Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma

Inconsistent prediction capability of ImmuneCells.Sig across different RNA-seq datasets

(2021) Xu Xiao et al.   Nature Communications

Reply to: “Inconsistent prediction capability of ImmuneCells.Sig across different RNA-seq datasets”

(2021) Donghai Xiong et al.   Nature Communications

Peripheral CD8+ T cell characteristics associated with durable responses to immune checkpoint blockade in patients with metastatic melanoma

(2020) Benjamin P. Fairfax et al.   NATURE MEDICINE

Transcriptional downregulation of MHC class I and melanoma de- differentiation in resistance to PD-1 inhibition

(2020) Jenny H. Lee et al.   Nature Communications

A peripheral immune signature of responsiveness to PD-1 blockade in patients with classical Hodgkin lymphoma

(2020) Fathima Zumla Cader et al.   NATURE MEDICINE

Predicting and affecting response to cancer therapy based on pathway-level biomarkers

(2020) Rotem Ben-Hamo et al.   Nature Communications

The PD-1 expression balance between effector and regulatory T cells predicts the clinical efficacy of PD-1 blockade therapies

(2020) Shogo Kumagai et al.   NATURE IMMUNOLOGY

A gene expression signature of TREM2hi macrophages and γδ T cells predicts immunotherapy response

(2020) Donghai Xiong et al.   Nature Communications

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

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

Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy

(2019) Tuba N. Gide et al.   CANCER CELL

Pembrolizumab versus ipilimumab in advanced melanoma (KEYNOTE-006): post-hoc 5-year results from an open-label, multicentre, randomised, controlled, phase 3 study

(2019) Caroline Robert et al.   LANCET ONCOLOGY

Proteomics of Melanoma Response to Immunotherapy Reveals Mitochondrial Dependence

(2019) Michal Harel et al.   CELL

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

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

IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma

(2019) Jason A. Carter et al.   NATURE MEDICINE

Reply to: ‘IMPRES does not reproducibly predict response to immune checkpoint blockade therapy in metastatic melanoma’

(2019) Noam Auslander et al.   NATURE MEDICINE

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

(2019) David Liu et al.   NATURE MEDICINE

T cell–induced CSF1 promotes melanoma resistance to PD1 blockade

(2018) Natalie J. Neubert et al.   Science Translational Medicine

MHC proteins confer differential sensitivity to CTLA-4 and PD-1 blockade in untreated metastatic melanoma

(2018) Scott J. Rodig et al.   Science Translational Medicine

Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response

(2018) Peng Jiang et al.   NATURE MEDICINE

Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma

(2018) Noam Auslander et al.   NATURE MEDICINE

Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA

(2018) K. G. Paulson et al.   Nature Communications

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

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

(2018) Razvan Cristescu et al.   SCIENCE

Pathway-based subnetworks enable cross-disease biomarker discovery

(2018) Syed Haider et al.   Nature Communications

IFN-γ–related mRNA profile predicts clinical response to PD-1 blockade

(2017) Mark Ayers et al.   JOURNAL OF CLINICAL INVESTIGATION

Ki67 Proliferation Index as a Tool for Chemotherapy Decisions During and After Neoadjuvant Aromatase Inhibitor Treatment of Breast Cancer: Results From the American College of Surgeons Oncology Group Z1031 Trial (Alliance)

(2017) Matthew J. Ellis et al.   JOURNAL OF CLINICAL ONCOLOGY

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy

(2017) Diego Chowell et al.   SCIENCE

Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy

(2017) Teresa Davoli et al.   SCIENCE

Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance

(2017) Whijae Roh et al.   Science Translational Medicine

Genomic landscape associated with potential response to anti-CTLA-4 treatment in cancers

(2017) Chan-Young Ock et al.   Nature Communications

Ex Vivo Profiling of PD-1 Blockade Using Organotypic Tumor Spheroids

(2017) Russell W. Jenkins et al.   Cancer Discovery

Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma

(2016) Willy Hugo et al.   CELL

The Tumor Microenvironment Represses T Cell Mitochondrial Biogenesis to Drive Intratumoral T Cell Metabolic Insufficiency and Dysfunction

(2016) Nicole E. Scharping et al.   IMMUNITY

Prolonged Survival in Stage III Melanoma with Ipilimumab Adjuvant Therapy

(2016) Alexander M.M. Eggermont et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2016) N. McGranahan et al.   SCIENCE

Melanoma-specific MHC-II expression represents a tumour-autonomous phenotype and predicts response to anti-PD-1/PD-L1 therapy

(2016) Douglas B. Johnson et al.   Nature Communications

Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade

(2016) P.-L. Chen et al.   Cancer Discovery

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Accurate Prediction and Validation of Response to Endocrine Therapy in Breast Cancer

(2015) Arran K. Turnbull et al.   JOURNAL OF CLINICAL ONCOLOGY

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Nivolumab in Previously Untreated Melanoma without BRAF Mutation

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

Genomic correlates of response to CTLA-4 blockade in metastatic melanoma

(2015) E. M. Van Allen et al.   SCIENCE

Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer

(2015) N. A. Rizvi et al.   SCIENCE

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma

(2014) Alexandra Snyder et al.   NEW ENGLAND JOURNAL OF MEDICINE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A combined oncogenic pathway signature ofBRAF,KRASandPI3KCAmutation improves colorectal cancer classification and cetuximab treatment prediction

(2012) Sun Tian et al.   GUT

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH