Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations

Abstract

Background Hypertrophic cardiomyopathy (HCM) is the most common genetic disease of the cardiac muscle, frequently caused by mutations in MYBPC3. However, little is known about the upstream pathways and key regulators causing the disease. Therefore, we employed a multi-omics approach to study the pathomechanisms underlying HCM comparing patient hearts harboring MYBPC3 mutations to control hearts. Results Using H3K27ac ChIP-seq and RNA-seq we obtained 9310 differentially acetylated regions and 2033 differentially expressed genes, respectively, between 13 HCM and 10 control hearts. We obtained 441 differentially expressed proteins between 11 HCM and 8 control hearts using proteomics. By integrating multi-omics datasets, we identified a set of DNA regions and genes that differentiate HCM from control hearts and 53 protein-coding genes as the major contributors. This comprehensive analysis consistently points toward altered extracellular matrix formation, muscle contraction, and metabolism. Therefore, we studied enriched transcription factor (TF) binding motifs and identified 9 motif-encoded TFs, including KLF15, ETV4, AR, CLOCK, ETS2, GATA5, MEIS1, RXRA, and ZFX. Selected candidates were examined in stem cell-derived cardiomyocytes with and without mutated MYBPC3. Furthermore, we observed an abundance of acetylation signals and transcripts derived from cardiomyocytes compared to non-myocyte populations. Conclusions By integrating histone acetylome, transcriptome, and proteome profiles, we identified major effector genes and protein networks that drive the pathological changes in HCM with mutated MYBPC3. Our work identifies 38 highly affected protein-coding genes as potential plasma HCM biomarkers and 9 TFs as potential upstream regulators of these pathomechanisms that may serve as possible therapeutic targets.

Mass-Spectrometry-Based Functional Proteomic and Phosphoproteomic Technologies and Their Application for Analyzing Ex Vivo and In Vitro Models of Hypertrophic Cardiomyopathy

“…Lumican modulates collagen assembly and is implicated in tissue fibrosis via TGF-β interaction [52]. In a similar experiment, Pei et al applied proteomics, chromatin sequencing, and RNA sequencing to HCM and control tissue [53]. As with Coats et al, they found decreased enrichment of fatty acid metabolism via their proteomic data, which was corroborated by decreased RNA expression and hypoacetylation of key genes.…”

“…First, there are robust experimental methods for extracting metabolites and protein/phosphoproteins from specimens simultaneously with minimal losses. For example, liquid-liquid extraction (LLE) procedures can be used to selectively separate metabolites and proteins by differences in solubility, with subsequent solid-phase microextraction (SPME) allowing for purification of metabolites with minimal matrix interferences that confound LC/MS [53].…”

Transcriptome Data Analysis of Primary Cardiomyopathies Reveals Perturbations in Arachidonic Acid Metabolism

“…Among the GSA-enriched KEGG metabolic pathways between cardiomyopathy and normal samples, glycolysis/gluconeogenesis, oxidative phosphorylation, nucleotides metabolism, amino acid biosynthesis, co-factor metabolism, and fatty acid precursor arachidonic acid metabolism were statistically significant. Previous studies have reported oxidative phosphorylation, glycolysis and fatty acid metabolism perturbation in individual cardiomyopathies (23,24). In this work, we carried out an integrated analysis of AA metabolic perturbation across cardiomyopathies.…”

“…These studies have reported a metabolic shift in energy sources during disease progression. HCM-focused transcriptome analysis showed down-regulated fatty acid metabolism (23). Similarly, in a DCM transcriptome analysis, mitochondrial dysfunction and oxidative phosphorylation pathways were significantly perturbed (24).…”

Cardiac myosin binding protein-C variants in paediatric-onset hypertrophic cardiomyopathy: natural history and clinical outcomes

“…The presence of common genetic variation at one or more of these loci may explain the variable disease expression observed in carriers of pathogenic sarcomeric variants 55 . Epigenetic factors may also influence HCM phenotype development by acting on signalling cascades, membrane receptors and transcription factors, or through proteomic upstream regulators of disease pathomechanisms, post-translational gene expression regulators and histone modification [56][57][58] .…”