Table 1.

Gene profiling studies in HIV-1-infected astrocytes and HIV-1- or SIV-infected brains discussed in this review

Citation	Cells	Microarray	Virus stimulus	Analysis	Genes regulated/ total	Conclusions
Astrocytes
Galey et al. 2003	Primary human  astrocytes	NIA immuno and  neuroarray	HIV-  gp120	HIV or gp120 vs  non-HIV	295/  2,306	Differential effect of HIV-1 and gp120 in astrocytes. Gp120 has more  profound effect but chemokine and cytokine induction occurs predomi-  nantly by HIV  infection
Kim et al. 2004	Primary human  astrocytes	Affymetrix U133  A/B	VSV-  HIV	VSV-HIV vs non-  VSV-HIV	734/ >44,000	Up-regulation of IFN antiviral responses, intercellular contacts, cell  adhesion, and signaling. Down-regulation of cell cycle, DNA replication,  and cell proliferation
Kramer-Hämmerle et al. 2005	Astrocytoma— Nef expressing  cells	BD Bioscience  Clontech	Nef	Native Nef vs  non-  myristoylated  Nef	400/  11,835	Up-regulation of small GTPase signaling, regulation of apoptosis, lipid  metabolism. JAK/STAT and MAPK signaling pathways
Borjabad and  Volsky 2009  (present work)	Primary mouse  astrocytes	Affymetrix U74v2	HIV	HIV vs  non-HIV	211/  36,000	Up-regulation of immune response, inflammation, signal transduction, and  chemotaxis. Down-regulation of signal transduction, development, and  protein modification processes
Brain tissue
Sui et al. 2003	Macaque—basal  ganglia	Clontech  chemokine and  cytokine array	SHIV	SIVE vs  non-SIVE	50/277	Changes in cytokine and its receptors expression during SHIV-encephalitis.  Up-regulated genes participating in promoting monocyte infiltration,  macrophage activation, and enhancement of virus replication. Down-  regulation of neutrophic factors
Roberts et al. 2003	Macaque—  frontal lobe	Affymetrix U95Av2	SIV	SIVE vs ni	98/  12,625	Up-regulation in SIVE of genes implicated in monocyte entry to the brain,  inflammation, IFN response, antigen presentation, production of neurotoxic  effects, transcription factors, and others
Roberts et al. 2004	Macaque—  frontal lobe	Affymetrix U95Av2	SIV	SIV vs ni	97/  12,625	Up-regulation in acute SIV infection of genes involved in IFN and IL-6  pathways. Many of these genes also up-regulated in long-term infection  and SIVE
Stephens et al. 2006	Macaque—  cortical brain	Clontech Cytokine  array	SHIV	SHIV vs ni	8	Up-regulated genes, including Cripto-1 and genes implicated in  inflammatory, neuroprotective, cognitive, and stress responses
Masliah et al. 2004	Human—frontal  cortex	Affymetrix U95Av2	HIV	HIVE vs  non-HIVE	133/  12,625	Up-regulated pathways included neuroimmune and antiviral response,  transcription, and signaling pathways. Down-regulated pathways included  synaptic plasticity and transmission, cell cycle, signaling molecules,  transcription factors, and cytoskeletal components