulation, which triggered DNA damage and genome instability and thereby induced PARP1 hyperactivation, leading to subsequent NAD + depletion and ATP loss, consequently activating mitochondrion-dependent necroptosis in intestinal epithelial cells. Importantly, restoration of cellular NAD + levels with NAD + or NMN supplementation, as well as suppression of ALKBH7, an α-ketoglutarate dioxygenase in mitochondria, rescued TDP-43 deficiency-induced cell death and intestinal inflammation. Furthermore, TDP-43 protein levels were significantly inversely correlated with γ-H2A.X and p-MLKL levels in clinical IBD samples, suggesting the clinical relevance of TDP-43 deficiency-induced mitochondrion-dependent necroptosis. Taken together, these findings identify a unique pathogenic mechanism that links oxidative stress to intestinal inflammation and provide a potent and valid strategy for IBD intervention.

Role played by MDSC in colitis-associated colorectal cancer and potential therapeutic strategies

“…Studies have shown that oxidative stress induces the misvocalization of nuclear RNA or the DNA-binding protein TDP-43, which further leads to the overaccumulation of the R-loop (i.e., DNA in the form of an RNA heterozygous strand structure formed by DNA and RNA), which in turn triggers DNA damage and instability in the genome, resulting in the over-activation of the key enzyme for DNA repair, PARP1. This further trigger depletion of the coenzyme NAD + and ATP deficiency, which promotes the onset of mitochondria-dependent necrotic apoptosis in intestinal epithelial cells, which in turn drives the onset of spontaneous intestinal inflammation (Yang et al 2024 ). In addition, excess ROS can cause damage to intestinal cells.…”

“…For example, the presence of commensal Gram-negative gut bacteria can lead to the accumulation of MDSCs (Zhang et al 2020 ). FadA adhesin produced by Clostridium nucleatum binds to E-calmodulin to produce pro-inflammatory factors and activates the TLR4/NF-κB signaling path way via lipopolysaccharide LPS to promote the recruitment of MDSCs to the infection site, this recruitment activates the Wnt/β-catenin signaling pathway, which further modulates the bacterial adhesion and invasion into the epithelial cells, ultimately, this process promotes the proliferation of colorectal cancer cells that Promotion of colorectal cancer (Yang et al 2024 ). Enterotoxin-producing bacterium Enterobacteriaceae fragilis (ETBF) induces Th17 recruitment and inhibits T-cell proliferation, contributing to a pro-inflammatory milieu that favors the production and differentiation of pre-tumorigenic monocyte-derived cells (MDSCs), as a consequence, the chances of developing colorectal cancer may increase (Thiele Orberg et al 2017 ).…”