Bespoke single cell molecular and tissue-scale analysis reveals mechanisms underpinning development and disease in complex developing cell populations

Abstract

Perturbation studies using gene knockouts have become a key tool for understanding the roles of regulatory genes in development and disease. Here we systematically characterise the effects of the knockout of the key developmental regulators T and Mixl1 in chimeric mouse embryos during gastrulation and organogenesis. We present a comprehensive and effective suite of tools for systematic characterisation of effects at the level of differential abundance of cell types, lineage development, and gene dysregulation. We apply this strategy to a novel chimera data set with Mixl1 knockout, and reveal a disruption in epicardium development in the absence of Mixl1, characterized by lack of upregulation along the lineage of the key transcription factor Tbx18 and Wnt regulator Sfrp5. Finally, we demonstrate the broad utility of our perturbSuite framework for testing progression and differential expression along lineages by applying it to published AML patient data. Specifically, we show how different responses to therapy are reflected in changes in gene expression along the myeloid trajectory between healthy and AML patients.