Integrating omics into the cardiac differentiation of human pluripotent stem cells

Abstract

Time-dependent extracellular manipulations of human pluripotent stem cells can yield as much as 90% pure populations of cardiomyocytes. While the extracellular control of differentiation generally entails dynamic regulation of well-known pathways such as Wnt, BMP, and Nodal signaling, the underlying genetic networks are far more complex and are poorly understood. Notably, the identification of these networks holds promise for understanding heart disease and regeneration. The availability of genome-wide experimentation, such as RNA and DNA sequencing, as well as high throughput surveying with small molecule and small interfering RNA libraries, now enables us to map the genetic interactions underlying cardiac differentiation on a global scale. Initial studies demonstrate the complexity of the genetic regulation of cardiac differentiation, exposing unanticipated novel mechanisms. However, the large datasets generated tend to be overwhelming and systematic approaches are needed to process the vast amount of data to improve our mechanistic understanding of the complex biology. Systems biology methods spur high hopes for parsing vast amounts of data into genetic interaction models that can be verified experimentally and ultimately yield functional networks that expose the genetic connections underlying biological processes.

Comparative Proteomic Analysis Reveals the Upregulation of Ketogenesis in Cardiomyocytes Differentiated from Induced Pluripotent Stem Cells

“…The cardiomyogenic differentiation efficiency was also confirmed by comparative proteomic data (Table S1, Supporting Information). Protein ratios of two markers were monitored, OCT4 for hiPSCs and MYL7 for CMs . OCT4 levels decreased by 0.33 and 0.14‐fold in CPCs and CMs, respectively.…”

“…Like their mRNA expression pattern, the differentiation markers OCT4 and MYL7 were altered in CMs as determined by quantitative proteomic analysis. Furthermore, we detected several differentiation indicators known as cardiomyocyte‐specific markers from the volcano plot analysis, including stage‐specific molecules, which can be used to distinguish the differentiation stages, such as MYH6, MYH7, HTNT1, GATA4, and DES for CMs and OCT4 for hiPSCs …”

Temporal Control of the WNT Signaling Pathway During Cardiac Differentiation Impacts Upon the Maturation State of Human Pluripotent Stem Cell Derived Cardiomyocytes

“…We and others have shown that microRNAs (miRs) and cardiac transcription factors (TFs), such as miR-200c, and a set of GATA4/6, NKX2-5, TBX5, HEY2, and HAND1/2 can cooperatively regulate the expression of genes critical for cardiac development and function ( Poon et al, 2011 ; Poon et al, 2013 ; Cerutti et al, 2014 ; Rojas-Munoz et al, 2014 ; Kathiriya et al, 2015 ; Poon et al, 2018 ). To investigate if these regulatory factors could contribute to the differential expression of genes involved in maturation between “1 + 2 + 2” and “2 + 2” cultures ( Figure 3 ), we identified binding sites of the cardiac TFs on the promoters of these ‘maturation genes’.…”

Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics

“…Among these are MESP1, which acts as a master regulator of cardiac lineage commitment [ 3 , 4 ]. The cardiac TFs GATA4, GATA6, NKX2-5, MEF2A/C, SRF, ISL1, TBX5, HAND1 and HAND2 subsequently play critical roles in regulation of early embryonic cardiogenesis [ 5 , 6 ]. The TFs HEY2 or NR2F2 and TBX5 direct ventricular or atrial identity [ 7 , 8 ].…”