Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire

Long-Term Outcomes and Retreatment Among Patients With Previously Treated, Programmed Death-Ligand 1‒Positive, Advanced Non‒Small-Cell Lung Cancer in the KEYNOTE-010 Study

(2020) Roy S. Herbst et al.   JOURNAL OF CLINICAL ONCOLOGY

Guidance Document: Validation of a High-Performance Liquid Chromatography-Tandem Mass Spectrometry Immunopeptidomics Assay for the Identification of HLA Class I Ligands Suitable for Pharmaceutical Therapies

(2020) Michael Ghosh et al.   MOLECULAR & CELLULAR PROTEOMICS

An RNA vaccine drives expansion and efficacy of claudin-CAR-T cells against solid tumors

(2020) Katharina Reinhard et al.   SCIENCE

Predicting Splicing from Primary Sequence with Deep Learning

(2019) Kishore Jaganathan et al.   CELL

Alternative Splicing in Tumors — A Path to Immunogenicity?

(2019) Jill E. Slansky et al.   NEW ENGLAND JOURNAL OF MEDICINE

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

(2019) Dongxue Wang et al.   Molecular Systems Biology

Phase II clinical trial of adoptive cell therapy for patients with metastatic melanoma with autologous tumor-infiltrating lymphocytes and low-dose interleukin-2

(2019) Linh T. Nguyen et al.   CANCER IMMUNOLOGY IMMUNOTHERAPY

ALK rearrangements: Biology, detection and opportunities of therapy in non-small cell lung cancer

(2019) Gina Rosas et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Pembrolizumab versus chemotherapy for previously untreated, PD-L1-expressing, locally advanced or metastatic non-small-cell lung cancer (KEYNOTE-042): a randomised, open-label, controlled, phase 3 trial

(2019) Tony S K Mok et al.   LANCET

Atezolizumab plus bevacizumab versus sunitinib in patients with previously untreated metastatic renal cell carcinoma (IMmotion151): a multicentre, open-label, phase 3, randomised controlled trial

(2019) Brian I Rini et al.   LANCET

Induction of neoantigen-reactive T cells from healthy donors

(2019) Muhammad Ali et al.   Nature Protocols

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

(2019) Markus W. Löffler et al.   Genome Medicine

Unique Neoantigens Arise from Somatic Mutations in Patients with Gastrointestinal Cancers

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

Minor intron splicing revisited: identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns

(2019) Anouk M. Olthof et al.   BMC GENOMICS

Microsatellite instability and immune checkpoint inhibitors: toward precision medicine against gastrointestinal and hepatobiliary cancers

(2019) Yuji Eso et al.   JOURNAL OF GASTROENTEROLOGY

Integrated genomic profiling expands clinical options for patients with cancer

(2019) Nike Beaubier et al.   NATURE BIOTECHNOLOGY

Five-Year Survival with Combined Nivolumab and Ipilimumab in Advanced Melanoma

(2019) James Larkin et al.   NEW ENGLAND JOURNAL OF MEDICINE

Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood

(2019) Songming Peng et al.   Cell Reports

Best practices for bioinformatic characterization of neoantigens for clinical utility

(2019) Megan M. Richters et al.   Genome Medicine

Immunopathologic Stratification of Colorectal Cancer for Checkpoint Blockade Immunotherapy

(2019) Nicolas J. Llosa et al.   Cancer Immunology Research

Multiomics Prediction of Response Rates to Therapies to Inhibit Programmed Cell Death 1 and Programmed Cell Death 1 Ligand 1

(2019) Joo Sang Lee et al.   JAMA Oncology

Next-Generation Sequencing in 305 Consecutive Patients: Clinical Outcomes and Management Changes

(2019) William Davis et al.   Journal of Oncology Practice

Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

(2019) Zach Rolfs et al.   Science Immunology

Response to Comment on “A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands”

(2019) Pouya Faridi et al.   Science Immunology

Advances in RNA Vaccines for Preventive Indications: A Case Study of A Vaccine Against Rabies

(2019) Armbruster et al.   Vaccines

A Non-interventional Clinical Trial Assessing Immune Responses After Radiofrequency Ablation of Liver Metastases From Colorectal Cancer

(2019) Markus W. Löffler et al.   Frontiers in Immunology

Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment

(2019) Alice Newey et al.   Journal for ImmunoTherapy of Cancer

A new synthetic toll-like receptor 1/2 ligand is an efficient adjuvant for peptide vaccination in a human volunteer

(2019) Hans-Georg Rammensee et al.   Journal for ImmunoTherapy of Cancer

Cancer immunotherapy with lymphocytes genetically engineered with T cell receptors for solid cancers

(2019) Lei Chen et al.   IMMUNOLOGY LETTERS

Peptide Channeling: The Key to MHC Class I Immunosurveillance?

(2019) Jonathan W. Yewdell et al.   TRENDS IN CELL BIOLOGY

Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations

(2018) Andrea Pellagatti et al.   BLOOD

Chimeric antigen receptor–modified T cells: CD19 and the road beyond

(2018) Alexander I. Salter et al.   BLOOD

Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation

(2018) Markus W. Löffler et al.   CANCER RESEARCH

Mapping the tumour human leukocyte antigen (HLA) ligandome by mass spectrometry

(2018) Lena Katharina Freudenmann et al.   IMMUNOLOGY

Chimeric Antigen Receptor (CAR) T-Cell Therapy for Thoracic Malignancies

(2018) Stefan Kiesgen et al.   Journal of Thoracic Oncology

Robust research needs many lines of evidence

(2018) Marcus R. Munafò et al.   NATURE

Adjuvant Pembrolizumab versus Placebo in Resected Stage III Melanoma

(2018) Alexander M.M. Eggermont et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tisagenlecleucel in Children and Young Adults with B-Cell Lymphoblastic Leukemia

(2018) Shannon L. Maude et al.   NEW ENGLAND JOURNAL OF MEDICINE

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

(2018) Michael Seiler et al.   Cell Reports

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

(2018) Reyka G. Jayasinghe et al.   Cell Reports

Antitumor activity of CAR-T cells targeting the intracellular oncoprotein WT1 can be enhanced by vaccination

(2018) Yasushi Akahori et al.   BLOOD

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

(2018) André Kahles et al.   CANCER CELL

Identification of non-mutated neoantigens presented by TAP-deficient tumors

(2018) Koen A. Marijt et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Exosomal PD-L1 contributes to immunosuppression and is associated with anti-PD-1 response

(2018) Gang Chen et al.   NATURE

Intron retention is a source of neoepitopes in cancer

(2018) Alicia C Smart et al.   NATURE BIOTECHNOLOGY

Combined analysis of antigen presentation and T cell recognition reveals restricted immune responses in melanoma

(2018) Shelly Kalaora et al.   Cancer Discovery

Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

(2018) David Gfeller et al.   Frontiers in Immunology

Lost in the crowd: identifying targetable MHC class I neoepitopes for cancer immunotherapy

(2018) Eric A. Wilson et al.   Expert Review of Proteomics

Initial results of pulmonary resection following neoadjuvant nivolumab in patients with resectable non-small cell lung cancer

(2018) Matthew J. Bott et al.   JOURNAL OF THORACIC AND CARDIOVASCULAR SURGERY

Pembrolizumab versus methotrexate, docetaxel, or cetuximab for recurrent or metastatic head-and-neck squamous cell carcinoma (KEYNOTE-040): a randomised, open-label, phase 3 study

(2018) Ezra E W Cohen et al.   LANCET

Actively personalized vaccination trial for newly diagnosed glioblastoma

(2018) Norbert Hilf et al.   NATURE

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

(2018) Derin B. Keskin et al.   NATURE

Immune Escape of Relapsed AML Cells after Allogeneic Transplantation

(2018) Matthew J. Christopher et al.   NEW ENGLAND JOURNAL OF MEDICINE

Tisagenlecleucel in Adult Relapsed or Refractory Diffuse Large B-Cell Lymphoma

(2018) Stephen J. Schuster et al.   NEW ENGLAND JOURNAL OF MEDICINE

Survival Outcomes in Patients With Previously Untreated BRAF Wild-Type Advanced Melanoma Treated With Nivolumab Therapy

(2018) Paolo A. Ascierto et al.   JAMA Oncology

A Pilot Prospective Study of Refractory Solid Tumor Patients for NGS-Based Targeted Anticancer Therapy

(2018) Young Mi Seol et al.   Translational Oncology

11 years' follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive early breast cancer: final analysis of the HERceptin Adjuvant (HERA) trial

(2017) David Cameron et al.   LANCET

Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis

(2017) Samra Turajlic et al.   LANCET ONCOLOGY

Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer

(2017) Ugur Sahin et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

Axicabtagene Ciloleucel CAR T-Cell Therapy in Refractory Large B-Cell Lymphoma

(2017) Sattva S. Neelapu et al.   NEW ENGLAND JOURNAL OF MEDICINE

The SysteMHC Atlas project

(2017) Wenguang Shao et al.   NUCLEIC ACIDS RESEARCH

The immunopeptidomic landscape of ovarian carcinomas

(2017) Heiko Schuster et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Is It Possible to Develop Cancer Vaccines to Neoantigens, What Are the Major Challenges, and How Can These Be Overcome?

(2017) Olivera J. Finn et al.   Cold Spring Harbor Perspectives in Biology

The Functional Impact of Alternative Splicing in Cancer

(2017) Héctor Climente-González et al.   Cell Reports

Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia

(2017) Stacy A. Malaker et al.   Cancer Immunology Research

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

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

An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes

(2017) Dorte B. Bekker-Jensen et al.   Cell Systems

Differential protein stability and clinical responses of EML4-ALK fusion variants to various ALK inhibitors in advanced ALK -rearranged non–small cell lung cancer

(2016) C.G. Woo et al.   ANNALS OF ONCOLOGY

The urgent need to recover MHC class I in cancers for effective immunotherapy

(2016) Federico Garrido et al.   CURRENT OPINION IN IMMUNOLOGY

Mass spectrometry-based antigen discovery for cancer immunotherapy

(2016) Michal Bassani-Sternberg et al.   CURRENT OPINION IN IMMUNOLOGY

Impact of Splicing Factor Mutations on Pre-mRNA Splicing in the Myelodysplastic Syndromes

(2016) Bon Ham Yip et al.   CURRENT PHARMACEUTICAL DESIGN

The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non‐coding RNA and synonymous mutations

(2016) Sven Diederichs et al.   EMBO Molecular Medicine

Opportunities and challenges for TCR mimic antibodies in cancer therapy

(2016) Aaron Y. Chang et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability

(2016) Bernhard Mlecnik et al.   IMMUNITY

IMA901, a multipeptide cancer vaccine, plus sunitinib versus sunitinib alone, as first-line therapy for advanced or metastatic renal cell carcinoma (IMPRINT): a multicentre, open-label, randomised, controlled, phase 3 trial

(2016) Brian I Rini et al.   LANCET ONCOLOGY

Graft versus self (GvS) against T-cell autoantigens is a mechanism of graft–host interaction

(2016) Nora Mirza et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A large fraction of HLA class I ligands are proteasome-generated spliced peptides

(2016) Juliane Liepe et al.   SCIENCE

Global proteogenomic analysis of human MHC class I-associated peptides derived from non-canonical reading frames

(2016) Céline M. Laumont et al.   Nature Communications

Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

(2016) Michal Bassani-Sternberg et al.   Nature Communications

Gapped sequence alignment using artificial neural networks: application to the MHC class I system

(2015) Massimo Andreatta et al.   BIOINFORMATICS

Correlation between Density of CD8+ T-cell Infiltrate in Microsatellite Unstable Colorectal Cancers and Frameshift Mutations: A Rationale for Personalized Immunotherapy

(2015) P. Maby et al.   CANCER RESEARCH

Complementary IMAC enrichment methods for HLA-associated phosphopeptide identification by mass spectrometry

(2015) Jennifer G Abelin et al.   Nature Protocols

PD-1 Blockade in Tumors with Mismatch-Repair Deficiency

(2015) Dung T. Le et al.   NEW ENGLAND JOURNAL OF MEDICINE

Pertuzumab, Trastuzumab, and Docetaxel in HER2-Positive Metastatic Breast Cancer

(2015) Sandra M. Swain et al.   NEW ENGLAND JOURNAL OF MEDICINE

Neoantigens in cancer immunotherapy

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

Immunogenicity of somatic mutations in human gastrointestinal cancers

(2015) E. Tran et al.   SCIENCE

Immunoinformatics and epitope prediction in the age of genomic medicine

(2015) Linus Backert et al.   Genome Medicine

An open-source computational and data resource to analyze digital maps of immunopeptidomes

(2015) Etienne Caron et al.   eLife

Long-term survival correlates with immunological responses in renal cell carcinoma patients treated with mRNA-based immunotherapy

(2015) Susanne M. Rittig et al.   OncoImmunology

CD20 alternative splicing isoform generates immunogenic CD4 helper T epitopes

(2014) Charline Vauchy et al.   INTERNATIONAL JOURNAL OF CANCER

Antigen-Dependent Integration of Opposing Proximal TCR-Signaling Cascades Determines the Functional Fate of T Lymphocytes

(2014) R. Wolchinsky et al.   JOURNAL OF IMMUNOLOGY

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing

(2014) Mahesh Yadav et al.   NATURE

HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL)

(2014) Daniel J. Kowalewski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Re-examining class-I presentation and the DRiP hypothesis

(2014) Kenneth L. Rock et al.   TRENDS IN IMMUNOLOGY

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

(2013) G. P. Linette et al.   BLOOD

Combination of sunitinib with anti-tumor vaccination inhibits T cell priming and requires careful scheduling to achieve productive immunotherapy

(2013) Ritika Jaini et al.   INTERNATIONAL JOURNAL OF CANCER

MHC Class I Antigen Processing and Presenting Machinery: Organization, Function, and Defects in Tumor Cells

(2013) P. Leone et al.   JNCI-Journal of the National Cancer Institute

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

The regulatory landscape for actively personalized cancer immunotherapies

(2013) Cedrik M Britten et al.   NATURE BIOTECHNOLOGY

MHC Class I-Associated Phosphopeptides Are the Targets of Memory-like Immunity in Leukemia

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

Identification of a Titin-Derived HLA-A1-Presented Peptide as a Cross-Reactive Target for Engineered MAGE A3-Directed T Cells

(2013) B. J. Cameron et al.   Science Translational Medicine

Getting Personal with Neoantigen-Based Therapeutic Cancer Vaccines

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

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival

(2012) Steffen Walter et al.   NATURE MEDICINE

The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation

(2011) E. Caron et al.   Molecular Systems Biology

gp100 Peptide Vaccine and Interleukin-2 in Patients with Advanced Melanoma

(2011) Douglas J. Schwartzentruber et al.   NEW ENGLAND JOURNAL OF MEDICINE

Phase II study of personalized peptide vaccination for castration-resistant prostate cancer patients who failed in docetaxel-based chemotherapy

(2011) Masanori Noguchi et al.   PROSTATE

Phase I Trial of a Personalized Peptide Vaccine for Patients Positive for Human Leukocyte Antigen–A24 With Recurrent or Progressive Glioblastoma Multiforme

(2010) Mizuhiko Terasaki et al.   JOURNAL OF CLINICAL ONCOLOGY

Sipuleucel-T Immunotherapy for Castration-Resistant Prostate Cancer

(2010) Philip W. Kantoff et al.   NEW ENGLAND JOURNAL OF MEDICINE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

A Pilot Study of Consolidative Immunotherapy in Patients with High-Risk Pediatric Sarcomas

(2008) C. L. Mackall et al.   CLINICAL CANCER RESEARCH

Booster vaccination of cancer patients with MAGE-A3 protein reveals long-term immunological memory or tolerance depending on priming

(2008) D. Atanackovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA