A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size.

The major barrier to an HIV cure is the HIV reservoir: latently-infected cells that persist despite effective antiretroviral therapy (ART). There have been few cohort-based studies evaluating host genomic or transcriptomic predictors of the HIV reservoir. We performed host RNA sequencing and HIV reservoir quantification (total DNA [tDNA], unspliced RNA [usRNA], intact DNA) from peripheral CD4+ T cells from 191 ART-suppressed people with HIV (PWH). After adjusting for nadir CD4+ count, timing of ART initiation, and genetic ancestry, we identified two host genes for which higher expression was significantly associated with smaller total DNA viral reservoir size, P3H3 and NBL1, both known tumor suppressor genes. We then identified 17 host genes for which lower expression was associated with higher residual transcription (HIV usRNA). These included novel associations with membrane channel (KCNJ2, GJB2), inflammasome (IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9, CXCL3, CXCL10), and innate immunity (TLR7) genes (FDR-adjusted q<0.05). Gene set enrichment analyses further identified significant associations of HIV usRNA with TLR4/microbial translocation (q = 0.006), IL-1/NRLP3 inflammasome (q = 0.008), and IL-10 (q = 0.037) signaling. Protein validation assays using ELISA and multiplex cytokine assays supported these observed inverse host gene correlations, with P3H3, IL-10, and TNF-α protein associations achieving statistical significance (p<0.05). Plasma IL-10 was also significantly inversely associated with HIV DNA (p = 0.016). HIV intact DNA was not associated with differential host gene expression, although this may have been due to a large number of undetectable values in our study. To our knowledge, this is the largest host transcriptomic study of the HIV reservoir. Our findings suggest that host gene expression may vary in response to the transcriptionally active reservoir and that changes in cellular proliferation genes may influence the size of the HIV reservoir. These findings add important data to the limited host genetic HIV reservoir studies to date.

Differences in expression of tumor suppressor, innate immune, inflammasome, and potassium/gap junction channel host genes significantly predict viral reservoir size during treated HIV infection.

The major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective antiretroviral therapy (ART). Most prior host genetic HIV studies have focused on identifying DNA polymorphisms (e.g., CCR5Δ32 , MHC class I alleles) associated with viral load among untreated "elite controllers" (~1% of HIV+ individuals who are able to control virus without ART). However, there have been few studies evaluating host genetic predictors of viral control for the majority of people living with HIV (PLWH) on ART. We performed host RNA sequencing and HIV reservoir quantification (total DNA, unspliced RNA, intact DNA) from peripheral CD4+ T cells from 191 HIV+ ART-suppressed non-controllers. Multivariate models included covariates for timing of ART initiation, nadir CD4+ count, age, sex, and ancestry. Lower HIV total DNA (an estimate of the total reservoir) was associated with upregulation of tumor suppressor genes NBL1 (q=0.012) and P3H3 (q=0.012). Higher HIV unspliced RNA (an estimate of residual HIV transcription) was associated with downregulation of several host genes involving inflammasome ( IL1A, CSF3, TNFAIP5, TNFAIP6, TNFAIP9 , CXCL3, CXCL10 ) and innate immune ( TLR7 ) signaling, as well as novel associations with potassium ( KCNJ2 ) and gap junction ( GJB2 ) channels, all q<0.05. Gene set enrichment analyses identified significant associations with TLR4/microbial translocation (q=0.006), IL-1ß/NRLP3 inflammasome (q=0.008), and IL-10 (q=0.037) signaling. HIV intact DNA (an estimate of the "replication-competent" reservoir) demonstrated trends with thrombin degradation ( PLGLB1 ) and glucose metabolism ( AGL ) genes, but data were (HIV intact DNA detected in only 42% of participants). Our findings demonstrate that among treated PLWH, that inflammation, innate immune responses, bacterial translocation, and tumor suppression/cell proliferation host signaling play a key role in the maintenance of the HIV reservoir during ART. Further data are needed to validate these findings, including functional genomic studies, and expanded epidemiologic studies in female, non-European cohorts. Author Summary: Although lifelong HIV antiretroviral therapy (ART) suppresses virus, the major barrier to an HIV cure is the persistence of infected cells that evade host immune surveillance despite effective ART, "the HIV reservoir." HIV eradication strategies have focused on eliminating residual virus to allow for HIV remission, but HIV cure trials to date have thus far failed to show a clinically meaningful reduction in the HIV reservoir. There is an urgent need for a better understanding of the host-viral dynamics during ART suppression to identify potential novel therapeutic targets for HIV cure. This is the first epidemiologic host gene expression study to demonstrate a significant link between HIV reservoir size and several well-known immunologic pathways (e.g., IL-1ß, TLR7, TNF-α signaling pathways), as well as novel associations with potassium and gap junction channels (Kir2.1, connexin 26). Further data are needed to validate these findings, including functional genomic studies and expanded epidemiologic studies in female, non-European cohorts.

Quantified Activity Patterns for Young Children in Beach Environments Relevant for Exposure to Contaminants.

In a study to evaluate beach play activities, 120 children were videotaped to observe and quantify factors that could influence their exposure to contaminants in the beach environment. Children aged 1 to 6 years were followed by researchers with video cameras at beaches (two in Miami, Florida and two in Galveston, Texas) for approximately one hour each. Factors evaluated included time spent in various beach locations, various activities engaged in, and various surfaces contacted (including contacts by hand and mouth). Activities recorded in the videos were transcribed to text files to allow for quantitative analyses. Across all sexes, age groups, and beaches, Wading was the most common activity and Seawater was the most common location where children played. The left hand was found to not be in contact with objects most of the time, while the right hand, considered the most dominant hand in most cases, contacted Plastic-Toys the most. Although activity patterns collection through videotaping and videotranslation can be labor-intensive, once collected, they can be widely useful for estimates of exposures to all contaminants in the beach environment (e.g., microorganisms and chemicals) as well as UV exposure, with considerations for whether the contaminants are found in water, sand or both. These activity patterns were collected to potentially look at exposures following the Deepwater Horizon 2010 Spill.

Soil-skin adherence measures from hand press trials in a Gulf study of exposures.

Marine oil spills and the resulting environmental contamination is common along coastal areas; however, information is lacking about the safety of impacted beaches for public use, especially for the most vulnerable population: children. One route of exposure for children at oil impacted beaches is through contact with sands. The purpose of this study was to evaluate beach sand skin adherence for children under the age of seven. Each of 122 children participated in a hand press trial conducted at one of four different U.S. beaches (two in Miami, FL, and two in Galveston, TX USA). During the hand press trials, hand conditions of the children were randomized (dry, wet, or with sunscreen), and soil adherence (mass of sand per palmar surface area of the hand) and the maximum pressure applied (force applied per area of hand) was measured and calculated. Each child was instructed to press their hands on a soil laden tray for 5 s and pressure of contact was measured using a scale. Results (n = 98) showed that the average soil adherence for both palmar hands across the four beaches ranged from 0.200 to 234 mg/cm2 with an average of 35.7 mg/cm2, with boys (40.4 mg/cm2) showing slightly higher means than girls (31.7 mg/cm2), but these differences were not significant even after adjusting for age. Among the three conditions evaluated, the highest loading was measured for children with wet hands (mean 65.3 mg/cm2), followed by dry hands (mean 24.5 mg/cm2). Sunscreen hands (mean 23.2 mg/cm2) had the lowest loadings. The pressure of contact ranged from 0.180 to 1.69 psi and varied by age groups and by height and weight, where pressure of contact did not have a significant influence on soil adherence. The average adhered sand grain size and average ambient sand grain size both had a statistically significant impact on hand soil adherence. Overall results from this study can be utilized in exposure and risk assessment models to evaluate the possible health impacts from contaminants found in beach sands.

Soil, Hand, and Body Adherence Measures across Four Beach Areas: Potential Influence on Exposure to Oil Spill Chemicals.

Skin adherence (SA) of soil affects exposure from soil contaminants through dermal routes via loading on the skin and through ingestion routes through hand to mouth activities. The objectives of this study were to evaluate the relationships between adherence versus child-specific and environmental factors. Two sets of soil-to-skin adherence were evaluated. The first was based on loading on hands following hand presses (Hand SA). The second was based on body rinses following one hour of play activities on the beach (Body SA). Results for 98-119 children conducted at four beach sites show that mean Hand SA was 35.7 mg/cm2 (std. dev. 41.8 mg/cm2), while Body SA based on full coverage was 352.3 mg/cm2 (std. dev. 250.4 mg/cm2). Statistically significant differences in Body SA were observed between male (419.2 mg/cm2) and female (300.4 mg/cm2) children (p < 0.05). No significant difference by sex was found for Hand SA. Other statistically different observations were that Hand SA (p < 0.05), but not Body SA, differed across the four beaches (p < 0.05). For Hand SA, this difference was associated soil size variability across the beaches. Hand and Body SA values measured during this study are recommended for use in risk assessments that evaluate beach exposures to oil spill chemicals for young children.