Genomic approaches to understanding variable expressivity in alagille syndrome and genetic susceptibility to biliary atresia

The biliary system facilitates transport of bile from the liver, where it is produced, to the gall bladder, where it is stored and later released to aid digestion. Obstruction and defects in the biliary system are a primary indication of liver transplantation in children. Alagille syndrome (ALGS) and biliary atresia (BA) are two cholangiopathies with different etiopathology, but both affect bile flow and can lead to end-stage liver disease. ALGS is a dominant, multisystemic disease caused by mutations in JAG1 or NOTCH2 characterized by intrahepatic ductopenia and variable expressivity. BA is a multifactorial disease characterized by necroinflammatory obliteration of the extrahepatic biliary tree with unknown etiology. I used genomic tools including genome-wide gene expression analysis, genome-wide association (GWA) studies of single nucleotide polymorphisms (SNPs) and copy number variation (CNVs), and exome sequence analysis to uncover the genetic component to variable expressivity in ALGS and susceptibility to BA. In the first part of this thesis, I searched for genetic modifiers of the ALGS phenotype by investigating the effects of the non-mutated JAG1 allele, characterizing downstream gene expression of Notch signaling, and performing a SNP and CNV GWA studies of liver disease severity. This work revealed that cardiac defects are correlated with liver disease severity and the presence of butterfly vertebrae. I uncovered an enhancer element upstream of THBS2 that may affect the progression of liver disease in ALGS patients. In the second part of this thesis, I looked for markers of genetic susceptibility to BA, using an association study, exome sequencing of unrelated patients, and exome sequencing and CNV analysis of familial recurrence of BA-associated phenotypes. This work suggested several BA candidate genes, including FOXA2, which we propose as a BA susceptibility gene. Additionally, fine mapping of a previously reported susceptibility locus demonstrated an intronic risk allele in ADD3. Exome sequencing of candidate genes and a pathway-enriched analysis revealed alterations in several other genes that support the hypothesis that BA is a genetically heterogeneous disorder. This work identifies multiple areas for future research to better understand the genetics of these two biliary disorders