HIV-associated dementia, Alzheimer's disease, multiple sclerosis, and schizophrenia: Gene expression review

Journal of the Neurological Sciences

Volumn 224, Issue 1-2, 2004, Pages 3-17

  Minagar, Alireza ^a,f   Shapshak, Paul ^b   Duran, Elda M ^c   Kablinger, Anita S ^d   Alexander, J Steven ^d   Kelley, Roger E ^d   Seth, Raman ^e   Kazic, Toni ^e  

^a Louisiana State Univ S   (United States)

^b Neurology

^c UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^d Louisiana State University School of Medicine Shreveport   (United States)

^e UNIVERSITY OF MISSOURI   (United States)

^f LOUISIANA STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Alzheimer's disease; Bioinformatics; Gene expression; HIV associated dementia; Microarray; Multiple sclerosis; Schizophrenia

Indexed keywords

ANTIRETROVIRUS AGENT; PROTEIN DERIVATIVE;

ALZHEIMER DISEASE; ANALYSIS OF VARIANCE; ASTROCYTE; BIOINFORMATICS; CELL CULTURE; CELL INTERACTION; COMPLEX FORMATION; CORRELATION ANALYSIS; DEMENTIA; DEMYELINATION; DISEASE ASSOCIATION; DISEASE COURSE; DNA MICROARRAY; DNA SEQUENCE; GENE CONTROL; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC CODE; GENETIC SUSCEPTIBILITY; GENETIC TRANSCRIPTION; HIGHLY ACTIVE ANTIRETROVIRAL THERAPY; HIV ASSOCIATED DEMENTIA; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IN SITU HYBRIDIZATION; MULTIPLE SCLEROSIS; NEUROTRANSMISSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PRIORITY JOURNAL; REVIEW; SCHIZOPHRENIA; STATISTICAL SIGNIFICANCE; TECHNIQUE; UNINDEXED SEQUENCE;

AIDS DEMENTIA COMPLEX; ALZHEIMER DISEASE; GENE EXPRESSION; GENE EXPRESSION PROFILING; HIV INFECTIONS; HUMANS; MULTIPLE SCLEROSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SCHIZOPHRENIA;

EID: 4644360165     PISSN: 0022510X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jns.2004.06.007     Document Type: Review

References (99)

1. D.H. Geschwind DNA microarrays: translation of the genome from laboratory to clinic Lancet Neurol. 2 2003 275 282
2. E.R. Marcotte, L.K. Srivastava, and R. Quirion cDNA microarray and proteomic approaches in the study of brain diseases: focus on schizophrenia and Alzheimer's disease Pharmacol. Ther. 100 1 2003 63 74
3. P. Shapshak, and R. Stengel Discovering Brain Mechanisms and the rules of Molecular Biology 6th World Multiconference on Systemics, Cybernetics and Informatics, Orlando, FL, July 14-18. www.iiis.org/sci2002/
4. A. Minagar, P. Shapshak, M. Heyes, R. Fujimura, C. Eisdorfer, and R. Ownby Microglia and astrocytes in neuro-AIDS, Alzheimer's disease, and multiple sclerosis J. Neurol. Sci. 202 2002 13 23
5. T. Kazic Semiotes a semantics for sharing Bioinformatics 16 2000 1129 1144 [Also at http://www.biocheminfo.org/repository/semiotes.ps]
6. K. Goodkin, F.L. Wilkie, M. Concha, D. Asthana, and P. Shapshak Subtle neuropsychologic impairment and minor cognitive-motor disorder in HIV-1 infection Neuroimaging Clin. N. Am., Neuroimaging of AIDS II 7 1997 561 579
7. K. Goodkin, and P. Shapshak Immune function, brain, and HIV-1 infection K. Goodkin A. Visser Psychoneuroimmunology: stress, mental disorders and health 1999 American Psychiatric Assoc. Press Washington, DC 243 315
8. K. Goodkin, T.T. Baldewicz, F.L. Wilkie, M.D. Tyll, and P. Shapshak HIV-1 infection of brain: a region-specific approach to its neuropathophysiology and therapeutic prospects Psychiatric Annals 31 2001 182 192
9. K. Sperber, and L. Shao Neurologic consequences of HIV infection in the ERA of HAART AIDS Patient Care STDs 17 10 2003 509 518
10. J. Torres-Munoz, P. Stockton, N. Tacoronte, B. Roberts, R.R. Maronpot, and C.K. Petito Detection of HIV-1 gene sequences in hippocampal neurons isolated from postmortem AIDS brains by laser capture microdissection J. Neuropathol. Exp. Neurol. 60 9 2001 (Sep.) 885 892
11. J. Hesselgesser, M. Halks-Miller, V. DelVecchio, S.C. Peiper, J. Hoxie, and D.L. Kolson CD4-independent association between HIV-1 gp120 and CXCR4: functional chemokine receptors are expressed in human neurons Curr. Biol. 7 2 1997 112 121
12. L. Resnick, J.R. Berger, P. Shapshak, and W.W. Tourtellotte Early penetration of the blood-brain-barrier by HTLV-III/LAV Neurology 38 1988 9 15
13. E.J. Singer, K. Syndulko, B.N. Fahy-Chandon, P. Shapshak, L. Resnick, and P. Schmid Cerebrospinal fluid p24 antigen levels and intrathecal immunoglobulin G synthesis are associated with cognitive disease severity in HIV-1 AIDS 8 1994 197 204
14. S. Gartner HIV infection and dementia Science 287 2000 602
15. S. Gartner, and Y. Liu Insights into the role of immune activation in HIV neuropathogenesis J. Neurovirol. 8 2002 69
16. T. Fischer-Smith, S. Croul, A.E. Sverstiuk, C. Capini, D. L'Heureux, and E.G. Regulir CNS invasion by CD14+/CD16+ peripheral blood-derived monocytes in HIV dementia: perivascular accumulation and reservoir of HIV infection J. Neurovirol. 7 6 2001 528 541
17. A. Ohagen, A. Devitt, K.J. Krunstman, P.R. Gorry, P.P. Rose, and B. Korber Genetic and functional analysis of full length HIV-1 env genes derived from brain and blood of patients with AIDS J. Virol. 77 22 2003 12336 12345
18. P. Shapshak, D.M. Segal, K.A. Crandall, R.K. Fujimura, B.T. Zhang, and K.Q. Xin Independent evolution of HIV type I in different brain regions AIDS Res. Hum. Retroviruses 15 9 1999 811 820
19. A. Morris, M. Marsden, K. Halcrow, E.S. Hughes, R.P. Brettle, and J.E. Bell 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. 73 10 1999 8720 8731
20. G.K. Geiss, R.E. Bumgarner, and M.C. An Large-scale monitoring of host cell gene expression during HIV-1 infection using cDNA microarrays Virology 266 2000 8 16
21. D. Galey, K. Becker, N. Haughey, A. Kalehua, D. Taub, and J. Woodward Differential transcriptional regulation by human immunodeficiency virus type 1 and gp120 in human astrocytes J. Neurovirol. 9 3 2003 358 371
22. P. Shapshak, D. Duncan, D. Minagar, P. Rodriguez de la Vega, R. Stewart, and C.K. Petito Elevated expression of IFN-γ in the HIV-1 infected brain Front. Biosci. 9 2004 1073 1081
23. J. Zeng, A. Ghorpade, D. Niemann, and R. Cotter Lymphotropic virions affect chemokine receptor-mediated neural signaling and apoptosis: Implications for HIV-1 associated dementia J. Virol. 73 10 1999 8256 8267
24. E.S. Roberts, M.A. Zandonatti, D.D. Watry, L.J. Madden, M.A. Henriksen, and H.S. Fox Induction of pathogenic sets of genes in macrophages and neurons in NeuroAIDS Am. J. Pathol. 162 2003 2041 2057
25. Y. Sui, R. Potula, D. Pinson, I. Adany, Z. Li, and J. Day Microarray analysis of cytokine and chemokine genes in the brains of macaques with SHIV-encephalitis J. Med. Primatol. 32 2003 229 239
26. M.T. Vahey, M.E. Nau, M. Taubman, J. Yalley-Ogunro, P. Silvera, and M.G. Lewis Patterns of gene expression in PBMNCs of Rhesus Macaques infected with SIVmac251 and exhibiting differential rates of disease progression AIDS Res. Hum. Retroviruses 19 2003 369 387
27. P. Shapshak, J. Torres-Munos, and C.K. Petito Bioinformatics in neurodegenerative diseases Proc. Virt. Conf. Genom. and Bioinf, North Dakota State University 2001 www.ndsu/virtual-genomics
28. P. Shapshak, R. Duncan, J.E. Torres-Munoz, and A. Minagar Problems and solutions in gene expression studies in AIDS J. Neurovirol. 9 2003 136
29. P. Shapshak, R. Duncan, J.E. Torres-Munoz, E.M. Duran, A. Minagar, and C.K. Petito Analytic approaches to differential Gene Expression in AIDS vs. Control Brains Front. Biosci. 9 2004 2935 2946
30. R. Bullock Cholinesterase inhibitors and vascular dementia: another string to their bow? CNS Drugs 18 2004 79 92
31. S.D. Ginsberg, S.E. Hemby, V.M. Lee, J.H. Eberwine, and J.Q. Trojanowski Expression profile of transcripts in Alzheimer's disease tangle-bearing CA1 neurons Ann. Neurol. 48 1 2000 77 87
32. J.F. Loring, X. Wen, J.M. Lee, J. Seilhamer, and R. Somogyi A gene expression profile of Alzheimer's disease DNA Cell Biol. 20 2001 683 695
33. G.M. Pasinetti Use of cDNA microarray in the search for molecular markers involved in the onset of Alzheimer's disease dementia J. Neurosci. Res. 65 6 2001 471 476
34. V. Colangelo, J. Schurr, M.J. Ball, R.P. Pelaez, N.G. Bazan, and W.J. Lukiw 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 J. Neurosci. Res. 70 3 2002 462 473
35. D.G. Walker, L.F. Lue, and T.G. Beach Increased expression of the urokinase plasminogen-activator receptor in amyloid beta peptide-treated human brain microglia and in AD brains Brain Res. 926 1-2 2002 69 79
36. W.W. Tourtellotte, S.N. Staugaitis, M.J. Walsh, P. Shapshak, R.W. Baumhefner, and A.R. Potvin The scientific basis of intra-BBB IgG synthesis Ann. Neurol. 17 1985 21 27
37. W.W. Tourtellotte, R.W. Baumheffner, P. Shapshak, and M. Osborne The status of intra-blood brain barrier IgG synthesis in multiple sclerosis Rev. Neurol. 57 1987 236 238
38. J.H. Noseworthy, C. Lucchinetti, M. Rodriguez, and B.G. Weinshenker Multiple sclerosis N. Engl. J. Med. 343 13 2000 938 952
39. L.W. Whitney, K.G. Becker, N.J. Tresser, C.I. Caballero-Ramos, P.J. Munson, and V.V. Prabhu Analysis of gene expression in multiple sclerosis lesions using cDNA microarrays Ann. Neurol. 46 3 1999 425 428
40. D. Chabas, S.E. Baranzini, D. Mitchell, C.C. Bernard, S.R. Rittling, and D.T. Denhardt The influence of the proinflammatory cytokine, osteopontin, on autoimmune demyelinating disease Science 294 5547 2001 1731 1735
41. C. Lock, G. Hermans, R. Pedotti, A. Brendolan, E. Schadt, and H. Garren Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis Nat. Med. 8 5 2002 500 508
42. F. Zavala, S. Abad, S. Ezine, V. Taupin, A. Masson, and J.F. Bach G-CSF therapy of ongoing experimental allergic encephalomyelitis via chemokine- and cytokine-based immune deviation J. Immunol. 168 4 2002 2011 2019
43. K.B. Abdul-Majid, A. Stefferl, C. Bourquin, H. Lassmann, C. Linington, and T. Olsson Fc receptors are critical for autoimmune inflammatory damage to the central nervous system in experimental autoimmune encephalomyelitis Scand. J. Immunol. 55 1 2002 70 81
44. R.J. Carmody, B. Hilliard, K. Maguschak, L.A. Chodosh, and Y.H. Chen Genomic scale profiling of autoimmune inflammation in the central nervous system: the nervous response to inflammation J. Neuroimmunol. 133 1-2 2002 95 107
45. M.P. Mycko, R. Papoian, U. Boschert, C.S. Raine, and K.W. Selmaj cDNA microarray analysis in multiple sclerosis lesions: detection of genes associated with disease activity Brain 126 Pt 5 2003 1048 1057
46. F. Koike, J. Satoh, S. Miyake, T. Yamamoto, M. Kawai, and S. Kikuchi Microarray analysis identifies interferon beta-regulated genes in multiple sclerosis J. Neuroimmunol. 139 1-2 2003 109 118
47. B. Capuano, I.T. Crosby, and E.J. Lloyd Schizophrenia: genesis, receptorology and current therapeutics Curr. Med. Chem. 9 5 2002 521 548
48. A.S. Kablinger, and A.M. Freeman III Prodromal schizophrenia and atypical antipsychotic treatment J. Nerv. Ment. Dis. 188 10 2000 642 652
49. B. Moghaddam, and M.E. Jackson Glutamatergic animal models of schizophrenia Ann. N. Y. Acad. Sci. 1003 2003 131 137
50. J.W. Olney, J.W. Newcomer, and N.B. Farber NMDA receptor hypofunction model of schizophrenia J. Psychiatr. Res. 33 1999 523 533
51. F.M. Benes The relationship between structural brain imaging and histopathologic findings in schizophrenia research Harv. Rev. Psychiatry 1 2 1993 100 109
52. F.M. Benes Alterations of neural circuitry within layer II of anterior cingulate cortex in schizophrenia J. Psychiatr. Res. 33 6 1999 511 512
53. B.K. Lipska, G.E. Jaskiw, and D.R. Weinberger Postpubertal emergence of hyperresponsiveness to stress and to amphetamine after neonatal excitotoxic hippocampal damage: a potential animal model of schizophrenia Neuropsychopharmacology 9 1993 67 75
54. B.C. Ho, N.C. Andreasen, P. Nopoulos, S. Arndt, V. Magnotta, and M. Flaum Progressive structural brain abnormalities and their relationship to clinical outcome: a longitudinal magnetic resonance imaging study early in schizophrenia Arch. Gen. Psychiatry 60 2003 585 594
55. G. Bartzokis, K.H. Nuechterlein, P.H. Lu, M. Gitlin, S. Rogers, and J. Mintz Dysregulated brain development in adult men with schizophrenia: a magnetic resonance imaging study Biol. Psychiatry 53 5 2003 412 421
56. E.F. Walker, D. Diforio, and K. Baum Developmental neuropathology and the precursors of schizophrenia Acta Psychiatr. Scand. Suppl. 395 1999 12 19
57. K. Mirnics, F.A. Middleton, A. Marquez, D.A. Lewis, and P. Levitt Molecular characterization of schizophrenia viewed by microarray analysis of gene expression in prefrontal cortex Neuron 28 2000 53 67
58. Y. Hakak, J.R. Walker, C. Li, W.H. Wong, K.L. Davis, and J.D. Buxbaum Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia Proc. Natl. Acad. Sci. U. S. A. 98 8 2001 4746 4751
59. M.P. Vawter, J.M. Crook, T.M. Hyde, J.E. Kleinman, D.R. Weinberger, and K.G. Becker Microarray analysis of gene expression in the prefrontal cortex in schizophrenia: a preliminary study Schizophrenia Res. 58 2002 11 20
60. S.E. Hemby, S.D. Ginsberg, B. Brunk, S.E. Arnold, J.Q. Trojanowski, and J.H. Eberwine Gene expression profile for schizophrenia: discrete neuron transcription patterns in the entorhinal cortex Arch. Gen. Psychiatry 59 2002 631 640
61. J. Golub, C.A. Ball, G. Binkley, J. Demeter, D.B. Finkelstein, and J.M. Hebert The Stanford Microarray Database: data access and quality assessment tools Nucleic Acids Res. 31 2003 94 96
62. P.J. Killon, G. Sherlock, and V.R. Iyer The Longhorn Array Database (LAD): an open-source, MIAME compliant implementation of the Stanford Microarray Database (SMD) BMC Bioinformatics 4 2003 32 38
63. L.H. Saal, C. Troein, J. Vallon-Christersson, S. Gruvberger, A. Borg, and C. Peterson BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data Genome Biol. 2002 [software0003.1-software0003.6.2002]
64. Altman RB, Klein TE, Jung T, Carrillo M, Hewett M, Rubin D, et al., 2003-present; PharmGKB. pharmgkb.org, http://pharmgkb.org/index.jsp.
65. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, and J.M. Cherry Gene Ontology: tool for the unification of biology Nat. Genet. 25 2000 25 29
66. B.L. Humphreys, and D.A.B. Lindberg The UMLS project: making the conceptual connection between users and the information they need Bull. Med. Libr. Assoc. 81 1993 170 177
67. MAGE-OM Working Group, 2003-present. MAGE-OM. MGED Society, http://www.mged.org/Workgroups/MAGE/mage-om.html.
68. Microarray Gene Expression Data Society, 2002-present. MGED Home. Microarray Gene Expression Data Society, http://www.mged.org/.
69. S.J. Nelson, L.F. Fuller, M.S. Earlbaum, M.S. Tuttle, D.D. Sherertz, and N.E. Olson The semantic structure of the UMLS metathesarus M.E. Frisse Sixteenth annual symposium on computer applications in medical care: a conference of the american medical informatics association 1993 McGraw-Hill New York 649 653
70. P.T. Spellman, M. Miller, J. Stewart, C. Troup, U. Sarkans, and S. Chervitz Design and implementation of microarray gene expression markup language (MAGE-ML) Genome Biol. 3 2002 [RESEARCH 0046.1-0046.9]
71. Gene Ontology Consortium, 2003-present. Gene Ontology Consortium. Gene Ontology Consortium, http://www.geneontology.org/.
72. Wiederhold G, Jannink J. Composing diverse ontologies. Stanford University, 1999; http://www-db.stanford.edu/SKC/publications/ifip99.html.
73. Genetic Information Research Institute, 2003-present. REPBASE UPDATE. Genetic Information Research Institute, http://www.girinst.org/RepbaseUpdate. html.
74. Murzin AG, Conte LL, Andreeva A, Howorth D, Ailey BG, Brenner SE, et al. SCOP: Structural Classification of Proteins. Cambridge University, 2003; http://scop.mrc-lmb.cam.ac.uk/scop/.
75. National Library of Medicine, 1966-present. MedLine/PubMed. National Library of Medicine, http://www.ncbi.nlm.nih.gov/entrez/query.fgci.
76. Alliance for Cellular Signaling, 2002-present. AFCS. Alliance for Cellular Signaling. Alliance for Cellular Signaling, http://www.afcs.org/.
77. Jiang J, Sanghi G, Kutikkad G, Bugrim A, Boyce S, Slomczynski J, et al. 2002-present. The Agora. University of Missouri, Columbia, MO, http://www.the-agora.org.
78. Futrelle RP, editor. 2003-present. Natural Language Processing of Biology Text. Northeastern University, http://www.ccs.neu.edu/home/futrelle/bionlp/.
79. National Institutes of Health, 2003-present. PubMed Central National Institutes of Health, http://www.pubmedcentralnih.gov/.
80. National Library of Medicine, 2003-present. Copyright Information and Downloading National Library of Medicine Data. National Library of Medicine, http://www.nlm.nih.gov/-databases/download.html.
81. Pustejovsky J, No JC, Luo WQ, Morrell M, Rumshisky A, Sauri R, et al. 2002-present. Medstract.org. Natural Language Processing and Computation Linguistics at Brandeis University. Brandeis University and Tufts University, http://www.medstract.org/.
82. M. Krauthammer, A. Rzhetsky, P. Morozov, and C. Friedman Using BLAST for identifying gene and protein names in journal articles Gene 259 2000 245 252
83. M. Krauthammer, P. Kra, I. Iossifov, S.M. Gomez, G. Hripcsak, and V. Hatzivassiloglou Of truth and pathways: chasing bits of information through myriads of articles Bioinformatics 18 2002 S249 S257
84. S. Raychaudhuri, H. Schutze, and R.B. Altman Using text analysis to identify functionally coherent gene groups Genome Res. 12 2002 1582 1590
85. S.C. Geller, J.P. Gregg, P. Hagerman, and D.M. Rocke Transformation and normalization of oligonucleotide microarray data Bioinformatics 19 2003 1817 1823
86. R. Nadon, E. Woody, P. Shi, N. Rghei, H. Hubschle, and E. Susko Statistical inference in array genomics D.H. Geschwind J.P. Gregg Microarrays for the neurosciences 2002 MIT Press Cambridge, MA 109 140
87. D.M. Rocke, and B. Durbin A model for measurement error for gene expression arrays J. Comp. Biol. 8 2001 557 569
88. A. Zien, J. Fluck, R. Zimmer, and T. Lengauer Microarrays: how many do you need? J. Comp. Biol. 10 2003 653 667
89. Spotfire, 2003-present. Spotfire. Spotfire, http://www.spotfire.com.
90. T.D. Moloshok, R.R. Klevecz, J.D. Grant, F.J. Manion, WF Speier 4th, and M.F. Ochs Application of Bayesian decomposition for analysing microarray data Bioinformatics 18 4 2002 566 575
91. D. Pe'er, A. Regev, G. Elidan, and N. Friedman Inferring subnetworks from perturbed expression profiles Bioinformatics 17 2001 S215 S224
92. T.R. Golub, D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, and J.P. Mesirov Molecular classification of cancer: class discovery and class prediction by gene expression monitoring Science 286 5439 1999 531 537
93. V.R. Iyer, M.B. Eisen, D.T. Ross, G. Schuler, T. Moore, and J.C. Lee The transcriptional program in the response of human fibroblasts to serum Science 283 5398 1999 83 87
94. M.B. Eisen, P.T. Spellman, P.O. Brown, and D. Botstein Cluster analysis and display of genome-wide expression patterns Proc. Natl. Acad. Sci. U. S. A. 95 1998 14863 14868
95. Dickerson JA, Cox Z, Wurtele ES, Fulmer AW. Creating metabolic and regulatory network models using fuzzy cognitive maps. Technical report; 2002. Iowa State University. http://clue.eng.iastate.edu/julied/publications/ NAFIPS01Metabolicfinalpdf.
96. F. Model, P. Adorjan, A. Olek, and C. Piepenbrock Feature selection for DNA methylation based cancer classification Bioinformatics 17 2001 1 8
97. D.V. Nguyen, and D.M. Rocke Tumor classification by partial least squares using Microarray gene expression data Bioinformatics 18 2002 39 50
98. E.F. Petricoin, K.C. Zoon, E.C. Kohn, J.C. Barrett, and L.A. Liotta Clinical proteomics: translating benchside promise into bedside reality Nat. Rev. Drug Discov. 1 2002 683 695
99. T. Akutsu, S. Miyano, and S. Kuhara Inferring qualitative relations in genetic networks and metabolic pathways Bioinformatics 16 2000 727 734