利用eQTL构建基因-基因网络挖掘类风湿性关节炎风险基因*

摘要目的：类风湿性关节炎是一种全身的慢性炎症型疾病，可能影响许多组织和器官，主要发作于灵活的关节。全世界人群中大 约有1%会患有类风湿性关节炎。目前已经证实了一些基因与类风湿性关节炎相关，但是这些基因只能解释一小部分遗传风险， 因此我们需要新的策略和方法来解决这个问题。方法：表达数量性状位点（eQTL）是指能够调控基因或蛋白质表达的基因组位点， 本文采用了eQTL数据构建基因- 基因网络并挖掘候选类风湿性关节炎风险基因。结果：首先，利用eQTL 数据,基于基因之间的 共调控系数，建立基因- 基因网络，我们建立了5 个不同阈值(0、0.2、0.4、0.6和0.8)的基因-基因网络；然后，在OMIM 和GAD数 据库中搜索已经证实的与类风湿性关节炎相关的186 个基因；最后我们将已证实与类风湿性关节炎相关的186 个基因分别投入 到这5 个网络中，利用基因与基因之间的相关性来挖掘到一些可能与类风湿性关节炎相关的候选风险基因。结论：本文基于 eQTL构建了基因-基因网络，结合已知类风湿性关节炎风险基因，挖掘未知风险基因，得到了较好的结果，证明了本方法的有效 性，且对于类风湿性关节炎的发病机制研究具有重要价值。除了类风湿性关节炎外，本方法还可推广到其它复杂疾病中，因此本 方法对人类复杂疾病的研究具有很强的学术理论价值和应用价值。     

Trans-omics pathway analysis suggests that eQTLs contribute to chondrocyte apoptosis of Kashin–Beck disease through regulating apoptosis pathway expression

Kashin–Beck disease (KBD) is a serious osteoarthropathia, mainly characterized by excessive chondrocyte necrosis and apoptosis. The molecular signaling pathways underlying KBD excessive chondrocyte apoptosis remain unclear, leading to a lack of effective medical interventions now. To clarify whether expression quantitative trait loci (eQTLs) contribute to excessive chondrocyte apoptosis of Kashin–Beck disease through regulating the expression of apoptosis pathways. We conducted a genome-wide eQTLs based pathway association analysis of KBD using Affymetrix Human SNP Array 6.0 in 1717 Chinese Han subjects. PLINK software was used for genome-wide association study (GWAS) of KBD. A modified gene set enrichment algorithm was applied for pathway association analysis based on GWAS results. The KBD-associated pathways were compared with abnormally expressed pathways in KBD articular cartilage, identified by microarray study of KBD. We identified 4 eQTLs pathways, which were not only significantly associated with KBD, but also abnormally expressed in KBD articular cartilage, including REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS (P = 0.008), MAHAJAN _RESPONSE_TO_IL1A_UP (P = 0.010), KEGG_PEROXISOME (P = 0.005) and MARKS_HDAC_TARGETS_UP (P = 0.006). Our results suggest that eQTLs contributed to KBD excessive chondrocyte apoptosis through regulating the expression of apoptosis related pathways. This study provides novel insight into the genetic susceptibility and therapeutic rationale of KBD.