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Updated: Aug 9, 2025

An Approach to Study Shape-Dependent Transcriptomics at a Single Cell Level
Published on: November 2, 2020
Multi-Omic Architecture of Obstructive Hypertrophic Cardiomyopathy
Ramin Garmany1,2, J Martijn Bos2,3,4, David J Tester2
1Mayo Clinic Medical Scientist Training Program, Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic Alix School of Medicine, Rochester, MN (R.G.).
Insights
Hypertrophic cardiomyopathy involves abnormal heart muscle growth. This study found that while gene expression downregulates key pathways, the heart muscle protein activity (proteome) upregulates them, particularly the RAS-MAPK cascade, suggesting its role in HCM.
Area of Science:
- Cardiovascular Biology
- Molecular Cardiology
- Systems Biology
Background:
- Hypertrophic cardiomyopathy (HCM) is a genetic heart muscle disease characterized by left ventricular hypertrophy.
- The precise molecular pathways driving HCM pathogenesis remain incompletely understood.
- Identifying these pathways is crucial for developing targeted therapies to manage HCM.
Purpose of the Study:
- To conduct a comprehensive multi-omic analysis of hypertrophy pathways in HCM.
- To elucidate the molecular mechanisms underlying cardiac hypertrophy in HCM patients.
Main Methods:
- Collected cardiac tissue samples from 97 HCM patients and 23 controls.
- Performed RNA sequencing, deep proteomic, and phosphoproteomic analyses.
- Utilized differential expression, gene set enrichment, and pathway analyses.
Main Results:
- Identified widespread transcriptional dysregulation with 1246 differentially expressed genes.
- Revealed downregulation of 10 hypertrophy pathways at the transcriptomic level.
- Found upregulation of 7 hypertrophy pathways at the proteomic level, primarily involving the RAS-MAPK signaling cascade, with evidence of its activation via hyperphosphorylation.
Conclusions:
- The ventricular proteome in HCM shows widespread activation of hypertrophy pathways, notably the RAS-MAPK cascade, irrespective of genotype.
- A counterregulatory transcriptional downregulation of these same pathways was observed.
- RAS-MAPK pathway activation is implicated as a critical factor in the hypertrophy characteristic of HCM.
Background:
Hypertrophic cardiomyopathy (HCM) is characterized by asymmetric left ventricular hypertrophy. Currently, hypertrophy pathways responsible for HCM have not been fully elucidated. Their identification could serve as a nidus for the generation of novel therapeutics aimed at halting disease development or progression. Herein, we performed a comprehensive multi-omic characterization of hypertrophy pathways in HCM.
Methods:
Flash-frozen cardiac tissues were collected from genotyped HCM patients (n=97) undergoing surgical myectomy and tissue from 23 controls. RNA sequencing and mass spectrometry-enabled deep proteome and phosphoproteomic assessment were performed. Rigorous differential expression, gene set enrichment, and pathway analyses were performed to characterize HCM-mediated alterations with emphasis on hypertrophy pathways.
Results:
We identified transcriptional dysregulation with 1246 (8%) differentially expressed genes and elucidated downregulation of 10 hypertrophy pathways. Deep proteomic analysis identified 411 proteins (9%) that differed between HCM and controls with strong dysregulation of metabolic pathways. Seven hypertrophy pathways were upregulated with antagonistic upregulation of 5 of 10 hypertrophy pathways shown to be downregulated in the transcriptome. Most upregulated hypertrophy pathways encompassed the rat sarcoma-mitogen-activated protein kinase signaling cascade. Phosphoproteomic analysis demonstrated hyperphosphorylation of the rat sarcoma-mitogen-activated protein kinase system suggesting activation of this signaling cascade. There was a common transcriptomic and proteomic profile regardless of genotype.
Conclusions:
At time of surgical myectomy, the ventricular proteome, independent of genotype, reveals widespread upregulation and activation of hypertrophy pathways, mainly involving the rat sarcoma-mitogen-activated protein kinase signaling cascade. In addition, there is a counterregulatory transcriptional downregulation of the same pathways. Rat sarcoma-mitogen-activated protein kinase activation may serve a crucial role in hypertrophy observed in HCM.
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