OBJECTIVE: Primary non-response (PNR) to anti-tumor necrosis factor-α (TNFα) biologics is a serious concern in patients with inflammatory bowel disease (IBD). We aimed to identify the genetic variants associated with PNR. DESIGN: Patients were recruited from outpatient GI clinics and PNR was determined using both clinical and endoscopic findings. A case-control genome-wide association study was performed in 589 IBD patients and associations were replicated in an independent cohort of 293 patients. Effect of the associated variant on gene expression and TNFα secretion was assessed by cell-based assays. Pleiotropic effects were investigated by Phenome-wide Association Study (PheWAS). RESULTS: We identified rs34767465 as associated with PNR to anti-TNF-α therapy (OR:2.07, 95%CI:1.46-2.94, p=2.43x10-7, [Replication OR:1.8, 95%CI:1.04-3.16, p=0.03]). rs34767465 is a multiple-tissue expression quantitative trait loci for FAM114A2. Using RNA-sequencing and protein quantification from HapMap lymphoblastoid cell lines (LCLs), we found a significant decrease in FAM114A2 mRNA and protein expression in both heterozygous and homozygous genotypes when compared to wild type LCLs. TNF-α secretion was significantly higher in THP-1 cells [differentiated into macrophages] with FAM114A2 knockdown versus controls. Immunoblotting experiments showed that depletion of FAM114A2 impaired autophagy related pathway genes suggesting autophagy mediated TNF-α secretion as a potential mechanism. PheWAS showed rs34767465 was associated with comorbid conditions found in IBD patients (derangement of joints [p=2.3x10-4], pigmentary iris degeneration [p=5.1x10-4], diverticulum of esophagus [p=6.3x10-4]). CONCLUSION: We identified a variant rs34767465 associated with PNR to anti-TNFα biologics, which increases TNFα secretion through mechanism related to autophagy. rs34767465 may also explain the comorbidities associated with IBD.

中文翻译：

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炎症性肠病患者原发性抗TNFα治疗无反应的遗传关联

目的：抗炎坏死因子-α（TNFα）生物制剂的原发性无应答（PNR）是炎症性肠病（IBD）患者的严重问题。我们旨在鉴定与PNR相关的遗传变异。设计：从门诊的GI诊所招募患者，并根据临床和内窥镜检查结果确定PNR。在589名IBD患者中进行了病例对照全基因组关联研究，并且在293名患者的独立队列中复制了关联。通过基于细胞的测定评估相关变体对基因表达和TNFα分泌的影响。多向性效应通过全现象关联研究（PheWAS）进行了研究。结果：我们确定rs34767465与PNR联用抗TNF-α（OR：2.07，95％CI：1.46-2.94，p = 2.43x10-7，[Replication OR：1.8，95％CI：1.04-3.16， p = 0.03]）。rs34767465是FAM114A2的多组织表达定量性状基因座。使用HapMap淋巴母细胞系（LCL）的RNA测序和蛋白质定量，我们发现与野生型LCL相比，杂合和纯合基因型的FAM114A2 mRNA和蛋白质表达均显着降低。具有FAM114A2抑制作用的THP-1细胞（分化为巨噬细胞）中的TNF-α分泌明显高于对照组。免疫印迹实验表明，FAM114A2耗竭会损害自噬相关途径基因，提示自噬介导的TNF-α分泌是一种潜在的机制。PheWAS显示rs34767465与IBD患者的合并症有关（关节异常[p = 2.3x10-4]，色素性虹膜变性[p = 5.1x10-4]，食道憩室[p = 6.3x10-4]）。结论：我们鉴定出了与抗TNFα生物制剂的PNR相关的变体rs34767465，该变体通过与自噬相关的机制增加了TNFα的分泌。rs34767465还可以解释与IBD相关的合并症。