Global quantification of mammalian gene expression noise

Abstract Even cells of the same type growing in the same environment show cell-to-cell differences in protein abundance, a phenomenon known as gene expression noise. This variability can be decomposed into intrinsic components, reflecting molecular randomness, and extrinsic components, arising from differences in cellular state. While gene expression noise has been studied genome-wide in microbes, its global organization remains largely unknown in mammalian cells. Here, we develop a spike-in-based stable isotope single-cell proteomics approach that enables robust quantification of protein-level gene expression noise across thousands of human proteins. We find that protein noise scales inversely with abundance until reaching a plateau, consistent with an extrinsic noise floor and conserved scaling principles observed in bacteria and yeast. Cell cycle stage and cell size contribute substantially to protein variability but do not fully account for the observed heterogeneity. Gene-specific features such as mRNA and protein half-lives and translation efficiency show only weak associations with protein noise, and variability at the mRNA level is a weak predictor of protein variability. Instead, protein noise is largely extrinsic, with coordinated variation across proteins encoding biologically organized cellular states. Consistently, coordinated proteome programs predict intercellular differences in proteome dynamics, linking protein variability to cellular function. Together, these results provide a proteome-wide view of gene expression noise in mammalian cells, establishing that protein-level variability encodes structured and functionally relevant differences in cellular state.