Bacteria-Specific Neutrophil Dysfunction Associated with Interferon-Stimulated Gene Expression in the Acute Respiratory Distress Syndrome

Acute respiratory distress syndrome (ARDS) is a poorly understood condition with greater than 30% mortality. Massive recruitment of neutrophils to the lung occurs in the initial stages of the ARDS. Significant variability in the severity and duration of ARDS-associated pulmonary inflammation could be linked to heterogeneity in the inflammatory capacity of neutrophils. Interferon-stimulated genes (ISGs) are a broad gene family induced by Type I interferons. While ISGs are central to anti-viral immunity, the potential exists for these genes to evoke extensive modification in cellular response in other clinical settings. In this prospective study, we sought to determine if ISG expression in circulating neutrophils from ARDS patients is associated with changes in neutrophil function. Circulating neutrophil RNA was isolated, and hierarchical clustering ranked patients' expression of three ISGs. Neutrophil response to pathogenic bacteria was compared between normal and high ISG-expressing neutrophils. High neutrophil ISG expression was found in 25 of 95 (26%) of ARDS patients and was associated with reduced migration toward interleukin-8, and altered responses to Staphylococcus aureus, but not Pseudomonas aeruginosa, which included decreased p38 MAP kinase phosphorylation, superoxide anion release, interleukin-8 release, and a shift from necrotic to apoptotic cell death. These alterations in response were reflected in a decreased capacity to kill S. aureus, but not P. aeruginosa. Therefore, the ISG expression signature is associated with an altered circulating neutrophil response phenotype in ARDS that may predispose a large subgroup of patients to increased risk of specific bacterial infections

Transcriptomic Signatures in Sepsis and a Differential Response to Steroids. From the VANISH Randomized Trial.

Non-commercial use onlyRATIONALE: There remains uncertainty about the role of corticosteroids in sepsis with clear beneficial effects on shock duration, but conflicting survival effects. Two transcriptomic sepsis response signatures (SRSs) have been identified. SRS1 is relatively immunosuppressed, whereas SRS2 is relatively immunocompetent. OBJECTIVES: We aimed to categorize patients based on SRS endotypes to determine if these profiles influenced response to either norepinephrine or vasopressin, or to corticosteroids in septic shock. METHODS: A post hoc analysis was performed of a double-blind, randomized clinical trial in septic shock (VANISH [Vasopressin vs. Norepinephrine as Initial Therapy in Septic Shock]). Patients were included within 6 hours of onset of shock and were randomized to receive norepinephrine or vasopressin followed by hydrocortisone or placebo. Genome-wide gene expression profiling was performed and SRS endotype was determined by a previously established model using seven discriminant genes. MEASUREMENTS AND MAIN RESULTS: Samples were available from 176 patients: 83 SRS1 and 93 SRS2. There was no significant interaction between SRS group and vasopressor assignment (P = 0.50). However, there was an interaction between assignment to hydrocortisone or placebo, and SRS endotype (P = 0.02). Hydrocortisone use was associated with increased mortality in those with an SRS2 phenotype (odds ratio = 7.9; 95% confidence interval = 1.6-39.9). CONCLUSIONS: Transcriptomic profile at onset of septic shock was associated with response to corticosteroids. Those with the immunocompetent SRS2 endotype had significantly higher mortality when given corticosteroids compared with placebo. Clinical trial registered with www.clinicaltrials.gov (ISRCTN 20769191).Supported by the UK National Institute for Health Research (NIHR) under Research for Patient Benefit program grant PB-PG-0610-22350, NIHR Clinician Scientist Award NIHR/CS/009/007, and NIHR Research Professor award RP-2015-06-018 (A.C.G.); also supported by the NIHR Imperial Biomedical Research Centre, the UK Intensive Care Foundation, Wellcome Trust grant 090532/Z/09/Z to core facilities at the Wellcome Centre for Human Genetics, Wellcome Trust Investigator Award 204969/Z/16/Z (J.C.K.), and by the NIHR Oxford Biomedical Research Centre

Range-wide sources of variation in reproductive rates of northern spotted owls

We conducted a range-wide investigation of the dynamics of site-level reproductive rate of northern spotted owls using survey data from 11 study areas across the subspecies geographic range collected during 1993–2018. Our analytical approach accounted for imperfect detection of owl pairs and misclassification of successful reproduction (i.e., at least one young fledged) and contributed further insights into northern spotted owl population ecology and dynamics. Both nondetection and state misclassification were important, especially because factors affecting these sources of error also affected focal ecological parameters. Annual probabilities of site occupancy were greatest at sites with successful reproduction in the previous year and lowest for sites not occupied by a pair in the previous year. Site-specific occupancy transition probabilities declined over time and were negatively affected by barred owl presence. Overall, the site-specific probability of successful reproduction showed substantial year-to-year fluctuations and was similar for occupied sites that did or did not experience successful reproduction the previous year. Site-specific probabilities for successful reproduction were very small for sites that were unoccupied the previous year. Barred owl presence negatively affected the probability of successful reproduction by northern spotted owls in Washington and California, as predicted, but the effect in Oregon was mixed. The proportions of sites occupied by northern spotted owl pairs showed steep, near-monotonic declines over the study period, with all study areas showing the lowest observed levels of occupancy to date. If trends continue it is likely that northern spotted owls will become extirpated throughout large portions of their range in the coming decades

An immune dysfunction score for stratification of patients with acute infection based on whole-blood gene expression

Dysregulated host responses to infection can lead to organ dysfunction and sepsis, causing millions of global deaths each year. To alleviate this burden, improved prognostication and biomarkers of response are urgently needed. We investigated the use of whole-blood transcriptomics for stratification of patients with severe infection by integrating data from 3149 samples from patients with sepsis due to community-acquired pneumonia or fecal peritonitis admitted to intensive care and healthy individuals into a gene expression reference map. We used this map to derive a quantitative sepsis response signature (SRSq) score reflective of immune dysfunction and predictive of clinical outcomes, which can be estimated using a 7- or 12-gene signature. Last, we built a machine learning framework, SepstratifieR, to deploy SRSq in adult and pediatric bacterial and viral sepsis, H1N1 influenza, and COVID-19, demonstrating clinically relevant stratification across diseases and revealing some of the physiological alterations linking immune dysregulation to mortality. Our method enables early identification of individuals with dysfunctional immune profiles, bringing us closer to precision medicine in infection.peer-reviewe

The effects of habitat, climate, and Barred Owls on long-term demography of Northern Spotted Owls

Estimates of species' vital rates and an understanding of the factors affecting those parameters over time and space can provide crucial information for management and conservation. We used mark–recapture, reproductive output, and territory occupancy data collected during 1985–2013 to evaluate population processes of Northern Spotted Owls (Strix occidentalis caurina) in 11 study areas in Washington, Oregon, and northern California, USA. We estimated apparent survival, fecundity, recruitment, rate of population change, and local extinction and colonization rates, and investigated relationships between these parameters and the amount of suitable habitat, local and regional variation in meteorological conditions, and competition with Barred Owls (Strix varia). Data were analyzed for each area separately and in a meta-analysis of all areas combined, following a strict protocol for data collection, preparation, and analysis. We used mixed effects linear models for analyses of fecundity, Cormack-Jolly-Seber open population models for analyses of apparent annual survival (ϕ), and a reparameterization of the Jolly-Seber capture–recapture model (i.e. reverse Jolly-Seber; RJS) to estimate annual rates of population change (λ[subscript]RJS) and recruitment. We also modeled territory occupancy dynamics of Northern Spotted Owls and Barred Owls in each study area using 2-species occupancy models. Estimated mean annual rates of population change (λ) suggested that Spotted Owl populations declined from 1.2% to 8.4% per year depending on the study area. The weighted mean estimate of λ for all study areas was 0.962 (± 0.019 SE; 95% CI: 0.925–0.999), indicating an estimated range-wide decline of 3.8% per year from 1985 to 2013. Variation in recruitment rates across the range of the Spotted Owl was best explained by an interaction between total winter precipitation and mean minimum winter temperature. Thus, recruitment rates were highest when both total precipitation (29 cm) and minimum winter temperature (−9.5°C) were lowest. Barred Owl presence was associated with increased local extinction rates of Spotted Owl pairs for all 11 study areas. Habitat covariates were related to extinction rates for Spotted Owl pairs in 8 of 11 study areas, and a greater amount of suitable owl habitat was generally associated with decreased extinction rates. We observed negative effects of Barred Owl presence on colonization rates of Spotted Owl pairs in 5 of 11 study areas. The total amount of suitable Spotted Owl habitat was positively associated with colonization rates in 5 areas, and more habitat disturbance was associated with lower colonization rates in 2 areas. We observed strong declines in derived estimates of occupancy in all study areas. Mean fecundity of females was highest for adults (0.309 ± 0.027 SE), intermediate for 2-yr-olds (0.179 ± 0.040 SE), and lowest for 1-yr-olds (0.065 ± 0.022 SE). The presence of Barred Owls and habitat covariates explained little of the temporal variation in fecundity in most study areas. Climate covariates occurred in competitive fecundity models in 8 of 11 study areas, but support for these relationships was generally weak. The fecundity meta-analysis resulted in 6 competitive models, all of which included the additive effects of geographic region and annual time variation. The 2 top-ranked models also weakly supported the additive negative effects of the amount of suitable core area habitat, Barred Owl presence, and the amount of edge habitat on fecundity. We found strong support for a negative effect of Barred Owl presence on apparent survival of Spotted Owls in 10 of 11 study areas, but found few strong effects of habitat on survival at the study area scale. Climate covariates occurred in top or competitive survival models for 10 of 11 study areas, and in most cases the relationships were as predicted; however, there was little consistency among areas regarding the relative importance of specific climate covariates. In contrast, meta-analysis results suggested that Spotted Owl survival was higher across all study areas when the Pacific Decadal Oscillation (PDO) was in a warming phase and the Southern Oscillation Index (SOI) was negative, with a strongly negative SOI indicative of El Niño events. The best model that included the Barred Owl covariate (BO) was ranked 4th and also included the PDO covariate, but the BO effect was strongly negative. Our results indicated that Northern Spotted Owl populations were declining throughout the range of the subspecies and that annual rates of decline were accelerating in many areas. We observed strong evidence that Barred Owls negatively affected Spotted Owl populations, primarily by decreasing apparent survival and increasing local territory extinction rates. However, the amount of suitable owl habitat, local weather, and regional climatic patterns also were related to survival, occupancy (via colonization rate), recruitment, and, to a lesser extent, fecundity, although there was inconsistency in regard to which covariates were important for particular demographic parameters or across study areas. In the study areas where habitat was an important source of variation for Spotted Owl demographics, vital rates were generally positively associated with a greater amount of suitable owl habitat. However, Barred Owl densities may now be high enough across the range of the Northern Spotted Owl that, despite the continued management and conservation of suitable owl habitat on federal lands, the long-term prognosis for the persistence of Northern Spotted Owls may be in question without additional management intervention. Based on our study, the removal of Barred Owls from the Green Diamond Resources (GDR) study area had rapid, positive effects on Northern Spotted Owl survival and the rate of population change, supporting the hypothesis that, along with habitat conservation and management, Barred Owl removal may be able to slow or reverse Northern Spotted Owl population declines on at least a localized scale.Keywords: Northern Spotted Owl, occupancy, population change, Strix varia, Strix occidentalis caurina, fecundity, Barred Owl, surviva

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity.

Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19

Magnitude and duration of acute-exercise intensity effects on symptoms of restless legs syndrome: a pilot study

Restless legs syndrome (RLS) is a neurological disorder that affects 5–15% of the population. There is increasing interest in exercise for managing the symptoms of RLS. To date, no research has examined the duration of acute-exercise intensity effects on RLS. The present study estimated the magnitude and duration of effect of two acute bouts of treadmill exercise at different intensities on severity of RLS. Eight participants (median age 44 years) with RLS completed three different conditions: rest, moderate-intensity exercise [50% heart rate reserve (HRR)], and vigorous-intensity exercise (70% HRR). RLS severity was measured with the International Restless Legs Syndrome Study Group (IRLS) Scale and daytime sleepiness was measured with the Epworth Sleepiness Scale (ESS) pre-condition, 24, and 48 h post-condition. There was no significant effect of time on IRLS or ESS for rest, moderate-intensity exercise, or vigorous-intensity exercise based on the Friedman test per condition. Effect sizes based on the z-value from the Wilcoxon Signed Ranks test indicated that moderate-intensity exercise had a moderate effect (r = 0.350) on IRLS in the first 24 h, but no effect on ESS. Vigorous-intensity exercise had a small effect on both IRLS (r = 0.191) and ESS (r = 0.210) in the first 24 h. Both conditions returned to normal or worsened within 48 h. Our results suggest that acute exercise, at either intensity, may have an immediate effect on RLS symptoms that dissipate within 48 h. These results highlight the importance of continual participation in exercise as a non-pharmacological approach to manage symptoms of RLS

Genomic insights into myasthenia gravis identify distinct immunological mechanisms in early and late onset disease

Objective: The purpose of this study was to identify disease relevant genes and explore underlying immunological mechanisms that contribute to early and late onset forms of myasthenia gravis. Methods: We used a novel genomic methodology to integrate genomewide association study (GWAS) findings in myasthenia gravis with cell-type specific information, such as gene expression patterns and promotor-enhancer interactions, in order to identify disease-relevant genes. Subsequently, we conducted additional genomic investigations, including an expression quantitative analysis of 313 healthy people to provide mechanistic insights. Results: We identified several genes that were specifically linked to early onset myasthenia gravis including TNIP1, ORMDL3, GSDMB, and TRAF3. We showed that regulators of toll-like receptor 4 signaling were enriched among these early onset disease genes (fold enrichment = 3.85, p = 6.4 × 10−3). In contrast, T-cell regulators CD28 and CTLA4 were exclusively linked to late onset disease. We identified 2 causal genetic variants (rs231770 and rs231735; posterior probability = 0.98 and 0.91) near the CTLA4 gene. Subsequently, we demonstrated that these causal variants result in low expression of CTLA4 (rho = −0.66, p = 1.28 × 10−38 and rho = −0.52, p = 7.01 × 10−22, for rs231735 and rs231770, respectively). Interpretation: The disease-relevant genes identified in this study are a unique resource for many disciplines, including clinicians, scientists, and the pharmaceutical industry. The distinct immunological pathways linked to early and late onset myasthenia gravis carry important implications for drug repurposing opportunities and for future studies of drug development

Epstein-Barr virus reactivation in sepsis due to community-acquired pneumonia is associated with increased morbidity and an immunosuppressed host transcriptomic endotype

Epstein-Barr virus (EBV) reactivation is common in sepsis patients but the extent and nature of this remains unresolved. We sought to determine the incidence and correlates of EBV-positivity in a large sepsis cohort. We also hypothesised that EBV reactivation would be increased in patients in whom relative immunosuppression was the major feature of their sepsis response. To identify such patients we aimed to use knowledge of sepsis response subphenotypes based on transcriptomic studies of circulating leukocytes, specifically patients with a Sepsis Response Signature endotype (SRS1) that we have previously shown to be associated with increased mortality and features of immunosuppression. We assayed EBV from the plasma of intensive care unit (ICU) patients with sepsis due to community-acquired pneumonia. In total 730 patients were evaluated by targeted metagenomics (n = 573 patients), digital droplet PCR (n = 565), or both (n = 408). We had previously analysed gene expression in peripheral blood leukocytes for a subset of individuals (n = 390). We observed a 37% incidence of EBV-positivity. EBV reactivation was associated with longer ICU stay (12.9 vs 9.2 days; p = 0.004) and increased organ failure (day 1 SOFA score 6.9 vs 5.9; p = 0.00011). EBV reactivation was associated with the relatively immunosuppressed SRS1 endotype (p = 0.014) and differential expression of a small number of biologically relevant genes. These findings are consistent with the hypothesis that viral reactivation in sepsis is a consequence of immune compromise and is associated with increasing severity of illness although further mechanistic studies are required to definitively illustrate cause and effect