Dopamine gene methylation patterns are associated with obesity markers and carbohydrate intake

Weighted single-step GWAS identified candidate genes associated with carcass traits in a Chinese yellow-feathered chicken population

Carcass traits in broiler chickens are complex traits that are influenced by multiple genes. To gain deeper insights into the genetic mechanisms underlying carcass traits, here we conducted a weighted single-step genome-wide association study (wssGWAS) in a population of Chinese yellow-feathered chicken. The objective was to identify genomic regions and candidate genes associated with carcass weight (CW), eviscerated weight with giblets (EWG), eviscerated weight (EW), breast muscle weight (BMW), drumstick weight (DW), abdominal fat weight (AFW), abdominal fat percentage (AFP), gizzard weight (GW), and intestine length (IL). A total of 1,338 broiler chickens with phenotypic and pedigree information were included in this study. Of these, 435 chickens were genotyped using a 600K single nucleotide polymorphism chip for association analysis. The results indicate that the most significant regions for 9 traits explained 2.38% to 5.09% of the phenotypic variation, from which the region of 194.53 to 194.63Mb on chromosome 1 with the gene RELT and FAM168A identified on it was significantly associated with CW, EWG, EW, BMW, and DW. Meanwhile, the 5 traits have a strong genetic correlation, indicating that the region and the genes can be used for further research. In addition, some candidate genes associated with skeletal muscle development, fat deposition regulation, intestinal repair, and protection were identified. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that the genes are involved in processes such as vascular development (CD34, FGF7, FGFR3, ITGB1BP1, SEMA5A, LOXL2), bone formation (FGFR3, MATN1, MEF2D, DHRS3, SKI, STC1, HOXB1, HOXB3, TIPARP), and anatomical size regulation (ADD2, AKT1, CFTR, EDN3, FLII, HCLS1, ITGB1BP1, SEMA5A, SHC1, ULK1, DSTN, GSK3B, BORCS8, GRIP2). In conclusion, the integration of phenotype, genotype, and pedigree information without creating pseudo-phenotype will facilitate the genetic improvement of carcass traits in chickens, providing valuable insights into the genetic architecture and potential candidate genes underlying carcass traits, enriching our understanding and contributing to the breeding of high-quality broiler chickens.

Type 3 IP3 receptor: Its structure, functions, and related disease implications

Cell-fate decisions depend on the precise and strict regulation of multiple signaling molecules and transcription factors, especially intracellular Ca2+ homeostasis and dynamics. Type 3 inositol 1,4,5-triphosphate receptor (IP3R3) is an a tetrameric channel that can mediate the release of Ca2+ from the endoplasmic reticulum (ER) in response to extracellular stimuli. The gating of IP3R3 is regulated not only by ligands but also by other interacting proteins. To date, extensive research conducted on the basic structure of IP3R3, as well as its regulation by ligands and interacting proteins, has provided novel perspectives on its biological functions and pathogenic mechanisms. This review aims to discuss recent advancements in the study of IP3R3 and provides a comprehensive overview of the relevant literature pertaining to its structure, biological functions, and pathogenic mechanisms.

DNA Methylation at ABCG1 and Long-term Changes in Adiposity and Fat Distribution in Response to Dietary Interventions: The POUNDS Lost Trial

OBJECTIVE

To examine whether participants with different levels of diabetes-related DNA methylation at ABCG1 might respond differently to dietary weight loss interventions with long-term changes in adiposity and body fat distribution.

RESEARCH DESIGN AND METHODS

The current study included overweight/obese participants from the POUNDS Lost trial. Blood levels of regional DNA methylation at ABCG1 were profiled by high-resolution methylC-capture sequencing at baseline among 673 participants, of whom 598 were followed up at 6 months and 543 at 2 years. Two-year changes in adiposity and computed tomography-measured body fat distribution were calculated.

RESULTS

Regional DNA methylation at ABCG1 showed significantly different associations with long-term changes in body weight and waist circumference at 6 months and 2 years in dietary interventions varying in protein intake (interaction P < 0.05 for all). Among participants assigned to an average-protein (15%) diet, lower baseline regional DNA methylation at ABCG1 was associated with greater reductions in body weight and waist circumference at 6 months and 2 years, whereas opposite associations were found among those assigned to a high-protein (25%) diet. Similar interaction patterns were also observed for body fat distribution, including visceral adipose tissue, subcutaneous adipose tissue, deep subcutaneous adipose tissue, and total adipose tissue at 6 months and 2 years (interaction P < 0.05 for all).

CONCLUSIONS

Baseline DNA methylation at ABCG1 interacted with dietary protein intake on long-term decreases in adiposity and body fat distribution. Participants with lower methylation at ABCG1 benefitted more in long-term reductions in body weight, waist circumference, and body fat distribution when consuming an average-protein diet.

Nutrition, DNA methylation and obesity across life stages and generations

Obesity is a complex multifactorial condition that often manifests in early life with a lifelong burden on metabolic health. Diet, including pre-pregnancy maternal diet, in utero nutrition and dietary patterns in early and late life, can shape obesity development. Growing evidence suggests that epigenetic modifications, specifically DNA methylation, might mediate or accompany these effects across life stages and generations. By reviewing human observational and intervention studies conducted over the past 10 years, this work provides a comprehensive overview of the evidence linking nutrition to DNA methylation and its association with obesity across different age periods, spanning from preconception to adulthood and identify future research directions in the field.

Epigenetic Mechanisms in Obesity: Broadening Our Understanding of the Disease

Now recognized as more than just the result of overeating or the consumption of poor-quality foods, obesity is understood to be a multifactorial disease, strongly correlated with a variety of environment-gene interactions. In addressing the complex public health issue of obesity, medical practitioners, along with their allied healthcare counterparts, face the challenge of reducing its prevalence by utilizing and sharing with patients the current, yet incomplete, scientific knowledge concerning the disease. While continued research is required to strengthen direct cause-effect relationships, substantial evidence links post-translational modifications such as DNA methylation and histone modifications of several candidate "obesity" genes to the predilection for obesity. Additional evidence supports the influence of maternal diet during the gestational period, individual diet, and other lifestyle and genetic factors in obesity. The purpose of this review is to synthesize the current information concerning epigenetic modifications that appear to support, or result from, the development of obesity. Such mechanisms may serve as therapeutic targets for developing novel prevention and/or treatment strategies for obesity or as epigenetic biomarkers for monitoring recovery.

Interaction of environmental factors with the polygenic risk scores of thinness-related genes in preventing obesity risk in middle-aged adults: The KoGES

BACKGROUND

Some persons are genetically resistant to obesity, but only a few studies have evaluated thinness genes for preventing obesity. We aimed to investigate the association of polygenic variants with being underweight and their interaction with the lifestyles of middle-aged and elderly persons and identify potential new genetic approaches for managing body weight.

METHODS

In total, 58,701 participants aged 40-77 years were recruited from urban hospitals in Korea. Underweight (case) was defined as body mass index (BMI) < 18.5 kg m2 (n = 991) and normal weight (control, n = 21,921) was defined as 18.5 ≤ BMI < 23 kg m2 . A genome-wide association study was run to identify thinness-related single nucleotide polymorphisms (SNPs) after adjustment for compound factors using Gplink. The generalised multifactor dimensionality reduction program was used to identify the genetic variants with SNP-SNP interactions. The polygenic risk score (PRS) was calculated by summing up the number of risk alleles in each SNP and classifying them into low-, medium- and high-PRS.

RESULTS

The best model included the ANK2_rs7656666, CAST_rs28042, SLC1A3_rs928431867, CHST12_rs2906173, ALOX5_rs1051713, RGS6_rs17180754, ST8SIA5_rs79491311 and DCC_rs35721894 alleles. The participants with high-PRS had a lower BMI (p < 0.0001) than those with low-PRS and were 3.834 (2.58-5.70) times more likely to be underweight after multivariate adjustment (p < 0.001). The selected SNPs were correlated with each other and highly expressed in brain-related genes. The genes with minor alleles of CAST_rs28042 and CHST12_rs2906173 exhibited a higher expression frequency in brain-related tissues. PRS had significant interactions with protein, sodium, indigestible carbohydrates, calcium intake and exercise (p < 0.05), influencing the underweight state. People with a high-PRS were more underweight than those with low-PRS under high protein, sodium, high calcium, low indigestible carbohydrate intake and low exercise by 3.75, 3.88, 7.05, 3.18 and 3.80 times, respectively (p < 0.0001).

CONCLUSIONS

In conclusion, adults having a high-PRS were significantly correlated with being underweight, especially in combination with a particular nutritional status. These results show the potential for thinness genes to be applied to personalised nutrition for preventing obesity through targeted gene therapy.

Hypomethylation of the dopamine transporter (DAT) gene promoter is associated with hyperphagia-related behavior in Prader-Willi syndrome: a case-control study

Prader-Willi syndrome (PWS), a neurodevelopmental disorder based on the loss of paternally derived but maternally imprinted genes on chromosome 15q11-13, is typically associated with hyperphagia-related behavior leading to massive obesity. Recently, there has been increasing evidence for dysregulated expression patterns of genes outside the PWS locus that influence the behavioral phenotype and for alterations in the dopaminergic system associated with weight regulation in PWS. In this study, we investigated the epigenetic regulation of the promoter regions of the dopamine transporter (DAT) and dopamine receptor D2 (DRD2) genes and their association with hyperphagia-related behavior in PWS. Methylation of the DAT and DRD2 promoter regions was examined by DNA bisulfite sequencing in 32 individuals with PWS and compared with a control group matched for sex, age, and body mass index (BMI). Hyperphagia-related behavior was assessed using the Hyperphagia Questionnaire for Clinical Trials (HQ-CT). Analysis by linear mixed models revealed a significant effect of factor group on mean DAT promoter methylation rate with decreased mean methylation in PWS (7.3 ± 0.4%) compared to controls (18.8 ± 0.6%), p < 0.001. In the PWS group, we further identified effects of HQ-CT score and BMI on DAT promoter methylation. Although also statistically significantly different (8.4 ± 0.2 in PWS, 10.5 ± 0.3 in controls, p < 0.001), DRD2 promoter methylation visually appeared to be evenly distributed between groups, raising concerns regarding a biological effect. Here, we provide evidence for altered epigenetic regulation of the DAT gene in PWS, which is associated with PWS-typical hyperphagia-related behaviors.

Role of DNA methylation in diabetes and obesity

Due to the fact that the upward trend of several metabolic disorders such as diabetes and obesity, in individuals especially monozygotic twins, who are under the same effects from the environment, are not similar, the role of epigenetic elements like DNA methylation needs taking into account. In this chapter, emerging scientific evidence supporting the strong relationship between changes in DNA methylation and those diseases' development was summarized. Changing in the expression level of diabetes/obesity-related genes through being silenced by methylation can be the underlying mechanism of this phenomenon. Genes with abnormal methylation status are potential biomarkers for early prediction and diagnosis. Moreover, methylation-based molecular targets should be investigated as a new treatment for both T2D and obesity.

Possible metabolic interplay between quality of life and fecal microbiota in a presenior population-Preliminary results

OBJECTIVES

The number of people aged ≥60 y is increasing worldwide, so establishing a relationship between lifestyle and health-associated factors, such as gut microbiota in an older population, is important. This study aimed to characterize the gut microbiota of a presenior population, and analyze the association between some bacteria and quality of life with the Short Form (SF) 36 questionnaire.

METHODS

Participants were adult men and women ages 50 to 80 y (n = 74). In addition to the SF-36 questionnaire, fecal samples were collected in cryotubes, and 16S RNA gene sequencing was performed to characterize microbial features. Participants were classified into two groups according to SF-36 punctuation. Linear and logistic regression models were performed to assess the possible association between any bacterial bowl and SF-36 score. Receiver operating characteristics curves were fitted to define the relative diagnostic strength of different bacterial taxa for the correct determination of quality of life.

RESULTS

A positive relationship was established between SF-36 score and Actinobacteria (P = 0.0310; R = 0.2510) compared with Peptostreptococcaceae (P = 0.0259; R = -0.2589), which increased with decreasing quality of life. Logistic regressions models and receiver operating characteristics curves showed that the relative abundance of Actinobacteria and Peptostreptococcaceae may be useful to predict quality of life in a presenior population (area under the curve: 0.71).

CONCLUSIONS

Quality of life may be associated with the relative abundance of certain bacteria, especially Actinobacteria and Peptostreptococcaceae, which may have a specific effect on certain markers and health care, which is important to improve quality of life in older populations.

Immunoinflammatory processes: Overlapping mechanisms between obesity and eating disorders?

Obesity and eating disorders are conditions that involve eating behaviors and are sometimes comorbid. Current evidence supports alterations in immunoinflammatory processes in both obesity and eating disorders. A plausible hypothesis is that immunoinflammatory processes may be involved in the pathophysiology of obesity and eating disorders. The aim of this review is to highlight the link between obesity and eating disorders, with a particular focus on immunoinflammatory processes. First, the relation between obesity and eating disorders will be presented, followed by a brief review of the literature on their association with immunoinflammatory processes. Second, developmental factors will be discussed to clarify the link between obesity, eating disorders, and immunoinflammatory processes. Genetic and epigenetic risk factors as well as the potential roles of stress pathways and early life development will be presented. Finally, implications of these findings for future research are discussed. This review highlighted biological and developmental aspects that overlap between obesity and EDs, emphasizing the need for biopsychosocial research approaches to advance current knowledge and practice in these fields.

ADHD co-morbidities: A review of implication of gene × environment effects with dopamine-related genes

ADHD is a major burden in adulthood, where co-morbid conditions such as depression, substance use disorder and obesity often dominate the clinical picture. ADHD has substantial shared heritability with other mental disorders, contributing to comorbidity. However, environmental risk factors exist but their interaction with genetic makeup, especially in relation to comorbid disorders, remains elusive. This review for the first time summarizes present knowledge on gene x environment (GxE) interactions regarding the dopamine system. Hitherto, mainly candidate (GxE) studies were performed, focusing on the genes DRD4, DAT1 and MAOA. Some evidence suggest that the variable number tandem repeats in DRD4 and MAOA may mediate GxE interactions in ADHD generally, and comorbid conditions specifically. Nevertheless, even for these genes, common variants are bound to suggest risk only in the context of gender and specific environments. For other polymorphisms, evidence is contradictory and less convincing. Particularly lacking are longitudinal studies testing the interaction of well-defined environmental with polygenic risk scores reflecting the dopamine system in its entirety.

An Overview of Epigenetics in Obesity: The Role of Lifestyle and Therapeutic Interventions

Obesity has become a global epidemic that has a negative impact on population health and the economy of nations. Genetic predispositions have been demonstrated to have a substantial role in the unbalanced energy metabolism seen in obesity. However, these genetic variations cannot entirely explain the massive growth in obesity over the last few decades. Accumulating evidence suggests that modern lifestyle characteristics such as the intake of energy-dense foods, adopting sedentary behavior, or exposure to environmental factors such as industrial endocrine disruptors all contribute to the rising obesity epidemic. Recent advances in the study of DNA and its alterations have considerably increased our understanding of the function of epigenetics in regulating energy metabolism and expenditure in obesity and metabolic diseases. These epigenetic modifications influence how DNA is transcribed without altering its sequence. They are dynamic, reflecting the interplay between the body and its surroundings. Notably, these epigenetic changes are reversible, making them appealing targets for therapeutic and corrective interventions. In this review, I discuss how these epigenetic modifications contribute to the disordered energy metabolism in obesity and to what degree lifestyle and weight reduction strategies and pharmacological drugs can restore energy balance by restoring normal epigenetic profiles.

Role of macronutrient intake in the epigenetics of obesity

Obesity is caused by a combination of hereditary and environmental factors. Despite extensive study, contemporary through diet, exercise, education, surgery, and pharmacological treatments, no effective long-term solution has been found to this epidemic. Over the last decade, there has been a tremendous advancement in understanding the science of epigenetics, as well as a rise in public interest in learning more about the influence of diet and lifestyle choices on the health of an individual. Without affecting the underlying DNA sequence, epigenetic alterations impact gene expression. Previous animal studies have shown a link between the type of diet and expression or suppression of obesity genes, but there are very few human studies that demonstrate the relationship between dietary intake and obesity gene expression. This review highlights the effects of carbohydrates, lipids, and protein intake from the diet on obesity-related genes.

The hypertriglyceridemic-waist phenotype as a valuable and integrative mirror of metabolic syndrome traits

Rates of non-communicable diseases (NCDs), such as obesity, diabetes, cardiovascular events and cancer, continue to rise worldwide, which require objective instruments for preventive and management actions. Diverse anthropometric and biochemical markers have been used to qualitatively evaluate degrees of disease, metabolic traits and evolution of nutritional status. The aim of this study was to integrate and assess the interactions between an anthropometric measurement, such as waist circumference (WC), and biochemical data, such as the triglyceride glucose index (TyG), in order to individually characterize metabolic syndrome (MetS) features considering the hypertriglyceridemic waist phenotype as a marker. An ancillary cross-sectional study was conducted using anthropometric measurements, such as weight, height, waist and hip circumferences, as well as fasting biochemical data of 314 participants. Different indices based on WC (WC, WC*TG and WC*TyG) were estimated to compute MetS components and accompanying comorbidities. ROC curves were fitted to define the strength of the analyses and the validity of the relationships. Associations were confirmed between anthropometric, biochemical and combined indices with some chronic disease manifestations, including hyperglycemia, hypertension and dyslipidemia. Both WC*TG and WC*TyG indices showed similar performance in diagnosing MetS (area under the ROC curve = 0.81). Interestingly, when participants were categorized according to a reference value of the WC*TyG index (842.7 cm*mg/dl), our results evidenced that subjects classified over this limit presented statistically higher prevalence of MetS and accompanying individual components with clinical relevance for interventions. These results revealed that WC*TyG mirrors the hypertriglyceridemic phenotype, which suggests may serve as a good indicator to define the metabolic syndrome phenotype and a suitable, sensitive, and simple proxy to complement others. A reference point was proposed with a good clinical performance and maximized sensitivity and specificity values.

Brain on food: The neuroepigenetics of nutrition

Humans have known for millennia that nutrition has a profound influence on health and disease, but it is only recently that we have begun mapping the mechanisms via which the dietary environment impacts brain physiology and behavior. Here we review recent evidence on the effects of energy-dense and methionine diets on neural epigenetic marks, gene expression, and behavior in invertebrate and vertebrate model organisms. We also discuss limitations, open questions, and future directions in the emerging field of the neuroepigenetics of nutrition.

Methylmercury Induces Metabolic Alterations in Caenorhabditis elegans: Role for C/EBP Transcription Factor

Methylmercury (MeHg) is a well-known neurotoxicant; however, its role in metabolic diseases has been gaining wider attention. We have previously shown that MeHg causes metabolic alterations in Caenorhabditis elegans, leading to decreased nicotinamide adenine dinucleotide cofactor, mitochondrial dysfunction, and oxidative stress. We were, therefore, interested in whether MeHg also affects nutrient metabolism, particularly lipid homeostasis, which may contribute to the development of metabolic conditions such as obesity or metabolic syndrome (MS). RNA from wild-type worms exposed to MeHg was collected immediately after treatment and used for gene expression analysis by DNA microarray. MeHg differentially regulated 215 genes, 17 genes involved in lipid homeostasis, and 12 genes involved in carbohydrate homeostasis. Of particular interest was cebp-1, the worm ortholog to human C/EBP, a pro-adipogenic transcription factor implicated in MS. MeHg increased the expression of cebp-1 as well as pro-adipogenic transcription factors sbp-1 and nhr-49, triglyceride synthesis enzyme acl-6, and lipid transport proteins vit-2 and vit-6. Concurrent with the altered gene expression, MeHg increased triglyceride levels, lipid storage, and feeding behaviors. Worms expressing mutant cebp-1 were protected from MeHg-induced alterations in lipid content, feeding behaviors, and gene expression, highlighting the importance of this transcription factor in the worm's response to MeHg. Taken together, our data demonstrate that MeHg induces biochemical, metabolic, and behavioral changes in C. elegans that can lead to metabolic dysfunction.

Integrative Genomic-Epigenomic Analysis of Clozapine-Treated Patients with Refractory Psychosis

Clozapine (CLZ) is the only antipsychotic drug that has been proven to be effective in patients with refractory psychosis, but it has also been proposed as an effective mood stabilizer; however, the complex mechanisms of action of CLZ are not yet fully known. To find predictors of CLZ-associated phenotypes (i.e., the metabolic ratio, dosage, and response), we explore the genomic and epigenomic characteristics of 44 patients with refractory psychosis who receive CLZ treatment based on the integration of polygenic risk score (PRS) analyses in simultaneous methylome profiles. Surprisingly, the PRS for bipolar disorder (BD-PRS) was associated with the CLZ metabolic ratio (pseudo-R2 = 0.2080, adjusted p-value = 0.0189). To better explain our findings in a biological context, we assess the protein-protein interactions between gene products with high impact variants in the top enriched pathways and those exhibiting differentially methylated sites. The GABAergic synapse pathway was found to be enriched in BD-PRS and was associated with the CLZ metabolic ratio. Such interplay supports the use of CLZ as a mood stabilizer and not just as an antipsychotic. Future studies with larger sample sizes should be pursued to confirm the findings of this study.

Food Addiction and Psychosocial Adversity: Biological Embedding, Contextual Factors, and Public Health Implications

The role of stress, trauma, and adversity particularly early in life has been identified as a contributing factor in both drug and food addictions. While links between traumatic stress and substance use disorders are well documented, the pathways to food addiction and obesity are less established. This review focuses on psychosocial and neurobiological factors that may increase risk for addiction-like behaviors and ultimately increase BMI over the lifespan. Early childhood and adolescent adversity can induce long-lasting alterations in the glucocorticoid and dopamine systems that lead to increased addiction vulnerability later in life. Allostatic load, the hypothalamic-pituitary-adrenal axis, and emerging data on epigenetics in the context of biological embedding are highlighted. A conceptual model for food addiction is proposed, which integrates data on the biological embedding of adversity as well as upstream psychological, social, and environmental factors. Dietary restraint as a feature of disordered eating is discussed as an important contextual factor related to food addiction. Discussion of various public health and policy considerations are based on the concept that improved knowledge of biopsychosocial mechanisms contributing to food addiction may decrease stigma associated with obesity and disordered eating behavior.

Biomolecules and Electrochemical Tools in Chronic Non-Communicable Disease Surveillance: A Systematic Review

Over recent three decades, the electrochemical techniques have become widely used in biological identification and detection, because it presents optimum features for efficient and sensitive molecular detection of organic compounds, being able to trace quantities with a minimum of reagents and sample manipulation. Given these special features, electrochemical techniques are regularly exploited in disease diagnosis and monitoring. Specifically, amperometric electrochemical analysis has proven to be quite suitable for the detection of physiological biomarkers in monitoring health conditions, as well as toward the control of reactive oxygen species released in the course of oxidative burst during inflammatory events. Besides, electrochemical detection techniques involve a simple and swift assessment that provides a low detection-limit for most of the molecules enclosed biological fluids and related to non-transmittable morbidities.

How Dietary Factors Affect DNA Methylation: Lesson from Epidemiological Studies

Over the past decades, DNA methylation has been proposed as a molecular mechanism underlying the positive or negative effects of diet on human health. Despite the number of studies on this topic is rapidly increasing, the relationship between dietary factors, changes in DNA methylation and health outcomes remains unclear. In this review, we summarize the literature from observational studies (cross-sectional, retrospective, or prospective) which examined the association of dietary factors (nutrients, foods, and dietary patterns) with DNA methylation markers among diseased or healthy people during the lifetime. Next, we discuss the methodological pitfalls by examining strengths and limitations of published studies. Finally, we close with a discussion on future challenges of this field of research, raising the need for large-size prospective studies evaluating the association between diet and DNA methylation in health and diseases for appropriate public health strategies.

Colorectal Cancer Early Detection in Stool Samples Tracing CpG Islands Methylation Alterations Affecting Gene Expression

Colorectal cancer (CRC) is a major cause of cancer mortality. Early diagnosis is relevant for its prevention and treatment. Since DNA methylation alterations are early events in tumourigenesis and can be detected in cell-free DNA, they represent promising biomarkers for early CRC diagnosis through non-invasive methods. In our previous work, we identified 74 early altered CpG islands (CGIs) associated with genes involved in cell cross-talking and cell signalling pathways. The aim of this work was to test whether methylation-based biomarkers could be detected in non-invasive matrices. Our results confirmed methylation alterations of GRIA4 and VIPR2 in CRC tissues, using MethyLight, as well as in stool samples, using a much more sensitive technique as droplet digital PCR. Furthermore, we analysed expression levels of selected genes whose promoter CGIs were hypermethylated in CRC, detecting downregulation at mRNA and protein levels in CRC tissue for GRIA4, VIPR2, SPOCK1 and SLC6A3. Most of these genes were already lowly expressed in colon normal tissues supporting the idea that cancer DNA methylation targets genes already barely expressed in the matched normal tissues. Our study suggests GRIA4 and VIPR2 as biomarkers for early CRC diagnosis using stool samples and confirms downregulation of genes hypermethylated in CRC.

The diet-microbiome tango: how nutrients lead the gut brain axis

Nutrients and the microbiome have a profound impact on the brain by influencing its development and function in health and disease. The mechanisms by which they shape brain function have only started to be uncovered. Here we propose that the interaction of diet with the microbiome is at the core of most mechanisms by which gut microbes affect host brain function. The microbiome acts on the host by altering the nutrients in the diet and by using them as precursors for synthetizing psychoactive metabolites. Diet is also a major modulator of gut microbiome composition making this another key mechanism by which they affect the host brain. Nutrient-microbiome-host interactions therefore provide an overarching framework to understand the function of the gut-brain axis.

Detecting multiple differentially methylated CpG sites and regions related to dimensional psychopathology in youths

Background

Psychiatric symptomatology during late childhood and early adolescence tends to persist later in life. In the present longitudinal study, we aimed to identify changes in genome-wide DNA methylation patterns that were associated with the emergence of psychopathology in youths from the Brazilian High-Risk Cohort (HRC) for psychiatric disorders. Moreover, for the differentially methylated genes, we verified whether differences in DNA methylation corresponded to differences in mRNA transcript levels by analyzing the gene expression levels in the blood and by correlating the variation of DNA methylation values with the variation of mRNA levels of the same individuals. Finally, we examined whether the variations in DNA methylation and mRNA levels were correlated with psychopathology measurements over time.

Methods

We selected 24 youths from the HRC who presented with an increase in dimensional psychopathology at a 3-year follow-up as measured by the Child Behavior Checklist (CBCL). The DNA methylation and gene expression data were compared in peripheral blood samples (n = 48) obtained from the 24 youths before and after developing psychopathology. We implemented a methodological framework to reduce the effect of chronological age on DNA methylation using an independent population of 140 youths and the effect of puberty using data from the literature.

Results

We identified 663 differentially methylated positions (DMPs) and 90 differentially methylated regions (DMRs) associated with the emergence of psychopathology. We observed that 15 DMPs were mapped to genes that were differentially expressed in the blood; among these, we found a correlation between the DNA methylation and mRNA levels of RB1CC1 and a correlation between the CBCL and mRNA levels of KMT2E. Of the DMRs, three genes were differentially expressed: ASCL2, which is involved in neurogenesis; HLA-E, which is mapped to the MHC loci; and RPS6KB1, the gene expression of which was correlated with an increase in the CBCL between the time points.

Conclusions

We observed that changes in DNA methylation and, consequently, in gene expression in the peripheral blood occurred concurrently with the emergence of dimensional psychopathology in youths. Therefore, epigenomic modulations might be involved in the regulation of an individual’s development of psychopathology.

Epigenome-wide DNA methylation in placentas from preterm infants: association with maternal socioeconomic status

This study evaluated the hypothesis that prenatal maternal socioeconomic status (SES) adversity is associated with DNA methylation in the placenta. SES adversity was defined by the presence of, as well as a summative count of, four factors: less than college education, single marital status, food and nutritional service assistance, and public health insurance. Epigenome-wide DNA methylation was assessed using the Illumina EPIC array in 426 placentas from a sample of infants born < 28 weeks of gestation from the Extremely Low Gestational Age Newborn cohort. Associations between SES adversity and DNA methylation were assessed with robust linear regressions adjusted for covariates and controlled the false discovery rate at < 10%. We also examined whether such associations were sex specific. Indicators of SES adversity were associated with differential methylation at 33 CpG sites. Of the 33 identified CpG sites, 19 (57.6%) displayed increased methylation, and 14 (42.4%) displayed decreased methylation in association with at least one of the SES adversity factors. Sex differences were observed in DNA methylation associated with summative SES score; in which placentas derived from female pregnancies showed more robust differential CpG methylation than placentas from male pregnancies. Maternal SES adversity was associated with differential methylation of genes with key role in gene transcription and placental function, potentially altering immunity and stress response. Further investigation is needed to evaluate the role of epigenetic differences in mediating the association between maternal socioeconomic status during pregnancy and later life health outcomes in children.

Comparative analysis of the influence of a high-fat/high-carbohydrate diet on the level of anxiety and neuromotor and cognitive functions in Wistar and DAT-KO rats

We compared anxiety, neuromotor, and cognitive functions in mutant rats with different allelic variants of dopamine transporter DAT knockout receiving balanced or excess in fat and fructose diet. The experiments were performed in DAT-/- homozygotes, DAT+/- heterozygotes, and DAT+/+ wild type rats. The genotype of DAT-KO rats was confirmed by restriction analysis of DAT gene compared to behavioral responses in the open field test (OF). Animals in the first groups of each strain were fed a balanced AIN93M diet; and those in the second groups with a high-fat/high-fructose diet. Neuromotor function was studied as grip strength, and behavioral responses were assessed in the elevated plus maze and conditioned passive avoidance response tests. The mass of the internal organs and white and brown fat, as well as selected lipid and nitrogen metabolism parameters in blood plasma were determined at the end of the experiment. DAT-/- had the highest specific grip strength, and showed an increase in initial exploratory activity in comparison with DAT+/- and DAT +/+. The exploratory activity was significantly reduced in the second test compared to the first one in DAT-/- and DAT+/- of first but not second group. Anxiety decreased with age in the second groups of DAT+/- and DAT+/+ (but not in DAT-/-) and was higher in DAT+/+ than in DAT+/- and DAT-/-. Excess fat and fructose resulted in the deterioration of short-term memory in DAT+/+. Lipidomic indices of blood plasma were less responsive to diet in DAT-/- and DAT-/+ in comparison to DAT+/+. The increased AsAT/AlAT activity ratio in DAT-/- compared with those in DAT+/+ suggests the activation of catabolism activity in the mutants. The consumption of excess fat and fructose significantly modified the effects produced by DAT gene allelic variants presumably due to the influence on the processes of dopamine metabolism.

Dopamine gene methylation patterns are associated with obesity markers and carbohydrate intake

INTRODUCTION

Dopamine (DA) is a neurotransmitter that regulates the rewarding and motivational processes underlying food intake and eating behaviors. This study hypothesized associations of DNA methylation signatures at genes modulating DA signaling with obesity features, metabolic profiles, and dietary intake.

METHODS

An adult population within the Methyl Epigenome Network Association project was included (n = 473). DNA methylation levels in white blood cells were measured by microarray (450K). Differentially methylated genes were mapped within the dopaminergic synapse pathway using the KEGG reference database (map04728). Subsequently, network enrichment analyses were run in the pathDIP portal. Associations of methylation patterns with anthropometric markers of general (BMI) and abdominal obesity (waist circumference), the blood metabolic profile, and daily dietary intakes were screened.

RESULTS

After applying a correction for multiple comparisons, 12 CpG sites were strongly associated (p < 0.0001) with BMI: cg03489495 (ITPR3), cg22851378 (PPP2R2D), cg04021127 (PPP2R2D), cg22441882 (SLC18A1), cg03045635 (DRD5), cg23341970 (ITPR2), cg13051970 (DDC), cg08943004 (SLC6A3), cg20557710 (CACNA1C), cg24085522 (GNAL), cg16846691 (ITPR2), and cg09691393 (SLC6A3). Moreover, average methylation levels of these genes differed according to the presence or absence of abdominal obesity. Pathway analyses revealed a statistically significant contribution of the aforementioned genes to dopaminergic synapse transmission (p = 4.78E-08). Furthermore, SLC18A1 and SLC6A3 gene methylation signatures correlated with total energy (p < 0.001) and carbohydrate (p < 0.001) intakes.

CONCLUSIONS

The results of this investigation reveal that methylation status on DA signaling genes may underlie epigenetic mechanisms contributing to carbohydrate and calorie consumption and fat deposition.