Transitory viremic surges in a human immunodeficiency virus-positive elite controller can shift the cellular transcriptome profile: a word of caution for microarray studies

A transcriptome-based model of central memory CD4 T cell death in HIV infection

BACKGROUND

Human central memory CD4 T cells are characterized by their capacity of proliferation and differentiation into effector memory CD4 T cells. Homeostasis of central memory CD4 T cells is considered a key factor sustaining the asymptomatic stage of Human Immunodeficiency Virus type 1 (HIV-1) infection, while progression to acquired immunodeficiency syndrome is imputed to central memory CD4 T cells homeostatic failure. We investigated if central memory CD4 T cells from patients with HIV-1 infection have a gene expression profile impeding proliferation and survival, despite their activated state.

METHODS

Using gene expression microarrays, we analyzed mRNA expression patterns in naive, central memory, and effector memory CD4 T cells from healthy controls, and naive and central memory CD4 T cells from patients with HIV-1 infection. Differentially expressed genes, defined by Log₂ Fold Change (FC) ≥ |0.5| and Log (odds) > 0, were used in pathway enrichment analyses.

RESULTS

Central memory CD4 T cells from patients and controls showed comparable expression of differentiation-related genes, ruling out an effector-like differentiation of central memory CD4 T cells in HIV infection. However, 210 genes were differentially expressed in central memory CD4 T cells from patients compared with those from controls. Expression of 75 of these genes was validated by semi quantitative RT-PCR, and independently reproduced enrichment results from this gene expression signature. The results of functional enrichment analysis indicated movement to cell cycle phases G1 and S (increased CCNE1, MKI67, IL12RB2, ADAM9, decreased FGF9, etc.), but also arrest in G2/M (increased CHK1, RBBP8, KIF11, etc.). Unexpectedly, the results also suggested decreased apoptosis (increased CSTA, NFKBIA, decreased RNASEL, etc.). Results also suggested increased IL-1β, IFN-γ, TNF, and RANTES (CCR5) activity upstream of the central memory CD4 T cells signature, consistent with the demonstrated milieu in HIV infection.

CONCLUSIONS

Our findings support a model where progressive loss of central memory CD4 T cells in chronic HIV-1 infection is driven by increased cell cycle entry followed by mitotic arrest, leading to a non-apoptotic death pathway without actual proliferation, possibly contributing to increased turnover.

Gene array data relevant to immunological and virological monitoring of human immunodeficiency virus type 1 infection

PURPOSE OF REVIEW

Immunomonitoring technologies are not only fast changing, but also have already revolutionized the way we look at treatments, diagnosis, and prognosis of a given disease. The purpose of the review is to provide a recent update on the use or possible use of array-based data in immunomonitoring of HIV patients.

RECENT FINDINGS

Since the inception of gene arrays, there has been a rapid surge in the development of a variety of array-based technologies, which comprise of gene and protein expression platforms. These have been instrumental in studying various immunological and genomic aspects of HIV disease at the subcellular level.

SUMMARY

Gene and protein array technologies are ideal for a high-throughput multiplexing of large datasets in determining the difference between diseased and nondiseased and pretreatment and posttreatment stages of HIV patients. Therefore, these technologies have the potential to revolutionize HIV immunomonitoring, treatment, diagnosis and prognosis. Although the array-based technologies have not yet replaced conventional immunomonitoring, the data coming out from high-throughput transcriptomic and proteomic studies and its global integration will lead to developing new generation of candidates and tools for immunomonitoring of HIV disease.

Transcriptome analysis of primary monocytes shows global down-regulation of genetic networks in HIV viremic patients versus long-term non-progressors

Despite significant contributions of monocytes to HIV persistence, the genomic basis of HIV-infection of monocytes and its association with plasma viremia remain elusive. To understand HIV interactions with monocytes during disease progression, monocytic transcriptomes from long-term non-progressors (LTNP), HIV+ patients with viral load <1000, with viral load >1000, and seronegative controls were analyzed using Illumina microarray. Differentially expressed genes were identified (fold change >2; adjusted p<0.05) and GSEA between HIV+ groups demonstrated that the down-regulation of the pathways including Toll-like receptor (TLR) signaling, cytokine-cytokine receptor interaction, cell cycle and apoptosis was significantly associated with the viremic groups, whereas their up-regulation with the LTNP group. The down-regulation of TLR pathway in the viremic patients was exemplified by the decreased expression of TLR with the subsequent tuning down of MAPK, NF-κB, JAK-STAT, and IRF cascades. These data provide the first transcriptomic distinction between HIV+ progressors and LTNPs based on primary monocytes.

Gene array studies in HIV-1 infection

HIV-1-infected individuals exhibit remarkable variation in the onset of disease. Virus replication and disease progression depend on host cellular transcription and gene regulation in virus-specific target cells. Both viral and host factors are implicated in this differential regulation. Gene arrays and transcriptome analyses might shed light on why some infected individuals remain asymptomatic while others progress rapidly to AIDS. Here we review developments in HIV research using gene array technologies and the unifying concepts that have emerged from these studies. Gene set enrichment analysis has revealed gene signatures linked to disease progression involving pathways related to metabolism, apoptosis, cell-cycle dysregulation, and T-cell signaling. Macrophages contain anti-apoptotic signatures. Also, HIV-1 regulates previously under-emphasized cholesterol biosynthesis and energy production pathways. Notably, cellular pathways linked to a subset of HIV-infected individuals known as non-progressors contribute to survival and anti-viral responses.

Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease

BACKGROUND

HIV preferentially infects CD4+ T cells, and the functional impairment and numerical decline of CD4+ and CD8+ T cells characterize HIV disease. The numerical decline of CD4+ and CD8+ T cells affects the optimal ratio between the two cell types necessary for immune regulation. Therefore, this work aimed to define the genomic basis of HIV interactions with the cellular transcriptome of both CD4+ and CD8+ T cells.

RESULTS

Genome-wide transcriptomes of primary CD4+ and CD8+ T cells from HIV+ patients were analyzed at different stages of HIV disease using Illumina microarray. For each cell subset, pairwise comparisons were performed and differentially expressed (DE) genes were identified (fold change >2 and B-statistic >0) followed by quantitative PCR validation. Gene ontology (GO) analysis of DE genes revealed enriched categories of complement activation, actin filament, proteasome core and proton-transporting ATPase complex. By gene set enrichment analysis (GSEA), a network of enriched pathways functionally connected by mitochondria was identified in both T cell subsets as a transcriptional signature of HIV disease progression. These pathways ranged from metabolism and energy production (TCA cycle and OXPHOS) to mitochondria meditated cell apoptosis and cell cycle dysregulation. The most unique and significant feature of our work was that the non-progressing status in HIV+ long-term non-progressors was associated with MAPK, WNT, and AKT pathways contributing to cell survival and anti-viral responses.

CONCLUSIONS

These data offer new comparative insights into HIV disease progression from the aspect of HIV-host interactions at the transcriptomic level, which will facilitate the understanding of the genetic basis of transcriptomic interaction of HIV in vivo and how HIV subverts the human gene machinery at the individual cell type level.

Differential gene expression of soluble CD8+ T-cell mediated suppression of HIV replication in three older children

Suppression of human immunodeficiency virus (HIV) replication by CD8+ T-cells (CD8 suppression) contributes to survival in adults and children <1 year. Soluble CD8 suppression can also be seen in some older children with AIDS. The factor responsible, CD8-derived antiviral factor (CAF), acts at the level of HIV RNA transcription. Differential gene expression techniques have been used to define the gene(s) mediating this phenomenon in adults. Recently, CAF has been linked to exosomes secreted by CD8+ T-cells. To compare the gene expression profiles from pediatric patients with each other, with those reported in 2 previous studies in adults and in those reportedly related to exosomes, we used differential gene expression to study three older children with HIV infection, one who did demonstrate soluble CD-8 suppression and two who did not. Eighteen differentially expressed genes were also seen in one adult study (P = 0.002, χ(2) test), and 38 such genes (P < 0.0001, χ(2) test) in a second adult study. In addition, two exosome components and some RNA's related to exosomal proteins were also differentially expressed. In children with HIV infection, we found significant differentially expressed genes that correlated to those previously reported in two studies in adults. Our data also lends some support to the recent identification of CAF with exosomes secreted by CD8+ T-cells.