Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

Cellular division is a fundamental source of cell-to-cell variability, and studies of transcript and protein abundances have revealed several hundred genes that are regulated by the cell cycle1-8. However, none of these studies provide single-cell resolution of protein expression, leaving an incomplete understanding of cell-to-cell heterogeneity and the roles of cycling transcripts and proteins. Here, we present the first comprehensive map of spatiotemporal heterogeneity of the human proteome by integrating proteomics at subcellular resolution, single-cell transcriptomics, and pseudotime measurements of individual cells within the cell cycle. We identify that 17% of the human proteome displays cell-to-cell variability, of which 26% is correlated to cell cycle progression, and we present the first evidence of cell cycle association for 235 proteins. Only 15% of proteomic cell cycle regulation is due to transcriptomic cycling, which points to other means of regulation such as post-translational modifications. For proteins regulated at the transcript level, we observe a 7.7 hour delay between peak expression of transcript and protein on average. This spatially resolved proteomic map of the cell cycle has been integrated into the Human Protein Atlas and serves as a valuable resource for accelerating molecular studies of the human cell cycle and cell proliferation.