Identification of drug candidates targeting monocyte reprogramming in people living with HIV

Introduction

People living with HIV (PLHIV) are characterized by functional reprogramming of innate immune cells even after long-term antiretroviral therapy (ART). In order to assess technical feasibility of omics technologies for application to larger cohorts, we compared multiple omics data layers.

Methods

Bulk and single-cell transcriptomics, flow cytometry, proteomics, chromatin landscape analysis by ATAC-seq as well as ex vivo drug stimulation were performed in a small number of blood samples derived from PLHIV and healthy controls from the 200-HIV cohort study.

Results

Single-cell RNA-seq analysis revealed that most immune cells in peripheral blood of PLHIV are altered in their transcriptomes and that a specific functional monocyte state previously described in acute HIV infection is still existing in PLHIV while other monocyte cell states are only occurring acute infection. Further, a reverse transcriptome approach on a rather small number of PLHIV was sufficient to identify drug candidates for reversing the transcriptional phenotype of monocytes in PLHIV.

Discussion

These scientific findings and technological advancements for clinical application of single-cell transcriptomics form the basis for the larger 2000-HIV multicenter cohort study on PLHIV, for which a combination of bulk and single-cell transcriptomics will be included as the leading technology to determine disease endotypes in PLHIV and to predict disease trajectories and outcomes.

Abacavir use is associated with increased prothrombin conversion

There is ongoing debate as to whether abacavir (ABC) increases the risk for cardiovascular disease(CVD) in people living with HIV (PLHIV) and the mechanisms underlying this possible association. We recently showed that the use of an ABC-containing regimen was independently associated with increased thrombin generation (TG). In the present study, we aim to explore these findings further, by studying the mechanistical processes that underly the global thrombin generation test via thrombin dynamics analysis. Thrombin dynamics analysis can pinpoint the cause of increased thrombin generation associated with ABC-use either to the procoagulant prothrombin conversion pathway or the anticoagulant thrombin inactivation pathway. In this cross-sectional study, 208 virally suppressed PLHIV were included, of whom 94 were on a ABC-containing regimen, 92 on a tenofovir disoproxil fumarate (TDF)-containing regimen, and the remainder on other regimens. We used Calibrated Automated Thrombinography to measure thrombin generation and perform thrombin dynamics analysis. The total amount of prothrombin conversion, as well as the maximum rate of prothrombin conversion were significantly increased in PLHIV on an ABC containing regimen compared to other treatment regimens. The levels of pro- and anticoagulant factors were comparable, indicating that the ABC-induced changes affect the kinetics of prothrombin conversion rather than procoagulant factor levels. Moreover, Von Willebrand Factor (VWF), active VWF and VWF pro-peptide levels were significantly higher in PLHIV than controls without HIV. However, they did not differ between ABC and non-ABC treated participants.

Targeted plasma proteomics reveals upregulation of distinct inflammatory pathways in people living with HIV

Despite antiretroviral therapy (ART), people living with HIV (PLHIV) display persistent inflammation leading to non-AIDS-related co-morbidities. To better understand underlying mechanisms, we compared targeted plasma inflammatory protein concentration (n = 92) between a cohort of 192 virally suppressed PLHIV, who were followed-up for five years, and 416 healthy controls (HC). Findings were validated in an independent cohort of 649 virally suppressed PLHIV and 98 HC. Compared to HC, PLHIV exhibited distinctively upregulated inflammatory proteins, including mucosal defense chemokines, CCR5 and CXCR3 ligands, and growth factors. Unsupervised clustering of inflammatory proteins clearly differentiated PLHIV with low (n = 123) and high inflammation (n = 65), the latter having a 3.4 relative risk (95% confidence interval 1.2-9.8) to develop malignancies and trend for cardiovascular events during a 5-year follow-up. The best protein predictors discriminating the two inflammatory endotypes were PD-L1, VEGFA, LAP TGF β-1, and TNFRSF9. Our data provide insights into co-morbidities associated inflammatory changes in PLHIV on long-term ART.

People with HIV have higher percentages of circulating CCR5+ CD8+ T cells and lower percentages of CCR5+ regulatory T cells

CCR5 is the main HIV co-receptor. We aimed to (1) compare CCR5 expression on immune cells between people living with HIV (PLHIV) using combination antiretroviral therapy (cART) and HIV-uninfected controls, (2) relate CCR5 expression to viral reservoir size and (3) assess determinants of CCR5 expression. This cross-sectional study included 209 PLHIV and 323 controls. Percentages of CCR5+ cells (%) and CCR5 mean fluorescence intensity assessed by flow cytometry in monocytes and lymphocyte subsets were correlated to host factors, HIV-1 cell-associated (CA)-RNA and CA-DNA, plasma inflammation markers and metabolites. Metabolic pathways were identified. PLHIV displayed higher percentages of CCR5+ monocytes and several CD8+ T cell subsets, but lower percentages of CCR5+ naive CD4+ T cells and regulatory T cells (Tregs). HIV-1 CA-DNA and CA-RNA correlated positively with percentages of CCR5+ lymphocytes. Metabolome analysis revealed three pathways involved in energy metabolism associated with percentage of CCR5+ CD8+ T cells in PLHIV. Our results indicate that CCR5 is differently expressed on various circulating immune cells in PLHIV. Hence, cell-trafficking of CD8+ T cells and Tregs may be altered in PLHIV. Associations between energy pathways and percentage of CCR5+ CD8+ T cells in PLHIV suggest higher energy demand of these cells in PLHIV.

Unbiased Metabolomics Links Fatty Acid Pathways to Psychiatric Symptoms in People Living with HIV

Psychiatric symptoms are prevalent in people living with HIV (PLWH), especially depression, anxiety, impulsivity, and substance use. Various biological mechanisms might play a role in the occurrence of psychiatric symptoms in this population. A hypothesis free, data-driven metabolomics approach can further our understanding of these mechanisms. In this study, we identified metabolic pathways associated with impulsivity, depression and substance use in 157 PLWH. First, Spearman’s rank correlations between metabolite feature intensities and psychiatric symptom levels were calculated, while controlling for age, gender and body mass index. Subsequently, a mummichog pathway analysis was performed. Finally, we analyzed which individual metabolites drove the observed effects. In our cohort of PLWH, fatty acid-related pathways were associated with both depressive as well as impulsive symptomatology. Substance use showed most extensive metabolic associations, and was positively associated with short chain fatty acids (SCFA’s), and negatively associated with glutamate levels. These findings suggest that PUFA metabolism might be associated with both internalising and externalising symptomatology in PLWH. Furthermore, glutamate and SCFA’s—microbiome derivatives with known neuroactive properties—might be involved in substance use in these patients. Future studies should explore potential causal mechanisms involved and whether these findings are HIV-specific.

Clonal hematopoiesis is associated with low CD4 nadir and increased residual HIV transcriptional activity in virally suppressed individuals with HIV

Clonal hematopoiesis, a common age-related phenomenon marked by expansion of cells with clonal hematopoiesis driver mutations, has been associated with all-cause mortality, cancer, and cardiovascular disease. People with HIV (PWH) are at risk for non-AIDS–related comorbidities such as atherosclerotic cardiovascular disease and cancer. In a cross-sectional cohort study, we compared clonal hematopoiesis prevalence in PWH on stable antiretroviral therapy with prevalence in a cohort of overweight individuals and a cohort of age- and sex-matched population controls. The prevalence of clonal hematopoiesis adjusted for age was increased and clone size was larger in PWH compared to population controls. Clonal hematopoiesis is associated with low CD4 nadir, increased residual HIV-1 transcriptional activity, and coagulation factors in PWH. Future studies on the effect of clonal hematopoiesis on the HIV reservoir and non-AIDS–related comorbidities are warranted.

Seasonal and Nonseasonal Longitudinal Variation of Immune Function

Different components of the immune response show large variability between individuals, but they also vary within the same individual because of host and environmental factors. In this study, we report an extensive analysis of the immune characteristics of 56 individuals over four timepoints in 1 single year as part of the Human Functional Genomics Project. We characterized 102 cell subsets using flow cytometry; quantified production of eight cytokines and two chemokines in response to 20 metabolic, bacterial, fungal, and viral stimuli; and measured circulating markers of inflammation. Taking advantage of the longitudinal sampling, both seasonal and nonseasonal sources of variability were studied. The circulating markers of inflammation IL-18, IL-18 binding protein, and resistin displayed clear seasonal variability, whereas the strongest effect was observed for α-1 antitrypsin. Cytokine production capacity also showed strong seasonal changes, especially after stimulation with the influenza virus, Borrelia burgdorferi, and Escherichia coli Furthermore, we observed moderate seasonality effects on immune cell counts, especially in several CD4⁺/CD8⁺ T cell subpopulations. Age of the volunteers was an important factor influencing IFN-γ and IL-22 production, which matched the strong impact of age on several T cell subsets. Finally, on average, genetics accounted for almost 50% of the interindividual variance not already explained by age, sex, and body mass index, although this varies strongly for different parameters. In conclusion, seasonality is an important environmental factor that influences immune responses, in addition to specific genetic and nongenetic host factors, and this may well explain the seasonal variation in the incidence and severity of immune-mediated diseases.