The regulation of the histone code during cardiac hypertrophy

心脏肥大过程中组蛋白密码的调节

• 批准号: 10373727
• 负责人: Maha Abdellatif
• 金额: $ 66.54万
• 依托单位: RBHS-NEW JERSEY MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-12-01 至 2022-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10373727
• 关键词: Acetylation; Aging; Butyryl-CoA dehydrogenase; CDK9 Protein Kinase; Carbohydrates; Cell Nucleus; Cells; ChIP-seq; Coenzyme A; Data; Diet; Dietary Fats; Disease Outcome; Disease Progression; Enzymes; Fat-Free Diets; Fatty Acids; Fatty acid glycerol esters; Gene Expression; Genes; Genetic Transcription; Genomics; Glucose; Goals; Health; Heart; Heart Hypertrophy; Heart failure; High Fat Diet; Histone Code; Histones; Human; Hypertrophy; Ketone Bodies; Ligase; Lysine; Mediating; Metabolic; Metabolism; Molecular; Mus; Nonesterified Fatty Acids; Nuclear; Outcome; Oxidoreductase; Pathologic; Regulation; Reporting; Role; Source; Stress; Sum; Transcriptional Regulation; acyl group; beta-Hydroxybutyrate; dietary; disease prognosis; genome-wide; histone methylation; histone modification; improved; improved outcome; ketogenic diet; ketogentic; knock-down; oxidation; pressure; promoter; recruit; transcriptome sequencing

Abstract Our goal is to investigate the impact of diet and pressure overload on the histone code, and how this influences changes in gene expression in the healthy and hypertrophied/failing hearts and, in turn, how it impacts progression of the disease. Deciphering the histone code and how diet can modify it, provides us an educated means to exploit it to our advantage, especially during pathological conditions. Acetylation and methylation of histone lysine (K) residues were the first histone modifications discovered and are, therefore, the most widely studied and understood. However, to-date, there are 11 confirmed modifiers of histone lysine residues, including the acyl groups butyryl (Bu), crotonyl (Cr), and b-hydroxybutyrate (bHB) 1, whose source, genomic distribution, and functional relevance, remain largely unknown in the heart, and are the focus of our study. Our recent findings uniquely show that dietary fat is a major regulator of histone butyrylation, including H3K9-butyryl (H3K9Bu). Using genome-wide chromatin immunoprecipitation-sequencing (ChIP-Seq), we show that H3K9Bu is abundant at all transcriptionally active promoters. Both a high-fat diet and stress accelerated the conversion of butyryl-CoA to crotonyl-CoA via acyl-CoA dehydrogenase short chain (ACADS), resulting in a substantial reduction in global promoter-H3K9Bu. A deletion of ACADS both in the mouse heart and in human cells reversed this effect and increased promoter and gene-body H3K9Bu. Paradoxically, though, a fat-free diet had the highest levels of H3K9Bu. Deletion of fatty acid synthetase (FASN), abolished H3K9Bu in cells maintained in a glucose-rich, fatty acid-free, but not in a fatty acid-rich, medium, proving that fatty acid synthesis from carbohydrates substitutes for dietary fat as a source butyryl-CoA. In contrast to H3K9Bu, there were minimal dietary-induced changes in H3K9-acetyl (H3K9ac) levels. Importantly, RNA-sequencing (RNA-Seq) revealed that diet-induced changes in H3K9Bu abundance in the mouse heart was associated with differential changes in gene expression, but only when stressed by pressure overload. Moreover, promoter-H3K9Bu levels inversely correlated with the extent of changes in gene expression levels, as evidenced by the more robust changes seen in the hearts of mice on a, short-term, high-fat vs a fat-free diet, as well as, after deletion of the ACADS. Interestingly, H3K9Bu abundance inversely correlated with H3K9-crotonyl (H3K9Cr) and Cdk9. In sum, our data uniquely show that H3K9Bu is enriched at active promoters, is negatively regulated by high-fat and stress in an ACADS-dependent fashion, and its abundance inversely correlates with stress-induced changes in gene expression. We are proposing that histone H3K9Bu, H3K9Cr, and H3K9-b-hydroxybutyryl (H3K9bHB), are products of the b-oxidation intermediates, butyryl-CoA, crotonyl-CoA, and b-hydroxybutyryl-CoA, or the ketone body, b-hydroxybutyrate, which serve as substrates for histones modifications. These marks are labile and differentially influence pressure overload-induced gene expression, but not baseline expression. Specifically, as H3K9Bu decreases it is replaced by H3K9Cr during a high-fat diet. This exchange exaggerates gene expression and worsens the outcome of cardiac failure. Conversely, H3K9bHB that increases during a ketogenic diet has the opposite effect, as it is reported to have beneficial effects on health and aging. This differential influence of the histone marks on gene expression is mediated by regulating the recruitment of Cdk9 to gene promoters. We hypothesize that 1) A high-fat diet (60 Kcal% fat, 20 Kcal% carb), or pressure overload, accelerates the conversion of nuclear butyryl- CoA to crotonyl-CoA in an ACADS-dependent manner, thus, reducing H3K9Bu and increasing H3K9Cr, which is responsible for exaggerating stress-induced gene expression and worsening the outcome of heart failure (HF). In contrast, a ketogenic diet (84 Kcal% fat, 0% carb) will produce high levels of b-hydroxybutyryl that will increase H3K9bHB, which curbs changes in stress-induced gene expression in a b-hydroxybutyrate dehydrogenase (BDH1)-dependent fashion, improving the outcome of HF. Supplementing a diet with b-hydroxybutyrate will also increase H3K9bHB, with similar beneficial effects. 2) Therefore, knockdown of ACADS reduces the conversion of butyryl-CoA to crotonyl-CoA, increasing H3K9Bu and improving the outcome of heart failure during a high-fat diet. Conversely, deletion or inhibition of BDH1 reduces H3K9bHB and worsens conditions. 3) H3K9Cr enhances the dynamics of cyclin-dependent kinase 9 (Cdk9) recruitment to promoters during stress, whereas, H3K9Bu and H3K9bHB temper it, thus, reducing the extent of changes in gene expression and improving disease outcome. The specific aims are: 1) Examine the effects of high-fat, ketogenic, and b-hydroxybutyrate-enriched diets on the genome-wide distribution and changes in H3K9Bu, H3K9Cr and H3K9bHB, changes in gene expression, and their impact on the progression of cardiac hypertrophy and failure. 2) Investigate the roles of ACADS and BDH1 in regulating the levels of H3K9Bu, H3K9Cr, and H3K9bHb, and the progression of cardiac hypertrophy and failure. 3) Investigate the role of Cdk9 in mediating the differential transcriptional regulation directed by promoter-H3K9Cr vs. H3K9Bu or H3K9bHB during cardiac hypertrophy and failure.

摘要 我们的目标是研究饮食和压力过载对组蛋白编码的影响，以及这如何影响 健康和肥大/衰竭心脏中基因表达的变化，以及它如何影响 疾病的进展。破译组蛋白密码以及饮食如何改变它，为我们提供了一个受过教育的 意味着利用它对我们有利，特别是在病理条件下。的乙酰化和甲基化 组蛋白赖氨酸（K）残基是最早发现的组蛋白修饰，因此也是最广泛的组蛋白修饰。 学习和理解。然而，到目前为止，有11个已证实的组蛋白赖氨酸残基修饰剂，包括 酰基丁酰基（Bu）、巴豆酰基（Cr）和β-羟基丁酸酯（bHB）1，其来源、基因组分布， 和功能相关性，在心脏中仍然很大程度上是未知的，并且是我们研究的重点。我们最近的发现 独特地表明膳食脂肪是组蛋白丁酰化的主要调节剂，包括H3 K9-丁酰（H3 K9 Bu）。 使用全基因组染色质免疫沉淀测序（ChIP-Seq），我们发现H3 K9 Bu是丰富的 在所有转录活性启动子上。高脂饮食和压力都加速了丁酰辅酶A的转化 通过酰基辅酶A脱氢酶短链（ACADS）转化为巴豆酰辅酶A，导致全球 启动子-H3 K9 Bu。在小鼠心脏和人类细胞中缺失ACADS可以逆转这种效应， 增加启动子和基因体H3 K9 Bu。奇怪的是，无脂饮食中的 H3K9Bu。脂肪酸合成酶（FATCH）的缺失，消除了维持在富含葡萄糖的脂肪酸环境中的细胞中的H3 K9 Bu。 无酸，但不是在富含脂肪酸的介质中，证明碳水化合物替代脂肪酸的合成 作为丁酰辅酶A的来源。与H3 K9 Bu相反，在H3 K9 Bu中存在最小的饮食诱导的变化。 H3 K9-乙酰基（H3 K9 ac）水平。重要的是，RNA测序（RNA-Seq）显示，饮食诱导的变化， 小鼠心脏中的H3 K9 Bu丰度与基因表达的差异变化相关，但仅 当压力过载时。此外，启动子-H3 K9 Bu水平与细胞凋亡的程度呈负相关。 基因表达水平的变化，如在A组小鼠心脏中观察到的更强烈的变化所证明的， 短期，高脂肪与无脂肪饮食，以及删除ACADS后。有趣的是，H3 K9 Bu丰度 与H3 K9-巴豆酰基（H3 K9 Cr）和Cdk 9呈负相关。总之，我们的数据唯一地表明H3 K9 Bu是 富含活性启动子，以ACADS依赖性方式受高脂和应激负调控， 其丰度与胁迫诱导的基因表达变化呈负相关。我们建议， 组蛋白H3 K9 Bu、H3 K9 Cr和H3 K9-b-羟基丁酰基（H3 K9 bHB）是b-氧化的产物 中间体，丁酰-CoA，巴豆酰-CoA和b-羟基丁酰-CoA，或酮体，b-羟基丁酸酯， 其用作组蛋白修饰的底物。这些标记是不稳定的，并对压力产生不同的影响 过负荷诱导的基因表达，但不是基线表达。具体地，随着H3 K9 Bu减少， H3 K9 Cr在高脂饮食中的作用这种交换夸大了基因表达， 心力衰竭相反，在生酮饮食期间增加的H3 K9 bHB具有相反的效果，因为它是 据报道，对健康和衰老有有益的影响。这种组蛋白标记对基因的差异影响 通过调节Cdk 9向基因启动子的募集来介导表达。我们假设：（1）A 高脂肪饮食（60千卡%脂肪，20千卡%碳水化合物），或压力过载，加速核丁酰基的转化， 辅酶A以ACADS依赖性方式转化为巴豆酰辅酶A，从而减少H3 K9 Bu并增加H3 K9 Cr， 是夸大应激诱导的基因表达和恶化心力衰竭（HF）结果的原因。 相比之下，生酮饮食（84千卡%脂肪，0%碳水化合物）将产生高水平的b-羟基丁酰基， H3 K9 bHB，抑制b-羟基丁酸脱氢酶中应激诱导的基因表达的变化 （BDH 1）依赖的方式，改善HF的结果。补充饮食与b-羟基丁酸也将 增加H3 K9 bHB，具有类似的有益效果。2)因此，ACADS的敲除降低了转化率， 丁酰辅酶A转化为巴豆酰辅酶A，增加H3 K9 Bu，改善高脂饮食期间心力衰竭的结局。 饮食.相反，BDH 1的缺失或抑制减少H3 K9 bHB和H3 K9 bHB的条件。3)H3 K9 Cr增强 细胞周期蛋白依赖性激酶9（Cdk 9）在应激过程中募集到启动子的动力学，而H3 K9 Bu 而H3 K9 bHB则可以调节它，从而降低基因表达的变化程度，改善疾病 结果。具体目的是：1）检查高脂肪，生酮和富含b-羟基丁酸的影响 H3 K9 Bu、H3 K9 Cr和H3 K9 bHB的全基因组分布和变化， 表达，以及它们对心脏肥大和衰竭进展的影响。2)调查以下人员的作用 ACADS和BDH 1对H3 K9 Bu、H3 K9 Cr和H3 K9 bHb水平的调节及心肌梗死的进展 肥大和衰竭。3)探讨Cdk 9在介导差异转录调控中的作用 在心肌肥厚和衰竭期间由启动子H3 K9 Cr vs. H3 K9 Bu或H3 K9 bHB指导。