Immunology
Abstract
Sepsis, a systemic inflammatory response to infection, remains a leading cause of mortality in intensive care units, with sepsis-induced immunosuppression being a critical pathophysiological process. In this study, we investigated the role of histone deacetylase 1 (HDAC1) in sepsis-induced CD8+ T cell exhaustion, a key driver of immunosuppression. Clinical analyses of patients with sepsis revealed that reduced peripheral blood lymphocyte levels, particularly CD8+ T cell depletion, strongly correlated with worsened outcomes. In a murine sepsis model, single-cell RNA-Seq revealed a significant decrease in the proportion of CD8+ T cells and an increase in the proportion of exhausted CD8+ T cells in mouse lungs. Adoptive transfer of CD8+ T cells effectively reduced sepsis mortality by preserving organ function. We further demonstrated that HDAC1 expression was significantly upregulated in CD8+ T cells from patients with sepsis. In vitro studies showed that HDAC1 inhibition preserved CD8+ T cell function by maintaining T cell activity and reducing the expression of inhibitory molecules such as PD-1. Pharmacological inhibition of HDAC1 reduced mortality and reversed CD8+ T cell exhaustion by restoring the balance between activator protein-1 (AP-1) and nuclear factor of activated T cells (NFAT). Additionally, we found that HDAC1 directly interacted with NFAT1, promoting its nuclear translocation and further enhancing the expression of inhibitory molecules. Our findings highlight HDAC1 as a potential therapeutic target for sepsis-induced immunosuppression. By elucidating the molecular mechanisms underlying HDAC1-mediated immunosuppression, we have provided potential strategies for developing immunomodulatory therapies for the treatment of sepsis.
Authors
Liu Di, Jiang-bo Fan, Rui Wang, You Li, Wan-da Bi, Si-yuan Huang, Heng-hai Nie, Xi-feng Feng, Hua-cai Zhang, Juan Du, Xiao-fei Huang, An-yong Yu, Zhe Xu, Fei Xia, Jian-xin Jiang, Shuang-shuang Dai, Xiang Xu, Zhen Wang, Ling Zeng
Abstract
Antibody-dependent enhancement (ADE) of infection is a well-described phenomenon for several viruses, including dengue, Ebola, respiratory syncytial virus, and HIV. ADE occurs when virus-antibody complexes engage Fc receptors (FcRs) and virus-specific receptors, enhancing infection under conditions of incomplete neutralization. The Coronavirus Immunotherapeutic Consortium (CoVIC) assembled a comprehensive dataset of functional properties for over 400 mAbs, enabling direct comparison of neutralization, Fc-mediated functions, receptor binding, and infection of immune cells. Infection rates in most primary human immune cell types were low, with modest increases observed for some mAbs. In contrast, macrophages were more susceptible to SARS-CoV-2 and exhibited substantial ADE with select mAbs. ADE was completely inhibited by FcR blockade and significantly reduced by antibody- or ceftazidime-mediated blocking of angiotensin-converting enzyme 2 (ACE2). Neutralization potency did not correlate with ADE, as both strongly and weakly neutralizing antibodies induced enhancement. Instead, ADE magnitude depended on an antibody’s ability to block spike protein binding to ACE2. Importantly, ADE resulted in productive infection with release of infectious virus. Evaluation of antibodies against the BA.1 (Omicron) variant revealed reduced or lost ADE for most mAbs, with increased ADE observed for several mAbs relative to the USA-WA1/2020 strain.
Authors
Natalia A. Kuzmina, Sivakumar Periasamy, Kritika Kedarinath, Keziah Hernandez, Caroline Atyeo, S. Moses Dennison, Kan Li, Daniel Bedinger, Sharon L. Schendel, Georgia D. Tomaras, Hanif Ali, Galit Alter, Erica Ollmann Saphire, Alexander Bukreyev
Abstract
BACKGROUND The SARS-CoV-2 pandemic provided a rare opportunity to study how human immune responses develop to a novel viral antigen delivered through different vaccine platforms. However, to date, no study has directly compared immune responses to all 3 FDA-approved COVID-19 vaccines at single-cell multiomic resolution.METHODS We longitudinally profiled SARS-CoV-2–naive adults (n = 31) vaccinated with BNT162b2, mRNA-1273, or Ad26.COV2.S, integrating plasma cytokines, antibody titers, and single-cell multiomic data (DOGMA-Seq).RESULTS We discovered a distinct, transient IFN program termed ISG-dim, which emerged specifically 1–2 days after the first mRNA dose in approximately 10% of myeloid cells. This state was characterized by ISGF3 complex activation and its target genes (e.g., MX1, MX2, DDX58), with transcriptional and epigenetic profiles distinct from the robust IFN program observed after mRNA boosting or a single Ad26.COV2.S dose (ISG-high). In vitro stimulation of human monocytes showed that IFN-α alone recapitulates ISG-dim, whereas both IFN-α and IFN-γ are required for ISG-high.CONCLUSION These findings define dose-dependent IFN programming in human myeloid cells and highlight mechanistic differences between priming and boosting, with implications for optimizing vaccine platform choice, dose scheduling, and formulation.FUNDING NIH grants AI142086, U19 AI135972, U01 AI165452, U01 AI165452, R01 AI160706, and P30 AG067988.
Authors
Giray Eryilmaz, Yilmaz Yucehan Yazici, Radu Marches, Eleni P. Mimitou, Lisa Kenyon-Pesce, Kim Handrejk, Sonia Jangra, Michael Schotsaert, Adolfo García-Sastre, George A. Kuchel, Jacques Banchereau, Duygu Ucar
Abstract
We previously demonstrated that blocking TGF-β with galunisertib, a safe, orally available small drug, reactivated latent SIV in vivo by shifting T cells toward a transitional effector phenotype. Here, we investigated the mechanisms underlying this effect using single-cell RNA sequencing, metabolic profiling, and high-dimensional spectral flow cytometry of samples from SIV-infected, antiretroviral therapy–treated (ART-treated) macaques before and after galunisertib. To characterize virus-transcribing, infected cells during ART, we developed a novel, sensitive SIV Transcripts Capture Assay (SCAP) that detected 127 SIV-expressing cells within lymph node single-cell transcriptome libraries. Galunisertib drove broad metabolic reprogramming in CD4+ T cells, with transcriptional upregulation of inflammatory and mitochondrial biosynthesis pathways, confirmed by Seahorse profiling. Metabolomics revealed increased energy metabolites and amino acids and enhanced metabolic flux without proliferation. SIV transcript–positive cells before galunisertib were metabolically quiescent compared with cells without detectable viral transcripts. After galunisertib, virus-expressing cells showed a dramatic metabolic activation, with upregulation of glycolysis, fatty acid metabolism, and TNF-α signaling. High-dimensional flow cytometry demonstrated effects beyond CD4+ T cells, including fewer tissue-resident memory T cells, but more inflammatory macrophages. In conclusion, SCAP represents a specific tool for characterizing rare SIV-infected cells transcribing virus during ART, and it reveals TGF-β as a key mediator of viral latency in vivo through metabolic suppression.
Authors
Romaila Abd-El-Raouf, Jakob Harrison-Gleason, Jinhee Kim, Ching Man Wai, Kayla L. Yerlioglu, Catarina Ananias-Saez, Alec Ksiazek, Jeffrey T. Poomkudy, Mariluz Araínga, Deepanwita Bose, Claudia Cicala, James Arthos, Francois J. Villinger, Ramon Lorenzo-Redondo, Elena Martinelli
Abstract
With the increasing use of genetic sequencing to investigate inborn errors of immunity, rare variants are frequently identified, yet their clinical relevance often remains uncertain. Establishing pathogenicity requires a multidisciplinary approach that integrates genetic, structural, functional, and clinical data. Here, we used such a strategy to investigate a previously unreported hemizygous missense variant — alanine (A) to threonine (T) at residue 518 — in Toll-like receptor 8 (TLR8), identified in 2 male siblings with recurrent infections and systemic inflammation, characterized by a proinflammatory immune signature and B cell dysregulation. Functional studies showed that the TLR8 A518T variant enhanced NF-κB activation and increased secretion of proinflammatory cytokines compared with WT TLR8 upon stimulation, consistent with a gain-of-function effect. Protein degradation and turnover assays revealed reduced abundance of the mutant TLR8 protein due to faster turnover and increased proteasomal degradation. Computational modeling predicted enhanced structural stabilization of the active TLR8 homodimer interface via additional water-mediated hydrogen bonds introduced by the A518T substitution. Together, these findings integrating structural modeling with functional assays identify a novel TLR8 ligand-specific gain-of-function mutation resulting in complex immunopathology in 2 siblings.
Authors
Nikolaos T. Skenteris, Elisa Luttermann, Sanjana Nair, Ioannis Evangelakos, Maria Pujantell, Marie Eggers, Fabian Hausmann, Marleen Bérouti, Benedetta Padoan, Felix J. Flomm, Janna M. Claussen, Benjamin Grünhagel, Anika Salfelder, Brigitte Beifuss, Saskia Biskup, Patrick Blümke, Katrin Rading, Heike Hildebrandt, Urte Matschl, Silke Giesemann-Jansen, Jana Hennesen, Viacheslav O. Nikolaev, Michael Kutsche, Christian Kubisch, Friedrich Koch-Nolte, Nicola M. Tomas, Eva Tolosa, Marc Lütgehetmann, Felix R. Stahl, Veit Hornung, Madeleine J. Bunders, Christian Schlein, Maya Topf, Ina Kötter, Marcus Altfeld
Abstract
The skin lesion erythema migrans (EM) is the first clinical sign of Lyme disease, an infection due to the tick-transmitted bacterium Borrelia burgdorferi (Bb). Previously, we used scRNA-Seq to characterize the cutaneous immune response in the EM lesion, focusing on B cells. Here, with an expanded sample size, we profiled T cell responses in EM lesions compared to autologous uninvolved skin. In addition to CD4+ T cell subsets known to be abundant in the EM lesion, we identified clonally expanded CD8+GZMK+IFNG+ T cells that comprised cells with high or intermediate IFNG expression. These cells exhibited significant differential expression of IFN-regulated genes and included subsets with low cytotoxic gene expression, suggesting an inflammatory potential that may contribute to early defense against Bb within the EM lesion. In addition, we found that endothelial cells, fibroblasts, and pericytes were the main producers of key T cell–recruiting chemokines. These studies using single-cell transcriptomics with adaptive immune receptor sequencing provide a comprehensive interrogation of the cutaneous T cell response to Bb infection and insight into the orchestration of the skin barrier defense to this vector-borne pathogen.
Authors
Edel Aron, Hailong Meng, Alexia A. Belperron, Paraskevas Filippidis, Kenneth R. Dardick, Steven H. Kleinstein, Linda K. Bockenstedt
Abstract
Alveolar macrophages (AMs) catabolize lipid-rich pulmonary surfactant to support gas exchange and have anti-inflammatory programming to limit tissue damage in response to minor challenges. GATA transcription factors (TFs) shape immune cell fates and GATA2 is expressed in a lung-specific manner in macrophages. GATA2 mutations and lung macrophage downregulation of GATA2 have been associated with chronic pulmonary pathologies in humans, but the role of GATA2 in coordinating AM function is not well defined. Using mice with myeloid-specific deletion of the GATA2 DNA binding C-terminal zinc finger domain, we show that GATA2 deficiency promotes enhanced inflammatory gene expression and metabolic dysfunction in AMs in response to type 2 stimuli. While homeostatic functions of AMs remain largely intact, GATA2 deficiency increases expression of type 2 response genes during IL-33-induced inflammation. Coincident with GATA2-dependent expression of genes in metabolic pathways, seahorse metabolic flux analysis indicates that AM metabolism is compromised in the absence of GATA2. AM GATA2-dependent gene networks are enriched for targets of TFs previously demonstrated to interact with GATA2 in other cellular contexts, including PU.1, PPARγ, and other regulators of AM function. Our data suggest that GATA2 modulates AM metabolic and transcriptomic programming to restrain responses and maintain AM identity during inflammation.
Authors
Morgan Jackson-Strong, Satarupa Ganguly, Aaron Francis, Flavia Rago, Jitendra Kanshana, Brandon A. Michalides, Lihong Teng, Omkar S. Betsur, Sonia Kruszelnicki, Karsen E. Shoger, Aaron Kim, Kay Bajpai, Amina Suleyman, Abigail Sekyere, Mika Hara, Varsha Sriram, Alok Kumar, Greg M. Delgoffe, Niranjana Natarajan, John F. Alcorn, Alison B. Kohan, Rachel A. Gottschalk
Abstract
The biological mechanisms underlying long COVID in the pediatric population are poorly understood. Our study aimed to characterize the immune pathophysiology of long COVID in children and young people (CYP). We analyzed major immune cell compartments in PBMCs, as well as specific SARS-CoV-2 antibody response in CYP with (n=99) and without (n=18) long COVID at three months following acute infection. Our findings indicate that pediatric long COVID is associated with a dysregulated immune response characterized by altered innate immunity and overactivated T-, B- and NK-cell responses. Furthermore, CYP with long COVID had an impaired humoral response to SARS-CoV-2 marked by a dysregulated B-cell compartment and lower levels of anti-RBD IgG and IgA. This correlated with reduced neutralizing capacity against SARS-CoV-2. Random forest analysis identified CCR6 expression on myeloid cells as the most relevant biomarker that distinguishes long COVID from control individuals with 79% accuracy.
Authors
Jon Izquierdo-Pujol, Núria Pedreño-Lopez, Tetyana Pidkova, Maria Nevot, Victor Urrea, Fernando Laguía, Francisco Muñoz-López, Judith Dalmau, Alba Gonzalez-Aumatell, Clara Carreras-Abad, María Méndez, Carlos Rodrigo, Marta Massanella, Julià Blanco, Jorge Carrillo, Benjamin Trinité, Javier Martinez-Picado, Sara Morón-López
Abstract
Authors
Sebastian Kämpf, Marjan Hematianlarki, Leon Altmann, Jessica M. Bright, Alyssa M. A. Toda, Zohreh Mirzapoor, Valentin Zollner, Anja Werner, Johanna Bulang, Barbara Radovani, Miriam Wöhner, William Avery, Mark J. Karbarz, Pamela B. Conley, Greg P. Coffey, Falk Nimmerjahn
Abstract
Adeno-associated viruses (AAVs) have been used in gene therapy, especially for inherited retinal diseases. Despite their effectiveness in gene transduction, immune responses to the AAV capsid and transgene products have been reported, which can compromise both the efficacy and safety of AAV-mediated therapies. The eye is regarded as an immune-privileged organ where immune activity is constitutively suppressed. Here, we highlight that immunomonitoring in an ocular gene transfer reveals variable immune responses, whatever the species (human clinical trial, non-human primates, mice), the site of injection, the cassette, and the dose. We further explored factors contributing to this variability, investigating the potential correlation among immune parameters in a controlled experimental setting. In a syngeneic murine model after a subretinal injection of AAV, our results highlight an inter-individual variability of immune parameters, emphasizing the importance of considering inherent variability among individuals while designing personalized therapies.
Authors
Duohao REN, Gaelle A. CHAUVEAU, Julie VENDOMELE, Emilie CABON, Audrey PINEIRO, Catherine VIGNAL-CLERMONT, Hanadi SALIBA, Giuseppe RONZITTI, Anne GALY, Deniz DALKARA, Juliette PULMAN, Divya AIL, Sylvain FISSON
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