Increasing cell size remodels the proteome and promotes senescence

Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the proteome changes with cell size. Protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA damage-, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology through remodeling the proteome and provide a rationale for cell size control and polyploidization. Overall design: Primary human lung fibroblasts (HLF) were arrested in G1 with the Cdk4/6 inhibitor Palbociclib and sorted by FACS into different 4 bins according to their size: bin1 = smallest and bin4 = largest. "Pre-sort" cells were also collected before sorting and "sort-all" cells were run through the FACs procedure without separating according to cell size. For each sample, 200,000 HLF cells were mixed with 100,000 D. melanogaster S2 cells as a spike-in and RNA was extracted for RNA-seq. Two biological replicates with two technical replicates each were performed for each condition.