Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis

• Published in: Nature communications Vol. 9; no. 1; pp. 4906 - 14
• Main Authors: Churko, Jared M., Garg, Priyanka, Treutlein, Barbara, Venkatasubramanian, Meenakshi, Wu, Haodi, Lee, Jaecheol, Wessells, Quinton N., Chen, Shih-Yu, Chen, Wen-Yi, Chetal, Kashish, Mantalas, Gary, Neff, Norma, Jabart, Eric, Sharma, Arun, Nolan, Garry P., Salomonis, Nathan, Wu, Joseph C.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 21.11.2018; Nature Publishing Group; Nature Portfolio
• Subjects: 13; 13/100; 38/91; 45; 631/208/514/1949; 631/532/2064/2158; Action Potentials; Basic Helix-Loop-Helix Transcription Factors - metabolism; Calcium; Calcium imaging; Calcium Signaling; Cardiomyocytes; Cell Differentiation; COUP Transcription Factor II - metabolism; CRISPR; Data processing; Differentiation; Disease control; Gene expression; Genetic Heterogeneity; Genome editing; Heart; Heterogeneity; Hierarchies; Humanities and Social Sciences; Humans; Induced Pluripotent Stem Cells; Medicine; multidisciplinary; Myocytes, Cardiac - metabolism; Physiology; Pluripotency; Population; Regulators; Repressor Proteins - metabolism; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Sequence Analysis, RNA; Single-Cell Analysis - methods; Splicing; Stem cells; T-Box Domain Proteins - metabolism; Transcription factors; Transcriptome
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-07333-4

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) have become a powerful tool for human disease modeling and therapeutic testing. However, their use remains limited by their immaturity and heterogeneity. To characterize the source of this heterogeneity, we applied complementary single-cell RNA-seq and bulk RNA-seq technologies over time during hiPSC cardiac differentiation and in the adult heart. Using integrated transcriptomic and splicing analysis, more than half a dozen distinct single-cell populations were observed, several of which were coincident at a single time-point, day 30 of differentiation. To dissect the role of distinct cardiac transcriptional regulators associated with each cell population, we systematically tested the effect of a gain or loss of three transcription factors ( NR2F2 , TBX5 , and HEY2 ), using CRISPR genome editing and ChIP-seq, in conjunction with patch clamp, calcium imaging, and CyTOF analysis. These targets, data, and integrative genomics analysis methods provide a powerful platform for understanding in vitro cellular heterogeneity. Human induced pluripotent stem cell derived cardiomyocytes are a powerful model for cardiogenesis and disease in vitro. Here the authors comprehensively map cardiac differentiation using multiple modalities, including single-cell RNA seq and CyTOF, in cells with a gain  or loss of function in key cardiac transcription factors.