Interpreting the regulatory mechanisms underlying the predisposition to substance use disorders

解释物质使用障碍倾向背后的调节机制

• 批准号: 10434023
• 负责人: Andreas Robert Pfenning
• 金额: $ 47.43万
• 依托单位: CARNEGIE-MELLON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10434023
• 关键词: Animal Model; Biological; Biological Assay; Brain; Brain Diseases; Brain region; CRISPR interference; Code; Complex; Computer Analysis; Data Set; Development; Disease; Drug Targeting; Enhancers; Epigenetic Process; Genes; Genetic; Genetic Variation; Genome; Genomics; Health; Human; Human Genetics; Link; Maps; Measures; Methods; Molecular; Mus; Nucleic Acid Regulatory Sequences; Pathway interactions; Personal Satisfaction; Predisposition; Proteins; Reporter; Research; Research Personnel; Smoking Behavior; Substance Use Disorder; Testing; Untranslated RNA; Work; addiction; cell type; epigenomics; flexibility; genetic variant; genome wide association study; genomic tools; in vivo; infancy; mouse model; neural circuit; nicotine exposure; relating to nervous system; substance use; therapy development; tool

Summary/Abstract Substance use disorders have a profound impact on human health and wellbeing. The development of new treatments for these disorders has remained difficult due to the complexity of the neural circuits and the underlying genetic mechanisms. Recent genome-wide association studies have begun to identify a few of loci associated with the predisposition to addiction, with many more loci are implicated with lower confidence. The majority of the genetic variants associated with complex brain disorders, including substance use, are likely to be located in non-coding regulatory regions, particularly enhancers, and not within protein-coding genes. Despite the importance of enhancer regions in the brain, the computational and experimental tools to study their function are still in their infancy. To work towards deciphering this critical biological mechanism underlying substance use disorders, we seek to build a framework to study the function of both human and mouse brain enhancer regions in vivo. First, we will analyze publically available genetic and epigenetic data sets to identify human genetic variation at enhancers regions that is likely to influence substance use predisposition. Next, we will measure the impact of that genetic variation using a high-throughput reporter assay, which has the ability to simultaneously test the activity of thousands of enhancers across the mouse brain in vivo under different conditions. Finally, we will validate those predictions using CRISPR interference on conserved orthologous enhancers in the mouse. In an initial test case, we will apply our methods to interpret a genome-wide association study of smoking behavior using cell type-specific human epigenomics. The key candidates that result from the computational analysis will be screened and validated in a mouse model of nicotine exposure. The result of our research effort will be a map that links high-confidence and low-confidence substance use-associated genetic variation to neural enhancer function. Furthermore, the flexible computational and experimental framework has the potential to study any combination of candidate enhancers and genetic variants in the context of different brain regions, different cell types, and different animal models.

摘要/摘要 药物使用障碍对人类健康和福祉产生深远影响。的发展 由于神经回路和神经系统的复杂性，针对这些疾病的新疗法仍然很困难 潜在的遗传机制。最近的全基因组关联研究已经开始确定一些基因座 与成瘾倾向相关，有更多的位点与较低的置信度有关。这 大多数与复杂的脑部疾病（包括物质使用）相关的遗传变异可能会导致 位于非编码调控区，特别是增强子，而不是蛋白质编码基因内。 尽管增强子区域在大脑中很重要，但研究的计算和​​实验工具 它们的功能仍处于起步阶段。 为了破译物质使用障碍背后的这一关键生物学机制，我们 寻求建立一个框架来研究人类和小鼠大脑增强子区域的体内功能。第一的， 我们将分析公开的遗传和表观遗传数据集，以识别人类遗传变异 可能影响物质使用倾向的增强子区域。接下来，我们将衡量影响 使用高通量报告基因检测来检测遗传变异，该检测能够同时检测 在不同条件下体内小鼠大脑中数千个增强子的活性。最后，我们将 使用 CRISPR 干扰小鼠保守的直系同源增强子来验证这些预测。在一个 初始测试案例，我们将应用我们的方法来解释吸烟行为的全基因组关联研究 使用细胞类型特异性的人类表观基因组学。计算分析得出的关键候选者 将在尼古丁暴露的小鼠模型中进行筛选和验证。 我们研究工作的结果将是一张连接高置信度和低置信度实质内容的地图 使用相关的遗传变异对神经增强子功能的影响。此外，灵活的计算和 实验框架有潜力研究候选增强子和遗传的任意组合 不同大脑区域、不同细胞类型和不同动物模型的变异。

项目成果

Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin.

• DOI: 10.1186/s12864-022-08450-7
• 发表时间: 2022-04-11
• 期刊: BMC genomics
• 影响因子: 4.4
• 作者: Kaplow IM;Schäffer DE;Wirthlin ME;Lawler AJ;Brown AR;Kleyman M;Pfenning AR
• 通讯作者: Pfenning AR

Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum.

• DOI: 10.1016/j.cub.2021.10.015
• 发表时间: 2021-12-20
• 期刊: CURRENT BIOLOGY
• 影响因子: 9.2
• 作者: He, Jing;Kleyman, Michael;Chen, Jianjiao;Alikaya, Aydin;Rothenhoefer, Kathryn M.;Ozturk, Bilge Esin;Wirthlin, Morgan;Bostan, Andreea C.;Fish, Kenneth;Byrne, Leah C.;Pfenning, Andreas R.;Stauffer, William R.
• 通讯作者: Stauffer, William R.

Machine learning sequence prioritization for cell type-specific enhancer design.

• DOI: 10.7554/elife.69571
• 发表时间: 2022-05-16
• 期刊: ELIFE
• 影响因子: 7.7
• 作者: Lawler, Alyssa J.;Ramamurthy, Easwaran;Brown, Ashley R.;Shin, Naomi;Kim, Yeonju;Toong, Noelle;Kaplow, Irene M.;Wirthlin, Morgan;Zhang, Xiaoyu;Phan, BaDoi N.;Fox, Grant A.;Wade, Kirsten;He, Jing;Ozturk, Bilge Esin;Byrne, Leah C.;Stauffer, William R.;Fish, Kenneth N.;Pfenning, Andreas R.
• 通讯作者: Pfenning, Andreas R.

HALPER facilitates the identification of regulatory element orthologs across species.

HALPER 有助于识别跨物种的调控元件直系同源物。

• DOI: 10.1093/bioinformatics/btaa493
• 发表时间: 2020
• 期刊: Bioinformatics (Oxford, England)
• 作者: Zhang,Xiaoyu;Kaplow,IreneM;Wirthlin,Morgan;Park,TaeYoon;Pfenning,AndreasR
• 通讯作者: Pfenning,AndreasR

Cell Type-Specific Oxidative Stress Genomic Signatures in the Globus Pallidus of Dopamine-Depleted Mice.

• DOI: 10.1523/jneurosci.1634-20.2020
• 发表时间: 2020-12-09
• 期刊: The Journal of neuroscience : the official journal of the Society for Neuroscience
• 作者: Lawler AJ;Brown AR;Bouchard RS;Toong N;Kim Y;Velraj N;Fox G;Kleyman M;Kang B;Gittis AH;Pfenning AR
• 通讯作者: Pfenning AR