Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice

Abstract

Cardiomyocyte differentiation derived from embryonic stem cells (ESCs) is a complex process involving molecular regulation of multiple levels. In this study, we first identify and compare differentially expressed gene (DEG) signatures of ESC-derived cardiomyocyte differentiation (ESCDCD) in humans and mice. Then, the multiscale embedded gene co-expression network analysis (MEGENA) of the human ESCDCD dataset is performed to identify 212 significantly co-expressed gene modules, which capture well the regulatory information of cardiomyocyte differentiation. Three modules respectively involved in the regulation of stem cell pluripotency, Wnt, and calcium pathways are enriched in the DEG signatures of the differentiation phase transition in the two species. Three human-specific cardiomyocyte differentiation phase transition modules are identified. Moreover, the potential regulation mechanisms of transcription factors during cardiomyocyte differentiation are also illustrated. Finally, several novel key drivers of ESCDCD are identified with the evidence of their expression during mouse embryonic cardiomyocyte differentiation. Using an integrative network analysis, the core molecular signatures and gene subnetworks (modules) underlying cardiomyocyte lineage commitment are identified in both humans and mice. Our findings provide a global picture of gene-gene co-regulation and identify key regulators during ESCDCD.

Personalized Medicine Approach in a DCM Patient with LMNA Mutation Reveals Dysregulation of mTOR Signaling

“…Cardiomyocytes derived from both WT and LMNA -KI mutated mES cells were examined for markers of several cell types ranging from early embryonic ectoderm to cardiomyocytes. Significant upregulation of Oct3/4 and Nanog , both markers for early embryonic ectoderm [ 21 , 22 ], in undifferentiated cells, show the degree and specificity of mES cells. On the other hand, markers for cardiomyocyte differentiation, Gata4 , Tbx20 , cTNT , α-Myh6 , Mlc2a, and Mlc2V , were significantly upregulated in differentiated WT and LMNA -KI cells.…”

“…Tbx20, which is expressed within E7.5, has been known to interact with several other proteins such as Nkx2-5, Gata4, and Gata5 and regulates the expression of various cardiac genes as well as coordinates cell proliferation and the process of cardiac differentiation [ 23 ]. Also, in mature cardiomyocytes, the expression of cTNT and α-Myh6 is crucial to maintaining the normal heart function [ 21 , 24 ]. Atrial and ventricular subtypes of cardiomyocytes can be distinguished by the expression of either Mlc2a (for atrial cardiomyocytes) or Mlc2V (for ventricular cardiomyocytes).…”

Regenerating Damaged Myocardium: A Review of Stem-Cell Therapies for Heart Failure

“…The long-coding RNA GATA6-AS1 also appears to be a key regulator of cardiomyocyte differentiation [72], because although GATA-AS1-knockout human iPSCs remained pluripotent, their ability to differentiate into cardiomyocytes was inhibited. Notably, when data generated from genome-wide RNA-sequencing analyses performed during four stages of murine and human ESC-CM differentiation (i.e., the ESC, mesoderm, cardiac progenitor, and cardiomyocyte stages) were analyzed via multiscale embedded gene co-expression network analysis (MEGENA), 212 significantly co-expressed gene modules were identified; the results from these analyses will provide a valuable foundation for future investigations that could lead to a more complete understanding of the molecular networks that govern PC-CM differentiation [73].…”

Regenerating Damaged Myocardium: A Review of Stem-Cell Therapies for Heart Failure

“…When doxycycline treatment was followed by two days of Wnt inhibition, the cells differentiated into monolayers of beating CMs that were largely indistinguishable from hESC-CMs obtained via the standard differentiation protocol; however, the doxycycline dose had to be precisely controlled, because too much or too little RNA GATA6-AS1 also appears to be a key regulator of cardiomyocyte differentiation [71], because although GATA-AS1knockout iPSCs remained pluripotent, their ability to differentiate into cardiomyocytes was inhibited. Notably, when data generated from genome-wide RNAseq analyses performed during four stages of murine and human ESC-CM differentiation (i.e., the ESC, mesoderm, cardiac progenitor, and cardiomyocyte stages) were analyzed via multiscale embedded gene co-expression network analysis (MEGENA), 212 significantly co-expressed gene modules were identified; the results from these analyses will provide a valuable foundation for future investigations that could lead to a more complete understanding of the molecular networks that govern PC-CM differentiation [72].…”