Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors

A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers

(2022) Ken-ichi Hanada et al.   CANCER CELL

CAR T cell killing requires the IFNγR pathway in solid but not liquid tumours

(2022) Rebecca C. Larson et al.   NATURE

Tuning T cell receptor sensitivity through catch bond engineering

(2022) Xiang Zhao et al.   SCIENCE

Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma

(2021) Giacomo Oliveira et al.   NATURE

Sensitive identification of neoantigens and cognate TCRs in human solid tumors

(2021) Marion Arnaud et al.   NATURE BIOTECHNOLOGY

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy

(2020) Greta Giordano-Attianese et al.   NATURE BIOTECHNOLOGY

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

TRM integrins CD103 and CD49a differentially support adherence and motility after resolution of influenza virus infection

(2020) Emma C. Reilly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-affinity oligoclonal TCRs define effective adoptive T cell therapy targeting mutant KRAS-G12D

(2020) Malcolm J. W. Sim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CXCR3 Ligands in Cancer and Autoimmunity, Chemoattraction of Effector T Cells, and Beyond

(2020) Nathan Karin   Frontiers in Immunology

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing

(2020) Timothy J. O’Donnell et al.   Cell Systems

Tumor infiltrating lymphocytes (TIL) therapy in metastatic melanoma: boosting of neoantigen-specific T cell reactivity and long-term follow-up

(2020) Joost H van den Berg et al.   Journal for ImmunoTherapy of Cancer

Biophysicochemical motifs in T cell receptor sequences distinguish repertoires from tumor-infiltrating lymphocytes and adjacent healthy tissue

(2019) Jared Ostmeyer et al.   CANCER RESEARCH

Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy

(2019) Yong-Chen Lu et al.   Cancer Immunology Research

A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancreatic Adenocarcinoma—A Proof of Antigen Discovery Feasibility in Three Patients

(2019) Michal Bassani-Sternberg et al.   Frontiers in Immunology

Preclinical evaluation of an affinity-enhanced MAGE-A4-specific T-cell receptor for adoptive T-cell therapy

(2019) Joseph P Sanderson et al.   OncoImmunology

Immune recognition of somatic mutations leading to complete durable regression in metastatic breast cancer

(2018) Nikolaos Zacharakis et al.   NATURE MEDICINE

TCRmodel: high resolution modeling of T cell receptors from sequence

(2018) Ragul Gowthaman et al.   NUCLEIC ACIDS RESEARCH

Sensitive and frequent identification of high avidity neo-epitope specific CD8+ T cells in immunotherapy-naive ovarian cancer

(2018) Sara Bobisse et al.   Nature Communications

InForm software: a semi-automated research tool to identify presumptive human hepatic progenitor cells, and other histological features of pathological significance

(2018) Anne S. Kramer et al.   Scientific Reports

Cancer Neoantigens

(2018) Ton N. Schumacher et al.   Annual Review of Immunology

Prediction of neoepitopes from murine sequencing data

(2018) Anne-Mette Bjerregaard et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

(2018) Wouter Scheper et al.   NATURE MEDICINE

Leveraging TCR Affinity in Adoptive Immunotherapy against Shared Tumor/Self-Antigens

(2018) Aaron M. Miller et al.   Cancer Immunology Research

CD49a Expression Defines Tissue-Resident CD8 + T Cells Poised for Cytotoxic Function in Human Skin

(2017) Stanley Cheuk et al.   IMMUNITY

In silicoand cell-based analyses reveal strong divergence between prediction and observation of T-cell–recognized tumor antigen T-cell epitopes

(2017) Julien Schmidt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Treatment of metastatic uveal melanoma with adoptive transfer of tumour-infiltrating lymphocytes: a single-centre, two-stage, single-arm, phase 2 study

(2017) Smita S Chandran et al.   LANCET ONCOLOGY

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer

(2017) Vinod P. Balachandran et al.   NATURE

Effects of thymic selection on T cell recognition of foreign and tumor antigenic peptides

(2017) Jason T. George et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

(2017) Martin Lauss et al.   Nature Communications

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity

(2017) Michal Bassani-Sternberg et al.   PLoS Computational Biology

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

(2017) Anne-Mette Bjerregaard et al.   Frontiers in Immunology

Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity

(2016) Michael Rasmussen et al.   JOURNAL OF IMMUNOLOGY

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

(2016) Alena Gros et al.   NATURE MEDICINE

T-Cell Transfer Therapy Targeting Mutant KRAS in Cancer

(2016) Eric Tran et al.   NEW ENGLAND JOURNAL OF MEDICINE

Control of the negative IREStrans-acting factor KHSRP by ubiquitination

(2016) Yu-An Kung et al.   NUCLEIC ACIDS RESEARCH

Durable Complete Response from Metastatic Melanoma after Transfer of Autologous T Cells Recognizing 10 Mutated Tumor Antigens

(2016) T. D. Prickett et al.   Cancer Immunology Research

Current tools for predicting cancer-specific T cell immunity

(2016) David Gfeller et al.   OncoImmunology

Identification of Rare High-Avidity, Tumor-Reactive CD8+ T Cells by Monomeric TCR-Ligand Off-Rates Measurements on Living Cells

(2015) M. Hebeisen et al.   CANCER RESEARCH

Neoantigens in cancer immunotherapy

(2015) T. N. Schumacher et al.   SCIENCE

Identifying Individual T Cell Receptors of Optimal Avidity for Tumor Antigens

(2015) Michael Hebeisen et al.   Frontiers in Immunology

Transient protein-protein interface prediction: datasets, features, algorithms, and the RAD-T predictor

(2014) Calem J Bendell et al.   BMC BIOINFORMATICS

Efficient Identification of Mutated Cancer Antigens Recognized by T Cells Associated with Durable Tumor Regressions

(2014) Y.-C. Lu et al.   CLINICAL CANCER RESEARCH

SHP-1 phosphatase activity counteracts increased T cell receptor affinity

(2013) Michael Hebeisen et al.   JOURNAL OF CLINICAL INVESTIGATION

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

(2013) Lucas Gregorio Nivón et al.   PLoS One

TCR-Ligand koff Rate Correlates with the Protective Capacity of Antigen-Specific CD8+ T Cells for Adoptive Transfer

(2013) M. Nauerth et al.   Science Translational Medicine

Getting Personal with Neoantigen-Based Therapeutic Cancer Vaccines

(2013) N. Hacohen et al.   Cancer Immunology Research

Functional Avidity: A Measure to Predict the Efficacy of Effector T Cells?

(2012) Selena Viganò et al.   Clinical & Developmental Immunology

Different affinity windows for virus and cancer-specific T-cell receptors: Implications for therapeutic strategies

(2012) Milos Aleksic et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Interplay between T Cell Receptor Binding Kinetics and the Level of Cognate Peptide Presented by Major Histocompatibility Complexes Governs CD8+T Cell Responsiveness

(2012) Melita Irving et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reversible Major Histocompatibility Complex I-Peptide Multimers Containing Ni2+-Nitrilotriacetic Acid Peptides and Histidine Tags Improve Analysis and Sorting of CD8+T Cells

(2011) Julien Schmidt et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SwissParam: A fast force field generation tool for small organic molecules

(2011) Vincent Zoete et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evidence for a TCR Affinity Threshold Delimiting Maximal CD8 T Cell Function

(2010) D. A. Schmid et al.   JOURNAL OF IMMUNOLOGY

MM-GBSA binding free energy decomposition and T cell receptor engineering

(2010) V. Zoete et al.   JOURNAL OF MOLECULAR RECOGNITION

Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

(2009) Daniel J Mandell et al.   NATURE METHODS

T-cell receptor binding affinities and kinetics: impact on T-cell activity and specificity

(2008) Jennifer D. Stone et al.   IMMUNOLOGY