Infectious disease
Abstract
Infectious diseases remain a global health challenge, driven by increasing antimicrobial-resistance and the threat of emerging epidemics. Mycobacterium tuberculosis and Staphylococcus aureus are leading causes of mortality worldwide. Trained immunity—a form of innate immune memory—offers a promising approach to enhance pathogen clearance. Here, we demonstrate that IFN-γ induces trained immunity in human monocytes through a mechanism involving mTORC1 activation, glutaminolysis, and epigenetic remodeling. Macrophages derived from IFN-γ–trained monocytes exhibited increased glycolytic activity with enhanced cytokine and chemokine responses upon stimulation or infection. Crucially, trained macrophages had increased production of reactive oxygen species which mediated enhanced bactericidal activity against methicillin-resistant S. aureus. Furthermore, ATAC-sequencing analysis of IFN-γ trained macrophages revealed increased chromatin accessibility in regions associated with host defence. Lastly, IFN-γ training restored impaired innate responses in macrophages from individuals homozygous for the TIRAP 180L polymorphism, a genetic variant associated with increased susceptibility to infection. These findings establish IFN-γ as a potent inducer of trained immunity in human monocytes and support its potential as a host-directed strategy to strengthen antimicrobial defenses, particularly in genetically susceptible individuals and high-risk clinical contexts.
Authors
Dearbhla M. Murphy, Isabella Batten, Aoife O'Farrell, Simon R. Carlile, Sinead A. O'Rourke, Chloe Court, Brenda Morris, Gina Leisching, Gráinne Jameson, Sarah A. Connolly, Adam H. Dyer, John P. McGrath, Emma McNally, Olivia Sandby-Thomas, Anjali Yennemadi, Conor M. Finlay, Clíona Ni Cheallaigh, Jean Dunne, Cilian Ó Maoldomhnaigh, Laura E. Gleeson, Aisling Dunne, Nollaig Bourke, Reinout van Crevel, Donal J. Cox, Niall Conlon, Arjun Raj, Rachel M. McLoughlin, Joseph Keane, Sharee A. Basdeo
Abstract
CD4 T cells are essential for immunity to M. tuberculosis (Mtb), and emerging evidence indicates that IL-17-producing Th17 cells contribute to immunity to Mtb. While identifying protective T cell effector functions is important for TB vaccine design, T cell antigen specificity is also likely to be important. To identify antigens that induce protective immunity, we reasoned that, as in other pathogens, effective immune recognition drives sequence diversity in individual Mtb antigens. We previously identified Mtb genes under evolutionary diversifying selection pressure whose products we term Rare Variable Mtb Antigens (RVMA). Here, in two distinct human cohorts with recent exposure to TB, we found that RVMA preferentially induce CD4 T cells that express RoRγt and produce IL-17, in contrast to ‘classical’ Mtb antigens that induce T cells that produce IFNγ. Together with emerging evidence showing human Th17 responses are associated with prevention of progression to TB disease, our results suggest that RVMA can be valuable antigens in vaccines for those already infected with Mtb to amplify existing antigen-specific Th17 responses to prevent TB disease.
Authors
Paul Ogongo, Liya Wassie, Anthony Tran, Devin Columbus, Julia Huffaker, Lisa Sharling, Gregory Ouma, Samuel Gurrion Ouma, Kidist Bobosha, Cecilia S. Lindestam Arlehamn, Neel R. Gandhi, Sara C. Auld, Jyothi Rengarajan, Cheryl L. Day, Artur Queiroz, Mariana Araújo-Pereira, Eduardo Fukutani, Bruno B. Andrade, John D. Altman, Henry M. Blumberg, Joel D. Ernst
Abstract
BACKGROUND After identifying 2 immunomarkers of acute injury, KIM-1 and LCN2, in all kidney biopsies from 31 patients with COVID-19 pneumonia and de novo kidney dysfunction, we investigated whether circulating markers of kidney epithelial injury are common in patients with laboratory-confirmed COVID-19 who require oxygen support but do not have critical illness.METHODS We studied 196 patients admitted to 15 hospitals with moderate to severe pneumonia who were enrolled in 2 independent randomized clinical trials. We measured 41 immune mediators and markers of kidney and endothelial injury in peripheral blood in these patients within 24 hours of randomization.RESULTS We constructed a generalized linear CORIMUNO model combining serum levels of KIM-1, LCN2, IL-10, and age at hospital admission that showed high discrimination for mortality (derivation cohort: AUC = 0.82, 95% CI: 0.73–0.92; validation cohort: AUC = 0.83, 95% CI: 0.74–0.92). An early rise in circulating kidney injury markers, in the absence of acute kidney injury criteria, was markedly associated with the risk of developing a severe form of COVID-19 and death within 3 months.CONCLUSION The CORIMUNO score may be a helpful tool for risk stratification, and for the first time to our knowledge, it identifies the overlooked impact of subclinical kidney injury on pneumonia outcomes.TRIAL REGISTRATION ClinicalTrials.gov NCT04324047, NCT04324073, and NCT04331808.FUNDING This research was funded by the French Ministry of Health, Programme Hospitalier de Recherche Clinique (PHRC COVID-19–20–0151, PHRC COVID-19–20–0029), Fondation de l’Assistance Publique Hôpitaux de Paris (Alliance Tous Unis Contre le Virus), Assistance Publique Hôpitaux de Paris, and grants from the Fondation pour la Recherche Médicale (FRM) (REA202010012514) and Agence Nationale de Recherches sur le Sida and emerging infectious diseases (ANRS) (ANRS0147) from the VINTED sponsorship.
Authors
Olivia Lenoir, Florence Morin, Anouk Walter-Petrich, Léa Resmini, Mohamad Zaidan, Nassim Mahtal, Sophie Ferlicot, Victor G. Puelles, Nicola Wanner, Julien Dang, Thibaut d’Izarny-Gargas, Jana Biermann, Benjamin Izar, Stéphanie Baron, Benjamin Terrier, Ziad A. Massy, Marie Essig, Aymeric Couturier, Olivia May, Xavier Belenfant, David Buob, Isabelle Brocheriou, Hassan Izzedine, Yannis Lombardi, Hélène François, Anissa Moktefi, Vincent Audard, Aurélie Sannier, Eric Daugas, Matthieu Jamme, Guylaine Henry, Isabelle Le Monnier de Gouville, Catherine Marie, Laurence Homyrda, Céline Verstuyft, Sarah Tubiana, Ouifiya Kafif, Valentine Piquard, Maxime Dougados, Tobias B. Huber, Marine Livrozet, Jean-Sébastien Hulot, Cedric Laouénan, Jade Ghosn, France Mentré, Alexandre Karras, Yazdan Yazdanpanah, Raphaël Porcher, Philippe Ravaud, Sophie Caillat-Zucman, Xavier Mariette, Olivier Hermine, Matthieu Resche-Rigon, Pierre-Louis Tharaux, CORIMUNO-19 collaborative group
Abstract
The activation of the NLRP3 inflammasome is a pivotal step in hyperinflammation in sepsis; however, the regulatory mechanisms underlying its activation are not fully understood. In this study, we found that 14-3-3ε facilitates NLRP3 inflammasome activation by enhancing NLRP3 K63 deubiquitination and promoting its translocation to the mitochondria-associated ER membranes (MAMs) for full activation. Mass spectrometry revealed that 14-3-3ε binds to NLRP3 in macrophages during sepsis. Plasma 14-3-3ε levels were elevated in patients with sepsis and were positively associated with disease severity. 14-3-3ε promoted NLRP3 inflammasome activation by facilitating NLRP3 aggregation and NLRP3–ASC assembly. The interaction between 14-3-3ε and NLRP3 was dependent on phosphorylation at the S194 site of NLRP3 NACHT domain. The NLRP3–14-3-3ε interaction promoted K63 deubiquitination and enhanced the translocation of NLRP3 to MAMs, which is necessary for full activation of NLRP3 inflammasome. Furthermore, macrophage-conditional KO of 14-3-3ε or treatment with BV02, a 14-3-3 inhibitor, improved the survival rate and alleviated organ injuries in septic mice. Taken together, our data indicate that 14-3-3ε functions as a positive regulator of the NLRP3 inflammasome and could be a target for sepsis treatment.
Authors
Xingyu Li, Siqi Ming, Can Cao, Yating Xu, Jingxian Shu, Ning Tan, Xi Huang, Yongjian Wu
Abstract
Functional antibody responses to malaria transmission-blocking vaccines (TBVs) are assessed using the Standard Membrane Feeding Assay (SMFA). This assay quantifies percentage reduction of oocyst levels in mosquitoes fed gametocytes mixed with antisera/antibodies, referred to as transmission-reducing activity (TRA). As TBVs advance to large clinical trials, new scalable assays are needed to characterize vaccine responses. Here, we developed an epitope-specific competitive ELISA platform (P230Compete) for TBV candidate Pfs230D1, based on single-chain variable fragments (scFv) against epitopes recognized by human monoclonal antibodies with high TRA. We quantified functional epitope-specific antibody responses (F) in Phase 1 Pfs230D1-EPA/AS01 vaccine trial participants, using 171 serum samples collected at two post-vaccination timepoints. Five antibody features were examined by P230Compete including total IgG (reported as ELISA units, EUF), IgG subclasses (IgG1F, IgG3F, IgG4F), and bound complement factor C1q (C1qF). EUF and IgG1F demonstrated strong correlation and excellent prediction of TRA≥80% in logistic regression analysis (AUC of 0.81 for both assays post-dose 3, and 0.80 and 0.76 post-dose 4). Furthermore, combining EUF and IgG1F showed even better predictive performance at each timepoint. P230Compete offers a promising proxy assay to replace SMFA in late-stage Pfs230D1 trials.
Authors
Cristina A. Meehan, Matthew V. Cowles, Robert D. Morrison, Yuyan Yi, Jingwen Gu, Jen C.C. Hume, Mina P. Peyton, Issaka Sagara, Sara A. Healy, Jonathan P. Renn, Patrick E. Duffy
Abstract
Mucosal secretory IgA (sIgA) plays a central role in protecting against the invasion of respiratory pathogen via the upper respiratory tract. To understand how intranasal booster induces mucosal sIgA response in humans, we first used liquid chromatography-tandem mass spectrometry for peptide identification of immunoglobulin (MS Ig-Seq) and single-cell B-cell receptor sequencing (scBCR-seq) to identify mucosal spike-specific sIgA monoclonal antibodies (mAbs) after intranasal booster. These mucosal sIgA mAbs exhibited enhanced neutralization up to 100-fold against SARS-CoV-2 variants compared to their monomeric IgG and IgA isotypes. Deep sequencing and longitudinal analysis of B-cell receptor repertoires revealed that nasal booster re-stimulates memory B cells primed by intramuscularly vaccination to undergo IgA class switching, somatic hypermutation, and clonal expansion. Single-cell sequencing revealed that intranasal booster upregulated the expression of mucosal homing receptors in spike-specific IgA-expressing B cells. This increase coincided with a transient increase of cytokines and chemokines that facilitate B cell recruitment in the nasal mucosa. Our findings demonstrate that intranasal booster can be an effective strategy for inducing upper respiratory mucosal sIgA and establishing mucosal immune protection.
Authors
Si Chen, Zhengyuan Zhang, Zihan Lin, Li Yin, Lishan Ning, Wenming Liu, Qian Wang, Chenchen Yang, Bo Feng, Ying Feng, Yongping Wang, Hengchun Li, Ping He, Huan Liang, Yichu Liu, Zhixia Li, Bo Liu, Yang Li, Diana Boraschi, Linbing Qu, Xuefeng Niu, Nanshan Zhong, Pingchao Li, Ling Chen
Abstract
Cardiac arrhythmias increase during acute SARS-CoV-2 infection and in long COVID syndrome, by unknown mechanisms. This study explored the acute and long-term effects of COVID-19 on cardiac electrophysiology and the cardiac conduction system (CCS) in a hamster model. Electrocardiograms and subpleural pressures were recorded by telemetry for 4 weeks after SARS-CoV-2 infection, and interferon-stimulated gene expression and macrophage infiltration of the CCS were assessed at 4 days and 4 weeks postinfection. COVID-19 induced pronounced tachypnea and cardiac arrhythmias, including bradycardia and persistent atrioventricular block, though no viral protein expression was detected in the heart. Arrhythmias developed rapidly, partially reversed, and then redeveloped, indicating persistent CCS injury. COVID-19 induced cardiac cytokine expression, connexin mislocalization, and CCS macrophage remodeling. Interestingly, sterile innate immune activation by direct cardiac injection of polyinosinic:polycytidylic acid (PIC) induced arrhythmias similar to those of COVID-19. PIC strongly induced cytokine secretion and interferon signaling in hearts, human induced pluripotent stem cell–derived cardiomyocytes, and engineered heart tissues, accompanied by alterations in excitation-contraction coupling. Importantly, the pulmonary and cardiac effects of COVID-19 were blunted by JAK/STAT inhibition or a mitochondrially targeted antioxidant, indicating that SARS-CoV-2 infection indirectly leads to arrhythmias by innate immune activation and redox stress, which could have implications for long COVID syndrome.
Authors
Deepthi Ashok, Ting Liu, Misato Nakanishi-Koakutsu, Joseph Criscione, Meghana Prakash, Alexis Tensfeldt, Byunggik Kim, Bryan Ho, Julian Chow, Morgan Craney, Mark J. Ranek, Brian L. Lin, Kyriakos Papanicolaou, Agnieszka Sidor, D. Brian Foster, Hee Cheol Cho, Andrew Pekosz, Jason Villano, Deok-Ho Kim, Brian O’Rourke
Abstract
Few HIV-specific epitopes restricted by non-classical HLA-E have been described, and even less is known about the functional profile of responding CD8 T cells (CD8s). This study evaluates the functional characteristics of CD8s targeting the Gag epitope KF11 (KAFSPEVIPMF) restricted by either HLA-E (E-CD8s) or HLA-B57 (B57-CD8s). CD8s from eight people with HIV (PWH) were cocultured with KF11 peptide presented by cell lines expressing HLA-B*57:01, HLA-E*01:01 or E*01:03. CD8 responses were analyzed using scRNA-seq and scTCR-seq. Supernatants were also assessed for soluble protein profiling. HLA-I multimers were developed to identify CD8s restricted by HLA-B57 and/or HLA-E ex vivo. B57-CD8s secreted higher levels of cytotoxic cytokines such as IFNγ, whereas E-CD8s produced more chemotactic cytokines, including RANTES, CXCL10 (IP-10), and IL27, findings which were corroborated through scRNA sequencing. TCR clonotypes stimulated by KF11 were cross-restricted by HLA-B*57 and HLA-E*01/03 as demonstrated by in vitro T cell reporter assays and ex vivo multimer screening. Ex vivo CD8s were singly restricted by HLA-B57 and HLA-E, with dual restriction only observed in PWH with lower viral load. These findings demonstrate that certain HIV-specific CD8s in PWH exhibit dual restriction by HLA-B*57 and HLA-E*01/03, leading to functionally distinct immune responses depending upon the restricting allele(s).
Authors
Kevin J. Maroney, Michael A. Rose, Allisa K. Oman, Abha Chopra, Hua-Shiuan Hsieh, Zerufael Derza, Rachel Waterworth, Mark A. Brockman, Spyros A. Kalams, Anju Bansal, Paul A. Goepfert
Abstract
Urinary tract infections (UTIs) are the most common severe bacterial infections in young children, often associated with vesicoureteral reflux (VUR). To explore host genetic-microbiota interactions and their clinical implications, we analyzed the urinary microbiota (urobiota) and conducted genome-wide association studies (GWAS) for bacterial abundance traits in pediatric UTI and VUR patients from the RIVUR and CUTIE cohorts. We identified four urobiota community types based on relative abundance, characterized by the genera Enterococcus, Prevotella, Pseudomonas, and Escherichia/Shigella, and their associations with VUR, age, and toilet training. Children with VUR exhibited decreased microbial diversity and increased abundance of genera that included opportunistic pathogens, suggesting a disrupted urobiota. We detected genome-wide significant genetic associations with urinary bacterial relative abundances, in or near candidate genes including CXCL12, ABCC1, and ROBO1, which are implicated in urinary tract development and response to infection. We showed that Cxcl12 is induced 12 hours after uropathogenic bacterial infection in mouse bladder. The association with CXCL12 suggests a genetic link between UTI, VUR and cardiovascular phenotypes later in life. These findings provide the first characterization of host genetic influences on the pediatric urobiota in UTI and VUR, offering insights into the interplay between disease, host genetics and the urobiota composition.
Authors
Miguel Verbitsky, Pavan Khosla, Daniel Bivona, Atlas Khan, Yask Gupta, Heekuk Park, Tian H. Shen, Aryan Ghotra, Katherine Xu, Iman A. Ghavami, Priya Krithivasan, Jeremiah Martino, Tanya Sezin, Tze Y. Lim, Victoria Kolupaeva, Nita A. Limdi, Yuan Luo, Hakon Hakonarson, Simone Sanna-Cherchi, Krzysztof Kiryluk, Cathy L. Mendelsohn, Anne-Catrin Uhlemann, Jonathan Barasch, Ali G. Gharavi
Abstract
BACKGROUND. Fecal Microbiota Transplantation (FMT) is the most effective therapy for recurrent Clostridioides difficile infection (rCDI), yet its mechanism of action remains poorly understood. METHODS. We report the results of a clinical trial of subjects undergoing FMT therapy for rCDI (n=16), analyzing colon biopsies, plasma, peripheral blood mononuclear cells, and stool at the time of FMT and two-month follow-up. Plasma and colon biopsy samples were also collected from healthy controls for comparison with rCDI patients. Microbiome composition, colonic gene expression, and immune changes were evaluated through high-throughput sequencing and immunoprofiling via flow cytometry. RESULTS. No subjects experienced recurrence at follow-up. FMT significantly altered the intestinal microbiome but had no significant impact on the systemic immune system. In contrast, FMT promoted broad changes in colonic transcriptional profiles compared to both pre-FMT and healthy control biopsies, inhibiting genes associated with pro-inflammatory signaling and upregulating type 2 immunity and proliferative pathways (Myc and mTORC1). FMT increased expression of IL-33 and the type 2 immune EGFR family ligand amphiregulin, potentially explaining upregulation of Myc and mTORC1 pathways. Spatial transcriptomics demonstrated that these changes were localized to the colonic epithelium. Comparison of transcriptional profiles with available single cell gene sets determined that post-FMT biopsies were enriched in signatures associated with proliferative cell types while repressing signatures of differentiated colonocytes. CONCLUSIONS. We conclude that FMT promotes proliferation of the colonic epithelium in rCDI patients, which may drive regeneration and protect against subsequent CDI. REGISTRATION. Clinicaltrials.gov NCT02797288. FUNDING. NIH grants R01 AI152477, R01 AI124214, and K23 AI163368.
Authors
G. Brett Moreau, Jiayi Tian, Nick R. Natale, Farha Naz, Mary K. Young, Uma Nayak, Mehmet Tanyüksel, Isaura Rigo, Gregory R. Madden, Mayuresh M. Abhyankar, Nicholas Hagspiel, Savannah Brovero, Mark Worthington, Brian Behm, Chelsea Marie, William A. Petri Jr., Girija Ramakrishnan
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