Pareto Optimality Reveals an Atlas of Cellular Archetypes

We sought to discover universal organizing principles behind phenotypic variation within cell types. Pareto optimality describes how trade-offs between optimal solutions account for variation, predicting that the boundary points of a data distribution reflect specialized functions. We hypothesized that Pareto optimality dominates transcriptomic variation across all cell types. We used the Tabula Sapiens atlas of single-cell RNA sequencing across cell types and tissues in the human body to test this hypothesis and discovered that most cell types adhere to this theory. This enabled us to use this principled method to characterize the functions performed by each cell type. These phenotypes are derived from an unbiased approach and do not incorporate ideas from existing biological models or theories, and yet in many cases they recapitulate our understanding of the functions of major cell types. Ultimately, we conclude that multi-objective optimization broadly shapes the observed phenotypic variation within cell types. This finding enables us to write explicit representations of the low-dimensional manifolds on which transcriptomes of single cells reside. This can inform the design of the next generation of virtual cell language models, which aim to statistically learn low-dimensional transcriptomic manifolds.