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Gene Expression in HIV-Associated Dementia

  • Chapter
Inflammatory Disorders of the Nervous System

Part of the book series: Current Clinical Neurology ((CCNEU))

Abstract

In past decades, the prime methods used for the study of genes and their respective products were Northern blots, Western blots, in situ hybridization, and immunocytochemistry. The applicability of these methods was restricted to the study of single genes or a few simultaneously (1,2).

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References

  1. Geschwind DH. DNA microarrays: translation of the genome from laboratory to clinic. Lancet Neurol 2003;2:275–282.

    Article  PubMed  CAS  Google Scholar 

  2. Minagar A, Shapshak P, Duran EM, et al. Gene expression in HIV-associated dementia, Alzheimer’s disease, multiple sclerosis, and schizophrenia. Under review, 2004.

    Google Scholar 

  3. Marcotte ER, Srivastava LK, Quirion R. cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer’s disease. Pharmacol Ther 2003;100:63–74.

    Article  PubMed  CAS  Google Scholar 

  4. Shapshak P, Stengel R. Discovering brain mechanisms and the rules of molecular biology. 6th World Multiconference on Systemics, Cybernetics and Informatics. Orlando, FL, July 14–18, 2002. Available from: www.iiis. org/sci2002/.

    Google Scholar 

  5. Goodkin K, Wilkie FL, Concha M, et al. Subtle neuropsychologic impairment and minor cognitive-motor disorder in HIV-1 infection. Neuroimaging of AIDS II. Neuroimaging Clin N Am, 1997;7:561–579.

    PubMed  CAS  Google Scholar 

  6. Goodkin K, Shapshak P, Wilkie FL, et al. Immune function, brain, and HIV-1 infection. In Goodkin K, Visser A, eds. Psychoneuroimmunology: Stress, Mental Disorders & Health. Washington, DC, American Psychiatric Association, 1999.

    Google Scholar 

  7. Goodkin K, Baldewicz TT, Wilkie FL, Tyll MD, Shapshak P. HIV-1 infection of brain: a region-specific approach to its neuropathophysiology and therapeutic prospects. Psychiatric Annals 2001;31:182–192.

    Google Scholar 

  8. Sperber K, Shao L. Neurologic consequences of HIV infection in the ERA of HAART. AIDS Patient Care STDs. 2003;17:509–518.

    Article  PubMed  Google Scholar 

  9. Torres-Munoz J, Stockton P, Tacoronte N, Roberts B, Maronpot RR, Petito CK. Detection of HIV-1 gene sequences in hippocampal neurons isolated from postmortem AIDS brains by laser capture microdissection. J Neuropathol Exp Neurol 2001;60:885–892.

    PubMed  CAS  Google Scholar 

  10. Hesselgesser J, Halks-Miller M, DelVecchio V, et al. CD4-independent association between HIV-1 gp120 and CXCR4: functional chemokine receptors are expressed in human neurons. Curr Biol 1997;7:112–121.

    Article  PubMed  CAS  Google Scholar 

  11. Fischer-Smith T, Croul S, Sverstiuk AE, et al. CNS invasion by CD14+/CD16+ peripheral blood-derived monocytes in HIV dementia: perivascular accumulation and reservoir of HIV infection. J Neurovirol. 2001;7:528–541.

    Article  PubMed  CAS  Google Scholar 

  12. Ohagen A, Devitt A, Kunstman KJ, et al. Genetic and functional analysis of full-length human immunodeficiency virus type 1 env genes derived from brain and blood of patients with AIDS. J Virol 2003;77:12,336–12,345.

    Article  PubMed  CAS  Google Scholar 

  13. Shapshak P, Segal DM, Crandall KA, et al. Independent evolution of HIV type I in different brain regions. AIDS Res Hum Retroviruses 1999;15:811–820.

    Article  PubMed  CAS  Google Scholar 

  14. Morris A, Marsden M, Halcrow K, et al. Mosaic structure of the HIV-1 genome infecting lymphoid cells and the brain: evidence for frequent in vivo recombination events in the evolution of region populations. J Virol 1999;73:720–731.

    Google Scholar 

  15. Eilbott DJ, Peress N, Burger H, et al. Human immunodeficiency virus type 1 in spinal cords of acquired immunodeficiency syndrome patients with myelopathy: expression and replication in macrophages. Proc Natl Acad Sci USA 1989;86:3337–3341.

    Article  PubMed  CAS  Google Scholar 

  16. Yoshioka M, Shapshak P, Sun NCJ, et al. Ferritin immunoreactivity in microglial nodules in AIDS brain, Acta Neuropathologica 1992;84:297–306.

    Article  PubMed  CAS  Google Scholar 

  17. Nukuna A, Gendelman HE, Limoges J, et al. Levels of HIV replicaton in macrophages determines the severity of murine HIV-1 encephalitis. J Neurovirol 2004;10(Suppl 1):82–90.

    PubMed  Google Scholar 

  18. Galey D, Becker K, Haughey N, et al. Differential transcriptional regulation by human immunodeficiency virus type 1 and gp120 in human astrocytes. J Neurovirol 2003;9:358–371.

    Article  PubMed  CAS  Google Scholar 

  19. Shapshak P, Duncan D, Minagar D, Rodriguez de la Vega P, Stewart R, Petito CK. Elevated expression of IFN-γ in the HIV-1 infected brain. Front Biosci 2004;9:1073–1081.

    Article  PubMed  CAS  Google Scholar 

  20. Vitkovic L, J Bockaert, C Jacque. Inflammatory cytokines: neuromodulators in normal brain? J Neurochem 2000;74:457–471.

    Article  PubMed  CAS  Google Scholar 

  21. Zeng J, Ghorpade A, Niemann D, et al. Lymphotropic virions affect chemokine receptor-mediated neural signaling and apoptosis: implications for HIV-1 associated dementia. J Virol 1999;73:8256–8267.

    Google Scholar 

  22. Geiss GK, Bumgarner RE, An MC, et al Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays. Virology 2000;266:8–16.

    Article  PubMed  CAS  Google Scholar 

  23. Roberts ES, Zandonatti MA, Watry DD, Madden LJ, Henriksen MA, Fox HS. Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS. Am J Pathol 2003;162;2041–2057.

    PubMed  CAS  Google Scholar 

  24. Sui Y, Potula R, Pinson D, et al. Microarray analysis of cytokine and chemokine genes in the brains of macaques with SHIV-encephalitis, J Med Primatol 2003;32:229–239.

    Article  PubMed  CAS  Google Scholar 

  25. Vahey MT, Nau ME, Taubman M, Yalley-Ogunro J, Silvera P, Lewis MG. Patterns of gene expression in PBMNCs of rhesus macaques infected with SIVmac251 and exhibiting differential rates of disease progression. AIDS Res Hum Retrov 2003;19:369–387.

    Article  CAS  Google Scholar 

  26. Shapshak P, Torres-Munos J, Petito CK. Bioinformatics in neurodegenerative diseases. Proc Virt Conf Genom Bioinf. North Dakota State University, 2001. Available from: www.ndsu/virtual-genomics.

    Google Scholar 

  27. Shapshak, P, Duncan, R, Torres-Munoz JE, Duran EM, Minagar A, Petito CK. Analytic approaches to differential gene expression in AIDS vs. control brains. Front Biosci 2004;9:2935–2946.

    Article  PubMed  CAS  Google Scholar 

  28. Liu G, Loraine AE, Shigeta R, et al. NetAffx: affymetrix probesets and annotations. Nucleic Acids Res 2003;31:82–86.

    Article  PubMed  CAS  Google Scholar 

  29. Kerr MK, Churchill GA. Bootstrapping cluster analysis: assessing the reliability of conclusions from microarray experiments. Proc Natl Acad Sci USA 2001;98:8961–8965.

    Article  PubMed  CAS  Google Scholar 

  30. Zien A, Fluck J, Zimmer R, Lengauer T. Microarrays: how many do you need? J Comp Biol 2003;10:653–667.

    Article  CAS  Google Scholar 

  31. Alter O, Brown PO, Botstein D. Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 2000;97:10,101–10,106.

    Article  PubMed  CAS  Google Scholar 

  32. Bicciato S, Luchini A, Di Bello C. PCA disjoint models for multiclass cancer analysis using gene expression data. Bioinformatics 2003;19:571–578.

    Article  PubMed  CAS  Google Scholar 

  33. Nguyen DV, Rocke DM. Tumor classification by partial least squares using Microarray gene expression data. Bioinformatics 2002;8:39–50.

    Article  Google Scholar 

  34. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 1998;95:14,863–14,868.

    Article  PubMed  CAS  Google Scholar 

  35. Huber W, Von Heydebreck A, Sultmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002;18(Suppl 1):S96–S104.

    PubMed  Google Scholar 

  36. Giles PJ, Kipling D. Normality of oligonucleotide microarray data and implications for parametric statistical analyses. Bioinformatics 2003;19:2254–2262.

    Article  PubMed  CAS  Google Scholar 

  37. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001;98:5116–5121.

    Article  PubMed  CAS  Google Scholar 

  38. Geschwind DH, Gregg JP. Microarrays for the Neurosciences. Cambridge, MA, MIT Press, 2002.

    Google Scholar 

  39. Sherlock G, Hernandez-Boussard T, Kasarskis A, et al. The Stanford Microarray Database. Nucleic Acids Res 2001;29:152–155.

    Article  PubMed  CAS  Google Scholar 

  40. Killon PJ, Sherlock G, Iyer VR. The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD). BMC Bioinfo 2003;4:32–38.

    Article  Google Scholar 

  41. Saal LH, Troein C, Vallon-Christersson J, Gruvberger S, Borg A, Peterson C. BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. Genome Biol: software0003.1-software 0003.6, 2002.

    Google Scholar 

  42. Ermolaeva O, Rastogi M, Pruitt KD, et al. Data management and analysis for gene expression arrays. Nature Genet 1998;20:19–23.

    Article  PubMed  CAS  Google Scholar 

  43. Brazma A, Parkinson H, Sarkans U, et al. ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Res 2003;31:68–71.

    Article  PubMed  CAS  Google Scholar 

  44. Gollub J, Ball CA, Binkley G, et al. The Stanford Microarray Database: data access and quality assessment tools. Nucleic Acids Res 2003;31:94–96.

    Article  PubMed  CAS  Google Scholar 

  45. Cornell M, Paton NW, Hedeler C, et al. GIMS: an integrated data storage and analysis environment for genomic and. Yeast 2003;20:1291–1306.

    Article  PubMed  CAS  Google Scholar 

  46. Aach J, Rindone W, Church G. Systematic management and analysis of yeast gene expression data. Genome Res 2000;10:431–445.

    Article  PubMed  CAS  Google Scholar 

  47. Dennis G Jr, Sherman BT, Hosack DA, et al. David: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003;4:P3.

    Article  PubMed  Google Scholar 

  48. Chen J, Zhao P, Massaro D, et al. The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. Nucleic Acids Res 2004;32:D578–D581.

    Article  PubMed  CAS  Google Scholar 

  49. Kasprzyk A, Keefe D, Smedley D, et al. Ensmart: a generic system for fast and flexible access to biological data. Genome Res 2004;14:160–169.

    Article  PubMed  CAS  Google Scholar 

  50. Grant JD, Somers LA, Zhang Y, Manion FJ, Bidaut G, Ochs MF. Fgdp: functional genomics data pipeline for automated, multiple microarray data analyses. Bioinformatics 2004;20:282–283.

    Article  PubMed  CAS  Google Scholar 

  51. Toga AW. Imaging databases and neuroscience. Neuroscientist 2002;8:423–436.

    Article  PubMed  Google Scholar 

  52. Van Horn JD, Grethe JS, Kostelec P, et al. The functional magnetic resonance imaging data center (FMRIDC): the challenges and rewards of large-scale databasing of neuroimaging studies. Phil Trans Roy Soc (London) B 2001;356:1323–1339.

    Article  Google Scholar 

  53. Dickson J, Drury H, van Essen D. “The surface management system” (SUMS) database: a surface-based database to aid cortical surface reconstruction, visualization and analysis. Phil Trans Roy Soc (London) B 2001;356:1277–1292.

    Article  CAS  Google Scholar 

  54. Peterson BE, Healy MD, Nadkarni PM, Miller PL, Shepherd GM. Modeldb: an environment for running and storing computational models and their results applied to neuroscience. J Am Med Inform Assoc 1996;3:389–398.

    PubMed  CAS  Google Scholar 

  55. Bota M, Arbib MA. Integrating databases and expert systems for the analysis of brain structures: connections, similarities, and homologies. Neuroinformatics 2004;2:19–58.

    Article  PubMed  Google Scholar 

  56. Brazma A, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (miame) — toward standards for microarray data. Nature Genet 2001;29:365–371.

    Article  PubMed  CAS  Google Scholar 

  57. MAGE-OM Working Group. MAGE-OM. MGED Society. 2003-present. Available from: www.mged.org/Work-groups/MAGE/mage-om.html.

    Google Scholar 

  58. MIAME Working Group. Minimum information about a microarray experiment ∼ MIAME. MGED Society. 2003-present. Available from: www.mged.org/-Workgroups/MIAME/miame.html.

    Google Scholar 

  59. MIAME Working Group. Minimum information about a microarray experiment, MIAME. MGED Society. 2003-present.

    Google Scholar 

  60. Spellman PT, Miller M, Stewart J, et al. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 2002;3:RESEARCH 0046.1-0046.9.

    Google Scholar 

  61. Ashburner M, Ball CA, Blake JA, et al. Gene Ontology: tool for the unification of biology. Nature Genet 2000;25:25–29.

    Article  PubMed  CAS  Google Scholar 

  62. EMAGE Editorial Office (2003-present). EMAGE gene expression database. Available from: http://genex.hgu.mrc.ac.uk/Emage/database/-emageIntro.html/.

  63. Amari SI, Beltrame F, Bjaalie JG, et al. Neuroinformatics: the integration of shared databases and tools towards integrative neuroscience. J Integ Neurosci 2002;1:117–128.

    Article  Google Scholar 

  64. Dashti AE, Ghandeharizadeh S, Stone J, Swanson LW, Thompson RH. Database challenges and solutions in neuro-scientific applications. Neuroimage 1997;5:97–115.

    Article  PubMed  CAS  Google Scholar 

  65. Gardner D, Knuth K, Abato M, et al. Common data model for neuroscience data and data model exchange. J Am Med Inform Assoc 2001;8:17–33.

    PubMed  CAS  Google Scholar 

  66. Gorin F, Hogarth M, Gertz M. The challenges and rewards of integrating diverse neuroscience. Neuroscientist 2001;7:18–27.

    PubMed  CAS  Google Scholar 

  67. Bowden DM, Martin RF. Neuronames brain hierarchy. Neuroimage 1995;2:63–83. Available from: www.mged.org/Workgroups/MIAME/miame.html.

    Article  PubMed  CAS  Google Scholar 

  68. Hole W, Srinivasan S. Adding NeuroNames to the UMLS Metathesaurus. Neuroinformatics 2003;1:61–63.

    Article  PubMed  Google Scholar 

  69. Bowden D, Dubach M. Neuronames 2002. Neuroinformatics 2003;1:43

    Article  PubMed  Google Scholar 

  70. Roland P, Svensson G, Lindeberg T, et al. A database generator for human brain imaging. Trends Neurosci 2001;24:562–564.

    Article  PubMed  CAS  Google Scholar 

  71. Kazic T. Semiotes a semantics for sharing. Bioinformatics 16:1129–1144. Available from: www.biocheminfo.org/repository/semiotes.ps.

    Google Scholar 

  72. Wiederhold G, Jannink J. Composing diverse ontologies. Stanford University. Available from: www.db.stanford.edu/SKC/publications/ifip99.html.

    Google Scholar 

  73. Chilukuri P, Kazic T. Semantic interoperability of heterogeneous systems. University of Missouri Bioinformatics Technical Report, 2004-01. Available from: www.biocheminfo.org/repository/parser.ps.

    Google Scholar 

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Author information

Authors and Affiliations

  1. Departments of Psychiatry and Behavioral Sciences, Neurology, Pathology, Comprehensive Drug Research Center, and Pediatrics McDonald Foundation Gene Team, University of Miami School of Medicine, Miami, FL

    Paul Shapshak PhD

  2. Department of Neurology, Louisiana State University Health Sciences Center, Shreveport, LA

    Alireza Minagar MD

  3. Departments of Psychiatry and Behavioral Sciences, University of Miami School of Medicine, Miami, FL

    Elda M. Duran MS & Fabiana Ziegler MD

  4. Department of Statistics, Baylor University, Waco, TX

    Wade Davis PhD

  5. Departments of Computer Science and Health Management Informatics, University of Missouri, Columbia, MO

    Raman Seth MBBS, MS & Toni Kazic PhD

Authors
  1. Paul Shapshak PhD
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  2. Alireza Minagar MD
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  3. Elda M. Duran MS
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  4. Fabiana Ziegler MD
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  5. Wade Davis PhD
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  6. Raman Seth MBBS, MS
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  7. Toni Kazic PhD
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Editor information

Editors and Affiliations

  1. Louisiana State University Health Science Center, Shreveport, LA

    Alireza Minagar MD  & J. Steven Alexander PhD  & 

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Shapshak, P. et al. (2005). Gene Expression in HIV-Associated Dementia. In: Minagar, A., Alexander, J.S. (eds) Inflammatory Disorders of the Nervous System. Current Clinical Neurology. Humana Press. https://doi.org/10.1385/1-59259-905-2:305

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  • DOI: https://doi.org/10.1385/1-59259-905-2:305

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-424-1

  • Online ISBN: 978-1-59259-905-9

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