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Yang AY, Davis-Porada J, Paik DH, George AB, Brown BH, Ruschke PL, Sims PA, Frankenstein Z, Saqi A, Farber DL
The Journal of experimental medicine
2026-01-05
PMID: 41081716
Animals
CD8-Positive T-Lymphocytes
Columbia University
Female
HIPC 2 (2015)
HIPC 3 (2022)
Humans
Immunity, Innate
Immunologic Memory
Inflammation
Interferon-gamma
Interleukin-10
Lung
Macrophages
Memory T Cells
Mice
Mice, Inbred C57BL
Orthomyxoviridae Infections
Abstract:
Respiratory viral infections establish tissue-resident memory T cells (TRM) in the lung, which provide optimal protection against subsequent infections, though the underlying mechanisms are incompletely understood. Here, we demonstrate in a mouse model of heterosubtypic influenza infection that lung TRM attenuate inflammation by macrophages during secondary versus primary responses, in part, through production of the immunoregulatory cytokine IL-10. During secondary infections, lung TRM were the predominant producers of early IL-10; inhibiting early IL-10 signaling resulted in increased macrophage-mediated inflammation, morbidity, and lung pathology. Moreover, lung TRM were shown to directly modulate lung macrophage responses and polarization in depletion experiments. Finally, IL-10 enhanced IFN-γ production by lung memory CD8+ T cells. Human influenza-specific TRM isolated from lungs recapitulated robust IL-10 expression associated with augmented effector responses of murine TRM. These data support a dual role of TRM in coordinating in situ secondary responses-augmenting effector responses for robust viral clearance while dampening inflammation to limit tissue damage.
Chihab LY, Cheng C, Hillman H, Khan N, Kearns K, Mondal M, Wang A, Seumois G, Vijayanand P, Drake WP, Veltkamp M, Janssen Bonás M, van Moorsel CHM, Joosten SA, van Meijgaarden KE, Palmieri F, Petrone L, Aiello A, Goletti D, De Silva AD, Tennekoon R, Dilani D, Scriba T, Fisher M, Luabeya AK, ...
Journal of immunology (Baltimore, Md. : 1950)
2025-10-17
PMID: 41105206
HIPC 2 (2015)
HIPC 3 (2022)
La Jolla Institute for Immunology
Abstract:
Sarcoidosis is a granulomatous systemic inflammatory disease predominantly affecting the lungs. It shares histopathological, clinical, and immune features with tuberculosis (TB). There are currently no diagnostic tests to formally identify sarcoidosis; instead, there is a need first to rule out the presence of other diseases, including TB. We hypothesized that Mycobacterium tuberculosis (Mtb)-specific immune signatures differ between sarcoidosis and TB. We characterized T-cell and monocyte signatures after Mtb antigen in vitro stimulation in the blood of patients with sarcoidosis compared to patients with TB disease and Mtb-sensitized and nonsensitized healthy controls using flow cytometry and transcriptomics on bulk PBMCs and sorted CD4 memory T cells. We found that sarcoidosis was associated with (1) a marked reduction in frequencies of antigen-reactive T cells in response to both Mtb peptides and Mtb lysate, (2) increased frequencies of monocytes, and (3) increased expression of monocyte-associated phagocytic genes compared to TB disease and Mtb-sensitized and nonsensitized healthy cohorts. A combination of Mtb peptide-specific T-cell and monocyte gene or flow cytometry signatures in Mtb peptide-stimulated PBMCs distinguished sarcoidosis from TB disease with high accuracy (area under the curve [AUC] = 0.91 and 0.96 for gene and flow cytometry signatures, respectively) and also distinguished sarcoidosis from Mtb-sensitized and nonsensitized healthy controls combined (AUC = 0.91 and 0.90 for gene and flow cytometry signatures, respectively). These findings highlight biological features that effectively distinguish sarcoidosis from TB and healthy populations and can be considered for the development of an optimized diagnostic method for sarcoidosis.
Pucella JN, Maqueda-Alfaro RA, Ni H, Bandeira Sulczewski F, Eichinger A, Esteva E, Ra AC, Das A, Perez OA, Feng J, Stoeckius M, Smibert P, Khodadadi-Jamayran A, Dolgalev I, Ivanova E, Sota S, Cadwell K, Koralov SB, Zhong J, Soni C, Stetson DB, Weisberg SP, Farber DL, Idoyaga J, Reizis B
Nature immunology
2025-10-14
PMID: 41087726
Columbia University
HIPC 2 (2015)
HIPC 3 (2022)
Abstract:
Plasmacytoid dendritic cells (pDCs) mount powerful antiviral type I interferon (IFN-I) responses, yet only a fraction of pDCs produces high levels of IFN-I. Here we report that peripheral pDCs in naive mice comprise three subsets (termed A, B and C) that represent progressive differentiation stages. This heterogeneity was generated by tonic IFN-I signaling elicited in part by the cGAS/STING and TLR9 DNA-sensing pathways. A small 'IFN-I-naive' subset (pDC-A) could give rise to other subsets; it was expanded in STING deficiency or after the IFN-I receptor blockade, but was abolished by exogenous IFN-I. In response to RNA viruses, pDC-A showed increased Bcl2-dependent survival and superior IFN-I responses, but was susceptible to virus infection. Conversely, the majority of pDCs comprised the 'IFN-I-primed' subsets (pDC-B/C) that showed lower IFN-I responses and poor survival, but did not support virus replication. Thus, tonic IFN-I signaling decreases the cytokine-producing capacity and survival of pDCs but increases their virus resistance, facilitating optimal antiviral responses.
Costa Monteiro AC, Pickering H, Sarma A, Taylor CS, Jenkins MM, Hsu FM, Nadel B, Levy O, Baden LR, Melamed E, Ehrlich LIR, McComsey GA, Sekaly RP, Cairns CB, Haddad EK, Shaw AC, Hafler DA, Montgomery RR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, ...
Critical care (London, England)
2025-10-14
PMID: 41088445
Adult
Aged
Child
Cohort Studies
COVID-19
Endothelial Cells
Female
HIPC 1 (2010)
HIPC 2 (2015)
HIPC 3 (2022)
Humans
Male
Middle Aged
Pilot Projects
Respiratory Distress Syndrome
Respiratory Insufficiency
Yale University
Abstract:
[{'@Label': 'BACKGROUND', '@NlmCategory': 'BACKGROUND', '#text': 'Elevated circulating endothelial cells (CECs), released from monolayers after insult, have been implicated in worse outcomes in ARDS and COVID-19, however there is no consensus proteomic phenotype that define CECs. We queried whether a transcriptomic approach would alternatively support the presence of endothelial cells in circulation and correlate with worsening respiratory failure.'}, {'@Label': 'METHODS', '@NlmCategory': 'METHODS', '#text': 'To test whether elevated endothelial cell signatures (ECS) in circulation plays a role in worse respiratory outcomes, we used unsupervised bulk-transcriptome deconvolution to quantify ECS% in two cohorts. Our pilot analysis included pediatric patients requiring invasive mechanical ventilation (CAF-PINT, NCT01892969). Our validation cohort included adult hospitalized patients with COVID-19 (IMPACC, NCT04378777), testing the association of ECS% to outcomes in patients at risk of acute respiratory failure/ARDS. Primary outcome was 28-day mortality.'}, {'@Label': 'RESULTS', '@NlmCategory': 'RESULTS', '#text': 'In CAF-PINT, day 0 ECS% was higher in non-survivors compared to survivors of respiratory failure (2.8%, IQR 2.4-3.4% versus 2.6%, IQR 2.2-3.0% n\u2009=\u2009244, p\u2009<\u20090.05, Wilcoxon rank-sum). In IMPACC, baseline ECS% (<\u200972\xa0h of hospitalization) was higher in COVID-19 non-survivors versus survivors (2.9%, IQR 2.6-3.4%, versus 2.7%, IQR 2.3-3.1%, n\u2009=\u2009932, p\u2009<\u20090.001, Wilcoxon rank-sum). Each 1% increase in baseline ECS% was significantly associated with mortality (adjusted OR 1.36, CI 1.03-1.79) by multivariable logistic regression. Increased baseline ECS% was associated with worse respiratory trajectories (2.5%, IQR 2.2-2.8% for trajectory with no oxygen requirements, 2.9%, IQR 2.6-3.4% for the trajectory with fatal outcome by day 28, n\u2009=\u2009932, p\u2009<\u20090.001, one-way ANOVA).'}, {'@Label': 'CONCLUSION', '@NlmCategory': 'CONCLUSIONS', '#text': 'Quantifying ECS by deconvolution supports a transcriptomics-driven approach towards the non-invasive evaluation of endothelial damage in respiratory outcomes. This is a first step towards elucidating mechanistic components linking endothelial damage to ARDS utilizing non-invasive, circulating transcriptomic data by leveraging a novel deconvolution approach.'}]
Moore AR, Zheng H, Ganesan A, Hasin-Brumshtein Y, Maddali MV, Levitt JE, van der Poll T, Lu J, Bouma HR, Scicluna BP, Giamarellos-Bourboulis EJ, Kotsaki A, Martin-Loeches I, Garduno A, Hinson J, Rothman RE, Sevransky J, Wright DW, Atreya MR, Moldawer LL, Efron PA, Kralovcova M, Karvunidis T, Giannini HM, Meyer NJ, ...
Nature medicine
2025-09-30
PMID: 41028543
HIPC 3 (2022)
Stanford
Abstract:
Critical care syndromes such as sepsis, acute respiratory distress syndrome (ARDS) and trauma continue to have unacceptably high morbidity and mortality, with progress limited by the inherent heterogeneity within syndromic illnesses. Although numerous immune endotypes have been proposed for sepsis and critical care, the similarities and differences between these endotypes remain unclear, hindering clinical translation. The SUBSPACE consortium is an international consortium that aims to advance precision medicine in critical care through the sharing of transcriptomic data. Here, evaluating the overlap of existing immune endotypes in sepsis across >7,074 samples from 37 independent cohorts, we developed cell-type-specific gene expression signatures to quantify dysregulation within immune compartments. Myeloid and lymphoid dysregulation were associated with disease severity and mortality across all cohorts. Importantly, this dysregulation was also observed in patients with ARDS, trauma and burns, suggesting a conserved mechanism across various critical illness syndromes. Moreover, analysis of randomized controlled trial data revealed that myeloid and lymphoid dysregulation are associated with differential mortality in patients treated with anakinra in the SAVE-MORE trial (n = 452) and corticosteroids in the VICTAS (n = 89) and VANISH (n = 117) trials, underscoring their prognostic and therapeutic implications. In conclusion, our proposed immunology-based framework for quantifying cellular compartment dysregulation offers a potentially valuable tool for understanding immune dysregulation in critical illness with prognostic and therapeutic significance.
Saglimbeni J, Esteva E, Canales J, Perez OA, Eichinger A, Huntley W, Khanna KM, Dolgalev I, Klar N, Adams S, Reizis B
Proceedings of the National Academy of Sciences of the United States of America
2025-09-23
PMID: 40953260
Animals
Breast Neoplasms
Columbia University
Eosinophils
Female
HIPC 2 (2015)
HIPC 3 (2022)
Humans
Interleukin-33
Macrophages
Mammary Neoplasms, Experimental
Mice
T-Lymphocytes, Regulatory
Tumor-Associated Macrophages
Tumor Microenvironment
Abstract:
Breast tumors harbor dynamic microenvironments, with multiple immune cell types playing opposing roles during tumor progression and/or response to therapy. Tumor-associated macrophages promote mammary tumorigenesis, whereas the role of mammary tissue macrophages (MTMs) remains incompletely understood. High-dimensional immunostaining of murine mammary tumor progression revealed that MTMs were localized in the peritumoral stroma and associated with eosinophils, which were previously shown to facilitate antitumor T cell responses. The depletion of MTMs accelerated tumorigenesis in both spontaneous and orthotopically transplanted mammary tumor models. Upon induction of a productive antitumor response via the depletion of regulatory T cells, MTMs assumed an alternatively activated state and expressed eotaxins, thereby attracting eosinophils to peritumoral regions. MTMs expressed the receptor for the alarmin IL-33, which induced both MTM activation and eosinophil recruitment. These results suggest that MTMs can sense IL-33 and recruit eosinophils to facilitate antitumor immunity, a mechanism that may operate during tumor progression and be further enhanced during productive antitumor responses.
Gervais A, Trespidi F, Ferrari A, Rovida F, Marchal A, Croce S, Cassaniti I, Moratti M, Uhrlaub JL, Florian DM, Stiasny K, Burdino E, Angelini M, Bizien L, Lilleri D, Codullo V, Freund T, Paran Y, Gadoth A, Biran R, Mancon A, Lucca C, Vogiatzis S, Pacenti M, Aubart M, ...
medRxiv : the preprint server for health sciences
2025-09-04
PMID: 40950468
HIPC 1 (2010)
HIPC 2 (2015)
HIPC 3 (2022)
Yale University
Abstract:
Mosquito-borne West Nile virus (WNV) infection is a growing global health problem. About 0.5% of infected individuals develop encephalitis. We previously showed that 40% of patients in six cohorts had WNV encephalitis because of circulating auto-antibodies (auto-Abs) neutralizing type I IFNs. In seven new cohorts, we found that the prevalence of auto-Abs was highest (40% [17-44%]) in patients with encephalitis, and very low in a small sample of individuals with asymptomatic or mild infection. In the 13 European, Middle-Eastern and American cohorts available, odds ratios for WNV encephalitis in individuals with these auto-Abs relative to those without them in a large sample of the general population untested for WNV infection range from ~20 (OR=17.7; 95% CI: 13.8-22.8, p<10-16) for auto-Abs neutralizing only 100 pg/mL IFN-α2 and/or IFN-ω to >2000 (OR=2218.4; 95% CI: 125.1-39337.7, p<10-16) for auto-Abs neutralizing high concentrations of IFN-α2 and high or low concentrations of IFN-ω. Pre-existing autoantibodies neutralizing type I IFNs are therefore causal for WNV encephalitis in about 40% of patients.
Johnson MM, Kaushik A, Kline OA, Smith EM, Zhou X, Pat Y, Buergi L, Aguilera J, Alkotob S, Simonin EM, Favaro A, Couto M, Bennett O, Chinthrajah RS, Parsons E, Shamji M, Burke M, Bondy M, Akdis M, Akdis CA, Nadeau KC
Nature medicine
2025-09-01
PMID: 40571754
Adult
Biomarkers
Case-Control Studies
DNA Methylation
Environmental Exposure
Female
Fires
HIPC 3 (2022)
Humans
Male
Middle Aged
Smoke
Stanford
Abstract:
Exposure to fire smoke has become a global health concern and is associated with increased morbidity and mortality. There is a lack of understanding of the specific immune mechanisms involved in smoke exposure, with preventive and targeted interventions needed. After exposure to fire smoke, which includes PM2.5, toxic metals and perfluoroalkyl and polyfluoroalkyl substances, epidemiology-based studies have demonstrated increases in respiratory (for example, asthma exacerbation), cardiac (for example, myocardial infarction, arrhythmias), neurological (for example, stroke) and pregnancy-related (for example, low birthweight, premature birth) outcomes. However, mechanistic studies exploring how smoke exposure disrupts cellular homeostasis are lacking. Therefore, we collected blood from smoke-exposed individuals (n = 31) and age-matched and sex-matched non-smoke-exposed controls (n = 29), and investigated these complex interactions using a single-cell exposomic approach based on both methylation and mass cytometry. Overall, our data demonstrated a strong association between smoke exposure and methylation at 133 disease-relevant gene loci, while immunophenotyping showed increased homing and activation biomarkers. We developed an application of mass cytometry to analyze single-cell/metal binding and found, for example, increased levels of mercury in dead cells and cadmium in the live and dead cell populations. Moreover, mercury levels were associated with years of smoke exposure. Several epigenetic sites across multiple chromosomes were associated with individual toxic metal isotopes in single immune cells. Our methods for detecting the effect of smoke exposure at the single-cell level and the study results may help to determine the timing of exposure and identify specific molecular targets that could be modified to prevent and manage exposure to smoke.
Wells SB, Rainbow DB, Mark M, Szabo PA, Ergen C, Caron DP, Maceiras AR, Rahmani E, Benuck E, Valiollah Pour Amiri V, Chen D, Wagner A, Howlett SK, Jarvis LB, Ellis KL, Kubota M, Matsumoto R, Mahbubani K, Saeb-Parsy K, Conde CD, Richardson L, Xu C, Li S, Mamanova L, Bolt L, ...
Nature immunology
2025-09-01
PMID: 40804529
Adult
Aged
Aging
B-Lymphocytes
Cell Lineage
Columbia University
Female
Gene Expression Profiling
HIPC 2 (2015)
HIPC 3 (2022)
Humans
Killer Cells, Natural
Lymphoid Tissue
Macrophages
Male
Middle Aged
Organ Specificity
T-Lymphocytes
Transcriptome
Young Adult
Abstract:
The immune system comprises multiple cell lineages and subsets maintained in tissues throughout the lifespan, with unknown effects of tissue and age on immune cell function. Here we comprehensively profiled RNA and surface protein expression of over 1.25 million immune cells from blood and lymphoid and mucosal tissues from 24 organ donors aged 20-75 years. We annotated major lineages (T cells, B cells, innate lymphoid cells and myeloid cells) and corresponding subsets using a multimodal classifier and probabilistic modeling for comparison across tissue sites and age. We identified dominant site-specific effects on immune cell composition and function across lineages; age-associated effects were manifested by site and lineage for macrophages in mucosal sites, B cells in lymphoid organs, and circulating T cells and natural killer cells across blood and tissues. Our results reveal tissue-specific signatures of immune homeostasis throughout the body, from which to define immune pathologies across the human lifespan.
Carrillo FAB, Ojeda S, Sanchez N, Plazaola M, Collado D, Miranda T, Saborio S, Mercado BL, Monterrey JC, Arguello S, Campredon L, Chu Z, Carlson CJ, Gordon A, Balmaseda A, Kuan G, Harris E
The Lancet. Child & adolescent health
2025-09-01
PMID: 40774783
Adolescent
Chikungunya Fever
Child
Child, Preschool
Dengue
Female
HIPC 2 (2015)
Humans
Male
Nicaragua
Prospective Studies
Zika Virus Infection
Abstract:
[{'@Label': 'BACKGROUND', '@NlmCategory': 'BACKGROUND', '#text': 'Dengue, chikungunya, and Zika are diseases of major human concern. Differential diagnosis of these three diseases is complicated in children and adolescents due to overlapping clinical features (signs, symptoms, and complete blood count results). Few studies have directly compared these three diseases. We aimed to use 18 years of primary care observations from a paediatric cohort to characterise the distinguishing features of dengue, chikungunya, and Zika.'}, {'@Label': 'METHODS', '@NlmCategory': 'METHODS', '#text': 'This single-centre prospective cohort study was based on the ongoing Pediatric Dengue Cohort Study (PDCS), which started on Aug 30, 2004, in District II of Managua, Nicaragua. The PDCS was initiated to study dengue virus infections in children who attended the Health Center Sócrates Flores Vivas (HCSFV) for their medical needs; over the years, the PDCS expanded the age range (2 to <10 years expanded to 2 to <18 years). The PDCS also expanded eligibility criteria to include chikungunya virus and Zika virus before they entered the geographical study area in August, 2014 and January, 2016, respectively. For this study, we included laboratory confirmed cases of dengue, chikungunya, and Zika enrolled in the PDCS between Jan 19, 2006, and Dec 31, 2023, and evaluated at the HCSFV. We assessed clinical features (clinical records and laboratory results) during the first 10 days of illness using generalised additive models, day-specific and disease-specific prevalence estimates, and machine learning models.'}, {'@Label': 'FINDINGS', '@NlmCategory': 'RESULTS', '#text': 'We characterised 1405 dengue, 517 chikungunya, and 522 Zika cases. The median age was 10·0 years (IQR 7·0-12·7); 1165 (47·7%) cases were male and 1279 (52·3%) were female. The prevalence of many clinical features shown by dengue, chikungunya, and Zika cases differed substantially overall, by age, and by day of illness. The presence of basophilia (prevalence difference 42·3% [95% CI 37·4 to 47·0]), monocytopenia (13·0% [10·0 to 16·4]), abdominal pain (19·1% [15·7 to 22·9]), and leukopenia (41·1% [36·2 to 45·6]) best distinguished dengue; the presence of arthralgia (60·5% [56·3 to 64·2]) and absence of papular rash (-14·9% [-17·2 to -12·7]), leukopenia (-32·0% [-36·7 to -27·1]), and conjunctival injection (-4·9% [-6·6 to -3·3]) best distinguished chikungunya; and the presence of generalised rash (35·0% [30·1 to 39·7]) and absence of fever (-37·3% [-41·7 to -33·0]), headache (-36·2% [-41·1 to -31·2]), myalgia (-30·1% [-33·9 to -26·2]), and lymphocytopenia (-41·9% [-46·6 to -37·1]) best distinguished Zika. Dengue and chikungunya cases showed similar temperature dynamics during acute illness, and their mean temperatures were higher than Zika cases. 62 laboratory confirmed afebrile dengue cases, which would not be captured by any widely used international case definition, presented most similarly to afebrile Zika cases, but five (8·1%) had warning signs of dengue disease severity. Based on boosted regression tree models, the presence of arthralgia and absence of basophilia and leukopenia most distinguished chikungunya, the presence of basophilia and leukopenia most distinguished dengue, and the absence of fever most distinguished Zika.'}, {'@Label': 'INTERPRETATIONS', '@NlmCategory': 'CONCLUSIONS', '#text': 'These findings substantially update the understanding of dengue, chikungunya, and Zika in a paediatric population and identify various clinical features that could improve differential diagnoses. The occurrence of afebrile dengue warrants reconsideration of current guidance.'}, {'@Label': 'FUNDING', '@NlmCategory': 'BACKGROUND', '#text': 'US National Institutes of Health.'}, {'@Label': 'TRANSLATION', '@NlmCategory': 'UNASSIGNED', '#text': 'For the Spanish translation of the abstract see Supplementary Materials section.'}]
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