Browse Articles

Plasmonic Enhancement of Fluorescence and Protein Dynamics in Living Mammalian Cells

ABSTRACT This study shows that coupling to designed plasmonic nanoparticles can modulate the electrophysiological function of proteins in living mammalian cells. Nanostar‐shaped particles, that are robust to biological noise, are designed to enable near‐field‐coupling to plasma membrane‐localized mutated Archaerhodopsin proteins in live cells. The coupled rhodopsins exhibit enhanced fluorescence and an increased response speed to membrane voltage. Incorporating this plasmonic enhancement into a Markov chain photocycle model of the Archaerhodopsin mutant QuasAr6a, shows an increased fluorescence emission rate and manipulation of the protein dynamics through a combination of photocycle transition rate enhancements. The results show an improvement in fluorescence and voltage‐response dynamics of the functional QuasAr6a Archaerhodopsin mutant, beyond what has been achievable through genetic engineering. This opens up possibilities for engineering the biological functionality of proteins through plasmonics: manipulating protein photocycles could improve light sensitivity, change optogenetic applications, and lead to fluorescent biosensors with enhanced dynamics.

Impact of temporal patterns in working contacts on epidemic spread

Abstract Most models for infectious disease spread simplify contact heterogeneity by assuming constant rates within a week. However, empirical studies show clear variation, such as reduced workplace contacts on weekends. In this work, we investigate the effects of daily variation in workplace contacts on the spread of respiratory infections using the individual-based framework GEMS (German Epidemic Micro-Simulation System) with a synthetic population of 5 million individuals. We compare the scenario with uniform daily contacts to the scenario with more contacts on workdays and fewer on weekends, keeping weekly totals constant. Simulations reveal that uniform contact rates yield higher prevalence for short latent periods (1–2 days) and lower prevalence for longer latencies (5–6 days). The effect diminishes for long infectious periods ( $$\ge$$ 7 days) but is more pronounced at lower basic reproduction numbers. Depending on the disease specification and the differences in weekday contacts, the impact of weekday heterogeneity can be very strong. These findings open new possibilities for weekday-dependent mitigation measures. We conclude that weekly contact dynamics should be explicitly incorporated into epidemic models to avoid systematic errors in reproduction number estimation.

A Cross-Species Nerve- and Airway-Associated Macrophage Program that Drives Lung Tumor Progression and Immunotherapy Resistance 2301331

Abstract Introduction Nerve- and airway-associated interstitial macrophages (NAMs) are a distinct subset of lung-resident macrophages with key immunoregulatory roles during respiratory viral infections. Previous research has highlighted their indispensable function in suppressing inflammation and promoting tissue homeostasis, establishing them as critical mediators of disease tolerance during lung infection. However, their role in the context of lung cancer remains largely unexplored. Methods To investigate the role of NAMs in lung tumor progression, we employed diphtheria toxin receptor (DTR) and gene-conditional knockout transgenic mouse models in combination with confocal microscopy and transcriptomic analyses of both murine and human lung tumor samples. Results Selective depletion of NAMs using transgenic NAM-DTR mice revealed a significant reduction in tumor burden across multiple lung tumor models. Furthermore, NAM depletion synergized with anti-PD-1 therapy to amplify CD8+ T cell responses and markedly enhance therapeutic efficacy. Extending these findings to patients, single-nucleus RNA sequencing of a lung cancer patient cohort demonstrated that higher NAM abundance in tumor biopsies was associated with both shorter overall survival and reduced progression-free survival. Consistent with this, transcriptomic analysis of a single-cell RNA sequencing dataset from an immunotherapy-treated cohort revealed that low-responder patients harbored a pronounced enrichment of NAMs compared to high-responders. Strikingly, within the low-responder group, NAM frequency exhibited a strong negative correlation with PD-1+TCF1+CD8+ T cells, the critical T cell reservoir required for durable responses to checkpoint blockade therapy. Conclusion Collectively, these findings identify NAMs as a previously underappreciated myeloid population that actively orchestrates an immunosuppressive tumor microenvironment and underscore their potential as a novel, targetable barrier to effective immunotherapy in lung cancer. Funding Source n/a Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

The Effects of Club Cell Protein 16 on Endothelial NFκB Signaling 2258195

Abstract Introduction Club Cell Protein 16 (CC16), one of the most abundant proteins in airway secretions, is primarily produced by Club Cells in the pulmonary epithelium; however, CC16 is readily detectable in circulation. Decreased CC16 concentrations in the serum have been associated with worse lung function in several chronic respiratory diseases, such as COPD and Asthma. CC16 has previously been shown to inhibit PLA2 activity, as well as NFκB activation in airway epithelial cells, yet little is known regarding CC16 interactions with endothelial cells. As such this study aimed to determine if CC16 plays an anti-inflammatory role in endothelial cells. Methods We investigated the effects of rCC16 on canonical NFκB signaling in endothelial cells using hTERT immortalized Human Aortic Endothelial Cells during IL-1β stimulation. Inflammatory factors were assessed by qRT-PCR (IL-6, IL-8, VCAM-1, and ICAM-1) and NFκB signaling pathways were examined by western blot analysis. Results While IL-1β increased all inflammatory factors examined, rCC16 led to significant reductions in both IL-6 and IL-8 when given concurrently during stimulation. Western blot analysis did not display observable trends in phosphorylated P65 at 15 minutes in IL-1β stimulated cells in which rCC16 was present compared to IL-1β stimulation alone. Conclusion These results suggest that CC16 is not merely a serum biomarker of lung function decline but may play an active role in circulation by limiting NFκB -driven inflammation in the endothelium. Further study into the mechanisms by which rCC16 may be effecting endothelial cells is necessary. Funding Source NIH funding: HL142769 Topic Categories Innate Immune Responses and Host Defense: Molecular Mechanisms (INM)

Prior antigen experience influences the development of alopecia areata in C3H/HeJ mice 2258436

Abstract Introduction Alopecia areata (AA) is an autoimmune disease of the hair follicle (HF) with a 2% lifetime incidence, characterized by well-defined patches of hair loss on the scalp. AA arises from the breakdown of HF immune privilege, leading to T cell infiltration and attack of the HF. Unlike humans who are continually exposed to diverse microbes, laboratory mice are maintained under specific pathogen—free (SPF) conditions, limiting their immune experience. Recent studies have shown that pet-store mice more closely replicate human immune responses. C3H/HeJ (C3H) mice are a common model to study AA and can be induced using skin grafts from affected mice; however, these mice are typically maintained in SPF facilities. This study aimed to determine whether immunologically experienced C3H mice, induced to develop AA, would harbor a skin environment that more closely mimics human patients. Methods To test this, we generated mice using a sequential infection model, replicating findings in pet-store mice, by infecting C3H mice with influenza A virus, vaccinia virus, Listeria monocytogenes, and lymphocytic choriomeningitis virus Armstrong at 5-day intervals. Results Sequentially infected mice, before disease induction, exhibited increased frequencies of antigen-experienced CD8 T cells in blood and skin-draining lymph nodes (SDLNs) compared to non-infected mice. They also showed elevated NKG2D+ CD8 T cells, a population known to drive AA. We hypothesized that AA onset would be accelerated following skin-graft induction. Surprisingly, previously infected mice developed AA at a reduced rate and exhibited fewer AA-associated T cells in SDLNs and skin compared to controls. Conclusion Ongoing studies will determine whether sequential infections alter precursor frequency of autoimmune T cells. Together, these data suggest that prior microbial exposure reshapes the immune landscape in C3H mice, attenuating AA-specific immune responses and supporting future studies to dissect how infections influence AA development. Funding Source n/a Topic Categories Basic Autoimmunity (BA)

The role of T cells in uterine turnover and homeostasis 2258113

Abstract Introduction The endometrium undergoes a coordinated and cyclic turnover that is unlike any other mammalian tissue. In mice, this process entails a 20-40% reduction in endometrial cellularity over a 12—24-hour time frame. This remarkable coordination raises fundamental questions about how such rapid and synchronized cell death is achieved across distinct cell types. Notably, the healthy, non-pregnant endometrium, in both mice and humans, harbors diverse immune cells that, in principle, could mediate or facilitate endometrial breakdown. T cells stand out as compelling candidates due to their ability to recognize and respond to tissue-restricted antigens. Therefore, we hypothesized that T cells specific for endometrial antigens act as physiological mediators of tissue breakdown, coordinating the timing and extent of endometrial cell death. Methods We integrated 3D volumetric imaging of optically cleared uteri with targeted genetic perturbations, temporally resolved manipulations across the estrous cycle, and adoptive transfer of defined T cell populations. Results We found that a population of conventional CD4+ T cells dynamically traffics from uterus-draining lymph nodes to the endometrium at defined stages of the estrous cycle, where they become locally activated in a TCR-dependent manner. Depletion of commensal microbes did not alter their activation or accumulation, indicating that these responses are most likely driven by self-antigens. Genetic ablation or acute depletion of CD4+ T cells markedly delayed endometrial degradation and disrupted the synchrony of epithelial and stromal cell death. Conclusion Our data identify a controlled autoimmune T cell response as a physiological mechanism that orchestrates the cyclical breakdown of the endometrium. These findings challenge the view of autoimmunity as exclusively pathological and position self-reactivity as an essential component of homeostasis, with broad implications for understanding immune regulation, tissue remodeling, and reproductive health. Funding Source This material is based upon work supported by the National Institute of General Medical Sciences of the National Institutes of Health under award number T32GM007753, the National Science Foundation Career Award, under award number 2442857, and by the National by the Ragon Institute under a Strategic Initiative grant. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or the National Institutes of Health. Topic Categories Basic Autoimmunity (BA)

Beta-adrenergic receptors ADRB1 and ADRB2 regulate formation of memory CD8 T cells 2260268

Abstract Introduction Memory CD8 T cells persist long term in tissues and protect the body against reinfection over multiple decades. Both lymphoid and non-lymphoid tissues are innervated by sympathetic nerves, which mediate the body’s response to stress and release the stress hormone noradrenaline. However, it is not understood how the sympathetic nerves in peripheral tissues control the function of immune cells and their response to acute viral infections. Methods To address this, we used genetic knockout mice to disrupt the expression of the noradrenaline receptors ADRB1 and ADRB2 on antigen-specific CD8 T cells during acute LCMV Armstrong infection. Results Our data show that loss of Adrb1 promotes the formation of memory precursor and central memory T cells, while loss of Adrb2 promotes terminal differentiation of CD8 T cells. RNA-seq analysis revealed that Adrb1-deficiency promotes memory gene expression programming. Expression of both Adrb1 and Adrb2 are regulated by type 1 interferons. Conclusion Given that Adrb1 and Adrb2 influence T cell differentiation in distinct and opposing manners, we hypothesize there is differential signaling downstream of the receptors, which we are currently investigating. These studies will yield insights into the mechanisms of communication between the nervous and immune systems and how they impact the immune response to acute viral infection. Funding Source n/a Topic Categories Neuroimmunology (NEUR)

Polysorbate 80 Impairs Esophageal Epithelial Barrier Function: Implications for Eosinophilic Esophagitis Pathogenesis 2260115

Abstract Introduction Eosinophilic esophagitis (EoE) is a chronic, immune-mediated disease characterized by esophageal dysfunction and eosinophilic inflammation. Worldwide EoE incidence and prevalence have increased substantially and coincide with increased global usage of dietary emulsifiers. We investigated the effects of polysorbate 80 (P80), a common emulsifier, on esophageal epithelial barrier function and inflammatory responses. Methods Immortalized esophageal epithelial cells (EPC2) were exposed to P80 concentrations ranging from 0.005% to 1%. Transepithelial electrical resistance (TEER), paracellular-flux, and cytotoxicity were assessed. Phase contrast, histology, immunofluorescence, and RT-PCR were performed. Results EPC2 cells exposed to concentrations of P80 >0.05% demonstrated decreased TEER, increased paracellular flux, and cytotoxicity consistent with epithelial barrier disruption. Histology and phase contrast microscopy revealed increased intercellular spaces, cellular detachment, and membrane disruption. mRNA expression of TSLP and IL33 increased (2.1-fold, p < 0.01 and 4.2-fold, p < 0.01, respectively) after 6 hours of exposure. Conclusion P80 at concentrations as low as 0.05% impairs esophageal barrier integrity and induces pro-inflammatory responses. These findings suggest that dietary emulsifiers like P80 may contribute to EoE pathogenesis by compromising epithelial barrier function, potentially facilitating immune activation. Funding Source na Topic Categories Mucosal and Regional Immunology (MUC)

A Specific Subset of Low-Density Neutrophils Aggravates Endothelial Denudation via NET-Mediated ANXA1 Sequestration: Implications for Plaque Erosion 2310364

Abstract Introduction Plaque erosion (PE) is a distinct pathological cause of acute coronary syndrome (ACS), characterized by neutrophil-mediated endothelial injury. However, the specific contribution of neutrophil heterogeneity, particularly low-density neutrophils (LDNs), to PE pathogenesis remains undefined. Methods We performed single-cell RNA sequencing and quantitative proteomics on peripheral blood from patients with optical coherence tomography (OCT)-verified PE-ACS, PR-ACS, and healthy controls. Findings were validated using flow cytometry and functional assays. Mechanistic pathways were investigated in an ApoE−/− mouse model of PE and human aortic endothelial cell (HAEC) co-cultures, utilizing CXCR2 inhibitors (AZD-5069) and NET inhibitors (GSK484). Results A distinct, pro-inflammatory LDN subset was significantly expanded in PE-ACS patients, correlating strongly with endothelial microvesicles and thrombus burden. These LDNs exhibited an immature (CD10−), hyperactive phenotype with enhanced chemotaxis and neutrophil extracellular trap (NET) release. We identified that these cells are recruited to erosion sites via the CXCL1/2-CXCR2 axis; pharmacological inhibition of CXCR2 significantly ameliorated PE phenotypes in mice. Mechanistically, PE LDN-derived NETs caused endothelial apoptosis and detachment. Specifically, these NETs impaired Annexin A1 (ANXA1)-mediated plasma membrane repair by physically sequestering ANXA1. An ANXA1 mimetic peptide rescued this impairment and reduced thrombus formation in vivo. Conclusion PE LDNs constitute a pathogenic neutrophil subset that drives PE-ACS. They are recruited via the CXCL1/2-CXCR2 axis and promote endothelial denudation and thrombosis by releasing NETs that compromise ANXA1-mediated membrane repair. Targeting the PE LDN-NET-ANXA1 axis represents a potential therapeutic strategy for PE. Funding Source National Natural Science Foundation of China (Grant No. 82170346); Grant of Shanghai Municipal Health Commission (NO. 202440145); Shanghai Science and Technology Committee (NO. 22Y11901600 and 22Y11909800) Topic Categories Immune Mechanisms of Human Disease (HUM)

Mucosal vaccination clears Clostridioides difficile colonization 2257244

Abstract Introduction Clostridioides difficile infection (CDI) is a leading cause of healthcare-associated infections in the United States. Recent vaccine strategies targeting the toxins responsible for CDI symptoms were unsuccessful in reducing C. difficile colonization in Phase III clinical trials. Colonization prevention or bacterial clearance would eliminate transmission of C. difficile spores and forestall recurrent CDI. Therefore, new vaccination strategies aim to identify novel surface antigens that promote mucosal immunity and bacterial clearance. Methods To start, we immunized mice with four candidate surface antigens by both parenteral and mucosal routes of administration and challenged with C. difficile. Three of these antigens reduced colonization burden in vivo, but only when administered by mucosal vaccination. We then immunized mice with a formula containing the three effective surface antigens and inactivated C. difficile toxins, again using both routes of administration. Results Both immunization routes protected against epithelial tissue damage, weight loss, and mortality. The mice that received mucosal immunization cleared both spores and vegetative bacteria, which was confirmed via tissue and fecal qPCR. However, those that received parenteral immunization were unable to do so, despite a robust systemic humoral response. We did not detect anti-surface-antigen systemic IgG nor fecal IgA in mice that received mucosal vaccination. Correlates of decolonization included fecal IgG responses to vegetative surface antigens, which reduce bacterial mobility, and a colonic, Th17-skewed tissue-resident memory T cell response against spore antigen. Conclusion We have demonstrated, for the first time, the clearance of C. difficile from the host after mucosal immunization. Our results demarcate notable differences in correlates of protection and pathogen clearance between administration routes and highlight mucosal immunization as the paramount strategy to elicit sterilizing immunity against CDI. Funding Source National Institutes of Health grant U19 AI174999 (my PI) Topic Categories Vaccines and Immunotherapy (VAC)

Positively Charged Polymer‐Brush MOFs for Large‐Area, Pressure‐Resistant Gas Separation Membranes (Adv. Mater. 43/2026)

Toward Practical Solid‐State Lithium Batteries With High‐Nickel Cathodes: An Interface‐Centered Perspective

ABSTRACT The global transition toward renewable energy and carbon neutrality has sharply increased the demand for energy‐storage systems with higher energy density, improved safety, and extended service life. Despite the dominance of lithium‐ion batteries, their development is greatly limited by the flammability and electrochemical instability of liquid electrolytes. Solid‐state lithium batteries (SSLBs) provide a promising alternative because solid‐state electrolytes (SSEs) eliminate electrolyte leakage, enhance thermal stability, and enable the use of high‐voltage cathodes and lithium‐metal anodes. Among candidate cathode materials, high‐nickel layered oxides (LiNi x Co y Mn 1‐ x ‐ y O 2 , x  ≥ 0.8) are the most viable for practical deployment, owing to their high specific capacity, moderate cost, and industrial maturity. However, their integration with SSEs introduces severe challenges, including structural degradation, oxygen release, and interfacial instability, which collectively impede lithium‐ion transport and compromise cycling durability. This review summarizes recent progress in SSLBs with high‐nickel cathodes, focusing on (1) structural and surface engineering of high‐nickel cathodes, (2) optimization of oxide‐, sulfide‐, halide‐, and polymer‐based SSEs, and (3) interface‐engineering strategies, including buffer layers and in situ interfacial design. Finally, perspectives are provided on material innovation, interfacial characterization, and scalable manufacturing, aiming to guide the development of next‐generation SSLBs that combine high energy density with intrinsic safety.

Artificial intelligence-based photographic detection of pink esthetic score attributes using a hybrid deep learning segmentation pipeline: a method development study

Abstract This study aimed to develop and internally validate a novel anatomy-driven artificial intelligence (AI) system for automated postoperative Pink Esthetic Score (PES) evaluation from intraoral photographs. Unlike most existing AI approaches, which rely on end-to-end prediction, the proposed pipeline derives PES attributes from anatomically grounded measurements. A hybrid analytical pipeline integrating instance segmentation and rule-based measurement was developed. Tooth crown segmentation was performed using Mask R-CNN, while gingival segmentation was performed using YOLOv11. Anatomical features were extracted from the segmented structures and converted into ordinal PES attributes through data-driven threshold calibration derived from the training dataset. The reference standard consisted of independent expert scoring of 82 postoperative intraoral photographs. Diagnostic accuracy, confusion matrix analyses, and regression metrics were calculated to evaluate agreement between automated and expert assessments. The hybrid segmentation-based system achieved accuracies of 91.5% for the mesial papilla, 85.4% for the distal papilla, 86.6% for the gingival margin, and 82.9% for gingival color assessment. Exact agreement between automated and expert total PES scores was observed in 57.3% of cases, increasing to 79.3% when a clinically relevant tolerance of ± 1 PES point was applied. Regression analysis demonstrated a mean absolute error of 0.76, a root mean squared error of 1.35, and an R² value of 0.49. An anatomy-driven segmentation framework may provide a transparent and reproducible approach for automated photographic PES attribute assessment in research settings.

Spatial IgA Plasma Cell Niches Drive Anti-Tumor Immunity in Pancreatic Cancer 2307077

Abstract Introduction Pancreatic ductal adenocarcinoma (PDAC) has the worst prognosis among major cancers, with a five-year survival rate below 10%. The tumor microenvironment (TME) strongly shapes immune responses, yet key immune cell interactions remain unclear. Plasma cells are abundant in PDAC tumors, but their roles in anti-tumor immunity are not well defined. We aimed to determine how spatially organized plasma cell populations influence immune cell function and patient survival within the PDAC TME. Methods We integrated two spatial transcriptomics cohorts with tumor and normal tissues from 71 PDAC patients, representing a large-scale spatial systems immunology analysis of plasma cells. We defined plasma cell niches within the TME and integrated these spatial features with TCGA PDAC data to test associations with patient survival. We modeled spatial cell-cell communication to link immune interactions with clinical outcomes and compared ligand-receptor signaling and spatial gene regulatory networks between IgA/M and IgG plasma cell niches. Results Plasma cell abundance increased with advanced lymph node metastasis stages (pN). IgA/M and IgG plasma cells formed distinct spatial niches in the PDAC TME. IgA/M niches were enriched for nearby T cells, NK cells, and antigen-presenting myeloid cells and were associated with stronger T cell cytotoxicity, clonal expansion, and longer patient survival. Tumor-derived LINE1 was associated with activation of MAF and IRF4 programs in IgA/M cells, which promoted TIMP1—CD63 signaling to myeloid cells and enhanced antigen presentation. Conclusion Distinct plasma cell niches actively shape cellular immune responses in the PDAC TME. IgA/M plasma cells support coordinated anti-tumor activity by T cells, NK cells, and myeloid cells and are linked to improved patient survival. These findings establish spatial plasma cell organization as a central regulator of tumor immunity and a promising target for immune-based strategies in pancreatic cancer. Funding Source n/a Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

Imipridone treatment activates canonical NFkB and inflammatory signaling in THP1 differentiated macrophages 2258348

Abstract Introduction Diffuse intrinsic pontine glioma (DIPG) is a devastating pediatric high-grade glioma and is the leading cause of brain cancer related mortality in children. Modeyso (ONC201/dordaviprone), the first in class imipridone, has been recently FDA approved for use in progressive H3K27M mutated diffuse midline gliomas (DMG) such as DIPG. We aim to better understand the effects of ONC201 on the predominantly-macrophage immune microenvironment of DIPG by characterizing their direct impact on bone marrow derived macrophages. Methods We conducted gene set enrichment analysis on RNA sequencing data derived from ONC201 DMG clinical trials. We next aimed to better understand NFκB signaling and cytokine production following imipridone treatment. We utilized the THP1 human-monocyte cancer cell line as a model for bone marrow derived macrophages by differentiating them using 200ng/mL PMA for 48 hours. Following differentiation, we treated the cells with 5µM or 2µM ONC201, 1.5µM or 0.75µM ONC206, or 0.1µM or 0.05µM ONC212 and collected lysates for western blot. Results Using the hallmarks gene set, we found that increased expression of genes associated with a baseline inflammatory, IFNα and IFNγ response were associated with patient radiographic response. By western blot, we found a dose dependent increase in protein levels of canonical NFκB subunits and increased phosphorylation of p65. At later time-points, we found an increase in ATF4 levels and subsequent decrease in inflammatory protein expression. We also identified an increase in pro-IL1β suggesting an activation of the NLRP3 inflammasome. However, we did not find an increase in the active form through western blotting. Conclusion We have identified a link between a more immunologically active TME and response to ONC201 in patients with DMG, and that changes in NFkB signaling occurred following imipridone treatment of the THP1 cell line. We will continue our analysis of changes in cytokine production through ELISA and luciferase reporter assays. Funding Source n/a Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)

Proximity Proteomics Identifies IFI16 as a Host Factor of Human Coronavirus Infection 2258522

Abstract Introduction Several proteomic approaches have been employed to determine the interacting partners of SARS-CoV-2 encoded proteins, with the goal of identifying protein targets for the design and evaluation of host-directed therapies against SARS-CoV-2. Proximity-dependent labelling followed by mass spectrometry (PDL-MS) is one such approach that has been employed in the study of interactions between SARS-CoV-2 proteins and the host cell. However, the proximity-dependent proteomic approaches employed in the study of SARS-CoV-2 so far have utilized either BioID or miniTurboID, a modified version of BioID. Methods We utilized split-TurboID, a versatile tool for probing the proximal partners of protein-protein interactions, to identify host proteins that are proximal partners of the non-structural proteins of SARS-CoV-2. We further carried out CRISPR-Ca9 knockout and CRISPRi knockdown assays to determine the role of the identified proximal partners of SARS-CoV-2 NSPs in human coronavirus infection. Results We identified IFI16, along with several RNA-binding proteins, as proximal partners of SARS-CoV-2 NSPs. Follow-up CRISPR-Cas9 knockout and CRISPRi knockdown of IFI16 in A549-ACE2 cells resulted in a decrease in human coronavirus infection. We further demonstrated reduced viral RNA replication and viral protein synthesis upon loss of IFI16. Interestingly, the loss of IFI16 results in reduced expression of type I IFNs and other interferon-stimulated genes. Conclusion Taken together, these data demonstrate that IFI16 promotes human coronavirus infection, and its role in coronavirus replication is independent of its role as a regulator of type I IFN gene expression. Funding Source VCIID COBRE (5P30GM118228-02) and TGIR COBRE (5P20GM125498-03) Topic Categories Viral Immunology (VIR)

Unraveling the Role of Dectin-1 in the Host Immune Response to Schistosoma mansoni Infection 2258129

Abstract Introduction Schistosomiasis is the second most prevalent parasitic disease, affecting over 250 million people worldwide. Schistosoma mansoni is a major causative agent, and current treatment relies solely on Praziquantel, raising concerns about reinfection and potential parasite resistance. Thus, further research is needed to better understand disease pathogenesis and identify alternative therapeutic targets. Given the glycan-rich nature of Schistosoma eggs and adult worms, C-type lectin receptors (CLRs) likely play a crucial role in pathogen recognition. Dectin-1, a CLR known for its role in fungal infections, may also regulate the immune response to S. mansoni infection, though its role remains unclear. We hypothesized that Dectin-1 contributes to inflammation during S. mansoni infection. Methods To investigate this, C57BL/6 and Dectin-1 knockout (KO) mice were infected with 80 S. mansoni cercariae via intraperitoneal injection, and after seven weeks, livers, spleens, mesenteric lymph nodes, and intestines were harvested for pathological and immunological analysis. Bone marrow-derived dendritic cells (BMDCs) from both genotypes were stimulated with live eggs to assess cytokine production and signaling pathways. Results Dectin-1 KO mice exhibited lower liver and spleen masses and reduced egg-induced hepatic immunopathology, as evidenced by smaller granulomas compared to wild-type mice. Moreover, Dectin-1 promoted the production of proinflammatory cytokines IL-1β and Th17 cell responses while suppressing the anti-inflammatory cytokine IL-10. Mechanistically, Raf-1 and NF-κB were identified as downstream mediators of Dectin-1 signaling in cytokine induction. Conclusion Our findings suggest that Dectin-1 decisively influences the course of the schistosome infection. Funding Source R01 AI018919/AI/NIAID NIH HHS/United States R01 AI148656/AI/NIAID NIH HHS/United States Topic Categories Microbial, Parasitic, and Fungal Immunology (MPF)

Disruption of the Lung Microbiome Early in Life Protects Mice from Systemic Lupus Erythematosus 2260267

Abstract Introduction Systemic lupus erythematosus (SLE) is an incurable autoimmune disease. While the disease is well characterized, the pathogenesis is not clearly understood. It is widely accepted that the gut microbiome plays a role in SLE progression, but there is less data about other mucosal microbiomes, such as in the lung. Methods We administered a mixture of vancomycin, neomycin, ampicillin, and metronidazole (ABX) or phosphate-buffer solution (PBS) via intranasal gavage every 3 days, starting at 4 weeks, until 7 of life (10 administrations) to lupus-prone MRL/lpr mice, collecting urine and weights weekly. At 15 weeks, we euthanized the mice and collected lymph organs, lungs, and kidneys. We extracted bacterial DNA from bronchial alveolar lavage fluid (BALF) and feces and performed bacterial 16S ribosomal sequencing. Results ABX mice had larger mediastinal lymph nodes (MsLN), but more distant lymph organs were the same size. However, ABX mice had decreased protein in their urine, indicating less severe lupus disease. ABX mice had decreased monocytes in their lung and increased CD4+ T cells. In the MsLN, ABX mice had decreased plasmablasts, IL-17-producing B cells, and interferon gamma producing T cells in their MsLN. ABX mice had fewer CD4-CD8- (DN) T cells and monocytes in their spleen. There was no difference in the lung microbiomes when comparing overall microbiota compositions, however, when comparing individual genus and family levels, there were clear differences. Further, when correlating the relative abundance of bacteria to disease parameters, we found that the lung microbiome, indicated by BALF, was more predictive of disease severity than the gut microbiome represented by the feces. Conclusion We found that intranasal antibiotics conferred protection against lupus, and that the lung microbiome was capable of predicting disease outcomes in lupus-prone mice. We believe that further study of the lung microbiome in inflammatory diseases is important, as it is a major site of microbe-host interaction. Funding Source NIH Topic Categories Basic Autoimmunity (BA)

Representation Learning on Population-Scale Proteomics to Stratify Immune Checkpoint Inhibitor Outcomes 2334712

Abstract Introduction High-throughput plasma proteomics has significant potential as a tool for monitoring immune checkpoint inhibitor (ICI) therapy and predicting immune-mediated adverse event (irAE) side effects. However, the high dimensionality of proteomic features relative to sample sizes in typical clinical cohorts limits robust analysis of the associations between proteins and irAEs. We hypothesized that a deep learning autoencoder trained on population-scale data could learn compressed representations of the plasma proteome, enabling improved sample stratification in smaller cohort settings. Methods We trained a masked autoencoder (MAE) on Olink proteomic data from over 50,000 UK Biobank participants to learn compressed proteomic embeddings. This pre-trained model was then applied to an independent clinical cohort of ICI-treated patients with longitudinal plasma proteomics samples paired with irAE phenotyping. The embeddings were used to predict the onset of irAEs and to identify proteomic signals of active irAEs. They were then compared to models trained on raw proteomic data. Results In irAE prediction and identification tasks, the MAE-derived embeddings demonstrated significantly improved robustness compared to models using raw protein levels. Models trained on pre-treatment samples were predictive of subsequent irAE development, identifying high-risk patients at a potentially clinically useful timepoint. Conclusion These results demonstrate that plasma proteomics has the potential to improve our understanding of individuals at risk for irAEs and that transfer learning from population-scale data can overcome sample size limitations in clinical ICI cohorts. Future work will focus on further expanding the biological interpretability of the latent features. Funding Source Penn Discretionary Fund Topic Categories Computational and Systems Immunology (COMP)

Regional Heterogeneity of Resident Memory CD8 T cells in the Human Brain 2259998

Abstract Introduction Resident memory T cells (TRM) reside in diverse tissues, including the central nervous system (CNS), where they provide rapid, site-specific immune responses upon secondary challenge. Mouse models have demonstrated the importance of CNS TRM in protection against neurotropic pathogens, involvement in neurological disorders, and maintenance of CNS homeostasis. However, understanding of human brain TRM has been limited by challenges in acquiring timely and adequate tissue samples. Methods We developed a unique pipeline combining on-site autopsies with rapid tissue dissociation to collect specimens from multiple CNS regions, including the cerebellum, hippocampus, frontal cortex, and meninges. Flow cytometry was used to quantify CD8+ TRM marked by canonical residency markers CD69+ CD103+. Single-cell RNA sequencing profiled TRM transcriptional signatures across regions. Additionally, barcoded tetramers identified virus-specific T cells, and TCR sequencing characterized clonal relationships between different regions. Results High frequencies of CD8+ TRM marked by CD69+ CD103+ were detected in all CNS tissues. Single-cell RNA sequencing revealed location-specific TRM signatures; meningeal T cells clustered distinctly, enriched for Granzyme B and Interferon-gamma, while hippocampus, cortex, and cerebellum TRM expressed TOX and HOBIT. Live tissue sampling from epilepsy surgeries showed analogous TRM signatures. Tetramer analysis identified influenza-, SARS-CoV-2-, Epstein-Barr virus (EBV)-, and cytomegalovirus (CMV)-specific T cells distributed throughout the brain. TCR sequencing demonstrated clonal overlap of virus-specific TRM clones across CNS regions, indicating an antigen-driven expansion that supports a durable, heterologous antiviral TRM repertoire in the brain. Conclusion These findings reveal regional heterogeneity and specialization of human brain TRM, underscoring their roles in neurological diseases and the need to understand their biology to develop targeted immunotherapies. Funding Source NIA R01 AG078761 Topic Categories Neuroimmunology (NEUR)