Multiomics Method Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem-Cell-Derived Cardiomyocytes.

Journal of Proteome Research
E. F. BayneYing Ge

Abstract

Human pluripotent stem-cell-derived cardiomyocytes (hPSC-CMs) show immense promise for patient-specific disease modeling, cardiotoxicity screening, and regenerative therapy development. However, thus far, hPSC-CMs in culture have not recapitulated the structural or functional properties of adult CMs in vivo. To gain global insight into hPSC-CM biology, we established a multiomics method for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multidimensional profiles of hPSC-CMs. Specifically, we developed a sequential extraction to capture metabolites and proteins from the same hPSC-CM monolayer cultures and analyzed these extracts using high-resolution mass spectrometry. Using this method, we annotated 205 metabolites/lipids and 4319 proteins 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 310 pathways identified using metabolomics and proteomics, 40 pathways were considered significantly overrepresented (false-discovery-rate-corrected p ≤ 0.05). Highly populated pathways included those involved in protein synthesis (ribosome, spliceosome), ATP generation (oxidative ph...Continue Reading

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