Mitochondrial DNA mutation triggers early-onset intestinal epithelial cell dysfunction during acute colitis [mtscATAC-seq]

Mitochondrial DNA (mtDNA) mutations cause multisystem disorders, involving gastrointestinal (GI) dysfunction. However, the mechanism underlying the selection against mutant mtDNA and the impact of pathogenic mtDNA mutations on intestinal epithelial cells (IECs) remain unclear. Here, we employed mitochondrial single-cell assay for transposase-accessible chromatin with sequencing (mtscATAC-seq) to examine the heteroplasmy of IECs in m.G5081A (mt-tRNA) and m.G12918A (mt-mRNA) mutant mouse models over a two-year lifespan. Our findings reveal age-dependent purifying selection against mutant mtDNA across nine IEC subtypes, a process originating in intestinal stem cells (ISCs) that does not strengthen during cellular differentiation. Combining the analysis of single-cell RNA sequencing, we found that young mice with high m.G5081A mutation loads exhibit IEC dysfunction, including impaired enterocyte differentiation and defective Paneth cell granule formation. The m.G5081A mutant mice exhibit increased susceptibility to DSS-induced acute colitis due to compromised intestinal barrier function and impaired wound healing caused by the mtDNA mutation. Collectively, our findings reveal the cellular dynamics of mtDNA selection in IECs and demonstrate the functional consequences of mitochondrial dysfunction on intestinal health, providing insights relevant to mitochondrial disease pathogenesis and management.