Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis
Nat Commun.. 2018-11-21;9(1):4906.
- 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.
- Consortium data used in this publication
- GSE81585
- Datasets
- DSR800JBR, DSR123YJD, DSR708PNY, DSR448QBY, DSR203VFL, DSR570MDA, DSR546NZS, DSR385LDV, DSR728MLZ, DSR510GLX, DSR594RNW, DSR460AFX, DSR360NXX, DSR964YUP, DSR709RWQ, DSR864VBI, DSR420MME, DSR438OVA, DSR442WBJ, DSR523BYW, DSR753PQV, DSR804FRN, DSR056NZI, DSR049INC, DSR289TPA, DSR908LAA, DSR785CVC, DSR009PYY, DSR479ETU, DSR703EAO, DSR510DCG, DSR523VBC, DSR114DGN, DSR255MJH, DSR987QRR, DSR707HLD, DSR039ZIN, DSR699GKY, DSR812PWH, DSR628XYG, DSR253OHG, DSR702VLZ, DSR910CXJ, DSR534WVZ, DSR462RQW, DSR748KEY, DSR609FKH, DSR303HZW, DSR888ZBQ, DSR369WKA, DSR286ZXO, DSR278GJW, DSR984GQF, DSR221VNW, DSR062UBY, DSR406HFH, DSR048JEU, DSR528YUV, DSR319BAH, DSR381AXH, DSR516JZH, DSR824LKP, DSR799KRH, DSR033FON, DSR457NJK, DSR134JTB, DSR669OGJ, DSR619HFK, DSR588GEP, DSR590ZPP, DSR866RIC, DSR549KYE, DSR356BUO, DSR111OVX, DSR546ZOC, DSR574ACJ, DSR846XIM, DSR707NJQ, DSR960ISM, DSR384FIT, DSR082OXX, DSR601PVN, DSR548YXN, DSR616QBR, DSR386UZR, DSR329EZQ, DSR266RUV, DSR054FJB, DSR102MFV, DSR414LZZ, DSR106BSY, DSR244KDG, DSR100RFF, DSR899VXA