Charting cellular differentiation trajectories with Ricci flow

Abstract

Complex biological processes, such as cellular differentiation, require an intricate rewiring of intra-cellular signalling networks. Previous characterisations of these networks revealed that promiscuity in signalling, quantified by a raised network entropy, underlies a less differentiated and malignant cell state. A theoretical connection between entropy and Ricci curvature has led to applications of discrete curvatures to characterise biological signalling networks at distinct time points during differentiation and malignancy. However, understanding and predicting the dynamics of biological network rewiring remains an open problem. Here we construct a framework to apply discrete Ricci curvature and Ricci flow to the problem of biological network rewiring. By investigating the relationship between network entropy and Forman-Ricci curvature, both theoretically and empirically on single-cell RNA-sequencing data, we demonstrate that the two measures do not always positively correlate, as has been previously suggested, and provide complementary rather than interchangeable information. We next employ discrete normalised Ricci flow, to derive network rewiring trajectories from transcriptomes of stem cells to differentiated cells, which accurately predict true intermediate time points of gene expression time courses. In summary, we present a differential geometry toolkit for investigation of dynamic network rewiring during cellular differentiation and cancer.