A single-cell and tissue-scale analysis suite resolves Mixl1’s role in heart development

TL;DR

This paper introduces COSICC, a new tool for analyzing gene perturbations in developing embryos, revealing key roles of T and Mixl1 in heart and mesoderm development.

Contribution

COSICC is a novel statistical suite for analyzing gene perturbation effects in complex developmental cell populations.

Findings

T plays a key cell-autonomous role in intermediate mesoderm and limb bud development.

Mixl1 depletion impairs the juxta-cardiac field, epicardium, and cardiac development.

COSICC addresses compositional bias in single-cell profiling of developmental defects.

Abstract

Perturbation studies using gene knockouts have become a key tool for understanding the roles of regulatory genes in development. However, large-scale studies dissecting the molecular role of development master regulators in every cell type throughout the embryo are technically challenging and scarce. Here, we systematically characterize the knockout effects of the key developmental regulators T/Brachyury and Mixl1 in gastrulation and early organogenesis using single-cell profiling of chimeric mouse embryos. For the analysis of these experimental data, we present COSICC, an effective suite of statistical tools to characterize perturbation effects in complex developing cell populations. We gain insights into T’s role in lateral plate mesoderm, limb development, and posterior intermediate mesoderm specification. Furthermore, we generate Mixl1−/− embryonic chimeras and reveal the role of this key transcription factor in discrete mesoderm lineages, in particular concerning developmental dysregulation of the recently identified juxta-cardiac field.

•COSICC enables multi-layered statistical analysis of gene perturbation effects•COSICC addresses compositional bias in single-cell profiling of development defects•T plays a key cell-autonomous role in intermediate mesoderm and limb bud development•Mixl1 depletion impairs juxta-cardiac field, epicardium, and cardiac development

COSICC enables multi-layered statistical analysis of gene perturbation effects

COSICC addresses compositional bias in single-cell profiling of development defects

T plays a key cell-autonomous role in intermediate mesoderm and limb bud development

Mixl1 depletion impairs juxta-cardiac field, epicardium, and cardiac development

Biocomputational method; Genomic analysis; Genomics

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