CD4 ⁺ T cell–dependent and CD4 ⁺ T cell–independent cytokine-chemokine network changes in the immune responses of HIV-infected individuals

Abstract

A vital defect in the immune systems of HIV-infected individuals is the loss of CD4+ T cells, resulting in impaired immune responses. We hypothesized that there were CD4+ T cell–dependent and –independent alterations in the immune responses of HIV-1+ individuals. To test this, we analyzed the secretion of cytokines and chemokines from stimulated peripheral blood mononuclear cell (PBMC) populations from HIV+ donors, healthy donors, and healthy donors with CD4+ T cells experimentally depleted. Multivariate analyses of 16 cytokines and chemokines at 6 and 72 hours after three stimuli (antibody-coated beads to stimulate T cells and R848 or LPS to stimulate innate immune cells) enabled integrative analysis of secreted profiles. Two major effects in HIV+ PBMCs were not reproduced upon depleting CD4+ T cell in healthy PBMCs: (i) HIV+ PBMCs maintained T cell–associated secreted profiles after T cell stimulation; (ii) HIV+ PBMCs showed impaired IFN-γ secretion early after innate stimulation. These changes arose from hyperactive T cells and debilitated natural killer (NK) cell, respectively. Modeling and experiments showed that early IFN-γ secretion predicted later differences in secreted profiles in vitro. This effect was recapitulated in healthy PBMCs by blocking the interferon-γ (IFN-γ) receptor. Thus, we identified a critical deficiency in NK cell responses of HIV-infected individuals, independent of CD4+ T cell depletion, which directs secreted profiles. Our findings illustrate a broad approach for identifying key disease-associated nodes in a multicellular, multivariate signaling network.

Systems analysis of dynamic transcription factor activity identifies targets for treatment in Olaparib resistant cancer cells

“…TRACER is distinct from other high‐throughput approaches that measure the abundance of mRNA or protein within cells, as the repeated measurement of activity for multiple TFs within the same cell populations enables monitoring of the cellular adaptation to the presence of the drug and provides information on active signaling pathways that enable resistance. We employed data‐driven modeling (Arnold et al, ; Beste et al, ) approaches that enable evaluation of relationships between TFs, rather than separate treatment of individual TFs. Network analysis of TF activity provided a unique perspective for both identifying tumor cells that are likely to be resistant to standard therapies as well as suggesting alternative multivariate targets for combinatorial treatment.…”

Advancing systems immunology through data-driven statistical analysis

“…Clustering analysis performed on whole proteome mass spectrometry profiles showed that HIV-infected patient CD4+ T cells on anti-retroviral therapy exhibited decreases in toll-like receptor 4 and type 1 interferon signaling relative to paired uninfected CD4+ T cell data [38]. To classify HIV+, T-cell depleted, and healthy PBMC samples, partial least squares discriminant analysis (PLS-DA)– which identifies linear combinations of variables to maximally separate known biological states –identified classification signatures based on measurements of 16 cytokines and chemokines, and then the underlying molecular changes could be associated with each group [39]. In a study from our lab, we measured phospho-signaling differences in uninfected and latent HIV-infected T cells and used PLS-DA to define signatures that predicted infection status and then identified changes in stress kinase signaling as a novel target for preferential infected-cell killing [40].…”

Demystifying the cytokine network: Mathematical models point the way

“…A recent study examined the profiles of cytokines produced by PBMC from healthy or HIV + individuals in response to three different stimuli [72]. Using partial least-squares discriminant analysis of these datasets they identified differences in the pattern of cytokine responses that depended on the stimulus and donor type.…”

“…In addition, a decision tree analysis revealed that HIV + donors had an early defect in the production of IFN-γ in response to innate stimuli. Further experiments revealed that this was an NK cell defect and that it had an impact on later production of cytokines by other immune cells [72]. …”