Principles of protein abundance regulation across single cells in a mammalian tissue

Protein synthesis and clearance are major regulatory steps of gene expression, but their in vivo regulatory roles across the cells comprising complex tissues remains unexplored. Here, we systematically quantify protein synthesis and clearance across over 4,200 cells from a primary tissue. Through integration with single-cell transcriptomics, we report the first quantitative analysis of how individual cell types regulate their proteomes across the continuum of gene expression. Our analysis quantifies the relative contributions of RNA abundance, translation, and protein clearance to the abundance variation of thousands of proteins. These results reveal an putative organizing principle: The contributions of both translation and protein clearance are linearly dependent on the cell growth rate. Further, we find that some proteins are primarily regulated by one mechanism (RNA abundance, translation, or clearance) across all cell types while the abundances of other proteins is dominated by different regulatory mechanisms across cell types. Our reliable multimodal measurements enabled quantifying and functionally interpreting molecular variation across single cells from the same cell type. The protein-protein correlations are substantially stronger than the mRNA-mRNA ones, which is mediated by protein clearance regulation. The protein-protein correlations are stronger not only for directly interacting proteins but also between functional sets of proteins. Further, these protein correlations allow identifying cell-type specific functional clusters. These clusters vary across cell types, revealing differences in metabolic processes coordination, partially mediated by protein clearance regulation. Our approach provides a scalable multiplexed framework for quantifying the regulatory processes shaping mammalian tissues and reveals organizing principles determining the relative contributions of translation and protein clearance to the proteomes of primary mammalian cells.