Clinical & Translational Immunology

In this study, we provide a comprehensive characterization of the alveolar immune landscape in patients suffering from severe acute respiratory failure, predominantly caused by pneumonia or acute respiratory distress syndrome, conditions defined by intense pulmonary inflammation and immune dysregulation. Despite diverse underlying causes, the overall composition of alveolar immune cells was largely consistent, with neutrophils and macrophages comprising the majority of cells. However, the maturation and activation states of immune cell subsets varied significantly, not only between patients with and without pneumonia, but also among pneumonia cases stratified by pathogen type. We also observed dynamic shifts in immune cell subsets over the disease course and found that an increased proportion of CD123bright immature neutrophils and a reduction in alveolar resident macrophages were associated with increased 28-day mortality. Integration with alveolar cytokine profiles revealed strong correlations between immune cell populations and the local cytokine milieu. These findings highlight the importance of assessing immune cell function, not merely abundance, through broad and longitudinal investigation to better understand the pathophysiology of acute respiratory failure and to guide precision immunomodulatory therapy.

PurposeSepsis-associated immunothrombosis significantly contributes to high mortality, yet the role of N-glycosylation in this process remains poorly understood. This study aimed to comprehensively profile the plasma N-glycosylation landscape in sepsis and elucidate how its specific reprogramming in the complement and coagulation cascades influences immunothrombotic balance and patient outcomes. MethodsWe performed in-depth 4D-DIA proteomic and N-glycomic analyses on plasma from 43 sepsis patients and 9 healthy controls. Differential expression, weighted gene co-expression network analysis (WGCNA), and protein-glycosylation correlation analyses were used to characterize molecular features. Clinical relevance was assessed via correlation and survival analyses. ResultsExtensive N-glycosylation reprogramming was observed in sepsis plasma,with marked enrichment in complement and coagulation pathways(KEGG p=7.76x10- {superscript 2}{superscript 1}).Pro-coagulant proteins(eg,vWF,fibrinogen)showed increased abundance together with enhanced site-specific glycosylation,potentially amplifying their activity.In contrast,key anticoagulant proteins(eg,SERPINC1)displayed unchanged glycosylation at critical sites despite abundance changes,which may impair function.Survival analysis revealed distinct prognostic values of glycoproteins and specific glycosylation sites.For instance,high vWF protein levels predicted mortality(HR=2.83),whereas elevated glycosylation at vWF N211 was associated with improved survival(HR=0.135),suggesting a negative regulatory role.These glycosylation markers correlated closely with disease severity and prognosis,representing potential early-warning biomarkers independent of current clinical coagulation indicators. ConclusionOur study demonstrates widespread reprogramming of the plasma proteome and N-glycome in sepsis.We propose that decoupling of protein function from abundance through N-glycosylation in the complement-coagulation network contributes to immunothrombotic imbalance.Specific N-glycosylation sites may serve as novel prognostic biomarkers,offering new perspectives for early risk stratification and glycosylation-targeted therapies in sepsis. Key PointsO_LISepsis plasma exhibits specific N-glycosylation reprogramming overwhelmingly focused on the complement and coagulation cascade. C_LIO_LIA dominant "glycosylation-dominated co-upregulation" mode in procoagulant factors, coupled with a "silent" glycosylation state in key anticoagulants, drives prothrombotic imbalance. C_LIO_LISite-specific N-glycosylation levels provide prognostic information distinct from, and often superior to, their carrier protein abundance, offering novel early-risk biomarkers. C_LI

Haemorrhage is the leading preventable cause of trauma death, primarily through ischaemic consequences that current treatments cannot adequately address. We combined human transcriptomic data (n=458) with a controlled porcine model of haemorrhagic shock to identify treatment-responsive molecular mechanisms. Using latent factorisation, we prioritised distinct molecular signatures of the human shock response, including stress signalling, neutrophil activation, and cytotoxic lymphocyte programmes. We assessed the behaviour of these pathways in the experimental porcine system, revealing that shock-initiated immune trajectories are not immutable: blood resuscitation normalised maladaptive transcriptomic changes whilst noradrenaline exacerbated them. While resuscitation modulated neutrophil, heat-shock, and barrier defence programmes, interferon and coagulation pathways were neither mortality-predictive nor treatment-responsive. A factor representing p38-MAPK/AP-1 stress signalling emerged as the dominant mortality-predictive pathway. An in silico small molecule screen identified p38 inhibitors as leading candidates for reversing shock-induced transcriptomic signatures. Our framework identifies modifiable pathways in trauma shock, prioritising p38-MAPK inhibition for therapeutic development and providing a systematic approach for trauma drug repurposing. One sentence summary: Human-porcine cross-analysis reveals treatment-modifiable molecular signatures of trauma shock, identifying potential therapeutic strategies.

In this report, experiments were performed to assess how Arylsulfatase B (ARSB; N-acetylgalactosamine-4-sulfatase) treatment might interact with Pembrolizumab and improve therapeutic responses in melanoma. ARSB acts to remove 4-sulfate groups from chondroitin 4-sulfate (C4S; chondroitin sulfate A; CSA). ARSB is required for the degradation of C4S, identified as an oncofetal, tumor-agnostic antigen. Previous reports showed that in syngeneic B16F10 mouse melanomas, ARSB inhibited progression of subcutaneous and metastatic pulmonary melanomas and improved survival by direct effects on melanoma cells. ARSB enhanced apoptosis, which was mediated by increased expression of Constitutive Photomorphogenic (COP)1, an E3 ubiquitin ligase. Combined treatment by recombinant human ARSB, directed at melanoma cells, and Pembrolizumab, directed at infiltrating cytotoxic lymphocytes, can lead to increased apoptosis by different mechanisms, to declines in metalloproteinases and invasiveness, and to altered expression of cytokines. Synergism between effects of ARSB and Pembrolizumab may further inhibit the progression of melanoma and improve treatment outcomes.

Coccidioidomycosis presents clinically as a spectrum ranging from self-limiting Uncomplicated Valley Fever (UVF) in most cases to life-threatening Disseminated Coccidioidomycosis (DCM) in rare individuals. A few patterns of immunologic deficits allowing for dissemination have been identified, though the specific defects in most individuals with DCM remain undefined. We hypothesized that chronic antigen exposure in DCM engenders a state of T cell exhaustion. From a cohort of over 300 subjects with confirmed diagnoses of coccidioidomycosis, circulating T cell phenotypes were characterized via flow cytometry and Coccidioides-specific T cell responses were measured using the Activation-Induced Marker (AIM) assay. Male sex was significantly associated with disseminated disease (odds ratio 2.5; 95% CI: 1.5 - 4.0). 52% of subjects showed Coccidioides-specific T cell responses in our AIM assay. We noted a significant difference in subjects sampled in the first year of diagnosis, where only 8% of DCM subjects had T cell responses during this time, as compared to 44% of UVF subjects (p = 0.04). Among DCM patients with detectable AIM responses, CD4+ T cells demonstrated an exhausted phenotype with elevated PD-1 expression compared to UVF subjects. In vitro PD-1 blockade augmented IFN{gamma} production in most tested DCM subjects. These findings suggest that dissemination may occur in some individuals during a period of impaired antigen-specific T-cell activity. Importantly, these responses can be augmented in vitro by PD-1 blocking antibodies, supporting further study of immune checkpoint therapy as an adjunct to antifungal treatment in disseminated coccidioidomycosis.

A multivariant total subclass analysis has been performed for a control cohort (n=15) and a long COVID patient cohort (n=15) measuring the IgG1, IgG2, IgG3, IgG4 and IgE response to the following 14 variants of SARS-CoV-2: Wuhan, Alpha, Delta, BA.1, BA.2, BA.5, EG.5.1, XBB.1.5, BA.2.75, CH.1.1, BA.2.12.1, BQ.1.1, JN.1, and KP.3. Significant differences (p < 0.05 and p < 0.005) between concentrations of IgG subclasses by variant were found in 24% of variants and in mean-normalised distributions. The medians of the mean-normalised distributions were significantly lower for IgG1 (p < 0.05) in long COVID patients compared with controls, and significantly higher (p < 0.005) for levels of IgG3, IgG4 and IgE for long COVID patients. A preliminary diagnostics classification analysis performed by variation of the mean-normalised upper and lower percentiles symmetrically for IgG3 showed a long COVID diagnostic sensitivity of 80%, and specificity of 80% for the 60th percentile threshold of the control cohort. Three types of long COVID can be identified: patients with at least one variant below the threshold (hypo-immune), patients with at least one variant above the threshold (hyperimmune) and patients with IgG3 levels within the reference range. The multivariant subclass spectrum indicates IgG4 and IgE elevations due to potential chronic antigen exposure from persistent virus or autoimmunity and may indicate potential therapeutic interventions.

BK polyomavirus (BKPyV) is a major complication in kidney transplant recipients (KTR), for whom no specific antiviral therapy is available. Modulation of immunosuppressive therapy results in virus clearance in most KTR with BKPyV DNAemia (controllers), but a significant minority fail to clear the virus (non-controllers). Here, we adapt LIBRA-seq, which links antibody sequence data to antigen specificity, to intact viral capsids of the four BKPyV genotypes to study and compare BKPyV-specific B-cell repertoires in controllers (n=8) versus non-controllers (n=3). Sequences were obtained for 5197 BKPyV-specific antibodies, and predicted antigen specificities were validated by ELISA and neutralizing assays (n=21 antibodies). We show that cross-genotype reactivity results from the recruitment of numerous broadly cross-reactive B-cell clones with preferential binding to the infecting genotype, making up 4,3% to 44,6% of the BKPyV-specific repertoire, while true broadly neutralizing antibodies are rare. The proportions of broadly-specific and isotype switched antibodies, rates of somatic hypermutation and repertoire diversity were comparable in both patient groups, indicating that there is no identifiable deficit in the humoral response mounted by BKPyV non-controllers, and supporting the notion that humoral immunity alone is insufficient to control established BKPyV replication. This work shows that LIBRA-seq can be successfully applied to a non-enveloped virus and provides a framework for analyzing antiviral B-cell repertoires and antibody specificity in clinically relevant settings. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/26345220v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@18ef2b6org.highwire.dtl.DTLVardef@1e0b7a2org.highwire.dtl.DTLVardef@3822fcorg.highwire.dtl.DTLVardef@180deea_HPS_FORMAT_FIGEXP M_FIG C_FIG

BackgroundImmune checkpoint inhibitors (ICIs) targeting the programmed death (ligand)-1 (PD-1/PD-L1) axis, like pembrolizumab, have significantly improved survival in non-small cell lung cancer (NSCLC). However, less than 50% of patients respond. Identifying early-response biomarkers is crucial to personalize therapy, thereby preventing ineffective, expensive and potentially harmful treatment. MethodsWe applied a novel ex vivo immunopharmacological bioassay to assess pembrolizumab-dependent T cell signalling in baseline peripheral blood mononuclear cells (PBMCs) from 64 NSCLC patients. PBMCs were stimulated with anti-CD3/CD28 with or without pembrolizumab, and phosphorylation states of PD-1-dependent T cell receptor (TCR) signalling pathways were measured by spectral flow cytometry. A composite signalling score was calculated representing the net pembrolizumab-induced phosphorylation response and patients were classified as low, optimal and high modulation responders based on this signalling score. Associations with progression-free survival and overall survival (OS) were evaluated using univariate Cox regression. ResultsPatients with optimal baseline pembrolizumab-induced signalling scores exhibited significantly higher signalling score outcomes than those with low modulation (p < 0.0001) and lower than patients with excessive modulation (p < 0.01) and had significantly longer OS (HR = 2.83, p = 0.013; and HR = 12.05, p = 0.003, respectively). Notably, conventional pharmacodynamic parameters, including half-maximal effective concentration (EC50) for PD-1 receptor occupancy and maximum IL-2 production (Emax), were not associated with clinical outcomes, underscoring the unique predictive value of the phosphorylation-based signalling score. In vivo, pembrolizumab-induced T cell activation changes and TCR signalling inhibition post-treatment correlated with shorter survival (HRs = 1.33-1.95), consistent with our ex vivo findings. ConclusionsWe demonstrate that a pretreatment signalling score derived from ex vivo pembrolizumab-modulated T cell phosphorylation identifies clinical response in NSCLC. This functional bioassay offers a novel approach to identify patients most likely to benefit from ICI therapy, potentially enabling personalised treatment decisions before therapy initiation. Graphical abstract textOur findings reveal that pretreatment, pembrolizumab-dependent modulation of T cell phosphorylation identifies clinical response in NSCLC. Furthermore, we introduce an overall signalling score, reflecting the net phosphorylation profile, which could serve as a potential predictive biomarker to distinguish responders from non-responders, thereby supporting biomarker-driven therapeutic strategies.

In approximately one third of patients, resected head and neck squamous cell carcinoma will recur. We postulated that the induction of tumor neoantigen-specific T cell responses could prevent relapse. To this end, we developed TG4050, an individualized neoantigen therapeutic vaccine encoding up to 30 patient-specific predicted tumor neoantigens delivered by a Modified Vaccinia Ankara virus viral vector. We tested TG4050 as single agent in a randomized phase I trial. We found that of 16 evaluable patients randomized to immediate vaccination with TG4050, none relapsed after a median follow-up of 30 months, while 3 relapsed in the 16 control arm patients randomized to observation and treatment with TG4050 after recurrence. Polyepitopic responses to vaccine neoantigens were detected in the blood of patients from both arms after treatment initiation. These responses were maintained throughout treatment and persisted for over one year after the last dose. Vaccine neoantigen-specific CD8+ T cells had an effector phenotype and displayed high expression of cytotoxic and tissue-resident markers. TCR repertoire analysis showed that vaccine neoantigen-specific CD8+ T cell responses were polyclonal and comprised both de novo responses and amplification of pre-existing tumor-infiltrating T cell clones. Together, this translational data is consistent with the model in which single-agent delivery of TG4050 induces long-lasting tumor neoantigen-specific cytotoxic T cell responses that prevent tumor recurrence.

Annual immunisation against both COVID-19 and seasonal influenza is now becoming standard of care, particularly ahead of anticipated winter waves. These vaccines may be co-administered on the same day or sequentially on separate days. Data on immunogenicity and the impact of consecutive vaccinations on spike-specific humoral and cellular immunity in dialysis patients remain limited. In this real-world observational study, SARS-CoV-2-specific immune responses were evaluated in dialysis patients receiving the monovalent XBB.1.5 vaccine followed by a quadrivalent influenza vaccine 14 days later, or either vaccine alone. Specific antibodies and T-cells were quantified and characterized using enzyme-linked immunosorbent assay and flow-cytometry. Baseline analyses from a reference-group prior to the vaccination season showed that most patients had detectable SARS-CoV-2- and influenza-specific immunity. Both the XBB.1.5 and the influenza vaccine substantially enhanced pre-existing antigen-specific humoral and cellular responses. When comparing XBB.1.5-vaccinated patients with and without subsequent influenza-vaccination, the magnitude of XBB.1.5-induced antibody or T-cell responses did not differ. Likewise, the influenza-vaccine had no non-specific effect on SARS-CoV-2-specific immune responses. Finally, spike-specific immunity remained stable over a six-month period and persisted at levels exceeding those of unvaccinated patients assessed during the same period. In conclusion, sequential administration of COVID-19 and influenza vaccines in dialysis patients is feasible and does not compromise the immunogenicity of either vaccine. Our data are encouraging in the context of ongoing development of additional mRNA-based vaccines that may require administration in close temporal proximity to seasonal influenza immunisation, and underscore the benefit of booster vaccination in individuals with impaired immune function.

The phase 1b TICIMEL clinical trial evaluated the safety, tolerability, and anti-tumor activity of combining the immune checkpoint inhibitors (ICI), ipilimumab and nivolumab, with tumor necrosis factor (TNF) blockers, certolizumab or infliximab, to treat advanced melanoma patients. A higher proportion of responses was observed in patients receiving ICI and certolizumab, while patients treated with ICI and infliximab demonstrated superior tolerability. Moreover, CITE-Seq analyses of circulating CD8 T cells showed that ICI plus certolizumab promoted an IFN signature, whereas ICI plus infliximab reduced the induction of genes associated with T cell activation. In preclinical models, ICI and TNF blockade with certolizumab increased IFN-{gamma}+ CD8 T cells and reduced regulatory T cells in tumors. The IgG1 Fc fragment of infliximab was identified as counteracting the benefits of TNF blockade. These findings underscore the importance of selecting the optimal TNF blocker to combine with ICI to enhance therapy efficacy in melanoma patients. ClinicalTrials.gov identifiers: NCT03293784; NCT05867004.

Regional lymph nodes (LNs) in the thoracic cavity serve as essential immunological hubs that coordinate humoral and cell-mediated responses against the development and progression of non-small cell lung cancer (NSCLC). To investigate immune dysregulation in the non-metastatic regional LNs of patients with aggressive NSCLC, we performed multimodal profiling on 36 LNs from 11 patients undergoing curative-intent resection including CITE-seq, scRNA-seq, and Imaging Mass Cytometry (IMC). Regional N1 LNs from patients with more aggressive disease (stage IB-IIIA) exhibited a significant enrichment of dysfunctional CD8 T cells and regulatory T cells (Tregs) compared to N2 LNs and LNs from patients with less aggressive disease (stage IA). These immune subsets were spatially co-localized with mature regulatory dendritic cells (mregDCs; CD1c, TIM3, LAMP3), forming an immunosuppressive niche uniquely enriched in the N1 LNs of higher-stage patients. Concurrently, higher-stage N1 LNs contained larger number of "decorticated" B-cell follicles characterized by decreased encapsulation of the mantle zone layer surrounding the germinal centers. This mantle zone disorganization was associated with increased spatial niches involving Tregs, CD68+ CD163 TIM3 Macrophages, CD163 TIM3dim Monocytic-Myeloid Derived Suppressor Cells (M-MDSC), plasma B cells, and a decrease in spatial niches involving CD4 T helper cells and fibroblastic reticular cells (FRCs). Together, our findings reveal parallel alterations in humoral and cell-mediated immunity within the regional LNs of patients with aggressive NSCLC.

Why do some individuals develop mild COVID-19 while others progress to severe disease remains a central challenge in SARS-CoV-2 immunology. In this study, we leveraged the BACO Cohort - a unique historical cohort of immunologically naive, hospitalized COVID-19 patients from the first pandemic wave - to investigate early immune determinants of clinical disease trajectories. Integrating bulk RNA-seq, Olink proteomics, and systems serology, we identified two fundamentally distinct immune trajectories according to disease phenotypes. Severe patients exhibited upregulation of proinflammatory genes and monocyte-associated transcripts, alongside downregulation of genes related to T cell responses and immune signaling. Notably, an upregulation of inhibitory Fc-receptor-associated gene was also found in severe cases. In contrast, mild cases showed coordinated lymphoid activation and limited inflammation. Building on these findings, we performed a functional profiling of Fc-effector activity in the polyclonal serum of the patients and found that monocyte-mediated phagocytosis was a common feature of mild disease. Interestingly, this response was mainly driven by rapid induction of S1-specific antibodies. Conversely, severe patients tended to generate higher levels of S2-biased antibodies early after infection with poor Fc-effector functionality. Together, these findings demonstrate that early S1-directed, Fc-competent humoral immunity is a key determinant of favorable COVID-19 outcomes, while delayed functional maturation and early S2 bias characterized severe disease in the BACO cohort.

Newly emerging influenza virus strains pose a constant threat as they encounter a population lacking neutralizing antibodies against the new strain. However, cross-reactive non-neutralizing antibodies (nnABs) may be present and assist in mitigating disease symptoms via various effector mechanisms, including antibody-dependent cellular cytotoxicity (ADCC). Although nnABs to influenza virus have received more attention lately, little information is available on their age-related prevalence, steady-state levels, functional properties, and changes in these parameters over time. Using longitudinal samples from adolescents, adults, and older adults, collected before and after the 2009 swine flu pandemic, we comprehensively characterized the specificity and functionality of nnAB responses against H1N1 pandemic 2009 (H1N1pdm09) virus. Remarkably, all participants exhibited cross-reactive antibodies to this virus before having encountered it through infection or vaccination, with the highest baseline levels observed in older adults. The levels of these IgG antibodies showed a strong correlation with engagement of fragment crystallizable {gamma} receptor IIIa (Fc{gamma}RIIIa) and ADCC activity, both of which were notably lower in adolescents compared to adults and older adults. Without infection or vaccination, average amounts of H1N1pdm09-reactive antibodies remained relatively stable on population level over the 5-year study period. However, on an individual level, substantial increases and decreases occurred. H1N1pdm09 infection or vaccination significantly enhanced specific antibody levels and the Fc{gamma}RIIIa-engaging capacity of these antibodies in all age groups. ADCC-mediating antibodies increased however only in adolescents, reaching the same level as observed in the adult groups. Taken together, our results demonstrate the presence of cross-reactive, non-neutralizing, functional, and boostable antibodies against a never-encountered influenza virus strain across all age groups. These antibodies can potentially contribute to protection from severe disease. Accordingly, in case of a newly emerging virus, their further enhancement by vaccination could be beneficial as an immediate protective measure before a strain-specific vaccine becomes available. Author summaryNearly everyone has contracted influenza and/or has been vaccinated against influenza several times over the years. While the antibodies raised during these earlier encounters will not prevent infection by a newly emerging influenza virus strain, they can help to protect from severe disease. Therefore, it is important to determine the prevalence and quantity of these antibodies, understand their mechanisms of action, assess their persistence over time, and examine potential age-related differences in these parameters. We studied antibody responses to the H1N1pdm09 virus in blood samples of young, adult, and older adult individuals from a large cohort study. Irrespective of age, all blood samples contained antibodies that reacted with a never-before-encountered influenza virus strain. The amounts of these antibodies were initially lower in adolescents but with time increased, reaching the same levels as observed in adults. Importantly, infection with or vaccination against the new virus strengthened the responses in all age groups. We conclude that boosting such broadly-reactive antibodies through vaccination could serve as an immediate strategy when a new virus emerges, buying critical time to develop a more specific vaccine.

BackgroundCoxsackie B viruses cause acute infections and have been linked to chronic diseases like cardiomyopathies, type 1 diabetes, and celiac disease. Despite their clinical significance, no vaccines exist for coxsackie B virus types. PRV-101, a new candidate vaccine covering five coxsackie B virus types, showed good immunogenicity and tolerability in a phase 1 trial (PROVENT). MethodsWe conducted an extended follow-up of the PROVENT trial to assess the long-term immune response and safety of PRV-101. A total of 26 participants from the original cohort (n=32) were enrolled for additional testing approximately two years post-immunization (11 high-dose, 10 low-dose, and 5 placebo). Coxsackie B virus -specific antibody responses were measured and compared to earlier time points. ResultsPRV-101 was safe with no late adverse effects or emergence of autoantibodies linked to type 1 diabetes or celiac disease. Neutralizing virus antibodies remained elevated, with a clear dose-dependent response. In the high-dose group, antibodies against all coxsackie B virus types reached presumably protective levels, except for coxsackie B virus 2, where two participants turned seronegative. ELISA tests confirmed elevated antibody levels against coxsackie B virus proteins. DiscussionThese results suggest that PRV-101 induces durable antibody responses lasting at least two years. The findings support the continued development of PRV-101 for preventing both acute coxsackie B virus infections and chronic diseases like type 1 diabetes and celiac disease.

BackgroundTumor-associated macrophages (TAMs) display context-dependent functional polarization, but whether their prognostic impact is consistent across tumor types remains unclear. MethodsWe analyzed RNA-sequencing and clinical data from The Cancer Genome Atlas (TCGA) lung adenocarcinoma (LUAD; n=648), lung squamous carcinoma (LUSC; n=623), and melanoma (SKCM; n=466). Cox proportional hazards models adjusted for age and AJCC stage evaluated per-standard deviation (SD) expression of TAM markers (FOLR2, TREM2) and T-cell markers (CD8A, CXCL9). Cross-histology interaction terms tested divergence between LUAD and LUSC. ResultsIn melanoma, higher FOLR2 (HR 0.87), TREM2 (HR 0.83), CD8A (HR 0.69), and CXCL9 (HR 0.67) independently predicted improved survival. LUAD showed largely neutral macrophage effects. In contrast, LUSC demonstrated an adverse association for FOLR2 (HR 1.28). Interaction analysis confirmed significant divergence for FOLR2 and TREM2 between LUAD and LUSC. ConclusionsTAM-associated prognostic effects reverse by tumor histology, supporting tumor-context-dependent macrophage polarization and informing macrophage-targeted therapeutic strategies.

BackgroundIn lung transplantation, de novo immunodominant donor-specific anti-HLA antibodies recognizing HLA-DQ antigens (dn-iDSA-DQ) are predominant and can induce chronic lung allograft dysfunction (CLAD). We previously developed a method to measure the active concentration of dn-iDSA-DQ. We aimed to determine whether this new quantitative biomarker is associated with transplantation outcomes. MethodsThis retrospective multicentre cohort study included 90 lung transplant recipients (LTRs) developing dn-iDSA-DQ, evidenced through single antigen flow beads (SAFB) follow-up. We measured the active concentration of dn-iDSA-DQ at the time of their first detection (T0) for all LTRs, and within the 2 years after DSA detection, whenever possible. SAFB dn-iDSA-DQ characteristics and clinical data were retrieved up to 5 years after DSA detection. ResultsWe tested 184 sera with SPR (n=90 at T0, n=94 within the 2 years after DSA detection), among which 63 (34.4%) had a quantifiable concentration of the dn-iDSA-DQ ([&ge;]0.3 nM). The median SAFB mean fluorescence intensity (MFI) of the dn-iDSA-DQ with a concentration [&ge;]0.3 nM was higher (p<0.0001), yet the correlation between SAFB MFI and active concentration was low (r=0.758, p<0.0001). In multivariate analysis, a concentration of the dn-iDSA-DQ [&ge;]0.3 nM at T0 was independently associated with a lower 2-year CLAD-free survival (HR 2.06, p=0.02). A concentration of the dn-iDSA-DQ [&ge;]0.3 nM within the 2 years from DSA detection was associated with a lower graft survival in univariate analysis. ConclusionsActive concentration of dn-iDSA-DQ appears as a valuable biomarker to identify pathogenic DSA at their first detection because of its association with CLAD.

The Endoplasmic Reticulum AminoPeptidase 2 (ERAP2) gene encodes an aminopeptidase involved in antigenic peptide processing for the MHC-I pathway. Genetic variants in the ERAP2 gene are associated with autoimmune conditions and infectious diseases. The linkage between genetic variants in the ERAP2 gene has given rise to the prevailing assumption that a single ERAP2 allotype with invariant amino acid sequence accounts for all immunological functions of ERAP2. Here, we show by analyzing exon-sequencing data from 160,000 individuals that 15 missense amino acid variants across the ERAP2 gene result in an array of different protein allotypes that are maintained in the European population. These allotypes can be divided into three haplotype groups, defined by the genotypes of two common splice-altering variants. We found novel associations between newly identified protein allotypes and immune-mediated diseases, suggesting that ERAP2 functional variation modifies disease susceptibility at the population level. An MHC class I antigen presentation assay revealed that disease-associated ERAP2 allotypes differ in their capacity to generate antigenic peptides for MHC-I presentation, resulting in differential activation of an antigen-specific T-cell receptor compared to non-disease-associated allotypes. These findings provide strong evidence that ERAP2 function is allotype-dependent and demonstrate that ERAP2 diversity shapes MHC-I antigen presentation and T-cell immunity. Significance statementThe ERAP2 enzyme modulates adaptive immunity and plays a role in autoimmunity, infection, and cancer. The authors discovered that a variety of protein allotypes of ERAP2 are maintained in the human population. Allotypes that increase disease risk for autoimmune and cardiovascular conditions are functionally distinct in their capacity to activate T-cells. The results of this study demonstrate that ERAP2 is a functionally diverse immune modulator that contributes to immune variation and influences susceptibility to immune-mediated diseases.

Antimicrobial peptides (AMPs) are essential components of the innate immune system, exhibiting diverse mechanisms of action. This study investigates the roles of cathelicidin (LL-37), alpha-defensins, and the S100 proteins S100A8 and S100A9 in systemic inflammation associated with sepsis, severe COVID-19, and acute pancreatitis using whole-blood bulk RNA-sequencing data. Gene co-expression network analysis revealed that during septic shock and severe COVID-19, cathelicidin and alpha-defensins act synergistically in innate immune responses, while S100A8 and S100A9 function through distinct pathways related to mitochondrial metabolism and ubiquitin ligase binding. In contrast, the acute pancreatitis network displayed a different pattern, with CAMP co-expressed alongside S100A8 and S100A9, whereas alpha-defensins were downregulated and associated with inhibited mucosal immune responses. These findings suggest that antimicrobial peptides contribute variably to systemic inflammation depending on the underlying insult, underscoring their complex, context-dependent roles in critical illness.

BackgroundSinonasal malignancies frequently present with symptoms overlapping chronic inflammatory conditions such as chronic rhinosinusitis (CRS), complicating early detection and delaying treatment. A fast, scalable, non-invasive approach capable of resolving immune and epithelial cell states across inflammatory and malignant disease from routine nasal swabs could substantially improve clinical screening, leading to the initiation of appropriate treatment. MethodsWe developed a deep learning-enabled single-cell morpholomic framework using the REM-I platform to generate a reference atlas of >641K cell brightfield images from purified immune cell populations. This reference atlas was applied to >2.5 million images obtained from nasal swabs spanning a clinical spectrum of health, CRS, and sinonasal carcinoma. Embeddings were integrated using dimensionality reduction for differential feature testing and comparative feature enrichment across disease states. FindingsAcross the disease continuum, sinonasal carcinoma samples exhibited distinct immune remodeling, including increased myeloid-like cell abundance and elevated small dark pixel intensity consistent with enhanced granulocyte activity. Basophil/NK-enriched clusters contained tumor-associated cells with deep learning-derived morphologic signatures not observed in CRS or healthy samples. Tumor-associated epithelial cells were significantly smaller and displayed disease-specific morpholomic patterns distinct from chronic inflammation. ConclusionsThis study establishes a deep learning-enabled single-cell morpholomic atlas of nasal swabs spanning healthy epithelium, chronic inflammation and sinonasal malignancies. Morpholomic cytology reveals reproducible immune and epithelial states associated with inflammatory and malignant disease and provides a scalable, non-invasive framework for cellular stratification in sinonasal pathology, supporting future applications in early point-of-care diagnostics.