Graphical abstract. From Ai et al., 2025. “Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts“, Molecular & Cellular Proteomics, 2025, 100910, ISSN 1535-9476, https://doi.org/10.1016/j.mcpro.2025.100910. Licensed under the terms of the Creative Commons CC-BY license.

Current understanding of induced pluripotent stem cell (iPSC)-derived cardiomyocytes (iCMs) as models for cardiovascular diseases and drug toxicology is limited by uncertainty about how iCMs compare to adult cardiomyocytes (aCMs), particularly at the single-cell proteomic level.

Previous studies faced technical challenges including slow processing times and limited throughput. The researchers aimed to map proteomic changes during iPSC to iCM differentiation and compare these to aCMs from different heart regions.

Using a simplified “one pot” label-free single cell proteomic approach, this quantitative study analysed 1,326 single cells across five differentiation timepoints, identifying 2,742 unique proteins. For adult cells, they successfully analysed 279 individual cardiomyocytes from three human hearts.

The setup utilised an Aurora Rapid CSI 5×75 C18 UHPLC column interfaced with a timsTOF single cell proteomics mass spectrometer.

This study revealed distinct cellular subtypes within cell populations, identifying two subgroups of cardiomyocytes separated by metabolic and myofibril proteins. The researchers discovered rare cells with hybrid proteomes containing both cardiac-specific and neuronal-enriched proteins in both aCMs and iCMs.

This work demonstrates the feasibility of large-scale single-cell proteomics across related cell types and provides new insights into cardiac cell development. The findings could impact future research in cardiovascular disease modeling and drug development by helping researchers better understand the limitations and capabilities of iPSC-derived cardiac models.

Publication
Molecular & Cellular Proteomics

Authors

Lizhuo Ai, Aleksandra Binek, Vladimir Zhemkov, Jae Hyung Cho, Ali Haghani, Simion Kreimer, Edo Israely, Madelyn Arzt, Blandine Chazarin, Niveda Sundararaman, Arun Sharma, Eduardo Marbán, Clive N. Svendsen, & Jennifer E. Van Eyk

Title

Single Cell Proteomics Reveals Specific Cellular Subtypes in Cardiomyocytes Derived from Human iPSCs and Adult Hearts