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| Open AccessAntigen presentation plays positive roles in the regenerative response to cardiac injury in zebrafish
An adequate immune response is necessary to promote heart regeneration. Here, the authors identified a link between antigen presentation, immune cells, and endocardial cells during the regenerative response to cardiac injury in the adult zebrafish.
- João Cardeira-da-Silva
- , Qianchen Wang
- & Didier Y. R. Stainier
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| Open AccessImmunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides
Abnormally expressed circular RNAs (circRNAs) represent an unexplored source of tumor-specific antigens in cancer. Here, the authors developed an immunopeptidomics workflow to identify human leukocyte antigen bound peptides specifically derived from the potential translation of these transcripts.
- Humberto J. Ferreira
- , Brian J. Stevenson
- & Michal Bassani-Sternberg
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| Open AccessThunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
Human leukocyte antigen (HLA) class I peptide ligands (HLAIps) are targets for developing vaccines and immunotherapies. Here the authors report Thunder-DDA-PASEF, an immunopeptidomics method which enhances the identification of vital HLAIps crucial for vaccine and immunotherapy development.
- David Gomez-Zepeda
- , Danielle Arnold-Schild
- & Stefan Tenzer
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| Open AccessDendritic cell-targeted therapy expands CD8 T cell responses to bona-fide neoantigens in lung tumors
Response to immune checkpoint inhibitors (ICIs) in patients with non-small cell lung cancer (NSCLC) remains suboptimal, even for tumors with elevated tumor mutational burden. Here the authors generate a model of NSCLC with enhanced mutational load, showing that, while still resistant to ICIs, hypermutated tumors become sensitive to dendritic cell-targeted therapy.
- Lucía López
- , Luciano Gastón Morosi
- & Federica Benvenuti
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| Open AccessEvidence for immune activation in pathogenesis of the HLA class II associated disease, podoconiosis
Podoconiosis is triggered by long term barefoot exposure to volcanic red clay soil. Here, Negash et al characterise the immune profile of podoconiosis patients to show this disease is associated with high levels of immune activation and inflammation.
- Mikias Negash
- , Menberework Chanyalew
- & Melanie J. Newport
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| Open AccessAssessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy
HLA-I plays a key role in triggering an immune response and predicting immune checkpoint efficacy. Here the authors develop a method for quantifying HLA-I neoantigen presentation capacity by integrating HLA-I allele divergence and neoantigens numbers, termed HAPS, to describe how immune checkpoint response may be mediated by HLA.
- Jiefei Han
- , Yiting Dong
- & Zhijie Wang
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Article
| Open AccessTumor reactive γδ T cells contribute to a complete response to PD-1 blockade in a Merkel cell carcinoma patient
Immune checkpoint blockade cancer therapy has been designed to enable tumor killing by conventional αβ T cells. Here authors show that in a Merkel cell carcinoma patient showing complete response to anti-PD-1 treatment, innate-like γδ T cells that specifically recognize the tumor cells expand, and likely contribute to therapeutic success.
- Scott C. Lien
- , Dalam Ly
- & Pamela S. Ohashi
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Article
| Open AccessHLA class I peptide polymorphisms contribute to class II DQβ0603:DQα0103 antibody specificity
Bead-based assays to assess the donor-specific antibody profile of solid organ transplant patients often produce discordant results relative to cell-based alternatives. In this study, the authors demonstrate that, for some MHC class-II-specific antibodies, discordance can be attributed to recognition of the MHC class-I-derived peptides bound to MHC class-II molecules.
- N. Remi Shih
- , Thoa Nong
- & Jar-How Lee
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Article
| Open Accessp53 suppresses MHC class II presentation by intestinal epithelium to protect against radiation-induced gastrointestinal syndrome
Radiation induced gastrointestinal syndrome is a complication of radiotherapy and the tumor suppressor p53 is implicated in protection from gastrointestinal toxicity. Here Wang and colleagues show that p53 protection against radiation-induced gastrointestinal syndrome involves intestinal stem cell function and inhibition of inflammation triggered by radiation via the IL12- p40/MHC-II axis.
- Jianming Wang
- , Chun-Yuan Chang
- & Wenwei Hu
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Article
| Open AccessBrain-to-gut trafficking of alpha-synuclein by CD11c+ cells in a mouse model of Parkinson’s disease
Despite being implicated in several neurological diseases, the gut-brain axis remains poorly understood. Here the authors describe a mechanism of communication between the brain and the gut in a Parkinson’s disease mouse model mediated by CD11c+ macrophages.
- Rhonda L. McFleder
- , Anastasiia Makhotkina
- & Chi Wang Ip
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Article
| Open AccessTOFIMS mass spectrometry-based immunopeptidomics refines tumor antigen identification
MS-based immunopeptidomics provides direct evidence for HLA peptide-antigen presentation, which is indispensable for therapeutic use. Here the authors present an ion mobility MS-based immunopeptidome workflow, largely expand benign reference databases and enables next generation tumor antigen discovery.
- Naomi Hoenisch Gravel
- , Annika Nelde
- & Juliane S. Walz
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Article
| Open AccessContinually recruited naïve T cells contribute to the follicular helper and regulatory T cell pools in germinal centers
B cell clonal expansion and affinity maturation takes place in germinal centers (GC) and is orchestrated by follicular T cells. Here authors show that naïve conventional T cells are continuously recruited to the GCs during the GC reaction and develop into follicular helper and regulatory T cells, thus quantitatively contribute to remodelling the GC overtime.
- Julia Merkenschlager
- , Riza-Maria Berz
- & Michel C. Nussenzweig
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Article
| Open AccessImmune synapse formation promotes lipid peroxidation and MHC-I upregulation in licensed dendritic cells for efficient priming of CD8+ T cells
CD4+ T cells have been shown to be important in CD8+ T cell responses through a process of DC:T cell interaction. Here the authors further characterise this DC:T cell interaction and show that after CD4+ T cell help these post-synaptic DCs have increased lipid peroxidation and increased MHC class I proteins associated with increased cross-presentation function.
- Diego Calzada-Fraile
- , Salvador Iborra
- & Francisco Sánchez-Madrid
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Article
| Open AccessDNMT and HDAC inhibition induces immunogenic neoantigens from human endogenous retroviral element-derived transcripts
Epigenetic therapies are known to synergize with immunotherapies through the de-repression of endogenous retroviral element (ERV)-encoded promoters. Here the authors identify treatment-induced neoantigens and validate their ability to induce T cell response and anti-tumor effects in vitro and in patient samples.
- Ashish Goyal
- , Jens Bauer
- & Christoph Plass
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Article
| Open AccessHydrophobic interactions dominate the recognition of a KRAS G12V neoantigen
Mutation associated neoantigens are a family of highly specific therapeutic targets for the treatment of cancer. Here, the authors describe the cryo-EM structure of an antibody bound to a neoantigen complex providing insights into the specificity of the antibody.
- Katharine M. Wright
- , Sarah R. DiNapoli
- & Sandra B. Gabelli
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| Open AccessCrystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing
The unusual crystal structures of MHC I-peptide complexes provide a visualization of the remarkable ability of the groove to adapt conformationally to bound peptides, explaining how MHC I molecules edit peptides in antigen presentation.
- Lenong Li
- , Xubiao Peng
- & Marlene Bouvier
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| Open AccessHigh-throughput characterization of HLA-E-presented CD94/NKG2x ligands reveals peptides which modulate NK cell activation
HLA-E is a highly conserved MHC-l recognized by NK and T cells. The authors characterize HLA-E-presented peptides recognized by CD94/NKG2x, identifying human and CMV-derived peptide ligands which can modulate NK cell activity when presented by HLA-E, including for selective NK cell activation.
- Brooke D. Huisman
- , Ning Guan
- & Michael E. Birnbaum
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| Open AccessRUFY3 regulates endolysosomes perinuclear positioning, antigen presentation and migration in activated phagocytes
RUFY proteins are known to regulate autophagy, cytoskeletal dynamics, migration and endosomal trafficking. Here, Char et al. show that iRUFY3 plays a role in perinuclear positioning, phagocyte migration and antigen presentation during Salmonella infection.
- Rémy Char
- , Zhuangzhuang Liu
- & Philippe Pierre
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| Open AccessMolecular mechanism of phosphopeptide neoantigen immunogenicity
Phosphorylated peptide antigens are present on cancer cells, but their role in cancer immunity is unknown. Here, the authors describe a molecular mechanism, by which a tumor-specific phosphopeptide found in acute myeloid leukemia is recognized by the human immune T cells.
- Yury Patskovsky
- , Aswin Natarajan
- & Michelle Krogsgaard
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| Open AccessUnraveling the glycosylated immunopeptidome with HLA-Glyco
Protein glycosylation plays a vital role in antigen recognition and immune modulation. Here, the authors present a computational workflow for identifying glycosylated peptides from mass spectrometry-based immunopeptidome data and investigate the properties of glycosylated MHC associated peptides.
- Georges Bedran
- , Daniel A. Polasky
- & Alexey I. Nesvizhskii
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| Open AccessAntigen recognition detains CD8+ T cells at the blood-brain barrier and contributes to its breakdown
Blood-brain barrier (BBB) breakdown and immune cell infiltration into the central nervous system are early hallmarks of multiple sclerosis. Here, the authors demonstrate that brain endothelial cells cross-present antigen to CD8+ T cells, thereby preventing their migration and initiating BBB breakdown.
- Sidar Aydin
- , Javier Pareja
- & Britta Engelhardt
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| Open AccessMolecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide
Cytotoxic lymphocytes (CTL) are important in the control of HIV and some HLA alleles are associated with protection or susceptibility to disease. Here the authors characterise an epitope where variants bind to HLA-B57 or HLA-B53 and they characterise the structural and functional TCR recognition differences.
- Xiaolong Li
- , Nishant Kumar Singh
- & Jia-huai Wang
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Article
| Open AccessCitrullination modulates antigen processing and presentation by revealing cryptic epitopes in rheumatoid arthritis
Antibodies directed against citrullinated proteins are commonly found in patients with rheumatoid arthritis. Here, the authors show that citrullination alters the peptide repertoire presented to T cells by altering protease cleavage and inducing protein destabilization, thereby exposing cryptic epitopes.
- Ashley M. Curran
- , Alexander A. Girgis
- & Erika Darrah
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Article
| Open AccessEnhancing CAR-T cell functionality in a patient-specific manner
‘Manufacturing CAR-T cells is a streamlined and highly regulated procedure involving T-cell-expansion and activation on a standardised platform. Here, the authors show that a personalized approach, taking the phenotypic attributes of individual patients’ T cells into account, leads to more efficient CAR-T cell manufacturing and better CAR-T cell functionality.
- David K. Y. Zhang
- , Kwasi Adu-Berchie
- & David J. Mooney
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Article
| Open AccessSARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19
Here, the authors report accelerated intrahost evolution of SARS-CoV-2 in an immunocompromised patient with non-Hodgkin’s lymphoma with 318 days long COVID-19, and show that changes in the viral genome resulted in escape from T cellular immune response.
- Oksana V. Stanevich
- , Evgeniia I. Alekseeva
- & Georgii A. Bazykin
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Article
| Open AccessCD1a promotes systemic manifestations of skin inflammation
Skin inflammation is often accompanied by systemic disease, yet the pathways that regulate this escalation are little known. Here authors show that transgenic expression of human CD1a in mice leads to the escalation of experimental skin inflammation and systemic inflammatory disease, and the generalized symptoms could be alleviated by blocking antibodies developed against CD1a.
- Clare S. Hardman
- , Yi-Ling Chen
- & Graham S. Ogg
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Article
| Open AccessA conserved population of MHC II-restricted, innate-like, commensal-reactive T cells in the gut of humans and mice
Interactions between the host immune response and the commensal microbiota play essential roles in health and disease. Here the authors identify a population of MHC class II, innate like, commensal reactive cells in the gut of mice and humans.
- Carl-Philipp Hackstein
- , Dana Costigan
- & Emily E. Thornton
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| Open AccessA class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry
MHC restriction depicts CD4+ T cell activation by MHC-II and CD8A+ by MHC-I, but rare T cells with mismatched MHC restriction have been reported. Here the authors use crystallography to describe features of such a mismatched TCR-MHC interaction and implicate an atypical TCR structure and TCR-MHC interface as contributing factors.
- Nishant K. Singh
- , Jesus A. Alonso
- & Brian M. Baker
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Article
| Open AccessExpanding cross-presenting dendritic cells enhances oncolytic virotherapy and is critical for long-term anti-tumor immunity
Strategies to advance T cell based immune therapies are mostly focusing on the improvement of CD8 T cell effector functions, such as cytotoxicity or recruitment to the tumor. Here authors show that by combining in situ vaccination with oncolytic Newcastle Disease Virus and Flt3L-driven dendritic cell expansion, the anti-tumor T cell response is amplified via increased antigen cross-presentation.
- Judit Svensson-Arvelund
- , Sara Cuadrado-Castano
- & Joshua D. Brody
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| Open AccessSymbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b
MR1 functions as an antigen presenting protein on cells in addition to MAIT cells. Here the authors use an early T cell-specific Bcl11b-deficient mouse that develops autoimmunity through a population of nonconventional MR1-restricted T cells and characterise their function.
- Kensuke Shibata
- , Chihiro Motozono
- & Sho Yamasaki
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Article
| Open AccessTumor factors stimulate lysosomal degradation of tumor antigens and undermine their cross-presentation in lung cancer
Dendritic cells (DC) present tumour antigens to T cells but this process is defective in the tumour microenvironment. Here the authors find that downregulation of cholesterol 25-hydroxylase underlies defective cross presentation of tumour antigens.
- Zhen Lu
- , Jinyun Chen
- & Serge Y. Fuchs
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| Open AccessAblation of CD8+ T cell recognition of an immunodominant epitope in SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.3
The T cell response to SARS-CoV-2 is important in protection from infection. Here the authors show by concentrating on a specific HLA haplotype that mutations in SARS-CoV-2 as new variants emerge can affect T cell recognition and reduce T cell responses to the virus.
- Srividhya Swaminathan
- , Katie E. Lineburg
- & Corey Smith
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| Open AccessThe type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α
The TYK2 gene is associated with development of type 1 diabetes. Here the authors show that TYK2 regulates β-cell development, but at the same time TYK2 inhibition in the islets prevents IFNα responses and enhances their survival against CD8+ T-cell cytotoxicity; representing a potent therapeutic target to halt T1D progression.
- Vikash Chandra
- , Hazem Ibrahim
- & Timo Otonkoski
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Article
| Open AccessStructural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation
The catalytic chaperone tapasin assists peptide loading onto MHC-I molecules for antigen presentation and immune recognition. Here, the authors present crystal structures that provide insights into the molecular mechanism of tapasin-mediated peptide exchange.
- Jiansheng Jiang
- , Daniel K. Taylor
- & Kannan Natarajan
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| Open AccessStructure of an MHC I–tapasin–ERp57 editing complex defines chaperone promiscuity
Adaptive immunity depends on cellular chaperone and quality control systems that are decisive for an effective presentation of foreign antigens via MHC I molecules. Here, the authors present the structure of a key chaperone-MHC I complex.
- Ines Katharina Müller
- , Christian Winter
- & Robert Tampé
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Article
| Open AccessMolecular basis of MHC I quality control in the peptide loading complex
The immune system monitors the health status of cells by surveilling fragments of foreign molecules from invaders presented on MHC I complexes at the cell surface. Here, the authors investigate the sequence of events of MHC I assembly and quality control cycle.
- Alexander Domnick
- , Christian Winter
- & Robert Tampé
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Article
| Open AccessAtypical sideways recognition of CD1a by autoreactive γδ T cell receptors
T cell receptors are generally thought to contact antigens presented in an end to end configuration. Here the authors show a geometrically alternate sideways mode of recognition of the antigen-presenting molecule CD1a by a γδ T cell receptor.
- Marcin Wegrecki
- , Tonatiuh A. Ocampo
- & Jamie Rossjohn
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Article
| Open AccessMultiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and weight regain in mice
Adipose immune cells contribute to obesity-related disease, but less is known about weight cycling. Here, authors show that weight loss reduces diabetes risk, but inflammatory adipose immune cell populations persist and may contribute to worsened diabetes risk upon weight regain.
- Matthew A. Cottam
- , Heather L. Caslin
- & Alyssa H. Hasty
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Article
| Open AccessT cell receptor and IL-2 signaling strength control memory CD8+ T cell functional fitness via chromatin remodeling
The strength and duration of interleukin-2 (IL-2) signals is known to regulate T cell memory. Here the authors show that T cell receptor signalling strength controls the requirement for IL-2 signals to form CD8+ T cell memory with high functional activity and a wide range of genes with open chromatin regions.
- Shu Shien Chin
- , Erik Guillen
- & Grégoire Lauvau
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Article
| Open AccessUbiquitin-like protein 3 (UBL3) is required for MARCH ubiquitination of major histocompatibility complex class II and CD86
Regulated trafficking of major histocompatibility complex class II and CD86 is a prerequisite of antigen presenting cell functionality. Authors show here that ubiquitin-like protein 3 is critically involved in the ubiquitination process that controls trafficking, with wide-ranging immunological consequences.
- Haiyin Liu
- , Kayla R. Wilson
- & Justine D. Mintern
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Article
| Open AccessMesenchymal stem cells transfer mitochondria to allogeneic Tregs in an HLA-dependent manner improving their immunosuppressive activity
Regulatory T (Treg) cells and mesenchymal stem cells (MSCs) are both cell populations capable of immune tolerance induction. Here the authors show that the transfer of mitochondria from mesenchymal stem cells to allogeneic Treg cells in an HLA-dependent manner results in enhanced immunosuppressive functions of Treg cells.
- Karolina Piekarska
- , Zuzanna Urban-Wójciuk
- & Natalia Maria Marek-Trzonkowska
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Article
| Open AccessCD4 and CD8 co-receptors modulate functional avidity of CD1b-restricted T cells
CD4 and CD8 co-receptors are routinely used to define distinct functional and phenotypic lineages of T cells. Here the authors show CD4 and CD8 also modulate the functional avidity of the CD1b-restricted response to mycobacterial lipid antigens
- Charlotte A. James
- , Yuexin Xu
- & Chetan Seshadri
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Article
| Open AccessSARS-CoV-2 inhibits induction of the MHC class I pathway by targeting the STAT1-IRF1-NLRC5 axis
The presentation of viral antigens to T cells via the MHC molecules is a critical component of the host response to viral infection. Here the authors suggest SARS-CoV-2 possesses the immune evasion strategy against the MHC class I pathway by targeting key transcriptional regulators.
- Ji-Seung Yoo
- , Michihito Sasaki
- & Koichi S. Kobayashi
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Article
| Open AccessSpecialized transendothelial dendritic cells mediate thymic T-cell selection against blood-borne macromolecules
T cells are selected in the thymus, through interaction with self-antigens, to remove autoreactive cells. Here the authors show that a specialized thymic dendritic cell subset juxtaposes to microvessels, requires CX3CR1/CX3CL1 for this positioning, and has processes extruding into the blood stream to sample soluble macromolecules and assist in T cell selection.
- Elisabeth H. Vollmann
- , Kristin Rattay
- & Ulrich H. von Andrian
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Article
| Open AccessAntigen presentation by lung epithelial cells directs CD4+ TRM cell function and regulates barrier immunity
The maintenance of T resident memory (TRM) cells within pulmonary tissues is incompletely understood. Here the authors show that antigen presentation by lung epithelial cells maintains function and phenotype of pulmonary TRM cells within specific locational niches.
- Anukul T. Shenoy
- , Carolina Lyon De Ana
- & Joseph P. Mizgerd
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Article
| Open AccessCas9-derived peptides presented by MHC Class II that elicit proliferation of CD4+ T-cells
There have been reports of immune responses against Cas9 which may impair clinical use. Here the authors scan a cohort comparable to the North American population vis-à-vis distribution of MHC-II variants to identify Cas9 peptides presented by MHC-II proteins and can stimulate CD4 + T-cells.
- Vijaya L. Simhadri
- , Louis Hopkins
- & Zuben E. Sauna
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Article
| Open AccessInterferon lambda 4 impairs hepatitis C viral antigen presentation and attenuates T cell responses
A genetic variant in the IFN-lambda 4 gene has been associated with poor hepatitis C virus prognosis but it is not clear how this functions. Here the authors show that IFN-lambda 4 promotes ER stress and inhibits presentation of HCV epitopes to CD8+ T cells.
- Qian Chen
- , Mairene Coto-Llerena
- & Markus H. Heim
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Article
| Open AccessHuman T cells engineered with a leukemia lipid-specific TCR enables donor-unrestricted recognition of CD1c-expressing leukemia
Leukaemia therapy may benefit from the use of antigens that are less restricted to individual donors. Here the authors engineered T cells with a TCR specific for a CD1c restricted lipid leukaemia antigen and show that they can protect against disease progression in mouse leukaemia xenograft models.
- Michela Consonni
- , Claudio Garavaglia
- & Giulia Casorati
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Article
| Open AccessFcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity
Neutrophils are versatile immune cells that may also serve as antigen-presenting cells (APC). Here the authors show that engaging FcγRs on neutrophils with immune complexes or an anti-FcγR-antigen conjugate induces neutrophil APC with comparable functions as classical dendritic cells, and with therapeutic potentials for cancer and infectious diseases.
- Vijayashree Mysore
- , Xavier Cullere
- & Tanya N. Mayadas