Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, 3584 CT, Utrecht, The Netherlands.
Regenerative Medicine Utrecht (RMU), University Medical Center Utrecht, University of Utrecht, 3584 CT, Utrecht, The Netherlands.
Clin Epigenetics. 2021 Mar 23;13(1):61. doi: 10.1186/s13148-021-01043-3.
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.
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.
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.
肥厚型心肌病（HCM）是最常见的心肌遗传性疾病，常由 MYBPC3 突变引起。然而，对于导致这种疾病的上游途径和关键调节因子知之甚少。因此，我们采用多组学方法研究 HCM 的发病机制，比较了携带 MYBPC3 突变的患者心脏和对照心脏。
使用 H3K27ac ChIP-seq 和 RNA-seq，我们分别在 13 例 HCM 和 10 例对照心脏之间获得了 9310 个差异乙酰化区域和 2033 个差异表达基因。我们使用蛋白质组学在 11 例 HCM 和 8 例对照心脏之间获得了 441 个差异表达蛋白。通过整合多组学数据集，我们确定了一组区分 HCM 和对照心脏的 DNA 区域和基因，以及 53 个主要贡献的蛋白编码基因。这项综合分析一致指向细胞外基质形成、肌肉收缩和代谢的改变。因此，我们研究了丰富的转录因子（TF）结合基序，并鉴定了 9 个基序编码的 TF，包括 KLF15、ETV4、AR、CLOCK、ETS2、GATA5、MEIS1、RXRA 和 ZFX。在有和没有突变的 MYBPC3 的干细胞衍生的心肌细胞中检查了选定的候选物。此外，与非心肌细胞群体相比，我们观察到心肌细胞中存在丰富的乙酰化信号和转录本。
通过整合组蛋白乙酰化组、转录组和蛋白质组谱，我们确定了主要的效应基因和蛋白质网络，这些基因和网络驱动了携带突变的 MYBPC3 的 HCM 的病理变化。我们的工作确定了 38 个受影响严重的蛋白编码基因作为潜在的 HCM 血浆生物标志物，并确定了 9 个 TF 作为这些发病机制的潜在上游调节剂，它们可能成为潜在的治疗靶点。
