title: MicroRNA regulation and its effects on cellular transcriptome in human immunodeficiency virus-1 (HIV-1) infected individuals with distinct viral load and CD4 cell counts.
abstract: BACKGROUND
  Disease progression in the absence of therapy varies significantly in HIV-1 infected individuals. Both viral and host cellular molecules are implicated; however, the exact role of these factors and/or the mechanism involved remains elusive. To understand how microRNAs (miRNAs), which are regulators of transcription and translation, influence host cellular gene expression (mRNA) during HIV-1 infection, we performed a comparative miRNA and mRNA microarray analysis using PBMCs obtained from infected individuals with distinct viral load and CD4 counts.
  
  
  METHODS
  RNA isolated from PBMCs obtained from HIV-1 seronegative and HIV-1 positive individuals with distinct viral load and CD4 counts were assessed for miRNA and mRNA profile. Selected miRNA and mRNA transcripts were validated using in vivo and in vitro infection model.
  
  
  RESULTS
  Our results indicate that HIV-1 positive individuals with high viral load (HVL) showed a dysregulation of 191 miRNAs and 309 mRNA transcripts compared to the uninfected age and sex matched controls. The miRNAs miR-19b, 146a, 615-3p, 382, 34a, 144 and 155, that are known to target innate and inflammatory factors, were significantly upregulated in PBMCs with high viral load, as were the inflammatory molecules CXCL5, CCL2, IL6 and IL8, whereas defensin, CD4, ALDH1, and Neurogranin (NRGN) were significantly downregulated. Using the transcriptome profile and predicted target genes, we constructed the regulatory networks of miRNA-mRNA pairs that were differentially expressed between control, LVL and HVL subjects. The regulatory network revealed an inverse correlation of several miRNA-mRNA pair expression patterns, suggesting HIV-1 mediated transcriptional regulation is in part likely through miRNA regulation.
  
  
  CONCLUSIONS
  Results from our studies indicate that gene expression is significantly altered in PBMCs in response to virus replication. It is interesting to note that the infected individuals with low or undetectable viral load exhibit a gene expression profile very similar to control or uninfected subjects. Importantly, we identified several new mRNA targets (Defensin, Neurogranin, AIF) as well as the miRNAs that could be involved in regulating their expression through the miRNA-mRNA interaction.
authors.affiliation: Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, 425 Parran Hall, 130 Desoto Street, Pittsburgh, PA 15261, USA.
authors.forename: Karolina
authors.initials: K
authors.lastname: Duskova
authors.forename: Pruthvi
authors.initials: P
authors.lastname: Nagilla
authors.forename: Hai-Son
authors.initials: HS
authors.lastname: Le
authors.forename: Priyadarshini
authors.initials: P
authors.lastname: Iyer
authors.forename: Anbupalam
authors.initials: A
authors.lastname: Thalamuthu
authors.forename: Jeremy
authors.initials: J
authors.lastname: Martinson
authors.forename: Ziv
authors.initials: Z
authors.lastname: Bar-Joseph
authors.forename: William
authors.initials: W
authors.lastname: Buchanan
authors.forename: Charles
authors.initials: C
authors.lastname: Rinaldo
authors.forename: Velpandi
authors.initials: V
authors.lastname: Ayyavoo
mesh_terms: D000328:Adult; D000368:Aged; D018791:CD4 Lymphocyte Count; D016000:Cluster Analysis; D016207:Cytokines / Q000032:analysis / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D015658:HIV Infections / Q000235:genetics* / Q000276:immunology / Q000378:metabolism; D015497:HIV-1 / Q000302:isolation & purification*; D054884:Host-Pathogen Interactions; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D008875:Middle Aged; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D018709:Statistics, Nonparametric; D059467:Transcriptome; D019562:Viral Load
chemical_list: D016207:Cytokines; D035683:MicroRNAs; D012333:RNA, Messenger