Stem Cell-Parenchymal Fusion: Communication and Gene Regulation

We investigated the cellular and molecular consequences of accidental cell fusion between mHL1 and mMSC cell lines using previously published single-cell RNA sequencing (scRNA-seq) data. We characterized the resulting cell types, their communication patterns, and underlying gene regulatory networks. Initial analyses identified four distinct cell types (mHL1, mHL1 fusion, mMSC, and mMSC fusion), which were also consolidated into three clusters via unsupervised learning. Differential gene expression analysis revealed diverse cell type associations with shared and exclusive gene expression. Single-cell compatible weighted gene co-expression network analysis (WGCNA) linked specific gene modules to distinct cell types and associated biological processes, including muscle contraction and metabolism in mHL1/mHL1 fusion, and extracellular matrix (ECM) formation and lipid metabolism in mMSC fusion. Cell-cell communication analysis revealed distinct intercellular communication patterns, with mMSC primarily acting as a ligand and mHL1 as both ligand and receptor. Reducing cell type complexity progressively simplified communication networks and altered pathway enrichment, while ECM-receptor pathways remained largely unchanged, with only minor shifts in ligand-receptor pairs. Interestingly, removing parental cells from the analysis altered cell type assignments, underscoring the influence of parental cell presence on fusion outcomes. Finally, gene regulatory network analysis identified key transcription factors (TFs) driving cell identity, distinguishing between master regulators and TFs with high cell-type specificity. These findings demonstrate the power of integrating multiple inter- and intra-cellular communication analysis approaches to dissect the complex interplay between cell type, communication, and gene regulation in cell fusion.