Commentary: Gene-environment interplay in the context of genetics, epigenetics, and gene expression

Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases

Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.

Assessing Relevance of External Cognitive Measures

The arrival of modern brain imaging technologies has provided new opportunities for examining the biological essence of human intelligence as well as the relationship between brain size and cognition. Thanks to these advances, we can now state that the relationship between brain size and intelligence has never been well understood. This view is supported by findings showing that cognition is correlated more with brain tissues than sheer brain size. The complexity of cellular and molecular organization of neural connections actually determines the computational capacity of the brain. In this review article, we determine that while genotypes are responsible for defining the theoretical limits of intelligence, what is primarily responsible for determining whether those limits are reached or exceeded is experience (environmental influence). Therefore, we contend that the gene-environment interplay defines the intelligent quotient of an individual.

Interactions Between Genetics, Lifestyle, and Environmental Factors for Healthcare

The occurrence and progression of diseases are strongly associated with a combination of genetic, lifestyle, and environmental factors. Understanding the interplay between genetic and nongenetic components provides deep insights into disease pathogenesis and promotes personalized strategies for people healthcare. Recently, the paradigm of systems medicine, which integrates biomedical data and knowledge at multidimensional levels, is considered to be an optimal way for disease management and clinical decision-making in the era of precision medicine. In this chapter, epigenetic-mediated genetics-lifestyle-environment interactions within specific diseases and different ethnic groups are systematically discussed, and data sources, computational models, and translational platforms for systems medicine research are sequentially presented. Moreover, feasible suggestions on precision healthcare and healthy longevity are kindly proposed based on the comprehensive review of current studies.

Parenting, Socioeconomic Status Risk, and Later Young Adult Health: Exploration of Opposing Indirect Effects via DNA Methylation

A sample of 398 African American youth, residing in rural counties with high poverty and unemployment, were followed from ages 11 to 19. Protective parenting was associated with better health, whereas elevated socioeconomic status (SES) risk was associated with poorer health at age 19. Genome-wide epigenetic variation assessed in young adulthood (age 19), was associated with both SES risk and protective parenting. Three categories of genes were identified whose methylation was associated with parenting, SES risk, and young adult health. Methylation was a significant mediator of the impact of parenting and SES risk on young adult health. Variation in mononuclear white blood cell types was also examined and controlled, showing that it did not account for observed effects of parenting and SES risk on health.

History of Family Psychiatry: From the Social Reform Era to the Primate Social Organ System

From early twentieth century social reform movements emerged the ingredients for both child and family psychiatry. Both psychiatries that involve children, parents, and families began in child guidance clinics. Post-World War II intellectual creativity provided the epistemological framework for treating families. Eleven founders (1950-1969) led the development of family psychiatry. Child and family psychiatrists disagreed over the issues of individual and family group dynamics. Over the past 25 years the emerging sciences of interaction, in the context of the Primate Social Organ System (PSOS), have produced the evidence for the family being the entity of treatment in psychiatry.

A developmental systems approach to executive function

According to recent claims from behavior genetics, executive function (EF) is almost entirely heritable. The implications of this claim are significant, given the importance of EF in academic, social, and psychological domains. This paper critically examines the behavior genetics approach to explaining individual differences in EF and proposes a relational developmental systems model that integrates both biological and social factors in the development of EF and the emergence of individual differences in EF. Problems inherent to behavioral genetics research are discussed, as is neuroscience research that emphasizes the plasticity of the prefrontal cortex. Empirical evidence from research on stress, social interaction, and intervention and training demonstrates that individual differences in EF are experience-dependent. Taken together, these findings challenge the claim that EF is almost entirely genetic but are consistent with an approach that considers biological differences in the context of social interaction.

Profiling of childhood adversity-associated DNA methylation changes in alcoholic patients and healthy controls

The increased vulnerability to alcohol dependence (AD) seen in individuals with childhood adversity (CA) may result in part from CA-induced epigenetic changes. To examine CA-associated DNA methylation changes in AD patients, we examined peripheral blood DNA methylation levels of 384 CpGs in promoter regions of 82 candidate genes in 279 African Americans [AAs; 88 with CA (70.5% with AD) and 191 without CA (38.2% with AD)] and 239 European Americans [EAs; 61 with CA (86.9% with AD) and 178 without CA (46.6% with AD)] using Illumina GoldenGate Methylation Array assays. The effect of CA on methylation of individual CpGs and overall methylation in promoter regions of genes was evaluated using a linear regression analysis (with consideration of sex, age, and ancestry proportion of subjects) and a principal components-based analysis, respectively. In EAs, hypermethylation of 10 CpGs in seven genes (ALDH1A1, CART, CHRNA5, HTR1B, OPRL1, PENK, and RGS19) were cross validated in AD patients and healthy controls who were exposed to CA. P values of two CpGs survived Bonferroni correction when all EA samples were analyzed together to increase statistical power [CHRNA5_cg17108064: P_adjust = 2.54×10⁻⁵; HTR1B_cg06031989: P_adjust = 8.98×10⁻⁵]. Moreover, overall methylation levels in the promoter regions of three genes (ALDH1A1, OPRL1 and RGS19) were elevated in both EA case and control subjects who were exposed to CA. However, in AAs, CA-associated DNA methylation changes in AD patients were not validated in healthy controls. Our findings suggest that CA could induce population-specific methylation alterations in the promoter regions of specific genes, thus leading to changes in gene transcription and an increased risk for AD and other disorders.

Epigenetic vestiges of early developmental adversity: childhood stress exposure and DNA methylation in adolescence

Fifteen-year-old adolescents (N = 109) in a longitudinal study of child development were recruited to examine differences in DNA methylation in relation to parent reports of adversity during the adolescents' infancy and preschool periods. Microarray technology applied to 28,000 cytosine-guanine dinucleotide sites within DNA derived from buccal epithelial cells showed differential methylation among adolescents whose parents reported high levels of stress during their children's early lives. Maternal stressors in infancy and paternal stressors in the preschool years were most strongly predictive of differential methylation, and the patterning of such epigenetic marks varied by children's gender. To the authors' knowledge, this is the first report of prospective associations between adversities in early childhood and the epigenetic conformation of adolescents' genomic DNA.

Array-based profiling of DNA methylation changes associated with alcohol dependence

BACKGROUND

Epigenetic regulation through DNA methylation may influence vulnerability to numerous disorders, including alcohol dependence (AD).

METHODS

Peripheral blood DNA methylation levels of 384 CpGs in the promoter regions of 82 candidate genes were examined in 285 African Americans (AAs; 141 AD cases and 144 controls) and 249 European Americans (EAs; 144 AD cases and 105 controls) using Illumina GoldenGate Methylation Array assays. Association of AD and DNA methylation changes was analyzed using multivariate analyses of covariance with frequency of intoxication, sex, age, and ancestry proportion as covariates. CpGs showing significant methylation alterations in AD cases were further examined in a replication sample (49 EA cases and 32 EA controls) using Sequenom's MassARRAY EpiTYPER technology.

RESULTS

In AAs, 2 CpGs in 2 genes (GABRB3 and POMC) were hypermethylated in AD cases compared with controls (p ≤ 0.001). In EAs, 6 CpGs in 6 genes (HTR3A, NCAM1, DRD4, MBD3, HTR2B, and GRIN1) were hypermethylated in AD cases compared with controls (p ≤ 0.001); CpG cg08989585 in the HTR3A promoter region showed a significantly higher methylation level in EA cases than in EA controls after Bonferroni correction (p = 0.00007). Additionally, methylation levels of 6 CpGs (including cg08989585) in the HTR3A promoter region were analyzed in the replication sample. Although the 6 HTR3A promoter CpGs did not show significant methylation differences between EA cases and EA controls (p = 0.067 to 0.877), the methylation level of CpG cg08989585 was nonsignificantly higher in EA cases (26.9%) than in EA controls (18.6%; p = 0.139).

CONCLUSIONS

The findings from this study suggest that DNA methylation profile appears to be associated with AD in a population-specific way and the predisposition to AD may result from a complex interplay of genetic variation and epigenetic modifications.

Hypermethylation of OPRM1 promoter region in European Americans with alcohol dependence

The μ-opioid receptor mediates rewarding effects of alcohol and illicit drugs. We hypothesized that altered DNA methylation in the μ-opioid receptor gene (OPRM1) might influence the vulnerability to alcohol dependence (AD). Genomic DNA was extracted from the peripheral blood of 125 European Americans with AD and 69 screened European American controls. Methylation levels of 16 CpGs in the OPRM1 promoter region were examined by bisulfite sequencing analysis. A multivariate analysis of covariance was conducted to analyze AD-associated methylation changes in the OPRM1 promoter region, using days of intoxication in the past 30 days, sex, age, ancestry proportion and childhood adversity (CA) as covariates. Three CpGs (80, 71, and 10 bp upstream of the OPRM1 translation start site) were more highly methylated in AD cases than in controls (CpG-80: P=0.033; CpG-71: P=0.004; CpG-10: P=0.008). Although these sites were not significant after correction for multiple comparisons, the overall methylation level of the 16 CpGs was significantly higher in AD cases (13.6%) than in controls (10.6%) (P=0.049). Sex and CA did not significantly influence OPRM1 promoter methylation levels. Our findings suggest that OPRM1 promoter hypermethylation may increase the risk for AD and other substance dependence disorders.

The expression levels of DNMT3a/3b and their relationship with meat quality in beef cattle

To identify the effects of the expression levels of DNMT3a and DNMT3b, coding the de novo methyltransferases DNMT3a and DNMT3b, on 16 beef carcass and quality traits, 50 beef cattle liver and ribeye muscle tissue samples were collected. Quantitative real-time RT-PCR was employed to quantify the expression level of these two genes, and a basic model included fixed effects of gender, age, and expression level of these two genes was used to analyze live weight; and slaughtering batches and aging days were added when beef carcass traits and beef quality traits were analyzed, respectively. Results showed that transcripts of DNMT3a and DNMT3b were present at significantly higher levels in liver tissue than in muscle tissue, and the expression level of DNMT3a was significantly higher than that of DNMT3b in both tissues. Regression analysis found that the expression levels of DNMT3a and DNMT3b were associated with several beef quality traits, which are important in beef breeding. Findings of the present study suggested that these two genes could significantly contribute to the improvement of beef quality genetically.

Gene X environment interactions in reading disability and attention-deficit/hyperactivity disorder

This article examines Gene x Environment (G x E) interactions in two comorbid developmental disorders--reading disability (RD) and attention-deficit/hyperactivity disorder (ADHD)--as a window on broader issues on G x E interactions in developmental psychology. The authors first briefly review types of G x E interactions, methods for detecting them, and challenges researchers confront in interpreting such interactions. They then review previous evidence for G x E interactions in RD and ADHD, the directions of which are opposite to each other: bioecological for RD and diathesis stress for ADHD. Given these results, the authors formulate and test predictions about G x E interactions that would be expected at the favorable end of each symptom dimension (e.g., above-average reading or attention). Consistent with their prediction, the authors found initial evidence for a resilience interaction for above-average reading: higher heritability in the presence of lower parental education. However, they did not find a G x E interaction at the favorable end of the ADHD symptom dimension. The authors conclude with implications for future research.

Gene x environment effects: stress and memory dysfunctions caused by stress and gonadal factor irregularities during puberty in control and TGF-alpha hypomorphic mice

The maturation of many neural functions occurs during puberty. An abnormal development of these processes, in the context of genetic vulnerability, may result in sex- and age-dependent penetrance of neuropsychiatric disorders. Reduced transforming growth factors-alpha (TGF-alpha) expression in Waved-1 (Wa-1) mice impairs the stress response and fear memory in adult males, but are absent or far less prominent in adult females and in pubertal males. Gonadectomy around the onset of puberty, when the mutant anatomical and behavioral phenotypes are undetectable, results in significant gene x environment effects. Adult control males show reduced physiological stress response as a result of gonadectomy, but not adult Wa-1 males. In females, pubertal gonadectomy elevates specific anxiety parameters only in adult control mice. There also are general sex-specific effects of pubertal gonadectomy on adult stress and fear memory. Surgical stress alone also induces sex- and genotype-dependent effects, albeit in different behavioral parameters than those affected by gonadectomy. We conclude that normal development of stress and memory processes is reliant on the levels of stress and gonadal factors during puberty, the effects of which are modulated by genetic factors and sex.

Ten good reasons to consider biological processes in prevention and intervention research

Most contemporary accounts of psychopathology acknowledge the importance of both biological and environmental influences on behavior. In developmental psychopathology, multiple etiological mechanisms for psychiatric disturbance are well recognized, including those operating at genetic, neurobiological, and environmental levels of analysis. However, neuroscientific principles are rarely considered in current approaches to prevention or intervention. In this article, we explain why a deeper understanding of the genetic and neural substrates of behavior is essential for the next generation of preventive interventions, and we outline 10 specific reasons why considering biological processes can improve treatment efficacy. Among these, we discuss (a) the role of biomarkers and endophenotypes in identifying those most in need of prevention; (b) implications for treatment of genetic and neural mechanisms of homotypic comorbidity, heterotypic comorbidity, and heterotypic continuity; (c) ways in which biological vulnerabilities moderate the effects of environmental experience; (d) situations in which Biology x Environment interactions account for more variance in key outcomes than main effects; and (e) sensitivity of neural systems, via epigenesis, programming, and neural plasticity, to environmental moderation across the life span. For each of the 10 reasons outlined we present an example from current literature and discuss critical implications for prevention.

Evidence for monozygotic twin (MZ) discordance in methylation level at two CpG sites in the promoter region of the catechol-O-methyltransferase (COMT) gene

Monozygotic (MZ) twin concordance for a range of psychiatric conditions is rarely 100%. It has been suggested that epigenetic factors, such as DNA methylation, may account for a proportion of the variation in behavioral traits observed between these genetically identical individuals. In this study we have quantitatively assessed the methylation status of two CpG sites in the promoter region of the COMT gene in 12 MZ twins-pairs discordant for birth weight, but otherwise clinically unaffected. DNA was obtained at age 5-years using buccal swabs, and modified using sodium-bisulfite treatment. Methylation profiles were assessed using Pyrosequencing, a technology enabling the precise degree of methylation to be assessed at any CpG site. We found that the degree of methylation at the two CpG sites was highly correlated, but there was considerable variation in the concordance of methylation levels between MZ twin-pairs. Some MZ twin-pairs showed a high degree of methylation concordance, whereas others differed markedly in their methylation profiles. Such epigenetic variation between genetically identical individuals may play a key role in the etiology of psychopathology, and explain the incomplete phenotypic concordance observed in MZ twins.

When parents have a history of conduct disorder: How is the caregiving environment affected?

Individuals with early-emerging conduct problems are likely to become parents who expose their children to considerable adversity. The current study tested the specificity of and alternative explanations for this trajectory. The sample included 246 members of a prospective, 30-year cohort study and their 3-year-old children. Parents who had a history of conduct disorder were specifically at elevated risk for socioeconomic disadvantage and relationship violence, but suboptimal parenting and offspring temperament problems were common to parents with any history of disorder. Recurrent disorder, comorbidity, and adversity in the family of origin did not fully account for these findings. The cumulative consequences of early-onset conduct disorder and assortative mating for antisocial behavior may explain the long-term effects of conduct disorder on young adult functioning.