Epigenomic profiling reveals DNA-methylation changes associated with major psychosis

Differential epigenomic and transcriptomic responses in subcutaneous adipose tissue between low and high responders to caloric restriction

BACKGROUND

Caloric restriction is recommended for the treatment of obesity, but it is generally characterized by large interindividual variability in responses. The factors affecting the magnitude of weight loss remain poorly understood. Epigenetic factors (ie, heritable but reversible changes to genomic function that regulate gene expression independently of DNA sequence) may explain some of the interindividual variability seen in weight-loss responses.

OBJECTIVE

The objective was to determine whether epigenetics and gene expression changes may play a role in weight-loss responsiveness.

DESIGN

Overweight/obese postmenopausal women were recruited for a standard 6-mo caloric restriction intervention. Abdominal subcutaneous adipose tissue biopsy samples were collected before (n = 14) and after (n = 14) intervention, and the epigenomic and transcriptomic profiles of the high and low responders to dieting, on the basis of changes in percentage body fat, were compared by using microarray analysis.

RESULTS

Significant DNA methylation differences at 35 loci were found between the high and low responders before dieting, with 3 regions showing differential methylation after intervention. Some of these regions contained genes known to be involved in weight control and insulin secretion, whereas others were localized in known imprinted genomic regions. Differences in gene expression profiles were observed only after dieting, with 644 genes being differentially expressed between the 2 groups. These included genes likely to be involved in metabolic pathways related to angiogenesis and cerebellar long-term depression.

CONCLUSIONS

These data show that both DNA methylation and gene expression are responsive to caloric restriction and provide new insights about the molecular pathways involved in body weight loss as well as methylation regulation during adulthood.

Differential DNA methylation correlates with differential expression of angiogenic factors in human heart failure

Epigenetic mechanisms such as microRNA and histone modification are crucially responsible for dysregulated gene expression in heart failure. In contrast, the role of DNA methylation, another well-characterized epigenetic mark, is unknown. In order to examine whether human cardiomyopathy of different etiologies are connected by a unifying pattern of DNA methylation pattern, we undertook profiling with ischaemic and idiopathic end-stage cardiomyopathic left ventricular (LV) explants from patients who had undergone cardiac transplantation compared to normal control. We performed a preliminary analysis using methylated-DNA immunoprecipitation-chip (MeDIP-chip), validated differential methylation loci by bisulfite-(BS) PCR and high throughput sequencing, and identified 3 angiogenesis-related genetic loci that were differentially methylated. Using quantitative RT-PCR, we found that the expression of these genes differed significantly between CM hearts and normal control (p<0.01). Moreover, for each individual LV tissue, differential methylation showed a predicted correlation to differential expression of the corresponding gene. Thus, differential DNA methylation exists in human cardiomyopathy. In this series of heterogenous cardiomyopathic LV explants, differential DNA methylation was found in at least 3 angiogenesis-related genes. While in other systems, changes in DNA methylation at specific genomic loci usually precede changes in the expression of corresponding genes, our current findings in cardiomyopathy merit further investigation to determine whether DNA methylation changes play a causative role in the progression of heart failure.

Epigenetics of schizophrenia

Epigenetic regulators of gene expression including DNA cytosine methylation and posttranslational histone modifications could play a role for some of the molecular alterations associated with schizophrenia. For example, in prefrontal cortex of subjects with schizophrenia, abnormal DNA or histone methylation at sites of specific genes and promoters is associated with changes in RNA expression. These findings are of interest from a neurodevelopmental perspective because there is increasing evidence that epigenetic markings for a substantial portion of genes and loci are highly regulated during the first years of life. Furthermore, there is circumstantial evidence that a subset of antipsychotic drugs, including the atypical, Clozapine, interfere with chromatin remodeling mechanisms. Challenges for the field include (1) no clear consensus yet regarding disease-associated changes, (2) the lack of cell-specific chromatin assays which makes it difficult to ascribe epigenetic alterations to specific cell populations, and (3) lack of knowledge about the stability or turnover of epigenetic markings at specific loci in (brain) chromatin. Despite these shortcomings, the study of DNA and histone modifications in chromatin extracted from diseased and control brain tissue is likely to provide valuable insight into the genomic risk architecture of schizophrenia, particularly in the large majority of cases for which a straightforward genetic cause still remains elusive,

Advancing paternal age is associated with deficits in social and exploratory behaviors in the offspring: a mouse model

Background

Accumulating evidence from epidemiological research has demonstrated an association between advanced paternal age and risk for several psychiatric disorders including autism, schizophrenia and early-onset bipolar disorder. In order to establish causality, this study used an animal model to investigate the effects of advanced paternal age on behavioural deficits in the offspring.

Methods

C57BL/6J offspring (n = 12 per group) were bred from fathers of two different ages, 2 months (young) and 10 months (old), and mothers aged 2 months (n = 6 breeding pairs per group). Social and exploratory behaviors were examined in the offspring.

Principal Findings

The offspring of older fathers were found to engage in significantly less social (p = 0.02) and exploratory (p = 0.02) behaviors than the offspring of younger fathers. There were no significant differences in measures of motor activity.

Conclusions

Given the well-controlled nature of this study, this provides the strongest evidence for deleterious effects of advancing paternal age on social and exploratory behavior. De-novo chromosomal changes and/or inherited epigenetic changes are the most plausible explanatory factors.

Epigenetics: molecular mechanisms and implications for disease

Epigenetics is rising to prominence in biology as a mechanism by which environmental factors have intermediate-term effects on gene expression without changing the underlying genetic sequence. This can occur through the selective methylation of DNA bases and modification of histones. There are wide-ranging implications for the gene-environment debate and epigenetic mechanisms are causing a reevaluation of many traditional concepts such as heritability. The reversible nature of epigenetics also provides plausible treatment or prevention prospects for diseases previously thought hard-coded into the genome. Here, we consider how growing knowledge of epigenetics is altering our understanding of biology and medicine, and its implications for future research.

Pharmacology of epigenetics in brain disorders

Epigenetics is a rapidly growing field and holds great promise for a range of human diseases, including brain disorders such as Rett syndrome, anxiety and depressive disorders, schizophrenia, Alzheimer disease and Huntington disease. This review is concerned with the pharmacology of epigenetics to treat disorders of the epigenome whether induced developmentally or manifested/acquired later in life. In particular, we will focus on brain disorders and their treatment by drugs that modify the epigenome. While the use of DNA methyl transferase inhibitors and histone deacetylase inhibitors in in vitro and in vivo models have demonstrated improvements in disease-related deficits, clinical trials in humans have been less promising. We will address recent advances in our understanding of the complexity of the epigenome with its many molecular players, and discuss evidence for a compromised epigenome in the context of an ageing or diseased brain. We will also draw on examples of species differences that may exist between humans and model systems, emphasizing the need for more robust pre-clinical testing. Finally, we will discuss fundamental issues to be considered in study design when targeting the epigenome.

Epigenetic inheritance in mammals: evidence for the impact of adverse environmental effects

The epigenome is the overall epigenetic state of a cell and represents the ensemble of chromatin modifications. It is an essential mechanism for the regulation of the genome that depends on modifications of DNA and histones but does not involve any change of the DNA sequence. It was previously assumed that in order for appropriate cellular development and differentiation to occur in mammals, the epigenome was fully erased and reestablished between generations. However, several examples of incomplete erasure at specific genes have been reported, and this is suggested to be associated with the epigenetic inheritance of gene profiles. Although the existence of such a mode of inheritance has been controversial, there is increasing evidence that it does occur in rodents and humans. In this review, we discuss the evidence that adverse environmental factors can affect not only the individuals directly exposed to these factors but also their offspring. Because the epigenome is sensitive to environmental influence and, in some cases, can, in part, be transmitted across generations, it provides a potential mechanism for the transgenerational transmission of the impact of environmental factors. Environmental factors examined include exposure to toxicants, diet, and postnatal care, and DNA methylation is the main mechanism discussed in this review.

The genetics of bipolar disorder

Bipolar disorder is a mood disorder characterized by impairing episodes of mania and depression. Twin studies have established that bipolar disorder is among the most heritable of medical disorders and efforts to identify specific susceptibility genes have intensified over the past two decades. The search for genes influencing bipolar disorder has been complicated by a paucity of animal models, limited understanding of pathogenesis, and the genetic and phenotypic complexity of the syndrome. Linkage studies have implicated several chromosomal regions as harboring relevant genes, but results have been inconsistent. It is now widely accepted that the genetic liability to bipolar disorder reflects the action of many genes of individually small effect, a scenario for which linkage studies are poorly suited. Thus, association studies, which are more powerful for the detection of modest effect loci, have become the focus of gene-finding research. A large number of candidate genes, including biological candidates derived from hypotheses about the pathogenesis of the disorder and positional candidates derived from linkage and cytogenetic studies, have been evaluated. Several of these genes have been associated with the disorder in independent studies (including BDNF, DAOA, DISC1, GRIK4, SLC6A4, and TPH2), but none has been established. The clinical heterogeneity of bipolar disorder and its phenotypic and genetic overlap with other disorders (especially schizophrenia, schizoaffective disorder, and major depressive disorder) have raised questions about the optimal phenotype definition for genetic studies. Nevertheless, genomewide association analysis, which has successfully identified susceptibility genes for a variety of complex disorders, has begun to implicate specific genes for bipolar disorder (DGKH, CACNA1C, ANK3). The polygenicity of the disorder means that very large samples will be needed to detect the modest effect loci that likely contribute to bipolar disorder. Detailed genetic dissection of the disorder may provide novel targets (both pharmacologic and psychosocial) for intervention.

One-carbon metabolism and schizophrenia: current challenges and future directions

Schizophrenia is a heterogeneous disease generally considered to result from a combination of heritable and environmental factors. Although its pathophysiology has not been fully determined, biological studies support the involvement of several possible components including altered DNA methylation, abnormal glutamatergic transmission, altered mitochondrial function, folate deficiency and high maternal homocysteine levels. Although these factors have been explored separately, they all involve one-carbon (C1) metabolism. Furthermore, C1 metabolism is well positioned to integrate gene-environment interactions by influencing epigenetic regulation. Here, we discuss the potential roles of C1 metabolism in the pathophysiology of schizophrenia. Understanding the contribution of these mechanisms could yield new therapeutic approaches aiming to counteract disease onset or progression.

Global leukocyte DNA methylation is not altered in euthymic bipolar patients

BACKGROUND

Bipolar disorder is a complex disorder hypothesized to involve an interaction of multiple susceptibility genes and environmental factors. The environmental factors may be mediated via epigenetic mechanisms such as DNA methylation. Since a different extent of DNA methylation has recently been reported in lymphoblastoid cells derived from monozygotic twins discordant for bipolar disorder, we hypothesized that bipolar patients exhibit a different extent of leukocyte global DNA methylation compared with healthy controls.

METHODS

DNA was extracted from peripheral blood leukocytes of 49 euthymic bipolar patients and 27 matched healthy controls. Percent of global genome DNA methylation was measured using the cytosine-extension method. Plasma homocysteine levels were measured by HPLC.

RESULTS

Leukocyte global DNA methylation did not differ between bipolar patients [62.3%+/-18.0 (S.D)] and control subjects (63.9%+/-14.6), p=0.70. Bipolar patients' plasma homocysteine levels (11.5 microM+/-4.8) did not differ from those of healthy controls (11.4+/-2.9), p=0.92.

LIMITATIONS

The assay we used, based on restriction by methylation-sensitive/insensitive enzymes followed by a radioactive DNA polymerase reaction was approved to accurately measure global DNA methylation, but has technical limitations i.e. restriction enzymes do not cleave all potential methylation sites in the genome and restriction sites may be altered by mutations or polymorphisms.

CONCLUSIONS

The lack of difference in leukocyte global DNA methylation between euthymic bipolar patients and healthy controls does not rule out the possibility that altered methylation of specific promoter regions is involved in the etiology of the disorder.

The LEARn model: an epigenetic explanation for idiopathic neurobiological diseases

Neurobiological disorders have diverse manifestations and symptomology. Neurodegenerative disorders, such as Alzheimer's disease, manifest late in life and are characterized by, among other symptoms, progressive loss of synaptic markers. Developmental disorders, such as autism spectrum, appear in childhood. Neuropsychiatric and affective disorders, such as schizophrenia and major depressive disorder, respectively, have broad ranges of age of onset and symptoms. However, all share uncertain etiologies, with opaque relationships between genes and environment. We propose a 'Latent Early-life Associated Regulation' (LEARn) model, positing latent changes in expression of specific genes initially primed at the developmental stage of life. In this model, environmental agents epigenetically disturb gene regulation in a long-term manner, beginning at early developmental stages, but these perturbations might not have pathological results until significantly later in life. The LEARn model operates through the regulatory region (promoter) of the gene, specifically through changes in methylation and oxidation status within the promoter of specific genes. The LEARn model combines genetic and environmental risk factors in an epigenetic pathway to explain the etiology of the most common, that is, sporadic, forms of neurobiological disorders.

Epigenetic mediation of environmental influences in major psychotic disorders

The major psychotic disorders schizophrenia and bipolar disorder are etiologically complex involving both heritable and nonheritable factors. The absence of consistently replicated major genetic effects, together with evidence for lasting changes in gene expression after environmental exposures, is consistent with the concept that the biologic underpinnings of these disorders are epigenetic in form rather than DNA sequence based. Psychosis-associated environmental exposures, particularly at key developmental stages, may result in long-lasting epigenetic alterations that impact on the neurobiological processes involved in pathology. Although direct evidence for epigenetic dysfunction in both schizophrenia and bipolar disorder is still limited, methodological technologies in epigenomic profiling have advanced. This means that we are at the exciting stage where it is feasible to start investigating molecular modifications to DNA and histones and examine the mechanisms by which environmental factors can act upon the genome to bring about epigenetic changes in gene expression involved in the etiology of these disorders. Given the dynamic nature of the epigenetic machinery and potential reversibility of epigenetic modifications, the understanding of such mechanisms is of key relevance for clinical psychiatry and for identifying new targets for prevention and/or intervention.

Histone modifications, DNA methylation, and schizophrenia

Studies have demonstrated that several schizophrenia candidate genes are especially susceptible to changes in transcriptional activity as a result of histone modifications and DNA methylation. Increased expression of epigenetic enzymes which generally reduce transcription have been reported in schizophrenia postmortem brain samples. An abnormal chromatin state leading to reduced candidate gene expression can be explained by aberrant coordination of epigenetic mechanisms in schizophrenia. Dynamic epigenetic processes are difficult to study using static measures such as postmortem brain samples. Therefore, we have developed a model using cultured peripheral blood mononuclear cells (PBMCs) capable of pharmacologically probing these processes in human subjects. This approach has revealed several promising findings indicating that schizophrenia subject PBMC chromatin may be less capable of responding to agents which normally 'open' chromatin. We suggest that the ability to appropriately modify chromatin structure may be a factor in treatment response. Several pharmacological approaches for targeting epigenetic processes are reviewed.

DNA methyltransferase 3B gene increases risk of early onset schizophrenia

OBJECTIVE

Consistent evidence indicated that aberrant DNA methylation may be involved in the development of schizophrenia. DNA methyltransferase 3B (DNMT3B) is the key methyltransferase in DNA methylation regulations. In this study, we investigated the association between DNMT3B polymorphisms and the susceptibility of early onset schizophrenia in Chinese Han population.

METHODS

Case-control (patients=381 and controls=472) and family based (trios=103) study was performed through genotyping two tag single nucleotide polymorphisms (rs2424908 and rs6119954) covering the whole DNMT3B gene. Single nucleotide polymorphism association and haplotype analysis were performed.

RESULTS

The frequency of G allele of rs6119954 was significantly higher in patients than that in controls (P=0.017). Genotype distribution of rs6119954 was significantly different between patients and controls (P=0.046). A haplotype-wise analysis revealed a higher frequency of the T-G (rs2424908-rs6119954) haplotype in patients than that in controls (P=0.033). In the transmission disequilibrium test analysis, G allele of rs6119954 was preferentially transmitted in the trios (P=0.030).

CONCLUSION

Our findings indicate that DNMT3B may be a candidate gene for susceptibility to early onset schizophrenia.

Epigenetics, genomic mutations and cognitive function

INTRODUCTION

There is growing interest in the role of single genes in cognitive functions. Association studies are the most commonly applied method in this field. This method assumes that the genetic information affecting cognitive processes is "static" and unchanging. However, there is accumulating evidence that dynamic genomic and epigenetic alterations can modulate complex cognitive processes, and influence susceptibility to disorders associated with impaired cognitive functioning.

METHODS

We present an overview of genomic and epigenetic mechanisms, and discuss the cognitive and psychiatric consequences of genomic and genetic abnormalities.

RESULTS

Genomic and epigenetic changes can affect complex cognitive functions, including learning and memory and are causative in several developmental and psychiatric disorders effecting language, social functioning and IQ.

CONCLUSIONS

Genomic and epigenetic disorders are "experiments of nature" that offer unique and valuable insight in to the physiology of general and specific cognitive functions.

Antipsychotic subtypes can be characterized by differences in their ability to modify GABAergic promoter methylation

Recent advances in schizophrenia and bipolar disorder research suggest that a dysfunction of GABAergic neurotransmission that is operative in telencephalic structures may be an important dynamic mechanism associated with psychosis. We propose that this dysfunction is probably mediated by the hypermethylation of glutamic acid decarboxylase (GAD67), reelin and other gene promoters expressed in GABAergic neurons. A pharmacological strategy that reduces the hypermethylation of GABAergic promoters is to administer drugs (i.e., valproate [VPA]) that induce DNA demethylation by facilitating chromatin remodeling. The enhanced clinical efficacy of atypical antipsychotics when co-administered with VPA prompted us to investigate whether this increased drug efficacy is related to a modification of GABAergic promoter methylation via chromatin remodeling. Our previous and present results strongly suggest that when associated with VPA, clozapine or sulpiride, but not haloperidol or olanzapine, facilitate chromatin remodeling. This molecular remodeling may contribute to the induction of reelin (RELN) and GAD67 (GAD1) promoter demethylation, and may reverse the downregulation of various GABAergic mRNAs and proteins detected in the telencephalon of patients with schizophrenia or bipolar disorders.

Common variants in polygenic schizophrenia

Common variant single-nucleotide polymorphisms at the MHC locus have recently been associated with schizophrenia. Together with known associations with rare copy-number variants affecting many genes, this reveals the highly polygenic etiology of the disease.

The molecular pathology of schizophrenia--focus on histone and DNA modifications

Dysfunction of cerebral cortex and other brain regions in schizophrenia is often accompanied by dysregulated expression of numerous genes. However, the underlying genetic risk architecture remains unclear for a large majority of cases. Therefore, the study of epigenetic regulators of gene expression, including covalent modifications of DNA and nucleosome core histones, offers an attractive alternative to further explore the molecular pathology of schizophrenia beyond the level of RNA quantification. Several studies reported alterations in DNA cytosine methylation and histone methylation at specific genes and promoters in postmortem brain of subjects with schizophrenia, often in conjunction with changes in levels of the corresponding RNAs. While evidence for such "epigenetic dysregulation" is increasing, many of the reported alterations await independent replication. Interestingly, studies across the lifespan indicate that DNA and histone methylation markings are developmentally regulated in human cerebral cortex, suggesting that at least some of the epigenetic changes in the brain of adult subjects with schizophrenia reflect disordered neurodevelopment.

Psychology and Epigenetics

The Human Genome Project mapped the complete DNA sequence that exists in each human cell, but questions remain about how genes are expressed. Epigenetics is defined as mechanisms of gene expression that can be maintained across cell divisions, and thus the life of the organism, without changing the DNA sequence. Recent research has identified important epigenetic mechanisms that play essential roles in normal and abnormal development. Of special significance for psychology are the findings that environmental and psychosocial factors can change the epigenome. Research also suggests that some experiences and epigenetic changes of an individual can be passed down to more than one generation of descendants. Linkages between epigenetics and psychopathology are emerging that point to new possibilities for conceptualizing, preventing, and treating disorders.

Epigenetic mechanisms in schizophrenia

Epidemiological research suggests that both an individual's genes and the environment underlie the pathophysiology of schizophrenia. Molecular mechanisms mediating the interplay between genes and the environment are likely to have a significant role in the onset of the disorder. Recent work indicates that epigenetic mechanisms, or the chemical markings of the DNA and the surrounding histone proteins, remain labile through the lifespan and can be altered by environmental factors. Thus, epigenetic mechanisms are an attractive molecular hypothesis for environmental contributions to schizophrenia. In this review, we first present an overview of schizophrenia and discuss the role of nature versus nurture in its pathology, where 'nature' is considered to be inherited or genetic vulnerability to schizophrenia, and 'nurture' is proposed to exert its effects through epigenetic mechanisms. Second, we define DNA methylation and discuss the evidence for its role in schizophrenia. Third, we define posttranslational histone modifications and discuss their place in schizophrenia. This research is likely to lead to the development of epigenetic therapy, which holds the promise of alleviating cognitive deficits associated with schizophrenia.

An upregulation of DNA-methyltransferase 1 and 3a expressed in telencephalic GABAergic neurons of schizophrenia patients is also detected in peripheral blood lymphocytes

Several lines of schizophrenia (SZ) research suggest that a functional downregulation of the prefrontal cortex GABAergic neuronal system is mediated by a promoter hypermethylation, presumably catalyzed by an increase in DNA-methyltransferase-1 (DNMT-1) expression. This promoter hypermethylation may be mediated not only by DNMT-1 but also by an entire family of de novo DNA-methyltransferases, such as DNA-methyltransferase-3a (DNMT-3a) and -3b (DNMT-3b). To verify the existence of an overexpression of DNMT-3a and DNMT-3b in the brain of schizophrenia patients (SZP), we compared their mRNA expression in Brodmann's area 10 (BA10) and in the caudate nucleus and putamen obtained from the Harvard Brain Tissue Resource Center (Belmont, MA) from both nonpsychiatric subjects (NPS) and SZP. Our results demonstrate that DNMT-3a and DNMT-1 are expressed and co-localize in distinct GABAergic neuron populations whereas DNMT-3b mRNA is virtually undetectable. We also found that unlike DNMT-1, which is frequently overexpressed in telencephalic GABAergic neurons of SZP, DNMT-3a mRNA is overexpressed only in layer I and II GABAergic interneurons of BA10. To ascertain whether these DNMT expression differences observed in brain tissue could also be detected in peripheral tissues, we studied whether DNMT-1 and DNMT-3a mRNAs were overexpressed in peripheral blood lymphocytes (PBL) of SZP. Both DNMT-1 and DNMT-3a mRNAs are expressed in the PBL and although DNMT-3a mRNA levels in the PBL are approximately 1/10 of those of DNMT-1, the comparison of the PBL content in NPS and SZP showed a highly significant 2-fold increase of both DNMT-1 and DNMT-3a mRNA in SZP. These changes were unaffected by the dose, the duration, or the type of antipsychotic treatment. The upregulation of DNMT-1 and to a lesser extent that of DNMT-3a mRNA in PBL of SZP supports the concept that this readily available peripheral cell type can express an epigenetic variation of specific biomarkers relevant to SZ morbidity. Hence, PBL studies may become useful to investigate a diagnostic epigenetic marker of SZ morbidity.

Chronic psychotropic drug treatment causes differential expression of Reelin signaling system in frontal cortex of rats

Disruption of the Reelin and GABAergic signaling systems have been observed in psychiatric disorders including autism, schizophrenia, bipolar disorder, and major depression. Less is known of therapeutic interventions that may help ameliorate the effects of these disruptions. The current study investigated whether chronic administration of psychotropic medications (clozapine, fluoxetine, haloperidol, lithium, olanzapine, and valproic acid) used in the treatment of psychiatric disorders alters levels of Reelin, its receptor Vldlr, downstream molecules Gsk3 beta, Dab-1, and Gad65/67 in rat prefrontal cortex as measured by qRT-PCR and SDS-PAGE and western blotting. qRT-PCR revealed that mRNAs for Reelin, Vldlr, Dab-1, Gsk3 beta, and Gad65 were each significantly altered by at least one of the drugs tested, and in the case of Reelin, Dab-1, and Gsk3 beta, by multiple drugs. To verify our results, we also performed SDS-PAGE and western blotting experiments. Again, several of the protein products for Reelin, Vldlr, Dab-1, Gsk3 beta, Gad65, and Gad67 were also significantly altered by multiple drugs. The present results suggest that the Reelin signaling and GABAergic systems are affected by commonly used psychotropic medications. These changes may help explain the efficacy of these drugs and provide further support for the investigation of the Reelin and GABAergic signaling systems as therapeutic targets for the treatment of neuropsychiatric diseases.

Fetal alcohol spectrum disorders: the epigenetic perspective

Ethanol is a classic teratogen capable of inducing a wide range of developmental abnormalities. Studies in animal models suggest that differences in timing and dosage underlie this variability, with three particularly important developmental periods: preconception, preimplantation, and gastrulation. These periods of teratogenesis correlate with peak periods of epigenetic reprogramming which, together with the evidence that ethanol interferes with one-carbon metabolism, DNA methylation, histone modifications, and noncoding RNA, suggests an important role for epigenetic mechanisms in the etiology of fetal alcohol spectrum disorders (FASDs). In addition to a number of testable hypotheses, an epigenetic model suggests that the concept of a "fetal alcohol spectrum" should be expanded to include "preconceptional effects." This proposal has important public health implications, highlighting the urgency of research into the epigenetic basis of FASDs.

Epigenomic profiling indicates a role for DNA methylation in early postnatal liver development

The question of whether DNA methylation contributes to the stabilization of gene expression patterns in differentiated mammalian tissues remains controversial. Using genome-wide methylation profiling, we screened 3757 gene promoters for changes in methylation during postnatal liver development to test the hypothesis that developmental changes in methylation and expression are temporally correlated. We identified 31 genes that gained methylation and 111 that lost methylation from embryonic day 17.5 to postnatal day 21. Promoters undergoing methylation changes in postnatal liver tended not to be associated with CpG islands. At most genes studied, developmental changes in promoter methylation were associated with expression changes, suggesting both that transcriptional inactivity attracts de novo methylation, and that transcriptional activity can override DNA methylation and successively induce developmental hypomethylation. These in vivo data clearly indicate a role for DNA methylation in mammalian differentiation, and provide the novel insight that critical windows in mammalian developmental epigenetics extend well beyond early embryonic development.

(Epi)genomics and neurodevelopment in schizophrenia: monozygotic twins discordant for schizophrenia augment the search for disease-related (epi)genomic alterations

Unlike stunning breakthroughs in the identification of genes for Mendelian disorders during the last three decades, gene identification in most complex disorders has been full of twists and turns and little progress. Doing more of the same will not guarantee success. The lessons learned argue for a need to reconsider genetic models that are appropriate for the disorder in question along with an interdisciplinary, systematic approach using genomic methods that have now become possible. We will use schizophrenia as an example to review the genetic progress to date that has been disappointing. We will argue that the causation of this complex disease may involve heterogeneous genomic changes of major effect. We will provide three approaches, retroviral transpositions, methylation, and copy number variations, to test this hypothesis. We will present arguments to suggest that such experiments will be most effective if undertaken on monozygotic twins. It will include our experience with associated experiments on the monozygotic twins discordant for schizophrenia. The results support that (epi)genomic changes of major effect, rather than accumulation of mutations of small effect, underlie the causation of this complex disease. More important, this experimental strategy will be an effective strategy for studies on other complex (behavioural) disorders as well.

Epigenetic mechanisms for nutrition determinants of later health outcomes

Epigenetic marking on genes can determine whether or not genes are expressed. Epigenetic regulation is mediated by the addition of methyl groups to DNA cytosine bases, of methyl and acetyl groups to proteins (histones) around which DNA is wrapped, and by small interfering RNA molecules. Some components of epigenetic regulation have evolved to permit control of whether maternal or paternal genes are expressed. The epigenetic imprinting of IGF2 expression is an example of maternal and paternal epigenetic marking that modulates fetal growth and fetal size. However, epigenetic regulation also permits the fetus and the infant to adapt gene expression to the environment in which it is growing; sometimes when this adjustment goes awry, the risk of chronic disease is increased. Recent progress in the understanding of nutritional influences on epigenetics suggests that nutrients that are part of methyl-group metabolism can significantly influence epigenetics. During critical periods in development, dietary methyl-group intake (choline, methionine, and folate) can alter DNA and histone methylation, which results in lifelong changes in gene expression. In rodent models, pregnant dams that were fed diets high in methionine, folic acid, and choline produced offspring with different coat colors or with kinked tails. A number of syndromes in humans can be caused by defective epigenetic regulation, including Rett syndrome. There are interesting examples of the effects of nutrition in early life that result in altered health in adults, and some of these could be the result of altered epigenetic regulation of gene expression.

Lasting epigenetic influence of early-life adversity on the BDNF gene

BACKGROUND

Childhood maltreatment and early trauma leave lasting imprints on neural mechanisms of cognition and emotion. With a rat model of infant maltreatment by a caregiver, we investigated whether early-life adversity leaves lasting epigenetic marks at the brain-derived neurotrophic factor (BDNF) gene in the central nervous system.

METHODS

During the first postnatal week, we exposed infant rats to stressed caretakers that predominately displayed abusive behaviors. We then assessed DNA methylation patterns and gene expression throughout the life span as well as DNA methylation patterns in the next generation of infants.

RESULTS

Early maltreatment produced persisting changes in methylation of BDNF DNA that caused altered BDNF gene expression in the adult prefrontal cortex. Furthermore, we observed altered BDNF DNA methylation in offspring of females that had previously experienced the maltreatment regimen.

CONCLUSIONS

These results highlight an epigenetic molecular mechanism potentially underlying lifelong and transgenerational perpetuation of changes in gene expression and behavior incited by early abuse and neglect.

Pathways from science findings to health benefits

There have been numerous exhortations for more 'translational research'. A selective review of historical examples of research leading to health benefits is used to consider the various forms of successful interplay between basic science and clinical applications. This is followed by a consideration of key neuroscience findings that might be relevant for translation, and then by a discussion of the challenges and opportunities in relation to mental disorders. The time-frame for the pathway from science findings to health benefits is usually long, and generally requires an interactive interplay among different scientific strategies. There is a false dichotomy between so-called basic and applied research and translation needs to proceed from the bedside to the laboratory as well as in the opposite direction. There is a key need for bridging research of the hypothesis-testing experimental medicine variety. Health benefits may involve either public health considerations or the treatment of individual patients, or both. There are now some opportunities for direct translational research but there is a much greater need for hypothesis-based bridging studies that occupy a crucial mid-phase in the pathway from science findings to health benefits.

Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation

Background

DNA methylation plays a vital role in normal cellular function, with aberrant methylation signatures being implicated in a growing number of human pathologies and complex human traits. Methods based on the modification of genomic DNA with sodium bisulfite are considered the 'gold-standard' for DNA methylation profiling on genomic DNA; however, they require relatively large amounts of DNA and may be prohibitively expensive when used on the large sample sizes necessary to detect small effects. We propose that a high-throughput DNA pooling approach will facilitate the use of emerging methylomic profiling techniques in large samples.

Results

Compared with data generated from 89 individual samples, our analysis of 205 CpG sites spanning nine independent regions of the genome demonstrates that DNA pools can be used to provide an accurate and reliable quantitative estimate of average group DNA methylation. Comparison of data generated from the pooled DNA samples with results averaged across the individual samples comprising each pool revealed highly significant correlations for individual CpG sites across all nine regions, with an average overall correlation across all regions and pools of 0.95 (95% bootstrapped confidence intervals: 0.94 to 0.96).

Conclusion

In this study we demonstrate the validity of using pooled DNA samples to accurately assess group DNA methylation averages. Such an approach can be readily applied to the assessment of disease phenotypes reducing the time, cost and amount of DNA starting material required for large-scale epigenetic analyses.

GABAergic promoter hypermethylation as a model to study the neurochemistry of schizophrenia vulnerability

The neuronal GABAergic mechanisms that mediate the symptomatic beneficial effects elicited by a combination of antipsychotics with valproate (a histone deacetylase inhibitor) in the treatment of psychosis (expressed by schizophrenia or bipolar disorder patients) are unknown. This prompted us to investigate whether the beneficial action of this combination results from a modification of histone tail covalent esterification or is secondary to specific chromatin remodeling. The results suggest that clozapine, or sulpiride associated with valproate, by increasing DNA demethylation with an unknown mechanism, causes a chromatin remodeling that brings about a beneficial change in the epigenetic GABAergic dysfunction typical of schizophrenia and bipolar disorder patients.

Recent advances in postmortem pathology and neurochemistry in schizophrenia

PURPOSE OF REVIEW

This is a review examining recent data from the study of the postmortem central nervous system (CNS) of patients with schizophrenia.

RECENT FINDINGS

Studies on the human CNS transcriptome suggest changes in pro-inflammatory pathways and myelination in schizophrenia, whereas changes in the proteome suggest that pathways involved in energy and metabolism may be particularly stressed. There appear to be complex changes in the expression of proposed candidate genes for schizophrenia such as NRG1, DISC1, RGS4 and DTNB1, and there are continued reports of alterations in central gamma-aminobutyric acidergic, dopaminergic, glutamatergic and cholinergic pathways in patients with the disorder. Data on epigenetic mechanisms and transcriptome regulation suggest that at least some changes in gene expression may be due to changes in levels of gene promoter methylation or microRNAs in the CNS of patients with schizophrenia.

SUMMARY

Postmortem CNS studies have begun to unravel changes in the epigenetic regulation of gene expression that may be central to how gene-environment interactions contribute to the onset of schizophrenia. In addition, a recent study indicates that it is possible to use biomarkers to segregate the syndrome of schizophrenia into more biologically homogeneous populations, which should decrease the biological complexity observed within that group within the schizophrenia syndrome.

Prospects for epigenetic epidemiology

Epigenetic modification can mediate environmental influences on gene expression and can modulate the disease risk associated with genetic variation. Epigenetic analysis therefore holds substantial promise for identifying mechanisms through which genetic and environmental factors jointly contribute to disease risk. The spatial and temporal variance in epigenetic profile is of particular relevance for developmental epidemiology and the study of aging, including the variable age at onset for many common diseases. This review serves as a general introduction to the topic by describing epigenetic mechanisms, with a focus on DNA methylation; genetic and environmental factors that influence DNA methylation; epigenetic influences on development, aging, and disease; and current methodology for measuring epigenetic profile. Methodological considerations for epidemiologic studies that seek to include epigenetic analysis are also discussed.

The reelin and GAD67 promoters are activated by epigenetic drugs that facilitate the disruption of local repressor complexes

The epigenetic down-regulation of genes is emerging as a possible underlying mechanism of the GABAergic neuron dysfunction in schizophrenia. For example, evidence has been presented to show that the promoters associated with reelin and GAD67 are down-regulated as a consequence of DNA methyltransferase (DNMT)-mediated hypermethylation. Using neuronal progenitor cells to study this regulation, we have previously demonstrated that DNMT inhibitors coordinately increase reelin and GAD67 mRNAs. Here, we report that another group of epigenetic drugs, histone deacetylase (HDAC) inhibitors, activate these two genes with dose and time dependence comparable with that of DNMT inhibitors. In parallel, both groups of drugs decrease DNMT1, DNMT3A, and DNMT3B protein levels and reduce DNMT enzyme activity. Furthermore, induction of the reelin and GAD67 mRNAs is accompanied by the dissociation of repressor complexes containing all three DNMTs, MeCP2, and HDAC1 from the corresponding promoters and by increased local histone acetylation. Our data imply that drug-induced promoter demethylation is relevant for maximal activation of reelin and GAD67 transcription. The results suggest that HDAC and DNMT inhibitors activate reelin and GAD67 expression through similar mechanisms. Both classes of drugs attenuate, directly or indirectly, the enzymatic and transcriptional repressor activities of DNMTs and HDACs. These data provide a mechanistic rationale for the use of epigenetic drugs, individually or in combination, as a potential novel therapeutic strategy to alleviate deficits associated with schizophrenia.

Epigenetic regulation in human brain-focus on histone lysine methylation

Alterations in RNA levels are frequently reported in brain of subjects diagnosed with autism, schizophrenia, depression, and other psychiatric diseases, but it remains unclear whether the underlying molecular pathology involves changes in gene expression, as opposed to alterations in messenger RNA processing. Pre-clinical studies have revealed that stress, drugs, and a variety of other environmental factors lead to changes in RNA levels in brain via epigenetic mechanisms, including modification of histone proteins. A number of site-specific modifications of the nucleosome core histones-including the trimethylated forms of histone H3 lysines K4, K9, and K27-are of particular interest for postmortem research, because these marks differentiate between active and inactive chromatin and seem to remain relatively stable during tissue autolysis. Therefore, histone methylation profiling at promoter regions could provide important clues about mechanisms of gene expression in human brain during development and in disease. Intriguingly, mutations within the genes encoding the H3K9-specific methyltransferase, EHMT1, and the H3K4-specific histone demethylase, JARID1C/SMCX, have been linked to mental retardation and autism, respectively. In addition, the H3K4-specific methyltransferase, MLL1, is essential for hippocampal synaptic plasticity and might be involved in cortical dysfunction of some cases of schizophrenia. Together, these findings emphasize the potential significance of histone lysine methylation for orderly brain development and also as a molecular toolbox to study chromatin function in postmortem tissue.

Searching for the true genetic vulnerability for schizophrenia

The search for a genetic basis for schizophrenia has taken a new turn recently with the publication of three reports of various rare copy-number variations that are associated with schizophrenia. While some of the findings may simply disappear as spurious reports, others remain interesting: that is, deletions in the Velocardiofacial syndrome region of chromosome 22, and regions of chromosome 1q21.1 and 15q13.3. These results will gain greater significance if future validation in family studies shows their segregation with illness within families, and when it is understood how the genes containing these variants affect the underlying neurochemistry and neuropathology characteristic of schizophrenia.

Cultural neuroscience and psychopathology: prospects for cultural psychiatry

There is a long tradition that seeks to understand the impact of culture on the causes, form, treatment, and outcome of psychiatric disorders. An early, colonialist literature attributed cultural characteristics and variations in psychopathology and behavior to deficiencies in the brains of colonized peoples. Contemporary research in social and cultural neuroscience holds the promise of moving beyond these invidious comparisons to a more sophisticated understanding of cultural variations in brain function relevant to psychiatry. To achieve this, however, we need better models of the nature of psychopathology and of culture itself. Culture is not simply a set of traits or characteristics shared by people with a common geographic, historical, or ethnic background. Current anthropology understands culture as fluid, flexible systems of discourse, institutions, and practices, which individuals actively use for self-fashioning and social positioning. Globalization introduces new cultural dynamics and demands that we rethink culture in relation to a wider domain of evolving identities, knowledge, and practice. Psychopathology is not reducible to brain dysfunction in either its causes, mechanisms, or expression. In addition to neuropsychiatric disorders, the problems that people bring to psychiatrists may result from disorders in cognition, the personal and social meanings of experience, and the dynamics of interpersonal interactions or social systems and institutions. The shifting meanings of culture and psychopathology have implications for efforts to apply cultural neuroscience to psychiatry. We consider how cultural neuroscience can refine use of culture and its role in psychopathology using the example of adolescent aggression as a symptom of conduct disorder.

Is schizophrenia the price of human central nervous system complexity?

The purpose of the present study was to determine if there is evidence to support the hypothesis that schizophrenia is a human-specific disorder associated with the need for highly complex central nervous system (CNS) development. A review was therefore undertaken of published literature relevant to the identification of human-specific CNS development. There was no clear evidence found at the macroscopic, microscopic or molecular level that suggests unique changes have occurred in the evolution of the human CNS. Rather, highly significant changes in the size of the frontal lobe, increases in numbers of specific cell types, changes in gene expression and changes in genome sequence all seem to be involved in the evolution of the human CNS. Human-specific changes in CNS development are wide ranging. The modification in CNS structure and function that has resulted from these changes affects many pathways and behaviours that appear to be also affected in subjects with schizophrenia. Therefore there is evidence to support the hypothesis that schizophrenia is a disease that develops because of derangements to human-specific CNS functions that have emerged since our species diverged from non-human primates.

The ghost in our genes: legal and ethical implications of epigenetics

Epigenetics is one of the most scientifically important, and legally and ethically significant, cutting-edge subjects of scientific discovery. Epigenetics link environmental and genetic influences on the traits and characteristics of an individual, and new discoveries reveal that a large range of environmental, dietary, behavioral, and medical experiences can significantly affect the future development and health of an individual and their offspring. This article describes and analyzes the ethical and legal implications of these new scientific findings.

DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia

BACKGROUND

The synapsin III (SYN III) gene on chromosome 22q is a candidate gene for schizophrenia susceptibility due to its chromosome location, neurological function, expression patterns and functional polymorphisms.

METHODS

This research has established the mRNA expression of SYN III in 22 adult human brain regions as well as the methylation specificity in the closest CpG island of this gene. The methylation specificity studied in 31 brain regions (from a single individual) was also assessed in 51 human blood samples (representing 20 people affected with schizophrenia and 31 normal controls) including a pair of monozygotic twin discordant for schizophrenia and 2 non-human primates.

RESULTS

The results show that the cytosine methylation in this genomic region is 1) restricted to cytosines in CpG dinucleotides 2) similar in brain regions and blood and 3) appears conserved in primate evolution. Two cytosines (cytosine 8 and 20) localized as the CpG dinucleotide are partially methylated in all brain regions studied. The methylation of these sites in schizophrenia and control blood samples was variable. While cytosine 8 was partially methylated in all samples, the distribution of partial to complete methylation at the cytosine 20 was 22:9 in controls as compared to 18:2 in schizophrenia (p = 0.82). Also, there is no difference in methylation between the affected and unaffected member of a monozygotic twin pair.

CONCLUSION

The variation in SYN III methylation studied is 1) not related to schizophrenia in the population sample or a monozygotic twin pair discordant for schizophrenia and 2) not related to the mRNA level of SYN IIIa in different human brain regions.

Epigenetic and pharmacoepigenomic studies of major psychoses and potentials for therapeutics

Individuals with neuropsychiatric diseases have epigenetic programming disturbances, both in the brain, which is the primary affected organ, and in secondary tissues. Epigenetic modulations are molecular modifications made to DNA, RNA and proteins that fine-tune genotype into phenotype and do not include DNA base changes. For instance, gene-expression modulation is linked to epigenetic codes in chromatin that consist of post-replication DNA methylation and histone protein modifications (e.g., methylation, acetylation and so on), particularly in gene-promoter regions. Epigenetic coding is modulated globally, and in a gene-specific manner by environmental exposures that include nutrition, toxins, drugs and so on. Analysis of epigenetic aberrations in diseases helps to identify dysfunctional genes and pathways, establish more robust cause–effect relationships than genetic studies alone, and identify new pharmaceutical targets and drugs, including nucleic acid reagents such as inhibitory RNAs. The emerging science of pharmacoepigenomics can impact the treatment of psychiatric and other complex diseases. In fact, some therapeutics now in use target epigenetic programming. In the near future, epigenetic interventions should help stabilize affected individuals and lead to prevention strategies.

Environmental studies of schizophrenia through the prism of epigenetics

Traditionally, etiological research of schizophrenia has been focused on elucidating predisposing genes and environmental risk factors. While numerous putative environmental hazards have been suggested, inconsistencies and methodological limitations of epidemiological studies have made it difficult to identify even a single exogenous cause of schizophrenia. Furthermore, there is increasing evidence that environmental risk factors may not play as much of a significant role in schizophrenia as previously suspected. In this article, we argue that molecular epigenetic studies can overcome the complexities of traditional epidemiological studies and may become a productive line of research in understanding the nongenetic mechanisms of schizophrenia.