Abstract

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.

Details

Title
Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis
Author
Churko, Jared M 1 ; Garg, Priyanka 2 ; Treutlein, Barbara 3 ; Venkatasubramanian, Meenakshi 4 ; Wu, Haodi 2 ; Lee, Jaecheol 2 ; Wessells, Quinton N 2 ; Shih-Yu, Chen 5 ; Wen-Yi, Chen 2 ; Chetal, Kashish 4 ; Mantalas, Gary 3 ; Neff, Norma 3 ; Jabart, Eric 6 ; Sharma, Arun 2   VIAFID ORCID Logo  ; Nolan, Garry P 5 ; Salomonis, Nathan 4 ; Wu, Joseph C 2 

1  Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Departments of Medicine and Radiology, Stanford University, Stanford, CA, USA; Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA 
2  Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Departments of Medicine and Radiology, Stanford University, Stanford, CA, USA 
3  Department of Bioengineering, Stanford University, Stanford, CA, USA 
4  Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA 
5  Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA 
6  Zephyrus Biosciences, Berkeley, CA, USA; Department of Biochemistry, Stanford University, Stanford, CA, USA 
Pages
1-14
Publication year
2018
Publication date
Nov 2018
Publisher
Nature Publishing Group
e-ISSN
20411723
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1038/s41467-018-07333-4
ProQuest document ID
2136548997
Copyright
© 2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.