Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

(2021) Sijin Cheng et al.   CELL

A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer

(2021) Ayse Bassez et al.   NATURE MEDICINE

Primary results from IMpassion131, a double-blind, placebo-controlled, randomised phase III trial of first-line paclitaxel with or without atezolizumab for unresectable locally advanced/metastatic triple-negative breast cancer

(2021) D. Miles et al.   ANNALS OF ONCOLOGY

Top 10 Challenges in Cancer Immunotherapy

(2020) Priti S. Hegde et al.   IMMUNITY

B cells are associated with survival and immunotherapy response in sarcoma

(2020) Florent Petitprez et al.   NATURE

Tertiary lymphoid structures improve immunotherapy and survival in melanoma

(2020) Rita Cabrita et al.   NATURE

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

Single-Cell Analyses Inform Mechanisms of Myeloid-Targeted Therapies in Colon Cancer

(2020) Lei Zhang et al.   CELL

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy

(2020) Martina Molgora et al.   CELL

cDC1 prime and are licensed by CD4+ T cells to induce anti-tumour immunity

(2020) Stephen T. Ferris et al.   NATURE

Baseline Frequency of Inflammatory Cxcl9-Expressing Tumor-Associated Macrophages Predicts Response to Avelumab Treatment

(2020) Yan Qu et al.   Cell Reports

1928O Meta-analysis of tumour and T cell intrinsic mechanisms of sensitization to checkpoint inhibition

(2020) K.R. Litchfield et al.   ANNALS OF ONCOLOGY

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

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

B Cells and T Follicular Helper Cells Mediate Response to Checkpoint Inhibitors in High Mutation Burden Mouse Models of Breast Cancer

(2019) Daniel P. Hollern et al.   CELL

Landscape and Dynamics of Single Immune Cells in Hepatocellular Carcinoma

(2019) Qiming Zhang et al.   CELL

Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade

(2019) Imran G. House et al.   CLINICAL CANCER RESEARCH

The Transcription Factor Tox2 Drives T Follicular Helper Cell Development via Regulating Chromatin Accessibility

(2019) Wei Xu et al.   IMMUNITY

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Massively multiplex chemical transcriptomics at single-cell resolution

(2019) Sanjay R. Srivatsan et al.   SCIENCE

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Immune checkpoint blockade therapy for cancer: An overview of FDA-approved immune checkpoint inhibitors

(2018) Kristian M. Hargadon et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

High-dimensional single-cell analysis predicts response to anti-PD-1 immunotherapy

(2018) Carsten Krieg et al.   NATURE MEDICINE

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

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

(2018) Thomas Duhen et al.   Nature Communications

MEF2B Instructs Germinal Center Development and Acts as an Oncogene in B Cell Lymphomagenesis

(2018) Paola Brescia et al.   CANCER CELL

Impact of Baseline Steroids on Efficacy of Programmed Cell Death-1 and Programmed Death-Ligand 1 Blockade in Patients With Non–Small-Cell Lung Cancer

(2018) Kathryn C. Arbour et al.   JOURNAL OF CLINICAL ONCOLOGY

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

(2018) Yannick Simoni et al.   NATURE

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

(2018) Hanjie Li et al.   CELL

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Atezolizumab and Nab-Paclitaxel in Advanced Triple-Negative Breast Cancer

(2018) Peter Schmid et al.   NEW ENGLAND JOURNAL OF MEDICINE

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Pembrolizumab in Patients With Advanced Triple-Negative Breast Cancer: Phase Ib KEYNOTE-012 Study

(2016) Rita Nanda et al.   JOURNAL OF CLINICAL ONCOLOGY

Triple-negative breast cancer: challenges and opportunities of a heterogeneous disease

(2016) Giampaolo Bianchini et al.   Nature Reviews Clinical Oncology

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

Effects of Systemically Administered Hydrocortisone on the Human Immunome

(2016) Matthew J. Olnes et al.   Scientific Reports

Immune Checkpoint Targeting in Cancer Therapy: Toward Combination Strategies with Curative Potential

(2015) Padmanee Sharma et al.   CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

The evaluation of tumor-infiltrating lymphocytes (TILs) in breast cancer: recommendations by an International TILs Working Group 2014

(2014) R. Salgado et al.   ANNALS OF ONCOLOGY

CD8+ T Cells Produce the Chemokine CXCL10 in Response to CD27/CD70 Costimulation To Promote Generation of the CD8+ Effector T Cell Pool

(2013) V. Peperzak et al.   JOURNAL OF IMMUNOLOGY

Innate and adaptive immune cells in the tumor microenvironment

(2013) Thomas F Gajewski et al.   NATURE IMMUNOLOGY

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Roles of BCL6 in normal and transformed germinal center B cells

(2012) Katia Basso et al.   IMMUNOLOGICAL REVIEWS

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

T cell exhaustion

(2011) E John Wherry   NATURE IMMUNOLOGY

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

New response evaluation criteria in solid tumours: Revised RECIST guideline (version 1.1)

(2008) E.A. Eisenhauer et al.   EUROPEAN JOURNAL OF CANCER