Preconditioning of human iPSCs with doxorubicin causes genome-wide transcriptional reprogramming in iPSC-derived cardiomyocytes linked to mitochondrial dysfunction and impaired cardiac regeneration

Westerhoff, M.; Brocke-Ahmadinejad, N.; Schaumkessel, Y.; Köhrer, K.; Dönmez, A.; Ghodrat, R.; Borchardt, A.; Enjuanes-Ruiz, L.; Tigges, J.; Koch, K.; Fritz, G.; Kondadi, A. K.; Reichert, A. S.

doi:10.1101/2025.04.18.649376

bioRxiv · 10.1101/2025.04.18.649376

Preconditioning of human iPSCs with doxorubicin causes genome-wide transcriptional reprogramming in iPSC-derived cardiomyocytes linked to mitochondrial dysfunction and impaired cardiac regeneration

Westerhoff, M.·Brocke-Ahmadinejad, N.·Schaumkessel, Y.·Köhrer, K.·Dönmez, A.·Ghodrat, R.·Borchardt, A.·Enjuanes-Ruiz, L.·Tigges, J.·Koch, K.·Fritz, G.·Kondadi, A. K.·Reichert, A. S.

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Abstract

BackgroundThe anthracycline doxorubicin (Dox) is a widely used genotoxic chemotherapeutic drug with known dose-limiting cardiotoxic effects. How Dox-induced damage either to cardiomyocytes or to cardiac stem cells, which may compromise cardiac regeneration, contributes to cardiotoxicity remains poorly understood. MethodsHere we used a human induced pluripotent stem cell (iPSC)-based model system to determine the sensitivity of stem cells (iPSCs) and iPSC-derived derived cardiomyocytes (iCMs) applying different treatment regimens of Dox. Next to a broad range of methods to determine cellular and mitochondrial functions we performed an in-depth whole genome transcriptome profiling in iPSCs as well as iCMs. ResultsAs compared to their differentiated counterparts, iPSCs are highly sensitive against even short pulse-treatments with low Dox concentrations. Using such rather mild treatment conditions, we observed major mitochondrial impairments as demonstrated by increased mitochondrial fragmentation, persistent loss of mitochondrial membrane potential, and reduced ATP levels, while neither a markedly increased nuclear DNA damage response nor apoptosis were detected. Albeit mitochondrial dysfunction was not accompanied by changes in mitochondrial ultrastructure or altered OXPHOS complex assembly, mitochondrial genome (mtDNA) organization was altered. This points to a possible role of mtDNA remodelling for contributing to the high susceptibility of iPSCs to Dox. Whole genome transcriptome profiling revealed major differences in the transcriptional response to Dox treatment between iPSCs and iCMs. We could show that a moderate and transient exposure of iPSCs to Dox is sufficient to cause major transcriptional changes as for example reflected by the downregulation of numerous pivotal genes regulating cellular homeostasis and energy metabolism in iPSCs. Furthermore, pulse-treatment with Dox at the iPSC stage, termed preconditioning here, shifts the global transcriptional landscape of iCMs towards the expression of genes associated with impaired cardiac muscle regeneration, disrupted energy metabolism, altered muscle contraction, and increased fibrosis. ConclusionsOur findings support the hypothesis that Dox-induced mitochondrial dysfunction and transcriptional preconditioning in stem cells results in an impaired regenerative capacity after differentiation. This highlights a potential critical role of stem cells in mediating Dox-induced cardiotoxicity.

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Westerhoff, M., Brocke-Ahmadinejad, N., Schaumkessel, Y., Köhrer, K., Dönmez, A., Ghodrat, R., Borchardt, A., Enjuanes-Ruiz, L., Tigges, J., Koch, K., Fritz, G., Kondadi, A. K., Reichert, A. S.. 2025-04-21. Preconditioning of human iPSCs with doxorubicin causes genome-wide transcriptional reprogramming in iPSC-derived cardiomyocytes linked to mitochondrial dysfunction and impaired cardiac regeneration. https://doi.org/10.1101/2025.04.18.649376

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