Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have shown immense promise for patient-specific disease modeling, cardiotoxicity screening, and regenerative therapy development. However, hPSC-CMs in culture have not recapitulated the structure or functional properties of adult CMs in vivo thus far. To gain global insight into hPSC-CM biology, we introduce a multi-omics strategy for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multi-dimensional profiles of hPSC-CMs. Here we developed a sequential extraction to capture metabolites and proteins from hPSC-CM monolayer cultures, and analyzed these extracts using high resolution mass spectrometry (MS). Using this strategy, we identified an average of 205 metabolites/lipids and 4,008 protein groups from 106 cells with high reproducibility. We further integrated the proteome and metabolome measurements to create network profiles of molecular phenotypes for hPSC-CMs. Out of the 310 total pathways identified using metabolomics and proteomics data, 40 pathways were considered significantly overrepresented (FDR-corrected p ≤ 0.05). Highly populated pathways included those involved in protein synthesis (ribosome, spliceosome), ATP generation (oxidative phosphorylation), and cardiac muscle contraction. This multi-omics method achieves deep coverage of metabolites and proteins, creating a multidimensional view of the hPSC-CM phenotype. This strategy can be used to generate biological hypotheses and identify biomarker candidates to advance the understanding of hPSC-CM differentiation and maturation.
Modeling Cardiovascular Diseases with Patient-Specific Human Pluripotent Stem Cell-Derived Cardiomyocytes