BACKGROUND:T cells are often enriched at barrier tissues, yet little is known of their roles in barrier sensing and relevance to associated disease. CD1a is a Major Histocompatibility Complex class I-like molecule expressed by Langerhans cells, which forms complexes with lipid antigens to facilitate recognition by non-classical CD1a-reactive T cells. OBJECTIVES:Langerhans cells are altered in lesional atopic dermatitis (AD) skin, but the role of CD1a in disease pathogenesis has not been extensively investigated. METHODS:Human skin challenge, single cell and spatial transcriptomic based approaches and functional immunology were used to assess the role of CD1a in AD pathogenesis. RESULTS:Skin allergen challenge in individuals with AD induced skin CCL17 and CCL22 concentrations that promoted CCR4+ T cell migration. Single cell resolution proteo-transcriptomics from human lesional AD skin tissue identified a dominant CCL17/22 source as a persistent population of activated skin CD1a+ dendritic cells (DCs) previously shown to be transiently enriched in human skin wounds. Single-cell resolution spatial tissue analyses showed that these cells were predominantly located within lesional sub-epidermal microcompartment clusters co-localising with distinct subpopulations of Th2 cells. Activated skin DCs expressed neutral sphingomyelinase, which processed inhibitory long chain sphingomyelin to drive Th2 cell CD1a-autoreactivity. CONCLUSIONS:In summary, the findings are consistent with human CD1a-autoreactive T cells sensing of chronic skin barrier compromise through detection of altered sphingomyelin cycle activity, with implications for the pathogenesis of atopic and related disease.

The early-life intestinal microenvironment plays a pivotal role in shaping immune cell development. Here, we identify a colonic Wnt4-expressing stromal cell, enriched during early-life, that promotes iNKT cell proliferation via BMP-MAPK signaling. These stromal cells are spatially associated with iNKT cells and macrophages and exhibit high Bmp2 expression during the neonatal period. Depletion of BMP2 in Wnt4+ stromal cells during, but not after, this time window leads to long-lasting reductions in iNKT cells. These stromal cells are shaped by microbial signals, as germ-free and early-life antibiotic-treated mice exhibit increased Wnt4+ stromal cell abundance and elevated Bmp2 expression, with excessive iNKT cell accumulation that lasts into adulthood. These persistent changes in iNKT cells due to early-life perturbations are associated with altered susceptibility to later-life mucosal disorders. Importantly, similar stromal cells are present in fetal and neonatal human colon, and human rBMP2 promotes iNKT cell growth. Together, our findings reveal a neonatal colonic stromal niche, orchestrated by microbial cues, that regulates colonic immune homeostasis in later-life.

Abstract At birth, the intestine must rapidly adapt to enable nutritional function and immune microbial tolerance. Here, integrating single-cell multi-omics and spatial transcriptomics we define the circuits underpinning this process. We identify asynchronous developmental trajectories with postnatal epithelial reprogramming characterised by coordinated changes in metabolism, junctional structure and innate defence. At birth epithelial stem cells demonstrate dynamic enhancer remodelling, with accessibility often preceding transcription. Fetal stemness elements remain accessible despite reduced transcription across epithelial lineages, retaining plasticity potential. Post-natal epithelia experience sequential homing of myeloid cells followed by innate T cells with peri-epithelial B cells localising later in infancy. Using developmentally staged organoids, we show that epithelial responses to inflammatory stimuli are age-dependent and constrained in early life. We identify BHLHE40 as an early-life regulator that attenuates the impact of interferon- and NF-κB–driven signalling. Altogether we define the events driving epithelial licensing and barrier adaptation at birth and through infancy.

Early immune processes in idiopathic pulmonary fibrosis (IPF) are poorly defined. Here, we integrate single-cell transcriptomics of lung digests and bronchoalveolar-lavaged cells (n = 108 patients), subcellular-resolution tissue spatial transcriptomics, and single-cell phospho-CyTOF of blood cells to define myeloid states associated with early stages of fibrosis. Two distinct myeloid gene transcriptional programs are increased in IPF compared to non-diseased controls—type I interferon-activated and fibrotic remodeling programs. At cell, organ, and patient levels, cell types with increased type I interferon-activated program (FABP4hi alveolar macrophages, classical monocytes, interstitial macrophages, and/or non-classical monocytes) are associated with architecturally better-preserved lung tissue, the alveolar barrier, and less fibrotic lung, or less severe disease. Circulating monocytes exhibit heightened type I interferon response that inversely correlate with severity of clinical disease. Our findings show that myeloid cells with increased type I interferon-activated gene programs are associated with less fibrotic stages of IPF.

Background:Two respiratory syncytial virus (RSV) vaccines are currently approved for use in adults aged 60 years and older in Canada. Objective:To conduct a multi-model comparison to explore the impact of alternate model structural and methodological assumptions on the estimated cost-effectiveness of RSV adult vaccination programs. Methods:We compared three static cost-utility models developed by the Public Health Agency of Canada, GSK and Pfizer using a common set of input parameters. Each model evaluated sequential incremental cost-effectiveness ratios in 2023 Canadian dollars per quality-adjusted life year (QALY) for a set of policy alternatives, with vaccine eligibility determined by combinations of age and chronic medical condition (CMC) status. Results were calculated for each vaccine separately for scenarios assuming two or three years of vaccine protection using the health system perspective and a 1.5% annual discount rate. Results:The three cost-utility models were broadly concordant across the scenarios modeled. In all scenarios, focusing on vaccination of people with CMCs was preferred over broader age-based policies. Respiratory syncytial virus vaccination for people with CMCs over the age of 70 years was most commonly identified as the optimal policy when using a cost-effectiveness threshold of $50,000/QALY. When only considering policies based on age criteria, vaccinating people over 80 years was cost-effective at this threshold. Conclusion:A multi-model comparison of Canadian cost-utility models shows that RSV vaccination programs for RSV are likely cost-effective for some groups of older adults in Canada. These findings were consistent across models, despite differences in model structure.

Background:In July 2024, Health Canada authorized a 21-valent pneumococcal conjugate vaccine (Pneu-C-21) for use in adults. Objective:To conduct a systematic review of the cost-effectiveness of Pneu-C-21 for preventing pneumococcal disease in adults. Methods:We conducted a systematic search of the literature and National Immunization Technical Advisory Groups' websites on July 3, 2024. We included economic evaluations that assessed Pneu-C-21 as a vaccination strategy among adults aged 18 years and older. Costs were adjusted to 2023 Canadian dollars. Results:We identified 10 studies in our search, five of which were summarized in our review. No economic evaluations were conducted in Canada. All economic evaluations used static cohort models and incorporated indirect effects from paediatric pneumococcal conjugate vaccination in primary or sensitivity analyses. Although incremental cost-effectiveness ratios were heterogeneous across included economic evaluations, overall, they qualitatively identified the same vaccination strategies as optimal within the given age and risk groups. Pneu-C-21 is likely to be cost-effective in adults aged 65 years and older and adults under the age of 65 years with specific high risk conditions. Conclusion:Pneu-C-21 is likely to be cost-effective in adults within specific age and risk groups. The applicability of the included economic evaluations to adults living in Canada is limited because the serotype-specific incidence of pneumococcal disease and the impact of indirect effects from pediatric vaccination varies by region and over time.

Background:Two pneumococcal conjugate vaccines, covering 15 and 20 Streptococcus pneumoniae serotypes (Pneu-C-15 and Pneu-C-20, respectively), were recently approved for use in the Canadian paediatric population. Objective:To assess the cost-effectiveness of Pneu-C-15 and Pneu-C-20 in unvaccinated infants initiating routine pneumococcal vaccination, compared to the currently used 13-valent conjugate vaccine (Pneu-C-13). Methods:A static cohort model was used to estimate sequential incremental cost-effectiveness ratios (ICERs in 2022 Canadian dollars per quality-adjusted life year [QALY]) of Pneu-C-13, Pneu-C-15 and Pneu-C-20 in the paediatric population starting their primary series. Costs and outcomes were calculated over a 10-year time horizon at the program level and a lifetime time horizon at the individual level and discounted at a rate of 1.5% per year. We explored the impact of uncertainties in model parameters and assumptions in scenario and sensitivity analyses. Results:Routine use of Pneu-C-20 and, to a lesser extent, Pneu-C-15 is projected to reduce pneumococcal disease burden, compared to Pneu-C-13. Based on product cost assumptions, sequential ICERs for Pneu-C-15 and Pneu-C-20 were $58,800 and $135,200 per QALY gained from the health system perspective and $18,272 and $93,416 per QALY gained from the societal perspective, excluding indirect effects. A reduction in serotype-attributable disease due to indirect vaccine effects of 5% or greater resulted in ICERs below $30,000 per QALY gained for Pneu-C-15 and Pneu-C-20, with the optimal strategy determined by the magnitude and time to reach a reduction in pneumococcal disease. Conclusion:Both Pneu-C-15 and Pneu-C-20 are expected to increase QALYs in Canadian children compared to Pneu-C-13 and may be cost-effective interventions.

Crohn’s disease often presents with fistulae, abnormal tunnels that connect the intestine to the skin or other organs. Despite their profound effect on morbidity, the molecular basis of fistula formation remains unclear, largely owing to the challenge of capturing intact fistula tracts and their inherent heterogeneity 1–3 . Here we construct a subcellular-resolution spatial atlas of 68 intestinal fistulae spanning diverse anatomical locations. We describe fistula-associated epithelial, immune and stromal cell states, revealing abnormal zonation of growth factors and morphogens linked to establishment of tunnelling anatomy. We identify fistula-associated stromal (FAS) fibroblasts, which are assembled in concentric layers: a proliferative, lumen-adjacent zone beneath neutrophil and macrophage-rich granulation tissue, an active lesion core of FAS cells and a quiescent, pro-fibrotic outer zone. We examine the architecture of the extracellular matrix in the fistula tract and demonstrate that FAS populations associate with distinct collagen structures, exhibiting properties ranging from proliferation, migration and extracellular matrix remodelling to dense collagen deposition and fibrosis. We define niches supporting epithelialization of fistula tunnels and a FAS-like population that is detected at the base of ulcers in non-penetrating Crohn’s disease. Our study demonstrates that common molecular pathways and cellular niches underpin fistulae across intestinal locations, revealing the cellular protagonists of fistula establishment and persistence. This resource will inform the development of model systems and interventions to mitigate aberrant fibroblast activity while preserving their regenerative properties in Crohn’s disease.

[This corrects the article DOI: 10.1371/journal.pone.0297093.].

Background: As COVID-19 becomes established as an endemic disease with widespread population immunity, there is uncertainty about the economic benefit of ongoing COVID-19 vaccination programs. We assessed the cost-effectiveness of a COVID-19 vaccination program similar to current Canadian recommendations, modelled as annual vaccination for people aged less than 65 years with chronic medical conditions and biannual vaccination for adults aged 65 years and older. Methods: Using a static individual-based model of medically attended COVID-19 in a population of one million people, we estimated costs (in 2023 Canadian dollars), quality-adjusted life years (QALYs), and incremental cost-effectiveness ratios (ICERs). We used health system and societal perspectives and a 1.5 % discount rate. Parameters were based on recent COVID-19 epidemiology, vaccine characteristics, and costs. Results: Between July 2024 and September 2025, a program similar to current Canadian recommendations was estimated to avert 3.1 % (95 % credible interval (CrI): 3.0 to 3.2 %) of outpatient cases, 8.8 % (95 % CrI: 7.3 to 10.4 %) of inpatient cases, 3.6 % (95 % CrI: 2.8 to 4.3 %) of PCC cases, and 9.4 % (95 % CrI: 5.6 to 13.8 %) of deaths compared to no vaccination. The number needed to vaccinate to prevent one hospitalization and one death was 1121 (95 % CrI: 941 to 1357) and 8656 (95 % CrI: 5848 to 14,915), respectively. For the health system perspective, the program would cost an additional $4.695 million but result in 221.17 QALYs gained, leading to an ICER of $21,227 per QALY compared to no vaccination. Vaccine price influenced cost-effectiveness, with higher prices reducing the likelihood the program met common cost-effectiveness thresholds. Conclusions: A program similar to current COVID-19 recommendations in Canada is likely effective and cost-effective compared to no vaccination. However, unlike some other research studies, alternate vaccination strategies that may offer better value for money were not evaluated.

Importance With shifting epidemiology and changes in the vaccine funding landscape, resource use considerations for COVID-19 vaccination programs are increasingly important. Objective To assess the cost effectiveness of COVID-19 vaccination programs, where eligibility is defined by combinations of age and chronic medical conditions, including a strategy similar to current Canadian recommendations. Design, Setting, and Participants Static, individual-based, probabilistic cost-utility model economic evaluation parameterized with recent data describing COVID-19 epidemiology, vaccine characteristics, and costs. The analysis used a 15-month time horizon from July 2024 to September 2025 and a modeled cohort of 1 million people with characteristics based on the Canadian population, stratified by age group and presence or absence of at least 1 chronic medical condition. Exposure Annual or biannual COVID-19 vaccination strategies offered to different age and medical risk groups, with annual vaccination occurring in October and November in the primary analysis. Main Outcomes and Measures Medically attended SARS-CoV-2 infections treated in outpatient and inpatient settings, including post-COVID condition cases and deaths. Costs in 2023 Canadian dollars, quality-adjusted life years (QALYs), and incremental cost-effectiveness ratios (ICERs), discounted at 1.5% for the health system and societal perspectives. Results Among 1 million simulated individuals, annual vaccination for adults aged 65 years and older consistently emerged as a cost-effective intervention, with ICERs less than CAD $50 000 per QALY compared with no vaccination for a range of model assumptions. Adding a second dose for adults aged 65 years and older or expanding programs to include vaccination for younger age groups, including those at higher risk of COVID-19 due to chronic medical conditions, generally resulted in ICERs greater than $50 000 per QALY. Shifting timing of vaccination programs to better align with periods of high COVID-19 case occurrence resulted in biannual vaccination for those aged 65 years and older being cost effective. Conclusions and Relevance In this economic evaluation of COVID-19 vaccination strategies, programs were observed to be cost effective when focused on groups at higher risk of disease. Optimal timing of programs improved the cost effectiveness of vaccination strategies. As COVID-19 transitioned to an endemic disease with high levels of population immunity, many jurisdictions revisited COVID-19 vaccination recommendations; these results identified COVID-19 vaccination programs that may provide good value for money.

BACKGROUND:A 21-valent pneumococcal conjugate vaccine (PCV21) was recently authorized in Canada to protect adults against invasive pneumococcal disease (IPD). OBJECTIVE:To assess the cost-effectiveness of PCV21 compared to current Canadian vaccination recommendations for adults of different age and risk groups. METHODS:We used a static cohort model to estimate lifetime incremental cost-effectiveness ratios (ICERs), in 2023 Canadian dollars per quality-adjusted life year (QALY), discounted at 1.5 %, in population cohorts aged 33 (midpoint of the 18-49 year age group), 50, and 65 years from the health system and societal perspectives. The primary analysis used 2022 serotype distributions for IPD cases. Additional analyses incorporated indirect effects from pediatric vaccination and used IPD serotype distributions from 2015 to 2019, to explore the impact of changes over time observed in some age groups. RESULTS:For population groups currently recommended to receive PCV20 in Canada (65 years and older, 50-64 years with additional risk factors for IPD, or 18-49 years with immunocompromising conditions), PCV21 was cost-effective at a $50,000 per QALY threshold and dominated PCV20 in most scenarios when PCV21 serotypes were more prevalent. When PCV20 serotypes were equally or more prevalent than PCV21 serotypes, results were more sensitive to assumptions about indirect effects and serotype replacement. For groups not currently recommended a conjugate vaccine (50-64 years without additional IPD risk factors and 18-49 years with chronic medical conditions or unhoused populations), use of a higher-valency conjugate vaccine was a cost-effective intervention compared to no vaccination, with the optimal vaccine dependent on the proportion of IPD attributable to PCV20 and PCV21 serotypes in the population of interest. Results were sensitive to vaccine price in most scenarios. INTERPRETATION:The use of PCV21 may be cost-effective in some populations, depending on the prevalence of IPD serotypes covered by PCV20 and PCV21.

The immune–epithelial–stromal interactions underpinning intestinal damage in celiac disease (CD) are incompletely understood. To address this, we performed single-cell transcriptomics (RNA sequencing; 86,442 immune, parenchymal and epithelial cells; 35 participants) and spatial transcriptomics (20 participants) on CD intestinal biopsy samples. Here we show that in CD, epithelial populations shifted toward a progenitor state, with interferon-driven transcriptional responses, and perturbation of secretory and enteroendocrine populations. Mucosal T cells showed numeric and functional changes in regulatory and follicular helper-like CD4 + T cells, intraepithelial lymphocytes, CD8 + and γδ T cell subsets, with skewed T cell antigen receptor repertoires. Mucosal changes remained detectable despite treatment, representing a persistent immune–epithelial ‘scar’. Spatial transcriptomics defined transcriptional niches beyond those captured in conventional histological scores, including CD-specific lymphoid aggregates containing T cell–B cell interactions. Receptor–ligand spatial analyses integrated with disease susceptibility gene expression defined networks of altered chemokine and morphogen signaling, and provide potential therapeutic targets for CD prevention and treatment.

Gasdermins are a family of structurally related proteins originally described for their role in pyroptosis. Gasdermin B (GSDMB) is currently the least studied, and while its association with genetic susceptibility to chronic mucosal inflammatory disorders is well established, little is known about its functional relevance during active disease states. Herein, we report increased GSDMB in inflammatory bowel disease, with single-cell analysis identifying epithelial specificity to inflamed colonocytes/crypt top colonocytes. Surprisingly, mechanistic experiments and transcriptome profiling reveal lack of inherent GSDMB-dependent pyroptosis in activated epithelial cells and organoids but instead point to increased proliferation and migration during in vitro wound closure, which arrests in GSDMB-deficient cells that display hyper-adhesiveness and enhanced formation of vinculin-based focal adhesions dependent on PDGF-A-mediated FAK phosphorylation. Importantly, carriage of disease-associated GSDMB SNPs confers functional defects, disrupting epithelial restitution/repair, which, altogether, establishes GSDMB as a critical factor for restoration of epithelial barrier function and the resolution of inflammation.

The success of checkpoint inhibitors (CPIs) for cancer has been tempered by immune-related adverse effects including colitis. CPI-induced colitis is hallmarked by expansion of resident mucosal IFNγ cytotoxic CD8+ T cells, but how these arise is unclear. Here, we track CPI-bound T cells in intestinal tissue using multimodal single-cell and subcellular spatial transcriptomics (ST). Target occupancy was increased in inflamed tissue, with drug-bound T cells located in distinct microdomains distinguished by specific intercellular signaling and transcriptional gradients. CPI-bound cells were largely CD4+ T cells, including enrichment in CPI-bound peripheral helper, follicular helper, and regulatory T cells. IFNγ CD8+ T cells emerged from both tissue-resident memory (TRM) and peripheral populations, displayed more restricted target occupancy profiles, and co-localized with damaged epithelial microdomains lacking effective regulatory cues. Our multimodal analysis identifies causal pathways and constitutes a resource to inform novel preventive strategies.

Background: Respiratory syncytial virus (RSV) vaccines could reduce disease burden and costs in older Canadian adults, but vaccination program cost-effectiveness is unknown. We evaluated the cost-effectiveness of different age cut-offs for RSV adult vaccination programs, with or without a focus on people with higher disease risk due to chronic medical conditions.Methods: We developed a static individual-based model of medically attended RSV disease to compare alternative age-, medical risk-, and age-plus medical risk-based vaccination policies. The model followed a multiage population of 100 000 people aged 50 years and older. Vaccine characteristics were based on RSV vaccines authorized in Canada as of May 2024, with vaccine protection assumed to last 2 years (or 3 years in scenario analyses). We calculated sequential incremental cost-effectiveness ratios in 2023 Canadian dollars per quality-adjusted life year (QALY) from the health-system and societal perspectives, discounted at 1.5%.Results: Although all vaccination strategies averted medically attended RSV disease, universal age-based strategies were not an efficient use of resources compared with medical risk-based strategies. Vaccinating adults aged 70 years and older with 1 or more chronic medical condition was the optimal strategy for a cost-effectiveness threshold of $50 000 per QALY. Results were sensitive to assumptions about vaccine price, but medical risk-based approaches remained optimal compared with age-based strategies, even when vaccine prices were low. Findings were robust to a range of alternative assumptions.Interpretation: Vaccination programs for RSV in some groups of older Canadians with underlying medical conditions are likely cost-effective. These findings can inform the design of vaccination programs.

Background: Health Canada recently authorized the RSVpreF pregnancy vaccine and nirsevimab to protect infants against respiratory syncytial virus (RSV) disease. Objective: Assess the cost-effectiveness of RSVpreF and nirsevimab programs in preventing RSV disease in infants, compared to a palivizumab program. Methods: We used a static cohort model of a Canadian birth cohort during their first RSV season to estimate sequential incremental cost-effectiveness ratios (ICERs) in 2023 Canadian dollars per quality-adjusted life year (QALY) for nine strategies implemented over a one-year time period, from the health system and societal perspectives. Sensitivity and scenario analyses were conducted to explore the impact of uncertainties on the results. Results: All-infants nirsevimab programs averted more RSV-related outcomes than year-round RSVpreF programs, with the most RSV cases averted in a seasonal nirsevimab program with catch-up. Assuming list prices for these immunizing agents, all-infants nirsevimab and year-round RSVpreF programs were never cost-effective, with ICERs far exceeding commonly used cost-effectiveness thresholds. Seasonal nirsevimab with catch-up for infants born outside the RSV season was a cost-effective program if prioritized for infants at moderate/high-risk (ICER <$28,000 per QALY) or those living in settings with higher RSV burden and healthcare costs, such as remote communities where transport would be complex (ICER of $5700 per QALY). Using a $50,000 per QALY threshold, an all-infants nirsevimab program could be optimal if nirsevimab is priced at <$110-190 per dose. A year-round RSVpreF for all pregnant women and pregnant people plus nirsevimab for infants at high-risk was optimal if nirsevimab is priced at >$110-190 per dose and RSVpreF priced at <$60-125 per dose. Interpretation: Prophylactic interventions can substantially reduce RSV disease in infants, and more focused nirsevimab programs are the most cost-effective option at current product prices.

Supplementary Figure 1 to 7, Supplementary Table 1