Gene expression profile analyses of cortical dysplasia by cDNA arrays

Whole Transcriptome Screening Reveals Myelination Deficits in Dysplastic Human Temporal Neocortex

Focal cortical dysplasias (FCDs) are local malformations of the human neocortex with strong epileptogenic potential. To investigate the underlying pathomechanisms, we performed a whole human transcriptome screening to compare the gene expression pattern of dysplastic versus nondysplastic temporal neocortex. Tissue obtained from FCD IIIa cases (mean age 20.5 years) who had undergone surgical treatment, due to intractable epilepsy, was compared with nondysplastic specimens (mean age 19.9 years) by means of Affymetrix arrays covering 28 869 genes. We found 211 differentially expressed genes (DEX) among which mainly genes important for oligodendrocyte differentiation and myelination were downregulated in FCD IIIa. These findings were confirmed as functionally important by Database for Annotation, Visualization, and Integrated Discovery (DAVID) analysis. The reduced expression of myelin-associated transcripts was confirmed for FCD Ia, IIa, and IIIa by real-time RT-qPCR. In addition, we found that the density of myelin basic protein mRNA-expressing oligodendrocytes and of 2',3'-cyclic nucleotide 3'-phosphodiesterase-positive myelin fibers was significantly reduced in dysplastic cortex. Moreover, high-resolution confocal imaging and 3D reconstruction revealed that the myelin fiber network was severely disorganized in dysplastic neocortex, indicating a disturbance of myelin sheath formation and maintenance in FCD.

Key proteins of activating cell death can be predicted through a kainic acid-induced excitotoxic stress

Epilepsy is a major neurological disorder characterized by spontaneous seizures accompanied by neurophysiological changes. Repeated seizures can damage the brain as neuronal death occurs. A better understanding of the mechanisms of brain cell death could facilitate the discovery of novel treatments for neurological disorders such as epilepsy. In this study, a model of kainic acid- (KA-) induced neuronal death was established to investigate the early protein markers associated with apoptotic cell death due to excitotoxic damage in the rat cortex. The results indicated that KA induces both apoptotic and necrotic cell death in the cortex. Incubation with high concentrations (5 and 500 μM, >75%) and low concentrations (0.5 pM: 95% and 50 nM: 8%) of KA for 180 min led to necrotic and apoptotic cell death, respectively. Moreover, proteomic analysis using two-dimensional gel electrophoresis and mass spectrometry demonstrated that antiapoptotic proteins, including heat shock protein 70, 3-mercaptopyruvate sulfurtransferase, tubulin-B-5, and pyruvate dehydrogenase E1 component subunit beta, were significantly higher in apoptosis than in necrosis induced by KA. Our findings provide direct evidence that several proteins are associated with apoptotic and necrotic cell death in excitotoxicity model. The results indicate that these proteins can be apoptotic biomarkers from the early stages of cell death.

Gene expression profile analysis in epilepsy by using the partial least squares method

PURPOSE

Epilepsy is a common chronic neurological disorder. We aim to investigate the underlying mechanism of epilepsy with partial least squares- (PLS-) based gene expression analysis, which is more sensitive than routine variance/regression analysis.

METHODS

Two microarray data sets were downloaded from the Gene Expression Omnibus (GEO) database. PLS analysis was used to identify differentially expressed genes. Gene ontology and network analysis were also implemented.

RESULTS

A total of 752 genes were identified to be differentially expressed, including 575 depressed and 177 overexpressed genes in patients. For GO enrichment analysis, except for processes related to the nervous system, we also identified overrepresentation of dysregulated genes in angiogenesis. Network analysis revealed two hub genes, CUL3 and EP300, which may serve as potential targets in further therapeutic studies.

CONCLUSION

Our results here may provide new understanding for the underlying mechanisms of epilepsy pathogenesis and will offer potential targets for producing new treatments.

Astrocyte immune responses in epilepsy

Astrocytes, the major glial cell type of the central nervous system (CNS), are known to play a major role in the regulation of the immune/inflammatory response in several human CNS diseases. In epilepsy-associated pathologies, the presence of astrogliosis has stimulated extensive research focused on the role of reactive astrocytes in the pathophysiological processes that underlie the development of epilepsy. In brain tissue from patients with epilepsy, astrocytes undergo significant changes in their physiological properties, including the activation of inflammatory pathways. Accumulating experimental evidence suggests that proinflammatory molecules can alter glio-neuronal communications contributing to the generation of seizures and seizure-related neuronal damage. In particular, both in vitro and in vivo data point to the role of astrocytes as both major source and target of epileptogenic inflammatory signaling. In this context, understanding the astroglial inflammatory response occurring in epileptic brain tissue may provide new strategies for targeting astrocyte-mediated epileptogenesis. This article reviews current evidence regarding the role of astrocytes in the regulation of the innate immune responses in epilepsy. Both clinical observations in drug-resistant human epilepsies and experimental findings in clinically relevant models will be discussed and elaborated, highlighting specific inflammatory pathways (such as interleukin-1β/toll-like receptor 4) that could be potential targets for antiepileptic, disease-modifying therapeutic strategies.

Impaired social recognition memory in recombination activating gene 1-deficient mice

The recombination activating genes (RAGs) encode two enzymes that play key roles in the adaptive immune system. RAG1 and RAG2 mediate VDJ recombination, a process necessary for the maturation of B- and T-cells. Interestingly, RAG1 is also expressed in the brain, particularly in areas of high neural density such as the hippocampus, although its function is unknown. We tested evidence that RAG1 plays a role in brain function using a social recognition memory task, an assessment of the acquisition and retention of conspecific identity. In a first experiment, we found that RAG1-deficient mice show impaired social recognition memory compared to mice wildtype for the RAG1 allele. In a second experiment, by breeding to homogenize background genotype, we found that RAG1-deficient mice show impaired social recognition memory relative to heterozygous or RAG2-deficient littermates. Because RAG1 and RAG2 null mice are both immunodeficient, the results suggest that the memory impairment is not an indirect effect of immunological dysfunction. RAG1-deficient mice show normal habituation to non-socially derived odors and habituation to an open-field, indicating that the observed effect is not likely a result of a general deficit in habituation to novelty. These data trace the origin of the impairment in social recognition memory in RAG1-deficient mice to the RAG1 gene locus and implicate RAG1 in memory formation.

Gene expression analysis of tuberous sclerosis complex cortical tubers reveals increased expression of adhesion and inflammatory factors

Cortical tubers in patients with tuberous sclerosis complex are associated with disabling neurological manifestations, including intractable epilepsy. While these malformations are believed to result from the effects of TSC1 or TSC2 gene mutations, the molecular mechanisms leading to tuber formation, as well as the onset of seizures, remain largely unknown. We used the Affymetrix Gene Chip platform to provide the first genome-wide investigation of gene expression in surgically resected tubers, compared with histological normal perituberal tissue from the same patients or autopsy control tissue. We identified 2501 differentially expressed genes in cortical tubers compared with autopsy controls. Expression of genes associated with cell adhesion, for example, VCAM1, integrins and CD44, or with the inflammatory response, including complement factors, serpinA3, CCL2 and several cytokines, was increased in cortical tubers, whereas genes related to synaptic transmission, for example, the glial glutamate transporter GLT-1, and voltage-gated channel activity, exhibited lower expression. Gene expression in perituberal cortex was distinct from autopsy control cortex suggesting that even in the absence of tissue pathology the transcriptome is altered in TSC. Changes in gene expression yield insights into new candidate genes that may contribute to tuber formation or seizure onset, representing new targets for potential therapeutic development.

Expression and localization of voltage dependent potassium channel Kv4.2 in epilepsy associated focal lesions

An increasing number of observations suggest an important role for voltage-gated potassium (Kv) channels in epilepsy. We studied the cell-specific distribution of Kv4.2, phosphorylated (p) Kv4.2 and the Kv4.2 interacting protein NCS-1 using immunocytochemistry in different epilepsy-associated focal lesions. In hippocampal sclerosis (HS), Kv4.2 and pKv4.2 immunoreactivity (IR) was reduced in the neuropil in regions with prominent neuronal cell loss. In both HS and malformations of cortical development (MCD), intense labeling was found in neuronal somata, but not in dendrites. Strong NCS-1 IR was observed in neurons in all lesion types. Western blot analysis demonstrated an increase of total Kv4.2 in all lesions and activation of the ERK pathway in HS and ganglioglioma. These findings indicate that Kv4.2 is expressed in both neuronal and glial cells and its regulation may involve potassium channel interacting proteins, alterations in the subcellular localization of the channel, as well as phosphorylation-mediated posttranslational modifications.

Immune and nervous systems share molecular and functional similarities: memory storage mechanism

One of the most complex and important features of both the nervous and immune systems is their data storage and retrieval capability. Both systems encounter a common and complex challenge on how to overcome the cumbersome task of data management. Because each neuron makes many synapses with other neurons, they are capable of receiving data from thousands of synaptic connections. The immune system B and T cells have to deal with a similar level of complexity because of their unlimited task of recognizing foreign antigens. As for the complexity of memory storage, it has been proposed that both systems may share a common set of molecular mechanisms. Here, we review the molecular bases of memory storage in neurons and immune cells based on recent studies and findings. The expression of certain molecules and mechanisms shared between the two systems, including cytokine networks, and cell surface receptors, are reviewed. Intracellular signaling similarities and certain mechanisms such as diversity, memory storage, and their related molecular properties are briefly discussed. Moreover, two similar genetic mechanisms used by both systems is discussed, putting forward the idea that DNA recombination may be an underlying mechanism involved in CNS memory storage.

Array analysis of epilepsy-associated gangliogliomas reveals expression patterns related to aberrant development of neuronal precursors

Gangliogliomas, the most frequent neoplasms in patients with pharmacoresistant focal epilepsies, are characterized by histological combinations of glial and dysplastic neuronal elements, a highly differentiated phenotype and rare gene mutations. Their molecular basis and relationship to other low-grade brain tumours are not completely understood. Systematic investigations of altered gene expression in gangliogliomas have been hampered by their cellular complexity, the lack of suitable control tissue and of sensitive expression profiling approaches. Here, we have used discrete microdissected ganglioglioma and adjacent control brain tissue obtained from the neurosurgical access to the tumour of identical patients (n = 6) carefully matched for equivalent glial and neuronal elements in an amount sufficient for oligonucleotide microarray hybridization without repetitive amplification. Multivariate statistical analysis identified a rich profile of genes with altered expression in gangliogliomas. Many differentially expressed transcripts related to intra- and intercellular signalling including protein kinase C and its target NELL2 in identical ganglioglioma cell components as determined by real-time quantitative RT-PCR (qRT-PCR) and in situ hybridization. We observed the LIM-domain-binding 2 (LDB2) transcript, critical for brain development during embryogenesis, as one of the strongest reduced mRNAs in gangliogliomas. Subsequent qRT-PCR in dysembryoplastic neuroepithelial tumours (n = 7) revealed partial expression similarities as well as marked differences from gangliogliomas. The demonstrated gene expression profile differentiates gangliogliomas from other low-grade primary brain tumours. shRNA-mediated silencing of LDB2 resulted in substantially aberrant dendritic arborization in cultured developing primary hippocampal neurons. The present data characterize novel molecular mechanisms operating in gangliogliomas that contribute to the development of dysplastic neurons and an aberrant neuronal network.

Gene expression profile analysis of epilepsy-associated gangliogliomas

Gangliogliomas (GG) constitute the most frequent tumor entity in young patients undergoing surgery for intractable epilepsy. The histological composition of GG, with the presence of dysplastic neurons, corroborates their maldevelopmental origin. However, their histogenesis, the pathogenetic relationship with other developmental lesions, and the molecular alterations underlying the epileptogenicity of these tumors remain largely unknown. We performed gene expression analysis using the Affymetrix Gene Chip System (U133 plus 2.0 array). We used GENMAPP and the Gene Ontology database to identify global trends in gene expression data. Our analysis has identified various interesting genes and processes that are differentially expressed in GG when compared with normal tissue. The immune and inflammatory responses were the most prominent processes expressed in GG. Several genes involved in the complement pathway displayed a high level of expression compared with control expression levels. Higher expression was also observed for genes involved in cell adhesion, extracellular matrix and proliferation processes. We observed differential expression of genes as cyclin D1 and cyclin-dependent kinases, essential for neuronal cell cycle regulation and differentiation. Synaptic transmission, including GABA receptor signaling was an under-expressed process compared with control tissue. These data provide some suggestions for the molecular pathogenesis of GG. Furthermore, they indicate possible targets that may be investigated in order to dissect the mechanisms of epileptogenesis and possibly counteract the epileptogenic process in these developmental lesions.

Pathophysiological mechanisms of focal cortical dysplasia: a critical review of human tissue studies and animal models

Cortical dysplasia (CD, also known as malformations of cortical development) are the pathological substrates in a large percentage of patients with pharmacoresistant epilepsy who may be amenable to surgical treatment. Therefore, research on the mechanisms of dysplastic lesion formation and epileptogenicity is of paramount importance for the prevention, detection, and treatment of CD-induced epilepsy. The purpose of this review is to discuss and critically evaluate the current state and results of human tissue experimentation (focusing on reported results of studies done on neocortical dysplastic tissue resected from patients with pharmacoresistant epilepsy), and to discuss some of the concerns related to research that uses surgically resected epileptic human tissue. The use of better animal models of CD as a tool toward the better understanding of the mechanisms of pathogenesis, epileptogenesis, and epileptogenicity of dysplastic lesions will be reviewed from the perspective of their usefulness in a model of translational research that should ultimately result in better diagnostic and therapeutic techniques of CD.

Gene expression, genetics, and genomics in epilepsy: some answers, more questions

The rapid technical progress made in molecular genetics has provided new strategies to study the molecular pathogenesis of human epilepsy. In particular, the abilities to assay the expression of many thousands of genes simultaneously with cDNA or oligonucleotide arrays and to rapidly screen thousands of DNA basepairs permits exciting insights into how human epilepsy may result from alterations in gene transcription and sequence. These approaches can show how monogenic and even complex genetic disorders lead to network alterations and seizures. Most recently, investigation of single nucleotide polymorphisms (SNPs) has shown that even subtle alterations in gene sequence across the genome can raise or lower seizure threshold. Clearly, there is a complex interplay between gene expression, genetics, and genomics which ultimately leads to seizure onset and epilepsy. Identifying the contribution that each plays in epileptogenesis may help define new therapeutic targets.

Genetic association studies in epilepsy pharmacogenomics: lessons learnt and potential applications

Although epilepsy is one of the most common neurological disorders and genetic factors are well known to play a role in response to antiepileptic drug (AED) treatment, the study of the pharmacogenetics of epilepsy has received relatively little attention and has not resulted in clinical applications to date. Our improved understanding of the pathogenesis of epilepsy and the mechanism of action of AEDs, together with recent advances in genetics and decreasing genotyping costs, have now paved the way for a more systematic application of pharmacogenetics in the field of epilepsy. It is hoped that the resulting knowledge will lead to a more rational treatment of epilepsy, development of more efficacious AEDs, and facilitation of clinical trials of new AEDs. However, there are formidable practical, methodological and theoretical hurdles to overcome before pharmacogenomic information will have any major utility in the clinical setting. Here, we discuss the evidence for a genetic contribution to AED response, review current knowledge in epilepsy pharmacogenetics and discuss potential future avenues with their implications, both for the clinical treatment of epilepsy and new AED development.

The potential of pharmacogenetics in the treatment of epilepsy

Pharmacogenetics studies how genetic variants influence individual drug responses. Although pharmacogenetics is currently the subject of intensive research in several disease domains, it remains relatively unexplored in the field of epilepsy. Drug treatment of epilepsy is characterized by unpredictability of efficacy, adverse drug reactions and optimal doses in individual patients. Moreover, a substantial fraction of patients develop drug refractory epilepsy despite optimal treatment. Insights in the pathogenesis of epilepsy and the mechanisms of action of antiepileptic drugs (AEDs) have improved our understanding of the genetic determinants of AED response. The first reports in epilepsy pharmacogenetics are becoming available, and large-scale pharmacogenetic studies are now possible thanks to recent advances in genetics and decreasing genotyping costs. It is hoped that ultimately, findings in epilepsy pharmacogenetics will lead to a more efficacious and less harmful treatment of epilepsy, development of more effective AEDs and facilitation of clinical trials of new AEDs. However, although pharmacogenetics will undoubtedly improve our insight into the mechanisms underlying response to AEDs and perhaps into the pathogenesis of drug refractory epilepsy, clinical application of any findings is expected to be a long process, and considerable practical and theoretical hurdles need to be overcome before pharmacogenetic information will prove of any major utility in the clinical setting. This review addresses current knowledge on genetic factors contributing to AED response and discusses the potential of epilepsy pharmacogenetics in the clinical treatment of epilepsy and new AED development.

HuR mRNA ligands expressed after seizure

HuR is a ubiquitously expressed AU-rich element (ARE)-binding protein that interacts with and stabilizes selective early response gene (ERG) mRNAs after cell activation or stress. To date, approximately 20 mRNAs have been unambiguously defined as HuR ligands. Given the discordance between the large number of ERG mRNAs and those few defined as ligands, we applied in vitro selection to isolate a broad range of HuR mRNA ligands using postseizure mouse hippocampal tissue. Selected mRNAs were converted into cDNA libraries and sequenced. Using this approach, we have identified over 600 novel, putative HuR mRNA ligands. These genes code for a variety of proteins, including transcription factors, signaling molecules, and kinases, but many have unknown function. Consistent with the means of their selection, several of these HuR ligands are differentially expressed in hippocampus after seizure. These results demonstrate a biochemical approach to identify and characterize the diverse repertoire of ligands for HuR and other regulatory mRNA-binding proteins.

Epileptogenesis-related genes revisited

The main goal of this study was to identify common features in the molecular response to epileptogenic stimuli across different animal models of epileptogenesis. Therefore, we compared the currently available literature on the global analysis of gene expression following epileptogenic insult to search for (i) highly represented functional gene classes (GO terms) within data sets, and (ii) individual genes that appear in several data sets, and therefore, might be of particular importance for the development of epilepsy due to different etiologies. We focused on two well-described models of brain insult that induce the development of spontaneous seizures in experimental animals: status epilepticus and traumatic brain injury. Additionally, a few papers describing gene expression in rat and human epileptic tissue were included for comparison. Our analysis revealed that epileptogenic insults induce significant changes in gene expression within a subset of pre-defined GO terms, that is, in groups of functionally linked genes. We also found individual genes for which expression changed across different models of epileptogenesis. Alterations in gene expression appear time-specific and underlie a number of processes that are linked with epileptogenesis, such as cell death and survival, neuronal plasticity, or immune response. Particularly, our analysis highlighted alterations in gene expression in glial cells as well as in genes involved in the immune response, which suggests the importance of gliosis and immune reaction in epileptogenesis.

T cell deficiency leads to cognitive dysfunction: implications for therapeutic vaccination for schizophrenia and other psychiatric conditions

The effects of the adaptive immune system on the cognitive performance and abnormal behaviors seen in mental disorders such as schizophrenia have never been documented. Here, we show that mice deprived of mature T cells manifested cognitive deficits and behavioral abnormalities, which were remediable by T cell restoration. T cell-based vaccination, using glatiramer acetate (copolymer-1, a weak agonist of numerous self-reactive T cells), can overcome the behavioral and cognitive abnormalities that accompany neurotransmitter imbalance induced by (+)dizocilpine maleate (MK-801) or amphetamine. The results, by suggesting that peripheral T cell deficit can lead to cognitive and behavioral impairment, highlight the importance of properly functioning adaptive immunity in the maintenance of mental activity and in coping with conditions leading to cognitive deficits. These findings point to critical factors likely to contribute to age- and AIDS-related dementias and might herald the development of a therapeutic vaccination for fighting off cognitive dysfunction and psychiatric conditions.