[Show abstract][Hide abstract] ABSTRACT: The emerging association of assisted reproductive technologies with adverse perinatal outcomes has prompted the in-depth examination of clinical and laboratory protocols and procedures and their possible effects on epigenetic regulatory mechanism(s). The application of various approaches to study epigenetic regulation to problems in reproductive medicine has the potential to identify relative risk indicators for particular conditions, diagnostic biomarkers of disease state, and prognostic indicators of outcome. Moreover, when applied genome-wide, these techniques are likely to find novel pathways of disease pathogenesis and identify new targets for intervention. The analysis of DNA methylation, histone modifications, transcription factors, enhancer binding and other chromatin proteins, DNase-hypersensitivity and, micro- and other noncoding RNAs all provide overlapping and often complementary snapshots of chromatin structure and resultant "gene activity." In terms of clinical application, the predictive power and utility of epigenetic information will depend on the power of individual techniques to discriminate normal levels of interindividual variation from variation linked to a disease state. At present, quantitative analysis of DNA methylation at multiple loci seems likely to hold the greatest promise for achieving the level of precision, reproducibility, and throughput demanded in a clinical setting.
Preview · Article · Jan 2016 · Cold Spring Harbor Perspectives in Medicine
[Show abstract][Hide abstract] ABSTRACT: We have identified a novel molecular phenotype that defines a subgroup of newborns who have highly disrupted epigenomes. We
profiled DNA methylation in cord blood of 114 children selected from the lowest and highest quintiles of the birth weight
distribution (irrespective of their mode of conception) at 96 CpG sites in genes we have found previously to be related to
birth weight or growth and metabolism. We identified those individuals in each group who differed from the mean of the distribution
by the greatest magnitude at each site and for the largest number of sites. Such ‘outlier’ individuals differ substantially
from the rest of the group in having highly disrupted methylation levels at many CpG sites. We find that children from the
lowest quintile of the birth weight distribution have a significantly greater number of disrupted CpGs than children from
the highest quintile of the birth weight distribution. Among children from the lowest quintile of the birth weight distribution,
‘outlier’ individuals are significantly more common among children conceived in vitro than children conceived in vivo. These observations are novel and potentially important because they associate a molecular phenotype (multiple and large
DNA methylation differences) in normal somatic tissues (cord blood) with both a prenatal exposure (conception in vitro) and a clinically important outcome (low birth weight). These observations suggest that some individuals are more susceptible
to environmentally mediated epigenetic alterations than others.
No preview · Article · Nov 2015 · Human Molecular Genetics
[Show abstract][Hide abstract] ABSTRACT: We, and others, have demonstrated previously that there are differences in DNA methylation and transcript levels of a number of genes in cord blood and placenta between children conceived using assisted reproductive technologies (ART) and children conceived in vivo. The source of these differences (the effect of ART versus the underlying infertility) has never been determined in humans. In this study, we have attempted to resolve this issue by comparing placental DNA methylation levels at 37 CpG sites in 16 previously identified candidate genes in independent populations of children conceived in vivo ('fertile control' group) with ART children conceived from two groups: either autologous oocytes with infertility in one or both parents ('infertile ART' group) or donor oocytes (obtained from young fertile donors) without male infertility ('donor oocyte ART' group).
Of the 37 CpG sites analyzed, significant differences between the three groups were found in 11 CpGs (29.73 %), using ANOVA. Tukey's post hoc test on the significant results indicated that seven (63.63 %) of these differences were significant between the donor oocyte ART and fertile control groups. In addition, 20 of the 37 CpGs analyzed had been identified as differentially methylated between ART and fertile control groups in an independent population in a prior study. Of these 20 CpG sites, 9 also showed significant differences in the present population. An additional 9 CpGs were found to be significantly different between the two groups. Of these 18 candidate CpGs, 12 CpGs (in seven candidate genes) also showed significant differences in placental DNA methylation levels between the donor oocyte ART and fertile control groups.
These data suggest strongly that the DNA methylation differences observed between ART and in vivo conceptions are associated with some aspect of ART protocols, not simply the underlying infertility.
[Show abstract][Hide abstract] ABSTRACT: Background
Genetic and epigenetic variations may be an important contributer to altered eating behaviors in childhood which may lead to weight gain and obesity later in life.Objective
This study aimed to evaluate epigenetic as well as genetic associations with appetite in young children.Subjects and methodsParticipants were 32 non-obese and 32 obese African–American children aged 5–6 years. Saliva was collected from each child, and RNA and DNA were extracted for analysis. Individuals were genotyped for eating- and obesity-associated single nucleotide polymorphisms in seven candidate genes (FTO, MAOA, SH2B1, LEPR, DNMT3B, BDNF and CCKAR), and DNA methylation levels were measured in the upstream promoter region of each. Transcript levels of MAOA and FTO were also assessed. The Children's Eating Behavior Questionnaire (CEBQ) was used to assess the aspects of appetite. Child obesity was assessed using measured height and weight, and percent body fat was measured by dual-energy X-ray absorptiometry.ResultsFood responsiveness was higher and satiety responsiveness was lower among obese than non-obese female children (P = 0.001 and P = 0.031), but did not differ among male children. Epigenetic analysis of the BDNF promoter revealed associations with altered satiety responsiveness among female children (P < 0.01).Conclusion
The findings provide new evidence of epigenetic associations with altered appetite among young African–American girls.
No preview · Article · Mar 2015 · Pediatric Obesity
[Show abstract][Hide abstract] ABSTRACT: We have validated differences in DNA methylation levels of candidate genes previously reported to discriminate between normal colon mucosa of colon cancer patients and normal colon mucosa of individuals without cancer. Here, we report that CpG sites in 16 of the 30 candidate genes selected show significant differences in mean methylation level in normal colon mucosa of 24 cancer patients and 24 controls. A support vector machine trained on these data and data for an additional 66 CpGs yielded an 18-gene signature, composed of 10 of the validated candidate genes plus eight additional candidates. This model exhibited 96% sensitivity and 100% specificity in a 40-sample training set and classified all eight samples in the test set correctly. Moreover, we found a moderate-strong correlation (Pearson coefficients r=0.253-0.722) between methylation levels in colon mucosa and methylation levels in peripheral blood for seven of the 18 genes in the support vector model. These seven genes, alone, classified 44 of the 48 patients in the validation set correctly and five CpGs selected from only two of the seven genes classified 41 of the 48 patients in the discovery set correctly. These results suggest that methylation biomarkers may be developed that will, at minimum, serve as useful objective and quantitative diagnostic complements to colonoscopy as a cancer-screening tool. These data also suggest that it may be possible to monitor biomarker methylation levels in tissues collected much less invasively than by colonoscopy.
Preview · Article · May 2014 · Cancer Prevention Research
[Show abstract][Hide abstract] ABSTRACT: Assisted reproductive technologies (ART) have been associated with several adverse perinatal outcomes involving placentation and fetal growth. It is critical to examine each intervention individually in order to assess its relationship to the described adverse perinatal outcomes. One intervention ubiquitously used in ART is superovulation with gonadotropins. Superovulation results in significant changes in the hormonal milieu, which persist during the peri-implantation and early placentation periods. Epidemiologic evidence suggests that the treatment-induced peri-implantation maternal environment plays a critical role in perinatal outcomes. In this study, using the mouse model, we have isolated the exposure to the peri-implantation period and we examine the effect of superovulation on placentation and fetal growth. We report that the non-physiologic peri-implantation maternal hormonal environment resulting from gonadotropin stimulation appears to have a direct effect on fetal growth, trophoblast differentiation and gene expression. This appears to be mediated, at least in part, through trophoblast expansion and invasion. Although the specific molecular and cellular mechanism(s) leading to these observations remain to be elucidated, identifying this modifiable risk factor will not only allow us to improve perinatal outcomes with ART, but help us understand the pathophysiology contributing to these outcomes.
Preview · Article · Dec 2013 · Biology of Reproduction
[Show abstract][Hide abstract] ABSTRACT: In eutherian mammals, one X-chromosome in every XX somatic cell is transcriptionally silenced through the process of X-chromosome inactivation (XCI). Females are thus functional mosaics, where some cells express genes from the paternal X, and the others from the maternal X. The relative abundance of the two cell populations (X-inactivation pattern, XIP) can have significant medical implications for some females. In mice, the 'choice' of which X to inactivate, maternal or paternal, in each cell of the early embryo is genetically influenced. In humans, the timing of XCI choice and whether choice occurs completely randomly or under a genetic influence is debated. Here, we explore these questions by analysing the distribution of XIPs in large populations of normal females. Models were generated to predict XIP distributions resulting from completely random or genetically influenced choice. Each model describes the discrete primary distribution at the onset of XCI, and the continuous secondary distribution accounting for changes to the XIP as a result of development and ageing. Statistical methods are used to compare models with empirical data from Danish and Utah populations. A rigorous data treatment strategy maximises information content and allows for unbiased use of unphased XIP data. The Anderson-Darling goodness-of-fit statistics and likelihood ratio tests indicate that a model of genetically influenced XCI choice better fits the empirical data than models of completely random choice.European Journal of Human Genetics advance online publication, 8 May 2013; doi:10.1038/ejhg.2013.84.
No preview · Article · May 2013 · European journal of human genetics: EJHG
[Show abstract][Hide abstract] ABSTRACT: Over the last decade, we have witnessed an explosion of information on genetic factors underlying common human diseases and disorders. This 'human genomics' information revolution has occurred as a backdrop to a rapid increase in the rates of many human disorders and diseases. For example, obesity, Type 2 diabetes, asthma, autism spectrum disorder and attention deficit hyperactivity disorder have increased at rates that cannot be due to changes in the genetic structure of the population, and are difficult to ascribe to changes in diagnostic criteria or ascertainment. A likely cause of the increased incidence of these disorders is increased exposure to environmental factors that modify gene function. Many environmental factors that have epidemiological association with common human disorders are likely to exert their effects through epigenetic alterations. This general mechanism of gene-environment interaction poses special challenges for individuals, educators, scientists and public policy makers in defining, monitoring and mitigating exposures.
[Show abstract][Hide abstract] ABSTRACT: Infant birth weight is a complex quantitative trait associated with both neonatal and long-term health outcomes. Numerous studies have been published in which candidate genes (IGF1, IGF2, IGF2R, IGF binding proteins, PHLDA2 and PLAGL1) have been associated with birth weight, but these studies are difficult to reproduce in man and large cohort studies are needed due to the large inter individual variance in transcription levels. Also, very little of the trait variance is explained. We decided to identify additional candidates without regard for what is known about the genes. We hypothesize that DNA methylation differences between individuals can serve as markers of gene "expression potential" at growth related genes throughout development and that these differences may correlate with birth weight better than single time point measures of gene expression.
We performed DNA methylation and transcript profiling on cord blood and placenta from newborns. We then used novel computational approaches to identify genes correlated with birth weight.
We identified 23 genes whose methylation levels explain 70-87% of the variance in birth weight. Six of these (ANGPT4, APOE, CDK2, GRB10, OSBPL5 and REG1B) are associated with growth phenotypes in human or mouse models. Gene expression profiling explained a much smaller fraction of variance in birth weight than did DNA methylation. We further show that two genes, the transcriptional repressor MSX1 and the growth factor receptor adaptor protein GRB10, are correlated with transcriptional control of at least seven genes reported to be involved in fetal or placental growth, suggesting that we have identified important networks in growth control. GRB10 methylation is also correlated with genes involved in reactive oxygen species signaling, stress signaling and oxygen sensing and more recent data implicate GRB10 in insulin signaling.
Single time point measurements of gene expression may reflect many factors unrelated to birth weight, while inter-individual differences in DNA methylation may represent a "molecular fossil record" of differences in birth weight-related gene expression. Finding these "unexpected" pathways may tell us something about the long-term association between low birth weight and adult disease, as well as which genes may be susceptible to environmental effects. These findings increase our understanding of the molecular mechanisms involved in human development and disease progression.
Full-text · Article · Apr 2012 · BMC Medical Genomics
[Show abstract][Hide abstract] ABSTRACT: We have compared DNA methylation in normal colon mucosa between patients with colon cancer and patients without cancer. We identified significant differences in methylation between the two groups at 114 to 874 genes. The majority of the differences are in pathways involved in the metabolism of carbohydrates, lipids, and amino acids. We also compared transcript levels of genes in the insulin signaling pathway. We found that the mucosa of patients with cancer had significantly higher transcript levels of several hormones regulating glucose metabolism and significantly lower transcript levels of a glycolytic enzyme and a key regulator of glucose and lipid homeostasis. These differences suggest that the normal colon mucosa of patients with cancer metabolizes dietary components differently than the colon mucosa of controls. Because the differences identified are present in morphologically normal tissue, they may be diagnostic of colon cancer and/or prognostic of colon cancer susceptibility.
Preview · Article · Mar 2012 · Cancer Prevention Research
[Show abstract][Hide abstract] ABSTRACT: We identified potential epigenetic biomarkers for chronic kidney disease progression by comparing site-specific DNA methylation levels in more than 14,000 genes between African American and Hispanic diabetes patients with end stage renal disease (ESRD) and diabetes patients without nephropathy. We identified 187 genes that are differentially methylated between the two groups on at least two CpG sites in each gene in DNA extracted from saliva. Of the 187 genes whose mean methylation levels differed between the two groups, 39 genes, or closely related gene family members, have been reported to be involved in kidney development or diabetic nephropathy, per se, or have been associated with dialysis-induced changes in gene expression in peripheral blood cells. The fact that such a substantial fraction (21%) of the 187 candidate genes have been implicated previously through genome association or transcription profiling studies suggests strongly that the DNA methylation differences we observe are associated with disease predisposition and/or treatment. The fact that these nephropathy and/or dialysis-associated differences between patients were identified in DNA extracted from saliva offers proof-of-principle that inter-individual epigenetic differences may prove useful as predictive biomarkers of disease susceptibility.
Full-text · Article · Jan 2011 · Epigenetics: official journal of the DNA Methylation Society
[Show abstract][Hide abstract] ABSTRACT: Lack of correlation between birth weight percentiles and IGF2 or IGF2R mRNA levels in cord blood and placenta. Birth weight percentiles in the in vitro and in vivo populations plotted versus cord blood transcript levels of (A) IGF2, (B) IGF2R, (C) IGF2/IGF2R, and placenta transcript levels of (D) IGF2, (E) IGF2R, and (F) IGF2/IGF2R. Although average birth weight was lower in the in vitro group, we found little correlation between birth weight and IGF2 or IGF2R transcript levels (regression lines are shown, straight and dashed lines for in vivo and in vitro populations, respectively, and the maximum r2of 0.2433 is found in (B), even when birth weights were corrected for gestational age [Min, et al; Oken, et al; Yarkoni, et al]. These findings are consistent with previous observations from studies in human IUGR placentae . [Min SJ, Luke B, Min L, Misiunas R, Nugent C, et al. (2004) Birth weight references for triplets. Am J Obstet Gynecol 191(3): 809-814. Oken E, Kleinman KP, Rich-Edwards J, Gillman MW (2003) A nearly continuous measure of birth weight for gestational age using a United States national reference. BMC Pediatr 8(3): 6. Yarkoni S, Reece EA, Holford T, O'Connor TZ, Hobbins JC (1987) Estimated fetal weight in the evaluation of growth in twin gestations: a prospective longitudinal study. Obstet Gynecol 69(4): 636-639.)
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[Show abstract][Hide abstract] ABSTRACT: Intra-individual variation in IGF2 mRNA expression. Steady-state IGF2 mRNA levels measured in five sections of placenta in 12 individuals. IGF2 transcript levels vary by more than an order of magnitude (n.b.: each unit on the vertical axis is a power of 2) between individuals and between samples within some individuals.
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