Detection of copy number variants reveals association of cilia genes with neural tube defects

Abstract

Background: Neural tube defects (NTDs) are one of the most common birth defects caused by a combination of genetic and environmental factors. Currently, little is known about the genetic basis of NTDs although up to 70% of human NTDs were reported to be attributed to genetic factors. Here we performed genome-wide copy number variants (CNVs) detection in a cohort of Chinese NTD patients in order to exam the potential role of CNVs in the pathogenesis of NTDs.

Methods: The genomic DNA from eighty-five NTD cases and seventy-five matched normal controls were subjected for whole genome CNVs analysis. Non-DGV (the Database of Genomic Variants) CNVs from each group were further analyzed for their associations with NTDs. Gene content in non-DGV CNVs as well as participating pathways were examined.

Results: Fifty-five and twenty-six non-DGV CNVs were detected in cases and controls respectively. Among them, forty and nineteen CNVs involve genes (genic CNV). Significantly more non-DGV CNVs and non-DGV genic CNVs were detected in NTD patients than in control (41.2% vs. 25.3%, p<0.05 and 37.6% vs. 20%, p<0.05). Non-DGV genic CNVs are associated with a 2.65-fold increased risk for NTDs (95% CI: 1.24-5.87). Interestingly, there are 41 cilia genes involved in non-DGV CNVs from NTD patients which is significantly enriched in cases compared with that in controls (24.7% vs. 9.3%, p<0.05), corresponding with a 3.19-fold increased risk for NTDs (95% CI: 1.27-8.01). Pathway analyses further suggested that two ciliogenesis pathways, tight junction and protein kinase A signaling, are top canonical pathways implicated in NTD-specific CNVs, and these two novel pathways interact with known NTD pathways.

Conclusions: Evidence from the genome-wide CNV study suggests that genic CNVs, particularly ciliogenic CNVs are associated with NTDs and two ciliogenesis pathways, tight junction and protein kinase A signaling, are potential pathways involved in NTD pathogenesis.

Figure 1. Summary of whole genomic copy number variants (CNVs) in the two groups; Wilcoxon rank-sum test was used for statistical analysis.

Figure 1A: Distribution of all called genomic CNVs by size. Figure 1B: Distribution of all called genomic CNVs by frequency.

Figure 2. Top bio-functional networks in NTD-affected cases.

The network “Cell Morphology, Developmental Disorder, Skeletal and Muscular Disorders” was identified in genes from NTD-specific CNVs by IPA (red indicates the duplication CNV, and green indicates deletion CNV). Genes are represented as nodes. Edges indicate known interactions between proteins (solid lines for direct interactions, dashed lines for mean indirect interactions). The gene shapes are indicative of molecular class. The canonical pathways (CP in the oval regions) were Tight junction signaling and Protein kinase A signaling.

Figure 3. Top bio-functional networks in known NTD candidate genes.

Pathways analysis identified “Organ Development, Embryonic Development, Tissue Development” in 223 known NTD candidate genes after literatures review. The known signaling pathways for neural tube closure including BMP signaling, SHH and Wnt/β-catenin signaling interact with two novel pathways in NTD-affected cases (CP in the oval regions).

Figure 4. Top bio-functional networks in the integrated list of 361 genes.

“Organ Development, Tissue Development, Embryonic Development” was identified as top network in the integrated list of 361 genes. The interactions exist between the novel pathway and the known pathway of NTDs.