[Show abstract][Hide abstract] ABSTRACT: Maternal one-carbon (1-C) metabolism provides methylgroups for fetal development and programing by DNA methylation as one of the underlying epigenetic mechanisms. We aimed to investigate maternal 1-C biomarkers, folic acid supplement use, and MTHFR C677T genotype as determinants of 1-C metabolism in early pregnancy in association with newborn DNA methylation levels of fetal growth and neurodevelopment candidate genes. The participants were 463 mother-child pairs of Dutch national origin from a large population-based birth cohort in Rotterdam, The Netherlands. In early pregnancy (median 13.0 weeks, 90% range 10.4-17.1), we assessed the maternal folate and homocysteine blood concentrations, folic acid supplement use, and the MTHFR C677T genotype in mothers and newborns. In newborns, DNA methylation was measured in umbilical cord blood white blood cells at 11 regions of the seven genes: NR3C1, DRD4, 5-HTT, IGF2DMR, H19, KCNQ1OT1, and MTHFR. The associations between the 1-C determinants and DNA methylation were examined using linear mixed models. An association was observed between maternal folate deficiency and lower newborn DNA methylation, which attenuated after adjustment for potential confounders. The maternal MTHFR TT genotype was significantly associated with lower DNA methylation. However, maternal homocysteine and folate concentrations, folic acid supplement use, and the MTHFR genotype in the newborn were not associated with newborn DNA methylation. The maternal MTHFR C677T genotype, as a determinant of folate status and 1-C metabolism, is associated with variations in the epigenome of a selection of genes in newborns. Research on the implications of these variations in methylation on gene expression and health is recommended.
[Show abstract][Hide abstract] ABSTRACT: The beneficial health effects of fruits and vegetables have been attributed to their polyphenol content. These compounds undergo many bioconversions in the body. Modeling polyphenol exposure of humans upon intake is a prerequisite for understanding the modulating effect of the food matrix and the colonic microbiome. This modeling is not a trivial task and requires a careful integration of measuring techniques, modeling methods and experimental design. Moreover, both at the population level as well as the individual level polyphenol exposure has to be quantified and assessed. We developed a strategy to quantify polyphenol exposure based on the concept of nutrikinetics in combination with population-based modeling. The key idea of the strategy is to derive nutrikinetic model parameters that summarize all information of the polyphenol exposure at both individual and population level. This is illustrated by a placebo-controlled crossover study in which an extract of wine/grapes and black tea solids was administered to twenty subjects. We show that urinary and plasma nutrikinetic time-response curves can be used for phenotyping the gut microbial bioconversion capacity of individuals. Each individual harbours an intrinsic microbiota composition converting similar polyphenols from both test products in the same manner and stable over time. We demonstrate that this is a novel approach for associating the production of two gut-mediated γ-valerolactones to specific gut phylotypes. The large inter-individual variation in nutrikinetics and γ-valerolactones production indicated that gut microbial metabolism is an essential factor in polyphenol exposure and related potential health benefits.
[Show abstract][Hide abstract] ABSTRACT: Is in vitro fertilization treatment with or without intracytoplasmatic sperm injection (IVF/ICSI) associated with changes in first and second trimester embryonic and fetal growth trajectories and birthweight in singleton pregnancies?
[Show abstract][Hide abstract] ABSTRACT: Deconvolution of noisy signals and images is an important task in various areas, examples are: chemometrics, biology and imaging. When the solution is required to be sparse, desirable results are obtained using penalized estimation techniques. Sparseness is realized by shrinking coefficients to zero. We use penalized regression with a penalty based on the L0 norm, as presented, for one dimensional data, in earlier work. Several extensions to this approach are presented. In case of blind deconvolution, a smoother is applied to improve the estimated impulse response, which is applicable to any unimodal response function. Results are demonstrated on pulse identification in endocrine data where it is aimed to model secretion pattern as a sparse series of spikes. Application to single-molecule fluorescence imaging is also demonstrated for functional superresolution in cell biology.
[Show abstract][Hide abstract] ABSTRACT: X-ray diffraction scans consist of series of counts; these numbers obey Poisson distributions with varying expected values. These scans are often smoothed and the Kα2 component is removed. This article proposes a framework in which both issues are treated. Penalized likelihood estimation is used to smooth the data. The penalty combines the Poisson log-likelihood and a measure for roughness based on ideas from generalized linear models. To remove the Kα doublet the model is extended using the composite link model. As a result the data are decomposed into two smooth components: a Kα1 and a Kα2 part. For both smoothing and Kα2 removal, the weight of the applied penalty is optimized automatically. The proposed methods are applied to experimental data and compared with the Savitzky–Golay algorithm for smoothing and the Rachinger method for Kα2 stripping. The new method shows better results with less local distortion. Freely available software in MATLAB and R has been developed.
Journal of Applied Crystallography 06/2014; 47(3). · 3.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Purpose: To introduce a method to optimize structural retinal nerve fiber layer (RNFL) models based on glaucomatous visual field data and to show how such an optimized model can be used to reduce noise in visual fields while preserving clinically important features. Methods: Correlation coefficients between age-adjusted deviation values of pairs of visual field test locations were calculated from 104 visual fields of moderately glaucomatous eyes. Distances between those test locations were defined for various parameters of a mathematical RNFL model. Then, the correspondence between the structural and functional data was defined by the spread, or variance, of the correlation coefficients for all distances. The model parameters that minimized this spread constituted the optimized model. To reduce noise in visual fields, the optimized model was used to smooth visual field data according to the RNFL's structure. The resulting fields were compared to visual fields that were smoothed based on the regular testing grid. Results: The optimal parameters for the RNFL model reduced the variance of the correlation coefficients by 85% and were well within the range of parameters previously determined from fundus photographs. Smoothing the visual fields based on the optimized RNFL-model strongly reduced noise while keeping important features. Conclusions: Mathematical RNFL models can be optimized based on visual field data, resulting in a strong structure-function relationship. Taking the RNFL's shape, as defined by such an optimized model, into account when smoothing visual fields results in better noise reduction while preserving important details.
[Show abstract][Hide abstract] ABSTRACT: To determine sociodemographic and life style-related risk factors and trimester specific maternal, placental, and fetal consequences of maternal anaemia and elevated haemoglobin levels in pregnancy.
In a population-based prospective cohort study of 7317 mothers, we measured haemoglobin levels in early pregnancy [gestational age median 14.4 weeks (inter-quartile-range 12.5-17.5)]. Anaemia (haemoglobin ≤11 g/dl) and elevated haemoglobin levels (haemoglobin ≥13.2 g/dl) were defined according to the WHO criteria. Maternal blood pressure, placental function and fetal growth were measured in each trimester. Data on gestational hypertensive disorders and birth outcomes was collected from hospitals.
Older maternal age, higher body mass index, primiparity and European descent were associated with higher haemoglobin levels (P < 0.05). Elevated haemoglobin levels were associated with increased systolic and diastolic blood pressure throughout pregnancy (mean differences 5.1 mmHg, 95% confidence interval [CI] 3.8, 6.5 and 4.1 mmHg, 95% CI 3.0, 5.2, respectively) and with a higher risk of third trimester uterine artery notching (RR 1.3, 95% CI 1.0, 1.7). As compared with maternal normal haemoglobin levels, not anaemia, but elevated haemoglobin levels were associated with fetal head circumference, length, and weight growth restriction from third trimester onwards (P < 0.05). Elevated haemoglobin levels were associated with increased risks of gestational hypertensive disorders (RR 1.4, 95% CI 1.1, 1.8) and adverse birth outcomes (RR 1.4, 95% CI 1.1, 1.7).
In a low-risk population, various sociodemographic and life style factors affect haemoglobin levels during pregnancy. Elevated haemoglobin levels are associated with increased risks of maternal, placental, and fetal complications.
Paediatric and Perinatal Epidemiology 02/2014; · 2.16 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: 17ß-Estradiol, an epigenetic modulator, is involved in the increased prevalence of migraine in women. Together with the prophylactic efficacy of valproate, which influences DNA methylation and histone modification, this points to the involvement of epigenetic mechanisms. Epigenetic studies are often performed on leukocytes, but it is unclear to what extent methylation is similar in other tissues. Therefore, we investigated methylation of migraine-related genes that might be epigenetically regulated (CGRP-ergic pathway, estrogen receptors, endothelial NOS, as well as MTHFR) in different migraine-related tissues and compared this to methylation in rat as well as human leukocytes. Further, we studied whether 17ß-estradiol has a prominent role in methylation of these genes. Female rats (n = 35) were ovariectomized or sham-operated and treated with 17β-estradiol or placebo. DNA was isolated and methylation was assessed through bisulphite treatment and mass spectrometry. Human methylation data were obtained using the Illumina 450k genome-wide methylation array in 395 female subjects from a population-based cohort study. We showed that methylation of the Crcp, Calcrl, Esr1 and Nos3 genes is tissue-specific and that methylation in leukocytes was not correlated to that in other tissues. Interestingly, the interindividual variation in methylation differed considerably between genes and tissues. Furthermore we showed that methylation in human leukocytes was similar to that in rat leukocytes in our genes of interest, suggesting that rat may be a good model to study human DNA methylation in tissues that are difficult to obtain. In none of the genes a significant effect of estradiol treatment was observed.
PLoS ONE 01/2014; 9(3):e87616. · 3.53 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Rayleigh and Raman scatter in fluorescence (excitation–emission) landscapes are a nuisance in two-way and three-way data modeling. We provide a method to clean individual emission spectra. The scatter can be represented accurately by Gaussian peaks, characterized by location, width and height. The analytic signal of interest effectively acts as a background to the scatter peaks. Modeling it locally as a smooth curve, using penalized least squares, allows accurate estimation of the parameters of scatter peaks. Once the peaks are modeled, they can be subtracted from the spectrum, almost completely removing the artifacts. Apart from local smoothness, no assumptions are made about the fluorescence spectra.
Chemometrics and Intelligent Laboratory Systems 01/2014; 130:1–5. · 2.29 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A peer-reviewed, open-access journal of population sciences open-access work is published under the terms of the Creative Commons Attribution NonCommercial License 2.0 Germany, which permits use, reproduction & distribution in any medium for non-commercial purposes, provided the original author(s) and source are given credit. See http://creativecommons.org/licenses/by-nc/2.0/de/
[Show abstract][Hide abstract] ABSTRACT: Can reliable size charts of human embryonic brain structures be created from three-dimensional ultrasound (3D-US) visualizations?
Reliable size charts of human embryonic brain structures can be created from high-quality images.
Previous studies on the visualization of both the cavities and the walls of the brain compartments were performed using 2D-US, 3D-US or invasive intrauterine sonography. However, the walls of the diencephalon, mesencephalon and telencephalon have not been measured non-invasively before. Last-decade improvements in transvaginal ultrasound techniques allow a better visualization and offer the tools to measure these human embryonic brain structures with precision.
This study is embedded in a prospective periconceptional cohort study. A total of 141 pregnancies were included before the sixth week of gestation and were monitored until delivery to assess complications and adverse outcomes.
For the analysis of embryonic growth, 596 3D-US scans encompassing the entire embryo were obtained from 106 singleton non-malformed live birth pregnancies between 7(+0) and 12(+6) weeks' gestational age (GA). Using 4D View (3D software) the measured embryonic brain structures comprised thickness of the diencephalon, mesencephalon and telencephalon, and the total diameter of the diencephalon and mesencephalon.
Of 596 3D scans, 161 (27%) high-quality scans of 79 pregnancies were eligible for analysis. The reliability of all embryonic brain structure measurements, based on the intra-class correlation coefficients (ICCs) (all above 0.98), was excellent. Bland-Altman plots showed moderate agreement for measurements of the telencephalon, but for all other measurements the agreement was good. Size charts were constructed according to crown-rump length (CRL).
The percentage of high-quality scans suitable for analysis of these brain structures was low (27%).
The size charts of human embryonic brain structures can be used to study normal and abnormal development of brain development in future. Also, the effects of periconceptional maternal exposures, such as folic acid supplement use and smoking, on human embryonic brain development can be a topic of future research.
This study was supported by the Department of Obstetrics and Gynaecology of the Erasmus University Medical Center. M.G. was supported by an additional grant from the Sophia Foundation for Medical Research (SSWO grant number 644). No competing interests are declared.
[Show abstract][Hide abstract] ABSTRACT: Attention deficit/hyperactivity disorder (ADHD) is a common and highly heritable psychiatric disorder. In addition, early life environmental factors contribute to the occurrence of ADHD. Recently, DNA methylation has emerged as a mechanism potentially mediating genetic and environmental effects. Here, we investigated whether newborn DNA methylation patterns of selected candidate genes involved in psychiatric disorders or fetal growth are associated with ADHD symptoms in childhood. Participants were 426 children from a large population based cohort of Dutch national origin. Behavioral data were obtained at age 6 years with the Child Behavior Checklist. For the current study, 11 regions at 7 different genes were selected. DNA methylation levels of cord blood DNA were measured for the 11 regions combined and for each region separately. We examined the association between DNA methylation levels at different regions and ADHD symptoms with linear mixed models. DNA methylation levels were negatively associated with ADHD symptom score in the overall analysis of all 11 regions. This association was largely explained by associations of DRD4 and 5-HTT regions. Other candidate genes showed no association between DNA methylation levels and ADHD symptom score. Associations between DNA methylation levels and ADHD symptom score were attenuated by co-occurring Oppositional defiant disorder and total symptoms. Lower DNA methylation levels of the 7 genes assessed at birth, were associated with more ADHD symptoms of the child at 6 years of age. Further studies are needed to confirm our results and to investigate the possible underlying mechanism.
Journal of Psychiatric Research 11/2013; · 4.09 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Are maternal characteristics and lifestyle factors associated with human embryonic growth trajectories?
Periconception maternal age is associated with increased, and smoking and alcohol use with decreased embryonic growth trajectories, estimated with crown-rump length (CRL) measurements.
Fetal weight is associated with health and disease in later life. Maternal characteristics and lifestyle factors affect fetal growth in the second and third trimesters of pregnancy and at birth; however, little is known about the association of these characteristics with first trimester embryonic growth.
In a tertiary centre, pregnant women were recruited and enrolled in a prospective periconception cohort study before 8 weeks of gestation. We selected 87 spontaneously conceived singleton pregnancies of women recruited in 2009 and 2010 that ended in non-malformed live births.
We performed weekly three-dimensional ultrasound scans from enrolment up to 13 weeks of gestation. At enrolment, a questionnaire was completed. Embryonic CRL measurements were performed using the V-Scope software in the BARCO I-Space. Associations between maternal characteristics and embryonic growth were assessed using square root transformed CRL as response in linear mixed model analyses, adjusted for potential confounders.
Four hundred and ninety-six scans from 87 pregnancies were included. In the multivariable analysis, maternal age was positively associated with first trimester CRL (difference per maternal year of age 0.024√mm (95% confidence interval (CI) 0.009, 0.040), P = 0.001). At 6 and 12 weeks of gestation, the CRL of an embryo from a 40-year-old mother was estimated 2.0 mm (61%) and 7.2 mm (14%) larger, respectively, compared with an embryo from a 20-year-old mother. Smoking of 10 or more cigarettes per day was negatively associated with CRL (difference -0.211√mm (95% CI -0.416, -0.006), P = 0.04), with embryos that were 0.9 mm (18.7%) and 3.1 mm (5.5%) smaller at 6 and 12 weeks, respectively, compared with non-smokers. Periconception alcohol use was negatively associated with CRL growth rate (difference -0.0025√mm (95% CI -0.0047, -0.0003)/day gestational age, P = 0.022), with embryos that were 0.2 mm (3%) and 1.1 mm (2%) smaller at 6 and 12 weeks, respectively, compared with non-alcohol users. Parity, BMI and moment of initiation of folic acid use were not significantly associated with embryonic CRL.
Due to the selection of pregnancies in a tertiary centre and the small number of pregnancies, the external validity of the results has to be confirmed using larger sample sizes and other population-based periconception cohort studies.
The association of maternal age and smoking with embryonic growth is in line with previous literature, whereas the association between embryonic growth and alcohol use is a new finding. However, concerning exposure to alcohol, the effect estimate was small and it is questionable whether this is of clinical value. More research is warranted to unravel underlying mechanisms and to assess the implications for preconception and early pregnancy care, such as the development and implementation of effective lifestyle interventions.
The work was funded by the Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Centre, Rotterdam, The Netherlands. The authors declare no conflicts of interest.
[Show abstract][Hide abstract] ABSTRACT: Purpose: Classical regression is based on certain assumptions that conflict with visual field data. We investigate and evaluate different regression models and their assumptions in order to determine point-wise visual field (VF) progression in glaucoma and to better predict future field loss for personalised clinical glaucoma management. Methods: Standard automated visual fields of 130 patients with primary glaucoma with a minimum of 6 years of follow-up were included. Sensitivity estimates at each VF location were regressed on time with classical linear and exponential regression models, as well as different variants of these models that take into account censoring and allow for robust fits. These models were compared for the best fit and for their predictive ability. The prediction was evaluated at 6 measurements (about 3 years) ahead using varying numbers of measurements. Results: For fitting the data, the classical uncensored linear regression model had the lowest root mean square error and 95th percentile of the absolute errors. These errors were reduced in all models when increasing the number of measurements used for the prediction of future measurements, with the classical uncensored linear regression model having the lowest values for these errors irrespective of how many measurements were included. Conclusion: All models performed similarly. Despite violation of its assumptions, the classical uncensored linear regression model appeared to provide the best fit for our data. In addition, this model appeared to perform the best when predicting future visual fields. However, more advanced regression models exploring any temporal-spatial relationships of glaucomatous progression are needed to reduce prediction errors to clinically meaningful levels.
[Show abstract][Hide abstract] ABSTRACT: The long-term follow-up results from the EORTC-26951 trial showed that the addition of PCV after radiotherapy increases survival in anaplastic oligodendrogliomas/oligoastrocytomas (AOD/AOA). However, some patients appeared to benefit more from PCV treatment than others.
We performed genome-wide methylation profiling of 115 samples included in the EORTC-26951 trial and extracted the CpG island hypermethylated phenotype (CIMP) and MGMT promoter-methylation (MGMT-STP27) status.
We first demonstrate that methylation profiling can be performed on archival tissues with a performance that is similar to snap frozen tissue samples. We then performed methylation profiling on EORTC-26951 clinical trial samples. Univariate analysis indicated that CIMP+ or MGMT-STP27 methylated tumors had an improved survival compared to CIMP- and/or MGMT-STP27 unmethylated tumors (median overall survival (OS) 1.05 v. 6.46 years and 1.06 v. 3.8 years, both P<0.0001 for CIMP and MGMT-STP27 status respectively). Multivariable analysis indicates that CIMP and MGMT-STP27 are significant prognostic factors for survival in presence of age, sex performance score and review diagnosis in the model. CIMP+ and MGMT-STP27 methylated tumors showed a clear benefit from adjuvant PCV chemotherapy: the median OS of CIMP+ samples in the RT and RT-PCV arms was 3.27 and 9.51 years respectively P=0.0033; for MGMT-STP27 methylated samples it was 1.98 and 8.65 years. There was no such benefit for CIMP- or MGMT-STP27 unmethylated tumors. MGMT-STP27 status remained significant in an interaction test (P=0.003). Statistical analysis of microarrays (SAM) identified 259 novel CpGs associated with treatment response.
MGMT-STP27 may be used to guide treatment decisions in this tumor type.
Clinical Cancer Research 08/2013; · 7.84 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Background:Perinatal environmental factors have been associated with the metabolic programming of children and consequent disease risks in later life. Epigenetic modifications that lead to altered gene expression may be involved. Here, we study early life environmental and constitutional factors in association with the DNA methylation of leptin (LEP), a non-imprinted gene implicated in appetite regulation and fat metabolism.Methods:We investigated maternal education, breastfeeding, and constitutional factors of the child at 17 mo of age. We measured the DNA methylation of LEP in whole blood and the concentration of leptin in serum.Results:Duration of breastfeeding was negatively associated with LEP methylation. Low education (≤12 y of education) was associated with higher LEP methylation. Boys had higher birth weight and lower LEP methylation than girls. An inverse association was established between birth weight per SD increase (+584 g) and LEP methylation. High BMI and leptin concentration were associated with lower methylation of LEP.Conclusion:The early life environment and constitutional factors of the child are associated with epigenetic variations in LEP. Future studies must reveal whether breastfeeding and the associated decrease in LEP methylation is an epigenetic mechanism contributing to the protective effect of breastfeeding against obesity.Pediatric Research (2013); doi:10.1038/pr.2013.95.
[Show abstract][Hide abstract] ABSTRACT: BACKGROUND: Epidemiological studies demonstrate that foetal growth restriction and low birth weight affect long-term health. Derangements in tissue-specific epigenetic programming of foetal and placental tissues are a suggested underlying mechanism of which DNA methylation is best understood. DNA methylation has been mostly investigated in DNA from white blood cells. To improve baseline understanding of tissue-specific DNA methylation, we examined variation in DNA methylation profiles of the imprinted foetal growth genes IGF2 and H19 in three different tissues from the same newborn obtained at the same time. FINDINGS: We obtained DNA from umbilical cord blood mononuclear cells (MNC; CD34+ and CD34--, n = 6), foetal side of the placenta (n = 5) and umbilical cord Wharton jelly (n = 5). DNA methylation of the IGF2 differentially methylated region (DMR) and H19 DMR was measured using quantitative mass spectrometry. Analysis of variance testing showed no statistical difference between total mean methylation of CD34+ and CD34-- MNC. Further comparisons were made with the pooled total MNC fraction. Mean IGF2 DMR methylation of Wharton jelly (P = 0.001) was 1.3 times higher than mean methylation of the pooled MNC. Placental mean methylation was 0.8 times lower (P <0.001) and Wharton jelly 0.9 times lower (P <0.001) than the pooled MNC of H19 DMR. CONCLUSION: The total MNC fraction is a rather homogeneous cell population for methylation studies of imprinted genes in umbilical cord blood white blood cells, but may not always reflect the methylation levels of IGF2 and H19 in other organs.