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Maternal-Fetal Medicine

Update on Gene-Environment Interactions and Birth Defects

Huiping Zhu, MD, PhD; Richard H. Finnell, PhD

Birth defects are structural malformations present in a baby at or before birth affecting multiple different organs. Here we discuss common etiologies thought to be affected by the interaction of genetics and the environment.

In the United States, 1 of every 33 babies is born with a birth defect. Established conditions such as chromosomal abnormalities and physical injury prior to or during birth may contribute to a small portion of all birth defects. Unfortunately for most cases, the causes remain unknown. After years of study, we have come to appreciate the fact that the more common birth defects represent complex traits with complex etiologies, which explains why very few genes that contribute to these defects are well known.

The term “gene-environment (GXE) interaction” is being used by scientists and clinicians from different disciplines to imply any kind of interplay between genes and environmental factors, including joint or synergistic effects. The ultimate goal of studying GXE interactions of birth defects is to provide individualized medicine, in terms of prevention and treatment, or to provide individualized lifestyle recommendation.1,2 On the other hand, from a public health perspective, the overall benefit of small changes at a population level is likely to be more significant than that of larger changes in high-risk individuals.

Currently, GXE interactions in the area of birth defects are investigated between environmental factors and candidate genes. Candidate genes and pathways are usually chosen from pertinent biological pathways, knock-out mouse studies, or genes responsible for syndromic congenital malformations. We will discuss 3 examples of GXE interactions that contribute to common birth defects etiology.

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Genes, nutrition, and neural tube defects: the folate story

The concept of nutritional genomics was introduced to the scientific community and the public rather recently, as genetic variation is now known to affect food tolerances and may also influence dietary requirements.3 A good example is the striking finding about the critical role of a simple vitamin, folic acid, in normal embryonic development. Epidemiologic and experimental studies demonstrated the benefit of folic acid supplementation in preventing neural tube defects (NTDs) and other congenital anomalies.

The mechanisms underlying those processes by which folic acid facilitates reduced NTD risk remains unknown. Nonetheless, there are some NTDs that are not preventable by folic acid supplementation. This has led to speculation that there is a subpopulation less responsive to folic acid supplementation than the general population.4 This decreased responsiveness could be due to variations in individual genetics. The folate-nonresponsive NTDs may also represent an entirely different pathogenetic mechanism at play that is responsible for these malformations.

This complex phenomenon has led multiple research groups to search for the presence of mutations or polymorphisms in genes associated with folate metabolism and transport as potential risk factors for NTDs.5 These genes include folate receptor α (FRα); reduced folate carrier (SLC19A1); 5,10-methylenetetrahydrofolate reductase (MTHFR); cystathionine β-synthase (CBS); methionine synthase (MTR); methionine synthase reductase (MTRR); methylenetetrahydrofolate dehydrogenase (MTHFD1); betaine-homocysteine methyltransferase (BHMT); and thymidylate synthase (TYMS). Interactions between maternal folate intake and several polymorphisms in folate genes (eg, MTHFR C677T, MTRR A66G, and SLC19A1 A80G) have been suggested by these studies. For example, in a population-based case-control study conducted in California, infants with an 80GG genotype of the SLC19A1 gene born to mothers who did not take vitamin supplementation during early pregnancy had a significantly higher risk for spina bifida.6

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Detoxification genes and anticonvulsant-induced birth defects

Anticonvulsant drugs have long been recognized as having a teratogenic potential capable of disrupting normal development in exposed infants. However, only about 3% to 10% of the infants who are exposed in utero will present with congenital malformations, and about 11% to 20% of these infants will exhibit neurodevelopment impairment with or without structural defects. In animal studies, there are clearly strain differences in anticonvulsant-induced NTD susceptibility, suggesting a strong genetic component in the susceptibility to valproic acid–induced exencephaly in mice, and likely an analogous situation exists for humans. The highly susceptible embryos are believed to carry genetic factors determining susceptibility to anticonvulsant drug–induced adverse fetal effects. In humans, it is estimated that 1% to 2% infants exposed to valproic acid in utero will present with spina bifida or other forms of NTDs.7

Genetic variations in infant and maternal genes involved in xenobiotic detoxification may modify risks of birth defects in response to maternal exposures to anticonvulsants. These enzymes are involved in metabolizing both endogenous compounds and a myriad of xenobiotic chemicals. Variant forms of both phase 1 (cytochrome P450) and phase 2 (eg, epoxide hydrolase, glutathione transferases, sulfotransferases, and N-acetyl transferases) enzymes are likely to increase risk of malformations because poor metabolizers may permit toxic compounds to persist longer in susceptible embryonic tissues, or because enhanced, rapid metabolizers for phase 1 enzymes may produce too many reactive intermediates that cannot be further detoxified quickly enough by phase 2 enzymes. Numerous phase 1–generated metabolic intermediates readily form protein and DNA adducts and cause oxidative stress, and as such, these reactive intermediates are often teratogenic, mutagenic, or carcinogenic.

Only a few clinical studies have investigated some of these enzyme variants with respect to risks of structural birth defects. Fetuses homozygous for the recessive allele would have low epoxide hydrolase (EPHX1) activity and would therefore be at risk if exposed to anticonvulsant drugs during gestation. Recently, the MTHFR C677T genotype was studied regarding the rates of major malformations following in utero exposure to antiepileptic drugs.8 The investigators found that the rate of major malformations was increased in offspring of mothers who carry at least 1 risk allele (T); however, neither genotype only nor anticonvulsant exposure only posed a significant increase in risk. These preliminary results suggest that genetic markers may prove useful in determining which infants are at increased risk for congenital malformations induced by anticonvulsant drugs.

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Maternal smoking, GXE, and orofacial clefts

Maternal smoking during pregnancy is associated with nonsyndromic cleft lip and/or palate (CL/P). Several animal studies demonstrated the adverse effects of cigarette smoking on development of cleft. GXE interactions have been investigated between maternal smoking and more than 2 dozen genes. Transforming growth factor α (TGFA) is the most intensively studied gene for GXE interaction effects on oral clefts. A large population-based case-control study investigated GXE interactions in CL/P and found a 2-fold increased risk associated with maternal smoking. The risk increased to 6-fold for infants who have the rare TGFA genotype.9

NOS3 gene encodes endothelial nitric oxide synthase, and its activity influences homocysteine concentration. Because smoking compromises NOS3 activity, genetic variation in the NOS3 gene could potentially interact with smoking and folic acid use in increasing the clefting risk.

In a California population-based case-control study, for those infants who had a least 1 variant allele for each NOS3 polymorphism, whose mothers smoked and did not use vitamins during early pregnancy, the CL/P risk was 4. 4 times higher for NOS3 -922G allele (95% confidence interval [CI], 2.1-10.2) and 4.6 times higher for 894T allele (95% CI, 1.8-10.7).10 Thus, the interaction between a genetic risk factor (NOS3 -922G allele or 894T allele) and 2 environmental factors (maternal smoking and folate intake) resulted in a 4-fold increase in risk for a craniofacial defect. Other genes that have been studied include aryl hydrocarbon receptor (AhR) pathway genes, several detoxification genes (CYP1A1, EPHX1), glutathione transferase gene family (GSTs), arylamine N-acetyltransferase gene family (NATs), hypoxia-induced factor-1 (HIF1), folate pathway genes (eg, MTHFR), muscle segment homeobox 1 (MSX1), and other developmental genes.11

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Methodology

The most commonly used epidemiologic study designs to test GXE interactions in the etiology of birth defects include population-based case-control, case-only, and family-based design. A case-control study is a retrospective design where cases and controls are sampled independently from the population. This method is simple and relatively inexpensive but usually suffers from bias due to population stratification.

When the main interest is GXE interaction and the candidate gene and environmental exposure are independent to each other, it is more efficient to analyze only the cases, ie, use a case-only study design. The main advantage is that no control is needed. However, several drawbacks limit the use of this design.2

Family-based design uses parents and the probands’ genotyping data and identifies allele association by comparing frequencies of “transmitted alleles” and “nontransmitted alleles.” This method has the advantage of avoiding the bias due to population stratification with both differential exposure and gene allele frequency. Family-based design is particularly suitable for birth defects research because the onsets are at birth, and parents are more likely to be available than when studying adult-onset diseases.

Sample size and statistical power have been a challenge for studying GXE interaction of structural birth defects, because these conditions are relatively rare and some of them could be lethal. In addition, the effect of each factor is rather small. Depending on the strength of the interaction and prevalence of exposure, as well as allele frequencies, sample size requirements to detect a significant GXE interaction are even larger than the sample sizes to identify a G or E marginal effect.

Another challenge for GXE interaction study of birth defects is the limited understanding of the mechanisms. Recent development of high-throughput genotyping technology and the HapMap project (www.hapmap.org) provided the opportunity for testing more variants and focusing on “tagging SNPs [single nucleotide polymorphisms]” that cover the whole gene region. Pathway-driven candidate gene studies that involve multiple genes/loci are becoming practical. But this raised the issues with multiple testing and further reduction of statistical power. Genome-wide association study (GWAS) seems to be the ultimate approach. However, to conduct large-scale GWAS in the area of birth defects research, a large number of DNA sample collection and robust analytic methods are required.

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Summary

Multiple genes with small effects interact with environmental factors to create a significant developmental disequilibrium beyond which these factors could have produced individually. We believe that it is the sum total of all these interacting elements from our genome and the environment that leads to the phenotypes in infants with complex birth defects. Although medicine is still far away from individualized preventive measures for birth defects, understanding how specific environmental factors interact with different genetic manifestations may yield critical clues that will ultimately lead to new approaches to avert preventable birth defects.

The authors report no actual or potential conflicts of interest in relation to this article.

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Huiping Zhu, MD, PhD, is Assistant Professor, and Richard H. Finnell, PhD, is Regents Professor, Center for Environmental and Genetic Medicine, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Houston.

References

1. Hunter DJ. Gene-environment interactions in human diseases. Nat Rev Genet. 2005;6(4):287-298.
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3. Stover PJ. Influence of human genetic variation on nutritional requirements. Am J Clin Nutr. 2006;83(2): 436S-442S.
4. Blom HJ, Shaw GM, den Heijer M, Finnell RH. Neural tube defects and folate: case far from closed. Nat Rev Neurosci. 2006;7(9):724-731.
5. Finnell RH, Shaw GM, Lammer EJ, Brandl KL, Carmichael SL, Rosenquist TH. Gene-nutrient interactions: importance of folates and retinoids during early embryogenesis. Toxicol Appl Pharmacol. 2004;198(2):75-85.
6. Shaw GM, Lammer EJ, Zhu H, Baker MW, Neri E, Finnell RH. Maternal periconceptional vitamin use, genetic variation of infant reduced folate carrier (A80G), and risk of spina bifida. Am J Med Genet. 2002;108(1):1-6.
7. Finnell RH. Genetic differences in susceptibility to anticonvulsant drug-induced developmental defects. Pharmacol Toxicol. 1991;69(4):223-227.
8. Kini U, Lee R, Jones A, et al; Liverpool Manchester Neurodevelopmental Study Group. Influence of the MTHFR genotype on the rate of malformations following exposure to antiepileptic drugs in utero. Eur J Med Genet. 2007; 50(6): 411-420.
9. Shaw GM, Wasserman CR, Lammer EJ, et al. Orofacial clefts, parental cigarette smoking, and transforming growth factor-alpha gene variants. Am J Hum Genet. 1996; 58(3):551-561.
10. Shaw GM, Iovannisci DM, Yang W, et al. Endothelial nitric oxide synthase (NOS3) genetic variants, maternal smoking, vitamin use, and risk of human orofacial clefts. Am J Epidemiol. 2005;162(12):1207-1214.
11. Shi M, Wehby GL, Murray JC. Review on genetic variants and maternal smoking in the etiology of oral clefts and other birth defects. Birth Defects Res C Embryo Today. 2008; 84(1):16-29.

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