Novel Variants of IGF2 Gene Are Linked With Neural Tube Defects-An In Silico to Clinical Approach in West Bengal, India

Background

Neural tube defects (NTDs) are defined as an incomplete closure of the neural tube (NT), with a prevalence of 1.2 per 1000 live births around the world. Methylation of the maternally imprinted gene Insulin-like growth factor 2 (IGF2) is one of the epigenetic mechanisms that contribute significantly to the development of NTDs. Its important functions are the fetal growth and metabolism, as well as cell division and differentiation.

Objectives

In a couple of studies, individual changes in IGF2 with single nucleotide variants (SNVs) have been found to be linked with NTDs as well as with other diseases. However, there is more need of studying so that we can better understand precisely this mechanism at the molecular level. In this study we tried to investigate the relationship between genetic variants of IGF2 and NT closure by screening all SNVs of IGF2 using both in silico methods and clinical experiments on human samples.

Methods

We enrolled 98 consecutive mothers carrying fetuses with NTDs as cases and 76 age-matched mothers with healthy babies as controls. Following an in silico analysis of the IGF2 gene, we designed three primers targeting a total of 180 exonic, 579 intronic, and 46 variants in the 3′ untranslated region (3′ UTR) for polymerase chain reaction (PCR) and subsequent sequencing. Statistical analyses were performed to assess associations between these genetic variants and NTDs. Additionally, quantitative real-time PCR (qRT-PCR) was conducted to analyze the mRNA expression levels of the target gene.

Results

This is the first study to enlist 11 non-synonymous variants [rs750845881(D93N), rs1290256492(P87H), rs755066389(P87T), rs150610908(G65D), rs762200142(R64C), rs868067982(G49C), rs778465733(R48L), rs1018841144(R48C), rs1057518115(C33R), rs112276039(C22R), rs1240151267(L16W)] in the regulation of IGF2 gene functions through in silico analysis. Further clinical validation in maternal samples showed a significant association between rs3213225 (C > T) (OR-2.076; CI-1.123-3.840; p-0.0209) and rs734351 (C > T) (OR-2.148; CI-1.167-3.956; p-0.0148) with increased disease risk. RNA expression study validated and supported all of these SNVs, indicating a strong correlation with NTD.

Conclusions

Our research strongly suggests that genetic variations in IGF2 may help explain the risk association with NTDs and could be valuable for diagnostic and therapeutic applications.