A dynamical systems treatment of transcriptomic trajectories in hematopoiesis

Inspired by Waddington's illustration of an epigenetic landscape, cell -fate transitions have been envisioned as bifurcating dynamical systems, wherein exogenous signaling dynamics couple to the enormously complex signaling and transcriptional machinery of a cell to elicit qualitative transitions in its collective state. Single-cell RNA sequencing (scRNA-seq), which measures the distributions of possible transcriptional states in large populations of differentiating cells, provides an alternate view, in which development is marked by the variations of a myriad of genes. Here, we present a mathematical formalism for rigorously evaluating, from a dynamical systems perspective, whether scRNA-seq trajectories display statistical signatures consistent with bifurcations and, as a case study, pinpoint regions of multistability along the neutrophil branch of hematopoeitic differentiation. Additionally, we leverage the geometric features of linear instability to identify the low-dimensional phase plane in gene expression space within which the multistability unfolds, highlighting novel genetic players that are crucial for neutrophil differentiation. Broadly, we show that a dynamical systems treatment of scRNA-seq data provides mechanistic insights into the high-dimensional processes of cellular differentiation, taking a step toward systematic construction of mathematical models for transcriptomic dynamics.

Automated summary

This study presents a mathematical formalism to analyze single-cell transcriptomic data from a dynamical systems perspective. It reveals the multistability of cellular differentiation and identifies the low-dimensional phase plane in gene expression space. The study also uncovers novel genetic players crucial for neutrophil differentiation.