N-myc and c-myc expression in Alzheimer disease, Huntington disease and Parkinson disease

Identification of Alzheimer's disease susceptibility genes by the integration of genomics and transcriptomics

BACKGROUND

Alzheimer's disease (AD) is a progressive neurodegenerative disease. With the deepening of clinical and genomic research, a series of biomarkers and risk factors related to AD have been identified. However, the exact molecular mechanism of AD is not completely understood.

METHODS

By combining expression quantitative trait loci (eQTLs) analysis with the results of genome-wide association studies (GWAS), the candidate genes (CG) related to AD were screened out accurately. We identified that intersection genes of differentially expressed genes (DEGs) and CG are the key genes. Then, GO, KEGG, and GSEA were utilized for functional enrichment analysis. Finally, we predicted AD responses to immunotherapy by the single sample gene set enrichment analysis (ssGSEA).

RESULTS

A total of 253 DEGs were identified. The three key genes (VASP, SURF2, and TARBP1) were identified by taking the intersection of DEGs and CG. Through Mendelian randomization (MR) analysis, it was found that the risk of AD was significantly increased when VASP expression increased (OR = 0.1.046), while the risk of AD was significantly decreased when SURF2 (OR = 0.897) and TARBP1(OR = 0.920) expression increased. Subsequently, the functional analysis indicated that the core genes were mainly enriched in Leukocyte Transendothelial Migration, cGMP-PKG signaling pathway, and Rap1 signaling pathway. Through ssGSEA analysis showed that all three core genes were significantly related to M2 macrophages.

CONCLUSIONS

Three core genes were screened by integrating eQTLs data, GWAS data and transfer group data, and the potential mechanism of diagnosis and treatment of AD was revealed.

Activation of Nuclear Factor-kappa B in the nucleus accumbens core is necessary for chronic stress-induced glutamate and neuro-immune alterations that facilitate cocaine self-administration

Stressful events are associated with impaired glutamate signaling and neuroimmune adaptations that may increase the vulnerability of individuals to cocaine addiction. We previously demonstrated that chronic stress induced reactive microglia and increased TNF-α expression in the nucleus accumbens core (NAcore), both alterations strongly linked with impaired glutamate homeostasis and the facilitation of cocaine self-administration. The nuclear factor kappa-B (NF-κB) is a critical regulator of many immune- and addiction-related genes, such as the gene coding for glutamate transporter (GLT-1), and it is considered a master regulator of inflammation, reported to be a key driver of microglia activation in psychiatric diseases. However, no studies have examined the role of NF-κB signaling within the NAcore in the neuroimmune and glutamate mechanism, underpinning stress-induced vulnerability to cocaine self-administration. Here we investigate whether viral dominant negative inhibition of I kappa B kinase (IKKdn), a signaling molecule responsible for NF-κB activation, would prevent stress-induced facilitation to cocaine self-administration and associated changes in accumbal GLT-1 and TNF-α expression. We also explore N-myc proto-oncogene protein (N-myc) levels as a link between NF-κB and stress-induced GLT-1 downregulation. For seven days (days 1-7), adult male rats were restrained for 2 h/day. Animals were administered an intra-NAcore with IKKdn or empty lentiviruses on day 14 after the first restraint stress session. Marked activation of NF-κB was detected in the NAcore of stressed subjects, along with increased NF-κB expression in astrocytes. Consistently, viral NF-κB inhibition prevented stress-induced facilitation of cocaine self-administration. Moreover, NF-κB blockade results in the restoration of stress-induced reduction in GLT-1 levels and was effective in suppressing stress-induced TNF-α within the NAcore. These findings suggest that accumbal NF-κB signaling exerts a central control over stress-altered downstream neuroimmune and glutamate function underlying vulnerability to cocaine use disorders.

Brain Plasticity and Cell Competition: Immediate Early Genes Are the Focus

Brain plasticity is at the basis of many cognitive functions, including learning and memory. It includes several mechanisms of synaptic and extrasynaptic changes, neurogenesis, and the formation and elimination of synapses. The plasticity of synaptic transmission involves the expression of immediate early genes (IEGs) that regulate neuronal activity, thereby supporting learning and memory. In addition, IEGs are involved in the regulation of brain cells' metabolism, proliferation, and survival, in the establishment of multicellular ensembles, and, presumably, in cell competition in the tissue. In this review, we analyze the current understanding of the role of IEGs (c-Fos, c-Myc, Arg3.1/Arc) in controlling brain plasticity in physiological and pathological conditions, including brain aging and neurodegeneration. This work might inspire new gene therapy strategies targeting IEGs to regulate synaptic plasticity, and potentially prevent or mitigate neurodegenerative diseases.

c-Myc and FOXO3a-The Everlasting Decision Between Neural Regeneration and Degeneration

The transcription factors c-Myc and FoxO3a play significant roles in neurodegenerative processes, yet their interaction in neurological disorders remains largely unexplored. In contrast, much of the available information about their relationship comes from cancer research. While it is well-established that FoxO3a inhibits c-Myc activity, this interaction represents only a basic understanding of a far more complex dynamic, which includes exceptions under specific conditions and the involvement of additional regulatory factors. Given the critical need to address this gap for the treatment and prevention of neurodegenerative disorders, this review consolidates current knowledge on the joint roles of these two factors in neuropathology. It also highlights their conformational flexibility, post-translational modifications, and outlines potential directions for future research.

MYC: there is more to it than cancer

MYC is a pleiotropic transcription factor involved in multiple cellular processes. While its mechanism of action and targets are not completely elucidated, it has a fundamental role in cellular proliferation, differentiation, metabolism, ribogenesis, and bone and vascular development. Over 4 decades of research and some 10,000 publications linking it to tumorigenesis (by searching PubMed for "MYC oncogene") have led to MYC becoming a most-wanted target for the treatment of cancer, where many of MYC's physiological functions become co-opted for tumour initiation and maintenance. In this context, an abundance of reviews describes strategies for potentially targeting MYC in the oncology field. However, its multiple roles in different aspects of cellular biology suggest that it may also play a role in many additional diseases, and other publications are indeed linking MYC to pathologies beyond cancer. Here, we review these physiological functions and the current literature linking MYC to non-oncological diseases. The intense efforts towards developing MYC inhibitors as a cancer therapy will potentially have huge implications for the treatment of other diseases. In addition, with a complementary approach, we discuss some diseases and conditions where MYC appears to play a protective role and hence its increased expression or activation could be therapeutic.

Triaging between post-translational modification of cell cycle regulators and their therapeutics in neurodegenerative diseases

Neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and Huntington's disease, present challenges in healthcare because of their complicated etiologies and absence of healing remedies. Lately, the emerging role of post-translational modifications (PTMs), in the context of cell cycle regulators, has garnered big interest as a potential avenue for therapeutic intervention. The review explores the problematic panorama of PTMs on cell cycle regulators and their implications in neurodegenerative diseases. We delve into the dynamic phosphorylation, acetylation, ubiquitination, SUMOylation, Glycation, and Neddylation that modulate the key cell cycle regulators, consisting of cyclins, cyclin-dependent kinases (CDKs), and their inhibitors. The dysregulation of these PTMs is related to aberrant cell cycle in neurons, which is one of the factors involved in neurodegenerative pathologies. Moreover, the effect of exogenous activation of CDKs and CDK inhibitors through PTMs on the signaling cascade was studied in postmitotic conditions of NDDs. Furthermore, the therapeutic implications of CDK inhibitors and associated alteration in PTMs were discussed. Lastly, we explored the putative mechanism of PTMs to restore normal neuronal function that might reverse NDDs.

Microbiome Depletion Increases Fentanyl Self-Administration and Alters the Striatal Proteome Through Short-Chain Fatty Acids

Opioid use disorder (OUD) is a public health crisis currently being exacerbated by increased rates of use and overdose of synthetic opioids, primarily fentanyl. Therefore, the identification of novel biomarkers and treatment strategies to reduce problematic fentanyl use and relapse to fentanyl taking is critical. In recent years, there has been a growing body of work demonstrating that the gut microbiome can serve as a potent modulator of the behavioral and transcriptional responses to both stimulants and opioids. Here, we advance this work to define how manipulations of the microbiome drive fentanyl intake and fentanyl-seeking in a translationally relevant drug self-administration model. Depletion of the microbiome of male rats with broad spectrum antibiotics leads to increased drug administration on increased fixed ratio, progressive ratio, and drug seeking after abstinence. Utilizing 16S  sequencing of microbiome contents from these animals, specific populations of bacteria from the gut microbiome correlate closely with levels of drug taking. Additionally, global proteomic analysis of the nucleus accumbens following microbiome manipulation and fentanyl administration to define how microbiome status alters the functional proteomic landscape in this key limbic substructure. These data demonstrate that an altered microbiome leads to marked changes in the synaptic proteome in response to repeated fentanyl treatment. Finally, behavioral effects of microbiome depletion are reversible by upplementation of the microbiome derived short-chain fatty acid metabolites. Taken together, these findings establish clear relevance for gut-brain signaling in models of OUD and lay foundations for further translational work in this space.

Myc beyond Cancer: Regulation of Mammalian Tissue Regeneration

Myc is one of the most well-known oncogenes driving tumorigenesis in a wide variety of tissues. From the brain to blood, its deregulation derails physiological pathways that grant the correct functioning of the cell. Its action is carried out at the gene expression level, where Myc governs basically every aspect of transcription. Indeed, in addition to its role as a canonical, chromatin-bound transcription factor, Myc rules RNA polymerase II (RNAPII) transcriptional pause-release, elongation and termination and mRNA capping. For this reason, it is evident that minimal perturbations of Myc function mirror malignant cell behavior and, consistently, a large body of literature mainly focuses on Myc malfunctioning. In healthy cells, Myc controls molecular mechanisms involved in pivotal functions, such as cell cycle (and proliferation thereof), apoptosis, metabolism and cell size, angiogenesis, differentiation and stem cell self-renewal. In this latter regard, Myc has been found to also regulate tissue regeneration, a hot topic in the research fields of aging and regenerative medicine. Indeed, Myc appears to have a role in wound healing, in peripheral nerves and in liver, pancreas and even heart recovery. Herein, we discuss the state of the art of Myc's role in tissue regeneration, giving an overview of its potent action beyond cancer.

Exploring the potential anti-Alzheimer disease mechanisms of Alpiniae Oxyphyliae Fructus by network pharmacology study and molecular docking

Alpiniae Oxyphyliae Fructus (AOF) (yizhi) is a frequently medicated Chinese herb for Alzheimer disease (AD) treatment. The present study investigated the components and potential mechanisms of AOF through network pharmacology analysis and molecular docking. The results showed that AOF contains at least 20 active ingredients and involves 184 target genes. A total of 301 AD-related genes were obtained from the DisGeNET, GeneCards, GEO, OMIM, and Alzheimer Disease: Genes databases. A total of 41 key targets were identified from the topology analysis of the AOF-AD target network. These key targets are involved in 105 signal pathways, such as the PI3K-Akt, HIF-1, and MAPK pathways, and can regulate gene transcription, cell death, cell proliferation, drug response, and protein phosphorylation. AOF's active ingredients, Chrysin, Isocyperol, Izalpinin, Linolenic acid, CHEMBL489541, Oxyphyllenone A, Oxyphyllenone B, and Oxyphyllol C, show high affinity to targets, including PPARG, ESR1, and AKT1. These findings provide a new basis for AOF application and anti-AD study.

Identification of hsa-miR-365b-5p's role in Alzheimer's disease: a combined analysis of miRNA and mRNA microarrays

BACKGROUND

Alzheimer's disease is a prevalent health problem with a heavy global burden. Definitely diagnosed by autopsy, the clear mechanism of Alzheimer's disease pathogenesis process needs to be illustrated. MicroRNAs are suggested to be involved in many diseases. We aimed to investigate the role of microRNA in Alzheimer's disease.

METHODS

We attempted to discover the role of microRNA in Alzheimer's disease by microarray bioinformatics analysis using autopsy sample data from the GEO database. Temporal cortex samples were included in this study. Bioinformatics analyses and visualization were processed based on R.

RESULTS

After filtering out significantly differential expressed microRNAs and genes, enrichment analyses of both microRNAs and genes were conducted, respectively. Then, we constructed a transcription factor- microRNA-mRNA network and a protein-protein interaction network. In parallel, we used the receiver operating characteristic curve to evaluate the diagnostic value of microRNA. Based on the evidence, we finally identified hsa-miR-365b-5p as a key target in Alzheimer's disease.

CONCLUSIONS

Hsa-miR-365b-5p act as a key target in Alzheimer's disease. It regulates Alzheimer's disease pathogenesis process via neuroinflammation, Wnt and oxidative stress pathway which provides a potential target for Alzheimer's disease treatment.

Gene expression data analysis using Hellinger correlation in weighted gene co-expression networks (WGCNA)

Weighted gene co-expression network analysis (WGCNA) is used to detect clusters with highly correlated genes. Measurements of correlation most typically rely on linear relationships. However, a linear relationship does not always model pairwise functional-related dependence between genes. In this paper, we first compared 6 different correlation methods in their ability to capture complex dependence between genes in three different tissues. Next, we compared their gene-pairwise coefficient results and corresponding WGCNA results. Finally, we applied a recently proposed correlation method, Hellinger correlation, as a more sensitive correlation measurement in WGCNA. To test this method, we constructed gene networks containing co-expression gene modules from RNA-seq data of human frontal cortex from Alzheimer's disease patients. To test the generality, we also used a microarray data set from human frontal cortex, single cell RNA-seq data from human prefrontal cortex, RNA-seq data from human temporal cortex, and GTEx data from heart. The Hellinger correlation method captures essentially similar results as other linear correlations in WGCNA, but provides additional new functional relationships as exemplified by uncovering a link between inflammation and mitochondria function. We validated the network constructed with the microarray and single cell sequencing data sets and a RNA-seq dataset of temporal cortex. We observed that this new correlation method enables the detection of non-linear biologically meaningful relationships among genes robustly and provides a complementary new approach to WGCNA. Thus, the application of Hellinger correlation to WGCNA provides a more flexible correlation approach to modelling networks in gene expression analysis that uncovers novel network relationships.

Oncogenic Pathways in Neurodegenerative Diseases

Cancer and neurodegenerative diseases are two of the leading causes of premature death in modern societies. Their incidence continues to increase, and in the near future, it is believed that cancer will kill more than 20 million people per year, and neurodegenerative diseases, due to the aging of the world population, will double their prevalence. The onset and the progression of both diseases are defined by dysregulation of the same molecular signaling pathways. However, whereas in cancer, these alterations lead to cell survival and proliferation, neurodegenerative diseases trigger cell death and apoptosis. The study of the mechanisms underlying these opposite final responses to the same molecular trigger is key to providing a better understanding of the diseases and finding more accurate treatments. Here, we review the ten most common signaling pathways altered in cancer and analyze them in the context of different neurodegenerative diseases such as Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases.

Neuroprotective Effects of Estradiol plus Lithium Chloride via Anti-Apoptosis and Neurogenesis Pathway in In Vitro and In Vivo Parkinson's Disease Models

Few pharmaceutical agents for slowing Parkinson's disease (PD) progression existed, especially for perimenopause females. The current general medications are mostly hormone replacement therapy and may have some side effects. Therefore, there is an urgent need for a novel treatment for PD. This study examined the possibility of estradiol plus lithium chloride (LiCl), one of the metal halides used as an alternative to salt. We showed that the combination of LiCl and estradiol could enhance neurogenesis proteins GAP-43 and N-myc in the human neuronal-like cells. We also further confirmed the neurogenesis activity in zebrafish. LiCl and LiCl plus estradiol could enhance 6-OHDA-induced upregulation of TGase-2b and Rho A mRNA expression. Besides, LiCl plus estradiol showed a synergic effect in anti-apoptotic activity. LiCl plus estradiol protected SH-SY5Y cells and zebrafish against 6-OHDA-induced damage on neurons than LiCl or estradiol alone groups via p-P38, p-Akt, Bcl-2, and caspase-3 cascade. The potential for developing this combination as a candidate treatment for PD is discussed.

Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease

AIMS

Reactive astrocytes in Alzheimer's disease (AD) have traditionally been demonstrated by increased glial fibrillary acidic protein (GFAP) immunoreactivity; however, astrocyte reaction is a complex and heterogeneous phenomenon involving multiple astrocyte functions beyond cytoskeletal remodelling. To better understand astrocyte reaction in AD, we conducted a systematic review of astrocyte immunohistochemical studies in post-mortem AD brains followed by bioinformatics analyses on the extracted reactive astrocyte markers.

METHODS

NCBI PubMed, APA PsycInfo and WoS-SCIE databases were interrogated for original English research articles with the search terms 'Alzheimer's disease' AND 'astrocytes.' Bioinformatics analyses included protein-protein interaction network analysis, pathway enrichment, and transcription factor enrichment, as well as comparison with public human -omics datasets.

RESULTS

A total of 306 articles meeting eligibility criteria rendered 196 proteins, most of which were reported to be upregulated in AD vs control brains. Besides cytoskeletal remodelling (e.g., GFAP), bioinformatics analyses revealed a wide range of functional alterations including neuroinflammation (e.g., IL6, MAPK1/3/8 and TNF), oxidative stress and antioxidant defence (e.g., MT1A/2A, NFE2L2, NOS1/2/3, PRDX6 and SOD1/2), lipid metabolism (e.g., APOE, CLU and LRP1), proteostasis (e.g., cathepsins, CRYAB and HSPB1/2/6/8), extracellular matrix organisation (e.g., CD44, MMP1/3 and SERPINA3), and neurotransmission (e.g., CHRNA7, GABA, GLUL, GRM5, MAOB and SLC1A2), among others. CTCF and ESR1 emerged as potential transcription factors driving these changes. Comparison with published -omics datasets validated our results, demonstrating a significant overlap with reported transcriptomic and proteomic changes in AD brains and/or CSF.

CONCLUSIONS

Our systematic review of the neuropathological literature reveals the complexity of AD reactive astrogliosis. We have shared these findings as an online resource available at www.astrocyteatlas.org.

Obscure Involvement of MYC in Neurodegenerative Diseases and Neuronal Repair

MYC is well known as a potent oncogene involved in regulating cell cycle and metabolism. Augmented MYC expression leads to cell cycle dysregulation, intense cell proliferation, and carcinogenesis. Surprisingly, its increased expression in neurons does not induce their proliferation, but leads to neuronal cell death and consequent development of a neurodegenerative phenotype. Interestingly, while cancer and neurodegenerative diseases such as Alzheimer's disease are placed at the opposite sides of cell division spectrum, both start with cell cycle dysregulation and stimulation of proliferation. It seems that MYC action directed toward neuron cell proliferation and neural tissue repair collides with evolutional loss of regenerative capacity of CNS neurons in order to strengthen synaptic structure, to protect our cognitive abilities and therefore character. Accordingly, there are abundant mechanisms that block its expression and action specifically in the brain. Moreover, while MYC expression in brain neurons during neurodegenerative processes is related to their death, there are obvious evidences that MYC action after physical injury is beneficial in case of peripheral nerve recovery. MYC might be a useful tool to repair brain cells upon development of neurodegenerative disease or CNS trauma, including stroke and traumatic brain and spinal cord injury, as even imperfect axonal growth and regeneration strategies will likely be of profound benefit. Understanding complex control of MYC action in the brain might have important therapeutic significance, but also it may contribute to the comprehension of development of neurodegenerative diseases.

Cell cycle re-entry of neurons and reactive neuroblastosis in Huntington's disease: Possibilities for neural-glial transition in the brain

Huntington's disease (HD) is an autosomal dominant pathogenic condition that causes progressive degeneration of GABAergic neurons in the brain. The abnormal expansion of the CAG repeats in the exon 1 of the Huntingtin gene (HTT gene) has been associated with the onset and progression of movement disorders, psychiatric disturbance and cognitive decline in HD. Microglial activation and reactive astrogliosis have been recognized as the key pathogenic cellular events in the brains of HD subjects. Besides, HD has been characterized by induced quiescence of neural stem cells (NSCs), reactive neuroblastosis and reduced survival of newborn neurons in the brain. Strikingly, the expression of the mutant HTT gene has been reported to induce the cell cycle re-entry of neurons in HD brains. However, the underlying basis for the induction of cell cycle in neurons and the fate of dedifferentiating neurons in the pathological brain remain largely unknown. Thus, this review article revisits the reports on the regulation of key signaling pathways responsible for altered cell cycle events in diseased brains, with special reference to HD and postulates the occurrence of reactive neuroblastosis as a consequential cellular event of dedifferentiation of neurons. Meanwhile, a substantial number of studies indicate that many neuropathogenic events are associated with the expression of potential glial cell markers by neuroblasts. Taken together, this article represents a hypothesis that transdifferentiation of neurons into glial cells might be highly possible through the transient generation of reactive neuroblasts in the brain upon certain pathological conditions.

Resveratrol Protects Optic Nerve Head Astrocytes from Oxidative Stress-Induced Cell Death by Preventing Caspase-3 Activation, Tau Dephosphorylation at Ser422 and Formation of Misfolded Protein Aggregates

Optic nerve head astrocytes (ONHAs) are the major cell type within the optic nerve head, providing both structural and nutrient support to the optic nerve. Astrocytes are necessary for the survival of neurons with controlled activation of astrocytes being beneficial to neurons. However, overactive astrocytes can be harmful and the loss of normal astrocyte function can be a primary contributor to neurodegeneration. The neuroprotective properties of reactive astrocytes can be lost or they might gain neurotoxic properties in neurodegenerative diseases. The activated astrocytes are crucial in the development of glaucoma, where they serve as a source for cytotoxic substances that participate in ganglion apoptosis. There is increasing evidence indicating that neuroinflammation is an important process in glaucoma. Under pathological conditions, astrocytes can induce an inflammatory response. Extensive evidence shows that inflammatory responses mediated by astrocytes can also influence pathology development, synapse health, and neurodegeneration. The elimination of activated astrocytes by apoptosis is also expected in unfavorable conditions. In neurodegenerative diseases, a common feature is the presence of aggregates found in astrocytes, which can disrupt astrocyte function in such a way as to be detrimental to the viability of neurons. The biological processes involved in vision loss in glaucoma are not well understood. Despite the rapid advances in our understanding of optic nerve head (ONH) structure and function, numerous potential contributions of the ONHAs to optic nerve damage remain unanswered. The present study investigated the role of ONHAs during oxidative stress in order to determine novel cell biological processes underlying glaucoma pathogenesis. ONHAs were exposed to chemically induced oxidative stress using tert-butyl hydroperoxide (tBHP) in order to model extracellular oxidative stress as it occurs in the glaucomatous retina and ONH. In order to determine the impact of an intervention approach employing potential glioprotective treatments for central nervous system tissue we pretreated cells with the polyphenolic phytostilbene and antioxidant trans-resveratrol (3,5,4'-trihydroxy-trans-stilbene). ONHAs exposed to tBHP-mediated oxidative stress displayed decreased viability and underwent apoptosis. In addition, increased levels of activated caspases, dephosphorylation of Tau protein at Ser422, an important site adjacent to the caspase cleavage site controlling Tau cleavage, caspase-mediated Tau cleavage, and cytoskeletal changes, specifically formation of neurofibrillary tangles (NFTs) were detected in ONHAs undergoing oxidative stress. When cells were pretreated with resveratrol cell viability increased along with a significant decrease in activated caspases, cleaved Tau, and NFT formation. Taken together, ONHAs appear to act similar to neurons when undergoing oxidative stress, where proteolytic cleavage of Tau by caspases leads to NFT formation. In addition, resveratrol appears to have promise as a potential protective treatment preventing ONHA dysfunction and degeneration. There is currently no cure for glaucoma or a neuro- and glioprotective treatment that directly targets the pathogenic mechanisms in the glaucomatous retina and optic nerve. The present study identified a potential mechanism underlying degeneration of astrocytes that is susceptible to pharmaco-therapeutic intervention in the eye and potentially elsewhere in the central nervous system. Identification of such mechanisms involved in glaucoma and other disorders of the eye and brain is critical to determine novel targets for effective therapies.

Cortical and Striatal Circuits in Huntington's Disease

Huntington's disease (HD) is a hereditary neurodegenerative disorder that typically manifests in midlife with motor, cognitive, and/or psychiatric symptoms. The disease is caused by a CAG triplet expansion in exon 1 of the huntingtin gene and leads to a severe neurodegeneration in the striatum and cortex. Classical electrophysiological studies in genetic HD mouse models provided important insights into the disbalance of excitatory, inhibitory and neuromodulatory inputs, as well as progressive disconnection between the cortex and striatum. However, the involvement of local cortical and striatal microcircuits still remains largely unexplored. Here we review the progress in understanding HD-related impairments in the cortical and basal ganglia circuits, and outline new opportunities that have opened with the development of modern circuit analysis methods. In particular, in vivo imaging studies in mouse HD models have demonstrated early structural and functional disturbances within the cortical network, and optogenetic manipulations of striatal cell types have started uncovering the causal roles of certain neuronal populations in disease pathogenesis. In addition, the important contribution of astrocytes to HD-related circuit defects has recently been recognized. In parallel, unbiased systems biology studies are providing insights into the possible molecular underpinnings of these functional defects at the level of synaptic signaling and neurotransmitter metabolism. With these approaches, we can now reach a deeper understanding of circuit-based HD mechanisms, which will be crucial for the development of effective and targeted therapeutic strategies.

Biological Functions of Plasmalogens

Plasmalogens (Pls) are one kind of phospholipids enriched in the brain and other organs. These lipids were thought to be involved in the membrane bilayer formation and anti-oxidant function. However, extensive studies revealed that Pls exhibit various beneficial biological activities including prevention of neuroinflammation, improvement of cognitive function, and inhibition of neuronal cell death. The biological activities of Pls were associated with the changes in cellular signaling and gene expression. Membrane-bound GPCRs were identified as possible receptors of Pls, suggesting that Pls might function as ligands or hormones. Aging, stress, and inflammatory stimuli reduced the Pls contents in cells, and addition of Pls inhibited inflammatory processes, which could suggest that reduction of Pls might be one of the risk factors for the diseases associated with inflammation. Oral ingestion of Pls showed promising health benefits among Alzheimer's disease (AD) patients, suggesting that Pls might have therapeutic potential in other neurodegenerative diseases.

Neurological Disorder Drug Discovery from Gene Expression with Tensor Decomposition

BACKGROUND

Identifying effective candidate drug compounds in patients with neurological disorders based on gene expression data is of great importance to the neurology field. By identifying effective candidate drugs to a given neurological disorder, neurologists would (1) reduce the time searching for effective treatments; and (2) gain additional useful information that leads to a better treatment outcome. Although there are many strategies to screen drug candidate in pre-clinical stage, it is not easy to check if candidate drug compounds can also be effective to human.

OBJECTIVE

We tried to propose a strategy to screen genes whose expression is altered in model animal experiments to be compared with gene expressed differentially with drug treatment to human cell lines.

METHODS

Recently proposed tensor decomposition (TD) based unsupervised feature extraction (FE) is applied to single cell (sc) RNA-seq experiments of Alzheimer's disease model animal mouse brain.

RESULTS

Four hundreds and one genes are screened as those differentially expressed during Aβ accumulation as age progresses. These genes are significantly overlapped with those expressed differentially with the known drug treatments for three independent data sets: LINCS, DrugMatrix, and GEO.

CONCLUSION

Our strategy, application of TD based unsupervised FE, is useful one to screen drug candidate compounds using scRNA-seq data set.

The role of astrocytic glutamate transporters GLT-1 and GLAST in neurological disorders: Potential targets for neurotherapeutics

Glutamate is the primary excitatory neurotransmitter in the central nervous system (CNS) which initiates rapid signal transmission in the synapse before its re-uptake into the surrounding glia, specifically astrocytes. The astrocytic glutamate transporters glutamate-aspartate transporter (GLAST) and glutamate transporter-1 (GLT-1) and their human homologs excitatory amino acid transporter 1 (EAAT1) and 2 (EAAT2), respectively, are the major transporters which take up synaptic glutamate to maintain optimal extracellular glutamic levels, thus preventing accumulation in the synaptic cleft and ensuing excitotoxicity. Growing evidence has shown that excitotoxicity is associated with various neurological disorders, including amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), manganism, ischemia, schizophrenia, epilepsy, and autism. While the mechanisms of neurological disorders are not well understood, the dysregulation of GLAST/GLT-1 may play a significant role in excitotoxicity and associated neuropathogenesis. The expression and function of GLAST/GLT-1 may be dysregulated at the genetic, epigenetic, transcriptional or translational levels, leading to high levels of extracellular glutamate and excitotoxicity. Consequently, understanding the regulatory mechanisms of GLAST/GLT-1 has been an area of interest in developing therapeutics for the treatment of neurological disorders. Pharmacological agents including β-lactam antibiotics, estrogen/selective estrogen receptor modulators (SERMs), growth factors, histone deacetylase inhibitors (HDACi), and translational activators have shown significant efficacy in enhancing the expression and function of GLAST/GLT-1 and glutamate uptake both in vitro and in vivo. This comprehensive review will discuss the regulatory mechanisms of GLAST/GLT-1, their association with neurological disorders, and the pharmacological agents which mediate their expression and function. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.

Reactive Astrocytes as Drug Target in Alzheimer's Disease

Alzheimer's disease is a neurodegenerative disease characterized by deposition of extracellular amyloid-β, intracellular neurofibrillary tangles, and loss of cortical neurons. However, the mechanism underlying neurodegeneration in Alzheimer's disease (AD) remains to be explored. Many of the researches on AD have been primarily focused on neuronal changes. Current research, however, broadens to give emphasis on the importance of nonneuronal cells, such as astrocytes. Astrocytes play fundamental roles in several cerebral functions and their dysfunctions promote neurodegeneration and, eventually, retraction of neuronal synapses, which leads to cognitive deficits found in AD. Astrocytes become reactive as a result of deposition of Aβ, which in turn have detrimental consequences, including decreased glutamate uptake due to reduced expression of uptake transporters, altered energy metabolism, altered ion homeostasis (K⁺ and Ca⁺), increased tonic inhibition, and increased release of cytokines and inflammatory mediators. In this review, recent insights on the involvement of, tonic inhibition, astrocytic glutamate transporters and aquaporin in the pathogenesis of Alzheimer's disease are provided. Compounds which increase expression of GLT1 have showed efficacy for AD in preclinical studies. Tonic inhibition mediated by GABA could also be a promising target and drugs that block the GABA synthesizing enzyme, MAO-B, have shown efficacy. However, there are contradictory evidences on the role of AQP4 in AD.

MicroRNA-455-3p as a potential peripheral biomarker for Alzheimer's disease

The purpose of our study was to identify microRNAs (miRNAs) as early detectable peripheral biomarkers in Alzheimer's disease (AD). To achieve our objective, we assessed miRNAs in serum samples from AD patients and Mild cognitive impairment (MCI) subjects relative to healthy controls. We used Affymetrix microarray analysis and validated differentially expressed miRNAs using qRT-PCR. We further validated miRNA data using AD postmortem brains, amyloid precursor protein transgenic mice and AD cell lines. We identified a gradual upregulation of four miRNAs: miR-455-3p, miR-4668-5p, miR-3613-3p and miR-4674. A fifth miRNA, mir-6722, was down-regulated in persons with AD and mild cognitive impairment compared with controls. Validation analysis by qRT-PCR showed significant upregulation of only miR-455-3p (P = 0.007) and miR-4668-5p (P = 0.016) in AD patients compared with healthy controls. Furthermore, qRT-PCR analysis of the AD postmortem brains with different Braak stages also showed upregulation of miR-455-3p (P = 0.016). However, receiver operating characteristic curves (ROC) curve analysis revealed a significant area under curve (AUC) value only for miR-455-3p in the serum (AUROC = 0.79; P = 0.015) and brains (AUROC = 0.86; P = 0.016) of AD patients. Expression analysis of amyloid precursor protein transgenic mice also revealed high level of mmu-miR-455-3p (P = 0.004) in the cerebral cortex (AD-affected) region of brain and low in the non-affected area, i.e. cerebellum. Furthermore, human and mouse neuroblastoma cells treated with the amyloid-β(1-42) peptide also showed a similarly higher expression of miR-455-3p. Functional analysis of differentially expressed miRNAs via the miR-path indicated that miR-455-3p was associated in the regulation of several biological pathways. Genes associated with these pathways were found to have a crucial role in AD pathogenesis. An increase in miR-455-3p expression found in AD patients and Aβ pathologies unveiled its biomarker characteristics and a precise role in AD pathogenesis.

Transactivation Domain of Human c-Myc Is Essential to Alleviate Poly(Q)-Mediated Neurotoxicity in Drosophila Disease Models

Polyglutamine (poly(Q)) disorders, such as Huntington's disease (HD) and spinocerebellar ataxias, represent a group of neurological disorders which arise due to an atypically expanded poly(Q) tract in the coding region of the affected gene. Pathogenesis of these disorders inside the cells begins with the assembly of these mutant proteins in the form of insoluble inclusion bodies (IBs), which progressively sequester several vital cellular transcription factors and other essential proteins, and finally leads to neuronal dysfunction and apoptosis. We have shown earlier that targeted upregulation of Drosophila myc (dmyc) dominantly suppresses the poly(Q) toxicity in Drosophila. The present study examines the ability of the human c-myc proto-oncogene and also identifies the specific c-Myc isoform which drives the mitigation of poly(Q)-mediated neurotoxicity, so that it could be further substantiated as a potential drug target. We report for the first time that similar to dmyc, tissue-specific induced expression of human c-myc also suppresses poly(Q)-mediated neurotoxicity by an analogous mechanism. Among the three isoforms of c-Myc, the rescue potential was maximally manifested by the full-length c-Myc2 protein, followed by c-Myc1, but not by c-MycS which lacks the transactivation domain. Our study suggests that strategies focussing on the transactivation domain of c-Myc could be a very useful approach to design novel drug molecules against poly(Q) disorders.

MEACA: efficient gene-set interpretation of expression data using mixed models.. [DOI: 10.1101/106781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Competitive gene-set analysis, or enrichment analysis, is widely used for functional interpretation of gene expression data. It tests a known category (e.g. pathway) of genes for enriched differential expression signals. Current methods do not properly capture inter-gene correlations and heterogeneity, resulting in mis-calibration and power loss. We propose MEACA, a new gene-set method based on mixed-effects models. MEACA flexibly incorporates unknown heterogeneity and correlations across genes, and does not need time-consuming permutations. Compared to existing methods, MEACA substantially improves type 1 error control and power in widely ranging scenarios. Real data applications demonstrate MEACA’s ability to recover biologically meaningful relationships.

Molecular changes in the postmortem parkinsonian brain

Parkinson disease (PD) is the second most common neurodegenerative disease after Alzheimer disease. Although PD has a relatively narrow clinical phenotype, it has become clear that its etiological basis is broad. Post-mortem brain analysis, despite its limitations, has provided invaluable insights into relevant pathogenic pathways including mitochondrial dysfunction, oxidative stress and protein homeostasis dysregulation. Identification of the genetic causes of PD followed the discovery of these abnormalities, and reinforced the importance of the biochemical defects identified post-mortem. Recent genetic studies have highlighted the mitochondrial and lysosomal areas of cell function as particularly significant in mediating the neurodegeneration of PD. Thus the careful analysis of post-mortem PD brain biochemistry remains a crucial component of research, and one that offers considerable opportunity to pursue etiological factors either by 'reverse biochemistry' i.e. from defective pathway to mutant gene, or by the complex interplay between pathways e.g. mitochondrial turnover by lysosomes. In this review we have documented the spectrum of biochemical defects identified in PD post-mortem brain and explored their relevance to metabolic pathways involved in neurodegeneration. We have highlighted the complex interactions between these pathways and the gene mutations causing or increasing risk for PD. These pathways are becoming a focus for the development of disease modifying therapies for PD. Parkinson's is accompanied by multiple changes in the brain that are responsible for the progression of the disease. We describe here the molecular alterations occurring in postmortem brains and classify them as: Neurotransmitters and neurotrophic factors; Lewy bodies and Parkinson's-linked genes; Transition metals, calcium and calcium-binding proteins; Inflammation; Mitochondrial abnormalities and oxidative stress; Abnormal protein removal and degradation; Apoptosis and transduction pathways. This article is part of a special issue on Parkinson disease.

MYC-repressed long noncoding RNAs antagonize MYC-induced cell proliferation and cell cycle progression

The transcription factor MYC is a proto-oncogene regulating cell proliferation, cell cycle, apoptosis and metabolism. The recent identification of MYC-regulated long noncoding RNAs (lncRNAs) expands our knowledge of the role of lncRNAs in MYC functions. Here, we identify MYC-repressed lncRNAs named MYCLo-4, -5 and -6 by comparing 3 categories of lncRNAs (downregulated in highly MYC-expressing colorectal cancer, up-regulated by MYC knockdown in HCT116, upregulated by MYC knockdown in RKO). The MYC-repressed MYCLos are implicated in MYC-modulated cell proliferation through cell cycle regulation. By screening cell cycle-related genes regulated by MYC and the MYC-repressed MYCLos, we identified the MYC-repressed gene GADD45A as a target gene of the MYC-repressed MYCLos such as MYCLo-4 and MYCLo-6.

Age-Dependent Alterations in the Interactions of NF-κB and N-myc with GLT-1/EAAT2 Promoter in the Pericontusional Cortex of Mice Subjected to Traumatic Brain Injury

Traumatic brain injury (TBI) is one of the major risk factors of dementia, aging, and cognitive impairments, etc. We have previously reported that expression of the astrocytic glutamate transporter GLT-1/EAAT2 is downregulated in the pericontusional cortex of adult and old mice in post-TBI time-dependent manner, and the process of decline starts before in old than in adult TBI mice. However, relationship between age- and TBI-dependent alterations in GLT-1/EAAT2 expression and interactions of transcription factors NF-κB and N-myc with their cognate GLT-1/EAAT2 promoter sequences, an important step of its transcriptional control, is not known. To understand this, we developed TBI mouse model by modified chronic head injury (CHI) method, analyzed expression of GFAP, TNF-α, and AQP4 by RT-PCR for its validation, and analyzed interactions of NF-κB and N-myc with GLT-1/EAAT2 promoter sequences by electrophoretic mobility shift assay (EMSA). Our EMSA data revealed that interactions of NF-κB and N-myc with GLT-1/EAAT2 promoter sequences was significantly elevated in the ipsi-lateral cortex of both adult and old TBI mice in post-TBI time-dependent manner; however, these interactions started immediately in the old compared to that in adult TBI mice, which could be attributed to our previously reported age- and post-TBI time-dependent differential expression of GLT-1/EAAT2 in the pericontusional cortex.

Proteome-wide characterization of signalling interactions in the hippocampal CA4/DG subfield of patients with Alzheimer's disease

Alzheimer’s disease (AD) is the most common form of dementia; however, mechanisms and biomarkers remain unclear. Here, we examined hippocampal CA4 and dentate gyrus subfields, which are less studied in the context of AD pathology, in post-mortem AD and control tissue to identify possible biomarkers. We performed mass spectrometry-based proteomic analysis combined with label-free quantification for identification of differentially expressed proteins. We identified 4,328 proteins, of which 113 showed more than 2-fold higher or lower expression in AD hippocampi than in control tissues. Five proteins were identified as putative AD biomarkers (MDH2, PCLO, TRRAP, YWHAZ, and MUC19 isoform 5) and were cross-validated by immunoblotting, selected reaction monitoring, and MALDI imaging. We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins. Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi. Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.

MicroRNA-145 as one negative regulator of astrogliosis

Astrogliosis occurs at the lesion site within days to weeks after spinal cord injury (SCI) and involves the proliferation and hypertrophy of astrocytes, leading to glia scar formation. Changes in gene expression by deregulated microRNAs (miRNAs) are involved in the process of central nervous system neurodegeneration. Here, we report that mir-145, a miRNA enriched in rat spinal neurons and astrocytes, was downregulated at 1 week and 1 month after SCI. Our in vitro studies using astrocytes prepared from neonatal spinal cord tissues indicated that potent inflammagen lipopolysaccharide downregulated mir-145 expression in astrocytes, suggesting that SCI-triggered inflammatory signaling pathways could play the inhibitory role in astrocytic mir-145 expression. To induce overexpression of mir-145 in astrocytes at the spinal cord lesion site, we developed a lentivirus-mediated pre-miRNA delivery system using the promoter of glial fibrillary acidic protein (GFAP), an astrocyte-specific intermediate filament. The results indicated that astrocyte-specific overexpression of mir-145 reduced astrocytic cell density at the lesion border of the injured spinal cord. In parallel, overexpression of mir-145 reduced the size of astrocytes and the number of related cell processes, as well as cell proliferation and migration. Through a luciferase reporter system, we found that GFAP and c-myc were the two potential targets of mir-145 in astrocytes. Together, the findings demonstrate the novel role of mir-145 in the regulation of astrocytic dynamics, and reveal that the downregulation of mir-145 in astrocytes is a critical factor inducing astrogliosis after SCI. GLIA 2015;63:194-205.

Early induction of c-Myc is associated with neuronal cell death

Neuronal cell cycle activation has been implicated in neurodegenerative diseases such as Alzheimer's disease, while the initiating mechanism of cell cycle activation remains to be determined. Interestingly, our previous studies have shown that cell cycle activation by c-Myc (Myc) leads to neuronal cell death which suggests Myc might be a key regulator of cell cycle re-entry mediated neuronal cell death. However, the pattern of Myc expression in the process of neuronal cell death has not been addressed. To this end, we examined Myc induction by the neurotoxic agents camptothecin and amyloid-β peptide in a differentiated SH-SY5Y neuronal cell culture model. Myc expression was found to be significantly increased following either treatment and importantly, the induction of Myc preceded neuronal cell death suggesting it is an early event of neuronal cell death. Since ectopic expression of Myc in neurons causes the cell cycle activation and neurodegeneration in vivo, the current data suggest that induction of Myc by neurotoxic agents or other disease factors might be a key mediator in cell cycle activation and consequent cell death that is a feature of neurodegenerative diseases.

Abnormal motor cortex plasticity in premanifest and very early manifest Huntington disease

BACKGROUND

Cognition is affected early in Huntington disease (HD), and in HD animal models there is evidence that this reflects abnormal synaptic plasticity. The authors investigated whether there is any evidence for abnormal synaptic plasticity using the human motor cortex-rTMS model and, if so, if there is any difference between premanifest HD gene carriers and very early manifest HD patients or any relationship with ratings of the severity of motor signs.

METHODS

Fifteen HD gene carriers (seven premanifest, eight very early manifest) and 14 control participants were given a continuous train of 100 bursts of theta burst stimulation (cTBS: three pulses at 50 Hz and 80% AMT repeated every 200 ms). The size of the motor-evoked potential was measured at regular intervals until 21 min after cTBS.

RESULTS

HD gene carriers and controls responded differently to theta burst stimulation (F(4.9,131.9)=1.37, p=0.048) with controls having more inhibition than HD gene carriers (F(1,27)=13.3, p=0.001). Across all time points, mean inhibition differed between the groups (F(2,26)=6.32, p=0.006); controls had more inhibition than either HD gene carrier subgroup (p=0.006 for premanifest and p=0.009 for early symptomatic), whereas there was no difference between premanifest and early symptomatic HD gene carriers. The measure of cortical plasticity was not associated with any clinical ratings (Unified Huntington Disease Rating Scale motor score, estimate of age at onset).

CONCLUSIONS

Motor cortex plasticity is abnormal in HD gene carriers but is not closely linked to the development of motor signs of HD.

Multifunctional roles of enolase in Alzheimer's disease brain: beyond altered glucose metabolism

Enolase enzymes are abundantly expressed, cytosolic carbon-oxygen lyases known for their role in glucose metabolism. Recently, enolase has been shown to possess a variety of different regulatory functions, beyond glycolysis and gluconeogenesis, associated with hypoxia, ischemia, and Alzheimer's disease (AD). AD is an age-associated neurodegenerative disorder characterized pathologically by elevated oxidative stress and subsequent damage to proteins, lipids, and nucleic acids, appearance of neurofibrillary tangles and senile plaques, and loss of synapse and neuronal cells. It is unclear if development of a hypometabolic environment is a consequence of or contributes to AD pathology, as there is not only a significant decline in brain glucose levels in AD, but also there is an increase in proteomics identified oxidatively modified glycolytic enzymes that are rendered inactive, including enolase. Previously, our laboratory identified alpha-enolase as one the most frequently up-regulated and oxidatively modified proteins in amnestic mild cognitive impairment (MCI), early-onset AD, and AD. However, the glycolytic conversion of 2-phosphoglycerate to phosphoenolpyruvate catalyzed by enolase does not directly produce ATP or NADH; therefore it is surprising that, among all glycolytic enzymes, alpha-enolase was one of only two glycolytic enzymes consistently up-regulated from MCI to AD. These findings suggest enolase is involved with more than glucose metabolism in AD brain, but may possess other functions, normally necessary to preserve brain function. This review examines potential altered function(s) of brain enolase in MCI, early-onset AD, and AD, alterations that may contribute to the biochemical, pathological, clinical characteristics, and progression of this dementing disorder.

The neuronal expression of MYC causes a neurodegenerative phenotype in a novel transgenic mouse

Many different proteins associated with the cell cycle, including cyclins, cyclin-dependent kinases, and proto-oncogenes such as c-MYC (MYC), are increased in degenerating neurons. Consequently, an ectopic activation of the cell cycle machinery in neurons has emerged as a potential pathogenic mechanism of neuronal dysfunction and death in many neurodegenerative diseases, including Alzheimer's disease. However, the exact role of cell cycle re-entry during disease pathogenesis is unclear, primarily because of the lack of relevant research models to study the effects of cell cycle re-entry on mature neurons in vivo. To address this issue, we developed a new transgenic mouse model in which forebrain neurons (CaMKII-MYC) can be induced to enter the cell cycle using the physiologically relevant proto-oncogene MYC to drive cell cycle re-entry. We show that such cell cycle re-entry results in neuronal cell death, gliosis, and cognitive deficits. These findings provide compelling evidence that dysregulation of cell cycle re-entry results in neurodegeneration in vivo. Our current findings, coupled with those of previous reports, strengthen the hypothesis that neurodegeneration in Alzheimer's disease, similar to cellular proliferation in cancer, is a disease that results from inappropriate cell cycle control.

Evidence that protease-activated receptor-2 mediates trypsin-induced reversal of stellation in cultured rat astrocytes

Serine proteases such as thrombin and trypsin play a key role in the development and repair processes in the central nervous system. Molecular actions of serine proteases include multiple cellular events like activation of protease-activated receptors (PARs). PARs belong to a family of G protein-coupled receptors that can be stimulated through their proteolytic cleavage by ligands. PAR-2 has been implicated in neurodegenerative diseases including astrogliosis. Although recent studies have shown that low concentration of trypsin activates PAR-2, its role in morphological changes in primary astrocytes has not been studied. In the present study, we investigated the effects of PAR-2 in astrocyte stellation in rat primary astrocyte culture. Both trypsin (0.1-1 U/ml) and a PAR-2-activating peptide SLIGRL-NH2 (1-50 microM) significantly reversed the stellation induced by serum deprivation in rat astrocytes. Treatment of astrocytes with trypsin or SLIGRL-NH2 resulted in a transient rise of the intracellular Ca2+ level and trypsin-induced morphological changes were blocked by BAPTA, a Ca2+ chelator. In addition, a protein kinase C (PKC) inhibitor, bisindolylmaleimide significantly inhibited the trypsin-induced morphological changes, whereas activation of PKC by phorbol-12-myristate-13-acetate acted as trypsin. Taken together, these results suggest that activation of PAR-2 by trypsin caused reversal of stellation in cultured astrocytes, in part, via the mobilization of intracellular Ca2+ and activation of PKC.

Discovery and development of biomarkers of neurological disease

The identification of clinically relevant biomarkers for neurological diseases poses unique challenges. These include an historical lack of availability of relevant tissues from the site of pathology, relatively poorly matured techniques for disease diagnosis, the complexity and cellular heterogeneity of the brain, and a clear deficiency of models for functional validation of candidate biomarkers. Here, the unique challenges that neurological disorders introduce to biomarker discovery are described and how modern technological advances in genomics, proteomics and metabolomics are overcoming these obstacles and are driving the discovery of novel biomarkers to improve early diagnosis and therapeutic treatment is discussed.

Possible involvement of the expression and phosphorylation of N-Myc in the induction of HMGA1a by hypoxia in the human neuroblastoma cell line

Increased expression of N-Myc and expression of the high mobility group protein A1a (HMGA1a) were observed in the nuclei of SK-N-SH cells following exposure to hypoxia. These observations were accompanied by the appearance of additional high molecular weight bands, which were eliminated by pretreatment with alkaline phosphatase. Immunoprecipitation showed phosphorylation of serine, threonine and tyrosine residues of N-Myc in the nucleus. These results suggest that hypoxia-induced signals in SK-N-SH cells lead to persistent expression of HMGA1a, which may induce expression of the transcription factor N-Myc, and that phosphorylation at serine, threonine and tyrosine residues of N-Myc occurs at an early stage after stimulation. Such signal consolidation processes could play a role in neuronal survival after hypoxia in neurons.

Positive and negative regulation of EAAT2 by NF-kappaB: a role for N-myc in TNFalpha-controlled repression

The glutamate transporter gene, EAAT2/GLT-1, is induced by epidermal growth factor (EGF) and downregulated by tumor necrosis factor alpha (TNFalpha). While TNFalpha is generally recognized as a positive regulator of NF-kappaB-dependent gene expression, its ability to control transcriptional repression is not well characterized. Additionally, the regulation of NF-kappaB by EGF is poorly understood. Herein, we demonstrate that both TNFalpha-mediated repression and EGF-mediated activation of EAAT2 expression require NF-kappaB. We show that EGF activates NF-kappaB independently of signaling to IkappaB. Furthermore, TNFalpha can abrogate IKKbeta- and p65-mediated activation of EAAT2. Our results suggest that NF-kappaB can intrinsically activate EAAT2 and that TNFalpha mediates repression through a distinct pathway also requiring NF-kappaB. Consistently, we find that N-myc is recruited to the EAAT2 promoter with TNFalpha and that N-myc-binding sites are required for TNFalpha-mediated repression. Moreover, N-myc overexpression inhibits both basal and p65-induced activation of EAAT2. Our data highlight the remarkable specificity of NF-kappaB activity to regulate gene expression in response to diverse cellular signals and have implications for glutamate homeostasis and neurodegenerative disease.

Biomarker identification in neurologic diseases: improving diagnostics and therapeutics

Identification of biomarkers in neurological disease remains impeded by many obstacles. Among them are the availability of tissue at the site of pathology, poor clinical diagnostics, the complexity of the brain and a general dearth of functional end points and models for validation. However, advances in technology have helped to overcome these challenges. Some of these advances include standardization and increased efficiency in brain banking, novel techniques for brain imaging, improved methods for reducing tissue heterogeneity including laser capture microdissection, high-throughput genomics, new functional validation techniques such as RNA interference, and the development of new animal models of neurologic disease. In order to efficiently handle the wealth of information that will be gleaned from these new technologies, new integrated databasing protocols will be necessary. Access to these databases by researchers and clinicians is critical to the continued progress being made in biomarker identification in neurological disease. These challenges and ways to overcome them are presented here in the context of a disease known to be a robust model for biomarker identification, Alzheimer's disease.

cDNA microarray analysis of changes in gene expression associated with MPP+ toxicity in SH-SY5Y cells

cDNA microarray analysis of 1-methyl-4-phenyl-pyridinium (MPP+) toxicity (1 mM, 72 h) in undifferentiated SH-SY5Y cells identified 48 genes that displayed a signal intensity greater than the mean of all differentially expressed genes and a two-fold or greater difference in normalized expression. RT-PCR analysis of a subset of genes showed that c-Myc and RNA-binding protein 3 (RMB3) expression decreased by approximately 50% after 72 h of exposure to MPP+ (1 mM) but did not change after 72 h of exposure to 6-hydroxydopamine (25 microM), rotenone (50 nM), and hydrogen peroxide (600 microM). Exposure of retinoic acid (RA)-differentiated SH-SY5Y cells to MPP+ (1 mM, 72 h) also resulted in a decrease in RMB3 expression and an increase in GADD153 expression. In contrast, c-Myc expression was slightly increased in RA-differentiated cells. Collectively, these data provide new insights into the molecular mechanisms of MPP+ toxicity and show that MPP+ can elicit distinct patterns of gene expression in undifferentiated and RA-differentiated SH-SY5Y cells.

Apoptosis in Huntington's disease

Huntington's disease (HD) is an autosomal dominant, fatal disorder. Patients display increasing motor, psychiatric and cognitive impairment and at autopsy, late-stage patient brains show extensive striatal (caudate and putamen), pallidal and cortical atrophy. The initial and primary target of degeneration in HD is the striatal medium spiny GABAergic neuron, and by end stages of the disease up to 95% of these neurons are lost [J. Neuropathol. Exp. Neurol. 57 (1998) 369]. The disease is caused by an elongation of a polyglutamine tract in the N-terminal of the huntingtin gene, but it is not known how this mutation leads to such extensive, but selective, cell death [Cell 72 (1993) 971]. There is substantial evidence from in vitro studies that connects apoptotic pathways and apoptosis with the mutant protein, and theories linking apoptosis to neuronal death in HD have existed for several years. Despite this, evidence of apoptotic neuronal death in HD is scarce. It may be that the processes involved in apoptosis, rather than apoptosis per se, are more important for HD pathogenesis. Upregulation of the proapoptotic proteins could lead to cleavage of huntingtin and as recent data has shown, the consequent toxic fragment may itself elicit toxic effects on the cell by disrupting transcription. In addition, the increased levels of proapoptotic proteins could contribute to slowly developing cell death in HD, selective for the striatal medium spiny GABAergic neurons and later spreading to other areas. Here we review the evidence supporting these mechanisms of pathogenesis in HD.

Phosphorylated c-MYC expression in Alzheimer disease, Pick's disease, progressive supranuclear palsy and corticobasal degeneration

Phosphorylated c-Myc (c-Myc-P) expression has been examined by immunohistochemistry, using an antibody that recognizes phosphorylated c-Myc at Thr58 and Ser62, in the brains of Alzheimer disease (AD), Pick's disease (PiD), progressive supranuclear palsy (PSP), corticobasal degeneration (CBD) and age-matched control cases, as well as in human medulloblastomas and central neuroblastomas. Strong c-Myc-P immunoreactivity was seen in dystrophic neurites and neurones with neurofibrillary tangles in AD, and in neurones and glial cells bearing abnormal tau deposits in PiD, PSP and CBD. Previous studies have shown active Ras and increased mitogen-activated protein kinase (MAPK/ERK) expression in neurones and glial cells with abnormal tau deposition in AD and other tauopathies. Since MAPKs phosphorylate c-Myc at Thr58 and Ser62, these observations implicate the Ras/MAP kinase pathway in c-Myc phosphorylation and accumulation in AD and other tauopathies. Previous studies have also shown activation of cell cycle associated proteins in neuronal death. The present results have shown colocalization of nuclear c-Myc-P and active, cleaved caspase-3, a major executioner of apoptosis, in medulloblastomas and central neuroblastomas, thus suggesting phosphorylated c-Myc expression in caspase-3-dependent apoptosis of tumour cells. However, no evidence of caspase-3 activation has been observed in neurones and glial cells with strong phosphorylated c-Myc immunoreactivity in AD, PiD, PSP and CBD. Therefore, it is not clear that the activation of the Ras/MAPK/c-Myc subprogramme leads to neuronal death in AD and other tauopathies.

Temporal profiling of methamphetamine-induced changes in gene expression in the mouse brain: Evidence from cDNA array

Methamphetamine (METH) is a neurodegenerative drug of abuse. Its toxicity is characterized by destruction of monoaminergic terminals and by apoptosis in cortical and striatal cell bodies. Multiple factors appear to control METH neurotoxicity, including free radicals and transcription factors. Here, using cDNA arrays, we show the temporal profile of gene expression patterns in the cortex of mice treated with this drug. We obtained two patterns of changes from 588 genes surveyed. First, an early pattern is characterized by upregulation of transcription factors, including members of the jun family. Second, a delayed pattern includes genes related to cell death and to DNA repair. A number of trophic factors were also activated at the later timepoint. These observations suggest that METH can activate a multigene machinery that participates in the production of its toxic effects. The resulting degenerative effects of the drug are thus the result of a balance between protoxic and antiapoptotic mechanisms triggered by its administration to these animals. These observations are of clinical relevance because of the recent identification of degenerative changes in the brains of METH abusers.