Clinical Genomics and Experimental Therapeutics

I. AUD中的表观基因组学和多组学： 我们继续在AUD人群和健康对照中进行大规模DNA表观基因组关联研究（EWAS）分析。据推测，酒精可能通过表观遗传修饰影响疾病结局：已知酒精会影响组蛋白的乙酰化和甲基化以及DNA的甲基化（Zakhari，2013）。DNA甲基化涉及由代谢物S-腺苷甲硫氨酸（SAM）提供的甲基基团添加到CpG二核苷酸的C。慢性酒精消耗导致SAM减少，这可导致整个表观基因组的低甲基化（Lu et al.，2000年）。酒精还影响叶酸循环，叶酸循环是生成甲硫氨酸以合成甲基所必需的（Mason和Choi，2005），并且高度反应性的酒精代谢物乙醛可以诱导DNA甲基转移酶（催化CpG甲基化的酶家族）的抑制以减少甲基化（Jangra等人，2016年，Garro等人，1991年）。醇代谢还通过增加活性氧（ROS）的形成而急剧消耗再甲基化所需的分子，这导致甲硫氨酸和SAM的产生减少（Chen等人，2011年）。 表观基因组关联研究（EWAS）已经鉴定了与酒精消耗和AUD相关的CpG（Lohoff et al.，2018年，Lohoff等人，2020，Longley等人，2021年）。然而，先前的研究在某种程度上受到小样本大小和较低捕获阵列的限制（Longley等人，2021年）。此外，只有少数研究将饮酒和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，我们在一个个体队列（n=8161）中进行了最大的酒精消费EWAS分析，我们正在继续使用翻译跨组织/跨表型方法跟踪AUD相关表型的主要发现，以确定与AUD相关的新的潜在靶点。应用各种其他计算基因组学方法来鉴定AUD的新药物靶标，包括孟德尔随机化和多组学研究（Mavrology等人，2022年）。 二. 老化（AUD） 研究表明，患有AUD的个体比健康对照早死亡，并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，在分子和表观遗传水平上理解这种关系是很重要的。为了更好地评估生物学年龄，已经开发了几种与实足年龄强相关的表观遗传时钟。这些时钟是采用特定CpG位点的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，该年龄与实足年龄高度相关。我们先前已经表明AUD与表观遗传年龄加速有关（罗森等人，2018），并在更大的样本中证实了我们的发现。在调整性别和血细胞组成后，与对照组相比，AUD的年龄加速了2.22岁（p = 1.85 10-5）（Luo等人，2020年）。我们继续研究AUD个体中衰老的表观遗传生物标志物，并合作/促成了迄今为止最大的表观遗传衰老GWAS（McCartney et al.，2021年）。鉴于端粒长度对衰老的已知影响，我们使用新的甲基化衍生评分研究了AUD中的端粒长度，并显示AUD个体中DNA端粒长度缩短（Jung et al.，2022年）。我们还开发了一种压力甲基化评分，用于跟踪AUD患者的压力暴露。 三. PCSK9（AUD） 目前约50%的肝病死亡率可归因于酒精滥用（Gao和Bataller，2011，雷姆等人，2013年，Seitz等人，2018年），但没有FDA批准的酒精相关性肝病（ALD）的治疗方案。因此，对能够减少酒精相关肝损伤的新治疗选择的需求正在出现。 我们最近已经表明，在慢性酒精暴露的大鼠模型中，PCSK 9抑制剂alirocumab减弱了酒精诱导的肝脏甘油三酯积累、肝细胞损伤和肝脏炎症（Lee et al.，2019年）。鉴于ALD新型治疗选择的临床需求未得到满足，我们在重度社交饮酒者中开始了alirocumab的安全性和耐受性研究。我们假设alirocumab在这一新的目标人群中耐受性良好且安全，alirocumab将减轻酒精诱导的肝损伤和炎症生物标志物。我们目前正在进行一项名为alirocumab在非寻求治疗的重度饮酒者中的安全性、耐受性和生物效应的I期、随机、双盲、安慰剂对照研究的临床试验（ClinicalTrials.gov标识符：NCT 04781322）。关于PCSK 9抑制减弱ALD和炎症的机制的其他临床前工作正在进行中。我们最近还使用药物靶向孟德尔随机化方法显示，PCSK 9抑制似乎对神经认知结果具有中性作用（Rosoff et al.，2022年）。

I. Epigenomics and multi-omics in AUD: We continue to work on large-scale DNA epigenome-wide association study (EWAS) analyses in AUD populations and healthy controls. It is hypothesized that alcohol may influence disease outcomes through epigenetic modifications: alcohol 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 collaborate/contributed to the largest GWAS of epigenetic aging to date (McCartney et al., 2021). Given the know effect of telomere length on aging, we investigated telomere length in AUD using a novel methylation derived score and showed shortened DNA telomere length in individuals with AUD (Jung et al., 2022). We have also developed a methylation score of stress that tracks stress exposure in individuals with AUD. 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).