Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma

CD3D is associated with immune checkpoints and predicts favorable clinical outcome in colon cancer

(2020) Yi Yang et al.   Immunotherapy

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

Manipulation of the Innate Immune Response by Varicella Zoster Virus

(2020) Chelsea Gerada et al.   Frontiers in Immunology

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

(2020) David Y. Oh et al.   CELL

The PD-1/PD-L1-Checkpoint Restrains T cell Immunity in Tumor-Draining Lymph Nodes

(2020) Floris Dammeijer et al.   CANCER CELL

Key Parameters of Tumor Epitope Immunogenicity Revealed Through a Consortium Approach Improve Neoantigen Prediction

(2020) Daniel K. Wells et al.   CELL

The first-week proliferative response of peripheral blood PD-1+CD8+ T cells predicts the response to anti-PD-1 therapy in solid tumors

(2019) Kyung Hwan Kim et al.   CLINICAL CANCER RESEARCH

Tumor mutational load predicts survival after immunotherapy across multiple cancer types

(2019) Robert M. Samstein et al.   NATURE GENETICS

CXCL5 induces tumor angiogenesis via enhancing the expression of FOXD1 mediated by the AKT/NF-κB pathway in colorectal cancer

(2019) Chun Chen et al.   Cell Death & Disease

A single dose of neoadjuvant PD-1 blockade predicts clinical outcomes in resectable melanoma

(2019) Alexander C. Huang et al.   NATURE MEDICINE

Randomized phase III KEYNOTE-045 trial of pembrolizumab versus paclitaxel, docetaxel, or vinflunine in recurrent advanced urothelial cancer: results of >2 years of follow-up

(2019) Y Fradet et al.   ANNALS OF ONCOLOGY

Analysis of the Association Between Adverse Events and Outcome in Patients Receiving a Programmed Death Protein 1 or Programmed Death Ligand 1 Antibody

(2019) V. Ellen Maher et al.   JOURNAL OF CLINICAL ONCOLOGY

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

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

Empty peptide-receptive MHC class I molecules for efficient detection of antigen-specific T cells

(2019) Sunil Kumar Saini et al.   Science Immunology

Immunohistochemical validation of COL3A1, GPR158 and PITHD1 as prognostic biomarkers in early-stage ovarian carcinomas

(2019) Hanna Engqvist et al.   BMC CANCER

Recruit or Reboot? How Does Anti-PD-1 Therapy Change Tumor-Infiltrating Lymphocytes?

(2019) Margaret K. Callahan et al.   CANCER CELL

UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma

(2019) Yochai Wolf et al.   CELL

T cell recognition of novel shared breast cancer antigens is frequently observed in peripheral blood of breast cancer patients

(2019) Nadia Viborg et al.   OncoImmunology

MHC-II neoantigens shape tumour immunity and response to immunotherapy

(2019) Elise Alspach et al.   NATURE

The CXCL5/CXCR2 axis is sufficient to promote breast cancer colonization during bone metastasis

(2019) Ricardo Romero-Moreno et al.   Nature Communications

TCR Repertoire Diversity of Peripheral PD-1+CD8+ T Cells Predicts Clinical Outcomes after Immunotherapy in Patients with Non–Small Cell Lung Cancer

(2019) Jiefei Han et al.   Cancer Immunology Research

CD4+ T Cell Help Is Required for the Formation of a Cytolytic CD8+ T Cell Subset that Protects against Chronic Infection and Cancer

(2019) Ryan Zander et al.   IMMUNITY

Cancer Neoepitopes for Immunotherapy: Discordance Between Tumor-Infiltrating T Cell Reactivity and Tumor MHC Peptidome Display

(2019) Stina L. Wickström et al.   Frontiers in Immunology

Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden

(2018) Matthew D. Hellmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Prevalence of PDL1 Amplification and Preliminary Response to Immune Checkpoint Blockade in Solid Tumors

(2018) Aaron M. Goodman et al.   JAMA Oncology

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

(2018) Yannick Simoni et al.   NATURE

PPAR-induced fatty acid oxidation in T cells increases the number of tumor-reactive CD8+ T cells and facilitates anti-PD-1 therapy

(2018) Partha S. Chowdhury et al.   Cancer Immunology Research

Predicting T cell recognition of MHC class I restricted neoepitopes

(2018) Zeynep Koşaloğlu-Yalçın et al.   OncoImmunology

Pan-tumor genomic biomarkers for PD-1 checkpoint blockade–based immunotherapy

(2018) Razvan Cristescu et al.   SCIENCE

Avelumab, an Anti–Programmed Death-Ligand 1 Antibody, In Patients With Refractory Metastatic Urothelial Carcinoma: Results From a Multicenter, Phase Ib Study

(2017) Andrea B. Apolo et al.   JOURNAL OF CLINICAL ONCOLOGY

Atezolizumab as first-line treatment in cisplatin-ineligible patients with locally advanced and metastatic urothelial carcinoma: a single-arm, multicentre, phase 2 trial

(2017) Arjun V Balar et al.   LANCET

First-line pembrolizumab in cisplatin-ineligible patients with locally advanced and unresectable or metastatic urothelial cancer (KEYNOTE-052): a multicentre, single-arm, phase 2 study

(2017) Arjun V Balar et al.   LANCET ONCOLOGY

Nivolumab in metastatic urothelial carcinoma after platinum therapy (CheckMate 275): a multicentre, single-arm, phase 2 trial

(2017) Padmanee Sharma et al.   LANCET ONCOLOGY

T-cell invigoration to tumour burden ratio associated with anti-PD-1 response

(2017) Alexander C. Huang et al.   NATURE

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

(2017) Vinod P. Balachandran et al.   NATURE

A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy

(2017) Marta Łuksza et al.   NATURE

Pembrolizumab as Second-Line Therapy for Advanced Urothelial Carcinoma

(2017) Joaquim Bellmunt et al.   NEW ENGLAND JOURNAL OF MEDICINE

Proliferation of PD-1+ CD8 T cells in peripheral blood after PD-1–targeted therapy in lung cancer patients

(2017) Alice O. Kamphorst et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of systemic and somatic factors to clinical response and resistance to PD-L1 blockade in urothelial cancer: An exploratory multi-omic analysis

(2017) Alexandra Snyder et al.   PLOS MEDICINE

An Analysis of Natural T Cell Responses to Predicted Tumor Neoepitopes

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

Efficacy and Safety of Durvalumab in Locally Advanced or Metastatic Urothelial Carcinoma

(2017) Thomas Powles et al.   JAMA Oncology

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial

(2016) Jonathan E Rosenberg et al.   LANCET

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

(2016) Se Jin Im et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

(2016) Amalie Kai Bentzen et al.   NATURE BIOTECHNOLOGY

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

Integrin and gene network analysis reveals that ITGA5 and ITGB1 are prognostic in non-small-cell lung cancer

(2016) Weiqi Zheng et al.   OncoTargets and Therapy

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

Pembrolizumab for the Treatment of Non–Small-Cell Lung Cancer

(2015) Edward B. Garon et al.   NEW ENGLAND JOURNAL OF MEDICINE

Nivolumab versus Everolimus in Advanced Renal-Cell Carcinoma

(2015) Robert J. Motzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Peripheral T cell receptor diversity is associated with clinical outcomes following ipilimumab treatment in metastatic melanoma

(2015) Michael A. Postow et al.   Journal for ImmunoTherapy of Cancer

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

OptiType: precision HLA typing from next-generation sequencing data

(2014) András Szolek et al.   BIOINFORMATICS

Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens

(2014) Matthew M. Gubin et al.   NATURE

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Tumor-associated macrophages subvert T-cell function and correlate with reduced survival in clear cell renal cell carcinoma

(2013) Stefanie Regine Dannenmann et al.   OncoImmunology

RazerS 3: Faster, fully sensitive read mapping

(2012) David Weese et al.   BIOINFORMATICS

Parallel detection of antigen-specific T cell responses by combinatorial encoding of MHC multimers

(2012) Rikke Sick Andersen et al.   Nature Protocols

Tumor Immunotherapy Directed at PD-1

(2012) Antoni Ribas   NEW ENGLAND JOURNAL OF MEDICINE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Parallel detection of antigen-specific T-cell responses by multidimensional encoding of MHC multimers

(2009) Sine Reker Hadrup et al.   NATURE METHODS

Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-Cell activation

(2008) Min Wang et al.   BMC GENOMICS

Conditional MHC class I ligands and peptide exchange technology for the human MHC gene products HLA-A1, -A3, -A11, and -B7

(2008) A. H. Bakker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA