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

IF 1.6 4区医学 Q4 DEVELOPMENTAL BIOLOGY

Birth Defects Research Pub Date : 2025-01-06 DOI:10.1002/bdr2.2428

Nirvika Paul, Susanta Sadhukhan, Srilagna Chatterjee, Anwesha Das, Dinesh Munian, Kausik Ganguly, Biswabandhu Bankura, Krishnendu Ghosh, Sudakshina Ghosh, Madhusudan Das

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引用次数: 0

Abstract

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.

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IGF2基因的新变异与神经管缺陷有关——印度西孟加拉邦的一个从计算机到临床的方法

神经管缺陷（NTDs）被定义为神经管（NT）的不完全闭合，在世界各地的患病率为每1000例活产1.2例。母体印迹基因胰岛素样生长因子2 （IGF2）的甲基化是NTDs发生的重要表观遗传机制之一。它的重要功能是胎儿的生长和代谢，以及细胞的分裂和分化。在一些研究中，已发现IGF2单核苷酸变异（snv）的个体变化与NTDs以及其他疾病有关。然而，为了更好地在分子水平上准确地理解这一机制，还需要进行更多的研究。在这项研究中，我们试图通过计算机方法和人体样本的临床实验筛选IGF2的所有snv，来研究IGF2遗传变异与NT关闭之间的关系。方法我们连续招募了98名携带被忽视热带病胎儿的母亲作为病例，76名年龄匹配的健康婴儿母亲作为对照。在对IGF2基因进行计算机分析后，我们设计了三个引物，针对3 ‘非翻译区（3 ’ UTR）的180个外显子、579个内含子和46个变体，用于聚合酶链反应（PCR）和随后的测序。进行统计分析以评估这些遗传变异与被忽视热带病之间的关系。采用实时荧光定量PCR （qRT-PCR）分析靶基因mRNA表达水平。本研究首次通过芯片分析获得了11个非同音变异体[rs750845881（D93N）、rs1290256492（P87H）、rs755066389（P87T）、rs150610908（G65D）、rs762200142（R64C）、rs868067982（G49C）、rs778465733（R48L）、rs1018841144（R48C）、rs1057518115（C33R）、rs112276039（C22R）、rs1240151267(L16W)]对IGF2基因功能的调控。在母体样本中进一步的临床验证显示rs3213225 (C >； T) (OR-2.076；ci - 1.123 - 3.840;p-0.0209)和rs734351 (C >； T) (OR-2.148；ci - 1.167 - 3.956;P-0.0148)，患病风险增加。RNA表达研究证实并支持所有这些snv，表明其与NTD有很强的相关性。我们的研究强烈表明，IGF2的遗传变异可能有助于解释与NTDs的风险关联，并可能在诊断和治疗应用中具有价值。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Birth Defects Research Medicine-Embryology

CiteScore

3.60

自引率

9.50%

发文量

153

期刊介绍： The journal Birth Defects Research publishes original research and reviews in areas related to the etiology of adverse developmental and reproductive outcome. In particular the journal is devoted to the publication of original scientific research that contributes to the understanding of the biology of embryonic development and the prenatal causative factors and mechanisms leading to adverse pregnancy outcomes, namely structural and functional birth defects, pregnancy loss, postnatal functional defects in the human population, and to the identification of prenatal factors and biological mechanisms that reduce these risks. Adverse reproductive and developmental outcomes may have genetic, environmental, nutritional or epigenetic causes. Accordingly, the journal Birth Defects Research takes an integrated, multidisciplinary approach in its organization and publication strategy. The journal Birth Defects Research contains separate sections for clinical and molecular teratology, developmental and reproductive toxicology, and reviews in developmental biology to acknowledge and accommodate the integrative nature of research in this field. Each section has a dedicated editor who is a leader in his/her field and who has full editorial authority in his/her area.