Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA.
J Hepatol. 2023 Dec;79(6):1385-1395. doi: 10.1016/j.jhep.2023.07.039. Epub 2023 Aug 11.
BACKGROUND & AIMS: Biliary atresia (BA) is poorly understood and leads to liver transplantation (LT), with the requirement for and associated risks of lifelong immunosuppression, in most children. We performed a genome-wide association study (GWAS) to determine the genetic basis of BA.
We performed a GWAS in 811 European BA cases treated with LT in US, Canadian and UK centers, and 4,654 genetically matched controls. Whole-genome sequencing of 100 cases evaluated synthetic association with rare variants. Functional studies included whole liver transcriptome analysis of 64 BA cases and perturbations in experimental models.
A GWAS of common single nucleotide polymorphisms (SNPs), i.e. allele frequencies >1%, identified intronic SNPs rs6446628 in AFAP1 with genome-wide significance (p = 3.93E-8) and rs34599046 in TUSC3 at sub-threshold genome-wide significance (p = 1.34E-7), both supported by credible peaks of neighboring SNPs. Like other previously reported BA-associated genes, AFAP1 and TUSC3 are ciliogenesis and planar polarity effectors (CPLANE). In gene-set-based GWAS, BA was associated with 6,005 SNPs in 102 CPLANE genes (p = 5.84E-15). Compared with non-CPLANE genes, more CPLANE genes harbored rare variants (allele frequency <1%) that were assigned Human Phenotype Ontology terms related to hepatobiliary anomalies by predictive algorithms, 87% vs. 40%, p <0.0001. Rare variants were present in multiple genes distinct from those with BA-associated common variants in most BA cases. AFAP1 and TUSC3 knockdown blocked ciliogenesis in mouse tracheal cells. Inhibition of ciliogenesis caused biliary dysgenesis in zebrafish. AFAP1 and TUSC3 were expressed in fetal liver organoids, as well as fetal and BA livers, but not in normal or disease-control livers. Integrative analysis of BA-associated variants and liver transcripts revealed abnormal vasculogenesis and epithelial tube formation, explaining portal vein anomalies that co-exist with BA.
BA is associated with polygenic susceptibility in CPLANE genes. Rare variants contribute to polygenic risk in vulnerable pathways via unique genes.
Liver transplantation is needed to cure most children born with biliary atresia, a poorly understood rare disease. Transplant immunosuppression increases the likelihood of life-threatening infections and cancers. To improve care by preventing this disease and its progression to transplantation, we examined its genetic basis. We find that this disease is associated with both common and rare mutations in highly specialized genes which maintain normal communication and movement of cells, and their organization into bile ducts and blood vessels during early development of the human embryo. Because defects in these genes also cause other birth defects, our findings could lead to preventive strategies to lower the incidence of biliary atresia and potentially other birth defects.
胆道闭锁（BA）的发病机制尚不清楚，导致大多数患儿需要进行肝移植（LT），并需要终生接受免疫抑制治疗，存在相关风险。我们进行了一项全基因组关联研究（GWAS），以确定 BA 的遗传基础。
我们对在美国、加拿大和英国中心接受 LT 治疗的 811 例欧洲 BA 病例和 4654 例基因匹配对照进行了 GWAS。对 100 例病例进行全基因组测序，评估罕见变异的合成关联。功能研究包括对 64 例 BA 病例进行全肝转录组分析和在实验模型中进行干扰。
常见单核苷酸多态性（SNP），即等位基因频率>1%的 GWAS 鉴定出 AFAP1 内含子 SNP rs6446628 具有全基因组显著性（p=3.93E-8）和 TUSC3 亚阈值全基因组显著性（p=1.34E-7）的 rs34599046，这两个 SNP 都得到了相邻 SNP 的可信峰的支持。与其他先前报道的 BA 相关基因一样，AFAP1 和 TUSC3 是纤毛生成和平面极性效应物（CPLANE）。在基于基因集的 GWAS 中，BA 与 102 个 CPLANE 基因中的 6005 个 SNP 相关（p=5.84E-15）。与非 CPLANE 基因相比，更多的 CPLANE 基因具有罕见变异（等位基因频率<1%），这些变异被预测算法分配了与肝胆异常相关的人类表型本体论术语，分别为 87%和 40%，p<0.0001。在大多数 BA 病例中，罕见变异存在于与 BA 相关常见变异不同的多个基因中。AFAP1 和 TUSC3 的敲低阻断了小鼠气管细胞中的纤毛生成。纤毛生成的抑制导致斑马鱼出现胆管发育不良。AFAP1 和 TUSC3 在胎儿肝类器官以及胎儿和 BA 肝脏中表达，但在正常或疾病对照肝脏中不表达。BA 相关变异和肝转录本的综合分析显示血管生成和上皮管形成异常，解释了与 BA 共存的门静脉异常。
BA 与 CPLANE 基因中的多基因易感性相关。罕见变异通过独特的基因在易感性途径中导致多基因风险。
大多数患有胆道闭锁的儿童需要进行肝移植才能治愈，胆道闭锁是一种发病机制尚不清楚的罕见疾病。移植免疫抑制增加了危及生命的感染和癌症的可能性。为了通过预防这种疾病及其向移植的进展来改善护理，我们研究了其遗传基础。我们发现，这种疾病与高度专业化基因中的常见和罕见突变有关，这些基因在人类胚胎早期维持细胞的正常通讯和运动，以及它们向胆管和血管的组织形成。由于这些基因的缺陷也会导致其他出生缺陷，我们的发现可能会导致预防策略的出现，以降低胆道闭锁的发病率，并可能降低其他出生缺陷的发病率。
