Methods for detecting interactions between genetic polymorphisms and prenatal environment exposure with a mother-child design

Environmental exposures during pregnancy: Mechanistic effects on immunity

In human studies, it is well established that exposures during embryonic and fetal development periods can influence immune health. Coupled with genetic predisposition, these exposures can alter lifetime chronic and infectious disease trajectory, and, ultimately, life expectancy. Fortunately, as research advances, mechanisms governing long-term effects of prenatal exposures are coming to light and providing the opportunity for intervention and risk reduction. For instance, human association studies have provided a foundation for the association of prenatal exposure to particulate matter with early immunosuppression and later allergic disease in the offspring. Only recently, the mechanisms mediating this response have been revealed and there is much we have yet to discover. Although cellular immune response is understood for many exposure scenarios, molecular pathways are still unidentified. This review will provide commentary and synthesis of the current literature regarding environmental exposures during pregnancy and mechanisms determining immune outcomes. Shared mechanistic features and current gaps in the state of the science are identified and discussed. To such purpose, we address exposures by their immune effect type: immunosuppression, autoimmunity, inflammation and tissue damage, hypersensitivity, and general immunomodulation.

Country-specific chemical signatures of persistent organic pollutants (POPs) in breast milk of French, Danish and Finnish women

The present study compares concentrations and chemical profiles of an extended range of persistent organic pollutants (dioxins, polychlorobiphenyls, brominated flame retardants and organochlorine pesticides) in breast milk samples from French (n = 96), Danish (n = 438) and Finnish (n = 22) women. Median exposure levels observed in French women (WHO-TEQ₂₀₀₅ PCDD/F = 6.1 pg/g l.w., WHO-TEQ₂₀₀₅ dl-PCB = 4.3 pg/g l.w., sum of 6 ndl-PCB = 85.2 ng/g l.w., sum of 7 i-PBDE = 1.5 ng/g l.w.) appeared overall lower than in Danish and Finnish women for all examined POPs, except for α-HBCD (2-fold higher level at 0.6 ng/g l.w.). Furthermore, the observed exposure levels of dioxins and PCBs were higher in Danish women (WHO-TEQ₂₀₀₅ PCDD/F = 13.2 pg/g l.w., WHO-TEQ₂₀₀₅ dl-PCB = 6.6 pg/g l.w., sum of 6 ndl-PCB = 162.8 ng/g l.w.) compared to Finnish women (WHO-TEQ₂₀₀₅ PCDD/F = 9.0 pg/g l.w., WHO-TEQ₂₀₀₅ dl-PCB = 4.6 pg/g l.w., sum of 6 ndl-PCB = 104.0 ng/g l.w.), whereas the concentrations of PBDEs were similar for Danish and Finnish women (sum of 7 i-PBDE = 4.9 and 5.2 ng/g l.w. respectively). The organochlorine (OC) pesticide contamination profile, determined in a subset of French samples, was dominated by p,p'-DDE (56.6%), followed by β-HCH (14.2%), HCB (9.7%) and dieldrin (5.2%), while other compounds were only minor contributors (<5%). The three countries appeared to be discriminated by the observed contamination patterns of the PCDD/F versus PCB, and the 1,2,3,6,7,8-HxCDD versus 1,2,3,4,7,8-HxCDD ratios, in addition to the relative contributions of specific congeners to the contamination profile (PCBs #118 and #156, PBDEs #28, #47, #99 and #153). In conclusion, unique chemical signatures were observed for each country on the basis of some POP congeners. Future biomonitoring studies will need to consider the high variability of individual exposure profiles in relation to multiple exposure sources but also physiological and metabolic differences.

Gene-environment interactions on growth trajectories

It has been suggested that children with larger brains tend to perform better on IQ tests or cognitive function tests. Prenatal head growth and head growth in infancy are two crucial periods for subsequent intelligence. Studies have shown that environmental exposure to air pollutants during pregnancy is associated with fetal growth reduction, developmental delay, and reduced IQ. Meanwhile, genetic polymorphisms may modify the effect of environment on head growth. However, studies on gene-environment or gene-gene interactions on growth trajectories have been quite limited partly due to the difficulty to quantitatively measure interactions on growth trajectories. Moreover, it is known that assessing the significance of gene-environment or gene-gene interactions on cross-sectional outcomes empirically using the permutation procedures may bring substantial errors in the tests. We proposed a score that quantitatively measures interactions on growth trajectories and developed an algorithm with a parametric bootstrap procedure to empirically assess the significance of the interactions on growth trajectories under the likelihood framework. We also derived a Wald statistic to test for interactions on growth trajectories and compared it to the proposed parametric bootstrap procedure. Through extensive simulation studies, we demonstrated the feasibility and power of the proposed testing procedures. We applied our method to a real dataset with head circumference measures from birth to age 7 on a cohort currently being conducted by the Columbia Center for Children's Environmental Health (CCCEH) in Krakow, Poland, and identified several significant gene-environment interactions on head circumference growth trajectories.

Methods for detecting interactions between imprinted genes and environmental exposures using birth cohort designs with mother-offspring pairs

Genomic imprinting is a form of epigenetic regulation in mammals in which the same allele of a gene is expressed differently depending on the parental origin of the allele. Traditionally, the detection of imprinted genes that affect complex diseases has been focused on linkage designs with pedigrees or case-parent designs with case-parent trios. In the past two decades, the birth cohort design with mother-offspring pairs has been applied to understand better the effect of environmental influences during pregnancy and beginning of life on the growth and development of children. No work has been done on the detection of imprinted genes using birth cohort designs. Moreover, although the importance of imprinting has been well recognized, no study has looked at how environmental exposures modify the effects of imprinted genes. In this study, we show that the proposed imprinting test using the birth cohort design with mother-offspring pairs is an efficient test for testing the interactions between imprinted genes and environmental exposures. Through extensive simulation studies and a real data application, the proposed imprinting test has demonstrated much improved power in detecting gene-environment interactions than that of a test assuming the Mendelian dominant model when the true underlying genetic model is imprinting.

Dissecting prenatal, postnatal, and inherited effects: ART and design

With the failure of common variants alone to explain the bulk of trait heritability, it becomes more important to understand the contribution of maternally inherited effects, prenatal effects, and postnatal environmental effects. These effects can be disentangled by studying families containing children conceived by assisted reproductive technologies (ART). We propose and develop a model that is an extension of the variance component model commonly used in pedigree analysis. Our model is flexible enough to allow any number of family members and degrees of relationship; thus, researchers can use both small and extended families simultaneously. Simulations demonstrate that our method has appropriate statistical properties and is robust to model misspecification and accurate in the presence of missing data. Most importantly, our method is able to disentangle maternally inherited effects from prenatal effects, which are confounded in traditional family studies. Our analyses also provide guidance to researchers designing studies that will use ART families to clarify genetic and environmental factors underlying traits.

Correlates of the FTO gene variant (rs9939609) and growth of American Indian infants

AIM

Obesity is a global, growing public-health problem. The detrimental health consequences of obesity are significant and include co-morbidities such as diabetes, coronary heart disease, and some types of cancer. To date, findings relating the A allele of the FTO variant rs9939609 to increased energy intake and risk for obesity have been fairly consistent across multiple populations. However, it is not known whether that relationship is also present in American Indian (AI) populations. The purpose of this study was to examine the minor allele frequency of the FTO variant rs9939609 and its associations with birth weight, weight for length (WFL) Z score, and amount of formula intake in AI infants.

DESIGN

A cross-sectional exploratory descriptive design was applied with a sample of 49 AI mother-infant dyads.

RESULTS

Mothers with an A allele had higher prepregnancy body mass index than those without an A allele, though difference was not statistically significant (p=0.08). Infants with an A allele tended to have higher birth weights, WFL Z score at age 14 to 20 weeks, and 24-h formula consumption compared with infants without an A-allele, though those differences were not statistically significant (p>0.05). Neither maternal nor infant A alleles were statistically significantly associated with birth weight, WFL Z score, and amount of formula intake in AI infants (p>0.05).

CONCLUSIONS

The findings do not confirm the association of the A allele of the FTO variant rs9939609 with birth weight, amount of formula intake, and WFL Z score in AI infants.