Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

(2021) Kevin Litchfield et al.   CELL

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Identification and Validation of T-cell Receptors Targeting RAS Hotspot Mutations in Human Cancers for Use in Cell-based Immunotherapy

(2021) Noam Levin et al.   CLINICAL CANCER RESEARCH

Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

(2021) Justina X. Caushi et al.   NATURE

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

(2021) Giacomo Oliveira et al.   NATURE

The T cell receptor repertoire of tumor infiltrating T cells is predictive and prognostic for cancer survival

(2021) Sara Valpione et al.   Nature Communications

Direct identification of neoantigen-specific TCRs from tumor specimens by high-throughput single-cell sequencing

(2021) Yong-Chen Lu et al.   Journal for ImmunoTherapy of Cancer

Neoantigen-driven B cell and CD4 T follicular helper cell collaboration promotes anti-tumor CD8 T cell responses

(2021) Can Cui et al.   CELL

Cancer statistics, 2020

(2020) Rebecca L. Siegel et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

(2020) Rita Cabrita et al.   NATURE

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

(2020) Hanjie Li et al.   CELL

Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer

(2020) David Y. Oh et al.   CELL

Rapid Identification and Evaluation of Neoantigen-reactive T-Cell Receptors From Single Cells

(2020) Biman C. Paria et al.   JOURNAL OF IMMUNOTHERAPY

Shared Immunogenic Poly-Epitope Frameshift Mutations in Microsatellite Unstable Tumors

(2020) Vladimir Roudko et al.   CELL

Stem-like CD8 T cells mediate response of adoptive cell immunotherapy against human cancer

(2020) Sri Krishna et al.   SCIENCE

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2019) Moshe Sade-Feldman et al.   CELL

Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade

(2019) Brian C. Miller et al.   NATURE IMMUNOLOGY

Type I interferon induces CXCL13 to support ectopic germinal center formation

(2019) Alice E. Denton et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

(2019) Suhas Vasaikar et al.   CELL

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

TOX is a critical regulator of tumour-specific T cell differentiation

(2019) Andrew C. Scott et al.   NATURE

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers

(2019) Maria R. Parkhurst et al.   Cancer Discovery

MHC-II neoantigens shape tumour immunity and response to immunotherapy

(2019) Elise Alspach et al.   NATURE

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium

(2019) Dmitry V Bagaev et al.   NUCLEIC ACIDS RESEARCH

An intra-tumoral niche maintains and differentiates stem-like CD8 T cells

(2019) Caroline S. Jansen et al.   NATURE

Antigen Identification for Orphan T Cell Receptors Expressed on Tumor-Infiltrating Lymphocytes

(2018) Marvin H. Gee et al.   CELL

A PDX/Organoid Biobank of Advanced Prostate Cancers Captures Genomic and Phenotypic Heterogeneity for Disease Modeling and Therapeutic Screening

(2018) Michael L. Beshiri et al.   CLINICAL CANCER RESEARCH

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

(2018) Yong-Chen Lu et al.   MOLECULAR THERAPY

Chimeric Antigen Receptor Therapy

(2018) Carl H. June et al.   NEW ENGLAND JOURNAL OF MEDICINE

Co-expression of CD39 and CD103 identifies tumor-reactive CD8 T cells in human solid tumors

(2018) Thomas Duhen et al.   Nature Communications

Bystander CD8+ T cells are abundant and phenotypically distinct in human tumour infiltrates

(2018) Yannick Simoni et al.   NATURE

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

(2018) Derin B. Keskin et al.   NATURE

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

(2018) Wouter Scheper et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Isolation of T-Cell Receptors Specifically Reactive with Mutated Tumor-Associated Antigens from Tumor-Infiltrating Lymphocytes Based on CD137 Expression

(2016) Maria Parkhurst et al.   CLINICAL CANCER RESEARCH

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Tumor- and Neoantigen-Reactive T-cell Receptors Can Be Identified Based on Their Frequency in Fresh Tumor

(2016) A. Pasetto et al.   Cancer Immunology Research

Prospective Derivation of a Living Organoid Biobank of Colorectal Cancer Patients

(2015) Marc van de Wetering et al.   CELL

Regulatory T Cells in Tumor-Associated Tertiary Lymphoid Structures Suppress Anti-tumor T Cell Responses

(2015) Nikhil S. Joshi et al.   IMMUNITY

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors

(2014) Alena Gros et al.   JOURNAL OF CLINICAL INVESTIGATION

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

Cardiovascular toxicity and titin cross-reactivity of affinity-enhanced T cells in myeloma and melanoma

(2013) G. P. Linette et al.   BLOOD

Tumor Exome Analysis Reveals Neoantigen-Specific T-Cell Reactivity in an Ipilimumab-Responsive Melanoma

(2013) Nienke van Rooij et al.   JOURNAL OF CLINICAL ONCOLOGY

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells

(2013) Paul F Robbins et al.   NATURE MEDICINE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Tumor Regression in Patients With Metastatic Synovial Cell Sarcoma and Melanoma Using Genetically Engineered Lymphocytes Reactive With NY-ESO-1

(2011) Paul F. Robbins et al.   JOURNAL OF CLINICAL ONCOLOGY

Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions

(2011) N. Halko et al.   SIAM REVIEW

Adoptive transfer of syngeneic T cells transduced with a chimeric antigen receptor that recognizes murine CD19 can eradicate lymphoma and normal B cells

(2010) J. N. Kochenderfer et al.   BLOOD

Case Report of a Serious Adverse Event Following the Administration of T Cells Transduced With a Chimeric Antigen Receptor Recognizing ERBB2

(2010) Richard A Morgan et al.   MOLECULAR THERAPY

T Cells Targeting Carcinoembryonic Antigen Can Mediate Regression of Metastatic Colorectal Cancer but Induce Severe Transient Colitis

(2010) Maria R Parkhurst et al.   MOLECULAR THERAPY

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS