Co-infection with HIV and HCV is common, and increasing evidence indicated that each can alter the course of infection of the other one
. However, little is known on the molecular basis of HIV and HCV interactions and their modulations on host responses. In this study, the gene expression profiles of CD4+ T cells in the treatment-naive HCV, HIV mono-infected and the HCV/HIV co-infected individuals were evaluated. For each cell subset, pairwise comparisons were performed and differentially expressed genes and significantly altered pathways were identified.
By using the GSEA analysis, groups of comprehensive pathways were identified. At first glance, it was obvious to notice that the major altered gene sets indentified in comparison between the HCV/HIV co-infections and HCV mono-infections were nearly same with those indentified in comparison between HIV and HCV mono-infections. Considering that CD4+ T cell was the major target of HIV and only a little specific CD4+ T cells was detected in the HCV infected individuals
[16, 17], it was reasonable that HCV only contribute a little to the global gene changes of CD4+ T cells in HCV/HIV co-infections (Table
One significant proportion of differentially expressed genes was associated with cell cycle which was significant up-regulated in both the HIV mono- and HCV/HIV co-infected individuals as compared with HCV mono-infected individuals (Figure
2). Functional analysis revealed that most of these gene sets involved in G1/S and G2/M transitions. In relate to G1/S transition, till now only one study has reported this phenomenon and the reason why HIV prefers to drive cells out of G1 to S phase is not clear yet
. One possible explanation is that the G1/S transition may regulate the latency of HIV
. The promotion of G1/S transition may facilitate HIV integration as indicated by the up-regulation of genes engaged mainly in DNA repair. The latter has been assumed to be required for the integration of HIV
[20, 21]. Another most affected phase was the G2/M transition
[22, 23]. As shown in Figure
2, 16 out of 33 genes that associated with G2/M transition were up-regulated in the HIV infected individuals, and most of them play important roles in the maintenance of centrosome normality and integrity. The Vpr (viral protein R) of HIV was reported to induce an accumulation of multiple centrosome-like structures in human cells that lead to cell cycle arrest or delay in the G2 phase
, thus positively support viral replication or facilitate viral spread by triggering cell death
. For HIV/HCV co-infection, the cell cycle arrest in G2 phase induced by HIV would lead to a depletion of CD4+ T cells
, and may partially result in a less efficient in HCV clearance
The second group of significantly up-regulated gene sets in both HIV mono- and HCV/HIV co-infections was genes related to innate immune response as compared with HCV mono-infections (Figure
3). In chronic infection, such as HIV, continuous ongoing innate immune responses may contribute more to disease progression rather than to limit viral replication
. Although the mechanisms are very complicated, functional analysis revealed that a group of overlapped genes were engaged in NF-κB regulation among these different innate immune pathways. This finding was also supported by other studies that NF-κB was mediated by Vpr and played a major role in HIV gene expression and pro-inflammatory cytokines induction
The third group of gene sets that is usually modulate by virus is the host cell transcription apparatus
. By providing direct gene pattern, our results confirmed that this strategy was also exploited both in the HIV mono- and HCV/HIV co-infected individuals. As seen in Figure
1C, many of the critical components that engaged in mRNA formation, elongation and maturation were up-regulated in the HIV mono- and HCV/HIV co-infected individuals. These implied that through up-regulating the mRNA editing genes, the HIV virus could facilitate the production of maturated transcripts which were needed for its own translation.
Gene sets in metabolic pathways, including carbohydrate, lipid, fatty acid, amino acid, nucleotide and even vitamin metabolisms, were all significantly changed in the co-infected group. Both of these two viruses have shown abilities to modulate partial of these pathways to facilitate their infections
[32–34]. The abnormalities in the whole metabolic net in co-infections may be a result of HIV-HCV interaction. By complement to each other, the damaging effects would be definitely aggravated, thus lead a more rapid disease progression in co-infections.
Results from our study also detected several pathways up-regulated in HCV infections. All of these pathways were directly or indirectly relate to pathway of GPCR signaling (Figure
1). By modulation several major effectors such as adenylyl cyclase, phospholipase C and the mitogen activated protein kinases (MAPKs), GPCR are involved in many diverse signaling events including visual sense, smell, immune system regulation and inflammation
[35, 36]. The significance of HCV on modulating GPCR signaling is not well understood yet. We speculate that the activation of GPCR signaling as exemplified by upregulation of chemokines (e.g., CCL22) may play important roles in lymphocytes chemotaxis, which could promote the activated lymphocytes to inflammatory sites and facilitate viral clearance
. However, an inappropriate activation of chemotaxis may also lead to unexpected damage of un-infected cells and accelerate the disease progression. Activation of GPCR pathways would lead to an increase in amount and duration of intracellular cyclic adenosine 3', 5’-monophosphate (cAMP) levels
. As an important regulator of immune cells, cAMP has a dual and opposite role during HIV infection
. cAMP can limit viral entry and replication
[40, 41], while it may also reduce HIV-specific antiviral immune responses and promote T cell dysfunctions
[42, 43]. The exact role of HCV-activated GPCR signaling on CD4+ T cells function and HIV infection needed to be further determined.