Biliary atresia is associated with polygenic susceptibility in ciliogenesis and planar polarity effector genes

Background Biliary atresia (BA) is poorly understood and requires liver transplantation (LT) in most children with lifelong risks of immunosuppression. Aims & Methods. To determine its genetic basis, we performed GWAS in 811 European BA cases treated with LT in US, Canadian and UK centers, and 4654 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. Results GWAS of common SNPs, 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 with 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 associated with 6005 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, 75% 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, fetal and BA liver but not normal or disease-control liver. 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. Conclusions Biliary atresia is associated with polygenic susceptibility in CPLANE genes. Rare variants contribute to polygenic risk in vulnerable pathways via unique genes. Impact and implications 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 specialised 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 can lead to preventive strategies to lower the incidence of biliary atresia and potentially other birth defects.