DNA Modifications and Neurological Disorders

Mounting evidence has recently underscored the importance of DNA methylation in normal brain functions. DNA methylation machineries are responsible for dynamic regulation of methylation patterns in discrete brain regions. In addition to methylation of cytosines in genomic DNA (5-methylcytosine; 5mC), other forms of modified cytosines, such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, can potentially act as epigenetic marks that regulate gene expression. Importantly, epigenetic modifications require cognate binding proteins to read and translate information into gene expression regulation. Abnormal or incorrect interpretation of DNA methylation patterns can cause devastating consequences, including mental illnesses and neurological disorders. Although DNA methylation was generally considered to be a stable epigenetic mark in post-mitotic cells, recent studies have revealed dynamic DNA modifications in neurons. Such reversibility of 5mC sheds light on potential mechanisms underlying some neurological disorders and suggests a new route to correct aberrant methylation patterns associated with these disorders.     

A genetic approach to ischemic stroke therapy

Stroke therapy will undergo a great revolution in the present decade. The knowledge of the human genome, gene interactions and proteomics will permit a new concept of drug development for stroke. Gene therapy by modification of gene expression will be useful to treat atherosclerosis and hypertensive microangiopathy, or in the acute phase, we will manipulate the acute gene expression induced by ischemia or the apoptotic gene program. However, a single abnormal gene, as in monogenic diseases, is easier to replace than several genes in complex multigenic disorders. Gene therapy, stem cell therapy and neurological grafts for stroke are still in the experimental phase, and many hurdles will have to be jumped before the introduction of these therapies into human clinical stroke trials. A more immediate clinical application of genetics to stroke therapy is the development of pharmacogenetics that analyzes the influence of genetic variability of individuals on drug response. A new era of personalized therapy is dawning where specific DNA biochips will help stroke clinicians to decide on the better use of thrombolytics, neuroprotectants, antithrombotics, statins or antihypertensives.     

Polymorphic variation as a driver of differential neuropeptide gene expression

The regulation of neuropeptide gene expression and their receptors in a tissue specific and stimulus inducible manner will determine in part behaviour and physiology. This can be a dynamic process resulting from short term changes in response to the environment or long term modulation imposed by epigenetically determined mechanisms established during life experiences. The latter underpins what is termed ‘nature and nurture, or ‘gene × environment interactions’. Dynamic gene expression of neuropeptides or their receptors is a key component of signalling in the CNS and their inappropriate regulation is therefore a predicted target underpinning psychiatric disorders and neuropathological processes. Finding the regulatory domains within our genome which have the potential to direct gene expression is a difficult challenge as 98% of our genome is non-coding and, with the exception of proximal promoter regions, such elements can be quite distant from the gene that they regulate. This review will deal with how we can find such domains by addressing both the most conserved non-exonic regions in the genome using comparative genomics and the most recent or constantly evolving DNA such as repetitive DNA or retrotransposons. We shall also explore how polymorphic changes in such domains can be associated with CNS disorders by altering the appropriate gene expression patterns which maintain normal physiology.     

Deep sequencing reveals increased DNA methylation in chronic rat epilepsy

Epilepsy is a frequent neurological disorder, although onset and progression of seizures remain difficult to predict in affected patients, irrespective of their epileptogenic condition. Previous studies in animal models as well as human epileptic brain tissue revealed a remarkably diverse pattern of gene expression implicating epigenetic changes to contribute to disease progression. Here we mapped for the first time global DNA methylation patterns in chronic epileptic rats and controls. Using methyl-CpG capture associated with massive parallel sequencing (Methyl-Seq) we report the genomic methylation signature of the chronic epileptic state. We observed a predominant increase, rather than loss of DNA methylation in chronic rat epilepsy. Aberrant methylation patterns were inversely correlated with gene expression changes using mRNA sequencing from same animals and tissue specimens. Administration of a ketogenic, high-fat, low-carbohydrate diet attenuated seizure progression and ameliorated DNA methylation mediated changes in gene expression. This is the first report of unsupervised clustering of an epigenetic mark being used in epilepsy research to separate epileptic from non-epileptic animals as well as from animals receiving anti-convulsive dietary treatment. We further discuss the potential impact of epigenetic changes as a pathogenic mechanism of epileptogenesis.     

Epigenetische Pathomechanismen der Epileptogenese

Recent studies point to a pathogenic role of epigenetic chromatin modifications during epileptogenesis. Epigenetic mechanisms are covalent posttranslational modifications of histone proteins and DNA, which can produce lasting alterations in chromatin structure and gene expression. They are increasingly recognized as fundamental regulatory processes in central nervous system development, synaptic plasticity, and memory, and also play a role in neurological disorders, such as schizophrenia or spinal muscular atrophy. The authors propose that the “methylation hypothesis??addresses the intriguing issue of seizure-induced epigenetic chromatin modifications, which aggravate the epileptogenic condition by targeting candidate epileptogenesis gene expression. Unravelling epigenetic pathomechanisms will open also new strategies to identify molecular targets for pharmacological treatment in epilepsies. This project will be supported by EpiGENet, one of four consortia from the newly established European EuroEPINOMICS initiative.     

The future of genomic profiling of neurological diseases using blood

Sequencing of the human genome and new microarray technology make it possible to assess all genes on a single chip or array. Recent studies show different patterns of gene expression related to different tissues and diseases, and these patterns of gene expression are beginning to be used for diagnosis and treatment decisions in various types of lymphoid and solid malignancies. Because of obvious problems obtaining brain tissue, progress in genomics of neurological diseases has been slow. To address this, we demonstrated that different types of acute injury in rodent brain produced different patterns of gene expression in peripheral blood. These animal studies have now been extended to human studies. Two groups have shown that there are specific genomic profiles in the blood of patients after ischemic stroke that are highly sensitive and specific for predicting stroke. Other recent studies demonstrate specific genomic profiles in the blood of patients with Down syndrome, neurofibromatosis, tuberous sclerosis, Huntington disease, multiple sclerosis, Tourette syndrome, and others. In addition, data demonstrate specific profiles of gene expression in the blood related to different drugs, toxins, and infections. Although all of these studies are still preliminary basic scientific endeavors, they suggest that this approach will have clinical applications to neurological diseases in humans.     

Gene expression profiling in multiple sclerosis brain

Multiple sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system and the leading cause of non-traumatic neurological disability in young adults in the United States and Europe. The clinical disease course is variable and starts with reversible episodes of neurological disability in the third or fourth decade of life. Microarray-based comparative gene profiling provides a snapshot of genes underlying a particular condition. Several large scale microarray studies have been conducted using brain tissue from MS patients. In this review, we summarize existing data from different gene expression profiling studies and how they relate to understand the pathogenesis of MS.     

Brain aromatase: new lessons from non-mammalian model systems

This review highlights recent studies of the anatomical and functional implications of brain aromatase (estrogen synthase) expression in two vertebrate lineages, teleost fishes and songbirds, that show remarkably high levels of adult brain aromatase activity, protein and gene expression compared to other vertebrate groups. Teleosts and birds have proven to be important neuroethological models for investigating how local estrogen synthesis leads to changes in neural phenotypes that translate into behavior. Region-specific patterns of aromatase expression, and thus estrogen synthesis, include the vocal and auditory circuits that figure prominently into the life history adaptations of vocalizing teleosts and songbirds. Thus, by targeting, for example, vocal motor circuits without inappropriate steroid exposure to other steroid-dependent circuits, such as those involved in either copulatory or spawning behaviors, the neuroendocrine system can achieve temporal and spatial specificity in its modulation of neural circuits that lead to the performance of any one behavior.     

Mitochondrial Etiology of Neuropsychiatric Disorders

The brain has the highest mitochondrial energy demand of any organ. Therefore, subtle changes in mitochondrial energy production will preferentially affect the brain. Considerable biochemical evidence has accumulated revealing mitochondrial defects associated with neuropsychiatric diseases. Moreover, the mitochondrial genome encompasses over a thousand nuclear DNA genes plus hundreds to thousands of copies of the maternally inherited mitochondrial DNA (mtDNA). Therefore, partial defects in either the nuclear DNA or mtDNA genes or combinations of the two can be sufficient to cause neuropsychiatric disorders. Inherited and acquired mtDNA mutations have recently been associated with autism spectrum disorder, which parallels previous evidence of mtDNA variation in other neurological diseases. Therefore, mitochondrial dysfunction may be central to the etiology of a wide spectrum of neurological diseases. The mitochondria and the nucleus communicate to coordinate energy production and utilization, providing the potential for therapeutics by manipulating nuclear regulation of mitochondrial gene expression.     

Rem2 signaling affects neuronal structure and function in part by regulation of gene expression

The central nervous system has the remarkable ability to convert changes in the environment in the form of sensory experience into long-term alterations in synaptic connections and dendritic arborization, in part through changes in gene expression. Surprisingly, the molecular mechanisms that translate neuronal activity into changes in neuronal connectivity and morphology remain elusive. Rem2, a member of the Rad/Rem/Rem2/Gem/Kir (RGK) subfamily of small Ras-like GTPases, is a positive regulator of synapse formation and negative regulator of dendritic arborization. Here we identify that one output of Rem2 signaling is the regulation of gene expression. Specifically, we demonstrate that Rem2 signaling modulates the expression of genes required for a variety of cellular processes from neurite extension to synapse formation and synaptic function. Our results highlight Rem2 as a unique molecule that transduces changes in neuronal activity detected at the cell membrane to morphologically relevant changes in gene expression in the nucleus.     

Neuronal Apoptosis Revealed by Genomic Analysis: Integrating Gene Expression Profiles with Functional Information

Apoptosis is a key physiological response that occurs during development of the nervous system, resulting in the death of nearly half of the embryonic neuronal population. Aberrant apoptotic mechanisms are thought to contribute significantly to many neurological disorders including Alzheimer’s disease. Although many experiments in the past have demonstrated the requirement of de novo gene expression during neuronal apoptosis, the complete spectrum of genes involved in distinct temporal domains is mostly unknown. To begin a comprehensive survey of the gene-based molecular mechanisms that underlie neuronal apoptosis, we have used the unprecedented experimental opportunities that genome sequences and the development of DNA microarray technology now provide to perform genome-wide expression analysis in different paradigms of neuronal apoptosis. In order to extract knowledge from gene expression information we have developed new informatics applications that enable clustering methods based on semantic characteristics, such as gene ontologies. This review will highlight the use of a genomic approach to identify the molecular program underlying neuronal apoptosis and illustrate how a semantic clustering method can be useful to extract more knowledge from microarray data.     

Epigenetics in psychiatry: Beyond DNA methylation

The global burden of psychopathologies appears to be underestimated, since the global psychiatric disorder burden is exceeding other medical burdens. To be able to address this problem more effectively, we need to better understand the etiology of psychiatric disorders. One of the hallmarks of psychiatric disorders appears to be epigenetic dysregulation. While some epigenetic modifications (such as DNA methylation) are well known and studied, the roles of others have been investigated much less. DNA hydroxymethylation is a rarely studied epigenetic modification, which as well as being an intermediate stage in the DNA demethylation cycle is also an independent steady cell state involved in neurodevelopment and plasticity. In contrast to DNA methylation, DNA hydroxymethylation appears to be related to an increase in gene expression and subsequent protein expression. Although no particular gene or genetic locus can be at this point linked to changes in DNA hydroxymethylation in psychiatric disorders, the epigenetic marks present good potential for biomarker identification because the epigenetic landscape is a result of the interplay between genes and environment, which both influence the development of psychiatric disorders, and because hydoxymethylation changes are particularly enriched in the brain and in synapse-related genes.     

Evolution of the nervous system: a critical evaluation of how genetic changes translate into morphological changes

Living creatures evolve, and this evolution allows them to adapt to an ever-changing milieu. Two main adaptive strategies coexist. The first involves genetic mutations taking place at the species level. The second strategy occurs at the individual level, and primarily involves changes in chromatin organization and brain circuits. We shall illustrate how the two modes of adaptation are interdependent, and will show the difference in their respective importance depending on the species. It will be proposed that changes in developmental strategies, genetically selected, can lead to more or less epigenetic freedom, sometimes with dramatic consequences. In particular it will be shown, taking chimpanzees and humans as examples, how minor genetic modifications can translate into nonlinear changes in brain structure and cultural practices, placing the two types of primates at a much greater distance than had been anticipated.     

Steroids in Duchenne muscular dystrophy: from clinical trials to genomic research

Steroids represent the only pharmacological palliative treatment for Duchenne muscular dystrophy. However, they do have side effects and despite a large number of published studies showing their efficacy, they are still not universally used. This is largely due to the lack of functional outcome and quality of life measures in most of the published studies and suggests that further trials might be required to answer some of the still unclear aspects of their role. Another important aspect of steroid therapy in Duchenne dystrophy is that we do not know how they work in dystrophic muscle. We have initiated a collaborative study on gene profiling using microarray in steroid-treated mdx mice. cDNA microarray studies were performed to examine the levels of skeletal muscle gene expression in a pool of mdx mice treated with prednisolone for 1 and 6 weeks. Interesting preliminary data on untreated mdx mice suggest that the gene profiling of young (7 weeks) versus older (12 weeks) mice is very significantly different. Furthermore, a large number of genes showed significant changes in expression at the mRNA level on treatment with prednisolone. These included structural protein genes; signalling genes and genes involved in immune response. Hopefully, analysis of this pattern of steroid-induced gene expression will provide some insight into understanding how glucocorticoids improve strength in Duchenne dystrophy, and may help in developing more effective and less toxic therapeutic approaches.     

Neurology and the Internet: a review

Nowadays, the Internet is the major source to obtain information about diseases and their treatments. The Internet is gaining relevance in the neurological setting, considering the possibility of timely social interaction, contributing to general public awareness on otherwise less-well-known neurological conditions, promoting health equity and improving the health-related coping. Neurological patients can easily find several online opportunities for peer interactions and learning. On the other hand, neurologist can analyze user-generated data to better understand patient needs and to run epidemiological studies. Indeed, analyses of queries from Internet search engines on certain neurological diseases have shown a strict temporal and spatial correlation with the “real world.” In this narrative review, we will discuss how the Internet is radically affecting the healthcare of people with neurological disorders and, most importantly, is shifting the paradigm of care from the hands of those who deliver care, into the hands of those who receive it. Besides, we will review possible limitations, such as safety concerns, financial issues, and the need for easy-to-access platforms.