Systems analysis of biliary atresia through integration of high-throughput biological data

Biliary atresia (BA), blockage of the proper bile flow due to loss of extrahepatic bile ducts, is a rare, complex disease of the liver and the bile ducts with unknown etiology. Despite ongoing investigations to understand its complex pathogenesis, BA remains the most common cause of liver failure requiring liver transplantation in children. To elucidate underlying mechanisms, we analyzed the different types of high-throughput genomic and transcriptomic data collected from the blood and liver tissue samples of children suffering from BA. Through use of a novel integrative approach, we identified potential biomarkers and over-represented biological functions and pathways to derive a comprehensive network showing the dysfunctional mechanisms associated with BA. One of the pathways highlighted in the integrative network was hypoxia signaling. Perturbation with hypoxia inducible factor activator, dimethyloxalylglycine, induced the biliary defects of BA in a zebrafish model, serving as a validation for our studies. Our approach enables a systems-level understanding of human BA biology that is highlighted by the interaction between key biological functions such as fibrosis, inflammation, immunity, hypoxia, and development The pooled RNA libraries were prepared using Illumina’s mRNA Sequencing Sample Preparation kit (#RS-930-1001) from the explanted liver tissue samples of 6 BA patients and 6 normal pre-implant liver allografts. The pooled RNA libraries for the BA and the normal groups were sequenced on Genome Analyzer II with 36 bp paired-end at the Wistar Institute, Philadelphia. CASAVA software was used to generate a table of exon, gene, and splice counts in both BA and normal groups