Characterization of the genetic determinants of context-specific DNA methylation in primary monocytes

To better understand inter-individual variation in sensitivity of DNA methylation (DNAm) to immune activity, we characterized effects of inflammatory stimuli on primary monocyte DNAm (n = 190). We find that monocyte DNAm is site-dependently sensitive to lipopolysaccharide (LPS), with LPS-induced demethylation occurring following hydroxymethylation. We identify 7,359 high-confidence immune-modulated CpGs (imCpGs) that differ in genomic localization and transcription factor usage according to whether they represent a gain or loss in DNAm. Demethylated imCpGs are profoundly enriched for enhancers and colocalize to genes enriched for disease associations, especially cancer. DNAm is age associated, and we find that 24-h LPS exposure triggers approximately 6 months of gain in epigenetic age, directly linking epigenetic aging with innate immune activity. By integrating LPS-induced changes in DNAm with genetic variation, we identify 234 imCpGs under local genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of disease-associated loci that modulate imCpG formation

IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma

Treatment with immune checkpoint blockade (ICB) frequently triggers immune-related adverse events (irAEs), causing considerable morbidity. In 214 patients receiving ICB for melanoma, we observed increased severe irAE risk in minor allele carriers of rs16906115, intronic to IL7. We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to IL7 in patients. Patients carrying the risk allele demonstrate increased pre-treatment B cell IL7 expression, which independently associates with irAE risk, divergent immunoglobulin expression and more B cell receptor mutations. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB-induced CD8+ T cell subset responses, skewing of T cell clonality and greater proportional repertoire occupancy by large clones. Finally, analysis of TCGA data suggests that risk allele carriers independently have improved melanoma survival. These observations highlight key roles for B cells and IL-7 in both ICB response and toxicity and clinical outcomes in melanoma

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Dog Walking and the Social Impact of the COVID-19 Pandemic on Loneliness in Older Adults

Pet ownership can provide important companionship and facilitate social connections, which may be particularly important to socially isolated older adults. Given the significant deleterious impact of loneliness on health and wellbeing in later life, many predicted that public safety measures imposed during the COVID-19 pandemic would greatly increase loneliness, particularly among vulnerable populations like older adults. We investigated whether dog walking buffers loneliness in the context of stressors imposed by the COVID-19 pandemic. Longitudinal survey data were obtained from a Florida community-based sample of adults (n = 466) aged 60+ years old in September 2018 and October 2020. Using OLS regression models, we tested: a) the association between the social consequences of COVID-19 and changes in loneliness, and b) the buffering effect of dog walking on this relationship. The high social consequences of COVID-19 were related to increases in loneliness. Walking a dog daily buffered the relationship. These results suggest potential therapeutic effects of dog walking for the promotion of mental health in older adults, particularly in the context of stressful situations that accentuate risks for loneliness

Delivery of Fall Prevention Interventions for At-Risk Older Adults in Rural Areas: Findings from a National Dissemination

Falls incidence rates and associated injuries are projected to increase among rural-dwelling older adults, which highlights the need for effective interventions to prevent falls and manage fall-related risks. The purpose of this descriptive study was to identify the geospatial dissemination of eight evidence-based fall prevention programs (e.g., A Matter of Balance, Stepping On, Tai Chi, Otago Exercise Program) across the United States (U.S.) in terms of participants enrolled, workshops delivered, and geospatial reach. These dissemination characteristics were compared across three rurality designations (i.e., metro areas; non-metro areas adjacent to metro areas; and, non-metro areas not adjacent to metro areas). Data were analyzed from a national repository of 39 Administration for Community Living (ACL) grantees from 2014–2017 (spanning 22 states). Descriptive statistics were used to assess program reach, delivery-site type, and completion rate by rurality. Geographic information systems (GIS) geospatially represented the collective reach of the eight interventions. Of the 45,812 participants who attended a fall prevention program, 12.7% attended workshops in non-metro adjacent areas and 6.6% attended workshops in non-metro non-adjacent areas. Of the 3755 workshops delivered (in over 550 unique counties), most were delivered in senior centers (26%), residential facilities (20%), healthcare organizations (13%), and faith-based organizations (9%). On average, the workshop attendance/retention rates were consistent across rurality (~70%). Findings highlight the need to diversify the delivery infrastructure for fall prevention programs to adequately serve older adults in rural areas. Ongoing efforts are needed to offer sustainable technical assistance and to develop scalable clinical-community referral systems to increase fall prevention program participation among rural-dwelling older adults

Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity

Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms

Gene expression profiling for molecular staging of cutaneous melanoma in patients undergoing sentinel lymph node biopsy

BACKGROUND: A gene expression profile (GEP) test able to accurately identify risk of metastasis for patients with cutaneous melanoma has been clinically validated. OBJECTIVE: We aimed for assessment of the prognostic accuracy of GEP and sentinel lymph node biopsy (SLNB) tests, independently and in combination, in a multicenter cohort of 217 patients. METHODS: Reverse transcription polymerase chain reaction (RT-PCR) was performed to assess the expression of 31 genes from primary melanoma tumors, and SLNB outcome was determined from clinical data. Prognostic accuracy of each test was determined using Kaplan-Meier and Cox regression analysis of disease-free, distant metastasis-free, and overall survivals. RESULTS: GEP outcome was a more significant and better predictor of each end point in univariate and multivariate regression analysis, compared with SLNB (P \u3c .0001 for all). In combination with SLNB, GEP improved prognostication. For patients with a GEP high-risk outcome and a negative SLNB result, Kaplan-Meier 5-year disease-free, distant metastasis-free, and overall survivals were 35%, 49%, and 54%, respectively. LIMITATIONS: Within the SLNB-negative cohort of patients, overall risk of metastatic events was higher ( approximately 30%) than commonly found in the general population of patients with melanoma. CONCLUSIONS: In this study cohort, GEP was an objective tool that accurately predicted metastatic risk in SLNB-eligible patients. Inc. All rights reserved

A mutation in the leptin receptor is associated with Entamoeba histolytica infection in children

Malnutrition substantially increases susceptibility to Entamoeba histolytica in children. Leptin is a hormone produced by adipocytes that inhibits food intake, influences the immune system, and is suppressed in malnourished children. Therefore we hypothesized that diminished leptin function may increase susceptibility to E. histolytica infection. We prospectively observed a cohort of children, beginning at preschool age, for infection by the parasite E. histolytica every other day over 9 years and evaluated them for genetic variants in leptin (LEP) and the leptin receptor (LEPR). We found increased susceptibility to intestinal infection by this parasite associated with an amino acid substitution in the cytokine receptor homology domain 1 of LEPR. Children carrying the allele for arginine (223R) were nearly 4 times more likely to have an infection compared with those homozygous for the ancestral glutamine allele (223Q). An association of this allele with amebic liver abscess was also determined in an independent cohort of adult patients. In addition, mice carrying at least 1 copy of the R allele of Lepr were more susceptible to infection and exhibited greater levels of mucosal destruction and intestinal epithelial apoptosis after amebic infection. These findings suggest that leptin signaling is important in mucosal defense against amebiasis and that polymorphisms in the leptin receptor explain differences in susceptibility of children in the Bangladesh cohort to amebiasis

Perspectives on ENCODE

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.11Nsciescopu