Biology subjects

Simmons, A. D.

Publications and source records attributed to Simmons, A. D..

3 recordsLinked to original sources

bioRxiv2026

Early multi-omic signatures and machine learning models predict cardiomyocyte differentiation efficiency and enable robust hPSC differentiation to cardiomyocytes

Protocols for generating cardiomyocytes (CMs) from human pluripotent stem cells (hPSCs) have existed for nearly two decades, yet manufacturing variability in terminal cell identity continues to limit clinical translation. To uncover the origin of fate divergence during hPSC-CM differentiation, we performed temporal transcriptomics, proteomics, and metabolomics of high and low efficiency differentiations. We identified significant early multi-omic divergence between differentiation batches and key pathways underlying fate divergence at critical differentiation stages included Wnt, MAPK, and glucose metabolism. Machine learning models trained on early candidate gene markers predicted hPSC-CM purity better than models using canonical cardiac development markers. Lastly, multi-omic insights informed perturbations, including Wnt and MAPK inhibition, which produced higher CM purities and yields. Our results showcase multi-omic analysis coupled with machine learning models as a powerful tool to identify cell fate determinants and enable robust manufacturing of complex cell products such as hPSC-derived cell therapies. TeaserMulti-omic analysis of hPSC-CM differentiation efficiency reveals early predictive features and enables robust differentiation.

cell biology↗

bioRxiv2025

Human Plasma-Like Medium Promotes Maturation of Human Pluripotent Stem Cell-Derived Cardiomyocytes

Maturing human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) in vitro is critical for advancing drug discovery and cardiotoxicity screening applications of these cells. However, the metabolic compositions of basal media used for hPSC-CM culture typically offer limited relevance to human cardiac physiology. Here, we examined how culture in Human Plasma-Like Medium (HPLM) versus conventional basal media affects the behavior of hPSC-CMs. Starting with Day 16 hPSC-CMs, we cultured cells for two weeks in either HPLM or RPMI-based media and then assessed maturation outcomes at Day 30. Compared to RPMI/B27 media containing either RPMI-defined (11.1 mM) or physiologic glucose levels (5 mM), HPLM/B27 markedly enhanced hPSC-CM maturity as evinced by concerted transcriptomic, structural, functional, and metabolic phenotypes. These effects included a higher extent of myosin heavy chain isoform switching (-MHC to {beta}-MHC), accelerated ventricular-specific myosin light chain isoform switching (MLC2a to MLC2v), elongated sarcomeres, increased multinucleation, enhanced calcium transient kinetics, and coordinated activation of oxidative and glycolytic metabolism. Collectively, these findings demonstrate that medium composition has substantial effects on hPSC-CM biology and also establish HPLM as a tool for driving hPSC-CM maturation in vitro. Translational Impact StatementHPLM was designed to more closely recapitulate the metabolic composition of human plasma and thus provides a physiological platform to promote hPSC-CM maturation. By enhancing structural, functional, and metabolic maturity, HPLM-cultured hPSC-CMs better approximate cardiac physiology, positioning them as improved models for cardiovascular disease research, drug-induced cardiotoxicity screening, and personalized therapeutic testing. This medium can integrate with existing maturation strategies, accelerating the translation of basic cardiac research into clinically predictive tools for the drug development pipeline. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/650456v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@a169eforg.highwire.dtl.DTLVardef@131e6f4org.highwire.dtl.DTLVardef@131d52dorg.highwire.dtl.DTLVardef@a2b248_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

A Multi-omics Strategy 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, hPSC-CMs in culture have not recapitulated the structural or functional properties of adult CMs in vivo thus far. To gain global insight into hPSC-CM biology, we established a multi-omics method for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multi-dimensional 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 (MS). Using this method, we annotated 205 metabolites/lipids and 4,008 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 (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, which provides a strong technological foundation to advance the understanding of hPSC-CM biology.

systems biology↗