Multilevel proteomic profiling of colorectal adenocarcinoma cell differentiation to characterize an intestinal epithelial model

Emergent advancements on the intestinal microbiome for human health and disease treatment necessitates well-defined intestinal cellular models to study and rapidly assess host, microbiome, and drug interactions. This study characterized molecular alterations during Caco-2 cell differentiation, an epithelial intestinal model, using quantitative multi-omic approaches. We demonstrated that both spontaneous and medium-induced cellular differentiations displayed similar protein and pathway changes, including the down-regulation of proteins related to translation and proliferation, and up-regulation of proteins related to cell adhesion, molecule binding and metabolic pathways. Acetyl-proteomics revealed decreased histone acetylation and increased acetylation in proteins associated with mitochondria functions in differentiated cells. Butyrate-containing differentiation medium accelerates differentiation, with earlier up-regulation of proteins related to differentiation and host-microbiome interactions. These results emphasize the controlled progression of Caco-2 differentiation toward a specialized intestinal epithelial-like cell. This further enhances their characterization, establishing their suitability for facilitating the effective evaluation of risk and quality in microbiome-directed therapeutics.