Table_1_Coordination among frequent genetic variants imparts substance use susceptibility and pathogenesis.DOCX

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.

明确关键遗传变异是全面理解物质使用障碍（Substance Use Disorders, SUDs）的核心步骤。本研究针对5个携带物质使用障碍的多代家系，利用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表型的候选遗传变异。本研究在GRIA3、NCOR1及SHANK1基因中鉴定出若干单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）以及罕见的蛋白功能改变变异；在LNPEP、LRP1与TBX2基因中鉴定出复合杂合变异，这些变异在神经递质-神经肽轴，尤其是多巴胺能通路上发挥重要作用。本研究还观察到，在参与突触受体结构与功能完整性维持的CHRNA4、CNR2、GABBR1、DRD4、NPAS4、ADH1B、ADH1C、OPRM1及GABBR2基因中，杂合变异与隐性变异的出现频率更高。对上游启动子区域的变异分析显示，NEK9、PRRX1、PRPF4B、CELA2A、RABGEF1及CRBN基因中存在调控变异，这些变异对多巴胺能调控至关重要。基于家系数据，本研究鉴定出与物质使用障碍相关的LNPEP、LRP1（含4个移码缺失）及TBX2（含2个移码缺失）基因中的杂合隐性等位基因。全基因组关联分析（Genome-Wide Association Study, GWAS）重叠分析鉴定出若干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，微小RNA（microRNA, miRNA）变异分析显示，mir-548 U与mir-532中存在显著变异。通路分析显示，上述遗传变异之间存在广泛协同作用，可赋予物质使用易感性并参与疾病发病机制。本研究鉴定出的变异在参与神经递质-神经肽轴的多巴胺能通路相关基因中富集度更高，提示这些变异对慢性物质使用的发生与维持具有多效性影响。不同频率下存在多种单倍剂量不足变异，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极强的协同作用。