Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity

Abstract

Analyses on the cellular level are indispensable to expand our understanding of complex tissues like the mammalian heart. Single-nucleus sequencing (snRNA-seq) allows for the exploration of cellular composition and cell features without major hurdles of single-cell sequencing. We used snRNA-seq to investigate for the first time an entire adult mammalian heart. Single-nucleus quantification and clustering led to an accurate representation of cell types, revealing 24 distinct clusters with endothelial cells (28.8%), fibroblasts (25.3%), and cardiomyocytes (22.8%) constituting the major cell populations. An additional RNA velocity analysis allowed us to study transcription kinetics and was utilized to visualize the transitions between mature and nascent cellular states of the cell types. We identified subgroups of cardiomyocytes with distinct marker profiles. For example, the expression of Hand2os1 distinguished immature cardiomyocytes from differentiated cardiomyocyte populations. Moreover, we found a cell population that comprises endothelial markers as well as markers clearly related to cardiomyocyte function. Our velocity data support the idea that this population is in a trans-differentiation process from an endothelial cell-like phenotype towards a cardiomyocyte-like phenotype. In summary, we present the first report of sequencing an entire adult mammalian heart, providing realistic cell-type distributions combined with RNA velocity kinetics hinting at interrelations.

“Single-nucleus RNA-seq2 reveals a functional crosstalk between liver zonation and ploidy”

“…In this context, single-nucleus RNA-seq has emerged as a complementary approach that relies on the unbiased assessment of nuclei from all cells present in a tissue [20,21,36]. The analysis of the nuclear transcriptome has been proven to be very powerful to study cell type diversity in the mouse and human tissues, including brain [21,[23][24][25][26][27]111]; spinal cord [50]; breast cancer [51]; kidney [29][30][31][32]; lung [28]; heart [33,34]; and a variety of human tumor samples [36].…”

“…Single-nucleus RNA-seq (snRNA-seq) has emerged as a complementary approach to study complex tissues at a single-cell level [20,21], including brain [21][22][23][24][25][26][27], lung [28], kidney [29][30][31][32] and heart [33,34] in mouse and human frozen samples [35,36]. However, there are no snRNA-seq methods tailored for frozen liver tissues.…”

Big Data Approaches in Heart Failure Research

“…Single-cell RNAseq has already been applied to study the cardiovascular system (reviewed in [77][78][79][80]). To date, studies have focused on the description of cardiac cell lineage heterogeneity and trajectory in mice [79,[81][82][83], as well as on human cardiogenesis [84][85][86][87][88].…”

The Roles of Noncardiomyocytes in Cardiac Remodeling

“…The heart is a complex multicellular tissue consisting of a heterogeneous population of CMs and morphologically and functionally distinct non-CMs (including fibroblasts, immune cells, pericytes and endothelial cells), with CMs accounting for approximately 22.8% of the total population and non-CMs accounting for the rest [8]. Cardiac remodeling is well regulated by cell apoptosis, proliferation, migration and differentiation in cardiac or extracardiac tissues.…”