Human morbid genetics revisited: relevance of epigenetics

Reelin promoter hypermethylation in schizophrenia

Reelin mRNA and protein levels are reduced by approximately 50% in various cortical structures of postmortem brain from patients diagnosed with schizophrenia or bipolar illness with psychosis. In addition, the mRNA encoding the methylating enzyme, DNA methyltransferase 1, is up-regulated in the same neurons that coexpress reelin and glutamic acid decarboxylase 67. We have analyzed the extent and pattern of methylation within the CpG island of the reelin promoter in genomic DNA isolated from cortices of schizophrenia patients and nonpsychiatric subjects. Ten (The Stanley Foundation Neuropathology Consortium) and five (Harvard Brain Collection) schizophrenia patients and an equal number of nonpsychiatric subjects were selected from each brain collection. Genomic DNA was isolated, amplified (from base pair -527 to base pair +322) after bisulphite treatment, and sequenced. The results show that within the promoter region there were interesting regional variations. There was increased methylation at positions -134 and 139, which is particularly important for regulation, because this portion of the promoter is functionally competent based on transient transfection assays. This promoter region binds a protein present in neuronal precursor nuclear extracts that express very low levels of reelin mRNA; i.e., an oligonucleotide corresponding to this region and that contains methylated cytosines binds more tightly to extracts from nonexpressing cells than the nonmethylated counterpart. Collectively, the data show that this promoter region has positive and negative properties and that the function of this complex cis element relates to its methylation status.

The neurodevelopmental model of schizophrenia: update 2005

Neurodevelopmental models of schizophrenia that identify longitudinal precursors of illness have been of great heuristic importance focusing most etiologic research over the past two decades. These models have varied considerably with respect to specificity and timing of hypothesized genetic and environmental 'hits', but have largely focused on insults to prenatal brain development. With heritability around 80%, nongenetic factors impairing development must also be part of the model, and any model must also account for the wide range of age of onset. In recent years, longitudinal brain imaging studies of both early and adult (to distinguish from late ie elderly) onset populations indicate that progressive brain changes are more dynamic than previously thought, with gray matter volume loss particularly striking in adolescence and appearing to be an exaggeration of the normal developmental pattern. This supports an extended time period of abnormal neurodevelopment in schizophrenia in addition to earlier 'lesions'. Many subtle cognitive, motor, and behavioral deviations are seen years before illness onset, and these are more prominent in early onset cases. Moreover, schizophrenia susceptibility genes and chromosomal abnormalities, particularly as examined for early onset populations (ie GAD1, 22q11DS), are associated with premorbid neurodevelopmental abnormalities. Several candidate genes for schizophrenia (eg dysbindin) are associated with lower cognitive abilities in both schizophrenic and other pediatric populations more generally. Postmortem human brain and developmental animal studies document multiple and diverse effects of developmental genes (including schizophrenia susceptibility genes), at sequential stages of brain development. These may underlie the broad array of premorbid cognitive and behavioral abnormalities seen in schizophrenia, and neurodevelopmental disorders more generally. Increased specificity for the most relevant environmental risk factors such as exposure to prenatal infection, and their interaction with susceptibility genes and/or action through phase-specific altered gene expression now both strengthen and modify the neurodevelopmental theory of schizophrenia.

Benefits and challenges brought by improved results fromin vitrofertilization

Abstract In vitro fertilization (IVF), in which preimplantation-stage embryos are produced after ovarian stimulation and retrieval of preovulatory oocytes, now accounts for almost 2% of all births in Australia. For clinics performing in the top quartile of national results, the chance of a live birth for a woman under 35 years from one round of egg retrieval and IVF treatment is greater than 50%, albeit still with a greater than 20% risk of twins or higher order multiple pregnancy. Similar or better live birth rates are now obtainable with the elective transfer of a single embryo at the stage of blastocyst (5-6 days in culture), a policy that if adopted for younger women can reduce the risk of twins in a clinic to less than 15%. Current developments centre around improvements to embryo culture and the testing of embryos for chromosomal normality and other genetic and epigenetic variables before transfer, made possible by licences for embryo research protocols now being issued under the Commonwealth's Research Involving Human Embryos Act 2002.

DNA methyltransferase 1 regulates reelin mRNA expression in mouse primary cortical cultures

The polygenic nature of complex psychiatric disorders suggests a common pathway that may be involved in the down-regulation of multiple genes through an epigenetic mechanism. To investigate the role of methylation in down-regulating the expression of mRNAs that may be associated with the schizophrenia phenotype, we have adopted a cell-culture model amenable to this line of investigation. We have administered methionine (2 mM) to primary cultures of cortical neurons prepared from embryonic day 16 mice and show that this treatment down-regulated reelin and glutamic acid decarboxylase 67 (GAD67) mRNA expression but not that corresponding to neuron-specific enolase mRNA. Moreover, methionine increased methylation of the reelin promoter, suggesting a possible mechanism for the observed change. These cultures contain a mixed population of neurons and glia. Approximately 83% of the neurons are GABAergic based on GAD immunoreactivity, and these neurons coexpress high levels of reelin and DNA methyltransferase (Dnmt) 1 immunoreactivity. To examine whether Dnmt1 regulates reelin gene expression, we used an antisense approach to reduce (knock down) Dnmt1 expression. The reduced Dnmt1 mRNA and protein were accompanied by increased reelin mRNA expression. More importantly, the Dnmt1 knockdown blocked the methionine-induced reelin and GAD67 mRNA down-regulation. These data support the hypothesis that the reduced amounts of reelin and GAD67 mRNAs documented in postmortem schizophrenia brain may be the consequence of a Dnmt1-mediated hypermethylation of the corresponding promoters.

Schizophrenia, epigenetics and ligand-activated nuclear receptors: a framework for chromatin therapeutics

Covalent modifications of DNA and its surrounding chromatin constitute an essential and powerful regulatory mechanism for gene transcription. Epigenetics is the study of this regulatory system. There is now strong albeit indirect evidence that epigenetic mechanisms contribute to the pathophysiology of schizophrenia. Furthermore, the discovery that valproic acid, a widely used psychotropic, has powerful epigenetic effects in clinically relevant concentrations suggests new therapeutic possibilities, i.e., drugs that act on chromatin structure. Fortunately, many proteins engaged in these processes, particularly chromatin remodeling, are accessible to pharmacological agents that have a high likelihood of crossing the blood brain barrier. This review will first summarize the essentials of the epigenetic regulatory system, then address the molecular evidence for altered epigenetic mechanisms in schizophrenia, and finally focus on the retinoic acid family of ligand-activated nuclear transcription factors as a likely system for new drug development in the management of schizophrenia-related symptoms.

Epigenetics and human disease

Epigenetics is comprised of the stable and heritable (or potentially heritable) changes in gene expression that do not entail a change in DNA sequence. The role of epigenetics in the etiology of human disease is increasingly recognized with the most obvious evidence found for genes subject to genomic imprinting. Mutations and epimutations in imprinted genes can give rise to genetic and epigenetic phenotypes, respectively; uniparental disomy and imprinting defects represent epigenetic disease phenotypes. There are also genetic disorders that affect chromatin structure and remodeling. These disorders can affect chromatin in trans or in cis, as well as expression of both imprinted and nonimprinted genes. Data from Angelman and Beckwith-Wiedemann syndromes and other disorders indicate that a monogenic or oligogenic phenotype can be caused by a mixed epigenetic and genetic and mixed de novo and inherited (MEGDI) model. The MEGDI model may apply to some complex disease traits and could explain negative results in genome-wide genetic scans.

Early maternal stress and health behaviours and offspring expression of psychosis in adolescence

OBJECTIVE

It has been suggested that influences operating early in life may affect the risk of postpubertal psychosis outcomes. This hypothesis was tested using a broad outcome of psychotic symptoms expressed in adolescence (prevalence: 15.6%).

METHOD

Findings are based on a longitudinal, population-based cohort study of 963 adolescents aged 15-20 years and their parents in the area of Munich, Germany. Trained psychologists assessed adolescents with the Munich-Composite International Diagnostic Interview. Independently, direct diagnostic interviews were conducted with the parents.

RESULTS

A range of medical complications of pregnancy and delivery, including lower birth weight, were not associated with the psychosis outcome. However, a number of maternal health behaviours and experiences did show associations, independent of confounders.

CONCLUSION

Not maternally reported medical complications of pregnancy and delivery, but maternal prenatal health behaviours predicted expression of psychosis along a continuum in adolescence. This effect may either be direct or constitute a proxy for later postnatal maternal behaviours associated with psychosis risk in the offspring.

Discovering endophenotypes for major depression

The limited success of genetic studies of major depression has raised questions concerning the definition of genetically relevant phenotypes. This paper presents strategies to improve the phenotypic definition of major depression by proposing endophenotypes at two levels: First, dissecting the depressive phenotype into key components results in narrow definitions of putative psychopathological endophenotypes: mood bias toward negative emotions, impaired reward function, impaired learning and memory, neurovegetative signs, impaired diurnal variation, impaired executive cognitive function, psychomotor change, and increased stress sensitivity. A review of the recent literature on neurobiological and genetic findings associated with these components is given. Second, the most consistent heritable biological markers of major depression are proposed as biological endophenotypes for genetic studies: REM sleep abnormalities, functional and structural brain abnormalities, dysfunctions in serotonergic, catecholaminergic, hypothalamic-pituitary-adrenocortical axis, and CRH systems, and intracellular signal transduction endophenotypes. The associations among the psychopathological and biological endophenotypes are discussed with respect to specificity, temporal stability, heritability, familiality, and clinical and biological plausibility. Finally, the case is made for the development of a new classification system in order to reduce the heterogeneity of depression representing a major impediment to elucidating the genetic and neurobiological basis of this common, severe, and often life-threatening illness.

Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: an HPLC-based study

The goal of the present study was to investigate inter-individual and age-dependent variation of global DNA methylation in human tissues. In this work, we examined 5-methyldeoxycytidine ((met)C) content by HPLC in human peripheral blood leukocytes obtained from 76 healthy individuals of ages varying from 4 to 94 years (yr), and 39 human placentas from various gestational stages. The HPLC analysis revealed a significant variation of (met)C across individuals and is consistent with the previous findings of age-dependent decrease of global methylation levels in human tissues. The age-dependent decrease of (met)C was relatively small, but statistically highly significant (p= 0.0002) in the aged group (65.9 +/- 8.9 [mean age +/- SD] yr; n = 22) in comparison to the young adult group (19.3 +/- 1.4 yr; n = 21). Males showed a subtle but statistically significant higher mean (met)C content than females. In contrast to the peripheral blood samples, DNA extracted from placentas exhibited gestational stage-dependent increase of methylation levels that appeared to inversely correlate with the expression levels of human endogenous retroviruses. These data may be helpful in further studies of DNA methylation, such as inheritance of epigenetic patterns, environment-induced changes, and involvement of epigenetic changes in disease.

Quantitative and theoretical analyses of the relation between older brothers and homosexuality in men

Meta-analysis of aggregate data from 14 samples representing 10,143 male subjects shows that homosexuality in human males is predicted by higher numbers of older brothers, but not by higher numbers of older sisters, younger brothers, or younger sisters. The relation between number of older brothers and sexual orientation holds only for males. This phenomenon has therefore been called the fraternal birth order effect. Research on birth order, birth weight, and sexual orientation suggests that the developmental pathway to homosexuality initiated by older brothers operates during prenatal life. Calculations assuming a causal relation between older brothers and sexual orientation have estimated the proportion of homosexual men who owe their sexual orientation to fraternal birth order at 15% in one study and 29% in another. The maternal immune hypothesis proposes that the fraternal birth order effect reflects the progressive immunization of some mothers to male-specific antigens by each succeeding male fetus and the increasing effects of such immunization on sexual differentiation of the brain in each succeeding male fetus. There are at least three possible mechanisms by which the mother's immune response could influence the fetus: the transfer of anti-male antibodies across the placenta from the maternal into the fetal compartment, the transfer of maternal cytokines across the placenta, and maternal immune reactions affecting the placenta itself. This hypothesis is consistent with recent studies showing that the quantity of fetal cells that enter the maternal circulation is greater than previously thought, and that the number of male-specific proteins encoded by Y-chromosome genes is greater than previously thought.

NDRG2: a novel Alzheimer's disease associated protein

Our understanding of the genes involved in Alzheimer's disease (AD) is incomplete. Using subtractive cloning technology, we discovered that the alpha/beta-hydrolase fold protein gene NDRG2 (NDRG family member 2) is upregulated at both the RNA and protein levels in AD brains. Expression of NDRG2 in affected brains was revealed in (1) cortical pyramidal neurons, (2) senile plaques and (3) cellular processes of dystrophic neurons. Overexpression of two splice variants encoding a long and short NDRG2 isoform in hippocampal pyramidal neurons of transgenic mice resulted in localization of both isoforms to dendritic processes. Taken together, our findings suggest that NDRG2 upregulation is associated with disease pathogenesis in the human brain and provide new insight into the molecular changes that occur in AD.

Genetics, epigenetics, and the environment: switching, buffering, releasing

Increasing evidence suggests that the interactions between genes and environment might play a critical role in the pathogenesis of complex diseases, such as asthma, that exhibit a heritable component but do not follow Mendel's laws. Gene-environment interactions are extremely complex and not linear, such that the same genetic variants might be associated with opposite phenotypes in different environments. This is particularly evident for innate immunity genes, which operate at the interface between the immune system and the pathogen world. This article examines gene-environment interactions by using CD14 as a model and argues that the conflicting results of epidemiologic studies on CD14*C-159T result from differences in environmental conditions essential to modulate CD14 gene expression. Furthermore, on the basis of how rapidly environmental changes have affected the incidence of immune diseases, I argue that a full understanding of gene-environment interactions requires that epigenetic as well as classical genetic mechanisms be taken into account. Recent data about the effect of diet on gene methylation and the release of hidden genetic variation by impairment of heat shock protein 90-mediated buffering systems offer eloquent examples of how epigenetic mechanisms might affect gene-environment interactions.

The origin of schizophrenia: genetic thesis, epigenetic antithesis, and resolving synthesis

Traditionally, it has been thought that schizophrenia results from the interaction of predisposing genes and hazardous environmental factors. In this article, the paradigm of "genes plus environment" is challenged, and a new interpretation is presented, in which the emphasis on DNA sequence variation is shared with epigenetic misregulation as a critical etiopathogenic factor. Partial epigenetic stability (metastability) of gene regulation is consistent with various nonmendelian irregularities of schizophrenia, such as the presence of clinically indistinguishable sporadic and familial cases, discordance of monozygotic twins, coincidence of peaks of susceptibility with major endocrine rearrangements, and fluctuating course of disease severity, among others. It is also suggested that stochastic epigenetic events might account for a substantial portion of phenotypic variance, which traditionally has been ascribed to environmental effects. This theoretic essay is constructed according to the principle of Hegelian dialectic reasoning (thesis-antithesis-synthesis), which serves the goal of showing that the best outcome of molecular genetic studies in schizophrenia (and perhaps other complex diseases) can be expected when components that effect chromatin structure and gene regulation are taken into account and investigated comprehensively.

DNA methylation as an epigenetic regulator of neural 5-lipoxygenase expression: evidence in human NT2 and NT2-N cells

Increased expression of 5-lipoxygenase is associated with various neuropathologies and may be related to epigenetic gene regulation. DNA methylation in promoter regions is typically associated with gene silencing. We found that human NT2 cells, which differentiate into neuron-like NT2-N cells, express 5-lipoxygenase and we investigated the relationship between 5-lipoxygenase expression and the methylation state of the 5-lipoxygenase core promoter. We used the demethylating agent 5-aza-2'-deoxycytidine and the histone deacetylase inhibitor valproate to alter DNA methylation and to induce histone modifications. 5-Lipoxygenase expression and DNA methylation were assayed with RT-PCR and bisulfite genomic sequencing, respectively. Neuronal differentiation of proliferating NT2 precursors decreased 5-lipoxygenase expression. 5-Aza-2'-deoxycytidine increased 5-lipoxygenase mRNA levels only in proliferating cells, whereas valproate increased 5-lipoxygenase mRNA levels in a cell cycle-independent manner. In both precursors and differentiated cells, CpG dinucleotides of the promoter were poorly methylated. In precursors, both 5-aza-2'-deoxycytidine and valproate further reduced the number of methylated CpGs. Moreover, we found evidence for cytosine methylation in CpWpG (W=adenine or thymine) and other asymmetrical sequences; CpWpG methylation was reduced by valproate in NT2-N but not in NT2 cells. This is the first report demonstrating that the dynamics of DNA methylation relates to neural 5-lipoxygenase gene expression.

Dnmt1 expression in pre- and postimplantation embryogenesis and the maintenance of IAP silencing

The methylation of intracisternal A-type particle (IAP) sequences is maintained during mouse embryogenesis. Methylation suppresses IAP expression and the potential for mutagenesis by retrotransposition, but it is not clear how methylation of these elements is maintained during the embryonic stages when the bulk of the genome is being demethylated. It has been suggested that the high levels of DNA methyltransferase-1 (Dnmt1) present during cleavage could be important for keeping IAPs methylated. To test this hypothesis, we combined mutant alleles of Dnmt1 with an agouti allele (A(iapy)), which provided a coat color readout for the methylation status of the IAP insertion in the agouti locus. We found that reduction in Dnmt1 levels directly impacted methylation at this locus, leading to stable transcriptional activation of the agouti gene in the adult. Specifically, the short maternal Dnmt1 protein was important in maintaining methylation at the A(iapy) locus in cleavage embryos, whereas the longer Dnmt1 isoform found in somatic cells was important in maintaining IAP methylation during the postimplantation stage. These results underscore the importance of maintaining proper maintenance of methylation patterns during gestation and suggest that interference with this process may stably affect gene expression patterns in the adult and may have profound phenotypic consequences.

Categories, Dimensions, and the Mental Health of Children and Adolescents

Concepts of mental disorder, and of the causal processes leading to disorder, have undergone radical changes over recent decades. Genetic findings, for example, have shown that (1) many conditions develop on the basis of a dimensional genetic liability; (2) the boundaries of some conditions extend much more broadly than indicated by the traditional diagnostic categories; and (3) there is substantial overlap between conditions previously thought to be distinctively different. On the other hand, genetic findings have also provided support for the validity of some diagnostic distinctions. Early molecular genetic research was conceptualized on the basis of the expectation that there would be disease-specific genes "for" schizophrenia, bipolar disorder, and the like. It has become apparent that, at best, this constitutes a misleading oversimplification. Almost all mental disorders (in childhood and adult life) have a multifactorial origin, and the genes are likely to operate through a range of direct and indirect routes. Gene-environment correlations and interactions are important, and there is a biological substrate for individual differences in responses to psychosocial stress and adversity, as well as for the effects of such stress and adversity on the organism. The empirical basis for these changes in concepts is reviewed, and the implications for clinical science and practice are considered.

Signal transduction and genes-to-behaviors pathways in psychiatric diseases

Although psychiatric diseases are among the most common and destructive of all human illnesses, the molecular and cellular mechanisms underlying their complex origins remain to be elucidated. Dysfunction of critical intracellular signaling pathways is very likely to be involved. This conclusion is based on a number of observations, including the short- and long-term cellular effects of psychiatric drugs; the critical role signaling pathways play in neurotransmitter, neuropeptide, and neurohormone communication; and the fact that signaling pathways are principle regulators of the diverse array of behavioral symptoms experienced by patients. The genomics era has brought to psychiatry an abundance of genetic linkage and candidate gene findings. The difficult task--now under way--is to discern the functional relevance of these results. Recent evidence suggests the involvement of the ubiquitous protein phosphatase 2B (calcineurin), a critical regulator of many signal transduction pathways, as a schizophrenia susceptibility gene. It is likely that genetic findings in severe psychiatric disorders will continue to implicate direct and indirect modulation of critical intracellular signaling pathways.

Using sex differences in psychopathology to study causal mechanisms: unifying issues and research strategies

BACKGROUND

Although there is an extensive literature, both speculative and empirical, on postulated differences between males and females in their rates of particular types of disorder, very little is known about the mechanisms that underlie these sex differences. The study of mechanisms is important because it may provide clues on aetiological processes. The review seeks to outline what is known, what are the methodological hazards that must be dealt with, and the research strategies that may be employed.

METHODS

We note the need for representative general samples, and for adequate measurement and significance testing if valid conclusions are to be drawn. We put forward three levels of causes that have to be considered: a genetically determined distal basic starting point; the varied consequences of being male or female; and the proximal risk or protective factors that are more directly implicated in the causal mechanisms that predispose to psychopathology. In delineating these, we argue that three key sets of evidential criteria have to be met: a) that the risk factors differ between males and females; b) that they provide for risk or protection within each sex; and c) that when introduced into a causal model, they eliminate or reduce the sex differences in the disorders being studied.

RESULTS

A male excess mainly applies to early onset disorders that involve some kind of neurodevelopmental impairment. A female excess mainly applies to adolescent-onset emotional disorders. No variables have yet met all the necessary criteria but some good leads are available. The possible research strategies that may be employed are reviewed.

CONCLUSIONS

The systematic investigation of sex differences constitutes an invaluable tool for the study of the causal processes concerned with psychopathology.

The Genetics of Adult-Onset Neuropsychiatric Disease: Complexities and Conundra?

Genetic factors play a major role in the etiology of adult-onset neurodegenerative and neuropsychiatric disorders. Several highly penetrant genes have been cloned for rare, autosomal-dominant, early-onset forms of neurodegenerative diseases. These genes have provided important insights into the mechanisms of these diseases (often altering neuronal protein processing). However, the genes associated with inherited susceptibility to late-onset neurodegenerative diseases, schizophrenia, and bipolar disorder appear to have smaller effects and are likely to interact with each other (and with nongenetic factors) to modulate susceptibility and/or disease phenotype. Several strategies have recently been applied to address this complexity, leading to the identification of a number of candidate susceptibility loci/genes.

Epigenetics and bipolar disorder: New opportunities and challenges

Despite significant effort, understanding of the molecular causes and mechanisms of bipolar disorder (BD) remains a major challenge. Numerous molecular genetic linkage and association studies have been conducted over the last two decades; however, the data are quite inconsistent or even controversial. This article develops an argument that molecular studies of BD would benefit significantly from adding an epigenetic (epiG) perspective. EpiG factors refer to modifications of DNA and chromatin that "orchestrate" the activity of the genome, including regulation of gene expression. EpiG mechanisms are consistent with various non-Mendelian features of BD such as the relatively high degree of discordance in monozygotic (MZ) twins, the critical age group for susceptibility to the disease, clinical differences in males and females, and fluctuation of the disease course, including interchanges of manic and depressive phases, among others. Apart from the phenomenological consistency, molecular epiG peculiarities may shed new light on the understanding of controversial molecular genetic findings. The relevance of epigenetics for the molecular studies of BD is demonstrated using the examples of genetic studies of BD on chromosome 11p and the X chromosome. A spectrum of epiG mechanisms such as genomic imprinting, tissue-specific effects, paramutagenesis, and epiG polymorphism, as well as epiG regulation of X chromosome inactivation, is introduced. All this serves the goal of demonstrating that epiG factors cannot be ignored anymore in complex phenotypes such as BD, and systematic large-scale epiG studies of BD have to be initiated.

Human endogenous retroviruses with transcriptional potential in the brain

Genetic studies of neuropsychiatric disorders have often produced conflicting results, which might partly result from the involvement of epigenetic modifications. We intended to explore the possible implication of DNA methylation and human endogenous retroviruses (HERVs) in neuropsychiatric disorders. In the present study, we identified two HERV loci that are expected to retain the transcriptional activity in the brain. One was located on chromosome 1q21-q22 and the other on 22q12. Interestingly, these regions were overlapped with or included in those of schizophrenia-susceptible loci, SCZD9 and SCZD4, respectively. Particularly, the HERV on 22q12 was located in the opposite direction 4 kb downstream of the Synapsin III gene. These HERV loci could afford clear targets for methylation and expression analyses in postmortem brains of patients with psychiatric disorders such as schizophrenia. In addition, we confirmed our previous finding that only a few of particular HERV-K loci were activated among a number of highly homologous loci in teratocarcinoma cell lines. These activated loci included ones common to all teratocarcinoma cell lines analyzed and depending on their male or female origin.

Impaired feedback regulation of XBP1 as a genetic risk factor for bipolar disorder

The pathophysiology of bipolar disorder is still unclear, although family, twin and linkage studies implicate genetic factors. Here we identified XBP1, a pivotal gene in the endoplasmic reticulum (ER) stress response, as contributing to the genetic risk factor for bipolar disorder. Using DNA microarray analysis of lymphoblastoid cells derived from two pairs of twins discordant with respect to the illness, we found downregulated expression of genes related to ER stress response in both affected twins. A polymorphism (-116C-->G) in the promoter region of XBP1, affecting the putative binding site of XBP1, was significantly more common in Japanese patients (odds ratio = 4.6) and overtransmitted to affected offspring in trio samples of the NIMH Bipolar Disorder Genetics Initiative. XBP1-dependent transcription activity of the -116G allele was lower than that of the -116C allele, and in the cells with the G allele, induction of XBP1 expression after ER stress was markedly reduced. Valproate, one of three mood stabilizers, rescued the impaired response by inducing ATF6, the gene upstream of XBP1. These results indicate that the -116C-->G polymorphism in XBP1 causes an impairment of its positive feedback system and increases the risk of bipolar disorder.

The application of functional genomics to Alzheimer's disease

Alzheimer's disease (AD) is a polygenic/complex disorder in which more than 50 genetic loci are involved. Primary and secondary loci are potentially responsible for the phenotypic expression of the disease under the influence of both environmental factors and epigenetic phenomena. The construction of haplotypes as genomic clusters integrating the different genotype combinations of AD-related genes is a suitable strategy to investigate functional genomics in AD. It appears that AD patients show about 3-5 times higher genetic variation than the control population. The analysis of genotype-phenotype correlations has revealed that the presence of the APOE-4 allele in AD, in conjunction with other loci distributed across the genome, influence disease onset, brain atrophy, cerebrovascular perfusion, blood pressure, beta-amyloid deposition, ApoE secretion, lipid metabolism, brain bioelectrical activity, cognition, apoptosis and treatment outcome. Pharmacogenomics studies also indicate that the therapeutic response in AD is genotype-specific and that approximately 15% of the cases with efficacy and/or safety problems are associated with a defective CYP2D6 gene. Consequently, the understanding of functional genomics in AD will foster productive pharmacogenomic studies in the search for effective medications and preventive strategies in AD.

Transposable elements: targets for early nutritional effects on epigenetic gene regulation

Early nutrition affects adult metabolism in humans and other mammals, potentially via persistent alterations in DNA methylation. With viable yellow agouti (A(vy)) mice, which harbor a transposable element in the agouti gene, we tested the hypothesis that the metastable methylation status of specific transposable element insertion sites renders them epigenetically labile to early methyl donor nutrition. Our results show that dietary methyl supplementation of a/a dams with extra folic acid, vitamin B(12), choline, and betaine alter the phenotype of their A(vy)/a offspring via increased CpG methylation at the A(vy) locus and that the epigenetic metastability which confers this lability is due to the A(vy) transposable element. These findings suggest that dietary supplementation, long presumed to be purely beneficial, may have unintended deleterious influences on the establishment of epigenetic gene regulation in humans.

Cell brain: a new focus in the postgenomic era

The centrosome, together with the embedded centrioles and connecting filaments, has come to be regarded as the 'brain' of a cell, analogous to the long known brain of an animal or a human being. It is through the 'brain' that different cellular activities are coordinated as a whole. In this article, comparative studies of the principles of life at varying levels and of the new roles of different cellular organelles in maintaining a healthy life for an organism provide further support to this theory, which is discussed based on the latest findings. Hopefully, this new theory can make a great contribution to break the paradigm of nucleus (or genes) as causes of all problems.

Imprinting evolution and the price of silence

In contrast to the biallelic expression of most genes, expression of genes subject to genomic imprinting is monoallelic and based on the sex of the transmitting parent. Possession of only a single active allele can lead to deleterious health consequences in humans. Aberrant expression of imprinted genes, through either genetic or epigenetic alterations, can result in developmental failures, neurodevelopmental and neurobehavioral disorders and cancer. The evolutionary emergence of imprinting occurred in a common ancestor to viviparous mammals after divergence from the egg-laying monotremes. Current evidence indicates that imprinting regulation in metatherian mammals differs from that in eutherian mammals. This suggests that imprinting mechanisms are evolving from those that were established 150 million years ago. Therefore, comparing genomic sequence of imprinted domains from marsupials and eutherians with those of orthologous regions in monotremes offers a potentially powerful bioinformatics approach for identifying novel imprinted genes and their regulatory elements. Such comparative studies will also further our understanding of the molecular evolution and phylogenetic distribution of imprinted genes.

Schizophrenia: from phenomenology to neurobiology

Schizophrenia is a common and debilitating illness, characterized by chronic psychotic symptoms and psychosocial impairment that exact considerable human and economic costs. The literature in electronic databases as well as citations and major articles are reviewed with respect to the phenomenology, pathology, treatment, genetics and neurobiology of schizophrenia. Although studied extensively from a clinical, psychological, biological and genetic perspective, our expanding knowledge of schizophrenia provides only an incomplete understanding of this complex disorder. Recent advances in neuroscience have allowed the confirmation or refutation of earlier findings in schizophrenia, and permit useful comparisons between the different levels of organization from which the illness has been studied. Schizophrenia is defined as a clinical syndrome that may include a collection of diseases that share a common presentation. Genetic factors are the most important in the etiology of the disease, with unknown environmental factors potentially modulating the expression of symptoms. Schizophrenia is a complex genetic disorder in which many genes may be implicated, with the possibility of gene-gene interactions and a diversity of genetic causes in different families or populations. A neurodevelopmental rather than degenerative process has received more empirical support as a general explanation of the pathophysiology, although simple dichotomies are not particularly helpful in such a complicated disease. Structural brain changes are present in vivo and post-mortem, with both histopathological and imaging studies in overall agreement that the temporal and frontal lobes of the cerebral cortex are the most affected. Functional imaging, neuropsychological testing and clinical observation are also generally consistent in demonstrating deficits in cognitive ability that correlate with abnormalities in the areas of the brain with structural abnormalities. The dopamine and other neurotransmitter systems are certainly involved in the treatment or modulation of psychotic symptoms. These broad findings represent the distillation of a large body of disparate data, but firm and specific findings are sparse, and much about schizophrenia remains unknown.

Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals

Cells of a multicellular organism are genetically homogeneous but structurally and functionally heterogeneous owing to the differential expression of genes. Many of these differences in gene expression arise during development and are subsequently retained through mitosis. Stable alterations of this kind are said to be 'epigenetic', because they are heritable in the short term but do not involve mutations of the DNA itself. Research over the past few years has focused on two molecular mechanisms that mediate epigenetic phenomena: DNA methylation and histone modifications. Here, we review advances in the understanding of the mechanism and role of DNA methylation in biological processes. Epigenetic effects by means of DNA methylation have an important role in development but can also arise stochastically as animals age. Identification of proteins that mediate these effects has provided insight into this complex process and diseases that occur when it is perturbed. External influences on epigenetic processes are seen in the effects of diet on long-term diseases such as cancer. Thus, epigenetic mechanisms seem to allow an organism to respond to the environment through changes in gene expression. The extent to which environmental effects can provoke epigenetic responses represents an exciting area of future research.

New phenotype of familial dilated cardiomyopathy and conduction disorders

BACKGROUND

Familial dilated cardiomyopathy (FDCM) is attributed to defects in cytoskeletal proteins, and different patterns of inheritance and phenotypic expressions according to assorted-protein modifications have been identified to date. We describe a clinical family study with 24 individuals in 3 generations affected by dilated cardiomyopathy (DCM) and cardiac conduction abnormalities.

METHODS AND RESULTS

After a follow-up period of 25 +/- 14 months, DCM developed in 7 male adults, 6 with associated arterioventricular block (AVB); and 10 female and 7 male adults had several degrees of isolated AVB. This particular clinical expression, with a strong predominance of dilation of the heart developing in the male population and the vertical distribution of patients affected with AVB, is consistent with autosomal dominant inheritance involving both cardiac abnormalities.

CONCLUSIONS

The presence of isolated AVB or that associated with DCM in a large number of individuals in the same family, in which members of the male sex seems to be predominantly affected by cardiac dilatation, differs from other FDCMs that have been described previously. This FDCM has an autosomal dominant pattern of inheritance with variable phenotypic expressivity, in which AVB may constitute in itself the only manifestation of this entity. To date, we have been unable to identify the mechanism of inheritance, and we advance some theoretical considerations about possible mechanisms.

Classical twin studies and beyond

Twin studies have been a valuable source of information about the genetic basis of complex traits. To maximize the potential of twin studies, large, worldwide registers of data on twins and their relatives have been established. Here, we provide an overview of the current resources for twin research. These can be used to obtain insights into the genetic epidemiology of complex traits and diseases, to study the interaction of genotype with sex, age and lifestyle factors, and to study the causes of co-morbidity between traits and diseases. Because of their design, these registers offer unique opportunities for selected sampling for quantitative trait loci linkage and association studies.

The Wnt signaling pathway in bipolar disorder

The Wnt signaling pathway is a highly conserved pathway critical for proper embryonic development. However, recent evidence suggests that this pathway and one of its key enzymes, glycogen synthase kinase 3beta, may play important roles in regulating synaptic plasticity, cell survival, and circadian rhythms in the mature CNS-all of which have been implicated in the pathophysiology and treatment of bipolar disorder. Furthermore, two structurally highly dissimilar medications used to treat bipolar disorder, lithium and valproic acid, exert effects on components of the Wnt signaling pathway. Together, these data suggest that the Wnt signaling pathway may play an important role in the treatment of bipolar disorder. Here, the authors review the modulation of the Wnt/GSK-3beta signaling pathway by mood-stabilizing agents, focusing on two therapeutically relevant aspects: neuroprotection and modulation of circadian rhythms. The future development of selective GSK-3beta inhibitors may have considerable utility not only for the treatment of bipolar disorder but also for a variety of classical neurodegenerative disorders.

Molecular genetic studies of schizophrenia: challenges and insights

Schizophrenia (SCZ) is a mental disease that affects approximately 1% of the population with life-long devastating consequences. Based on evidence for a major contribution of genetic factors, a decade of extensive efforts has been dedicated to the search of DNA sequence variations that increase the risk to SCZ. Search for genes in rare multiplex SCZ families with a large number of affected individuals and quasi-Mendelian mode of inheritance using genetic linkage methodology has been one of the favorite strategies in psychiatric genetics. Although several genomic regions were suggested for linkage to SCZ, not a single gene causing or predisposing to SCZ has been identified thus far. Furthermore, it is not clear whether the genes of familial SCZ are also involved in sporadic cases that represent the overwhelming majority of SCZ patients. For sporadic cases, genetic association studies comparing the distribution of allelic frequencies of candidate genes in SCZ patients and controls have been performed but the outcome of such studies has also been quite modest. Several factors such as possible involvement of numerous interactive genes of minor effect, yet unknown environmental effects and diagnostic ambiguities of the disease have made genetic studies in SCZ quite unproductive. In terms of future studies, a genome-wide association search is a promising approach; however, this approach requires genotyping of thousands of genetic markers in large samples. In addition, a detailed analysis of the genes, expression of which changes under the influence of environmental factors, can indicate good candidates for genetic association studies. In this connection, investigations of the epigenetic regulation of genes and not only the DNA sequence variation, may be necessary for complete understanding of the etiopathogenic mechanisms of SCZ.

Maternal methyl supplements in mice affect epigenetic variation and DNA methylation of offspring

This study was designed to determine if maternal dietary methyl supplements increase DNA methylation and methylation-dependent epigenetic phenotypes in mammalian offspring. Female mice of two strains were fed two levels of dietary methyl supplement or control diet prior to and during pregnancy. Offspring of these mice vary in phenotype, which is epigenetically determined and affects health and 2-y survival. Phenotype and DNA methylation of a long terminal repeat (LTR) controlling expression of the agouti gene were assayed in the resulting offspring. Methyl supplements increase the level of DNA methylation in the agouti LTR and change the phenotype of offspring in the healthy, longer-lived direction. This shows that methyl supplements have strong effects on DNA methylation and phenotype and are likely to affect long-term health. Optimum dietary supplements for the health and longevity of offspring should be intensively investigated. This should lead to public policy guidance that teaches optimal, rather than minimal, dose levels of maternal supplements.

Endophenotypes in bipolar disorder

The search for genes in bipolar disorder has provided numerous genetic loci that have been linked to susceptibility to developing the disorder. However, because of the genetic heterogeneity inherent in bipolar disorder, additional strategies may need to be employed to fully dissect the genetic underpinnings. One such strategy involves reducing complex behaviors into their component parts (endophenotypes). Abnormal neurophysiological, biochemical, endocrinological, neuroanatomical, cognitive, and neuropsychological findings are characteristics that often accompany psychiatric illness. It is possible that some of these may eventually be useful in subdefining complex genetic disorders, allowing for improvements in diagnostic assessment, genetic linkage studies, and development of animal models. Findings in patients with bipolar disorder that may eventually be useful as endophenotypes include abnormal regulation of circadian rhythms (the sleep/wake cycle, hormonal rhythms, etc.), response to sleep deprivation, P300 event-related potentials, behavioral responses to psychostimulants and other medications, response to cholinergics, increase in white matter hyperintensities (WHIs), and biochemical observations in peripheral mononuclear cells. Targeting circadian rhythm abnormalities may be a particularly useful strategy because circadian cycles appear to be an inherent evolutionarily conserved function in all organisms and have been implicated in the pathophysiology of bipolar disorder. Furthermore, lithium has been shown to regulate circadian cycles in diverse species, including humans, possibly through inhibition of glycogen synthase kinase 3-beta (GSK-3beta), a known target of lithium.

Epigenetics and DNA methylation come of age in toxicology

A wide variety of chemical and physical agents have the potential to produce adverse effects by causing heritable changes to the genome, resulting in heritable alterations in phenotype. These are often assumed to be a consequence of mutation. However, mutagenesis is not the only mechanism underlying heritable alterations to the genome. It is important to understand that there may also be an epigenetic basis for this. DNA methylation is the epigenetic mechanism that this review focuses upon. We indicate how altered methylation may play a key role in a variety of chemical-induced toxicities, including, but not limited to, carcinogenesis, and we point out how an assessment of methylation status can provide important information as a component of an overall safety assessment.

Gene-environment interplay in relation to emotional and behavioral disturbance

The conceptual and methodological issues involved in the study of gene-environment correlations (rGE) and interactions (GxE) are discussed in historical context. Quantitative genetic findings are considered with respect to rGE and GxE in relation to emotional and behavioral disturbance. Key conceptual and substantive implications are outlined in relation to both genetic and environmental risk mediation, with a brief note on evolutionary considerations.

The chromosome 1;11 translocation provides the best evidence supporting genetic etiology for schizophrenia and bipolar affective disorders

Genetics is assumed to cause susceptibility to psychosis, but no major locus has been identified. These disorders cosegregate with a chromosome 1;11 translocation in a Scottish pedigree where 50% of the carriers are diseased. A genetic model originally proposed to explain the basis of these illnesses predicts such an outcome.

Major psychosis and chromosome 22: genetics meets epigenetics

Elucidation of genetic factors in schizophrenia and bipolar disorder remains a challenging task to psychiatric researchers. As a rule, data from genetic linkage and association studies are quite controversial. In this article, we further explore the possibility that in addition to DNA sequences variation, a putative epigenetic dysregulation of brain genes plays an important role in the etiopathogenesis of major psychosis. We provide an epigenetic interpretation of unclear genetic findings specifically pertaining to chromosome 22 in schizophrenia and bipolar disorder. It is suggested that epigenetic strategies, when applied in conjunction with traditional genetic ones, may significantly expedite the uncovering of the molecular causes of major psychosis.

Pharmacogenomics for the treatment of dementia

Alzheimer's disease (AD) is a genetically complex disorder associated with multiple genetic defects either mutational or of susceptibility. Current AD genetics does not explain in full the etiopathogenesis of AD, suggesting that environmental factors and/or epigenetic phenomena may also contribute to AD pathology and phenotypic expression of dementia. The genomics of AD is still in its infancy, but is helping us to understand novel aspects of the disease including genetic epidemiology, multifactorial risk factors, pathogenic mechanisms associated with genetic networks and genetically-regulated metabolic cascades. AD genomics is also fostering new strategies in pharmacogenomic research and prevention. Functional genomics, proteomics, pharmacogenomics, high-throughput methods, combinatorial chemistry and modern bioinformatics will greatly contribute to accelerating drug development for AD and other complex disorders. The multifactorial genetic dysfunction in AD includes mutational loci (APP, PS1, PS2) and diverse susceptibility loci (APOE, A2M, AACT, LRP1, IL1A, TNF, ACE, BACE, BCHE, CST3, MTHFR, GSK3B, NOS3) distributed across the human genome, probably converging in common pathogenic mechanisms that lead to premature neuronal death. Genomic associations integrate polygenic matrix models to elucidate the genomic organization of AD in comparison to the control population. Using APOE-related monogenic models it has been demonstrated that the therapeutic response to drugs (e.g., cholinesterase inhibitors, non-cholinergic compounds) in AD is genotype-specific. A multifactorial therapy combining three different drugs yielded positive results during 6-12 months in approximately 60% of the patients. With this therapeutic strategy, APOE-4/4 carriers were the worst responders and patients with the APOE-3/4 genotype were the best responders. Other polymorphic variants (PS1, PS2) also influence the therapeutic response to different drugs in AD patients, suggesting that the final pharmacological outcome is the result of multiple genomic interactions, including AD-related genes and genes associated with drug metabolism, disposition, and elimination. The pharmacogenomics of AD may contribute in the future to optimise drug development and therapeutics, increasing efficacy and safety, and reducing side-effects and unnecessary costs.

Molecular genetics and the epidemiology of bipolar disorder

The methodologies of epidemiology and molecular genetics are complementary approaches to identifying risk factors in bipolar disorder. Genetic linkage studies have revealed several chromosomal loci likely to contain genes that increase the risk of bipolar disorder, but major uncertainties remain about the mode of inheritance of the condition and the definition of the phenotype. Epidemiological findings have contributed to both these areas and have led to new hypotheses about causation. For example, the analysis of variability of age at onset of bipolar disorder led to studies of anticipation and a possible role of dynamic DNA repeat sequence mutations. Future epidemiological studies that aim to identify risk factors for bipolar disorder at the population level will be able to measure the interactions of genome sequence variation with other risk factors in the domain of demography, childhood experiences, exposure to adversity and availability of social support.