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Transcriptomic analysis reveals a statin-induced core molecular signature in human iPSC-CMs

ABSTRACT: Statins prevent cardiovascular disease via their salutary function as inhibitors of cholesterol biosynthesis and mediators of pleiotropic effects on the cardiovascular system. The current study focuses on the class effect of statins on the transcriptome of human iPSC-derived cardiomyocytes (iPSC-CMs), applied at serum peak concentrations. We report a comprehensive transcriptomic analysis of iPSC-CMs derived from four healthy donors and different differentiation batches following treatment with fluvastatin, simvastatin, atorvastatin, and lovastatin. Our data display dynamic transcriptional networks and reveal a statin-induced molecular signature in iPSC-CMs independent of genetic background and technical variability. Finally, in-depth pathway enrichment analysis uncovers that all statins affect mainly metabolic properties of iPSC-CMs and particularly the regulation of cholesterol biosynthesis and fatty acid metabolism. Our study provides a global insight into the cardiomyocyte effects of statins revealing novel aspects of their role on cardiomyocyte metabolic regulation, when applied at clinically relevant concentrations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE113546 | GEO | 2020/04/29

REPOSITORIES: GEO

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Project description:Background: Cholesterol pathway inhibition by statins prevents breast cancer development in mouse models of breast cancer but their efficacy is not very high (about 50%) . Therefore, the goal of this study is to investigate if the fluvastatin mediated upregulation in the steroid biosynthesis pathway genes limit the efficacy of statin chemoprevention. Methods: A published gene signature of statin resistance was validated in cell line-based models of inherent and acquired resistance during breast cancer. These signatures were next validated in a mouse model of hormone receptor negative breast cancer. Results: We found more than 70% of a published multi-gene fluvastatin resistance signature to be significantly upregulated in an inherently resistant cell line relative to fluvastatin sensitive cell line. We found this inherent statin resistance gene signature to be also shared with the signature of acquired resistance to fluvastatin (13 / 23 total genes). These 13 inherent resistance genes and 10 additional genes mapped to 2 of the top 3 deregulated pathways that are steroid-, and terpenoid backbone- biosynthesis pathway. Next, we tested if one or multiple genes of statin resistance signature, could predict efficacy of statin chemoprevention in the SV40 C3TAg transgenic mouse model. We found upregulation of a large number (19/24) of genes in the tumor bearing mammary glands, suggesting that upregulation of these pathways drives resistance to statin chemoprevention. A subset of 13-genes from this panel was significantly associated with response to statin treatment, as was the expression level of HMGCR alone in a mouse model of breast cancer. Lastly, we studied if a 10-day period of fluvastatin treatment to SV40C3 TAg mice, can also trigger the upregulation of these genes and provide an early signal of statin resistance. These experiments showed that a 10-day period is insufficient to cause a feedback upregulation in steroid biosynthesis pathway genes and thus cannot be used as an early biomarker to detect resistance to fluvastatin. Conclusions: High basal or restorative upregulation in the steroid biosynthesis pathway gene expression after fluvastatin treatment appears to be strongly associated with resistance to statin chemoprevention for breast cancer and may serve as a biomarker to identify patients that are most likely to respond to statins or develop resistance.

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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Transcriptomic analysis reveals a statin-induced core molecular signature in human iPSC-CMs

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