Research of the Month

November 2018

Nat Commun. 2018 Nov 19;9(1):4877

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

Jia G, Preussner J, Chen X, Guenther S, Yuan X, Yekelchyk M, Kuenne C, Looso M, Zhou Y, Teichmann S, Braun T

Heart is the first organ that emerges during mammalian embryonic development. The long-lasting challenges for understanding heart development are to characterize cell fate transition, specification and hierarchical lineage descendants of cardiac progenitor cells (CPCs), and underlying gene regulatory networks and epigenetic mechanisms that orchestrate such processes. However, the cell fate decisions of CPCs during cardiogenesis remain unclear due to limited cell numbers. Recently, the revolutionary single-cell analysis techniques such as single-cell RNA sequencing (scRNA-seq) and ATAC-seq (transposase-accessible chromatin profiling, scATAC-seq) allow researchers to comprehensively characterize thousands of transcriptomes at the single cell level in a high-throughput manner.

 In this study, the ECCPS investigators comprehensively analyzed Nkx2.5+ and Isl1+ cardiac progenitor cells at embryonic day 7.5, 8.5 and 9.5 using single-cell RNA sequencing, representing the first in vivo transcriptome-wide interrogation of the first and second heart fields during early mammalian cardiogenesis. By reconstructing developmental trajectories and transcriptional regulator networks, they showed when and how the progenitor cell fate is committed to a specific lineage: multipotent Isl1+ CPCs pass through an attractor state before separating into different developmental branches, whereas extended expression of Nkx2-5 commits CPCs to an unidirectional cardiomyocyte fate. Using transposase-accessible chromatin with high throughput sequencing (ATAC-seq) approach, they showed that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl1 and Nkx2-5. Moreover, using knockout mice, they investigated the molecular function of Isl1 and demonstrate its key role in subpopulation and lineage establishment in the second heart field. The study reveals the heterogeneity of cardiac progenitor cells and establishes a reference model and general framework for studying early cardiogenesis at single-cell resolution.

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