Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology.

Evidence suggests that innate and adaptive cellular responses mediate resistance to the influenza virus and confer protection after vaccination. However, few studies have resolved the contribution of cellular responses within the context of preexisting antibody titers. Here, we measured the peripheral immune profiles of 206 vaccinated or unvaccinated adults to determine how baseline variations in the cellular and humoral immune compartments contribute independently or synergistically to the risk of developing symptomatic influenza. Protection correlated with diverse and polyfunctional CD4+ and CD8+ T, circulating T follicular helper, T helper type 17, myeloid dendritic and CD16+ natural killer (NK) cell subsets. Conversely, increased susceptibility was predominantly attributed to nonspecific inflammatory populations, including γδ T cells and activated CD16- NK cells, as well as TNFα+ single-cytokine-producing CD8+ T cells. Multivariate and predictive modeling indicated that cellular subsets (1) work synergistically with humoral immunity to confer protection, (2) improve model performance over demographic and serologic factors alone and (3) comprise the most important predictive covariates. Together, these results demonstrate that preinfection peripheral cell composition improves the prediction of symptomatic influenza susceptibility over vaccination, demographics or serology alone.

ER Stress Sensor XBP1 Controls Anti-tumor Immunity by Disrupting Dendritic Cell Homeostasis.

Dendritic cells (DCs) are required to initiate and sustain T cell-dependent anti-cancer immunity. However, tumors often evade immune control by crippling normal DC function. The endoplasmic reticulum (ER) stress response factor XBP1 promotes intrinsic tumor growth directly, but whether it also regulates the host anti-tumor immune response is not known. Here we show that constitutive activation of XBP1 in tumor-associated DCs (tDCs) drives ovarian cancer (OvCa) progression by blunting anti-tumor immunity. XBP1 activation, fueled by lipid peroxidation byproducts, induced a triglyceride biosynthetic program in tDCs leading to abnormal lipid accumulation and subsequent inhibition of tDC capacity to support anti-tumor T cells. Accordingly, DC-specific XBP1 deletion or selective nanoparticle-mediated XBP1 silencing in tDCs restored their immunostimulatory activity in situ and extended survival by evoking protective type 1 anti-tumor responses. Targeting the ER stress response should concomitantly inhibit tumor growth and enhance anti-cancer immunity, thus offering a unique approach to cancer immunotherapy.

Necroptosis blockade prevents lung injury in severe influenza.

Severe influenza A virus (IAV) infections can result in hyper-inflammation, lung injury and acute respiratory distress syndrome1-5 (ARDS), for which there are no effective pharmacological therapies. Necroptosis is an attractive entry point for therapeutic intervention in ARDS and related inflammatory conditions because it drives pathogenic lung inflammation and lethality during severe IAV infection6-8 and can potentially be targeted by receptor interacting protein kinase 3 (RIPK3) inhibitors. Here we show that a newly developed RIPK3 inhibitor, UH15-38, potently and selectively blocked IAV-triggered necroptosis in alveolar epithelial cells in vivo. UH15-38 ameliorated lung inflammation and prevented mortality following infection with laboratory-adapted and pandemic strains of IAV, without compromising antiviral adaptive immune responses or impeding viral clearance. UH15-38 displayed robust therapeutic efficacy even when administered late in the course of infection, suggesting that RIPK3 blockade may provide clinical benefit in patients with IAV-driven ARDS and other hyper-inflammatory pathologies.

Spliced X-box binding protein 1 couples the unfolded protein response to hexosamine biosynthetic pathway.

The hexosamine biosynthetic pathway (HBP) generates uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) for glycan synthesis and O-linked GlcNAc (O-GlcNAc) protein modifications. Despite the established role of the HBP in metabolism and multiple diseases, regulation of the HBP remains largely undefined. Here, we show that spliced X-box binding protein 1 (Xbp1s), the most conserved signal transducer of the unfolded protein response (UPR), is a direct transcriptional activator of the HBP. We demonstrate that the UPR triggers HBP activation via Xbp1s-dependent transcription of genes coding for key, rate-limiting enzymes. We further establish that this previously unrecognized UPR-HBP axis is triggered in a variety of stress conditions. Finally, we demonstrate a physiologic role for the UPR-HBP axis by showing that acute stimulation of Xbp1s in heart by ischemia/reperfusion confers robust cardioprotection in part through induction of the HBP. Collectively, these studies reveal that Xbp1s couples the UPR to the HBP to protect cells under stress.

The transcription factor XBP1 is selectively required for eosinophil differentiation.

The transcription factor XBP1 has been linked to the development of highly secretory tissues such as plasma cells and Paneth cells, yet its function in granulocyte maturation has remained unknown. Here we discovered an unexpectedly selective and absolute requirement for XBP1 in eosinophil differentiation without an effect on the survival of basophils or neutrophils. Progenitors of myeloid cells and eosinophils selectively activated the endoribonuclease IRE1α and spliced Xbp1 mRNA without inducing parallel endoplasmic reticulum (ER) stress signaling pathways. Without XBP1, nascent eosinophils exhibited massive defects in the post-translational maturation of key granule proteins required for survival, and these unresolvable structural defects fed back to suppress critical aspects of the transcriptional developmental program. Hence, we present evidence that granulocyte subsets can be distinguished by their differential reliance on secretory-pathway homeostasis.

The miR-126-VEGFR2 axis controls the innate response to pathogen-associated nucleic acids.

miR-126 is a microRNA expressed predominately by endothelial cells and controls angiogenesis. We found miR-126 was required for the innate response to pathogen-associated nucleic acids and that miR-126-deficient mice had greater susceptibility to infection with pseudotyped HIV. Profiling of miRNA indicated that miR-126 had high and specific expression by plasmacytoid dendritic cells (pDCs). Moreover, miR-126 controlled the survival and function of pDCs and regulated the expression of genes encoding molecules involved in the innate response, including Tlr7, Tlr9 and Nfkb1, as well as Kdr, which encodes the growth factor receptor VEGFR2. Deletion of Kdr in DCs resulted in reduced production of type I interferon, which supports the proposal of a role for VEGFR2 in miR-126 regulation of pDCs. Our studies identify the miR-126-VEGFR2 axis as an important regulator of the innate response that operates through multiscale control of pDCs.

Mycobacterium abscessus resists the innate cellular response by surviving cell lysis of infected phagocytes.

Mycobacterium abscessus is the most pathogenic species among the predominantly saprophytic fast-growing mycobacteria. This opportunistic human pathogen causes severe infections that are difficult to eradicate. Its ability to survive within the host was described mainly with the rough (R) form of M. abscessus, which is lethal in several animal models. This R form is not present at the very beginning of the disease but appears during the progression and the exacerbation of the mycobacterial infection, by transition from a smooth (S) form. However, we do not know how the S form of M. abscessus colonizes and infects the host to then multiply and cause the disease. In this work, we were able to show the hypersensitivity of fruit flies, Drosophila melanogaster, to intrathoracic infections by the S and R forms of M. abscessus. This allowed us to unravel how the S form resists the innate immune response developed by the fly, both the antimicrobial peptides- and cellular-dependent immune responses. We demonstrate that intracellular M. abscessus was not killed within the infected phagocytic cells, by resisting lysis and caspase-dependent apoptotic cell death of Drosophila infected phagocytes. In mice, in a similar manner, intra-macrophage M. abscessus was not killed when M. abscessus-infected macrophages were lysed by autologous natural killer cells. These results demonstrate the propensity of the S form of M. abscessus to resist the host's innate responses to colonize and multiply within the host.

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data.

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems, such as cell signaling and epigenetic regulation. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Protein positional isomers refer to a set of proteoforms with identical total mass and set of modifications, but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, the current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for the relative quantification of PI within a single tool. Benchmarking IsoForma's performance against two existing workflows produced comparable results and improvements in speed. Overall, IsoForma provides a streamlined process for quantifying PI, reduces the analysis time, and offers an essential framework for developing customized proteoform analysis workflows. The software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

Alleviating misclassified germline variants in underrepresented populations: A strategy using popmax.

PURPOSE: Germline variant interpretation often depends on population-matched control cohorts. This is not feasible for population groups that are underrepresented in current population reference databases. METHODS: We classify germline variants with population-matched controls for 2 ancestrally diverse cohorts of patients: 132 early-onset or familial colorectal carcinoma patients from Singapore and 100 early-onset colorectal carcinoma patients from the United States. The effects of using a population-mismatched control cohort are simulated by swapping the control cohorts used for each patient cohort, with or without the popmax computational strategy. RESULTS: Population-matched classifications revealed a combined 62 pathogenic or likely pathogenic (P/LP) variants in 34 genes across both cohorts. Using a population-mismatched control cohort resulted in misclassification of non-P/LP variants as P/LP, driven by the absence of ancestry-specific rare variants in the control cohort. Popmax was more effective in alleviating misclassifications for the Singapore cohort than the US cohort. CONCLUSION: Underrepresented population groups can suffer from higher rates of false-positive P/LP results. Popmax can partially alleviate these misclassifications, but its efficacy still depends on the degree with which the population groups are represented in the control cohort.

Heavy metal stress and mitogen activated kinase transcription factors in plants: Exploring heavy metal-ROS influences on plant signalling pathways.

Due to their stationary nature, plants are exposed to a diverse range of biotic and abiotic stresses, of which heavy metal (HM) stress poses one of the most detrimental abiotic stresses, targeting diverse plant processes. HMs instigate the overproduction of reactive oxygen species (ROS), and to mitigate the adverse effects of ROS, plants induce multiple defence mechanisms. Besides the negative implications of overproduction of ROS, these molecules play a multitude of signalling roles in plants, acting as a central player in the complex signalling network of cells. One of the ROS-associated signalling mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signalling pathway which transduces extracellular stimuli into intracellular responses. Plant MAPKs have been implicated in signalling involved in stress response, phytohormone regulation, and cell cycle cues. However, the influence of various HMs on MAPK activation has not been well documented. In this review, we address and summarise several aspects related to various HM-induced ROS signalling. Additionally, we touch on how these signals activate the MAPK cascade and the downstream transcription factors that influence plant responses to HMs. Moreover, we propose a workflow that could characterise genes associated with MAPKs and their roles during plant HM stress responses.

Landscape of germline pathogenic variants in patients with dual primary breast and lung cancer.

BACKGROUND: Cancer predisposition is most often studied in the context of single cancers. However, inherited cancer predispositions can also give rise to multiple primary cancers. Yet, there is a paucity of studies on genetic predisposition in multiple primary cancers, especially those outside of well-defined cancer predisposition syndromes. This study aimed to identify germline variants associated with dual primary cancers of the breast and lung. METHODS: Exome sequencing was performed on germline DNA from 55 Singapore patients (52 [95%] never-smokers) with dual primaries in the breast and lung, confirmed by histopathology. Using two large control cohorts: the local SG10K_Health (n = 9770) and gnomAD non-cancer East Asians (n = 9626); and two additional local case cohorts of early-onset or familial breast cancer (n = 290), and lung cancer (n = 209), variants were assessed for pathogenicity in accordance with ACMG/AMP guidelines. In particular, comparisons were made with known pathogenic or likely pathogenic variants in the ClinVar database, pathogenicity predictions were obtained from in silico prediction software, and case-control association analyses were performed. RESULTS: Altogether, we identified 19 pathogenic or likely pathogenic variants from 16 genes, detected in 17 of 55 (31%) patients. Six of the 19 variants were identified using ClinVar, while 13 variants were classified pathogenic or likely pathogenic using ACMG/AMP guidelines. The 16 genes include well-known cancer predisposition genes such as BRCA2, TP53, and RAD51D; but also lesser known cancer genes EXT2, WWOX, GATA2, and GPC3. Most of these genes are involved in DNA damage repair, reaffirming the role of impaired DNA repair mechanisms in the development of multiple malignancies. These variants warrant further investigations in additional populations. CONCLUSIONS: We have identified both known and novel variants significantly enriched in patients with primary breast and lung malignancies, expanding the body of known cancer predisposition variants for both breast and lung cancer. These variants are mostly from genes involved in DNA repair, affirming the role of impaired DNA repair in the predisposition and development of multiple cancers.

The tip of the iceberg: Generalism in undergraduate medical education, a systems thinking analysis.

PURPOSE: There is a shortage of generalist physicians globally impacting health equity and access to care. An important way in which medical schools can demonstrate social accountability is by graduating learners interested in careers in generalism. While generalism is endorsed as a matter of principle in medical education, how this translates into curricula is less clear. The aim of this study was to identify how generalism is understood and supported by family physician educational leaders in undergraduate medical education (UME) in Canada. METHODS: We conducted a qualitative study, interviewing 38 family medicine leaders in UME across all 17 Canadian medical schools. We examined the data with template analysis, informed by the iceberg model of systems thinking. RESULTS: Four themes were identified: (1) Teaching and learning strategies in support of generalism-a consistent range existed across UME curricula; (2) Curriculum patterns-changes in leadership and curriculum reform created positive or negative feedback loops that promoted or hindered initiatives to support generalism; (3) Curriculum structures-organ-system-based curricula and availability of generalist faculty presented particular challenges to teaching generalist approaches; (4) Mental models and ways of knowing-the preponderance of biomedical frameworks of thinking in curricula unconsciously undermined generalist approaches to patient care. CONCLUSIONS: UME programmes promoted generalism through a range of teaching activities and strategies, but these efforts were countered by curriculum structures and mental models that perpetuate epistemic inequity between biomedical approaches to medical education and generalist models of care. Novel curricular frameworks are needed to align undergraduate programmes' commitment to social accountability with community-based need.

Exploring Whether and How People Experiencing High Deprivation Access Diagnostic Services: A Qualitative Systematic Review.

INTRODUCTION: To contribute to addressing diagnostic health inequalities in the United Kingdom, this review aimed to investigate determinants of diagnostic service use amongst people experiencing high deprivation in the United Kingdom. METHODS: A systematic review was conducted using three databases (EBSCO, Web of Science and SCOPUS) to search studies pertaining to diagnostic service use amongst people experiencing high deprivation. Search terms related to diagnostics, barriers and facilitators to access and deprivation. Articles were included if they discussed facilitators and/or barriers to diagnostic service access, contained participants' direct perspectives and focussed on individuals experiencing high deprivation in the United Kingdom. Articles were excluded if the full text was unretrievable, only abstracts were available, the research did not focus on adults experiencing high deprivation in the United Kingdom, those not including participants' direct perspectives (e.g., quantitative studies) and papers unavailable in English. RESULTS: Of 14,717 initial papers, 18 were included in the final review. Determinants were grouped into three themes (Beliefs and Behaviours, Emotional and Psychological Factors and Practical Factors), made up of 15 sub-themes. These were mapped to a conceptual model, which illustrates that Beliefs and Behaviours interact with Emotional and Psychological Factors to influence Motivation to access diagnostic services. Motivation then influences and is influenced by Practical Factors, resulting in a Decision to Access or Not. This decision influences Beliefs and Behaviours and/or Emotional and Psychological Factors such that the cycle begins again. CONCLUSION: Decision-making regarding diagnostic service use for people experiencing high deprivation in the United Kingdom is complex. The conceptual model illustrates this complexity, as well as the mediative, interactive and iterative nature of the process. The model should be applied in policy and practice to enable understanding of the factors influencing access to diagnostic services and to design interventions that address identified determinants. PATIENT OR PUBLIC CONTRIBUTION: Consulting lived experience experts was imperative in understanding whether and how the existing literature captures the lived experience of those experiencing high deprivation in South England. The model was presented to lived experience experts, who corroborated findings, highlighted significant factors for them and introduced issues that were not identified in the review.

Effect of the Nurse Work Environment on Older Hispanic Surgical Patient Readmissions.

BACKGROUND: Readmissions following hospitalization for common surgical procedures are prevalent among older adults and are disproportionally experienced by Hispanic patients. One potential explanation for these disparities is that Hispanic patients may receive care in hospitals with lower-quality nursing care. OBJECTIVES: The objective of this study was to evaluate the relationship between the hospital-level work environment of nurses and hospital readmissions among older Hispanic patients. METHODS: Using linked data sources from 2014 to 2016, we conducted a cross-sectional analysis of 522 hospitals and 732,035 general, orthopedic, and vascular surgical patients (80,978 Hispanic patients and 651,057 non-Hispanic White patients) in four states. Multivariable logistic regression models were employed to determine the relationship between the work environment and older Hispanic patient readmissions at multiple time periods (7, 30, and 90 days). RESULTS: In final adjusted models that included an interaction between work environment and ethnicity, an increase in the quality of the work environment resulted in a decrease in the odds of readmission that was greater for older Hispanic surgical patients at all time periods. Specifically, an increase in three of the five work environment subscales (Nurse Participation in Hospital Affairs, Nursing Foundations for Quality of Care, and Staffing and Resource Adequacy) was associated with a reduction in the odds of readmission that was greater for Hispanic patients than their non-Hispanic White counterparts. DISCUSSION: System-level investments in the work environment may reduce Hispanic patient readmission disparities. This study's findings may be used to inform the development of targeted interventions to prevent hospital readmissions for Hispanic patients.

Pre- and post-COVID-19 gender trends in authorship for paediatric radiology articles worldwide: a systematic review.

BACKGROUND: Gender inequalities in academic medicine persist despite progress over the past decade. Evidence-based targeted interventions are needed to reduce gender inequalities. OBJECTIVE: This systematic review aimed to investigate the impact of COVID-19 on gender trends in authorship of paediatric radiology research worldwide. MATERIALS AND METHODS: This prospectively registered, PRISMA-compliant systematic review searched the following databases: PubMed, MEDLINE, Web of Science, and Scopus from January 1, 2018, to May 29, 2023, with no restrictions on country of origin. Screening and data extraction occurred independently and in duplicate. Gender of first, last, and corresponding authors were determined using an artificial intelligence-powered, validated, multinational database ( www.genderize.io ). Two time periods were categorised according to the Johns Hopkins Center for Systems Science and Engineering: pre-COVID (prior to March 2020) and peak and post-COVID (March 2020 onwards). One-sample binomial testing was used to analyse proportion of authorship based on gender. Categorical variables were described as frequencies and percentages, and compared using testing chi-square or Fisher exact testing, with a threshold of P<0.05 representing statistical significance. RESULTS: In total, 922 articles were included with 39 countries represented. A statistically significant difference in authorship based on gender persisted during the peak and post-COVID time period (March 2020 onwards) where women represented a statistically significant lower proportion of last (35.5%) and corresponding (42.7%) authors (P<0.001, P=0.001, respectively). Statistically significant differences for first authors were not found in either period (P=0.08 and P=0.48). CONCLUSION: This study identifies differences in gender trends for authorship in paediatric radiology research worldwide. Future efforts to increase authorship by women are needed.

Normal Proteasome Function Is Needed to Prevent Kidney Graft Injury during Cold Storage Followed by Transplantation.

Kidney transplantation is the preferred treatment for end-stage kidney disease (ESKD). However, there is a shortage of transplantable kidneys, and donor organs can be damaged by necessary cold storage (CS). Although CS improves the viability of kidneys from deceased donors, prolonged CS negatively affects transplantation outcomes. Previously, we reported that renal proteasome function decreased after rat kidneys underwent CS followed by transplantation (CS + Tx). Here, we investigated the mechanism underlying proteasome dysfunction and the role of the proteasome in kidney graft outcome using a rat model of CS + Tx. We found that the key proteasome subunits ß5, α3, and Rpt6 are modified, and proteasome assembly is impaired. Specifically, we detected the modification and aggregation of Rpt6 after CS + Tx, and Rpt6 modification was reversed when renal extracts were treated with protein phosphatases. CS + Tx kidneys also displayed increased levels of nitrotyrosine, an indicator of peroxynitrite (a reactive oxygen species, ROS), compared to sham. Because the Rpt6 subunit appeared to aggregate, we investigated the effect of CS + Tx-mediated ROS (peroxynitrite) generation on renal proteasome assembly and function. We treated NRK cells with exogenous peroxynitrite and evaluated PAC1 (proteasome assembly chaperone), Rpt6, and ß5. Peroxynitrite induced a dose-dependent decrease in PAC1 and ß5, but Rpt6 was not affected (protein level or modification). Finally, serum creatinine increased when we inhibited the proteasome in transplanted donor rat kidneys (without CS), recapitulating the effects of CS + Tx. These findings underscore the effects of CS + Tx on renal proteasome subunit dysregulation and also highlight the significance of proteasome activity in maintaining graft function following CS + Tx.

Exploring the relationships between resilience, burnout, work engagement, and intention to leave among nurses in the context of the COVID-19 pandemic: a cross-sectional study.

BACKGROUND: Nurses have faced significant personal and professional stressors during the COVID-19 pandemic that have contributed to increased rates of burnout, intention to leave, and poorer work engagement. Resilience has been identified as a critical factor influencing job outcomes; however, the dynamics of this association have not yet been investigated within the context of the Thai workforce. The study objective was to determine the associations between resilience and job outcomes, including burnout, intention to leave, and work engagement among nurses working in Thailand during the COVID-19 pandemic. METHODS: This cross-sectional study gathered data from a sample of 394 registered nurses employed across 12 hospitals. The research instruments comprised the Connor-Davidson Resilience Scale (CD-RISC), the Maslach Burnout Inventory-Health Services Survey (MBI-HSS), a questionnaire assessing the intention to leave the job, and the Utrecht Work Engagement Scale (UWES). To determine the associations among the measured variables, multivariate logistic regression analyses were conducted. RESULTS: One-third of nurses experienced emotional exhaustion and depersonalization, and about half experienced reduced personal accomplishment; one-tenth of nurses intended to leave their job. Nurses who exhibited higher levels of resilience were found to have a significantly reduced likelihood of experiencing high emotional exhaustion, depersonalization, and a diminished sense of personal accomplishment. Conversely, these nurses were more likely to report higher levels of work engagement than their less resilience. CONCLUSION: The COVID-19 pandemic offers important lessons learned about promoting the well-being of the nursing workforce and protecting against adverse job outcomes. While we identified resilience as a significant predictor of several nurse outcomes, other work environment factors should be considered. Government and hospital administrations should allocate resources for individual and organizational-level interventions to promote resilience among frontline nurses so that hospitals will be better prepared for the next public health emergency and patient and nurse outcomes can be optimized.