Placental NEGR1 DNA methylation is associated with BMI and neurodevelopment in preschool-age children

Association between epigenome-wide DNA methylation changes and early neurodevelopment in preschool children: Evidence from a former impoverished county in Central China

BACKGROUND

Existing epigenome-wide association studies (EWAS) investigating the association between DNA methylation (DNAm) and child neurodevelopment have been predominantly conducted within Western populations, and yielded inconsistent results, leading to a significant gap within non-Western setting, particularly in resource-limited rural areas of Central China.

OBJECTIVES

To investigate the association between altered epigenome-wide DNAm and neurodevelopment in preschool children from resource-limited rural areas of Central China.

METHODS

This case-control study involved 64 preschoolers. We assessed children's neurodevelopment using the Gesell Developmental Diagnostic Scale. The neurodevelopmental potential was expressed as a global developmental quotient (DQ) score. We conducted an EWAS with an Illumina Infinium MethylationEPIC v1.0 BeadChip array, using blood samples from 32 suspected developmental delay children (DQ scores < 85) and 32 controls (DQ scores ≥ 85). Differentially methylated probes (DMPs) and differentially methylated regions (DMRs) between the suspected developmental delay and control groups were analyzed. Multivariate linear regression models were used to evaluate the association between global DQ scores and DNAm. Functional enrichment analyses were conducted using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). The BECon tool was utilized to estimate the concordance of CpGs between blood and the human brain.

RESULTS

A total of 66 DMRs (PFDR < 0.05) were identified between the two groups, but no DMPs were found. After FDR correction, 844 methylated CpG sites exhibited significant associations with the global DQ scores in children. Genes annotated by methylated CpGs were mainly enriched in the "oxytocin signaling pathway", "mTOR signaling pathway", and "thyroid hormone signaling pathway". They were also involved in the "regulation of cell development", "cell-cell junction", and "ATPase activity". Among the top 20 CpGs, nine global DQ scores related-CpGs had blood-brain DNA methylation correlations, and six CpGs among them had an absolute Spearman correlation coefficient bigger than 0.2.

CONCLUSIONS

Preschoolers from a former impoverished county exhibited epigenome-wide DNAm changes strongly linked to early neurodevelopment. This study enhances our understanding of the epigenetic landscape associated with early neurodevelopment, and suggests the potential for developmenting epigenetic biomarkers that could facilitate the early identification of children at a higher risk of compromised neurodevelopment, as well as holding implication to inform novel interventions, especially in underprivileged regions.

Cohort profile: the Genetics of Glucose regulation in Gestation and Growth (Gen3G) - a prospective prebirth cohort of mother-child pairs in Sherbrooke, Canada, 3-year and 5-year follow-up visits

PURPOSE

Initiated in 2010, the Genetics of Glucose regulation in Gestation and Growth (Gen3G) prospective cohort investigates the pathophysiology of impaired glycaemic regulation in pregnancy and evaluates its impact on both the mothers and her offspring health trajectory. Follow-up visits 3 and 5 years after delivery aimed to investigate pregnancy-related risk factors such as maternal obesity and gestational hyperglycaemia in relation to the mother's metabolic health after pregnancy, and with offspring health outcomes such as risk of obesity and neurodevelopmental problems in early childhood. We also investigated molecular mechanisms involved in the fetal programming of these later health outcomes.

PARTICIPANTS

Of the 1024 women originally recruited in the first trimester of pregnancy, we have targeted the 854 who had complete glucose tolerance test data and the 724 newborns who provided placenta and/or cord blood samples for follow-up recruitment. Of these, 695 mother-child dyads agreed to be contacted for the prospective follow-up visits. 448 and 521 mother-child dyads completed the research visits at 3 and 5 years after delivery respectively.

FINDINGS TO DATE

At both visits, we collected the mother's and child's medical history, lifestyle (using validated questionnaires), sociodemographic status, anthropometric measurements, mother's blood samples, child's saliva samples and growth charts. At the 5-year-old visit, we additionally collected the mother's and child's urine and stool samples and the child's blood samples; we performed a 75 g oral glucose tolerance test in the mothers and assessed the body composition in children using dual-energy X-ray absorptiometry. Using the Gen3G rich longitudinal data set, we have enhanced the understanding of the pathophysiology and characterisation of the heterogeneity of gestational diabetes mellitus, and we have shown that gestational hyperglycaemia and insulin resistance are associated with offspring epigenetics (DNA methylation) variations in the placenta, cord blood and blood at 5 years of age, as well as with offspring anthropometric, metabolic and neurodevelopmental outcomes in early childhood.

FUTURE PLANS

We are currently conducting a prospective follow-up of mothers and their children 12 years after delivery to study how prenatal and early-life metabolic factors may programme childhood adiposity and obesogenic dietary behaviours. This follow-up should be completed by the end of 2026.

Unraveling the genetic links between depression and type 2 diabetes

BACKGROUND

Type 2 diabetes (T2D) is a chronic metabolic disorder that has high comorbidity with mental disorders. The genetic relationships between T2D and depression are far from being well understood.

METHODS

We performed genetic correlation, polygenic overlap, Mendelian randomization (MR) analyses, cross-trait meta-analysis, and Bayesian colocalization analysis to assess genetic relationships between T2D and depression, in the forms of major depressive disorder (MDD) and depressed affect (DAF). Then, the summary data-based MR (SMR) analysis was performed to prioritize genes contributing to MDD and to T2D from functional perspective. MDD-driven signaling pathways were constructed to understand the influence of MDD on T2D at the molecular level.

RESULTS

T2D has positive genetic correlations both with MDD (rg = 0.14) and with DAF (rg = 0.19). The polygenic overlap analysis showed that about 60 % of causal variants for T2D are shared with MDD and DAF. The MR analysis indicated that genetic liabilities to both MDD (OR: 1.24, 95 % CI: 1.11-1.38) and DAF (OR: 1.48, 95 % CI: 1.23-1.78) are associated with an increased risk for T2D, while genetic liability to T2D is not associated with the risk for MDD (OR: 1.00, 95 % CI: 0.99-1.01) or DAF (OR: 1.01, 95 % CI: 1.00-1.02). The cross-trait meta-analysis identified 271 genomic loci, of which 29 were novel. Genetic predisposition to MDD and T2D shares six overlapping loci, involving some well-characterized genes, such as TCF4 and NEGR1. Colocalization analysis revealed three shared chromosome regions between MDD and T2D, which covers mediator genes including SCYL1, DENND1A, and MAD1L1. Molecular pathway analysis suggests mechanisms that promote the development of T2D through inflammatory pathways overactive in patients with MDD. The SMR analysis and the meta-analysis highlighted seven genes with functional implications for both MDD and T2D, including TNKS2, CCDC92, FADS1, ERI1, THUMPD3, NUCKS1, and PM20D1.

CONCLUSIONS

Our study points out that depression, in the forms of MDD and DAF, may increase the risk of T2D. Analysis of underlying genetic variation and the molecular pathways, connecting depression and T2D, indicate that the pathophysiological foundations of these two conditions have a notable overlap.

Maternal Hyperglycemia in Pregnancy and Offspring Internalizing and Externalizing Behaviors

OBJECTIVE

To examine the associations between exposure to gestational diabetes mellitus (GDM) and maternal glycemic markers during pregnancy and offspring behaviors at 3 and 5 years. We hypothesized that exposure to maternal hyperglycemia would be associated with more behavioral problems in offspring.

METHODS

We included 548 mother-child pairs from the prospective pre-birth Gen3G cohort (Canada). Glycemic markers were measured during a 75 g oral glucose tolerance test (OGTT) in the second trimester of pregnancy. Based on OGTT, we classified 59 women (10.8%) as having GDM according to international diagnostic criteria. Mothers reported offspring behavior using the Strengths and Difficulties Questionnaire (SDQ) at 3 and 5 years, and the Child Behavior Checklist (CBCL) at 5 years. We used linear mixed models and multivariate regression to assess the associations between GDM or glycemic markers and children's behavior, adjusted for child sex and age, and maternal demographic factors, body mass index and family history of diabetes.

RESULTS

Exposure to GDM was associated with higher SDQ externalizing scores at 3 and 5 years [B = 1.12, 95% CI (0.14, 2.10)] in fully adjusted linear mixed models. These results were supported by the CBCL at 5 years. Higher levels of maternal glucose at 1 h and 2 h during OGTT were associated with greater SDQ externalizing scores. Fasting glucose levels were not associated with child behavior scores. We did not observe associations between glycemic markers and internalizing behaviors.

CONCLUSIONS

Exposure to higher levels of maternal glycemia during pregnancy was associated with more externalizing behaviors in children at 3 and 5 years.

Epigenome-Wide Associations of Placental DNA Methylation and Behavioral and Emotional Difficulties in Children at 3 Years of Age

The placenta is a key organ for fetal and brain development. Its epigenome can be regarded as a biochemical record of the prenatal environment and a potential mechanism of its association with the future health of the fetus. We investigated associations between placental DNA methylation levels and child behavioral and emotional difficulties, assessed at 3 years of age using the Strengths and Difficulties Questionnaire (SDQ) in 441 mother-child dyads from the EDEN cohort. Hypothesis-driven and exploratory analyses (on differentially methylated probes (EWAS) and regions (DMR)) were adjusted for confounders, technical factors, and cell composition estimates, corrected for multiple comparisons, and stratified by child sex. Hypothesis-driven analyses showed an association of cg26703534 (AHRR) with emotional symptoms, and exploratory analyses identified two probes, cg09126090 (intergenic region) and cg10305789 (PPP1R16B), as negatively associated with peer relationship problems, as well as 33 DMRs, mostly positively associated with at least one of the SDQ subscales. Among girls, most associations were seen with emotional difficulties, whereas in boys, DMRs were as much associated with emotional than behavioral difficulties. This study provides the first evidence of associations between placental DNA methylation and child behavioral and emotional difficulties. Our results suggest sex-specific associations and might provide new insights into the mechanisms of neurodevelopment.

Gestational Weight Gain Relates to DNA Methylation in Umbilical Cord, Which, In Turn, Associates with Offspring Obesity-Related Parameters

Excessive gestational weight gain (GWG) has a negative impact on offspring's health. Epigenetic modifications mediate these associations by causing changes in gene expression. We studied the association between GWG and DNA methylation in umbilical cord tissue; and determined whether the DNA methylation and the expression of corresponding annotated genes were associated with obesity-related parameters in offspring at 6 years of age. The methylated CpG sites (CpGs) associated with GWG were identified in umbilical cord tissue by genome-wide DNA methylation (n = 24). Twelve top CpGs were validated in a wider sample by pyrosequencing (n = 87), and the expression of their 5 annotated genes (SETD8, TMEM214, SLIT3, RPTOR, and HOXC8) was assessed by RT-PCR. Pyrosequencing results validated the association of SETD8, SLIT3, and RPTOR methylation with GWG and showed that higher levels of SETD8 and RPTOR methylation and lower levels of SLIT3 methylation relate to a higher risk of obesity in the offspring. The association of SETD8 and SLIT3 gene expression with offspring outcomes paralleled the association of methylation levels in opposite directions. Epigenetic changes in the umbilical cord tissue could explain, in part, the relationship between GWG and offspring obesity risk and be early biomarkers for the prevention of overweight and obesity in childhood.

DNA methylation in people with anorexia nervosa: Epigenome-wide patterns in actively ill, long-term remitted, and healthy-eater women

OBJECTIVES

Recent studies have reported altered methylation levels at disorder-relevant DNA sites in people who are ill with Anorexia Nervosa (AN) compared to findings in people with no eating disorder (ED) or in whom AN has remitted. The preceding implies state-related influences upon gene expression in people with AN. This study further examined this notion.

METHODS

We measured genome-wide DNA methylation in 145 women with active AN, 49 showing stable one-year remission of AN, and 64 with no ED.

RESULTS

Comparisons revealed 205 differentially methylated sites between active and no ED groups, and 162 differentially methylated sites between active and remitted groups (Q < 0.01). Probes tended to map onto genes relevant to psychiatric, metabolic and immune functions. Notably, several of the genes identified here as being differentially methylated in people with AN (e.g. SYNJ2, PRKAG2, STAT3, CSGALNACT1, NEGR1, NR1H3) have figured in previous studies on AN. Effects also associated illness chronicity and lower BMI with more pronounced DNA methylation alterations, and remission of AN with normalisation of DNA methylation.

CONCLUSIONS

Findings corroborate earlier results suggesting reversible DNA methylation alterations in AN, and point to particular genes at which epigenetic mechanisms may act to shape AN phenomenology.

Recent progress in epigenetics of obesity

Nowadays, obesity is one of the largest public health problems worldwide. In the last few decades, there has been a marked increase in the obesity epidemic and its related comorbidities. Worldwide, more than 2.2 billion people (33%) are affected by overweight or obesity (712 million, 10%) and its associated metabolic complications. Although a high heritability of obesity has been estimated, the genetic variants conducted from genetic association studies only partially explain the variation of body mass index. This has led to a growing interest in understanding the potential role of epigenetics as a key regulator of gene-environment interactions on the development of obesity and its associated complications. Rapid advances in epigenetic research methods and reduced costs of epigenome-wide association studies have led to a great expansion of population-based studies. The field of epigenetics and metabolic diseases such as obesity has advanced rapidly in a short period of time. The main epigenetic mechanisms include DNA methylation, histone modifications, microRNA (miRNA)-mediated regulation and so on. DNA methylation is the most investigated epigenetic mechanism. Preliminary evidence from animal and human studies supports the effect of epigenetics on obesity. Studies of epigenome-wide association studies and genome-wide histone modifications from different biological specimens such as blood samples (newborn, children, adolescent, youth, woman, man, twin, race, and meta-analysis), adipose tissues, skeletal muscle cells, placenta, and saliva have reported the differential expression status of multiple genes before and after obesity interventions and have identified multiple candidate genes and biological markers. These findings may improve the understanding of the complex etiology of obesity and its related comorbidities, and help to predict an individual's risk of obesity at a young age and open possibilities for introducing targeted prevention and treatment strategies.

Spatiotemporal expression of IgLON family members in the developing mouse nervous system

Differential expression of cell adhesion molecules in neuronal populations is one of the many mechanisms promoting the formation of functional neural circuits in the developing nervous system. The IgLON family consists of five cell surface immunoglobulin proteins that have been associated with various developmental disorders, such as autism spectrum disorder, schizophrenia, and major depressive disorder. However, there is still limited and fragmented information about their patterns of expression in certain regions of the developing nervous system and how their expression contributes to their function. Utilizing an in situ hybridization approach, we have analyzed the spatiotemporal expression of all IgLON family members in the developing mouse brain, spinal cord, eye, olfactory epithelium, and vomeronasal organ. At one prenatal (E16) and two postnatal (P0 and P15) ages, we show that each IgLON displays distinct expression patterns in the olfactory system, cerebral cortex, midbrain, cerebellum, spinal cord, and eye, indicating that they likely contribute to the wiring of specific neuronal circuitry. These analyses will inform future functional studies aimed at identifying additional roles for these proteins in nervous system development.