Immunity

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.

Immune imprinting, also known as immune history, is a core aspect of adaptive immunity that influences antibody responses to future antigen exposures. Nevertheless, the impact of sequential flavivirus vaccinations on epitope targeting and antibody activity in humans remains incompletely understood. This question is particularly important in regions where the inactivated Japanese encephalitis virus (JEV) vaccines and the live-attenuated dengue virus (DENV) vaccines are used, as both have been associated with an increased risk of symptomatic dengue infection and severe illness. We studied the impact of prior inactivated JEV IXIARO vaccination and simultaneous vaccination on humoral immunity following live-attenuated dengue CYD-TDV vaccination. Long-term analysis showed that JEV IXIARO priming guides the dengue vaccine-induced antibody response toward conserved fusion loop epitopes (FLEs) of the DENV envelope protein, as indicated by 4G2 FLE-bias. This imprinting was characterized by higher levels of 4G2 FLE-like antibodies, rapid recall responses after dengue vaccination, and broad but low-potency neutralization across dengue serotypes and Zika virus. Notably, 4G2 FLE-focused responses correlated with higher Fc{gamma}RIIa-mediated antibody-dependent enhancement relative to neutralization potency, suggesting functional effects beyond neutralization. To better understand epitope dominance within the native envelope, we used a structurally defined fusion loop epitope mutant (FLE-mut) envelope dimer assay. Disrupting fusion loop accessibility significantly decreased antibody binding, confirming that FLE-specific antibodies are a major component of the response after sequential vaccination. Importantly, a complete series of live-attenuated dengue vaccine reduced 4G2 FLE bias, encouraged the recruitment of non-fusion-loop epitopes, and lessened Fc{gamma}RIIa-biased antibody activity. Overall, these results show that vaccination platform, timing, and regimen are critical determinants of epitope dominance and antibody quality following flavivirus vaccination.

IntroductionVery preterm birth (<32 weeks of gestation) disrupts key developmental programs and exposes infants to a highly vulnerable postnatal period. However, the molecular trajectories underlying early postnatal adaptation remain poorly characterized, largely due to limitations in longitudinal sampling and the need for minimally invasive approaches. MethodsHere, we applied an integrated longitudinal proteomic and lipidomic analysis to plasma extracellular vesicles (EVs) from very preterm infants, spanning the developmental window from birth to term-equivalent age. EVs were enriched from plasma micro-volumes (10 {micro}L) using an automated Mag-Net-based workflow and analyzed by high-resolution mass spectrometry. Longitudinal molecular changes were modeled using linear mixed-effects models, and cross-omics integration was performed through correlation network analysis and module detection. Associations with clinical outcomes were assessed using a module-level competitive testing framework. ResultsWe quantified 1,528 EV-associated proteins and 421 lipid species across 74 longitudinal samples. The EV proteome underwent extensive and structured remodeling over time, characterized by a progressive decrease in proteins related to translation and early growth processes and a concomitant increase in immune-related components, including complement and immunoglobulin-associated proteins. In contrast, lipidomic remodeling involved a more selective subset of species but followed coordinated temporal patterns. Lipids increasing toward term-equivalent age were enriched for triacylglycerols and ether-linked phosphatidylcholines, while specific membrane-associated species decreased, indicating selective structural reorganization rather than global class-level shifts. Cross-omics integration revealed five coordinated protein-lipid modules, each capturing coherent longitudinal programs. Several modules showed significant associations with clinical features of prematurity, particularly brain injury, highlighting that EV molecular trajectories reflect clinically relevant biological states. Module-based associations were more robust than single-feature signals, especially for lipidomic data. ConclusionsTogether, these results demonstrate that EV-based multi-omics enables longitudinal molecular profiling in very preterm infants using minimal sample volumes and captures coordinated biological programs linked to development and clinical outcomes. This framework provides a scalable and biologically informative approach for studying neonatal adaptation and vulnerability in fragile clinical populations.

BackgroundInfluenza vaccination and bacterial colonization both shape immunity in the respiratory tract, yet their combined impact on the human lung mucosa remains poorly understood. Secondary bacterial pneumonia following influenza infection is a leading cause of mortality, underscoring the need to define how vaccines and microbes intersect at the airway interface. MethodsUsing the Experimental Human Pneumococcal Challenge (EHPC) model, we examined how intramuscular inactivated (TIV) and nasal live attenuated (LAIV) influenza vaccines, with or without Streptococcus pneumoniae colonization, modulate lower airway immunity. Bronchoalveolar lavage samples from 22 adults were profiled by single-cell RNA-seq (>40,000 cells), flow cytometry, cytokine multiplexing, and macrophage functional assays. FindingsLAIV recipients who became colonized with S. pneumoniae displayed heightened influenza-specific CD4{square} T cell responses and enhanced alveolar macrophage (AM) opsonophagocytic activity, showing that nasal bacterial colonization can act as natural mucosal adjuvant. Single-cell transcriptomics revealed four AM gene modules; among them, an interferon-driven "anti-microbial" program correlated with enhanced phagocytosis, whereas a complement- and antigen-presentation module associated with IFN{gamma}-iNOS/ROS signaling was attenuated in colonized vaccinees. Given that AMs are poor antigen-presenting cells, this shift likely reflects reprogramming toward cytokine-mediated immune modulation rather than direct T cell activation. The elevated influenza-specific CD4{square} T cell responses may instead represent feedback from enhanced local activation. Together, these data indicate that vaccination and colonization synergize to rewire AM-T cell communication, fine-tuning antiviral and antibacterial defenses. Similar transcriptional perturbations in public COVID-19 and lung cancer datasets underscore the broader relevance of these macrophage modules across lung disease contexts. ConclusionsOur findings define how influenza vaccination and pneumococcal colonization converge in the human lung to reprogram AM-T cell crosstalk, enhancing local immune responses and protective immunity. By uncovering conserved macrophage modules and mechanisms that shape mucosal defense, this study provides a framework for designing next-generation respiratory vaccines and strategies to mitigate post-viral bacterial pneumonia.

Epstein-Barr virus (EBV) is strongly implicated as an essential environmental trigger of multiple sclerosis (MS), yet the host genetic mechanisms governing EBV activity and how infection triggers the disease are not known. We developed a pipeline to quantify EBV DNA from whole-genome sequencing data and applied it to population-scale cohorts. Using this pipeline, we performed a cross-ancestry genome-wide association study (GWAS) of EBV DNA positivity in 617,186 individuals and identified 39 independent susceptibility risk loci, with the strongest associations in the HLA region. We validated this finding in our independent cohort (N=94) and found that quantitative PCR (qPCR)-confirmed EBV DNA positive individuals were enriched in the top decile of EBV polygenic risk scores (PRS) containing newly discovered loci. A significant overlap with genetic variants associated with MS risk was observed. PRS and Mendelian randomization analyses further supported a causal role of EBV activity on MS risk, which was also seen in other autoimmune diseases. A meta-analysis of qPCR based case-control studies showed elevated EBV DNA positivity in MS. By establishing a single-cell RNA-seq method optimized for EBV detection, we identified EBV-infected B cells, primarily in memory B cells, atypical B cells and antibody-secreting cells from MS and healthy individuals. Notably, EBV-infected memory B cells and atypical B cells showed strong upregulation of cytokines and costimulatory signals that influence T cell activation, IFNg secreting Tregs, and regulators of B cell differentiation and survival. EBV-infected memory B cells also upregulated risk genes from both the EBV and MS GWAS, suggesting that EBV-infected B cells constitute a critical hub that modulates T cell responses while simultaneously activating MS susceptibility pathways within the B cell compartment. Together, these findings define a genetic and cellular framework linking EBV infection to the initiation of MS.

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.

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

Antiphospholipid syndrome (APS) and systemic sclerosis (SSc) are immune-mediated multisystem autoimmune diseases with distinct clinical phenotypes but overlapping pathogenic themes, including immune dysregulation, chronic inflammation, and endothelial injury. Using peripheral blood transcriptome datasets from the Gene Expression Omnibus (GSE102215: 9 APS/9 controls; GSE231691: 49 SSc/18 controls), we performed differential expression analysis within each cohort (limma; |log2FC|>1, P<0.05) and identified 281 genes dysregulated in the same direction in both diseases (100 upregulated and 181 downregulated). Enrichment analyses highlighted interferon-related and cytokine/inflammatory signaling programs in APS and SSc. To derive a compact diagnostic signature, we combined random forest feature ranking with a single-hidden-layer artificial neural network, prioritizing five shared candidate biomarkers (S100A8, IER5L-AS1, LTK, PRR5-ARHGAP8, and PCDH1). Each gene showed consistent case-control differences in both cohorts (P<0.001) and achieved good discrimination (AUC>0.75), with S100A8 performing most consistently (AUC=0.98 in APS; AUC=0.88 in SSc). CIBERSORT deconvolution indicated a myeloid-skewed blood profile in both diseases, characterized by higher neutrophil and monocyte/macrophage signals; SSc additionally showed stronger inferred CD4+ T cell and NK cell signals. S100A8 expression correlated with inferred neutrophil abundance in both cohorts (APS r=0.62; SSc r=0.58; P<0.05). Finally, miRNA-target prediction and DSigDB drug-signature enrichment generated regulatory and pharmacologic hypotheses, including immune-regulatory miRNAs (e.g., miR-155 and miR-146a) and candidate compounds (celecoxib, tamibarotene, HMN-176, and XMD14-99). Overall, these results nominate shared blood transcriptional markers and immune correlates across APS and SSc for follow-up validation.

AimsGestational diabetes mellitus (GDM) is the most common pregnancy-related medical complication. GDM is linked to aberrant immune responses in both mothers and offsprings, specifically, the subsequent development of inflammatory diseases. Whereas prior research has focused on specific immune cell subsets, a comprehensive overview of the impacts of GDM on maternal and fetal immune landscape is lacking. Here, we aim to comprehensively decipher how GDM modulates various immune cell populations in mothers and offsprings. MethodsA prospective, longitudinal case-control study was carried out. Maternal blood from GDM-affected (GDM, n=18) and non-GDM-affected (Ctrl, n=21) mothers were collected at ante-(36-38 weeks of gestation) and post-partum (6-8 weeks post-partum) timepoints. Cord blood from GDM (n=7) and Ctrl (n=11) pregnancies were collected upon C-section. They were analyzed with the state-of-the-art cytometry by time of flight (CyTOF) with a 40-marker panel. Additionally, a publicly available RNA-seq dataset for cord blood mononuclear cells was re-analyzed to confirm results from CyTOF experiments. ResultsCompared to Ctrl, GDM was associated with more activated maternal T cell subsets ante-partum, including increased CD45RO+ and Ki67+ CD4+ T cell populations, which reverted post-partum. GDM-affected maternal innate lymphoid cell (ILC) also exhibited increased granzyme B production ante-partum. On the other hand, in GDM-impacted cord blood, fetal T and B cells were more activated, displaying less naive and more effector phenotypes, further supported by RNA-seq analyses. ConclusionsOur comprehensive analyses revealed that GDM is linked to profound changes in the immune landscapes of the mothers (ante-/post-partum) and foetuses (at birth), casting novel insights towards GDM pathophysiology. Longitudinal immune profiling might be warranted for early detection and stratification of risk, and development of targeted interventions to prevent inflammatory disorders in GDM mothers and their offspring. Research in contextO_LIWhat is already known about this subject? O_LIThe maternal and intrauterine environments are important contributors to long-term health outcomes of mothers and offsprings. C_LIO_LISome maternal and fetal immunity changes have been observed in gestational diabetes mellitus (GDM)-affected pregnancies. C_LIO_LIGDM is associated with increased risk of later-life metabolic and inflammatory diseases in mothers as well as offsprings. C_LI C_LIO_LIWhat is the key question? O_LIWhat are the longitudinal alterations in maternal and fetal immune landscapes in GDM-affected pregnancies? C_LI C_LIO_LIWhat are the new findings? O_LIHigh-dimensional immune profiling provided the most comprehensive overview of alterations in maternal and fetal immune landscapes associated with GDM. C_LIO_LIGDM is associated with skewing of maternal CD4+ T cell and ILC towards activated phenotypes ante-partum. C_LIO_LIGDM is linked to more activated fetal T and B cell profiles. C_LI C_LIO_LIHow might this impact on clinical practice in the foreseeable future? O_LIUnderstanding the complex alterations in the maternal and fetal immune landscape in GDM-affected pregnancy provides insights into the long-term impacts of GDM on the mother and offspring. C_LI C_LI

BackgroundGastroenteric tract requires robust tolerogenic mechanisms to tolerize foreign antigens like foods and microbiota. This is critical to establish the immune homeostasis, which upon disruption, might contribute to a plethora of atopic disorders, including food allergy and eosinophilic esophagitis (EOE). Recently, there was a new subset of tolerizing dendritic cells (tolDCs), PRDM16 tolDC, discovered in the gut of mice and humans, which confers protection against food allergy. Whether an analogous population of it exist in the esophagus is unknown, especially in the context of EOE, another atopic disease associated with dietary antigens. MethodsWe thoroughly analyzed the human esophagus cell atlas single cell RNA-seq dataset and the myeloid DC-VERSE dataset, in an attempt to identify and characterize the esophageal counterpart of the intestinal PRDM16 tolDC. ResultsWe identified the esophageal counterpart of intestinal PRDM16 tolDC as a conventional type II DC subtype expressing PRDM16, termed as cDC2C (PRDM16). We demonstrated the similarities between PRDM16 tolDC and cDC2C (PRDM16) regarding their transcriptomic and functional profiles. Importantly, we found that cDC2C (PRDM16) were expanded during EOE and exhibited an anti-inflammatory phenotype, suggesting their protective role in EOE. Notably, these tolerogenic DCs were not found in other atopic diseases beyond the gastroenteric tract. ConclusionsWe here defined a novel tolerogenic DC population in human esophagus and demonstrated their implications in the pathophysiology of EOE. These findings would provide novel insights towards the tolerogenic mechanisms along the gastroenteric tract and possess translational relevance for EOE diagnosis and interventions.

Epigenetic clocks and scores have been investigated as potential biomarkers of later-life health outcomes following early-life exposures. In pediatric settings, DNA methylation (DNAm) is often measured in saliva; however, most clocks and scores have been trained in adult blood. Therefore, we assessed the performance, correlation, longitudinal stability, and association with early-life adversity (ELA) for established epigenetic measures in matched pediatric blood and saliva samples. Leveraging the Kids2Health cohort of 291 children (3-12 years, 56% exposed to ELA), we assessed DNAm (Illumina EPICv2) from matched blood and saliva. We calculated 22 commonly used epigenetic measures (chronological and biological clocks, scores for body mass index [BMI], C-reactive protein [CRP], cognition, maternal smoking, telomere length) and compared them with corresponding measured phenotypes (chronological age, BMI, CRP, IQ, telomere length). Overall, performance of epigenetic clocks and scores in children varied widely. Nine epigenetic measures were significantly and equally correlated with their corresponding phenotype across tissues. Six measures were highly correlated between blood and saliva (r[&ge;]0.7). All age acceleration estimates showed low to moderate cross-tissue correlations (r=0.20-0.68). Epigenetic scores indicating lower cognitive ability and elevated inflammation were associated with ELA and low SES in both tissues. We additionally provide epigenome-wide blood-saliva correlations across 815,069 CpGs. The results indicate limited generalizability of adult-trained epigenetic clocks and scores to pediatric blood and saliva, even when accounting for cell type composition. We advise caution for cross-tissue and cross-age-range applications of epigenetic measures in research and clinical settings and provide a resource to optimize epigenetic biomarkers in children.

BackgroundSickle Cell Anaemia (SCA), a genetic blood disorder caused by a single mutation in the beta globin gene, displays a highly variable clinical course. Hydroxyurea (HU), an effective treatment, has an unclear mechanism of action. Plasma proteins can act as biomarkers for understanding disease states and response to HU treatment in SCA patients. MethodsPlasma proteome profiling of 31 healthy individuals and 76 SCA patients, including those with and without HU treatment, was performed using a high-performance liquid chromatography system and Orbitrap mass spectrometer. Statistical analysis was performed to identify differentially abundant proteins (DAPs) between SCA patients and healthy controls. Subgroup analyses were performed to look at the impact of HU treatment on plasma proteome. ResultsOur analysis yielded 43 DAPs in the plasma of SCA patients. Global correlation and protein-protein network analysis revealed that these proteins are part of a robust interaction network. Proteins showing higher abundance (LBP, ORM1 and TFRC) were primarily associated with immune response whereas those with reduced abundance (FBLN1 and F13B) were linked to blood coagulation and proteolysis. Differential abundance of several proteins such as CD14, FCN3, LFALS3BP, LAP and TGFBI was observed in either male or female patients indicating influence of gender. Importantly, HU treatment was associated with elevated levels of haptoglobin (HP) and hemopexin (HPX), key proteins involved in free hemoglobin scavenging. Notably, DAPs such as F10, LPA, and FCN3 overlapped with proteins previously reported to be differentially abundant in beta-thalassemia patients. Moreover, multiple proteins, including APOL1, AZGP1, FBLN1, GPLD1, HPX, LGALS3BP, and TFRC correlated with clinical parameters, such as blood transfusion frequency and, vaso-occlusive crisis, and WBC and platelet counts. ConclusionsThis study identifies novel differentially abundant plasma proteins in SCA, expanding the current repertoire of disease-associated biomarkers and proteins modulated by hydroxyurea therapy. The observed overlap with beta-thalassemia associated signatures reinforces shared pathophysiological mechanisms between these hemoglobinopathies. Several of these proteins show significant correlations with key clinical parameters and disease complications, offering insights into disease mechanisms and potential utility in disease management. Collectively, these findings provide a strong foundation for translational validation in larger, independent cohorts.

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.

Pathogenic organisms are typically thought to be constrained by a tradeoff between the rate and duration of transmission, an assumption that underpins a considerable body of evolutionary theory. Here we test for a transmission-duration tradeoff using detailed historical malaria infection data from an era prior to widespread use of antibiotics when humans were deliberately infected with malaria parasites as treatment for neurosyphilis (malariatherapy). These time series follow individual human infections until recovery or treatment with antimalarial drugs due to acute need (a proxy for virulence), and include data on the abundance of specialized transmission stages that can be used to project parasite fitness. We fit a model to estimate initial parasite multiplication rates (PMRs) and find that faster within-host multiplication extends infection duration (time until recovery) and enhances parasite fitness without a discernible cost, such as increased virulence. Initial PMRs exhibit strain-specific differences, a feature required for evolution by natural selection, but our results contradict the idea that the evolution of human malaria parasites is constrained by a transmission-duration tradeoff. Significance statementPathogenic organisms are usually assumed to face a tradeoff such that aggressively exploiting host resources enables more efficient transmission but at the cost of shorter infections. If such a classic transmission-duration tradeoff is not general, then it is not clear what prevents pathogenic organisms from evolving to exploit their hosts ever more aggressively. We use historical data from human malaria infections to show a remarkable lack of evidence for a transmission-duration tradeoff, since faster parasite multiplication tends to prolong infections and enable more efficient transmission. Therefore, classic predictions regarding the evolution of infection-induced harm to hosts may not apply to human malaria parasites, and efforts to locate general evolutionary constraints on pathogenic organisms should look beyond a classic tradeoff. FundingThis work was supported by the Cornell University College of Agriculture & Life Sciences (M.A.G.). L.M.C. was partially supported by the National Science Foundation Grant # 2144680. Data availabilityAll supporting data and code are provided as supplemental files. NoteFor ease of reviewing, this MS includes all elements (including figures) embedded in the text. If accepted, we would be happy to provide elements as separate files.

BackgroundTuberculosis (TB) and HIV co-infection cause profound immune dysregulation. Understanding how these infections alter immune cell distribution across systemic and tissue compartments is critical for improving therapeutic and vaccine strategies. MethodsFlow cytometry was used to quantify CD4 and CD8 T cells, B cells, and tissue-resident memory (TRM) T and B cells in peripheral blood mononuclear cells (PBMCs), lung tissue, bronchoalveolar lavage (BAL), spleen, and lung-draining hilar lymph nodes (HLN) from individuals with pulmonary TB (PTB), disseminated TB (Diss TB), HIV only, or both TB and HIV infections. ResultsCD4 T cell frequencies were significantly reduced in multiple compartments of HIV infected subjects, irrespective of TB status, indicating systemic immune suppression. CD8 T-cell frequencies were elevated in the blood of HIV-infected individuals, suggesting a compensatory response to CD4 T-cell loss. B-cell frequencies were reduced in PBMCs and lung tissue of TB subjects, regardless of HIV status. Notably, CD4 TRM T cells were specifically depleted in lung tissue of HIV/TB co-infected individuals, whereas TRM B cells were selectively depleted in TB subjects, independent of HIV infection. ConclusionTB and HIV drive distinct and compartment-specific TRM cell loss in infected tissues. HIV primarily targets CD4 TRM T cells, while TB specifically depletes TRM B cells, highlighting separate mechanisms of tissue-resident immune disruption. These findings emphasize the importance of tissue-specific immune analyses and provide new insights for targeted vaccine and immunotherapy strategies.

Population-based studies of circulating blood proteins have provided profound insights into human biology. However, short-lived changes often remained undetected. To address this, we performed a comprehensive longitudinal dried blood spot (DBS) self-sampling study in 808 young adults of the BAMSE cohort during 2020-2022. We profiled serological, autoimmune, and proteomic phenotypes in relation to SARS-CoV-2 exposures (infection, vaccination), physiological traits, genetic variation, and blood counts. Data-driven seroclustering revealed dynamic immune response to both exposures, while analysis of anti-interferon autoantibodies (AAbs) uncovered associations of pre-existing stable AAbs with prolonged COVID-19 symptoms. Genome-wide mapping determined 664 pQTLs, with cis-pQTLs associated showing increased longitudinal stability. We also identified relationships between blood cell counts and DBS proteins beyond the hematocrit effects. Paired pre- and post-exposure highlighted transient alterations for infection (e.g. LAP3) and vaccinations (e.g. TIMP3). Multi-molecular phenotyping in self-sampling can capture dynamic immune trajectories, informing precision medicine efforts with clinically valuable insights on short-term variability in health phenotypes.

Sjogrens disease (SjD) is a chronic autoimmune disorder characterized by inflammation of the exocrine glands, leading to dry mouth and dry eyes. This study investigates the role of interleukin-9 (IL-9) and T helper 9 (Th9) cells in the pathogenesis of SjD. We found that serum IL-9 levels were significantly elevated in SjD patients and correlated with clinical laboratory parameters, including autoantibody production. In a mouse model of SjD, IL-9 and Th9-associated cytokines were also elevated, and Th9 cells were enriched in the salivary glands. Our results suggest that IL-9 is produced by multiple cell types, including macrophages, CD4+ T cells, and NK cells, and that Th9 cells contribute to the development of SjD by promoting inflammation and autoantibody production. We also found that Th9 and Th17 polarization conditions increased Th2 and Th17 cells in SjD mice, indicating a shared epigenetic program that renders T cells permissive to multiple differentiation pathways. Anti-IL-9 treatment had a sex-dependent effect, reducing autoantibody production in male mice but worsening focal glandular infiltration in female mice. Our findings suggest that IL-9 plays a complex role in SjD pathobiology, contributing to both local immunoregulation and systemic autoantibody response. Overall, this study offers new insights into the role of IL-9 and Th9 cells in SjD, highlighting the potential for therapeutic targeting of the IL-9/Th9 axis in the treatment of this disease.

Cutaneous leishmaniasis (CL) is a skin disease caused by Leishmania infection, for which no licensed human vaccine exists. Protective immunity is largely T cell-mediated and depends on antigen presentation by MHC molecules, yet the naturally presented epitopes during human disease remain poorly defined. To address this gap, we performed mass spectrometry-based immunopeptidomics on lesional biopsies from 27 Ethiopian CL patients spanning the full clinical spectrum. We newly identified 333 MHC-I and 247 MHC-II epitopes from 398 L. aethiopica proteins, including 19 peptides and 51 antigens recurrently presented across patients of which several were also epitope-rich. Some peptides were also detected during early infection in a L. aethiopica-infected THP-1 monocyte model, highlighting their relevance from disease onset. Notably, despite the broad predictive coverage of NetMHCpan and NetMHCIIpan, these tools missed 20-70% of the naturally presented epitopes while predicting millions of candidates, underscoring the limitations of prediction-only vaccine pipelines. This first comprehensive map of the Leishmania immunopeptidome in human disease reveals conserved and prevalent antigens that can inform rational vaccine design and deepen our understanding of protective T cell responses in leishmaniasis.

Multiple sclerosis (MS) therapies primarily rely on lymphocyte depletion or trafficking blockade, carrying risks of systemic immunosuppression; however, such treatments have limited efficacy in secondary progressive multiple sclerosis (SPMS). Thus, drugs that target stage-specific inflammation without broad immunosuppression are an unmet clinical need. In this double-blind, placebo-controlled phase II trial, 30 patients with relapsing MS received weekly oral OCH or placebo for 24 weeks. In the pre-specified SPMS subgroup (n=12), OCH achieved complete relapse prevention (p=0.0003), prolonged relapse-free survival (p=0.0079), no new lesions (0/6), with no evidence of disease activity (NEDA-3) in 5/6 patients. In comparison, for the placebo-treated group, 5/6 patients suffered relapses, 2/6 patients developed new lesions, and no placebo-treated SPMS achieved NEDA-3. Invariant natural killer T (iNKT) cells, a regulatory lymphocyte population that is numerically and functionally impaired in MS, are a potential target for MS therapy. Glycolipid OCH is a selective iNKT cell stimulator, skewing the cytokine environment towards Th2. OCH treatment resulted in increased IL-4-producing Th cells in patient peripheral blood while decreasing pathogenic GM-CSF-producing Th cells. Parallel studies in mouse models of MS (EAE) corroborated this mechanism and further revealed that OCH activated gut iNKT cells. Disease amelioration by OCH depended on IL-4 and its efficacy was further enhanced by depletion of B cells. These data revealed the gut-brain axis mediation of progressive-stage pathology distinct from relapsing-remitting MS. Findings from this bidirectional translational study uncover mechanistic differences between SPMS and other types of MS and highlight divergent roles for B cells and Th cells. Furthermore, OCH exerts its therapeutic benefit via targeting mechanisms that are distinct from currently available drugs; exploiting iNKT cell regulatory potential to reprogram pathogenic T helper responses without lymphocyte depletion. The unique yet effective nature of OCH treatment positions it as an attractive future oral therapy for SPMS. One Sentence SummaryThe iNKT cell activating ligand OCH suppresses disease activity selectively in secondary progressive MS in a phase II clinical trial, revealing stage-specific IL-4-mediated immune cell interactions in MS pathology.

Vaccination frequently elicits suboptimal immunogenicity in organ transplant recipients, particularly those on long-term immunosuppressive therapy, highlighting the need for improved understanding of immunosuppression mechanisms and optimized vaccination strategies. This study enrolled a cohort of 132 individuals and observed significantly lower antibody levels in kidney transplant recipients (KTRs) compared to non-transplant controls (non-KTRs). Antibody levels were inversely associated with both the dosage and duration of immunosuppressive therapy. Complementary small animal studies demonstrated that immunosuppressive treatment dosage-dependently and reversibly impaired antibody production, primarily by depleting immune cells, notably B cells. A single shot of adenoviral vector-based vaccines demonstrated enhanced immunogenicity relative to two shots of alum-adjuvanted protein vaccines, inducing potent neutralizing antibodies (NAbs) and a Th1-biased T-cell response even under continuous immunosuppression. The enhanced response was driven by reduced interference from pre-existing antibodies, sustained transgene expression, and the reprogramming of lipid metabolism to activate T and B cells. Our findings advocate for tailored vaccination strategies, positioning adenoviral vectors as a candidate modality for this vulnerable population.