Nady El Hajj

CpG sites with continuously increasing or decreasing methylation from early to late human fetal brain development

Normal human brain development is dependent on highly dynamic epigenetic processes for spatial and temporal gene regulation. Recent work identified wide-spread changes in DNA methylation during fetal brain development. We profiled CpG methylation in frontal cortex of 27 fetuses from gestational weeks 12-42, using Illumina 450K methylation arrays. Sites showing genome-wide significant correlation with gestational age were compared to a publicly available data set from gestational weeks 3-26. Altogether, we identified 2016 matching developmentally regulated differentially methylated positions (m-dDMPs): 1767m-dDMPs were hypermethylated and 1149 hypomethylated during fetal development. M-dDMPs are underrepresented in CpG islands and gene promoters, and enriched in gene bodies. They appear to cluster in certain chromosome regions. M-dDMPs are significantly enriched in autism-associated genes and CpGs. Our results promote the idea that reduced methylation dynamics during fetal brain development may predispose to autism. In addition, m-dDMPs are enriched in genes with human-specific brain expression patterns and/or histone modifications. Collectively, we defined a subset of dDMPs exhibiting constant methylation changes from early to late pregnancy. The same epigenetic mechanisms involving methylation changes in cis-regulatory regions may have been adopted for human brain evolution and ontogeny.

DNA methylation signatures in cord blood of ICSI children

Abstract STUDY QUESTION Does ICSI induce specific DNA methylation changes in the resulting offspring? SUMMARY ANSWER Although several thousand analyzed CpG sites (throughout the genome) displayed significant between-group methylation differences, both ICSI and spontaneously conceived children varied within the normal range of methylation variation. WHAT IS KNOWN ALREADY Children conceived by ART have increased risks for medical problems at birth and to the extent of present knowledge also in later life (i.e. impaired metabolic and cardiovascular functions). One plausible mechanism mediating these ART effects are epigenetic changes originating in the germ cells and/or early embryos and persisting during further development. STUDY DESIGN, SIZE, DURATION We compared the cord blood methylomes and candidate gene methylation patterns of newborns conceived through ICSI or spontaneously. PARTICIPANTS/MATERIALS, SETTING, METHODS Umbilical cord bloods were obtained from healthy newborn singletons conceived spontaneously (53 samples), through ICSI (89) or IVF (34). Bisulfite-converted DNA samples of 48 ICSI and 46 control pregnancies were used for genome-wide analyses with Illuminas 450K methylation arrays. Candidate genes from the methylation screen were analyzed in all three groups by bisulfite pyrosequencing. MAIN RESULTS AND THE ROLE OF CHANCE Altogether, 4730 (0.11%) of 428 227 analyzed CpG sites exhibited significant between-group methylation differences, but all with small (β < 10%) or very small (β < 1%) effect size. ICSI children showed a significantly decreased DNA methylation age at birth, lagging approximately half a week behind the controls. ART-susceptible CpGs were enriched in CpG islands with low methylation values (0–20%) and in imprinting control regions (ICRs). Eighteen promoter regions (six in microRNA and SNORD RNA genes), four CpG islands (three in genes including one long non-coding RNA), and two ICRs contained multiple significant sites. Three differentially methylated regions were studied in more detail by bisulfite pyrosequencing. ATG4C and SNORD114-9 could be validated in an independent ICSI group, following adjustment for maternal age and other confounding factors. ATG4C was also significant in the IVF group. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION The observed epigenetic effects are small and there are numerous potential confounding factors such as parental age and infertility. Although our study meets current standards for epigenetic screens, sample size is still two orders of magnitude below that of genome-wide association studies. WIDER IMPLICATIONS OF THE FINDINGS Our study suggests an impact of ICSI on the offsprings epigenome(s), which may contribute to phenotypic variation and disease susceptibility in ART children. Epigenetic regulation of gene expression by different classes of non-coding RNAs may be a key mechanism for developmental programming through ART. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by a research grant (no. 692185) from the European Union (ERA of ART). There are no competing interests.

Epigenetic signatures of gestational diabetes mellitus on cord blood methylation

BackgroundIntrauterine exposure to gestational diabetes mellitus (GDM) confers a lifelong increased risk for metabolic and other complex disorders to the offspring. GDM-induced epigenetic modifications modulating gene regulation and persisting into later life are generally assumed to mediate these elevated disease susceptibilities. To identify candidate genes for fetal programming, we compared genome-wide methylation patterns of fetal cord bloods (FCBs) from GDM and control pregnancies.Methods and resultsUsing Illumina’s 450K methylation arrays and following correction for multiple testing, 65 CpG sites (52 associated with genes) displayed significant methylation differences between GDM and control samples. Four candidate genes, ATP5A1, MFAP4, PRKCH, and SLC17A4, from our methylation screen and one, HIF3A, from the literature were validated by bisulfite pyrosequencing. The effects remained significant after adjustment for the confounding factors maternal BMI, gestational week, and fetal sex in a multivariate regression model. In general, GDM effects on FCB methylation were more pronounced in women with insulin-dependent GDM who had a more severe metabolic phenotype than women with dietetically treated GDM.ConclusionsOur study supports an association between maternal GDM and the epigenetic status of the exposed offspring. Consistent with a multifactorial disease model, the observed FCB methylation changes are of small effect size but affect multiple genes/loci. The identified genes are primary candidates for transmitting GDM effects to the next generation. They also may provide useful biomarkers for the diagnosis, prognosis, and treatment of adverse prenatal exposures.

Epigenetic dysregulation of protocadherins in human disease

Protocadherins (Pcdhs) are a group of cell-cell adhesion molecules that are highly expressed in the nervous system and have a major function in dendrite development and neural circuit formation. However, the role protocadherins play in human health and disease remains unclear. Several recent studies have associated epigenetic dysregulation of protocadherins with possible implications for disease pathogenesis. In this review, we briefly recap the various epigenetic mechanisms regulating protocadherin genes, particularly the clustered Pcdhs. We further outline research describing altered epigenetic regulation of protocadherins in neurological and psychiatric disorders, as well as in cancer and during aging. We additionally present preliminary data on DNA methylation dynamics of clustered protocadherins during fetal brain development, as well as the epigenetic differences distinguishing adult neuronal and glial cells. A deeper understanding of the role of protocadherins in disease is crucial for designing novel diagnostic tools and therapies targeting brain disorders.

Gene expression and epigenetic aberrations in F1-placentas fathered by obese males: Molecular aberrations using an obese mice model

Gene expression and/or epigenetic deregulation may have consequences for sperm and blastocysts, as well as for the placenta, together potentially contributing to problems observed in offspring. We previously demonstrated specific perturbations of fertilization, blastocyst formation, implantation, as well as aberrant glucose metabolism and adiposity in offspring using a mouse model of paternal obesity. The current investigation analyzed gene expression and methylation of specific CpG residues in F1 placentas of pregnancies fathered by obese and normal‐weight male mice, using real‐time PCR and bisulfite pyrosequencing. Our aim was to determine if paternal obesity deregulated placental gene expression and DNA methylation when compared to normal‐weight males. Gene methylation of sperm DNA was analyzed and compared to placentas to address epigenetic transmission. Of the 10 paternally expressed genes (Pegs), 11 genes important for development and transport of nutrients, and the long‐terminal repeat Intracisternal A particle (IAP) elements, derived from a member of the class II endogenous retroviral gene family, we observed a significant effect of paternal diet‐induced obesity on deregulated expression of Peg3, Peg9, Peg10, and the nutrient transporter gene Slc38a2, and aberrant DNA methylation of the Peg9 promoter in F1 placental tissue. Epigenetic changes in Peg9 were also found in sperm from obese fathers. We therefore propose that paternal obesity renders changes in gene expression and/or methylation throughout the placental genome, which could contribute to the reproductive problems related to fertility and to the metabolic, long‐term health impact on offspring.

Natural Killer Cell Immunoglobulin-like Receptor (KIR) genotypes in Follicular Lymphoma patients: Results of a pilot study

AIMSnThe Natural Killer Cell Immunoglobulin-like Receptor (KIR) genotype profiling in Follicular Lymphoma has not been reported before in the literature.nnnMATERIALS AND METHODSnDNA extracted from 20 Follicular Lymphoma patients and 62 healthy controls was analyzed for KIR genotyping using a polymerase chain reaction/sequence specific primers technique (PCR/SSP) for the presence of 16 KIR gene and pseudogene loci.nnnRESULTSnThe AA, AB, and BB genotype frequencies were, respectively, 20%, 60% and 20% with an A:B ratio of 1:1. KIR 2DL4, KIR 3DL2, KIR 3DL3, and KIR 3DP1*003 were presented in all individuals. No significant difference between patients and controls was detected.nnnCONCLUSIONnKIR genotyping profile does not seem to be associated with Follicular Lymphoma. The results presented in this pilot research represent the first international report about this important clinical entity.

Distribution of killer cell immunoglobulin-like receptor (KIR) genotypes in patients with familial Mediterranean fever.

Genotypic profiles of the natural killer cell immunoglobulin-like receptors (KIR) have been reported to vary among different ethnic groups and variable clinical entities. This study represents the first report on its distribution among patients with familial Mediterranean fever (FMF). We studied 56 unrelated Lebanese FMF patients, had their DNA typed using sequence-specific primer (SSP) technique for the presence of 16 KIR gene and pseudogene loci, and compared them to the general Lebanese population. The AA1 genotype was the most frequent in both the FMF and control groups. Six new KIR profiles were identified. The FMF group showed a higher prevalence of KIR 3DP1*003 (p<0.05) and an increase in the BB genotype compared with controls. The results lead to an interesting future research question of whether or not KIR genotype is involved in the predisposition to or pathogenesis of FMF. This is the first report that describes the KIR genotypic profile in this important clinical disease.

Killer cell immunoglobulin-like receptor genotypes in Behçet's disease patients: any role for the 3DP1*001/002 pseudogene?

AIMSnGenotypic profiles of the natural killer cell immunoglobulin-like receptors (KIR) have been reported to vary among different ethnic groups and variable clinical entities. This study represents the second report on its distribution among patients with Behçets disease (BD). We studied 43 unrelated Lebanese Behçets patients, had their DNA typed using sequence-specific primer technique for the presence of 16 KIR genes and pseudogenes loci, and compared them to the general Lebanese population.nnnRESULTSnIn addition to sharing common features with the general population, the AA genotype was still the most frequent--however, with five new KIR profiles identified. There was no statistically significant distribution of the different KIR genes between the cases (BD patients) and controls (Lebanese population); however, KIR3DP1*001/002 was found to be significantly different between the BD patients and the Lebanese population, but this significance was lost after correction for all KIR loci.nnnCONCLUSIONnThe results lead to an interesting future research question of whether or not KIR genotype is involved in the predisposition to or pathogenesis of BD especially that a pseudogene is controversially in question. This is the second report that describes the KIR genotypic profile in such an important clinical disease but the first to shed a light on the possible role of a pseudogene.

Killer Cell Immunoglobulin-Like Receptor (KIR) Genotypes in Patients with Recurrent Tonsillitis

AIMSnThis study represents the first report on the distribution of killer cell immunoglobulin-like receptor (KIR) genotype among recurrent tonsillitis patients. We recruited 34 Lebanese pediatric patients diagnosed with recurrent tonsillitis and had their DNA typed using sequence-specific primer technique for the presence of 16 KIR loci.nnnRESULTSnWe observed that 25 different KIR genotypes were present similar to the general control population with the same KIR gene content. There was no statistically significant difference in the distribution of the activating and inhibitory KIR genes between the two categories. Like in the general control population, we noted a predominance of the AB genotype; however, the KIR genotypic distribution among the tonsillitis patients was much more heterogeneous with even new genotypes not reported in the control group.nnnCONCLUSIONSnAlthough the sample size is small, this first study observes an interesting heterogeneous KIR gene profile in recurrent tonsillitis that warrants larger and further research in the area for the true biological and clinical significance of this observation.

Allele-specific methylation of imprinted genes in fetal cord blood is influenced by cis-acting genetic variants and parental factors

Aim: To examine the effects of genetic variation, parental age and BMI on parental allele-specific methylation of imprinted genes in fetal cord blood samples. Methodology: We have developed SNP genotyping and deep bisulphite sequencing assays for six imprinted genes to determine parental allele-specific methylation patterns in diploid somatic tissues. Results: Multivariate linear regression analyses revealed a negative correlation of paternal age with paternal MEG3 allele methylation in fetal cord blood. Methylation of the maternal PEG3 allele showed a positive correlation with maternal age. Paternal BMI was positively correlated with paternal MEST allele methylation. In addition to parental origin, allele-specific methylation of most imprinted genes was largely dependent on the underlying SNP haplotype. Conclusion: Our study supports the idea that parental factors can have an impact, although of small effect size, on the epigenome of the next generation, providing an additional layer of complexity to phenotypic diversity.