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Critical for cellular maintenance and repair, autophagy recycles damaged or redundant cellular components. Dysregulated autophagy is associated with progressive cellular injury in various liver pathologies. However, the role of autophagy in intestinal failure-associated liver disease has not previously been investigated. Using a preclinical murine model of short bowel syndrome, we explored the role of autophagy impairment at early and late time points. Regardless of sex, small bowel resected (SBR) mice demonstrated significant liver injury compared to sham controls, exhibiting elevated serum transaminases, altered liver histology, and increased mRNA expression of endoplasmic reticulum stress marker (Ddit3) and oxidative stress marker ( Nqo1) . Autophagy impairment was supported by increased p62 mRNA and protein expression in SBR liver and then confirmed with qualitative autophagy flux assay which suggested alteration of autophagy induction in SBR liver. Single nuclear RNA sequencing identified a cluster of hepatocytes in the SBR liver with increased p62 expression. These hepatocytes showed enrichment of genes related to the PI3K-Akt and ErbB pathways both which converge on mTORC1. Immunohistochemical distribution of pS6 confirmed increased mTORC1 activation in the SBR hepatocytes. Overall autophagy dysregulation is correlated with mTORC1 activation in SBR mice and is associated with greater liver injury.