title: Transcriptome analyses identify key cellular factors associated with HIV-1-associated neuropathogenesis in infected men.
abstract: HIV-1 viral proteins and host inflammatory factors have a direct role in neuronal toxicity in vitro; however, the contribution of these factors in vivo in HIV-1-associated neurocognitive disorder (HAND) is not fully understood. We applied novel Systems Biology approaches to identify specific cellular and viral factors and their related pathways that are associated with different stages of HAND.
  
  
  
  A cross-sectional study of individuals enrolled in the Multicenter AIDS Cohort Study including HIV-1-seronegative (N = 36) and HIV-1-seropositive individuals without neurocognitive symptoms (N = 16) or with mild neurocognitive disorder (MND) (N = 8) or HIV-associated dementia (HAD) (N = 16).
  
  
  
  A systematic evaluation of global transcriptome of peripheral blood mononuclear cells (PBMCs) obtained from HIV-1-seronegative individuals and from HIV-1-positive men without neurocognitive symptoms, or MND or HAD was performed.
  
  
  
  MND and HAD were associated with specific changes in mRNA transcripts and microRNAs in PBMCs. Comparison of upstream regulators and TimePath analyses identified specific cellular factors associated with MND and HAD, whereas HIV-1 viral proteins played a greater role in HAD. In addition, expression of specific microRNAs - miR-let-7a, miR-124, miR-15a and others - were found to correlate with mRNA gene expression and may have a potential protective role in asymptomatic HIV-1-seropositive individuals by regulating cellular signal transduction pathways downstream of chemokines and cytokines.
  
  
  
  These results identify signature transcriptome changes in PBMCs associated with stages of HAND and shed light on the potential contribution of host cellular factors and viral proteins in HAND development.
authors.affiliation: aDepartment of Infectious Diseases & Microbiology, Graduate School of Public Health, University of Pittsburgh bComputer Science Department, School of Computer Science, Carnegie Mellon University cMolecular Biology Information Service, University of Pittsburgh dComputational Biology and Machine Learning Department, Carnegie Mellon University, Pittsburgh, Pennsylvania eDepartment of Radiology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois fDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland gDepartment of Neurology, David Geffen School of Medicine, University of California Los Angeles, California hDepartment of Psychiatry, Rush University Medical Center, Chicago, Illinois iDepartment of Neurology, Johns Hopkins Bayview Medical Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
authors.forename: Narasimhan J
authors.initials: NJ
authors.lastname: Venkatachari
authors.forename: Siddhartha
authors.initials: S
authors.lastname: Jain
authors.forename: Leah
authors.initials: L
authors.lastname: Walker
authors.forename: Shalmali
authors.initials: S
authors.lastname: Bivalkar-Mehla
authors.forename: Ansuman
authors.initials: A
authors.lastname: Chattopadhyay
authors.forename: Ziv
authors.initials: Z
authors.lastname: Bar-Joseph
authors.forename: Charles
authors.initials: C
authors.lastname: Rinaldo
authors.forename: Ann
authors.initials: A
authors.lastname: Ragin
authors.forename: Eric
authors.initials: E
authors.lastname: Seaberg
authors.forename: Andrew
authors.initials: A
authors.lastname: Levine
authors.forename: James
authors.initials: J
authors.lastname: Becker
authors.forename: Eileen
authors.initials: E
authors.lastname: Martin
authors.forename: Ned
authors.initials: N
authors.lastname: Sacktor
authors.forename: Velpandi
authors.initials: V
authors.lastname: Ayyavoo
mesh_terms: D015526:AIDS Dementia Complex / Q000503:physiopathology*; D002478:Cells, Cultured; D003430:Cross-Sectional Studies; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D015658:HIV Infections / Q000150:complications*; D015497:HIV-1 / Q000472:pathogenicity*; D054884:Host-Pathogen Interactions; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000502:physiology* / Q000821:virology*; D008297:Male; D049490:Systems Biology / Q000379:methods