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Wu iPSC-CM MM11 label-free proteomics

ABSTRACT: Label-free proteomics from iPSC-CMs and cardiomyocytes.

INSTRUMENT(S): timsTOF Ultra

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Arianne Caudal

PROVIDER: MSV000098942 | MassIVE | Tue Aug 26 14:08:00 BST 2025

SECONDARY ACCESSION(S): PXD067761

REPOSITORIES: MassIVE

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Project description:The cardiomyocytes (CMs) differentiation of 12 validated iPSC lines were induced using the Gibco PSC Cardiomyocyte Differentiation Kit and following manufacturer method with minor modifications (Thermo Fisher Scientific, Waltham, MA, USA). The differentiation kit consists of a set of serum-free and xeno-free media that enable efficient differentiation of human iPSCs into spontaneously contracting functional cardiomyocytes in 14 days. On day 14 of the differentiation, spontaneously contracting CMs were characterized by immunocytochemistry (ICC) analysis of cardiac mesoderm marker NKX2-5, and mature cardiomyocyte marker TNNT2 and genome-wide mRNA sequencing of the 12 iPSC lines and generated 12 CM lines were performed. The CMs differentiated from all the 12 iPSC lines expressed NKX2-5 and TNNT2 cardiomyocyte markers. Based on the criteria normalized read count (NRC) ≥ 20 in all 12 CM samples, a total of 12280 genes were found expressed. The average correlation coefficient at 95% CI between 12 CM samples, calculated based on all expressed genes, was 0.92 ± 0.02, suggesting a uniform differentiation of generated CMs across 12 samples. The expression of the well-known CMs genes/markers MYH6, MYL4, MYL3, MYL7, NPPA, NPPB, MYH7, NKX2-5, TBX5, TNNT2, ACTN2, TNNC1 and MB, was significantly up-regulated across all 12 CM samples (FDR corrected p-value ≤ 0.05 and fold change absolute (FC-abs) ≥ 2.0); whereas the expression of pluripotency markers and the ectodermal markers was significantly down regulated. The endodermal markers SOX17 and CLDN6 were below the expression threshold of NRC ≥ 20. A differential gene expression analysis of iPSC’s and CM’s expressed transcription identified 4,191 genes that were significantly differentially expressed (DE) between iPSCs and differentiated CMs. The 2,116 DE genes that were significantly up regulated in differentiated CMs showed significantly high enrichment in cardiovascular system development and functions (571 mRNAs; FDR adjusted p-value range: 1.75x10-66 – 1.61x10-14) and predicted activation of the functions associated with development of human heart and cardiovascular system.

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Wu iPSC-CM MM11 label-free proteomics

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