Fine mapping on chromosome 10q24.2 implicates ADD3 in biliary atresia

Abstract

Biliary Atresia (BA [OMIM 210500]) is a major cause of neonatal cholestasis (arrest of the normal flow bile) and is characterized by progressive fibrosclerosing and inflammatory obliteration of the extrahepatic biliary system during the first few weeks of life. The only current treatment is surgical (portoenterostomy -Kasai operation). The condition presents mainly sporadically, with only a few familial cases reported. BA is a rare congenital disorder whose incidence varies widely among populations (from 1 in 5,000 in Asians to 1 in 18,000 in Caucasians), being most common in East Asia and Polynesia. Through a genome-wide association study (GWAS) on Chinese individuals we identified the association of a 129Kb BA-associated region on chromosome 10q24.2 encompassing two biologically plausible genes, ADD3 and XPNPEP1. The strongest association was for a Single Nucleotide Polymorphism (SNP; rs17095355; p=6.94x10-9), intergenic between ADD3 and XPNPEP1. To determine the genetic architecture within this region we increased the genotype density by genotyping 117 tag-SNPs in 339 Chinese BA patients and 389 Chinese controls and also used imputation. rs17095355 remained the most associated marker within the region (p=6.06 x10-9). To elucidate the risk-contribution model of regional variation, we performed stepwise regression and sequential conditional test of the genotyped SNPs with BA phenotype. The disease risk model included 6 SNPs (i.e. rs975442, rs17095355, rs10509906, rs11194975, rs2501577 and rs11194997), in which rs975442, rs10509906, rs11194975, rs11194997 were variants newly included in the fine mapping study but not in GWAS. In this model, rs10509906 was independently associated with BA (p=0.018 conditioned on rs17095355). This model explains 8.9% of the phenotypic variation (R2=0.031 in GWAS) and indicates that multiple variants may contribute to BA susceptibility. The risk alleles of rs17095355 and rs10509906 were ancestral, suggesting an ancestral-susceptibility model of BA pathogenesis. We found that the haplotype comprising the risk allele of rs17095355 was associated with reduced ADD3 gene expression in liver of BA patients. Thus, our data suggests that ADD3 expression level in BA liver may contribute to BA pathogenesis. ADD3 is a component of the actin-adducin-spectin complex which is known to be associated with pathologic cholestasis.