Gene expression in HIV-associated neurocognitive disorders: A meta-analysis

Journal of Acquired Immune Deficiency Syndromes

Volumn 70, Issue 5, 2015, Pages 479-488

  Siangphoe, Umaporn ^a   Archer, Kellie J ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Gene expression; HIV associated neurocognitive disorders; Meta analysis; Postmortem brain samples

Indexed keywords

INTERFERON; TRANSCRIPTOME;

ANTIGEN PRESENTATION; APOLIPOPROTEIN L 6 GENE; ARTICLE; BRAIN TISSUE; ENCEPHALITIS; GENE EXPRESSION; GLYCOPROTEIN NMB GENE; HIV ASSOCIATED DEMENTIA; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTED PATIENT; IMMUNE SYSTEM; META ANALYSIS; PRIORITY JOURNAL; PROTEASOME ACTIVATOR SUBUNIT 1 ANTISENSE RNA 1 GENE; PROTEASOME ACTIVATOR SUBUNIT 1 GENE; PROTEASOME ACTIVATOR SUBUNIT 2 GENE; TRIPARTITE MOTIF CONTAINING 69 GENE; UBIQUITIN CONJUGATING ENZYME E2L 6 GENE; UPREGULATION; WHITE MATTER; BRAIN; COMPLICATION; GENE EXPRESSION REGULATION; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; METABOLISM; NEUROCOGNITIVE DISORDERS; PATHOLOGY; PHYSIOLOGY; POSTMORTEM CHANGE;

BRAIN; GENE EXPRESSION REGULATION; HIV INFECTIONS; HUMANS; NEUROCOGNITIVE DISORDERS; POSTMORTEM CHANGES; TRANSCRIPTOME;

EID: 84947718249     PISSN: 15254135     EISSN: 10779450     Source Type: Journal    
DOI: 10.1097/QAI.0000000000000800     Document Type: Article

References (67)

1. Haddow LJ, Floyd S, Copas A, et al. A systematic review of the screening accuracy of the HIV dementia scale and international HIV dementia scale. PLoS One. 2013;8:e61826.
2. Brew BJ, Chan P. Update on HIV dementia and HIV-associated neurocognitive disorders. Curr Neurol Neurosci Rep. 2014;14:468.
3. Stevenson M. HIV-1 pathogenesis. Nat Med. 2003;9:853-860.
4. Ellis R, Langford D, Masliah E. HIV and antiretroviral therapy in the brain: neuronal injury and repair. Nat Rev Neurosci. 2007;8:33-44.
5. Gendelman HE, Lipton SA, Tardieu M, et al. The neuropathogenesis of HIV-1 infection. J Leukoc Biol. 1994;56:389-398.
6. Gendelman HE, Tardieu M. Macrophages/microglia and the pathophys-iology of CNS injuries in AIDS. J Leukoc Biol. 1994;56:387-388.
7. Kaul M, Garden GA, Lipton SA. Pathways to neuronal injury and apoptosis in HIV-associated dementia. Nature. 2001;410:988-994.
8. Minagar A, Shapshak P, Fujimura R, et al. The role of macrophage/microglia and astrocytes in the pathogenesis of three neurologic disorders: HIV-associated dementia, alzheimer disease, and multiple sclerosis. J Neurol Sci. 2002;202:13-23.
9. Vivithanaporn P, Heo G, Gamble J, et al. Neurologic disease burden in treated HIV/AIDS predicts survival: a population-based study. Neurology. 2010;75:1150-1158.
10. Valcour VG. HIV, aging, and cognition: emerging issues. Top Antivir Med. 2013;21:119-123.
11. Heaton RK, Clifford DB, Franklin DR Jr, et al. HIV-associated neuro-cognitive disorders persist in the era of potent antiretroviral therapy: CHARTER study. Neurology. 2010;75:2087-2096.
12. Grant I, Franklin DR Jr, Deutsch R, et al. Asymptomatic HIV-associated neurocognitive impairment increases risk for symptomatic decline. Neurology. 2014;82:2055-2062.
13. Zipursky AR, Gogolishvili D, Rueda S, et al. Evaluation of brief screening tools for neurocognitive impairment in HIV/AIDS: a systematic review of the literature. AIDS. 2013;27:2385-2401.
14. Ananworanich J, Avihingsanon A. HIV and noncommunicable diseases: the Asian perspective. J Acquir Immune Defic Syndr. 2014;67(suppl 1): S99-S103.
15. Peluso MJ, Spudich S. Treatment of HIV in the CNS: effects of antiretroviral therapy and the promise of non-antiretroviral therapeutics. Curr HIV/AIDS Rep. 2014;11:353-362.
16. Peluso MJ, Ferretti F, Peterson J, et al. Cerebrospinal fluid HIV escape associated with progressive neurologic dysfunction in patients on antiretroviral therapy with well controlled plasma viral load. AIDS. 2012;26:1765-1774.
17. Chan P, Brew BJ. HIV associated neurocognitive disorders in the modern antiviral treatment era: prevalence, characteristics, biomarkers, and effects of treatment. Curr HIV/AIDS Rep. 2014;11:317-324.
18. Ellis RJ, Badiee J, Vaida F, et al. CD4 nadir is a predictor of HIV neurocognitive impairment in the era of combination antiretroviral therapy. AIDS. 2011;25:1747-1751.
19. Heaton RK, Franklin DR, Ellis RJ, et al. HIV-associated neuro-cognitive disorders before and during the era of combination anti-retroviral therapy: differences in rates, nature, and predictors. J Neurovirol. 2011;17:3-16.
20. Barrett T, Wilhite SE, Ledoux P, et al. NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 2013;41:D991-D995.
21. Edgar R, Domrachev M, Lash AE. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30:207-210.
22. Rustici G, Kolesnikov N, Brandizi M, et al. ArrayExpress update-trends in database growth and links to data analysis tools. Nucleic Acids Res. 2013;41:D987-D990.
23. Hubble J, Demeter J, Jin H, et al. Implementation of GenePattern within the stanford microarray database. Nucleic Acids Res. 2009;37: D898-D901.
24. Borjabad A, Volsky DJ. Common transcriptional signatures in brain tissue from patients with HIV-associated neurocognitive disorders, Alzheimer's disease, and multiple sclerosis. J Neuroimmune Pharmacol. 2012;7:914-926.
25. Gelman BB, Soukup VM, Schuenke KW, et al. Acquired neuronal channelopathies in HIV-associated dementia. J Neuroimmunol. 2004; 157:111-119.
26. Masliah E, Roberts ES, Langford D, et al. Patterns of gene dysregulation in the frontal cortex of patients with HIV encephalitis. J Neuroimmunol. 2004;157:163-175.
27. Shapshak P, Duncan R, Torres-Munoz JE, et al. Analytic approaches to differential gene expression in AIDS versus control brains. Front Biosci. 2004;9:2935-2946.
28. Everall I, Salaria S, Roberts E, et al. Methamphetamine stimulates interferon inducible genes in HIV infected brain. J Neuroimmunol. 2005; 170:158-171.
29. Borjabad A, Morgello S, Chao W, et al. Significant effects of antiretroviral therapy on global gene expression in brain tissues of patients with HIV-1-associated neurocognitive disorders. PLoS Pathog. 2011;7:e1002213.
30. Gelman BB, Chen T, Lisinicchia JG, et al. The national NeuroAIDS tissue consortium brain gene array: two types of HIV-associated neuro-cognitive impairment. PLoS One. 2012;7:e46178.
31. Rudy J, Valafar F. Empirical comparison of cross-platform normalization methods for gene expression data. BMC Bioinformatics. 2011; 12:467.
32. Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res. 2012;40:3785-3799.
33. Ramasamy A, Mondry A, Holmes CC, et al. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med. 2008; 5:e184.
34. Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.
35. McClintick JN, Edenberg HJ. Effects of filtering by present call on analysis of microarray experiments. BMC Bioinformatics. 2006;7:49.
36. Miller CJ. Simpleaffy: Very simple high level analysis of Affymetrix data. R package version 2.44.0. Available at: http://www.bioconductor.org, http://bioinformatics.picr.man.ac.uk/simpleaffy/.
37. Dumur CI, Nasim S, Best AM, et al. Evaluation of quality-control criteria for microarray gene expression analysis. Clin Chem. 2004;50:1994-2002.
38. Bolstad BM, Irizarry RA, Astrand M, et al. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003;19:185-193.
39. Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4:249-264.
40. Irizarry RA, Bolstad BM, Collin F, et al. Summaries of affymetrix GeneChip probe level data. Nucleic Acids Res. 2003;31:e15.
41. Gautier L, Cope L, Bolstad BM, et al. A affy-analysis of affymetrix GeneChip data at the probe level. Bioinformatics. 2004;20:307-315.
42. Carlson M. hgu95av2.db: Affymetrix Human Genome U95 Set Annotation Data (chip hgu95av2). R package version 2.14.0.
43. Carlson M. hgu133plus2.db: Affymetrix Human Genome U133 Plus 2.0 Array Annotation Data (chip hgu133plus2). R package version 2.14.0.
44. Huber W, Gentleman R. Matchprobes: a bioconductor package for the sequence-matching of microarray probe elements. Bioinformatics. 2004; 20:1651-1652.
45. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:Article3.
46. Smyth GK. Limma: linear models for microarray data. In: Gentleman VCR, Dudoit S, Irizarry R, Huber W, eds. Bioinformatics and computational biology solutions using R and Bioconductor. New York: Springer, 2005:397-420.
47. Chang LC, Lin HM, Sibille E, et al. Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline. BMC Bioinformatics. 2013;14:368.
48. Ghosh D, Barette TR, Rhodes D, et al. Statistical issues and methods for meta-analysis of microarray data: a case study in prostate cancer. Funct Integr Genomics. 2003;3:180-188.
49. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B. 1995;51:289-300.
50. Choi JK, Yu U, Kim S, et al. Combining multiple microarray studies and modeling interstudy variation. Bioinformatics. 2003;19(suppl 1): i84-i90.
51. Marot G, Foulley JL, Mayer CD, et al. Moderated effect size and P-value combinations for microarray meta-analyses. Bioinformatics. 2009;25: 2692-2699.
52. Ihnatova I. MAMA: Meta-Analysis of MicroArray. R package version 2.2.1. 2013.
53. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28:27-30.
54. Kanehisa M, Goto S, Sato Y, et al. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2014;42: D199-D205.
55. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25-29.
56. Carlson M. GO.db: A Set of Annotation Maps Describing the Entire Gene Ontology. R package version 2.14.0.
57. Morgan M, Falcon S, Gentleman R. GSEABase: Gene Set Enrichment Data Structures and Methods. R package version 1.26.0.
58. Warde-Farley D, Donaldson SL, Comes O, et al. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010;38: W214-W220.
59. Maglott D, Ostell J, Pruitt KD, et al. Entrez gene: gene-centered information at NCBI. Nucleic Acids Res. 2005;33:D54-D58.
60. Gelman BB. Neuropathology of hand with suppressive antiretroviral therapy: encephalitis and neurodegeneration reconsidered. Curr HIV/AIDS Rep. 2015;12:272-279.
61. Antinori A, Arendt G, Becker JT, et al. Updated research nosology for HIV-associated neurocognitive disorders. Neurology. 2007;69:1789-1799.
62. Wiley CA, Achim C. Human immunodeficiency virus encephalitis is the pathological correlate of dementia in acquired immunodeficiency syndrome. Ann Neurol. 1994;36:673-676.
63. Clifford DB, Ances BM. HIV-associated neurocognitive disorder. Lancet Infect Dis. 2013;13:976-986.
64. Rappaport J, Volsky DJ. Role of the macrophage in HIV-associated neurocognitive disorders and other comorbidities in patients on effective antiretroviral treatment. J Neurovirol. 2015;21:235-241.
65. Gelman BB, Lisinicchia JG, Chen T, et al. Prefrontal dopaminergic and enkephalinergic synaptic accommodation in HIV-associated neurocognitive disorders and encephalitis. J Neuroimmune Pharmacol. 2012;7:686-700.
66. Levine AJ, Miller JA, Shapshak P, et al. Systems analysis of human brain gene expression: mechanisms for HIV-associated neurocognitive impairment and common pathways with Alzheimer's disease. BMC Med Genomics. 2013;6:4.
67. Rung J, Brazma A. Reuse of public genome-wide gene expression data. Nat Rev Genet. 2013;14:89-99.