☆ 4.8 Review

Antigen-specificity measurements are the key to understanding T cell responses

FRONTIERS IN IMMUNOLOGY (2023)

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Thymic development of unconventional T cells: how NKT cells, MAIT cells and γδ T cells emerge

Daniel G. Pellicci et al.

NATURE REVIEWS IMMUNOLOGY (2020)

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Clonal expansion of innate and adaptive lymphocytes

Nicholas M. Adams et al.

NATURE REVIEWS IMMUNOLOGY (2020)

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T cell receptor β repertoires as novel diagnostic markers for systemic lupus erythematosus and rheumatoid arthritis

Xiao Liu et al.

ANNALS OF THE RHEUMATIC DISEASES (2019)

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Clonal Vγ6+Vδ4+ T cells promote IL-17-mediated immunity against Staphylococcus aureus skin infection

Mark C. Marchitto et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity

Neerja Thakkar et al.

BMC BIOINFORMATICS (2019)

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NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline

Ryan O. Schenck et al.

BMC BIOINFORMATICS (2019)

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Bystander responses impact accurate detection o f murine and human antigen-specific CD8+ T cells

Matthew D. Martin et al.

JOURNAL OF CLINICAL INVESTIGATION (2019)

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Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires

Sofie Gielis et al.

FRONTIERS IN IMMUNOLOGY (2019)

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Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

Hanjie Li et al.

CELL (2019)

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The Immune Epitope Database (IEDB): 2018 update

Randi Vita et al.

NUCLEIC ACIDS RESEARCH (2019)

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Is TCR/pMHC Affinity a Good Estimate of the T-cell Response? An Answer Based on Predictions From 12 Phenotypic Models

Jesus Galvez et al.

FRONTIERS IN IMMUNOLOGY (2019)

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Host Transcriptomics as a Tool to Identify Diagnostic and Mechanistic Immune Signatures of Tuberculosis

Julie G. Burel et al.

FRONTIERS IN IMMUNOLOGY (2019)

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ImmunoMap: A Bioinformatics Tool for T-cell Repertoire Analysis

John-William Sidhom et al.

CANCER IMMUNOLOGY RESEARCH (2018)

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B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle

Simone Rizzetto et al.

BIOINFORMATICS (2018)

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Human blood MAIT cell subsets defined using MR1 tetramers

Nicholas A. Gherardin et al.

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Disease-driving CD4+ T cell clonotypes persist for decades in celiac disease

Louise F. Risnes et al.

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Transcriptomic Analysis of CD4+ T Cells Reveals Novel Immune Signatures of Latent Tuberculosis

Julie G. Burel et al.

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HLA-DRB1 Shared Epitope Alleles and Disease Activity Are Correlated with Reduced T Cell Receptor Repertoire Diversity in CD4+T Cells in Rheumatoid Arthritis

Keiichi Sakurai et al.

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An Efficient Single-Cell RNA-Seq Approach to Identify Neoantigen-Specific T Cell Receptors

Yong-Chen Lu et al.

MOLECULAR THERAPY (2018)

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Personalized vaccines for cancer immunotherapy

Ugur Sahin et al.

SCIENCE (2018)

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The human Vδ2+ T-cell compartment comprises distinct innate-like Vγ9+ and adaptive Vγ9- subsets

Martin S. Davey et al.

NATURE COMMUNICATIONS (2018)

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BALDR: a computational pipeline for paired heavy and light chain immunoglobulin reconstruction in single-cell RNA-seq data

Amit A. Upadhyay et al.

GENOME MEDICINE (2018)

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Immune Response Regulation by Antigen Receptors' Clone-Specific Nonself Parts

Hilmar Lemke

FRONTIERS IN IMMUNOLOGY (2018)

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Limited Pulmonary Mucosal-Associated Invariant T Cell Accumulation and Activation during Mycobacterium tuberculosis Infection in Rhesus Macaques

Keith D. Kauffman et al.

INFECTION AND IMMUNITY (2018)

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Identification and Analysis of Islet Antigen-Specific CD8+ T Cells with T Cell Libraries

Hideki Ogura et al.

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Type II NKT Cells: An Elusive Population With Immunoregulatory Properties

Avadhesh Kumar Singh et al.

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Predicting T cell recognition of MHC class I restricted neoepitopes

Zeynep Kosaloglu-Yalcin et al.

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Host resistance to pulmonary Mycobacterium tuberculosis infection requires CD153 expression

Michelle A. Sallin et al.

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Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition

Dina Schneidman-Duhovny et al.

PLOS ONE (2018)

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Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database

Swapnil Mahajan et al.

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Activation-induced Markers Detect Vaccine-Specific CD4+ T Cell Responses Not Measured by Assays Conventionally Used in Clinical Trials

Georgina Bowyer et al.

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BASIC: BCR assembly from single cells

Stefan Canzar et al.

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Islet-Derived CD4 T Cells Targeting Proinsulin in Human Autoimmune Diabetes

Aaron W. Michels et al.

DIABETES (2017)

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Shared αβ TCR Usage in Lungs of Sarcoidosis Patients with Lofgren's Syndrome

Angela M. Mitchell et al.

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Dense Array of Spikes on HIV-1 Virion Particles

Armando Stano et al.

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Quantifiable predictive features define epitope-specific T cell receptor repertoires

Pradyot Dash et al.

NATURE (2017)

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Identifying specificity groups in the T cell receptor repertoire

Jacob Glanville et al.

NATURE (2017)

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Antigen receptor repertoire profiling from RNA-seq data

Dmitriy A. Bolotin et al.

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Global Assessment of Dengue Virus-Specific CD4+ T Cell Responses in Dengue-Endemic Areas

Alba Grifoni et al.

FRONTIERS IN IMMUNOLOGY (2017)

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Definition of Human Epitopes Recognized in Tetanus Toxoid and Development of an Assay Strategy to Detect Ex Vivo Tetanus CD4+ T Cell Responses

Ricardo da Silva Antunes et al.

PLOS ONE (2017)

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Deep sequencing of blood and gut T-cell receptor β-chains reveals gluten-induced immune signatures in celiac disease

Dawit A. Yohannes et al.

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Novel tools to assist neoepitope targeting in personalized cancer immunotherapy

S. K. Saini et al.

ANNALS OF ONCOLOGY (2017)

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Vγ9Vδ2 T cell activation by strongly agonistic nucleotidic phosphoantigens

Morgane Moulin et al.

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Differential Recognition of Mycobacterium tuberculosis-Specific Epitopes as a Function of Tuberculosis Disease History

Thomas J. Scriba et al.

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Overview of methodologies for T-cell receptor repertoire analysis

Elisa Rosati et al.

BMC BIOTECHNOLOGY (2017)

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Evolution of MHC-based technologies used for detection of antigen-responsive T cells

Amalie Kai Bentzen et al.

CANCER IMMUNOLOGY IMMUNOTHERAPY (2017)

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Human γδ T cells are quickly reconstituted after stem-cell transplantation and show adaptive clonal expansion in response to viral infection

Sarina Ravens et al.

NATURE IMMUNOLOGY (2017)

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Successive annual influenza vaccination induces a recurrent oligoclonotypic memory response in circulating T follicular helper cells

Ramin Sedaghat Herati et al.

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Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer

Lisle E. Mose et al.

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Regulatory T Cell Specificity Directs Tolerance versus Allergy against Aeroantigens in Humans

Petra Bacher et al.

CELL (2016)

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Th1 versus Th2 T cell polarization by whole-cell and acellular childhood pertussis vaccines persists upon re-immunization in adolescence and adulthood

Tara Bancroft et al.

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Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with the allergen-specific modulation of immune reactivity

D. Hinz et al.

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Type II NKT cells: a distinct CD1d-restricted immune regulatory NKT cell subset

Suryasarathi Dasgupta et al.

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A Subset of Protective γ9δ2 T Cells Is Activated by Novel Mycobacterial Glycolipid Components

Mei Xia et al.

INFECTION AND IMMUNITY (2016)

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Characterization of T-cell Receptor Repertoire in Inflamed Tissues of Patients with Crohn's Disease Through Deep Sequencing

Christopher G. Chapman et al.

INFLAMMATORY BOWEL DISEASES (2016)

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An antigen-specific, four-color, B-cell FluoroSpot assay utilizing tagged antigens for detection

Peter Jahnmatz et al.

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Comment on A Cytokine-Independent Approach To Identify Antigen-Specific Human Germinal Center T Follicular Helper Cells and Rare Antigen-Specific CD4+ T Cells in Blood

Laura Cook et al.

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A Cytokine-Independent Approach To Identify Antigen-Specific Human Germinal Center T Follicular Helper Cells and Rare Antigen-Specific CD4+ T Cells in Blood

Jennifer M. Dan et al.

JOURNAL OF IMMUNOLOGY (2016)

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Research Techniques Made Simple: Monitoring of T-Cell Subsets using the ELISPOT Assay

Christian Moebs et al.

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Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes

Amalie Kai Bentzen et al.

NATURE BIOTECHNOLOGY (2016)

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Genetic variation in MHC proteins is associated with T cell receptor expression biases

Eilon Sharon et al.

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Prospective identification of neoantigen-specific lymphocytes in the peripheral blood of melanoma patients

Alena Gros et al.

NATURE MEDICINE (2016)

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Ultra-high-throughput sequencing of the immune receptor repertoire from millions of lymphocytes

Jonathan R. McDaniel et al.

NATURE PROTOCOLS (2016)

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Persistent donor derived Vδ4 T cell clones may improve survival for recurrent T cell acute lymphoblastic leukemia after HSCT and DLI

Ling Xu et al.

ONCOTARGET (2016)

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pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens

Jasreet Hundal et al.

GENOME MEDICINE (2016)

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A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans

Cecilia S. Lindestam Arlehamn et al.

PLOS PATHOGENS (2016)

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Targeting cancer-specific mutations by T cell receptor gene therapy

Thomas Blankenstein et al.

CURRENT OPINION IN IMMUNOLOGY (2015)

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Analysis of the functional WT1-specific T-cell repertoire in healthy donors reveals a discrepancy between CD4+ and CD8+ memory formation

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IMMUNOLOGY (2015)

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More tricks with tetramers: a practical guide to staining T cells with peptide-MHC multimers

Garry Dolton et al.

IMMUNOLOGY (2015)

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Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes

Sinu Paul et al.

JOURNAL OF IMMUNOLOGICAL METHODS (2015)

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Antigen Specificity of Type I NKT Cells Is Governed by TCR β-Chain Diversity

Garth Cameron et al.

JOURNAL OF IMMUNOLOGY (2015)

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Human CD8+ T-Cell Responses Against the 4 Dengue Virus Serotypes Are Associated With Distinct Patterns of Protein Targets

Daniela Weiskopf et al.

JOURNAL OF INFECTIOUS DISEASES (2015)

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The burgeoning family of unconventional T cells

Dale I. Godfrey et al.

NATURE IMMUNOLOGY (2015)

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The TB-specific CD4+ T cell immune repertoire in both cynomolgus and rhesus macaques largely overlap with humans

Bianca R. Mothe et al.

TUBERCULOSIS (2015)

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Type II nKT cells in inflammation, autoimmunity, microbial immunity, and cancer

Idania Marrero et al.

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High Reproducibility of ELISPOT Counts from Nine Different Laboratories

Srividya Sundararaman et al.

CELLS (2015)

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Quantitative and qualitative characterization of expanded CD4+ T cell clones in rheumatoid arthritis patients

Kazuyoshi Ishigaki et al.

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Tracking global changes induced in the CD4 T-cell receptor repertoire by immunization with a complex antigen using short stretches of CDR3 protein sequence

Niclas Thomas et al.

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Different subsets of natural killer T cells may vary in their roles in health and disease

Vipin Kumar et al.

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T-cell Receptor (TCR)-Peptide Specificity Overrides Affinity-enhancing TCR-Major Histocompatibility Complex Interactions

David K. Cole et al.

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Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity

Fei Duan et al.

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Transcriptional Profile of Tuberculosis Antigen-Specific T Cells Reveals Novel Multifunctional Features

Cecilia Lindestam Arlehamn et al.

JOURNAL OF IMMUNOLOGY (2014)

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The Role of the gamma delta T Cell in Allergic Diseases

Rui Zheng et al.

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Triple Cytokine FluoroSpot Analysis of Human Antigen-Specific IFN-γ, IL-17A and IL-22 Responses

Tomas Dillenbeck et al.

Cells (2014)

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The Adaptable Major Histocompatibility Complex (MHC) Fold: Structure and Function of Nonclassical and MHC Class I-Like Molecules

Erin J. Adams et al.

ANNUAL REVIEW OF IMMUNOLOGY, VOL 31 (2013)

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Antigen-Reactive T Cell Enrichment for Direct, High-Resolution Analysis of the Human Naive and Memory Th Cell Repertoire

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JOURNAL OF IMMUNOLOGY (2013)

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Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization

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NATURE BIOTECHNOLOGY (2013)

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Memory T Cells in Latent Mycobacterium tuberculosis Infection Are Directed against Three Antigenic Islands and Largely Contained in a CXCR3+CCR6+ Th1 Subset

Cecilia S. Lindestam Arlehamn et al.

PLOS PATHOGENS (2013)

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Selection of Self-Reactive T Cells in the Thymus

Gretta L. Stritesky et al.

ANNUAL REVIEW OF IMMUNOLOGY, VOL 30 (2012)

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CD4(+)T Cells: Differentiation and Functions

Rishi Vishal Luckheeram et al.

CLINICAL & DEVELOPMENTAL IMMUNOLOGY (2012)

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Strategy of lipid recognition by invariant natural killer T cells: 'one for all and all for one'

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New and improved methods for measuring lymphocyte proliferation in vitro and in vivo using CFSE-like fluorescent dyes

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JOURNAL OF IMMUNOLOGICAL METHODS (2012)

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MHC Class II Tetramers

Gerald T. Nepom

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Protein structure prediction from sequence variation

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Why must T cells be cross-reactive?

Andrew K. Sewell

NATURE REVIEWS IMMUNOLOGY (2012)

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γδ T cell Receptor Ligands and Modes of Antigen Recognition

Eric Champagne

ARCHIVUM IMMUNOLOGIAE ET THERAPIAE EXPERIMENTALIS (2011)

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Deep Sequencing of the Human TCRγ and TCRβ Repertoires Suggests that TCRβ Rearranges After ab and γδ T Cell Commitment

Anna M. Sherwood et al.

SCIENCE TRANSLATIONAL MEDICINE (2011)

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Interrogating the repertoire: broadening the scope of peptide-MHC multimer analysis

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NATURE REVIEWS IMMUNOLOGY (2011)

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MHC-peptide tetramers for the analysis of antigen-specific T cells

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EXPERT REVIEW OF VACCINES (2010)

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Adaptive immunity

Francisco A. Bonilla et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2010)

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Human cytomegalovirus elicits fetal γδ T cell responses in utero

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Evolving concepts of specificity in immune reactions

Herman N. Eisen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

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An αβ T Cell Receptor Structure at 2.5 Å and Its Orientation in the TCR-MHC Complex

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iNKT cell autoreactivity: what is 'self' and how is it recognized?

Laurent Gapin

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Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells

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BLOOD (2009)

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Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

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GENOME RESEARCH (2009)

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Tricks with tetramers: how to get the most from multimeric peptide-MHC

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IMMUNOLOGY (2009)

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Increasing functional avidity of TCR-redirected T cells by removing defined N-glycosylation sites in the TCR constant domain

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JOURNAL OF EXPERIMENTAL MEDICINE (2009)

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Techniques to Improve the Direct Ex Vivo Detection of Low Frequency Antigen-Specific CD8+ T Cells with Peptide-Major Histocompatibility Complex Class I Tetramers

Pratip K. Chattopadhyay et al.

CYTOMETRY PART A (2008)

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Tracking Antigen-Driven Responses by Flow Cytometry: Monitoring Proliferation by Dye Dilution

Paul K. Wallace et al.

CYTOMETRY PART A (2008)

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Multifunctional TH1 cells define a correlate of vaccine-mediated protection against Leishmania major

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Human TCR-Binding affinity is governed by MHC class restriction

David K. Cole et al.

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Patterns of somatic mutation in human cancer genomes

Christopher Greenman et al.

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Nonpeptide antigens, presentation mechanisms, and immunological memory of human Vγ2Vδ2 T cells:: discriminating friend from foe through the recognition of prenyl pyrophosphate antigens

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IMMUNOLOGICAL REVIEWS (2007)

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Human autoimmune diseases are specific antigen-driven T-cell diseases: identification of the antigens

Chris D. Platsoucas et al.

IMMUNOLOGIC RESEARCH (2007)

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Specificity on a knife-edge:: the αβ T cell receptor

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CURRENT OPINION IN STRUCTURAL BIOLOGY (2006)

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Dextramers:: New generation of fluorescent MHC class I/peptide multimers for visualization of antigen-specific CD8+ T cells

P Batard et al.

JOURNAL OF IMMUNOLOGICAL METHODS (2006)

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MHC multimer technology: current status and future prospects

AH Bakker et al.

CURRENT OPINION IN IMMUNOLOGY (2005)

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Solving the protein sequence metric problem

WR Atchley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

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Prevention of autoimmunity by targeting a distinct, noninvariant CD1d-reactive T cell population reactive to sulfatide

A Jahng et al.

JOURNAL OF EXPERIMENTAL MEDICINE (2004)

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Central memory and effector memory T cell subsets: Function, generation, and maintenance

F Sallusto et al.

ANNUAL REVIEW OF IMMUNOLOGY (2004)

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The effect of specific immunotherapy on T-cell receptor repertoire in patients with allergy to house-dust mite

K Sade et al.

ALLERGY (2003)

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Shattuck Lecture - diversity of the immune repertoire and immunoregulation

RS Schwartz

NEW ENGLAND JOURNAL OF MEDICINE (2003)

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Tracking T cells with tetramers: New tales from new tools

P Klenerman et al.

NATURE REVIEWS IMMUNOLOGY (2002)

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V beta 18.1(+) and V alpha 2.3(+) T-cell subsets are associated with house dust mite allergy in human subjects

MF Kircher et al.

JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY (2002)

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Cutting edge: A major fraction of human bone marrow lymphocytes are Th2-like CD1d-reactive T cells that can suppress mixed lymphocyte responses

MA Exley et al.

JOURNAL OF IMMUNOLOGY (2001)

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T cell receptor Vβ expression in patients with allergic asthma before and after repeated low-dose allergen inhalation

J Wahlström et al.

CLINICAL IMMUNOLOGY (2001)

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Naive CTLs require a single brief period of antigenic stimulation for clonal expansion and differentiation

MJB van Stipdonk et al.

NATURE IMMUNOLOGY (2001)

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Memory CD8+ T cell differentiation:: initial antigen encounter triggers a developmental program in naive cells

SM Kaech et al.

NATURE IMMUNOLOGY (2001)

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Antigen recognition by human γδ T cells:: pattern recognition by the adaptive immune system

CT Morita et al.

SPRINGER SEMINARS IN IMMUNOPATHOLOGY (2000)

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Evaluation of the modified ELISPOT assay for gamma interferon production in cancer patients receiving antitumor vaccines

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CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY (2000)

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