An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes

Tumor-associated high endothelial venules mediate lymphocyte entry into tumors and predict response to PD-1 plus CTLA-4 combination immunotherapy

(2022) Assia Asrir et al.   CANCER CELL

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

(2021) Kevin Litchfield et al.   CELL

Monocyte-derived S1P in the lymph node regulates immune responses

(2021) Audrey Baeyens et al.   NATURE

Expansible residence decentralizes immune homeostasis

(2021) Sathi Wijeyesinghe et al.   NATURE

Lesion-level heterogeneity of radiologic progression in patients treated with pembrolizumab

(2021) B.G. Topp et al.   ANNALS OF ONCOLOGY

PD-1+ Tcf1+ CD8+ T cells from established chronic infection can form memory while retaining a stableimprint of persistent antigen exposure

(2021) Mélanie Charmoy et al.   Cell Reports

Peripheral T cell expansion predicts tumour infiltration and clinical response

(2020) Thomas D. Wu et al.   NATURE

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

(2020) Jean-Christophe Beltra et al.   IMMUNITY

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart 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

PD-1hi CD8+ resident memory T cells balance immunity and fibrotic sequelae

(2019) Zheng Wang et al.   Science Immunology

Tick-TOX, it’s time for T cell exhaustion

(2019) Thomas H. Mann et al.   NATURE IMMUNOLOGY

Proliferating Transitory T Cells with an Effector-like Transcriptional Signature Emerge from PD-1+ Stem-like CD8+ T Cells during Chronic Infection

(2019) William H. Hudson et al.   IMMUNITY

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

(2019) Caroline S. Jansen et al.   NATURE

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

(2019) David Liu et al.   NATURE MEDICINE

PD-1 is required to maintain stem cell properties in human dental pulp stem cells

(2018) Yao Liu et al.   CELL DEATH AND DIFFERENTIATION

CD103+Tumor-Resident CD8+T Cells Are Associated with Improved Survival in Immunotherapy-Naïve Melanoma Patients and Expand Significantly During Anti–PD-1 Treatment

(2018) Jarem Edwards et al.   CLINICAL CANCER RESEARCH

The Transcription Factor Runx3 Establishes Chromatin Accessibility of cis -Regulatory Landscapes that Drive Memory Cytotoxic T Lymphocyte Formation

(2018) Dapeng Wang et al.   IMMUNITY

A Yin and Yang in Epithelial Immunology: The Roles of the α E (CD103)β 7 Integrin in T Cells

(2018) Jan-Hendrik B. Hardenberg et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

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

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

Tim-3 co-stimulation promotes short-lived effector T cells, restricts memory precursors, and is dispensable for T cell exhaustion

(2018) Lyndsay Avery et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of PD-1 during effector CD8 T cell differentiation

(2018) Eunseon Ahn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Thomas Duhen et al.   Nature Communications

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

(2018) Yannick Simoni et al.   NATURE

Armed and Ready: Transcriptional Regulation of Tissue-Resident Memory CD8 T Cells

(2018) Felix M. Behr et al.   Frontiers in Immunology

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

(2018) Hanjie Li et al.   CELL

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

(2018) Moshe Sade-Feldman et al.   CELL

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers

(2018) Wouter Scheper et al.   NATURE MEDICINE

Transforming of the Tumor Microenvironment: Implications for TGF-β Inhibition in the Context of Immune-Checkpoint Therapy

(2018) Stefanie Löffek   Journal of Oncology

Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells

(2017) Ruth Brignall et al.   JOURNAL OF IMMUNOLOGY

Survival of tissue-resident memory T cells requires exogenous lipid uptake and metabolism

(2017) Youdong Pan et al.   NATURE

Origin and differentiation of human memory CD8 T cells after vaccination

(2017) Rama S. Akondy et al.   NATURE

Runx3 programs CD8+ T cell residency in non-lymphoid tissues and tumours

(2017) J. Justin Milner et al.   NATURE

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Suboptimal T-cell receptor signaling compromises protein translation, ribosome biogenesis, and proliferation of mouse CD8 T cells

(2017) Thomas C. J. Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

Optimal Generation of Tissue-Resident but Not Circulating Memory T Cells during Viral Infection Requires Crosspriming by DNGR-1 + Dendritic Cells

(2016) Salvador Iborra et al.   IMMUNITY

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

(2016) Andrea Schietinger 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

Cell cycle arrest caused by MEK/ERK signaling is a mechanism for suppressing growth of antigen-hyperstimulated effector T cells

(2016) Shizuka Ohtsuka et al.   INTERNATIONAL IMMUNOLOGY

Local antigen in nonlymphoid tissue promotes resident memory CD8+T cell formation during viral infection

(2016) Tahsin N. Khan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Brain-resident memory T cells represent an autonomous cytotoxic barrier to viral infection

(2016) Karin Steinbach et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Antigen-dependent competition shapes the local repertoire of tissue-resident memory CD8 + T cells

(2016) Andreas Muschaweckh et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Immediate Dysfunction of Vaccine-Elicited CD8+T Cells Primed in the Absence of CD4+T Cells

(2016) Nicholas M. Provine et al.   JOURNAL OF IMMUNOLOGY

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

(2016) Se Jin Im et al.   NATURE

Programs for the persistence, vigilance and control of human CD8+ lung-resident memory T cells

(2016) Pleun Hombrink et al.   NATURE IMMUNOLOGY

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data

(2016) Martin Barron et al.   Scientific Reports

The Transcription Factor NFAT Promotes Exhaustion of Activated CD8 + T Cells

(2015) Gustavo J. Martinez et al.   IMMUNITY

CCCTC-binding factor controls the homeostatic maintenance and migration of Langerhans cells

(2015) Tae-Gyun Kim et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Genetic absence of PD-1 promotes accumulation of terminally differentiated exhausted CD8+T cells

(2015) Pamela M. Odorizzi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

CD8+CD103+Tumor–Infiltrating Lymphocytes Are Tumor-Specific Tissue-Resident Memory T Cells and a Prognostic Factor for Survival in Lung Cancer Patients

(2015) Fayçal Djenidi et al.   JOURNAL OF IMMUNOLOGY

Cutting Edge: CD69 Interference with Sphingosine-1-Phosphate Receptor Function Regulates Peripheral T Cell Retention

(2015) Laura K. Mackay et al.   JOURNAL OF IMMUNOLOGY

Human skin is protected by four functionally and phenotypically discrete populations of resident and recirculating memory T cells

(2015) Rei Watanabe et al.   Science Translational Medicine

Cancer Immunotherapy with Immunomodulatory Anti-CD137 and Anti-PD-1 Monoclonal Antibodies Requires BATF3-Dependent Dendritic Cells

(2015) A. R. Sanchez-Paulete et al.   Cancer Discovery

High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci

(2014) Kwangwoo Kim et al.   ANNALS OF THE RHEUMATIC DISEASES

Distinct Dendritic Cell Subsets Dictate the Fate Decision between Effector and Memory CD8+ T Cell Differentiation by a CD24-Dependent Mechanism

(2014) Taeg S. Kim et al.   IMMUNITY

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Resident memory CD8 T cells trigger protective innate and adaptive immune responses

(2014) J. M. Schenkel et al.   SCIENCE

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

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Tumor-Infiltrating Lymphocytes Expressing the Tissue Resident Memory Marker CD103 Are Associated with Increased Survival in High-Grade Serous Ovarian Cancer

(2013) J. R. Webb et al.   CLINICAL CANCER RESEARCH

Antigen Availability Determines CD8+ T Cell-Dendritic Cell Interaction Kinetics and Memory Fate Decisions

(2013) Sarah E. Henrickson et al.   IMMUNITY

T cells in the human metastatic melanoma microenvironment express site-specific homing receptors and retention integrins

(2013) Elise P. Salerno et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Sensing and alarm function of resident memory CD8+ T cells

(2013) Jason M Schenkel et al.   NATURE IMMUNOLOGY

The developmental pathway for CD103+CD8+ tissue-resident memory T cells of skin

(2013) Laura K Mackay et al.   NATURE IMMUNOLOGY

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Tolerance and exhaustion: defining mechanisms of T cell dysfunction

(2013) Andrea Schietinger et al.   TRENDS IN IMMUNOLOGY

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

(2012) Travis A. Doering et al.   IMMUNITY

Antigen-Independent Differentiation and Maintenance of Effector-like Resident Memory T Cells in Tissues

(2012) K. A. Casey et al.   JOURNAL OF IMMUNOLOGY

The Molecular Signature of Tissue Resident Memory CD8 T Cells Isolated from the Brain

(2012) L. M. Wakim et al.   JOURNAL OF IMMUNOLOGY

Progressive Loss of Memory T Cell Potential and Commitment to Exhaustion during Chronic Viral Infection

(2012) J. M. Angelosanto et al.   JOURNAL OF VIROLOGY

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

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

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The prognostic influence of tumour-infiltrating lymphocytes in cancer: a systematic review with meta-analysis

(2011) M J M Gooden et al.   BRITISH JOURNAL OF CANCER

Exhaustion of tumor-specific CD8+ T cells in metastases from melanoma patients

(2011) Lukas Baitsch et al.   JOURNAL OF CLINICAL INVESTIGATION

The genomic complexity of primary human prostate cancer

(2011) Michael F. Berger et al.   NATURE

Consensus-Phenotype Integration of Transcriptomic and Metabolomic Data Implies a Role for Metabolism in the Chemosensitivity of Tumour Cells

(2011) Rachel Cavill et al.   PLoS Computational Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Differentiation and Persistence of Memory CD8+ T Cells Depend on T Cell Factor 1

(2010) Xinyuan Zhou et al.   IMMUNITY

CD69 Suppresses Sphingosine 1-Phosophate Receptor-1 (S1P1) Function through Interaction with Membrane Helix 4

(2010) Alexander J. Bankovich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Memory T cells persisting within the brain after local infection show functional adaptations to their tissue of residence

(2010) L. M. Wakim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Tumor antigen-specific CD8 T cells infiltrating the tumor express high levels of PD-1 and are functionally impaired

(2009) M. Ahmadzadeh et al.   BLOOD

PD-1-Mediated Suppression of IL-2 Production Induces CD8+ T Cell Anergy In Vivo

(2009) S. Chikuma et al.   JOURNAL OF IMMUNOLOGY

Memory T cells in nonlymphoid tissue that provide enhanced local immunity during infection with herpes simplex virus

(2009) Thomas Gebhardt et al.   NATURE IMMUNOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Functional and genomic profiling of effector CD8 T cell subsets with distinct memory fates

(2008) Surojit Sarkar et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Selective expansion of a subset of exhausted CD8 T cells by  PD-L1 blockade

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