Immunology articles within Nature Communications

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  • Article
    | Open Access

    Oncolytic viruses promote an inflammatory response and elicit anti-tumor immunity. Here the authors show, unexpectedly, that the oncolytic virus, VSVIFNβ, induces type I interferon responses that, when combined with chimeric antigen receptor (CAR) T therapy, lead to the attrition of both CAR T and conventional T cells, thus dampening their anti-tumor activity.

    • Laura Evgin
    • , Amanda L. Huff
    •  & Richard Vile

  • Article
    | Open Access

    Emergence of ABL1 kinase inhibitor resistant clones may cause disease relapse in Philadelphia chromosome-positive acute lymphoblastic leukemia. Here, the authors show interleukin 7 receptor (IL7R) signaling to contribute to this resistance mechanism, and that targeting the IL7R pathway may suppress incurable drug-resistant leukemia forms.

    • Hend Abdelrasoul
    • , Anila Vadakumchery
    •  & Hassan Jumaa

  • Article
    | Open Access

    The mechanisms underlying immunpathologies in dengue virus (DENV) infection are incompletely understood. Here, authors show that TLR2 recognizes DENV particles inducing cytokine expression and activating vascular endothelium cells in vitro, and that TLR2 expression on monocytes correlates with disease severity in patients.

    • José A. Aguilar-Briseño
    • , Vinit Upasani
    •  & Izabela A. Rodenhuis-Zybert

  • Article
    | Open Access

    Information on immune receptor repertoire provides important insights on disease progression and therapy development, but can be expensive and time-consuming to obtain. Here the authors report ImReP, a computational method that can extract detailed immune repertoire information from existing tissue-specific RNA sequencing data.

    • Igor Mandric
    • , Jeremy Rotman
    •  & Serghei Mangul

  • Article
    | Open Access

    B cell development is tightly regulated in a stepwise manner to ensure proper generation of repertoire diversity via somatic gene rearrangements. Here, the authors show that a transcription factor, Erg, functions at the earliest stage to critically control two downstream factors, Ebf1 and Pax5, for modulating this gene rearrangement process.

    • Ashley P. Ng
    • , Hannah D. Coughlan
    •  & Warren S. Alexander

  • Article
    | Open Access

    Here, Kuroda et al. screen a library of nearly 400 interferon-stimulated genes (ISGs) and identify several ISGs that inhibit Ebola virus entry, viral transcription/replication, or virion formation. The study provides insights into interactions between Ebola and the host cells.

    • Makoto Kuroda
    • , Peter J. Halfmann
    •  & Yoshihiro Kawaoka

  • Article
    | Open Access

    Immune cells are important regulators of adipose tissue function, including adaptive thermogenesis. Here the authors show that mice with Krüppel-like factor 3 (KLF3) deficiency in bone marrow-derived cells have increased adipose tissue beiging which may at least in part be due to altered eosinophil paracrine signaling.

    • Alexander J. Knights
    • , Emily J. Vohralik
    •  & Kate G. R. Quinlan

  • Article
    | Open Access

    Developing broadly applicable neoantigen-directed adoptive cell therapies (ACTs) is challenging because each cancer patient has an unique neoantigen repertoire. Here, the authors present the crystal structures of tumor-specific T cell receptors (TCRs) that recognize a shared neoepitope arising from the R175H driver mutation in the p53 oncogene (p53R175H) alone and bound to p53R175H–HLA-A2, which are of interest for the structure-guided design of TCRs to improve T cell potency for ACT.

    • Daichao Wu
    • , D. Travis Gallagher
    •  & Roy A. Mariuzza

  • Article
    | Open Access

    Type I IFN has apposing effects in neuromyelitis optica spectrum disorder (NMOSD) and multiple sclerosis (MS). Here the authors perform molecular profiling of NMOSD patients and mouse mechanistic experiments of neuro-inflammation to show that IFN-I stimulates pathogenic Th17 via IL-6 production by B cells.

    • Agnieshka M. Agasing
    • , Qi Wu
    •  & Robert C. Axtell

  • Article
    | Open Access

    Fatty acid oxidation (FAO) is thought to contribute to high spare respiratory capacity (SRC), which in turn affects CD8+ T cell function. Here, the authors show that ex vivo virtual memory T cells (and not antigen experienced memory T cells) have high SRC, a metabolic state that it is affected by ageing and IL-15 signalling and not directly by FAO.

    • Kylie M. Quinn
    • , Tabinda Hussain
    •  & Nicole L. La Gruta

  • Article
    | Open Access

    Splenic marginal zone macrophages can establish immune tolerance and limit the development of systemic lupus erythematosus (SLE). Here the authors show that these cells do this by clearing apoptotic cells, and defects in these cells result in the generation of self-reactive double negative T cells that are known to contribute to SLE pathogenesis.

    • Hao Li
    • , Iannis E. Adamopoulos
    •  & George C. Tsokos

  • Article
    | Open Access

    An effective vaccine for human papillomavirus (HPV) needs to protect from several genotypes. Here, Wang et al. provide a strategy to produce single capsomere-hybrid virus-like particle (chVLP) composed of capsomers of different genotypes and show that a nona-type chVLP induces similar levels of neutralizing antibodies as an approved HPV vaccine.

    • Daning Wang
    • , Xinlin Liu
    •  & Shaowei Li

  • Article
    | Open Access

    REV7 has emerged as a critical regulator of DNA double-strand breaks repair. Here, the authors show that REV7 is crucial for both antibody class switch recombination and somatic hypermutation in activated B cells, in addition to their survival upon AID-deamination.

    • Dingpeng Yang
    • , Ying Sun
    •  & Fei-Long Meng

  • Article
    | Open Access

    Mutations that affect Treg cell function can cause lethal autoimmunity, but whether correcting these mutations can reverse established disease is unclear. Here, the authors correct Treg cell-specific Brg1 mutation in a minor fraction of Treg cells, which supercharges these cells to rescue mice from otherwise fatal IPEX-like autoimmunity.

    • Yongqin Li
    • , Yuxin Chen
    •  & Tian Chi

  • Article
    | Open Access

    Anti-Ly6G or ant-Gr1 antibodies are commonly used to deplete neutrophils in vivo. Here the authors provide mechanistic insight into why these approaches may not specifically or durably reduce the number of neutrophils in mice, and also present a new method that overcomes these limitations to have potentially wide applicability in experimental studies.

    • Gael Boivin
    • , Julien Faget
    •  & Etienne Meylan

  • Article
    | Open Access

    T cell receptors (TCR) are internalized when activated by their ligands. Here the authors show that the internalized TCRs are localized to endosomes expressing IRAP and Syntaxin 6 to maintain intracellular signalling capacity, whose importance is shown by the absence of efficient polyclonal anti-tumour response in mice with T-specific conditional deletion of IRAP.

    • Irini Evnouchidou
    • , Pascal Chappert
    •  & Loredana Saveanu

  • Article
    | Open Access

    White adipose inflammation can occur in obesity and is at least in part mediated by inflammatory immune cells. Here the authors show that the Type I Interferon/Interferon alpha-beta receptor axis promotes an inflammatory, glycolysis associated adipocyte phenotype.

    • Calvin C. Chan
    • , Michelle S. M. A. Damen
    •  & Senad Divanovic

  • Article
    | Open Access

    Immunopeptidomics allows identifying the cellular repertoire of MHC-bound peptides, but quantifying them remains challenging. Here, the authors present a method to efficiently generate internal peptide MHC standards and calibration curves, facilitating relative and absolute quantitative immunopeptidomics.

    • Lauren E. Stopfer
    • , Joshua M. Mesfin
    •  & Forest M. White

  • Article
    | Open Access

    Characterisation of the human antibody response to SARS-CoV-2 can help the design of serological tests and vaccines. Here, the authors identify two linear epitopes in SARS-CoV-2 spike protein that elicit neutralising antibodies in several patients and could thus be useful for serology and vaccine development.

    • Chek Meng Poh
    • , Guillaume Carissimo
    •  & Lisa F. P. Ng

  • Article
    | Open Access

    Milk breastfeeding and prebiotic-supplemented formulas have varying effects on the infant gut microbiome. Here, in a randomized controlled clinical trial, the authors investigate the effects of a Lactobacillus paracasei-fermented formula on the immune defense mechanisms, microbiota and its metabolome in full term infants.

    • Paola Roggero
    • , Nadia Liotto
    •  & Maria Rescigno

  • Article
    | Open Access

    Over 100 million of opioid prescriptions are issued yearly in the USA alone, but the impact of opioid use on the immune system is barely characterized. Here the authors report antiviral immune response is blunted in several types of blood cells from opioid-dependent individuals, and when healthy donor cells are exposed to morphine in a dish.

    • Tanya T. Karagiannis
    • , John P. Cleary Jr
    •  & Christine S. Cheng

  • Article
    | Open Access

    Poly-functional helper T cells can have a stronger effect than mono-functional T cells, but whether the response is qualitatively different is not clear. Here the authors show that a population of IL-17+IL-22+, but not single IL-22+, CD4+ T cells are induced by TGF-β, enriched in patients with colorectal cancer (CRC) and drive CRC progression in mice.

    • Laura Garcia Perez
    • , Jan Kempski
    •  & Samuel Huber

  • Article
    | Open Access

    Memory B cells are important for protecting the host from pathogen rechallenge, but their properties and locations remain ill-defined. Here the authors show, using single-cell transcriptomics and repertoire analyses, that mouse spleen and bone marrow host distinct populations of isotype-switched memory B cells to potentially optimize for rapid recall responses.

    • René Riedel
    • , Richard Addo
    •  & Andreas Radbruch

  • Article
    | Open Access

    The characteristics of immune cells in the peripheral nervous system (PNS) are not fully understood. Here the authors examine the transcriptomic profile and ontogeny of macrophages from the PNS, show they are derived from both embryonic and hematopoietic precursors, and that they have some shared features with microglia.

    • Peter L. Wang
    • , Aldrin K. Y. Yim
    •  & Gwendalyn J. Randolph

  • Article
    | Open Access

    There is currently no licensed SARS-CoV-2 vaccine. Here, the authors generate an optimized DNA vaccine candidate encoding the SARS-CoV-2 spike antigen, demonstrating induction of specific T cells and neutralizing antibody responses in mice and guinea pigs. These initial results support further development of this vaccine candidate.

    • Trevor R. F. Smith
    • , Ami Patel
    •  & Kate E. Broderick

  • Article
    | Open Access

    Nodular lymphocyte-predominant Hodgkin lymphoma with IgD+ lymphocyte-predominant (LP) cells is a rare clinical distinct lymphoma subset of B-cell origin. Here the authors show that antigens expressed by Moraxella catarrhalis are recognized by B cell receptors of IgD+ LP cells, suggesting the contribution of chronic antigen stimulation to lymphomagenesis.

    • Lorenz Thurner
    • , Sylvia Hartmann
    •  & Michael Pfreundschuh

  • Article
    | Open Access

    Type 1 diabetes is associated with autoimmune destruction of pancreatic beta-cells. Here the authors compose a large-scale electron microscopy image data base of pancreatic organ donor tissue to enable data mining and further understanding of the disease.

    • Pascal de Boer
    • , Nicole M. Pirozzi
    •  & Ben N. G. Giepmans

  • Article
    | Open Access

    Vaccine mismatch and changes in antigenicity due to vaccine strain egg adaptation can affect seasonal influenza vaccine effectiveness. Here, Gouma et al. show that the egg-adapted 3c3.A H3N2 vaccine strain elicits antibodies with limited reactivity to a wildtype 3c3.A strain and currently circulating 3c2.A H3N2 strains.

    • Sigrid Gouma
    • , Madison Weirick
    •  & Scott E. Hensley

  • Article
    | Open Access

    Zika virus (ZIKV) poses a significant public health threat, but the immune landscape changes following ZIKV infection is still unclear. Here, the authors show, using flow cytometry and transcriptomic data, that ZIKV induces a multitude of immune responses, with plasmacytoid dendritic cells poised centrally to interact with other immune cell types.

    • Xiaoming Sun
    • , Stephane Hua
    •  & Xu G. Yu

  • Article
    | Open Access

    The role of sexual practice in HIV-associated gut microbiota remains poorly understood. Here, in a cohort of chronically treated HIV-infected people, the authors show microbiome signatures to be independent of sex and sexual practice and that the extent of dysbiosis correlates with nadir CD4, inflammatory markers, and comorbidities.

    • I. Vujkovic-Cvijin
    • , O. Sortino
    •  & I. Sereti

  • Article
    | Open Access

    Neutrophils mobilize rapidly and travel through the vasculature and microcirculation en masse in response to inflammatory stimuli. Here the authors use a microfluidic device and intravital microscopy to show neutrophils move through tissues in a highly ordered pattern, taking turns to file into alternate branches at bifurcations.

    • Xiao Wang
    • , Mokarram Hossain
    •  & Daniel Irimia

  • Article
    | Open Access

    Immune tolerance is mediated by the deletion of autoreactive T cells via medullary thymic epithelial cells (mTEC) and dendritic cells (DC), and by the induction of regulatory T cells (Treg). Here the authors show that mTEC receiving toll-like receptor signaling control the recruitment of CD14+Sirpα+ DC population that is capable of inducing Treg for establishing tolerance.

    • Matouš Vobořil
    • , Tomáš Brabec
    •  & Dominik Filipp

  • Article
    | Open Access

    Extracellular vesicles can carry immunoregulatory cytokines such as TGF-β. Here the authors use CD11b-deficient mice and macrophages to show that such vesicles carrying TGF-β are produced in response to Candida albicans infections and can limit the proinflammatory response partly via a positive feedback on TGF-β production by endothelial cells.

    • Luke D. Halder
    • , Emeraldo A. H. Jo
    •  & Christine Skerka

  • Article
    | Open Access

    Sepsis due to multidrug resistant pathogens is the most common cause of death in intensive care units. Here, the authors report that fecal microbiota transplant (FMT) can rescue mice from lethal sepsis of pathogens isolated from stool of a critically ill patient and show that FMT reverses the immunosuppressive effect induced by the pathogen community.

    • Sangman M. Kim
    • , Jennifer R. DeFazio
    •  & John C. Alverdy

  • Article
    | Open Access

    Inflammasome activation is a response to bacterial infection but can cause damage and spread infection. Here, the authors use live single-cell imaging to show two mechanisms by which M. tuberculosis causes damage to human macrophage cell plasma membranes, resulting in activation of the NLRP3 inflammasome, pyroptosis and release of infectious particles.

    • Kai S. Beckwith
    • , Marianne S. Beckwith
    •  & Trude H. Flo

  • Article
    | Open Access

    Upon infection with cytomegalovirus, CD8+ T cells undergo prolific expansion in a process known as memory inflation. Here the authors define a population of Tcf1 expressing cells within the inflationary pool that is critical in fuelling this process.

    • Suzanne P. M. Welten
    • , Alexander Yermanos
    •  & Annette Oxenius

  • Article
    | Open Access

    Renal macrophages (RMs) can be of bone marrow or embryonic origin, but their abundance, fate and metabolic profiles in physiological and pathogenic settings are still unclear. Here the authors show, by characterizing these two RMs in multiple transgenic mouse lines, that they exhibit distinct dynamics, homeostasis, immune activity, and metabolic properties.

    • Fengming Liu
    • , Shen Dai
    •  & Xuebin Qin

  • Article
    | Open Access

    Macrophage activation is integral to innate immunity and inflammation, and involves transcriptome remodeling leading to the rapid upregulation of pro- and anti-inflammatory effector genes. Here the authors show that the negative elongation factor (NELF) complex controls the transcription of anti-inflammatory genes through Pol II pause release.

    • Li Yu
    • , Bin Zhang
    •  & Xiaoyu Hu

  • Article
    | Open Access

    One cause of relapse in cancer patients treated with chimeric antigen receptor (CAR) T cells is the loss of CAR-targeted antigens, which is particularly common in multiple myeloma (MM). Here the authors engineer a CAR recognizing two common MM-associated antigens and demonstrate its superiority to single-antigen CARs in a mouse model of MM.

    • Eugenia Zah
    • , Eunwoo Nam
    •  & Yvonne Y. Chen

  • Article
    | Open Access

    Macrophages undergo a Warburg-like switch from oxidative phosphorylation to glycolysis in response to inflammatory stimulus. Here the authors show that fungal melanin can trigger this switch in human macrophages by sequestering calcium in the phagosome and enabling protection against Aspergillus fumigatus infection.

    • Samuel M. Gonçalves
    • , Cláudio Duarte-Oliveira
    •  & Agostinho Carvalho

  • Article
    | Open Access

    Chronic graft versus host disease (cGvHD) is a major cause of morbidity and mortality in allogeneic bone marrow transplantation. Here the authors identify a recurrent activating mTOR mutation in expanded donor T-cell clones of 3 cGvHD patients, which suggests somatic mutations may contribute to GvHD pathogenesis and opens avenues to targeted therapies.

    • Daehong Kim
    • , Giljun Park
    •  & Satu Mustjoki

  • Article
    | Open Access

    In macrophages, IL-1β secretion is mediated by N-GSDMD pores in the plasma membrane (PM). Here the authors show that in neutrophils, IL-1β secretion occurs in the absence of PM pores, via autophagosomes; N-GSDMD does not traffic to PM but to azurophilic granules, thereby releasing neutrophil elastase which cleaves further N-GSDMD into alternative fragments.

    • Mausita Karmakar
    • , Martin Minns
    •  & Eric Pearlman

  • Article
    | Open Access

    Immune infiltration provides critical information for health and disease, yet it is unclear what factors influence infiltration levels. Here, the authors analyze human tissue transcriptomes from the Genotype-Tissue Expression project to find infiltration patterns regulated by age, sex and host genetic information.

    • Andrew R. Marderstein
    • , Manik Uppal
    •  & Olivier Elemento

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