Differential gene expression in HIV-infected individuals following ART.
Previous studies of the effect of ART on gene expression in HIV-infected individuals have identified small numbers of modulated genes. Since these studies were underpowered or cross-sectional in design, a paired analysis of peripheral blood mononuclear cells (PBMCs), isolated before and after ART, from a robust number of HIV-infected patients (N=32) was performed. Gene expression was assayed by microarray and 4157 differentially expressed genes (DEGs) were identified following ART using multivariate permutation tests. Pathways and gene ontology (GO) terms over-represented for DEGs reflected the transition from a period of active virus replication before ART to one of viral suppression (e.g., repression of JAK-STAT signaling) and possible prolonged drug exposure (e.g., oxidative phosphorylation pathway) following ART. CMYC was the DEG whose product made the greatest number of interactions at the protein level in protein interaction networks (PINs), which has implications for the increased incidence of Hodgkin's lymphoma (HL) in HIV-infected patients. The differential expression of multiple genes was confirmed by RT-qPCR including well-known drug metabolism genes (e.g., ALOX12 and CYP2S1). Targets not confirmed by RT-qPCR (i.e., GSTM2 and RPL5) were significantly confirmed by droplet digital (ddPCR), which may represent a superior method when confirming DEGs with low fold changes. In conclusion, a paired design revealed that the number of genes modulated following ART was an order of magnitude higher than previously recognized.
Fundació irsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; Veterans Affairs San Diego Healthcare System, San Diego, CA 92161, USA; Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
Marta
M
Massanella
Akul
A
Singhania
Nadejda
N
Beliakova-Bethell
Rose
R
Pier
Steven M
SM
Lada
Cory H
CH
White
Josué
J
Pérez-Santiago
Julià
J
Blanco
Douglas D
DD
Richman
Susan J
SJ
Little
Christopher H
CH
Woelk
D023241:Antiretroviral Therapy, Highly Active; D020869:Gene Expression Profiling; D015658:HIV Infections / Q000188:drug therapy* / Q000473:pathology*; D006801:Humans; D008297:Male; D046228:Microarray Analysis; D060888:Real-Time Polymerase Chain Reaction
Antiretroviral therapy; Droplet digital PCR; Gene expression; HIV; Microarray; Paired analysis