Integrated transcriptomic and proteomic profiling of colonic tissue in interleukin-10-deficient mice

Interleukin (IL)-10, a prominent anti-inflammatory cytokine predominantly secreted by various immune cells, plays a crucial role in the pathophysiological mechanisms of inflammatory bowel disease (IBD). Mice deficient in IL-10 (IL-10^-/-) progressively develop features of idiopathic enterocolitis as they mature. To advance our understanding of the molecular mechanisms underpinning chronic enterocolitis in IL-10^-/- mice, we performed an extensive analysis of the transcriptome and proteome of colonic tissue from these mice manifesting colitis. The study employed bulk RNA sequencing (RNA-seq) and four-dimensional (4D) label-free mass spectrometry (MS) to facilitate an integrated analysis of the resultant omics data. Following an extensive series of quality control evaluations, 635 genes and 1,071 proteins were identified as differentially expressed. The principal aim of this integrated analysis was to elucidate novel signaling pathways and identify potential therapeutic targets for IBD treatment.