Pangenomics of nicotine abuse in the hybrid rat diversity panel

吸烟成瘾及其许多共病疾病-从癌症到COPD -有很大的影响。 全球影响。尽管我们对影响成瘾的大脑回路有着深刻的见解， 较少涉及导致成瘾风险的高水平个体差异的遗传变异， 烟草及其主要的精神活性物质尼古丁。很大一部分的脆弱性， 青少年吸烟和成年后复吸是由于遗传的基因差异。响应于 NIDA PAR-21-244，这个U 01专注于发现和理解这些复杂的遗传和分子生物学。 因素，使用一个强大的新资源-杂交大鼠多样性小组（HRDP）。HRDP的独特之处在于它 集成：1.一个非常高水平的遗传多样性类似于混合人群; 2。的方法 控制和改变药物暴露，系统地研究基因与环境和基因与药物之间的相互作用， 行动; 3.整合遗传、基因组和分子数据的完整定量“成瘾组”的方法， 用于推动精准医学的机制化发展。HRDP由91个不同的， 完全同基因大鼠，包括近交系和F1杂种（用于双杂交）：所有大鼠均“开放获取”，可供 研究成瘾的各个方面我们有三个目标：目标1。从青春期开始，我们将收集行为数据 使用我们建立的尼古丁静脉自我给药的有限进入操作模型， （IVSA），之后将是一个扩展访问模式。通过将这两个模型并置， 青春期有限的、间歇性吸烟的初始阶段，以及随后的持续性、习惯性吸烟， 导致尼古丁依赖。我们的实验设计是性别平衡和交错，以尽量减少批量 影响;我们量化尼古丁摄入量，尼古丁的动机，戒断严重程度，尽管寻求延长， 缺乏强化和线索诱导的药物寻求恢复;目的2.我们产生端粒到端粒 (T2T)HRDP关键菌株的基因组组装并构建大鼠泛基因组。我们利用排序 为人类T2 T组装建立的方法，基于高度准确的Pacific Biosciences（PacBio） HiFi长读取（20 kb）和牛津纳米孔（ONT）超长（>100 kb）数据;目标3。我们用泛基因组 改进的基因分型和QTL作图。人类基因组研究表明，泛基因组减少了基因组 “暗物质”--极大地改进了基因分型。我们将绘制每种尼古丁依赖行为的基因位点， 相关的表型网络，并通过与hu- 男人GWAS。结合人类吸烟的大鼠模型、高级长读基因组测序、T2 T组装 和泛基因组学，我们将准确地定义高影响力的遗传变异和分子网络与 尼古丁激发的行为，模拟人类吸烟的关键阶段。

Addiction to smoked tobacco and its many comorbid diseases – from cancer to COPD – have a massive global impact. Although we have deep insights into brain circuits that influence addiction, we understand much less about the genetic variants responsible for the high level of individual variability in the risk for addiction to smoked tobacco and its principal psychoactive agent, nicotine. A large fraction of the vulnerability to initially smoke cigarettes in adolescence and to relapse in adults is due to heritable genetic differences. In response to NIDA PAR-21-244, this U01 is focused on discovering and understanding these complex genetic and molecular factors, using a powerful new resource – the hybrid rat diversity panel (HRDP). The HRDP is unique in that it integrates: 1. A very high level of genetic diversity similar to that of admixed human populations; 2. Ways to control and change drug exposures and to systematically study gene-by-environment and gene-by-drug inter- actions; 3. Ways to integrate a full quantitative "addictome" of genetic, genomic, and molecular data that can be used to promote the mechanistic development of Precision Medicine. The HRDP consists of 91 different, fully isogenic rats, both inbred and F1 hybrids (used for diallel crosses): all are "open access" and available to study facets of addiction. We have 3 aims: Aim 1. Beginning in adolescence, we will collect behavioral data from the HRDP using our established limited access operant model of nicotine intravenous self-administration (IVSA), which will be followed by an extended access model. By juxtaposing these two models, we emulate the initial phase of limited, episodic smoking during adolescence, and the subsequent persistent, habitual smoking, which leads to nicotine dependence. Our experimental design is sex-balanced and interleaved to minimize batch effects; we quantify nicotine intake, motivation for nicotine, withdrawal severity, prolongation of seeking despite lack of reinforcement, and cue-induced reinstatement of drug seeking; Aim 2. We generate telomere-to-telomere (T2T) genome assemblies of key strains of the HRDP and construct a rat pangenome. We use the sequencing methods established for the human T2T assembly, based on the highly accurate Pacific Biosciences (PacBio) HiFi long-read (20kb) and Oxford Nanopore (ONT) ultralong (>100 kb) data; Aim 3. We use the pangenome for improved genotyping and QTL mapping. Human genomic studies have shown that pangenomes reduce genomic "dark matter" – greatly improving genotyping. We will map gene loci for each nicotine-dependent behavior and associated phenome networks and evaluate the translational relevance of candidate genes by comparison to hu- man GWAS. Combining rat models of human smoking, advanced long read genome sequencing, T2T assemblies and pangenomics, we will accurately define high impact genetic variants and molecular networks associated with nicotine motivated behavior that models the key stages of human smoking.