Development and the epigenome: the 'synapse' of gene-environment interplay

The Impact of Early Childhood Life Adversity on Peripubertal Accelerated Epigenetic Aging and Psychopathology

OBJECTIVE

To examine longitudinal associations between early life threat and deprivation on epigenetic age acceleration at ages 9 and 15, and examine associations of age acceleration on later internalizing and externalizing symptoms.

METHOD

The study examines a large (n= 2,039) and racially diverse (Black/African American = 44%, Latino = 18%, White = 5 %) sample from a national dataset. Epigenetic age acceleration was estimated using the pediatric buccal epigenetic clock. Early life threat and deprivation were measured using composites from the Parent-Child Conflict Tactics Scale and county-level violent and property crime rate data. Internalizing and externalizing symptoms came from parent-reported Child Behavior Checklist. Path analysis models examined associations of threat and deprivation at age 3 on epigenetic age acceleration at ages 9 and 15. Experiences of threat were further broken down into threat experienced in the home and in the community.

RESULTS

Home threat experienced at 3 predicted age acceleration at 9 and 15, and community threat experienced at 3 predicted age acceleration at 15, but not 9. Deprivation was not a significant predictor of accelerated aging. Age acceleration at age 9 predicted externalizing, but not internalizing, symptoms at 15. Community threat had a direct effect on externalizing. No association emerged with internalizing.

CONCLUSION

Findings revealed that threat, not deprivation, was predictive of age acceleration, demonstrating support for this pattern longitudinally, using an epigenetic clock that is accurate in children. They provide critical nuance to the examination of threat and highlight associated risks and possible intervention points for externalizing symptoms.

Incorporating the Molecular Mimicry of Environmental Antigens into the Causality of Autoimmune Hepatitis

Molecular mimicry between foreign and self-antigens has been implicated as a cause of autoimmune hepatitis in experimental models and cross-reacting antibodies in patients. This review describes the experimental and clinical evidence for molecular mimicry as a cause of autoimmune hepatitis, indicates the limitations and uncertainties of this premise, and encourages investigations that assess diverse environmental antigens as sources of disease-relevant molecular mimics. Pertinent articles were identified in PubMed using multiple search phrases. Several pathogens have linear or conformational epitopes that mimic the self-antigens of autoimmune hepatitis. The occurrence of an acute immune-mediated hepatitis after vaccination for severe acute respiratory syndrome (SARS)-associated coronavirus 2 (SARS-CoV-2) has suggested that vaccine-induced peptides may mimic disease-relevant tissue antigens. The intestinal microbiome is an under-evaluated source of gut-derived antigens that could also engage in molecular mimicry. Chaperone molecules may enhance the pathogenicity of molecular mimics, and they warrant investigation. Molecular mimics of immune dominant epitopes within cytochrome P450 IID6, the autoantigen most closely associated with autoimmune hepatitis, should be sought in diverse environmental antigens and assessed for pathogenicity. Avoidance strategies, dietary adjustments, vaccine improvement, and targeted manipulation of the intestinal microbiota may emerge as therapeutic possibilities. In conclusion, molecular mimicry may be a missing causality of autoimmune hepatitis. Molecular mimics of key immune dominant epitopes of disease-specific antigens must be sought in diverse environmental antigens. The ubiquity of molecular mimicry compels rigorous assessments of peptide mimics for immunogenicity and pathogenicity in experimental models. Molecular mimicry may complement epigenetic modifications as causative mechanisms of autoimmune hepatitis.

Associations of peripheral blood DNA methylation and estimated monocyte proportion differences during infancy with toddler attachment style

Attachment is a motivational system promoting felt security to a caregiver resulting in a persistent internal working model of interpersonal behavior. Attachment styles are developed in early social environments and predict future health and development outcomes with potential biological signatures, such as epigenetic modifications like DNA methylation (DNAm). Thus, we hypothesized infant DNAm would associate with toddler attachment styles. An epigenome-wide association study (EWAS) of blood DNAm from 3-month-old infants was regressed onto children's attachment style from the Strange Situation Procedure at 22-months at multiple DNAm Cytosine-phosphate-Guanine (CpG) sites. The 26 identified CpGs associated with proinflammatory immune phenotypes and cognitive development. In post-hoc analyses, only maternal cognitive-growth fostering, encouraging intellectual exploration, contributed. For disorganized children, DNAm-derived cell-type proportions estimated higher monocytes -cells in immune responses hypothesized to increase with early adversity. Collectively, these findings suggested the potential biological embedding of both adverse and advantageous social environments as early as 3-months-old.

Charting the social neuroscience of human attachment (SoNeAt)

This introduction aims to set out the potential as well as some of the pitfalls of the newly emerging area of the Social Neuroscience of Human Attachment (SoNeAt). To organize and interconnect the burgeoning empirical studies in this line of research, including those in this special issue, we outline a programmatic framework including an extension of our conceptual proposals NAMA and NAMDA to guide future research. We hope that this special issue will act as a stimulus for redoubling our efforts advancing the newly emerging SoNeAt area bridging attachment theory and social neuroscience.

An integrative framework and recommendations for the study of DNA methylation in the context of race and ethnicity

Human social epigenomics research is critical to elucidate the intersection of social and genetic influences underlying racial and ethnic differences in health and development. However, this field faces major challenges in both methodology and interpretation with regard to disentangling confounded social and biological aspects of race and ethnicity. To address these challenges, we discuss how these constructs have been approached in the past and how to move forward in studying DNA methylation (DNAm), one of the best-characterized epigenetic marks in humans, in a responsible and appropriately nuanced manner. We highlight self-reported racial and ethnic identity as the primary measure in this field, and discuss its implications in DNAm research. Racial and ethnic identity reflects the biological embedding of an individual's sociocultural experience and environmental exposures in combination with the underlying genetic architecture of the human population (i.e., genetic ancestry). Our integrative framework demonstrates how to examine DNAm in the context of race and ethnicity, while considering both intrinsic factors-including genetic ancestry-and extrinsic factors-including structural and sociocultural environment and developmental niches-when focusing on early-life experience. We reviewed DNAm research in relation to health disparities given its relevance to race and ethnicity as social constructs. Here, we provide recommendations for the study of DNAm addressing racial and ethnic differences, such as explicitly acknowledging the self-reported nature of racial and ethnic identity, empirically examining the effects of genetic variants and accounting for genetic ancestry, and investigating race-related and culturally regulated environmental exposures and experiences.

Supplementary Information

The online version contains supplementary material available at 10.1007/s44155-023-00039-z.

Childhood Trauma and Epigenetics: State of the Science and Future

PURPOSE OF REVIEW

There is a great deal of interest regarding the biological embedding of childhood trauma and social exposures through epigenetic mechanisms, including DNA methylation (DNAm), but a comprehensive understanding has been hindered by issues of limited reproducibility between studies. This review presents a summary of the literature on childhood trauma and DNAm, highlights issues in the field, and proposes some potential solutions.

RECENT FINDINGS

Investigations of the associations between DNAm and childhood trauma are commonly performed using candidate gene approaches, specifically involving genes related to neurological and stress pathways. Childhood trauma is defined in a wide range of ways in several societal contexts. However, although variations in DNAm are frequently found in stress-related genes, unsupervised epigenome-wide association studies (EWAS) have shown limited reproducibility both between studies and in relating these changes to exposures. The reproducibility of childhood trauma DNAm studies, and the field of social epigenetics in general, may be improved by increasing sample sizes, standardizing variables, making use of effect size thresholds, collecting longitudinal and intervention samples, appropriately accounting for known confounding factors, and applying causal analysis wherever possible, such as "two-step epigenetic Mendelian randomization."

Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies

Biomedical research has grown increasingly cooperative through the sharing of consortia-level epigenetic data. Since consortia preprocess data prior to distribution, new processing pipelines can lead to different versions of the same dataset. Similarly, analytic frameworks evolve to incorporate cutting-edge methods and best practices. However, it remains unknown how different data and analytic versions alter the results of epigenome-wide analyses, which could influence the replicability of epigenetic associations. Thus, we assessed the impact of these changes using data from the Avon Longitudinal Study of Parents and Children (ALSPAC) cohort. We analysed DNA methylation from two data versions, processed using separate preprocessing and analytic pipelines, examining associations between seven childhood adversities or prenatal smoking exposure and DNA methylation at age 7. We performed two sets of analyses: (1) epigenome-wide association studies (EWAS); (2) Structured Life Course Modelling Approach (SLCMA), a two-stage method that models time-dependent effects. SLCMA results were also compared across two analytic versions. Data version changes impacted both EWAS and SLCMA analyses, yielding different associations at conventional p-value thresholds. However, the magnitude and direction of associations was generally consistent between data versions, regardless of p-values. Differences were especially apparent in analyses of childhood adversity, while smoking associations were more consistent using significance thresholds. SLCMA analytic versions similarly altered top associations, but time-dependent effects remained concordant. Alterations to data and analytic versions influenced the results of epigenome-wide analyses. Our findings highlight that magnitude and direction are better measures for replication and stability than p-value thresholds.

Missing Causality and Heritability of Autoimmune Hepatitis

BACKGROUND

Autoimmune hepatitis has an unknown cause and genetic associations that are not disease-specific or always present. Clarification of its missing causality and heritability could improve prevention and management strategies.

AIMS

Describe the key epigenetic and genetic mechanisms that could account for missing causality and heritability in autoimmune hepatitis; indicate the prospects of these mechanisms as pivotal factors; and encourage investigations of their pathogenic role and therapeutic potential.

METHODS

English abstracts were identified in PubMed using multiple key search phases. Several hundred abstracts and 210 full-length articles were reviewed.

RESULTS

Environmental induction of epigenetic changes is the prime candidate for explaining the missing causality of autoimmune hepatitis. Environmental factors (diet, toxic exposures) can alter chromatin structure and the production of micro-ribonucleic acids that affect gene expression. Epistatic interaction between unsuspected genes is the prime candidate for explaining the missing heritability. The non-additive, interactive effects of multiple genes could enhance their impact on the propensity and phenotype of autoimmune hepatitis. Transgenerational inheritance of acquired epigenetic marks constitutes another mechanism of transmitting parental adaptations that could affect susceptibility. Management strategies could range from lifestyle adjustments and nutritional supplements to precision editing of the epigenetic landscape.

CONCLUSIONS

Autoimmune hepatitis has a missing causality that might be explained by epigenetic changes induced by environmental factors and a missing heritability that might reflect epistatic gene interactions or transgenerational transmission of acquired epigenetic marks. These unassessed or under-evaluated areas warrant investigation.

The immune factors driving DNA methylation variation in human blood

Epigenetic changes are required for normal development, yet the nature and respective contribution of factors that drive epigenetic variation in humans remain to be fully characterized. Here, we assessed how the blood DNA methylome of 884 adults is affected by DNA sequence variation, age, sex and 139 factors relating to life habits and immunity. Furthermore, we investigated whether these effects are mediated or not by changes in cellular composition, measured by deep immunophenotyping. We show that DNA methylation differs substantially between naïve and memory T cells, supporting the need for adjustment on these cell-types. By doing so, we find that latent cytomegalovirus infection drives DNA methylation variation and provide further support that the increased dispersion of DNA methylation with aging is due to epigenetic drift. Finally, our results indicate that cellular composition and DNA sequence variation are the strongest predictors of DNA methylation, highlighting critical factors for medical epigenomics studies.

Social Epigenomics: Conceptualizations and Considerations for Oral Health

Advances in high-throughput technologies and the generation of multiomics, such as genomic, epigenomic, transcriptomic, and metabolomic data, are paving the way for the biological risk stratification and prediction of oral diseases. When integrated with electronic health records, survey, census, and/or epidemiologic data, multiomics are anticipated to facilitate data-driven precision oral health, or the delivery of the right oral health intervention to the right individuals/populations at the right time. Meanwhile, multiomics may be modified by a multitude of social exposures, cumulatively along the life course and at various time points from conception onward, also referred to as the socio-exposome. For example, adverse exposures, such as precarious social and living conditions and related psychosocial stress among others, have been linked to specific genes being switched "on and off" through epigenetic mechanisms. These in turn are associated with various health conditions in different age groups and populations. This article argues that considering the impact of the socio-exposome in the biological profiling for precision oral health applications is necessary to ensure that definitions of biological risk do not override social ones. To facilitate the uptake of the socio-exposome in multiomics oral health studies and subsequent interventions, 3 pertinent facets are discussed. First, a summary of the epigenetic landscape of oral health is presented. Next, findings from the nondental literature are drawn on to elaborate the pathways and mechanisms that link the socio-exposome with gene expression-or the biological embedding of social experiences through epigenetics. Then, methodological considerations for implementing social epigenomics into oral health research are highlighted, with emphasis on the implications for study design and interpretation. The article concludes by shedding light on some of the current and prospective opportunities for social epigenomics research applied to the study of life course oral epidemiology.

Epigenetic Aspects and Prospects in Autoimmune Hepatitis

The observed risk of autoimmune hepatitis exceeds its genetic risk, and epigenetic factors that alter gene expression without changing nucleotide sequence may help explain the disparity. Key objectives of this review are to describe the epigenetic modifications that affect gene expression, discuss how they can affect autoimmune hepatitis, and indicate prospects for improved management. Multiple hypo-methylated genes have been described in the CD4⁺ and CD19⁺ T lymphocytes of patients with autoimmune hepatitis, and the circulating micro-ribonucleic acids, miR-21 and miR-122, have correlated with laboratory and histological features of liver inflammation. Both epigenetic agents have also correlated inversely with the stage of liver fibrosis. The reduced hepatic concentration of miR-122 in cirrhosis suggests that its deficiency may de-repress the pro-fibrotic prolyl-4-hydroxylase subunit alpha-1 gene. Conversely, miR-155 is over-expressed in the liver tissue of patients with autoimmune hepatitis, and it may signify active immune-mediated liver injury. Different epigenetic findings have been described in diverse autoimmune and non-autoimmune liver diseases, and these changes may have disease-specificity. They may also be responses to environmental cues or heritable adaptations that distinguish the diseases. Advances in epigenetic editing and methods for blocking micro-ribonucleic acids have improved opportunities to prove causality and develop site-specific, therapeutic interventions. In conclusion, the role of epigenetics in affecting the risk, clinical phenotype, and outcome of autoimmune hepatitis is under-evaluated. Full definition of the epigenome of autoimmune hepatitis promises to enhance understanding of pathogenic mechanisms and satisfy the unmet clinical need to improve therapy for refractory disease.

The continuing evolution of birth cohort studies: achievements and challenges

Well-designed birth cohorts are able to estimate prevalence/distribution of various health events/outcomes, and to link early-life origins with adult health and function. The past two decades have seen a surge in the establishment of new birth cohorts and their accompanying research. We discussed distinct designs of current birth cohort studies, reviewed their achievements, and highlighted insights obtained from birth cohort studies, as well as challenges we are facing. Birth cohort studies are providing increasing opportunities to identify determining factors for short- and long-term health, yielding substantial evidence to uncover biological mechanisms of diseases and phenotypes, and providing further insights for public health. Dynamic monitoring, accurate measurements, long-term follow-ups and collaborative efforts are warranted in new birth cohorts to elucidate the nature of life course relationships in contemporary generation.

Infant DNA methylation: an early indicator of intergenerational trauma?

Exposure to adverse childhood experiences (ACEs) increases risk for mental and physical health problems. Intergenerationally, mothers' ACEs predict children's health problems including neurodevelopmental and behavioural problems and poorer physical health. Theories of intergenerational trauma suggest that ACEs experienced in one generation negatively affect the health and well-being of future generations, with DNA methylation (DNAm) being one of several potential biological explanations. To begin exploring this hypothesis, we tested whether infant DNA methylation associated with intergenerational trauma. Secondary analysis employed data from the Alberta Pregnancy Outcomes and Nutrition (APrON) study. Subsample data were collected from mothers during pregnancy and postpartum on measures of distress, stress and ACEs and from infants at 3 months of age on DNAm from blood (n = 92) and buccal epithelial cells (BECs; n = 124; primarily nonoverlapping individuals between tissues). Blood and BECs were examined in separate analyses. Preliminary associations identified in blood and BECs suggest that infant DNAm patterns may relate to maternal ACEs. For the majority of ACE-related DNAm sites, neither maternal perinatal distress, nor maternal cortisol awakening response (CAR; a measure of hypothalamic-pituitary-adrenocortical axis function), substantially reduced associations between maternal ACEs and infant DNAm. However, accounting for maternal perinatal distress and cortisol substantially changed the effect of ACEs in a greater proportion of blood DNAm sites than BEC DNAm sites in the top ACEs-associated correlated methylated regions (CMRs), as well as across all CMRs and all remaining CpGs (that did not fall into CMRs). Possible DNAm patterns in infants, thus, might capture a signature of maternal intergenerational trauma, and this effect appears to be more dependent on maternal perinatal distress and CAR in blood relative to BECs.

Intersection of Epigenetic and Immune Alterations: Implications for Fetal Alcohol Spectrum Disorder and Mental Health

Prenatal alcohol exposure can impact virtually all body systems, resulting in a host of structural, neurocognitive, and behavioral abnormalities. Among the adverse impacts associated with prenatal alcohol exposure are alterations in immune function, including an increased incidence of infections and alterations in immune/neuroimmune parameters that last throughout the life-course. Epigenetic patterns are also highly sensitive to prenatal alcohol exposure, with widespread alcohol-related alterations to epigenetic profiles, including changes in DNA methylation, histone modifications, and miRNA expression. Importantly, epigenetic programs are crucial for immune system development, impacting key processes such as immune cell fate, differentiation, and activation. In addition to their role in development, epigenetic mechanisms are emerging as attractive candidates for the biological embedding of environmental factors on immune function and as mediators between early-life exposures and long-term health. Here, following an overview of the impact of prenatal alcohol exposure on immune function and epigenetic patterns, we discuss the potential role for epigenetic mechanisms in reprogramming of immune function and the consequences for health and development. We highlight a range of both clinical and animal studies to provide insights into the array of immune genes impacted by alcohol-related epigenetic reprogramming. Finally, we discuss potential consequences of alcohol-related reprogramming of immune/neuroimmune functions and their effects on the increased susceptibility to mental health disorders. Overall, the collective findings from animal models and clinical studies highlight a compelling relationship between the immune system and epigenetic pathways. These findings have important implications for our understanding of the biological mechanisms underlying the long-term and multisystem effects of prenatal alcohol exposure, laying the groundwork for possible novel interventions and therapeutic strategies to treat individuals prenatally exposed to alcohol.

Prenatal Adversity Alters the Epigenetic Profile of the Prefrontal Cortex: Sexually Dimorphic Effects of Prenatal Alcohol Exposure and Food-Related Stress

Prenatal adversity or stress can have long-term consequences on developmental trajectories and health outcomes. Although the biological mechanisms underlying these effects are poorly understood, epigenetic modifications, such as DNA methylation, have the potential to link early-life environments to alterations in physiological systems, with long-term functional implications. We investigated the consequences of two prenatal insults, prenatal alcohol exposure (PAE) and food-related stress, on DNA methylation profiles of the rat brain during early development. As these insults can have sex-specific effects on biological outcomes, we analyzed epigenome-wide DNA methylation patterns in prefrontal cortex, a key brain region involved in cognition, executive function, and behavior, of both males and females. We found sex-dependent and sex-concordant influences of these insults on epigenetic patterns. These alterations occurred in genes and pathways related to brain development and immune function, suggesting that PAE and food-related stress may reprogram neurobiological/physiological systems partly through central epigenetic changes, and may do so in a sex-dependent manner. Such epigenetic changes may reflect the sex-specific effects of prenatal insults on long-term functional and health outcomes and have important implications for understanding possible mechanisms underlying fetal alcohol spectrum disorder and other neurodevelopmental disorders.

Genes, Environments, and Time: The Biology of Adversity and Resilience

Exposures to adverse environments, both psychosocial and physicochemical, are prevalent and consequential across a broad range of childhood populations. Such adversity, especially early in life, conveys measurable risk to learning and behavior and to the foundations of both mental and physical health. Using an interactive gene-environment-time (GET) framework, we survey the independent and interactive roles of genetic variation, environmental context, and developmental timing in light of advances in the biology of adversity and resilience, as well as new discoveries in biomedical research. Drawing on this rich evidence base, we identify 4 core concepts that provide a powerful catalyst for fresh thinking about primary health care for young children: (1) all biological systems are inextricably integrated, continuously "reading" and adapting to the environment and "talking back" to the brain and each other through highly regulated channels of cross-system communication; (2) adverse environmental exposures induce alterations in developmental trajectories that can lead to persistent disruptions of organ function and structure; (3) children vary in their sensitivity to context, and this variation is influenced by interactions among genetic factors, family and community environments, and developmental timing; and (4) critical or sensitive periods provide unmatched windows of opportunity for both positive and negative influences on multiple biological systems. These rapidly moving frontiers of investigation provide a powerful framework for new, science-informed thinking about health promotion and disease prevention in the early childhood period.

Early Biomarkers and Intervention Programs for the Infant Exposed to Prenatal Stress

Functional development of affective and reward circuits, cognition and response inhibition later in life exhibits vulnerability periods during gestation and early childhood. Extensive evidence supports the model that exposure to stressors in the gestational period and early postnatal life increases an individual's susceptibility to future impairments of functional development. Recent versions of this model integrate epigenetic mechanisms of the developmental response. Their understanding will guide the future treatment of the associated neuropsychiatric disorders. A combination of non-invasively obtainable physiological signals and epigenetic biomarkers related to the principal systems of the stress response, the Hypothalamic-Pituitary axis (HPA) and the Autonomic Nervous System (ANS), are emerging as the key predictors of neurodevelopmental outcomes. Such electrophysiological and epigenetic biomarkers can prove to timely identify children benefiting most from early intervention programs. Such programs should ameliorate future disorders in otherwise healthy children. The recently developed Early Family-Centered Intervention Programs aim to influence the care and stimuli provided daily by the family and improving parent/child attachment, a key element for healthy socio-emotional adult life. Although frequently underestimated, such biomarker-guided early intervention strategy represents a crucial first step in the prevention of future neuropsychiatric problems and in reducing their personal and societal impact.

Maternal Stress During Pregnancy Predicts Infant Infectious and Noninfectious Illness

OBJECTIVES

To examine the association between prenatal stress and infant physical health in the first year of life within an understudied, racially and ethnically diverse, highly stressed community sample. We expected that greater stress exposure would predict higher rates of infant illness.

STUDY DESIGN

Low-income, racially/ethnically diverse, overweight women with low medical risk pregnancies were recruited (2011-2014) during pregnancy. Pregnancy Stressful Life Events were assessed retrospectively (mean, 11.88 months postpartum). Perceived stress was assessed twice during pregnancy (at a mean of 17.4 weeks and again at a mean of 25.6 weeks) and at 6 months postpartum. Women with live births (n = 202) were invited; 162 consented to the offspring study. Medical records from pediatric clinics and emergency departments for 148 infants were abstracted for counts of total infectious illnesses, total noninfectious illness, and diversity of illnesses over the first year of life.

RESULTS

The final analytic sample included 109 women (mean age, 28.08 years) and their infants. In covariate-adjusted negative binomial models, maternal perceptions of stress across pregnancy were positively associated with infant illness. Each 1-point increase in average stress was associated with a 38% increase in incidence of infant infections (Incidence rate ratio, 1.38; 95% CI, 1.01-1.88; P < .05), a 73% increase in noninfectious illness (IRR, 1.73; 95% CI, 1.34-2.23; P < .05), and a 53% increase in illness diversity (IRR, 1.53; 95% CI, 1.25, 1.88; P < .01); effect sizes were larger for perceived stress later in pregnancy. Stressful life events count and postnatal stress were not uniquely associated with illness.

CONCLUSIONS

In line with recommendations from the American Academy of Pediatrics to screen for maternal perinatal depression, screening and support for stress reduction during pregnancy may benefit both maternal and child health.

The impact of COVID-19 on the learning and achievement of vulnerable Canadian children and youth

Many children and youth in Canada are identified as vulnerable due to educational, environmental, and social factors. They are more likely to be negatively affected by events that cause significant upheaval in daily life. The changes imposed by COVID-19, such as physical distancing, school closures, and reductions in community-based services all have the potential to weaken the systems of support necessary for these children to learn and develop. Existing inequities in educational outcomes experienced by vulnerable children prior to the pandemic have been greatly exacerbated as cracks in our support structures are revealed. Many children and youth have experienced disengagement, chronic attendance problems, declines in academic achievement, and decreased credit attainment during the pandemic, with the impact far deeper for those already at-risk. This chapter examines what is known to date regarding the impact of COVID-19 on vulnerable children and youth and provides recommendations to guide postpandemic planning. Vulnerable children, youth, and their families require access to reliable high-speed internet, effective and inclusive learning spaces, and a range of coordinated social services. All stakeholders need to develop and fund initiatives that address these critical areas to ensure that educational opportunities for all children and youth can be realized.

Genes and environments, development and time

A now substantial body of science implicates a dynamic interplay between genetic and environmental variation in the development of individual differences in behavior and health. Such outcomes are affected by molecular, often epigenetic, processes involving gene-environment (G-E) interplay that can influence gene expression. Early environments with exposures to poverty, chronic adversities, and acutely stressful events have been linked to maladaptive development and compromised health and behavior. Genetic differences can impart either enhanced or blunted susceptibility to the effects of such pathogenic environments. However, largely missing from present discourse regarding G-E interplay is the role of time, a "third factor" guiding the emergence of complex developmental endpoints across different scales of time. Trajectories of development increasingly appear best accounted for by a complex, dynamic interchange among the highly linked elements of genes, contexts, and time at multiple scales, including neurobiological (minutes to milliseconds), genomic (hours to minutes), developmental (years and months), and evolutionary (centuries and millennia) time. This special issue of PNAS thus explores time and timing among G-E transactions: The importance of timing and timescales in plasticity and critical periods of brain development; epigenetics and the molecular underpinnings of biologically embedded experience; the encoding of experience across time and biological levels of organization; and gene-regulatory networks in behavior and development and their linkages to neuronal networks. Taken together, the collection of papers offers perspectives on how G-E interplay operates contingently within and against a backdrop of time and timescales.

Epigenetics, Development, and Psychopathology

Epigenetic mechanisms govern the transcription of the genome. Research with model systems reveals that environmental conditions can directly influence epigenetic mechanisms that are associated with interindividual differences in gene expression in brain and neural function. In this review, we provide a brief overview of epigenetic mechanisms and research with relevant rodent models. We emphasize more recent translational research programs in epigenetics as well as the challenges inherent in the integration of epigenetics into developmental and clinical psychology. Our objectives are to present an update with respect to the translational relevance of epigenetics for the study of psychopathology and to consider the state of current research with respect to its potential importance for clinical research and practice in mental health.

Epigenetic aging in children from a small-scale farming society in The Congo Basin: Associations with child growth and family conflict

Developmental environments influence individuals' long-term health trajectories, and there is increasing emphasis on understanding the biological pathways through which this occurs. Epigenetic aging evaluates DNA methylation at a suite of distinct CpG sites in the genome, and epigenetic age acceleration (EAA) is linked to heightened chronic morbidity and mortality risks in adults. Consequently, EAA provides insights on trajectories of biological aging, which early life experiences may help shape. However, few studies have measured correlates of children's epigenetic aging, especially outside of the U.S. and Europe. In particular, little is known about how children's growth and development relate to EAA in ecologies in which energetic and pathogenic stressors are commonplace. We studied EAA from dried blood spots among Bondongo children (n = 54) residing in a small-scale, fisher-farmer society in a remote region of the Republic of the Congo. Here, infectious disease burdens and their resultant energy demands are high. Children who were heavier for height or taller for age, respectively, exhibited greater EAA, including intrinsic EAA, which is considered to measure EAA internal to cells. Furthermore, we found that children in families with more conflict between parents had greater intrinsic EAA. These results suggest that in contexts in which limited energy must be allocated to competing demands, more investment in growth may coincide with greater EAA, which parallels findings in European children who do not face similar energetic constraints. Our findings also indicate that associations between adverse family environments and greater intrinsic EAA were nonetheless observable but only after adjustment for covariates relevant to the energetically and immunologically demanding nature of the local ecology.

Biological embedding of experience: A primer on epigenetics

Biological embedding occurs when life experience alters biological processes to affect later life health and well-being. Although extensive correlative data exist supporting the notion that epigenetic mechanisms such as DNA methylation underlie biological embedding, causal data are lacking. We describe specific epigenetic mechanisms and their potential roles in the biological embedding of experience. We also consider the nuanced relationships between the genome, the epigenome, and gene expression. Our ability to connect biological embedding to the epigenetic landscape in its complexity is challenging and complicated by the influence of multiple factors. These include cell type, age, the timing of experience, sex, and DNA sequence. Recent advances in molecular profiling and epigenome editing, combined with the use of comparative animal and human longitudinal studies, should enable this field to transition from correlative to causal analyses.

DNA methylation of HPA-axis genes and the onset of major depressive disorder in adolescent girls: a prospective analysis

The stress response system is disrupted in individuals with major depressive disorder (MDD) as well as in those at elevated risk for developing MDD. We examined whether DNA methylation (DNAm) levels of CpG sites within HPA-axis genes predict the onset of MDD. Seventy-seven girls, approximately half (n = 37) of whom were at familial risk for MDD, were followed longitudinally. Saliva samples were taken in adolescence (M age = 13.06 years [SD = 1.52]) when participants had no current or past MDD diagnosis. Diagnostic interviews were administered approximately every 18 months until the first onset of MDD or early adulthood (M age of last follow-up = 19.23 years [SD = 2.69]). We quantified DNAm in saliva samples using the Illumina EPIC chip and examined CpG sites within six key HPA-axis genes (NR3C1, NR3C2, CRH, CRHR1, CRHR2, FKBP5) alongside 59 genotypes for tagging SNPs capturing cis genetic variability. DNAm levels within CpG sites in NR3C1, CRH, CRHR1, and CRHR2 were associated with risk for MDD across adolescence and young adulthood. To rule out the possibility that findings were merely due to the contribution of genetic variability, we re-analyzed the data controlling for cis genetic variation within these candidate genes. Importantly, methylation levels in these CpG sites continued to significantly predict the onset of MDD, suggesting that variation in the epigenome, independent of proximal genetic variants, prospectively predicts the onset of MDD. These findings suggest that variation in the HPA axis at the level of the methylome may predict the development of MDD.

Designing resilience research: Using multiple methods to investigate risk exposure, promotive and protective processes, and contextually relevant outcomes for children and youth

BACKGROUND

Inconsistent, poorly designed research on resilience in the human sciences has contributed to epistemological and ontological ambiguity which has fuelled claims that resilience as a concept is poorly theorized.

OBJECTIVE

Building on research with abused and neglected children around the world, the objective of this paper is to show that studies of resilience must account for: (a) risk exposure (of relevance in different contexts); (b) promotive and protective processes (internal and external resources associated with resilience across systems); and (c) desired outcomes (as privileged by stakeholders in different cultures and contexts).

METHOD

By identifying common aspects of resilience research from a purposeful selection of studies (ones with weak and strong methodologies), this paper identifies three dimensions of well-designed studies of childhood resilience.

RESULTS

Attention to all three dimensions enhances both the empirical validity (in the quantitative research paradigm) and phenomenological trustworthiness (in qualitative research) of resilience research with children and families. Challenges researching resilience can also be resolved by designing studies that account for all three dimensions. These challenges include the lack of systemic thinking to account for contextual factors and other external threats to child wellbeing, and the excessive generalization of findings.

CONCLUSION

This three-part model for resilience research reflects the very best practices among resilience researchers and has the potential to address the definitional and methodological ambiguity that plague studies of resilience.

The epigenome of twins as a perfect laboratory for studying behavioural traits

The debate upon the relative importance of nature vs nurture in the development of human behaviour can be traced back to ancient times. Traditional epidemiology and genetic epidemiology have confirmed the association of environmental and genetic factors with behavioural traits. Current genomic studies are identifying genetic variants associated with various behavioural traits. However, exploring the relationship of abundant environmental factors with the complex epigenome that mediates human behaviour is just at its beginning. Identical twins can serve as perfect experiments for studying the environmental impact on behavioural epigenetics advantaged by enriched power in association analysis due to controlling of their genetic make-ups. Recent development in causal inference using twin-based models adds more values in twins. This review briefly introduces the various approaches in making use of twins in studying behavioural epigenetics from experiment design to practical applications. Exploring the epigenome of twins using the powerful twin-based study designs and analytical approaches will help identifying causal epigenetic markers mediating environmental exposures and behavioural traits enabling both pharmaceutical intervention and effective prevention.

Children's DAT1 Polymorphism Moderates the Relationship Between Parents' Psychological Profiles, Children's DAT Methylation, and Their Emotional/Behavioral Functioning in a Normative Sample

Parental psychopathological risk is considered as one of the most crucial features associated with epigenetic modifications in offspring, which in turn are thought to be related to their emotional/behavioral profiles. The dopamine active transporter (DAT) gene is suggested to play a significant role in affective/behavioral regulation. On the basis of the previous literature, we aimed at verifying whether children’s DAT1 polymorphisms moderated the relationship between parents’ psychological profiles, children’s emotional/behavioral functioning, and DAT1 methylation in a normative sample of 79 families with school-age children (Ntot = 237). Children’s biological samples were collected through buccal swabs, while Symptom Check-List-90 item Revised, Adult Self Report, and Child Behavior Check-List/6–18 was administered to assess parental and children’s psychological functioning. We found that higher maternal externalizing problems predicted the following: higher levels of children’s DAT1 methylation at M1, but only among children with 10/10 genotype; higher levels of methylation at M2 among children with 10/10 genotype; while lower levels for children with a 9-repeat allele. There was also a positive relationship between fathers’ externalizing problems and children’s externalizing problems, only for children with a 9-repeat allele. Our findings support emerging evidence of the complex interplay between genetic and environmental factors in shaping children’ emotional/behavioral functioning, contributing to the knowledge of risk variables for a child’s development and psychological well-being.

Nature and mental health: An ecosystem service perspective

A growing body of empirical evidence is revealing the value of nature experience for mental health. With rapid urbanization and declines in human contact with nature globally, crucial decisions must be made about how to preserve and enhance opportunities for nature experience. Here, we first provide points of consensus across the natural, social, and health sciences on the impacts of nature experience on cognitive functioning, emotional well-being, and other dimensions of mental health. We then show how ecosystem service assessments can be expanded to include mental health, and provide a heuristic, conceptual model for doing so.

Child maltreatment, adaptive functioning, and polygenic risk: A structural equation mixture model

This study used a structural equation mixture model to examine associations between child maltreatment, polygenic risk, and indices of adaptive functioning. Children aged 6 to 13 years (N = 1,004), half maltreated, half nonmaltreated, were recruited to attend a research day camp. Multi-informant indicators of prosocial behavior, antisocial behavior, withdrawn behavior, and depression were collected and used in a latent class analysis. Four classes emerged, characterizing "well-adjusted," "externalizing," "internalizing," and "socially dominant" groups. Twelve genetic variants, previously reported in the Gene × Environment literature, were modeled as one weighted polygenic risk score. Large main effects between maltreatment and adaptive functioning were observed (Wald = 35.3, df = 3, p &lt; .0001), along with evidence of a small Gene × Environment effect (Wald = 13.5, df = 3, p = .004), adjusting for sex, age, and covariate interaction effects.

Genetic Contributions to Loneliness and Their Relevance to the Evolutionary Theory of Loneliness

Loneliness is a negative and distressing emotional state that arises from a discrepancy between one's desired and achieved levels of social connectedness. The evolutionary theory of loneliness (ETL) posits that experiencing loneliness is an inherited adaptation that signals that salutary social relations are endangered or damaged and prompts people to reconnect to significant others. The basic tenets of the ETL has led researchers to examine the genetic underpinnings of loneliness. The current review provides an updated overview of genetic studies on loneliness and discusses the importance of genetic research for the ETL. The most recent studies suggest that the many genes that contribute to a small degree to differences in loneliness partially overlap with genes that contribute to neuroticism, but not with depression. In addition, the genetic studies discussed in this review show that genes are unlikely to have a direct effect on loneliness. Instead, environmental factors determine in a dynamic fashion how genes that contribute to loneliness are expressed. Future research on epigenetic processes, such as DNA methylation, can further elucidate the dynamic interplay between genes and the environment and how this interplay contributes to loneliness.

Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation

Background

The widespread use of accessible peripheral tissues for epigenetic analyses has prompted increasing interest in the study of tissue-specific DNA methylation (DNAm) variation in human populations. To date, characterizations of inter-individual DNAm variability and DNAm concordance across tissues have been largely performed in adult tissues and therefore are limited in their relevance to DNAm profiles from pediatric samples. Given that DNAm patterns in early life undergo rapid changes and have been linked to a wide range of health outcomes and environmental exposures, direct investigations of tissue-specific DNAm variation in pediatric samples may help inform the design and interpretation of DNAm analyses from early life cohorts. In this study, we present a systematic comparison of genome-wide DNAm patterns between matched pediatric buccal epithelial cells (BECs) and peripheral blood mononuclear cells (PBMCs), two of the most widely used peripheral tissues in human epigenetic studies. Specifically, we assessed DNAm variability, cross-tissue DNAm concordance and genetic determinants of DNAm across two independent early life cohorts encompassing different ages.

Results

BECs had greater inter-individual DNAm variability compared to PBMCs and highly the variable CpGs are more likely to be positively correlated between the matched tissues compared to less variable CpGs. These sites were enriched for CpGs under genetic influence, suggesting that a substantial proportion of DNAm covariation between tissues can be attributed to genetic variation. Finally, we demonstrated the relevance of our findings to human epigenetic studies by categorizing CpGs from published DNAm association studies of pediatric BECs and peripheral blood.

Conclusions

Taken together, our results highlight a number of important considerations and practical implications in the design and interpretation of EWAS analyses performed in pediatric peripheral tissues.

Electronic supplementary material

The online version of this article (10.1186/s13072-018-0245-6) contains supplementary material, which is available to authorized users.

Social Environment and Epigenetics

Our social environment, from the microscopic to the macro-social, affects us for the entirety of our lives. One integral line of research to examine how interpersonal and societal environments can get "under the skin" is through the lens of epigenetics. Epigenetic mechanisms are adaptations made to our genome in response to our environment which include tags placed on and removed from the DNA itself to how our DNA is packaged, affecting how our genes are read, transcribed, and interact. These tags are affected by social environments and can persist over time; this may aid us in responding to experiences and exposures, both the enriched and the disadvantageous. From memory formation to immune function, the experience-dependent plasticity of epigenetic modifications to micro- and macro-social environments may contribute to the process of learning from comfort, pain, and stress to better survive in whatever circumstances life has in store.

The role of the gut microbiota in schizophrenia: Current and future perspectives

OBJECTIVES

Schizophrenia is a poorly understood chronic disease. Its pathophysiology is complex, dynamic, and linked to epigenetic mechanisms and microbiota involvement. Nowadays, correlating schizophrenia with the environment makes sense owing to its multidimensional implications: temporal and spatial variability. Microbiota involvement and epigenetic mechanisms are factors that are currently being considered to better understand another dimension of schizophrenia.

METHODS

This review summarises and discusses currently available information, focussing on the microbiota, epigenetic mechanisms, technological approaches aimed at performing exhaustive analyses of the microbiota, and psychotherapies, to establish future perspectives.

RESULTS

The connection between the microbiota, epigenetic mechanisms and technological developments allows for formulating new approaches objectively oriented towards the development of alternative psychotherapies that may help treat schizophrenia.

CONCLUSIONS

In this review, the gut microbiota and epigenetic mechanisms were considered as key regulators, revealing a potential new aetiology of schizophrenia. Likewise, continuous technological advances (e.g. culturomics), aimed at the microbiota-gut-brain axis generate new evidence on this concept.

An epigenetic pathway approach to investigating associations between prenatal exposure to maternal mood disorder and newborn neurobehavior

Following recent advances in behavioral and psychiatric epigenetics, researchers are increasingly using epigenetic methods to study prenatal exposure to maternal mood disorder and its effects on fetal and newborn neurobehavior. Despite notable progress, various methodological limitations continue to obscure our understanding of the epigenetic mechanisms underpinning prenatal exposure to maternal mood disorder on newborn neurobehavioral development. Here we detail this problem, discussing limitations of the currently dominant analytical approaches (i.e., candidate epigenetic and epigenome-wide association studies), then present a solution that retains many benefits of existing methods while minimizing their shortcomings: epigenetic pathway analysis. We argue that the application of pathway-based epigenetic approaches that target DNA methylation at transcription factor binding sites could substantially deepen our mechanistic understanding of how prenatal exposures influence newborn neurobehavior.

The biological embedding of early-life socioeconomic status and family adversity in children's genome-wide DNA methylation

Aim:

To examine variation in child DNA methylation to assess its potential as a pathway for effects of childhood social adversity on health across the life course.

Materials & methods:

In a diverse, prospective community sample of 178 kindergarten children, associations between three types of social experience and DNA methylation within buccal epithelial cells later in childhood were examined.

Results:

Family income, parental education and family psychosocial adversity each associated with increased or decreased DNA methylation (488, 354 and 102 sites, respectively) within a unique set of genomic CpG sites. Gene ontology analyses pointed to genes serving immune and developmental regulation functions.

Conclusion:

Findings provided support for DNA methylation as a biomarker linking early-life social experiences with later life health in humans.

Understanding the effects of education through the lens of biology

Early educational interventions aim to close gaps in achievement levels between children. However, early interventions do not eliminate individual differences in populations and the effects of early interventions often fade-out over time, despite changes of the mean of the population immediately following the intervention. Here, we discuss biological factors that help to better understand why early educational interventions do not eliminate achievement gaps. Children experience and respond to educational interventions differently. These stable individual differences are a consequence of biological mechanisms that support the interplay between genetic predispositions and the embedding of experience into our biology. Accordingly, we argue that it is not plausible to conceptualize the goals of educational interventions as both a shifting of the mean and a narrowing of the distribution of a particular measure of educational attainment assumed to be of utmost importance (such as a standardized test score). Instead of aiming to equalize the performance of students, the key goal of educational interventions should be to maximize potential at the individual level and consider a kaleidoscope of educational outcomes across which individuals vary. Additionally, in place of employing short-term interventions in the hope of achieving long-term gains, educational interventions need to be sustained throughout development and their long-term, rather than short-term, efficacy be evaluated. In summary, this paper highlights how biological research is valuable for driving a re-evaluation of how educational success across development can be conceptualized and thus what policy implications may be drawn.

Children's biobehavioral reactivity to challenge predicts DNA methylation in adolescence and emerging adulthood

A growing body of research has documented associations between adverse childhood environments and DNA methylation, highlighting epigenetic processes as potential mechanisms through which early external contexts influence health across the life course. The present study tested a complementary hypothesis: indicators of children's early internal, biological, and behavioral responses to stressful challenges may also be linked to stable patterns of DNA methylation later in life. Children's autonomic nervous system reactivity, temperament, and mental health symptoms were prospectively assessed from infancy through early childhood, and principal components analysis (PCA) was applied to derive composites of biological and behavioral reactivity. Buccal epithelial cells were collected from participants at 15 and 18 years of age. Findings revealed an association between early life biobehavioral inhibition/disinhibition and DNA methylation across many genes. Notably, reactive, inhibited children were found to have decreased DNA methylation of the DLX5 and IGF2 genes at both time points, as compared to non‐reactive, disinhibited children. Results of the present study are provisional but suggest that the gene's profile of DNA methylation may constitute a biomarker of normative or potentially pathological differences in reactivity. Overall, findings provide a foundation for future research to explore relations among epigenetic processes and differences in both individual‐level biobehavioral risk and qualities of the early, external childhood environment.

DNA methylation in adolescents with anxiety disorder: a longitudinal study

Anxiety disorders (AD) typically manifest in children and adolescents and might persist into adulthood. However, there are still few data concerning epigenetic mechanisms associated with onset, persistence or remission of AD over time. We investigated a cohort of adolescents and young adults at baseline (age; 13.19 ± 2.38) and after 5 years and classified them according to the AD diagnosis and their longitudinal trajectories into 4 groups: (1) Typically Developing Comparisons (TDC; control group, n = 14); (2) Incident (AD in the second evaluation only, n = 11); (3) Persistent (AD in both evaluations, n = 14) and (4) Remittent (AD in the first evaluation only, n = 8). DNA methylation was evaluated with the Infinium HumanMethylation450 BeadChip from saliva samples collected at both evaluations. Gene set enrichment analysis was applied to consider biological pathways. We found decreased DNA methylation in TDC group while the chronic cases of AD presented hypermethylation in central nervous system development pathways. Moreover, we showed that this persistent group also presented hypermethylation while the other three groups were associated with hypomethylation in nervous system development pathway. Incidence and remission groups were associated with increased and decreased methylation in neuron development pathways, respectively. Larger studies are likely to detect specific genes relevant to AD.

Lifelong Impacts of Moderate Prenatal Alcohol Exposure on Neuroimmune Function

In utero alcohol exposure is emerging as a major risk factor for lifelong aberrant neuroimmune function. Fetal alcohol spectrum disorder encompasses a range of behavioral and physiological sequelae that may occur throughout life and includes cognitive developmental disabilities as well as disease susceptibility related to aberrant immune and neuroimmune actions. Emerging data from clinical studies and findings from animal models support that very low to moderate levels of fetal alcohol exposure may reprogram the developing central nervous system leading to altered neuroimmune and neuroglial signaling during adulthood. In this review, we will focus on the consequences of low to moderate prenatal alcohol exposure (PAE) on neuroimmune interactions during early life and at different stages of adulthood. Data discussed here will include recent studies suggesting that while abnormal immune function is generally minimal under basal conditions, following pathogenic stimuli or trauma, significant alterations in the neuroimmune axis occur. Evidence from published reports will be discussed with a focus on observations that PAE may bias later-life peripheral immune responses toward a proinflammatory phenotype. The propensity for proinflammatory responses to challenges in adulthood may ultimately shape neuron–glial-immune processes suspected to underlie various neuropathological outcomes including chronic pain and cognitive impairment.

Unitary Physiology

The common relationships among a great variety of biological phenomena seem enigmatic when considered solely at the level of the phenotype. The deep connections in physiology, for example, between the effects of maternal food restriction in utero and the subsequent incidence of metabolic syndrome in offspring, the effects of microgravity on cell polarity and reproduction in yeast, stress effects on jellyfish, and their endless longevity, or the relationship between nutrient abundance and the colonial form in slime molds, are not apparent by phenotypic observation. Yet all of these phenomena are ultimately determined by the Target of Rapamycin (TOR) gene and its associated signaling complexes. In the same manner, the unfolding of evolutionary physiology can be explained by a comparable application of the common principle of cell-cell signaling extending across complex developmental and phylogenetic traits. It is asserted that a critical set of physiologic and phenotypic adaptations emanated from a few crucial, ancestral receptor gene duplications that enabled the successful terrestrial transition of vertebrates from water to land. In combination, mTor and its cognate receptors and a few crucial genetic duplications provide a mechanistic common denominator across a diverse spectrum of biological responses. The proper understanding of their purpose yields a unified concept of physiology and its evolutionary development. © 2018 American Physiological Society. Compr Physiol 8:761-771, 2018.

DNA methylation as a predictor of fetal alcohol spectrum disorder

Background

Fetal alcohol spectrum disorder (FASD) is a developmental disorder that manifests through a range of cognitive, adaptive, physiological, and neurobiological deficits resulting from prenatal alcohol exposure. Although the North American prevalence is currently estimated at 2-5%, FASD has proven difficult to identify in the absence of the overt physical features characteristic of fetal alcohol syndrome. As interventions may have the greatest impact at an early age, accurate biomarkers are needed to identify children at risk for FASD. Building on our previous work identifying distinct DNA methylation patterns in children and adolescents with FASD, we have attempted to validate these associations in a different clinical cohort and to use our DNA methylation signature to develop a possible epigenetic predictor of FASD.

Methods

Genome-wide DNA methylation patterns were analyzed using the Illumina HumanMethylation450 array in the buccal epithelial cells of a cohort of 48 individuals aged 3.5-18 (24 FASD cases, 24 controls). The DNA methylation predictor of FASD was built using a stochastic gradient boosting model on our previously published dataset FASD cases and controls (GSE80261). The predictor was tested on the current dataset and an independent dataset of 48 autism spectrum disorder cases and 48 controls (GSE50759).

Results

We validated findings from our previous study that identified a DNA methylation signature of FASD, replicating the altered DNA methylation levels of 161/648 CpGs in this independent cohort, which may represent a robust signature of FASD in the epigenome. We also generated a predictive model of FASD using machine learning in a subset of our previously published cohort of 179 samples (83 FASD cases, 96 controls), which was tested in this novel cohort of 48 samples and resulted in a moderately accurate predictor of FASD status. Upon testing the algorithm in an independent cohort of individuals with autism spectrum disorder, we did not detect any bias towards autism, sex, age, or ethnicity.

Conclusion

These findings further support the association of FASD with distinct DNA methylation patterns, while providing a possible entry point towards the development of epigenetic biomarkers of FASD.

Early-life adversity and long-term neurobehavioral outcomes: epigenome as a bridge?

Accumulating evidence suggests that adversities at critical periods in early life, both pre- and postnatal, can lead to neuroendocrine perturbations, including hypothalamic-pituitary-adrenal axis dysregulation and inflammation persisting up to adulthood. This process, commonly referred to as biological embedding, may cause abnormal cognitive and behavioral functioning, including impaired learning, memory, and depressive- and anxiety-like behaviors, as well as neuropsychiatric outcomes in later life. Currently, the regulation of gene activity by epigenetic mechanisms is suggested to be a key player in mediating the link between adverse early-life events and adult neurobehavioral outcomes. Role of particular genes, including those encoding glucocorticoid receptor, brain-derived neurotrophic factor, as well as arginine vasopressin and corticotropin-releasing factor, has been demonstrated in triggering early adversity-associated pathological conditions. This review is focused on the results from human studies highlighting the causal role of epigenetic mechanisms in mediating the link between the adversity during early development, from prenatal stages through infancy, and adult neuropsychiatric outcomes. The modulation of epigenetic pathways involved in biological embedding may provide promising direction toward novel therapeutic strategies against neurological and cognitive dysfunctions in adult life.

Dynamic stress-related epigenetic regulation of the glucocorticoid receptor gene promoter during early development: The role of child maltreatment

Epigenetics processes may play a vital role in the biological embedding of early environmental adversity and the development of psychopathology. Accumulating evidence suggests that maltreatment is linked to methylation of the glucocorticoid receptor gene, nuclear receptor subfamily 3, group C, member 1 (NR3C1), which is a key regulator of the hypothalamus-pituitary-adrenal axis. However, prior work has been exclusively cross-sectional, greatly constraining our understanding of stress-related epigenetic processes over time. In the current study, we examined the effect of maltreatment and other adversity on change in NR3C1 methylation among at-risk preschoolers to begin to characterize within-child epigenetic changes during this sensitive developmental period. Participants were 260 preschoolers (3-5 years old, 53.8% female), including 51.5% with moderate to severe maltreatment in the past 6 months. Child protection records, semistructured interviews, and parent reports were used to assess child stress exposure. Methylation of exons 1D and 1F of NR3C1 via saliva DNA were measured at two time points approximately 6 months apart. Results indicate that maltreated children evidence higher baseline levels of NR3C1 methylation, significant decreases in methylation over time, and then at follow-up, lower levels of methylation, relative to nonmaltreated preschoolers. Findings from the current study highlight the complex nature of stress-related epigenetic processes during early development.

Epigenetic correlates of neonatal contact in humans

Animal models of early postnatal mother–infant interactions have highlighted the importance of tactile contact for biobehavioral outcomes via the modification of DNA methylation (DNAm). The role of normative variation in contact in early human development has yet to be explored. In an effort to translate the animal work on tactile contact to humans, we applied a naturalistic daily diary strategy to assess the link between maternal contact with infants and epigenetic signatures in children 4–5 years later, with respect to multiple levels of child-level factors, including genetic variation and infant distress. We first investigated DNAm at four candidate genes: the glucocorticoid receptor gene, nuclear receptor subfamily 3, group C, member 1 (NR3C1), μ-opioid receptor M1 (OPRM1) and oxytocin receptor (OXTR; related to the neurobiology of social bonds), and brain-derived neurotrophic factor (BDNF; involved in postnatal plasticity). Although no candidate gene DNAm sites significantly associated with early postnatal contact, when we next examined DNAm across the genome, differentially methylated regions were identified between high and low contact groups. Using a different application of epigenomic information, we also quantified epigenetic age, and report that for infants who received low contact from caregivers, greater infant distress was associated with younger epigenetic age. These results suggested that early postnatal contact has lasting associations with child biology.

BECon: a tool for interpreting DNA methylation findings from blood in the context of brain

Tissue differences are one of the largest contributors to variability in the human DNA methylome. Despite the tissue-specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well-documented. Here, we aimed to provide a resource to the community to aid interpretation of blood-based DNA methylation results in the context of brain tissue. We used paired samples from 16 individuals from three brain regions and whole blood, run on the Illumina 450 K Human Methylation Array to quantify the concordance of DNA methylation between tissues. From these data, we have made available metrics on: the variability of cytosine-phosphate-guanine dinucleotides (CpGs) in our blood and brain samples, the concordance of CpGs between blood and brain, and estimations of how strongly a CpG is affected by cell composition in both blood and brain through the web application BECon (Blood-Brain Epigenetic Concordance; https://redgar598.shinyapps.io/BECon/). We anticipate that BECon will enable biological interpretation of blood-based human DNA methylation results, in the context of brain.

Epigenomic Susceptibility to the Social World: Plausible Paths to a "Newest Morbidity"

This article-presented on the celebratory occasion of Dr Robert Haggerty's 91st birthday-describes how a 1962 article by Dr Haggerty and his colleague Dr Roger Meyer launched a previously unexplored, pediatric research enterprise by asserting that: "There are little precise data to explain why one person becomes ill with an infecting agent and another not." Noting a prospective association between family stressors and the acquisition of β-hemolytic streptococcal infections, the article introduced a generation of young academic pediatricians-the author of the present article among them-to the possibility of causal linkages among children's adversity exposures, compromised immunological processes, and the development of immune-mediated, acute or chronic diseases of childhood. That research agenda has led, over the past 40 years, to the advent of psychoneuroimmunology as a field of study, to the recognition of childhood stress and adversity as potential etiologic agents among childhood morbidities, and to the discovery of differential susceptibility to social adversities within populations of children.