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

Abstract

Formation and segregation of cell lineages forming the heart have been studied extensively but the underlying gene regulatory networks and epigenetic changes driving cell fate transitions during early cardiogenesis are still only partially understood. Here, we comprehensively characterize mouse cardiac progenitor cells (CPCs) marked by Nkx2-5 and Isl1 expression from E7.5 to E9.5 using single-cell RNA sequencing and transposase-accessible chromatin profiling (ATAC-seq). By leveraging on cell-to-cell transcriptome and chromatin accessibility heterogeneity, we identify different previously unknown cardiac subpopulations. Reconstruction of developmental trajectories reveal that multipotent Isl1+ CPC pass through an attractor state before separating into different developmental branches, whereas extended expression of Nkx2-5 commits CPC to an unidirectional cardiomyocyte fate. Furthermore, we show that CPC fate transitions are associated with distinct open chromatin states critically depending on Isl1 and Nkx2-5. Our data provide a model of transcriptional and epigenetic regulations during cardiac progenitor cell fate decisions at single-cell resolution.

Fate of developmental mechanisms of myocardial plasticity in the postnatal heart

“…3), indicates that Isl1 is translationally silenced in these cells. These findings are reminiscent of previous developmental studies suggesting that the Isl1 and Nkx2-5 CPC-GRNs suppress each other during early CM differentiation of aSHF CPCs (Jia et al, 2018;Prall et al, 2007). Of note, consistent with our previous findings, a small fraction of Isl1 + cells (27/483) and Nkx2-5 + cells (5/426) co-expressed the proto-oncogene Kit (Hatzistergos et al, 2016;Hatzistergos et al, 2015).…”

Cardiac competence of the paraxial head mesoderm fades concomitant with a shift towards the head skeletal muscle programme

“…Our data indicate that generic cardiac competence in the head mesoderm fades after HH5/6. Yet Isl1, which marks cells with myocardial but also vascular, smooth or head skeletal muscle potential (Jia et al, 2018;Nathan et al, 2008), and Hand2, a marker for head and trunk lateral mesoderm (Firulli et al, 2005;Lopez-Sanchez et al, 2009), could be activated in the PHM as late as HH10 and its expression dorsally expanded at HH13/14. This suggests that the PHM remains Bmp responsive.…”

“…They also control cardiogenesis directly, with Smad1/5/8-Smad4 complexes transactivating genes encoding key cardiac transcription factors such as Isl1, Nkx2.5, Gata4 and Tbx2 (Hami et al, 2011;Liberatore et al, 2002;Lien et al, 2002;Shirai et al, 2009;Si et al, 2014). Mesodermal cells expressing the pioneer factor Isl1 still have non-cardiogenic options, however the expression of Nkx2.5 drives cells towards a cardiomyocyte fate (Gao et al, 2019;Jia et al, 2018). Nkx2.5 is not sufficient for cardiomyocyte differentiation, but the combinatorial expression of cardiogenic transcription factors allows beating cardiomyocytes to form, both in vivo and in vitro (Ieda et al, 2010;Luna-Zurita et al, 2016;Zhou et al, 2012).…”

Combinatorial prediction of marker panels from single-cell transcriptomic data

“…Single-cell transcriptomic technologies have enabled the exciting discovery of novel cell populations within various in vivo contexts (Baron et al, 2016;Chapuy et al, 2019;Jia et al, 2018;Kernfeld et al, 2018;Kurtulus et al, 2019;Paul et al, 2015;Satija et al, 2015;Shekhar et al, 2016;Singer et al, 2016;Spallanzani et al, 2019;Vento-Tormo et al, 2018;Villani et al, 2017). Following the discovery of a new cell population of interest based on full transcriptome analysis (of typically a few thousand genes), follow-up studies require succinct gene-marker panels by which the cells of interest can be distinguished from the general cell population ( Figure 1).…”