Clinical Genomics and Experimental Therapeutics

一、澳大利亚的表观基因组学和多重组学： 酒精可能通过表观遗传修饰影响疾病结果，并已知影响组蛋白的乙酰化和甲基化以及DNA的甲基化(Zakhari，2013)。DNA甲基化包括在CpG二核苷酸的C位加一个甲基，由代谢物S-腺苷甲硫氨酸(SAM)提供。长期饮酒导致SAM减少，这可能导致整个表观基因组的低甲基化(Lu等人，2000年)。酒精还影响叶酸循环，而叶酸循环是合成甲基团所需的蛋氨酸(Mason和Choi，2005)，高活性的酒精代谢物乙醛可诱导抑制DNA甲基转移酶，DNA甲基转移酶是催化CpG甲基化的酶家族，以减少甲基化(Jangra等人，2016，Garro等人，1991年)。酒精代谢还通过增加活性氧物种(ROS)的形成，急剧耗尽重新甲基化所需的分子，从而导致蛋氨酸和SAM的产生减少(Chen等人，2011年)。 表观基因组范围的关联研究(Ewas)已经确定了与酒精消费和AUD相关的CPG(Lohoff等人，2018，Lohoff等人，2020，Longley等人，2021)。然而，先前的研究受到小样本量和较低捕获阵列的某种限制(Longley等人，2021年)。此外，只有少数研究将酒精摄入量和AUD Ewas数据与详细的生物学验证联系起来。为了解决文献中的这些差距，我们对单个个体队列(n=8161)的酒精消费进行了最大规模的Ewas分析，我们正在继续使用翻译跨组织/跨表型方法跟踪AUD相关表型的最新发现，以确定与AUD相关的新的潜在靶点。各种其他计算基因组方法被应用于确定AUD的新药靶点，包括孟德尔随机化和多组学研究(Mavroatis等人，2022)。 二、澳元的老化 研究表明，与健康对照组相比，患有AUD的人死亡更早，而且全因死亡的风险显著增加(Westman等人，2015年，Larame等人，2015年)。鉴于AUD在衰老过程中的潜在作用，在分子、表观遗传学水平上理解这种关系是很重要的。为了更好地评估生物年龄，已经开发了几个与时间年龄密切相关的表观遗传学时钟。这些时钟是采用特定CpG位点甲基化水平的加权平均值来计算DNA甲基化年龄(dNaM年龄)的算法，该年龄与时间年龄高度相关。我们先前已经证明AUD与表观遗传年龄加速有关(Rosen等人，2018年)，并在更大的样本中证实了我们的发现。在调整了性别和血细胞成分后，AUD患者的年龄比对照组快了2.22岁(p=1.85×10-5)(Luo等人，2020)。我们继续研究AUD患者衰老的表观遗传生物标记物，并开发了一种压力甲基化评分，跟踪AUD患者的压力暴露(Jung等人，2022)。此外，我们对衰老进行了多组学分析，并确定了几个新的靶点(Mavromatis等人，2023)(Rosoff等人，2023)。 三、澳元中的PCSK9 目前约50%的肝病死亡可归因于酒精滥用(Gao和Bataller，2011，Rehm等人，2013，Seitz等人，2018)，但FDA尚未批准酒精相关性肝病(ALD)的治疗方案。因此，对能够减少与酒精相关的肝损伤的新治疗方案的需求正在大量和日益增长。 我们最近表明，PCSK9抑制剂alirocumab可以减轻酒精诱导的肝甘油三酯蓄积、肝细胞损伤和慢性酒精暴露大鼠的肝脏炎症(Lee等人，2019年)。考虑到ALD的新治疗选择的临床需求尚未得到满足，我们开始了一项针对大量社交饮酒者的alirocumab的安全性和耐受性研究。我们假设，在这个新的目标人群中，alirocumab将具有良好的耐受性和安全性，并且alirocumab将减轻酒精诱导的肝损伤和炎症生物标志物。我们目前正在进行这项名为A阶段的临床试验，随机、双盲、安慰剂对照，研究alirocumab在未寻求治疗的重度饮酒者中的安全性、耐受性和生物效应(ClinicalTrials.gov标识符：NCT04781322)。关于PCSK9抑制减轻ALD和炎症的机制的其他临床前工作正在进行中。我们最近还表明，使用药物靶向孟德尔随机化方法，PCSK9抑制似乎对神经认知结果具有中性影响(Rosoff等人，2022)。

I. Epigenomics and multi-omics in AUD: Alcohol may influence disease outcomes through epigenetic modifications and is known to affect the acetylation and methylation of histones and the methylation of DNA (Zakhari, 2013). DNA methylation involves the addition of a methyl group, donated by the metabolite, S-adenosylmethionine (SAM), to the C of CpG dinucleotides. Chronic alcohol consumption leads to a reduction in SAM, which can lead to hypomethylation across the epigenome (Lu et al., 2000). Alcohol also impacts the folate cycle which is necessary for the generation of methionine for the synthesis of methyl groups (Mason and Choi, 2005) and the highly reactive alcohol metabolite acetaldehyde can induce inhibition of DNA methyltransferases, the family of enzymes that catalyze CpG methylation, to reduce methylation (Jangra et al., 2016, Garro et al., 1991). Alcohol metabolism also acutely depletes molecules needed for re-methylation by increasing reactive oxygen species (ROS) formation, which results in decreased production of methionine and SAM (Chen et al., 2011). Epigenome-wide association studies (EWAS) have identified CpGs that are associated with alcohol consumption and AUD (Lohoff et al., 2018, Lohoff et al., 2020, Longley et al., 2021). However, prior studies were somewhat limited by small sample sizes and lower capture arrays (Longley et al., 2021). In addition, only a few studies exist linking alcohol consumption and AUD EWAS data with detailed biological validation. To address these gaps in the literature, we conducted the largest EWAS analyses of alcohol consumption in a single cohort of individuals (n=8161) and we are continuing to follow up top findings in AUD relevant phenotypes using a translational cross-tissue/cross-phenotypic approach to identify novel potential targets relevant to AUD. Various other computational genomic approaches are applied to identify new drug targets for AUD, including Mendelian Randomization and multi-omics studies (Mavromatis et al., 2022). II. Aging in AUD Studies have shown that individuals with AUD die earlier than healthy controls and are at a significantly increased risk for all-cause mortality (Westman et al., 2015, Larame et al., 2015). Given the potential role of AUD in the aging process, it is important to understand this relationship on a molecular, epigenetic level. To better assess biological age, several epigenetic clocks that robustly correlate with chronological age have been developed. These clocks are algorithms that take the weighted average of methylation levels at specific CpG sites to calculate DNA methylation age (DNAm age), which is highly correlated with chronological age. We have previously shown that AUD is associated with epigenetic age acceleration (Rosen et al., 2018) and confirmed our finding in a larger sample. There was a 2.22-year age acceleration in AUD compared to controls after adjusting for gender and blood cell composition (p = 1.85 10-5)(Luo et al., 2020). We continue to work on epigenetic biomarkers of aging in individuals with AUD and have developed a methylation score of stress that tracks stress exposure in individuals with AUD (Jung et al., 2022). In addition, we have conducted multi-omic analyses of aging and identified several novel targets (Mavromatis et al., 2023)(Rosoff et al., 2023). III. PCSK9 in AUD Approximately 50% of all liver disease mortality is currently attributable to alcohol misuse (Gao and Bataller, 2011, Rehm et al., 2013, Seitz et al., 2018), yet there are no FDA approved treatment options for alcohol-associated liver disease (ALD). Thus, a substantial and increasing need is emerging for new therapeutic options capable of reducing alcohol-associated liver damage. We have recently shown that the PCSK9 inhibitor alirocumab attenuates alcohol-induced hepatic triglyceride accumulation, hepatocellular injury and hepatic inflammation in a rat model of chronic alcohol exposure (Lee et al., 2019). Given the unmet clinical need for novel treatment options for ALD, we started a safety and tolerability study of alirocumab in heavy social drinkers. We hypothesize that alirocumab will be well tolerated and safe in this new target population and alirocumab will attenuate alcohol-induced liver damage and inflammatory biomarkers. We are currently conducting this clinical trial entitled A Phase I, Randomized, Double-Blind, Placebo-Controlled, Study of Safety, Tolerability, and Bioeffects of alirocumab in Non-treatment Seeking Heavy Drinkers (ClinicalTrials.gov Identifier: NCT04781322). Additional preclinical work is ongoing on the mechanisms by which PCSK9 inhibition attenuates ALD and inflammation. We have also recently shown that PCSK9 inhibition appears to have a neutral effect on neurocognitive outcomes using a drug-target Mendelian Randomization approach (Rosoff et al., 2022).