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Spatial discordances between mRNAs and proteins in the intestinal epithelium

ABSTRACT: A cell’s proteome is an important determinant of its functional state, however the use of transcriptomes as reliable proxies for cellular proteomes is debatable. In the small intestine, nutrient absorbing enterocytes operate for four days as they migrate along villi, highly graded microenvironments. Spatial transcriptomics demonstrated profound zonation in enterocyte gene expression, but how this variability translates to protein content is unclear. Here, we used spatial sorting to generate global spatial maps of enterocyte proteins and mRNAs along the villus axis. We found that both were zonated, yet often spatially anti-correlated. We developed a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, and demonstrate that space-independent protein-synthesis delays can explain the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the intestinal epithelium and highlights the importance of protein measurements for inferring states of tissue cells that operate outside of steady state.

ORGANISM(S): Mus musculus

PROVIDER: GSE164746 | GEO | 2021/10/09

REPOSITORIES: GEO

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