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Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism

ABSTRACT: Background: The histone demethylase KDM1A is a multi-faceted regulator of critical developmental processes, including mesodermal and cardiac tube formation during mice gastrulation. The fine-tuning of KDM1A splicing has been linked to regulating the transcriptional program of excitable cells such as neurons. However, it is unknown whether modulating the expression of KDM1A isoforms is crucial for the specification and maintenance of cell identity of other cell types sensitive to electrical cues such as the cardiomyocytes. Objective: We investigated the role of ubKDM1A and KDM1A+2a ubiquitous splice variants during cardiomyogenesis and evaluated their impact on the regulation of cardiac differentiation in vitro. Methods and Results: We discovered a temporal modulation of ubKDM1A and KDM1A+2a isoform levels during human and mouse fetal cardiac development. Therefore, we generated human embryonic stem cells (hESCs) exclusively devoid of one or both isoforms and assessed their potential to derive cardiomyocytes. KDM1A depletion severely impaired cardiac differentiation. Conversely, KDM1A+2a-/- hESCs give rise to functional cardiomyocytes, displaying increased beating amplitude and frequency compared to wild-type cells. Transcriptomic profiling revealed that KDM1A-/- cardiomyocytes fail to activate an effective cardiac transcriptional program, while the depletion of KDM1A+2a enhances the expression of key cardiogenic markers. Notably, the impaired cardiac differentiation of KDM1A-/- cells can be rescued by re-expressing ubKDM1A or catalytically deficient ubKDM1A-K661A, but not by KDM1A+2a or KDM1A+2a-K661A. These data demonstrate a divergent role of the two KDM1A isoforms that is independent of their enzymatic activity. Through an exhaustive biochemical and genome-wide binding characterization, we excluded that the opposite ubKDM1A- and KDM1A+2a-mediated regulation of cardiac differentiation resides into differential substrate specificity, H3K4 demethylation efficiency, core-partners binding affinity, or alternative genome binding profiles. Conclusions: Our findings suggest the existence of a divergent scaffolding role of KDM1A splice variants during hESC differentiation into cardiomyocytes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE189944 | GEO | 2022/07/01

REPOSITORIES: GEO

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Project description:Human embryonic and induced pluripotent stem cells (hESCs/iPSCs) are promising cell sources for cardiac regenerative medicine. To realize hESC/iPSC-based cardiac cell therapy, efficient induction, purification, and transplantation methods for cardiomyocytes should be required. Though marker gene transduction or fluorescent-based purification methods were reported, fast, efficient and scalable purification methods with no genetic modification are essential for clinical purposes but have not been established yet. In this study, we used microarrays to detail the global gene program during cardiac differentiation and to identify cardiac-specific cell surface markers. hiPSCs (201B6) were differentiated toward cardiomyocytes using a modified-directed differentiation protocol (high density culture in RPMI+B27-insulin, sequential administration of Activin A 100ng/mL 1 day, BMP4 10ng/mL+bFGF 10ng/mL 4 days, and Dkk1 100ng/mL 2 days). Beating clusters were first observed at day 8-9 and spread by day 11 after Activin A administration. Cardiac troponin-T (cTnT)-positive cells appeared at day 7-8 after induction and were observed in 30-70% of cells at day 11. qPCR and genome-wide analysis reflected differentiation processes from the undifferentiated state to cardiomyocytes. Rapid downregulation of pluripotent stem cell markers such as NANOG and POU5F1 was observed within 2 days of differentiation. Early and cardiac mesodermal genes (T, MESP1, KDR, ISL1) were expressed during day 2-5, and cardiac genes (NKX2-5, MYH6, MYH7, MYL2, and MYL7) were expressed after day 7. We identified VCAM1 as a cardiac-specific cell surface marker by microarray and flow cytometry. Human induced pluripotent stem cells (iPSCs; 201B6) were differentiated toward cardiomyocytes (RPMI+B27 medium supplemented d0-1 Activin A, d1-5 BMP4+bFGF, d5-7 Dkk1). RNA was extracted from cells at day 0, day 2, day 5, day 7, day 9, and day 11. Cardiomyocytes appeared after day 7 and reached about 50% of total cells at day 11.

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Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism

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