Next-generation sequencing identifies novel genes with rare variants in total anomalous pulmonary venous connection

Abstract

BackgroundTotal anomalous pulmonary venous connection (TAPVC) is recognized as a rare congenital heart defect (CHD). With a high mortality rate of approximately 80%, the survival rate and outcomes of TAPVC patients are not satisfactory. However, the genetic aetiology and mechanism of TAPVC remain elusive. This study aimed to investigate the underlying genomic risks of TAPVC through next-generation sequencing (NGS).MethodsRare variants were identified through whole exome sequencing (WES) of 78 sporadic TAPVC cases and 100 healthy controls using Fisher's exact test and gene-based burden test. We then detected candidate gene expression patterns in cells, pulmonary vein tissues, and embryos. Finally, we validated these genes using target sequencing (TS) in another 100 TAPVC cases.FindingsWe identified 42 rare variants of 7 genes (CLTCL1, CST3, GXYLT1, HMGA2, SNAI1, VAV2, ZDHHC8) in TAPVC cases compared with controls. These genes were highly expressed in human umbilical vein endothelial cells (HUVECs), mouse pulmonary veins and human embryonic hearts. mRNA levels of these genes in human pulmonary vein samples were significantly different between cases and controls. Through network analysis and expression patterns in zebrafish embryos, we revealed that SNAI1, HMGA2 and VAV2 are the most important genes for TAPVC.InterpretationOur study identifies novel candidate genes potentially related to TAPVC and elucidates the possible molecular pathogenesis of this rare congenital birth defect. Furthermore, SNAI1, HMGA2 and VAV2 are novel TAPVC candidate genes that have not been reported previously in either humans or animals.FundNational Natural Science Foundation of China.

HMGA Genes and Proteins in Development and Evolution

“…Hmga2 developmental expression has been studied by in situ hybridization and transgenic promoter analysis in the mouse [34,35] and by in situ hybridization in Xenopus early embryogenesis [36][37][38][39]. A very short description of hmga2 expression in the zebrafish was published recently [40].…”

“…A recent report has analyzed very succinctly the pattern of expression of hmga2 in zebrafish, concluding that the mRNA distribution of hmga2 transcripts parallels that of snai1, reported to be expressed in the primitive veins and in the head region at 20 hours post fertilization (hpf), in the developing posterior cardinal veins at 24 and 30 hpf, and in the heart at 48 and 72 hpf [40]. snai1 is expressed in the developing pharyngeal arches [52], so it looks as if zebrafish hmga2 pattern of expression is quite similar to that of Xenopus.…”

“…A graphic synopsis of Hmga1 and Hmga2 developmental expression in a generalized vertebrate embryo is presented in Figure 2. developing posterior cardinal veins at 24 and 30 hpf, and in the heart at 48 and 72 hpf [40]. snai1 is expressed in the developing pharyngeal arches [52], so it looks as if zebrafish hmga2 pattern of expression is quite similar to that of Xenopus.…”

In Silico Analysis Identifies Differently Expressed lncRNAs as Novel Biomarkers for the Prognosis of Thyroid Cancer

“…The coexpressed DEG-lncRNA pairs with the absolute value of Pearson correlation coefficient ≥ 0:75 were selected, and the coexpression network was established by using cytoscape software. Cytoscape e differentially expressed genes on chromosomes Under-expressed genes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Gene coexpression analysis could be applied to related genes of unknown function with GO or to analysis candidate disease genes or to predict transcriptional regulatory mechanism [16].…”

Network‐Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma

“…The KEGG (Kyoto Encyclopedia of Genes and Genomes) [ 22 ], GO (Gene Ontology) [ 23 , 24 ], and immune cell-based overrepresentation enrichment analysis were implemented in R with clusterProfiler package [ 25 ], which used overrepresentation enrichment analysis (ORA) to identify enriched KEGG pathways, GO terms, and immune cells. The gene markers for immune cells were extracted from the previously published study [ 26 ].…”