Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer

Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer

(2022) Adriana M. Mujal et al.   Cancer Immunology Research

Mitochondrial stress induced by continuous stimulation under hypoxia rapidly drives T cell exhaustion

(2021) Nicole E. Scharping et al.   NATURE IMMUNOLOGY

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma

(2021) David A. Braun et al.   CANCER CELL

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

(2021) Kevin Bi et al.   CANCER CELL

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

(2021) Sijin Cheng et al.   CELL

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

Fibroblast-macrophage reciprocal interactions in health, fibrosis, and cancer

(2021) Matthew B. Buechler et al.   IMMUNITY

A unified atlas of CD8 T cell dysfunctional states in cancer and infection

(2021) Yuri Pritykin et al.   MOLECULAR CELL

Transient rest restores functionality in exhausted CAR-T cells through epigenetic remodeling

(2021) Evan W. Weber et al.   SCIENCE

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

(2021) Giacomo Oliveira et al.   NATURE

BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells

(2021) Hyungseok Seo et al.   NATURE IMMUNOLOGY

BATF regulates progenitor to cytolytic effector CD8+ T cell transition during chronic viral infection

(2021) Yao Chen et al.   NATURE IMMUNOLOGY

Single-cell analysis of the pan-cancer immune microenvironment and scTIME portal

(2021) Fang Hong et al.   Cancer Immunology Research

Discovering dominant tumor immune archetypes in a pan-cancer census

(2021) Alexis J. Combes et al.   CELL

Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms

(2020) Jean-Christophe Beltra et al.   IMMUNITY

Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

(2020) Yonatan Katzenelenbogen et al.   CELL

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

(2020) Martina Molgora et al.   CELL

Impaired mitochondrial oxidative phosphorylation limits the self-renewal of T cells exposed to persistent antigen

(2020) Santosha A. Vardhana et al.   NATURE IMMUNOLOGY

ZipSeq: barcoding for real-time mapping of single cell transcriptomes

(2020) Kenneth H. Hu et al.   NATURE METHODS

Early precursor T cells establish and propagate T cell exhaustion in chronic infection

(2020) Daniel T. Utzschneider et al.   NATURE IMMUNOLOGY

SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution

(2020) Rafael J. Argüello et al.   Cell Metabolism

SLAMF7 Signaling Reprograms T Cells toward Exhaustion in the Tumor Microenvironment

(2020) Patrick O’Connell et al.   JOURNAL OF IMMUNOLOGY

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

(2019) Imran Siddiqui et al.   IMMUNITY

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

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

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

(2019) Johanna Wagner et al.   CELL

Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity

(2019) Mikhail Binnewies et al.   CELL

TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection

(2019) Francesca Alfei et al.   NATURE

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

(2019) Andrew C. Scott et al.   NATURE

TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion

(2019) Omar Khan et al.   NATURE

Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection

(2019) Chen Yao et al.   NATURE IMMUNOLOGY

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

(2019) Ansuman T. Satpathy et al.   NATURE BIOTECHNOLOGY

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

(2019) Caroline S. Jansen et al.   NATURE

OUP accepted manuscript

(2018)   BIOINFORMATICS

A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade

(2018) Daniela S. Thommen et al.   NATURE MEDICINE

Understanding the tumor immune microenvironment (TIME) for effective therapy

(2018) Mikhail Binnewies et al.   NATURE MEDICINE

A natural killer–dendritic cell axis defines checkpoint therapy–responsive tumor microenvironments

(2018) Kevin C. Barry et al.   NATURE MEDICINE

Macrophages impede CD8 T cells from reaching tumor cells and limit the efficacy of anti–PD-1 treatment

(2018) Elisa Peranzoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Moshe Sade-Feldman et al.   CELL

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Transcription Factor IRF4 Promotes CD8 + T Cell Exhaustion and Limits the Development of Memory-like T Cells during Chronic Infection

(2017) Kevin Man et al.   IMMUNITY

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Visualizing dynamic microvillar search and stabilization during ligand detection by T cells

(2017) En Cai et al.   SCIENCE

Critical Role for CD103 + /CD141 + Dendritic Cells Bearing CCR7 for Tumor Antigen Trafficking and Priming of T Cell Immunity in Melanoma

(2016) Edward W. Roberts et al.   CANCER CELL

Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis

(2016) Andrea Schietinger et al.   IMMUNITY

Bioenergetic Insufficiencies Due to Metabolic Alterations Regulated by the Inhibitory Receptor PD-1 Are an Early Driver of CD8 + T Cell Exhaustion

(2016) Bertram Bengsch et al.   IMMUNITY

Expansion and Activation of CD103 + Dendritic Cell Progenitors at the Tumor Site Enhances Tumor Responses to Therapeutic PD-L1 and BRAF Inhibition

(2016) Hélène Salmon et al.   IMMUNITY

High antigen levels induce an exhausted phenotype in a chronic infection without impairing T cell expansion and survival

(2016) Daniel T. Utzschneider et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2016) Se Jin Im et al.   NATURE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade

(2016) K. E. Pauken et al.   SCIENCE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

The prognostic landscape of genes and infiltrating immune cells across human cancers

(2015) Andrew J Gentles et al.   NATURE MEDICINE

CD8+ Tumor-Infiltrating T Cells Are Trapped in the Tumor-Dendritic Cell Network

(2015) Alexandre Boissonnas et al.   NEOPLASIA

Dissecting the Tumor Myeloid Compartment Reveals Rare Activating Antigen-Presenting Cells Critical for T Cell Immunity

(2014) Miranda L. Broz et al.   CANCER CELL

PD-1 blockade induces responses by inhibiting adaptive immune resistance

(2014) Paul C. Tumeh et al.   NATURE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Low-Dose Irradiation Programs Macrophage Differentiation to an iNOS+/M1 Phenotype that Orchestrates Effective T Cell Immunotherapy

(2013) Felix Klug et al.   CANCER CELL

Macrophage Regulation of Tumor Responses to Anticancer Therapies

(2013) Michele De Palma et al.   CANCER CELL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Marginating Dendritic Cells of the Tumor Microenvironment Cross-Present Tumor Antigens and Stably Engage Tumor-Specific T Cells

(2012) John J. Engelhardt et al.   CANCER CELL

Network Analysis Reveals Centrally Connected Genes and Pathways Involved in CD8+ T Cell Exhaustion versus Memory

(2012) Travis A. Doering et al.   IMMUNITY

Prognostic Significance of Tumor-Associated Macrophages in Solid Tumor: A Meta-Analysis of the Literature

(2012) Qiong-wen Zhang et al.   PLoS One

Leukocyte composition of human breast cancer

(2011) B. Ruffell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD40 Agonists Alter Tumor Stroma and Show Efficacy Against Pancreatic Carcinoma in Mice and Humans

(2011) G. L. Beatty et al.   SCIENCE

Leukocyte Complexity Predicts Breast Cancer Survival and Functionally Regulates Response to Chemotherapy

(2011) David G. DeNardo et al.   Cancer Discovery

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

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