Deciphering the genetic etiology of rare congenital disorders through genomic analysis of rare variants

Abstract

Congenital diseases are a group of medical conditions that are present at birth and influenced, in part, by genetic variations. Tetralogy of Fallot (TOF) and biliary atresia (BA) are examples of rare congenital multifactorial diseases, in which rare genetic variations are believed to play important roles in their etiology. TOF is a common type of congenital heart defect (CHD). Rare coding mutations are known to underlie abnormal cardiac development, yet the contribution of rare noncoding variants to disease pathogenesis has been underexplored. To systematically assess the contribution of noncoding de novo variants (NC DNVs) to TOF, we explored the whole genome sequencing (WGS) data on 141 Chinese nonsyndromic TOF trios (CHN-TOF) and compared the results to Pediatric Cardiac Genomics Consortium (PCGC) of primarily European ancestries. Chinese but not the PCGC TOF patients showed a notably increased burden of damaging NC DNVs. In Chinese, NC and coding DNVs were predominantly associated with cardiomyocyte differentiation and chamber/valve/aorta development, respectively. When combined, these DNVs were significantly enriched in the NOTCH signaling pathway and outflow tract morphogenesis, with genes harbored NC DNVs (e.g., EFNB2, HEY2, and PITX2) interacting with NOTCH1 and FLT4 in a tight protein-protein interaction (PPI) network. Co-expression of genes with coding mutations, NC DNVs, and in NOTCH/VEGF signaling in cardiac mesoderm and cardiomyocyte progenitors further implies that noncoding mutations may increase the risk of TOF via perturbing the regulation of gene expression in fetal cardiac development. Overall, this study unveils a substantial contribution of damaging NC DNVs to TOF and implicates dysregulation of NOTCH signaling during cardiac differentiation as a major disease mechanism in the Chinese population. BA is a rare pediatric cholangiopathy and is the commonest reason for liver transplantation in the pediatric population. Elucidating the genetic predisposition of BA may help decode the underlying molecular mechanisms to improve disease outcomes. To uncover novel disease-susceptibility genetic factors, rare damaging mutations were identified in a dataset of whole exome/genome sequencing of 188 BA patients and 324 unaffected parents. Bioinformatic analyses discovered four gene sets associated with the development of BA: (i) cilium, (ii) extracellular matrix (ECM), (iii) NOTCH, and (iv) transforming growth factor-beta (TGFβ) signaling pathways. Integration with transcriptome data helped prioritize genes associated with disease progression to liver fibrosis or cirrhosis, including MAT1A and THBS1. Cell type enrichment and gene expression deconvolution analyses using scRNA-seq data further highlighted the significance of hepatic stellate cells (HSCs) and their interplay with ECM in BA. Overall, this study utilized various genomic methodologies to uncover novel disease-susceptibility genes, biological processes, and pathways involved in the development or progression of BA. In summary, our studies revealed a significant contribution of NC DNVs to TOF and identified multiple susceptibility genes/pathways/cell types implicated in the etiology of BA. In addition, we highlighted the tremendous power of diverse genomic methodologies and transcriptomic information in elucidating the etiology of congenital disorders, which will pave the way for the development of personalized treatment to improve the diagnosis and prognosis of these complex diseases.