Progress in the use of microarray technology to study the neurobiology of disease

The diverse functions of the brain are mediated by neurons and glia whose phenotype is defined by a dynamically maintained set of gene transcripts, or 'transcriptome'. Large-scale analysis of gene expression in postmortem brain using microarray technology has the potential to elucidate molecular changes that occur in disease states. There are unique challenges associated with studies of postmortem brain, including limited sample sizes and variable clinical phenotypes that are typical of complex disorders. Nevertheless, recent microarray-based studies have implicated both individual dysregulated genes and abnormal patterns of gene expression in brain disorders.

[1]  W. Markesbery,et al.  Incipient Alzheimer's disease: Microarray correlation analyses reveal major transcriptional and tumor suppressor responses , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[2]  Jonathan Pevsner,et al.  Global up-regulation of chromosome 21 gene expression in the developing Down syndrome brain. , 2003, Genomics.

[3]  J. Pierri,et al.  Alterations in chandelier neuron axon terminals in the prefrontal cortex of schizophrenic subjects. , 1999, The American journal of psychiatry.

[4]  J. Wendel,et al.  Polyploid formation in cotton is not accompanied by rapid genomic changes , 2001 .

[5]  John Quackenbush Microarray data normalization and transformation , 2002, Nature Genetics.

[6]  E. Mufson,et al.  Gene Expression Profiles of Cholinergic Nucleus Basalis Neurons in Alzheimer's Disease , 2002, Neurochemical Research.

[7]  Ash A. Alizadeh,et al.  Genome-wide analysis of DNA copy-number changes using cDNA microarrays , 1999, Nature Genetics.

[8]  R. Tibshirani,et al.  Significance analysis of microarrays applied to the ionizing radiation response , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[9]  S. Ludwin,et al.  Microarray analysis of gene expression in multiple sclerosis and EAE identifies 5-lipoxygenase as a component of inflammatory lesions , 2001, Journal of Neuroimmunology.

[10]  M. Gerstein,et al.  Comparing protein abundance and mRNA expression levels on a genomic scale , 2003, Genome Biology.

[11]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

[12]  Jorge R. Oksenberg,et al.  Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis , 2002, Nature Medicine.

[13]  L. Lazzeroni,et al.  Gene expression patterns vary in clonal cell cultures from Rett syndrome females with eight different MECP2 mutations , 2002, BMC Medical Genetics.

[14]  W H Wong,et al.  Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[15]  D. Lewis,et al.  Disease-specific changes in regulator of G-protein signaling 4 (RGS4) expression in schizophrenia , 2001, Molecular Psychiatry.

[16]  Terry Speed,et al.  Normalization of cDNA microarray data. , 2003, Methods.

[17]  P. Coleman,et al.  Defects in expression of genes related to synaptic vesicle traffickingin frontal cortex of Alzheimer’s disease , 2003, Neurobiology of Disease.

[18]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[19]  J. Trent,et al.  Analysis of gene expression in multiple sclerosis lesions using cDNA microarrays , 1999 .

[20]  Peter B. Jones,et al.  Oligodendrocyte dysfunction in schizophrenia and bipolar disorder , 2003, The Lancet.

[21]  Michael C O'Donovan,et al.  Support for RGS4 as a susceptibility gene for schizophrenia , 2004, Biological Psychiatry.

[22]  H. Causton,et al.  MGED comes of age , 2003, Genome Biology.

[23]  Eric P. Hoffman,et al.  Gene Expression Profiling in Postmortem Rett Syndrome Brain: Differential Gene Expression and Patient Classification , 2001, Neurobiology of Disease.

[24]  R. Quirion,et al.  cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer's disease. , 2003, Pharmacology & therapeutics.

[25]  Paul J. Harrison,et al.  The relative importance of premortem acidosis and postmortem interval for human brain gene expression studies: selective mRNA vulnerability and comparison with their encoded proteins , 1995, Neuroscience Letters.

[26]  K. Selmaj,et al.  cDNA microarray analysis in multiple sclerosis lesions: detection of genes associated with disease activity. , 2003, Brain : a journal of neurology.

[27]  G. Pasinetti,et al.  Use of cDNA microarray in the search for molecular markers involved in the onset of Alzheimer's disease dementia , 2001, Journal of neuroscience research.

[28]  Peter B. Jones,et al.  Gene expression analysis in schizophrenia: Reproducible up-regulation of several members of the apolipoprotein L family located in a high-susceptibility locus for schizophrenia on chromosome 22 , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[29]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[30]  Károly Mirnics,et al.  Microarrays in brain research: the good, the bad and the ugly , 2001, Nature Reviews Neuroscience.

[31]  Cheng Li,et al.  Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application , 2001, Genome Biology.

[32]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[33]  H. Zoghbi,et al.  Modelling brain diseases in mice: the challenges of design and analysis , 2003, Nature Reviews Genetics.

[34]  M. Morley,et al.  Making and reading microarrays , 1999, Nature Genetics.

[35]  J. Trojanowski,et al.  Gene expression profile for schizophrenia: discrete neuron transcription patterns in the entorhinal cortex. , 2002, Archives of general psychiatry.

[36]  Avrum Spira,et al.  Guidelines: Expression profiling — best practices for data generation and interpretation in clinical trials , 2004 .

[37]  J M Lee,et al.  A gene expression profile of Alzheimer's disease. , 2001, DNA and cell biology.

[38]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[39]  J. Pierri,et al.  Gene Expression Profiling Reveals Alterations of Specific Metabolic Pathways in Schizophrenia , 2002, The Journal of Neuroscience.

[40]  Shuichi Tsutsumi,et al.  Distinction in gene expression profiles of oligodendrogliomas with and without allelic loss of 1p , 2002, Oncogene.

[41]  Michael Gill,et al.  Confirming RGS4 as a susceptibility gene for schizophrenia , 2004, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[42]  B. Devlin,et al.  Association and linkage analyses of RGS4 polymorphisms in schizophrenia. , 2002, Human molecular genetics.

[43]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[44]  M. Ball,et al.  Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: Transcription and neurotrophic factor down‐regulation and up‐regulation of apoptotic and pro‐inflammatory signaling , 2002, Journal of neuroscience research.

[45]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[46]  R. Harris,et al.  Application of DNA microarrays to study human alcoholism. , 2001, Journal of biomedical science.

[47]  Paul J. Harrison Schizophrenia: a disorder of neurodevelopment? , 1997, Current Opinion in Neurobiology.

[48]  J. Weingarten,et al.  Predominance of neuronal mRNAs in individual Alzheimer's disease senile plaques , 1999, Annals of neurology.

[49]  R. Yolken,et al.  The Stanley Foundation brain collection and Neuropathology Consortium , 2000, Schizophrenia Research.

[50]  M. Bannon,et al.  Gene expression profile of the nucleus accumbens of human cocaine abusers: evidence for dysregulation of myelin , 2004, Journal of neurochemistry.

[51]  D. Lockhart,et al.  Expression monitoring by hybridization to high-density oligonucleotide arrays , 1996, Nature Biotechnology.

[52]  Daniel R Weinberger,et al.  Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study , 2002, Schizophrenia Research.

[53]  David A Lewis,et al.  The Human Brain Revisited: Opportunities and Challenges in Postmortem Studies of Psychiatric Disorders , 2002, Neuropsychopharmacology.

[54]  Jane Pickett Current Investigations in Autism Brain Tissue Research , 2001, Journal of autism and developmental disorders.

[55]  F. Middleton,et al.  Gene Expression Profiling with DNA Microarrays: Advancing Our Understanding of Psychiatric Disorders , 2002, Neurochemical Research.

[56]  Pat Levitt,et al.  Analysis of complex brain disorders with gene expression microarrays: schizophrenia as a disease of the synapse , 2001, Trends in Neurosciences.

[57]  R. Harris,et al.  Gene expression in human alcoholism: microarray analysis of frontal cortex. , 2000, Alcoholism, clinical and experimental research.

[58]  R. Myers,et al.  DNA microarray analysis of functionally discrete human brain regions reveals divergent transcriptional profiles , 2003, Neurobiology of Disease.

[59]  Pat Levitt,et al.  Molecular Characterization of Schizophrenia Viewed by Microarray Analysis of Gene Expression in Prefrontal Cortex , 2000, Neuron.

[60]  M K Kerr,et al.  Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[61]  Susan M. Chang,et al.  Grade II astrocytomas are subgrouped by chromosome aberrations. , 2003, Cancer genetics and cytogenetics.

[62]  J. Trojanowski,et al.  Expression profile of transcripts in Alzheimer's disease tangle‐bearing CA1 neurons , 2000, Annals of neurology.

[63]  R. Jaenisch,et al.  Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[64]  J. Trent,et al.  Analysis of gene expression in mutiple sclerosis lesions using cDNA microarrays. , 1999, Annals of neurology.