Cells and gene expression programs in the adult human heart

Monika Litvinukova; Carlos Talavera-Lopez; Henrike Maatz; Daniel Reichart; Catherine L. Worth; Eric L. Lindberg; Masatoshi Kanda; Krzysztof Polanski; Eirini S. Fasouli; Sara Samari; Kenny Roberts; Elizabeth Tuck; Matthias Heinig; Daniel DeLaughter; Barbara McDonough; Hiroko Wakimoto; Joshua M. Gorham; Emily Nadelmann; Krishnaa T. Mahbubani; Kourosh Saeb-Parsy; Giannino Patone; Joseph J Boyle; Hongbo Zhang; Hao Zhang; Anissa Viveiros; Gavin Oudit; Omer Bayraktar; J. G. Seidman; Christine Seidman; Michela Noseda; Norbert Hubner; Sarah A. Teichmann

Overview of the cellular landscape of the adult human heart Samples were obtained from six cardiac regions including the free wall of each chamber (left/right ventricle, left/right atrium), denoted as LV, RV, LA, RA, and from the LV apex (AX) and interventricular septum (SP). To capture the heterogeneity of cardiac cell populations, samples were collected as transmural tissue segments that span the three cardiac layers (epicardium, myocardium and endocardium; Figure 1A ) from 14 normal hearts (seven females, seven males) of North American and British organ donors (ages 40-75 years; Figure 1B and Supplementary Table A1 ). We isolated single cells and single nuclei, as the large sizes of cardiomyocyte (CM) are not captured by the 10X Genomics Chromium platform. Fresh tissues were mechanically and enzymatically processed to dissociate single cells, and subsequently cardiac immune cells were enriched from the cell fraction using CD45+ magnetic selection. Single nuclei were isolated from frozen heart tissues and purified by fluorescent activated cell sorting. The transcriptome of single cells and nuclei were profiled using the 10X Genomics Single Cell Gene Expression Solution ( Figure 1A ). After processing, all data from nuclei, cells and CD45+ enriched cells were batch-aligned using a generative deep variational autoencoder 5 , prior to unsupervised clustering. After processing and quality controls, we obtained a total of 45,870 cells, 78,023 CD45+ enriched cells and 363,213 We found differences in the distribution of cell types across donors, even within the same region, and correlations between different cell types at the same site ( Supplementary Table A3 ). For example, in LV, AX, SP and RV tissues, the proportions of vCM and FB were negatively correlated ( p -value=2.0e-4), while there was a positive correlation among the proportions of PC, SMC, and NC cells ( p -value<1e-4). We suggest that these data reflect random sampling that included vessels with EC, PC, SMC, and concurrently fewer CM.