Genome-wide cheater screen reveals safeguards for cell cooperation during embryogenesis

Ensuring cooperation among formerly autonomous cells has been a central challenge in the evolution of multicellular organisms. One solution is monoclonality, but this option does not eliminate genetic and epigenetic variability, leaving room for exploitative behavior. We therefore hypothesized that embryonic development must be protected by robust regulatory mechanisms that prevent aberrant clones from superseding wild-type cells. Using a genome-wide screen in murine induced pluripotent stem cells, we identified a network of genes (centered on p53, topoisomerase 1, and olfactory receptors) whose downregulation caused the cells to replace wild-type cells, both in vitro and in the mouse embryo—without perturbing normal development. These genes thus appear to fulfill an unexpected role in fostering cell cooperation. We mixed knockdown (Top1 or p53) and mock embryonic stem cells and collected mRNA on day 4 of coculture, while cells were in the growth phase. These conditions allowed direct comparisons within a single cell type rather than a mixture of different cell types as seen under differentiation conditions. To extract information specific to cell cooperation as opposed to canonical p53 and Top1 functions, we compared results obtained from our mixed (1:4) culture with those obtained after mixing mRNA (also 1:4) from p53- or Top1-knockdown cells and mock cells that were grown homotypically.