This project will map disease pathways for biliary atresia (BA), which has failed all therapy and requires liver transplantation (LTx), using genetic susceptibility as a common basis. BA causes liver failure at birth and accounts for up to half of all pediatric LTx, worldwide, but has an uncertain etiology. BA leads to scarred and atretic bile ducts, which fail to drain the liver. Some children also have anomalous left-right patterning of extrahepatic organs. Preliminary genome-wide association study (GWAS) of single nucleotide polymorphisms (SNPs) in BA cases, and other evidence from human BA and experimental models lead us to propose the following specific aims: Aim 1. We will confirm whether BA associates with SNPs in manosidase-1-α-2 (MAN1A2), and in genes which signal via hedgehog, epidermal and transforming growth factors and genes for ciliogenesis. These pathways are abnormal in liver from BA cases, zebrafish with knockdown of man1a2, and Man1a2 -/- (knockout) mice. We will identify novel potentially causal variants with targeted sequencing of significant SNP loci. Aim 2. We will confirm whether knockdown of man1a2 and other candidates induces biliary dysgenesis and cardiac and hepatic heterotaxy in zebrafish, impaired ciliogenesis in the ex vivo mouse airway epithelia model of ciliogenesis, and dysregulation of the abovementioned developmental pathways in the liver transcriptome. Aim 3. We will construct putative pathways for BA with those significant SNP loci and dysregulated genes which show interactions in an integrated systems analysis of data from Aims 1 and 2. These loci will also implicate aberrant inflammatory and stress responses. We will corroborate pathways with combined perturbations of a developmental gene with an inflammatory and a stress response gene in zebrafish and ex vivo ciliogenesis models. We expect that aberrant developmental, inflammatory and stress response signaling contributes to hepatic and extrahepatic BA. We will genotype the largest homogeneous cohort of 800 Caucasian BA cases with LTx from three of the world's largest pediatric LTx centers: the Children's Hospital of Pittsburgh, King's College Hospital, London, UK, Birmingham Children's Hospital, UK. We will perform whole genome transcriptome (RNA) sequencing of liver samples from 80 of these cases. We will use experimental and bioinformatics resources of the Universities of Pittsburgh and California, San Diego, and the Center for Applied Genomics, Philadelphia. At the end of our project, we will have expanded our knowledge about pathogenesis of BA and related birth defects and identified candidate strategies to prevent or overcome delayed biliary morphogenesis. The international collaboration of leaders in hepatology (Kelly, Dhawan, Squires), transplant surgery (Sharif, Sindhi), genomics (Weeks, Hakonarson, Higgs), pathology (Ranganathan) and systems biology/bioinformatics (Subramanian, Higgs) is well suited to this task.