HIV and cancer in the Veterans Health Administration System

Computationally inferred cell-type specific epigenome-wide DNA methylation analysis unveils distinct methylation patterns among immune cells for HIV infection in three cohorts

BACKGROUND

Epigenome-wide association studies (EWAS) have identified CpG sites associated with HIV infection in blood cells in bulk, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. In this study, we aim to identify differentially methylated CpG sites for HIV infection in immune cell types: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes.

METHODS

Applying a computational deconvolution method, we performed a cell-type based EWAS for HIV infection in three independent cohorts (Ntotal = 1,382). DNA methylation in blood or in peripheral blood mononuclear cells (PBMCs) was profiled by an array-based method and then deconvoluted by Tensor Composition Analysis (TCA). The TCA-computed CpG methylation in each cell type was first benchmarked by bisulfite DNA methylation capture sequencing in a subset of the samples. Cell-type EWAS of HIV infection was performed in each cohort separately and a meta-EWAS was conducted followed by gene set enrichment analysis.

RESULTS

The meta-analysis unveiled a total of 2,021 cell-type unique significant CpG sites for five inferred cell types. Among these inferred cell-type unique CpG sites, the concordance rate in the three cohorts ranged from 96% to 100% in each cell type. Cell-type level meta-EWAS unveiled distinct patterns of HIV-associated differential CpG methylation, where 74% of CpG sites were unique to individual cell types (false discovery rate, FDR <0.05). CD4+ T-cells had the largest number of unique HIV-associated CpG sites (N = 1,624) compared to any other cell type. Genes harboring significant CpG sites are involved in immunity and HIV pathogenesis (e.g. CD4+ T-cells: NLRC5, CX3CR1, B cells: IFI44L, NK cells: IL12R, monocytes: IRF7), and in oncogenesis (e.g. CD4+ T-cells: BCL family, PRDM16, monocytes: PRDM16, PDCD1LG2). HIV-associated CpG sites were enriched among genes involved in HIV pathogenesis and oncogenesis that were enriched among interferon-α and -γ, TNF-α, inflammatory response, and apoptotic pathways.

CONCLUSION

Our findings uncovered computationally inferred cell-type specific modifications in the host epigenome for people with HIV that contribute to the growing body of evidence regarding HIV pathogenesis.

Cell-type specific EWAS identifies genes involved in HIV pathogenesis and oncogenesis among people with HIV infection

Epigenome-wide association studies (EWAS) of heterogenous blood cells have identified CpG sites associated with chronic HIV infection, which offer limited knowledge of cell-type specific methylation patterns associated with HIV infection. Applying a computational deconvolution method validated by capture bisulfite DNA methylation sequencing, we conducted a cell type-based EWAS and identified differentially methylated CpG sites specific for chronic HIV infection among five immune cell types in blood: CD4+ T-cells, CD8+ T-cells, B cells, Natural Killer (NK) cells, and monocytes in two independent cohorts (N total =1,134). Differentially methylated CpG sites for HIV-infection were highly concordant between the two cohorts. Cell-type level meta-EWAS revealed distinct patterns of HIV-associated differential CpG methylation, where 67% of CpG sites were unique to individual cell types (false discovery rate, FDR <0.05). CD4+ T-cells had the largest number of HIV-associated CpG sites (N=1,472) compared to any other cell type. Genes harboring statistically significant CpG sites are involved in immunity and HIV pathogenesis (e.g. CX3CR1 in CD4+ T-cells, CCR7 in B cells, IL12R in NK cells, LCK in monocytes). More importantly, HIV-associated CpG sites were overrepresented for hallmark genes involved in cancer pathology ( FDR <0.05) (e.g. BCL family, PRDM16, PDCD1LGD, ESR1, DNMT3A, NOTCH2 ). HIV-associated CpG sites were enriched among genes involved in HIV pathogenesis and oncogenesis such as Kras-signaling, interferon-α and -γ, TNF-α, inflammatory, and apoptotic pathways. Our findings are novel, uncovering cell-type specific modifications in the host epigenome for people with HIV that contribute to the growing body of evidence regarding pathogen-induced epigenetic oncogenicity, specifically on HIV and its comorbidity with cancers.

Cancer in patients with and without HIV infection in the national cancer registry of Rwanda

OBJECTIVE

As antiretroviral therapy (ART) has been widely scaled up in Rwanda, life expectancies among people with HIV (PWH) have increased. With increasing viral suppression, AIDS-defining cancers (ADCs) typically decrease; however, as the PWH population ages, non-AIDS-defining cancers (NADCs) will be expected to increase. The aim of this study was to compare cancer diagnoses between PWH and patients without HIV in Rwanda and to describe the changes in the number and types of cancer over time.

DESIGN

Retrospective cohort study.

METHODS

Rwanda National Cancer Registry (RNCR) recorded the HIV status, primary site, and morphological description for cancer diagnoses from 2007 to 2018. Descriptive analyses were carried out by cancer group (HIV+ and HIV-). A portion of patients whose HIV status was unknown (63%) were excluded from the present analysis.

RESULTS

Among the 20 258 cases registered in the Registry, there were 1048 PWH and 6359 HIV- individuals. The proportion of ADCs were significantly higher in the PWH group compared to those without HIV ( P  < 0.001). Among PWH, there was a longitudinal increase in NADCs and a decrease in ADCs ( P  < 0.001) over time. Among the ADCs in the PWH group, there was a significant decline in Kaposi sarcoma cases over time.

CONCLUSIONS

The study demonstrates a decreasing frequency of ADCs driven by declines in Kaposi sarcoma diagnoses and an increased frequency of NADCs among PWH in Rwanda over time. These findings support a need for focusing early detection and management efforts on NADCs, as they begin to play a larger role in the disease processes that affect the aging PWH population.

Treatment and comorbidity burden among people living with HIV: a review of systematic literature reviews

Background

As the human immunodeficiency virus (HIV) treatment landscape continues to evolve, the prolonged life expectancy and long-term exposure to antiretroviral drugs have modified the burden associated with living with HIV.

Objective

To better understand the current treatment and comorbidity burden in people living with HIV (PLWH).

Methods

Peer-reviewed systematic literature reviews (SLRs) between 2017 and 2020 that included US studies and examined drug adherence/pill burden, resistance burden, or comorbidities in PLWH were identified. Methods and findings were extracted for the overall studies and examined in the subset of US studies.

Results

Among 665 publications identified, 47 met the inclusion criteria (drug adherence/pill burden: 5; resistance: 3; comorbidities: 40). While antiretroviral drug adherence levels varied across SLRs, single-tablet regimens (STR) were associated with higher adherence versus multiple-tablet regimens. STRs were also associated with lower risk of treatment discontinuation, higher cost-effectiveness, and lower risk of hospitalization. Longer survival resulted in a high comorbidity burden, with non-AIDS causes accounting for 47% of deaths among PLWH in the US. HIV doubled the risk of cardiovascular disease and was associated with other health problems, including bone and muscle diseases, depression, and cancers. Several antiretroviral regimens were associated with chronic diseases, including cardiometabolic conditions. Lifetime HIV costs are substantially increasing, driven by antiretroviral, adverse event, and comorbidity treatment costs cumulated due to longer survival times.

Conclusions

There is a considerable burden associated with HIV and antiretroviral treatment, highlighting the benefits of less complex and safer regimens, and the unmet need for effective preventative interventions.

Rapid Antiretroviral Therapy Program: Development and Evaluation at a Veterans Affairs Medical Center in the Southern United States

Early HIV viral suppression (VS) improves individual health outcomes and decreases onward transmission. We designed an outpatient clinic protocol to rapidly initiate antiretroviral therapy (ART) in a large Veterans Health Administration (VA) HIV clinic. A pre-post evaluation was performed using a retrospective cohort study design for new diagnoses of HIV infection from January 2012 to February 2020. Time-to-event analyses were performed using the Cox proportional hazards model with the intervention group as the main exposure adjusted for integrase inhibitor usage, baseline viral load, age, gender, and race. Most of the patients were men (historical control: 94.8%, n = 55; Rapid Start: 94.8%, n = 55) and Black or African American persons (historical control: 87.9%, n = 51; Rapid Start: 82.8%, n = 48). More patients initiated treatment with an integrase inhibitor-based regimen in the Rapid Start group (98.3%, n = 57) compared with the historical control group (39.7%, n = 23). Compared with controls, the Rapid Start patients were significantly more likely to achieve VS at any given time during the study period (hazard ratio 2.65; p < 0.001). Median days (interquartile range) from diagnosis to VS decreased from 180.5 (102.5-338.5) to 62 (40-105) (p < 0.001), first appointment to VS decreased from 123 (68.5-237.5) to 45 (28-82) (p < 0.001), referral to first visit decreased from 20 (10-43) to 1 (0-3) (p < 0.001), and from first visit to ART dispense date decreased from 27.5 (3-50) to 0 (0-0) (p = 0.01). Prioritizing immediate ART initiation can compress the HIV care continuum from diagnosis to linkage to VS. Implementation of the Rapid Start Protocol should be considered at all VA facilities providing HIV care.

Cancer immunotherapy in adult patients with HIV

The availability of antiretroviral therapy (ART) has increased the life expectancy of people with HIV (PWH) and reduced the incidence of AIDS-associated malignancies, yet PWH have a significantly increased incidence of malignancy and less favorable outcomes of cancer treatment compared with the general population.Immunotherapy has revolutionized cancer therapy, becoming the standard of care for various malignancy treatments. However, PWH are an underserved population with limited access to clinical trials and cancer treatment.This review of the available evidence on different classes of cancer immunotherapy in PWH is mostly based on case reports, case series, but few prospective studies and clinical trials due to the exclusion of PWH from most oncologic clinical trials. The results of the available evidence support the safety of immunotherapy in PWH. Immunotherapy has similar effectiveness in PWH, an acceptable toxicity profile, and has no clinically significant impact on HIV viral load and CD4-T cell count. In addition, there is no reported change in the incidence of opportunistic infections and other complications for PWH with well-controlled viremia.This review aims to briefly summarize the current state of immunotherapy in cancer, guide clinicians in the management of immunotherapy in cancer PWH, and encourage the inclusion of PWH in clinical trials of cancer immunotherapy.

Cancer Microbiology

Microbes play important roles in cancer from direct carcinogenic effects to their use in treatment. Cancers caused by microorganisms account for approximately 15% of cancers, mostly in low- and middle-income countries. Unique features of infectious carcinogens include their transmissibility, mutability, and specific immune interactions, which provide challenges and opportunities for cancer prevention and treatment. For these agents, infection control through exposure reduction, antivirals, antibiotics, and vaccines is cancer control. In addition, developing evidence suggests that microorganisms including the human microbiome can indirectly modulate cancer formation and influence the effectiveness and toxicity of cancer treatments. Finally, microorganisms themselves can be used to prevent or treat cancer. The convergence of these factors signals the emergence of a new field, Cancer Microbiology. Recognition of Cancer Microbiology will spur research, stimulate cross-disciplinary training, inform drug development, and improve public health.

Natural killer cell exhaustion in lung cancer

OBJECTIVES

Lung cancer is one of the most frequently diagnosed cancers worldwide. However, the potential causes of lung cancer oncogenesis are still unclear. This study aims to explore the phenomenon and mechanism of NK cell exhaustion in lung cancer and lay the foundation for developing a targeting strategy to ameliorate immune cell exhaustion in cancer.

MATERIALS AND METHODS

NK cells were isolated from the blood samples of lung cancer patients and healthy volunteers. After culture in vitro, the colony forming ability, cytotoxicity, apoptosis and receptor expression of NK cells in the peripheral blood from the lung cancer patients and the volunteers were analyzed by flow cytometry and the corresponding methods. The correlation between the NK cell profile and lung cancer occurrence was analyzed as well.

RESULTS

The colony formation and cytotoxicity of the NK cells from the lung cancer group were significantly decreased compared to whose of the NK cells from volunteers. The expression of NKG2A was upregulated and CD226 was downregulated significantly in the lung cancer group compared with the control group. Furthermore, through correlation analysis, the colony forming level, cytotoxicity and CD226 expression level were significantly negatively correlated with lung cancer, and the expression level of NKG2A was significantly positively correlated with lung cancer. Moreover, the impaired colony formation of NK cells was significantly correlated with NK cell functional exhaustion in lung cancer.

CONCLUSIONS

The downregulated CD226 expression and the upregulated NKG2A expression may serve as potential markers of NK cells exhaustion in lung cancer.

A supervised exercise intervention fails to improve subjective and objective sleep measures among older adults with and without HIV

BACKGROUND

Chronic sleep disruption can have significant negative health effects and prior studies suggest that people with HIV (PWH) have disproportionately higher rates of sleep problems.

METHODS

We evaluated baseline sleep of sedentary, older adults (50-75 years) with (n = 28) and without HIV (n = 29) recruited into a 24-week exercise study. Subjective sleep quality was assessed with the Pittsburgh Sleep Quality Index (PSQI); objective sleep parameters were assessed using wrist-worn actigraphy. Regression models were used to investigate changes in outcomes.

RESULTS

Fifty-seven participants completed the intervention. At baseline, PWH had significantly lower sleep efficiency (88.7 [95% CI 86, 91]%) compared to controls (91.8 [95% CI 91, 93]%; p = 0.02); other sleep measures indicated poorer sleep among PWH but did not reach statistical significance (p ≥ 0.12). Overall, sleep outcomes did not significantly change with the exercise intervention (all p > 0.05). In adjusted analyses, PWH demonstrated a decrease in total sleep time (-22.1 [-43.7, -0.05] p = 0.045) and sleep efficiency (-1.3 [-2.5, -.01], p = 0.03) during the 24 weeks of exercise; these differences were attenuated and no longer significant after adjusting for exercise intensity. At the completion of the intervention, compared to controls, PWH had significantly poorer sleep by PSQI score (2.2 [0.6, 3.8]; p = 0.006) and sleep efficiency (-2.8 [-5.4,-0.2]%; p = 0.04).

CONCLUSIONS

In this study, sleep disturbance was more prevalent in sedentary older PWH compared to uninfected controls. An exercise intervention had minimal effect on sleep impairments among PWH nor controls. Among older adults, interventions beyond cardiovascular and resistance exercise may be needed to significantly alter subjective and objective sleep outcomes.