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

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 phosphorylation),
and cardiac muscle contraction. This multiomics method achieves a
deep coverage of metabolites and proteins, creating a multidimensional
view of the hPSC-CM phenotype, which provides a strong technological
foundation to advance the understanding of hPSC-CM biology. Raw data
are available in the MassIVE repository with identifier MSV000088010.