Table_3_Coordination among frequent genetic variants imparts substance use susceptibility and pathogenesis.XLSX

Determining the key genetic variants is a crucial step to comprehensively understand substance use disorders (SUDs). In this study, utilizing whole exome sequences of five multi-generational pedigrees with SUDs, we used an integrative omics-based approach to uncover candidate genetic variants that impart susceptibility to SUDs and influence addition traits. We identified several SNPs and rare, protein-function altering variants in genes, GRIA3, NCOR1, and SHANK1; compound heterozygous variants in LNPEP, LRP1, and TBX2, that play a significant role in the neurotransmitter-neuropeptide axis, specifically in the dopaminergic circuits. We also noted a greater frequency of heterozygous and recessive variants in genes involved in the structural and functional integrity of synapse receptors, CHRNA4, CNR2, GABBR1, DRD4, NPAS4, ADH1B, ADH1C, OPRM1, and GABBR2. Variant analysis in upstream promoter regions revealed regulatory variants in NEK9, PRRX1, PRPF4B, CELA2A, RABGEF1, and CRBN, crucial for dopamine regulation. Using family-and pedigree-based data, we identified heterozygous recessive alleles in LNPEP, LRP1 (4 frameshift deletions), and TBX2 (2 frameshift deletions) linked to SUDs. GWAS overlap identified several SNPs associated with SUD susceptibility, including rs324420 and rs1229984. Furthermore, miRNA variant analysis revealed notable variants in mir-548 U and mir-532. Pathway studies identified the presence of extensive coordination among these genetic variants to impart substance use susceptibility and pathogenesis. This study identified variants that were found to be overrepresented among genes of dopaminergic circuits participating in the neurotransmitter-neuropeptide axis, suggesting pleiotropic influences in the development and sustenance of chronic substance use. The presence of a diverse set of haploinsufficient variants in varying frequencies demonstrates the existence of extraordinary coordination among them in attributing risk and modulating severity to SUDs.

明确核心遗传变异是全面解析物质使用障碍（substance use disorders, SUDs）的关键环节。本研究针对5个携带物质使用障碍的多代家系的全外显子组测序数据，采用整合组学方法，挖掘可赋予物质使用障碍易感性、并影响成瘾特征的候选遗传变异。本研究在GRIA3、NCOR1及SHANK1等基因中鉴定出多个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）与罕见蛋白功能改变变异；在LNPEP、LRP1及TBX2基因中发现复合杂合变异，上述变异在神经递质-神经肽轴，尤其是多巴胺能环路中发挥关键调控作用。我们还观察到，参与突触受体结构与功能完整性维持的基因（涵盖CHRNA4、CNR2、GABBR1、DRD4、NPAS4、ADH1B、ADH1C、OPRM1及GABBR2）中，杂合变异与隐性变异的检出频率显著升高。对上游启动子区域的变异分析显示，NEK9、PRRX1、PRPF4B、CELA2A、RABGEF1及CRBN等基因存在调控变异，这些变异对多巴胺能调控至关重要。借助基于家系与谱系的数据集，我们鉴定出与物质使用障碍相关的LNPEP、LRP1（含4处移码缺失）及TBX2（含2处移码缺失）的杂合隐性等位基因。全基因组关联研究（Genome-Wide Association Study, GWAS）重叠分析鉴定出多个与物质使用障碍易感性相关的单核苷酸多态性，包括rs324420与rs1229984。此外，miRNA变异分析发现mir-548 U及mir-532存在显著变异。通路富集分析显示，上述遗传变异间存在广泛协同效应，共同介导物质使用易感性与疾病发病机制。本研究鉴定的变异在参与神经递质-神经肽轴的多巴胺能环路相关基因中富集度显著升高，提示其在慢性物质使用的发生与维持过程中发挥多效性调控作用。不同频率的多样单倍剂量不足变异的存在，表明这些变异在赋予物质使用障碍风险及调节疾病严重程度方面存在精妙的协同调控机制。