Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence

Epigenetic regulation of T cell exhaustion

(2022) Julia A. Belk et al.   NATURE IMMUNOLOGY

Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions

(2021) Ryan A. Flynn et al.   CELL

In vivo CRISPR screening reveals nutrient signaling processes underpinning CD8+ T cell fate decisions

(2021) Hongling Huang et al.   CELL

In vivo CD8+ T cell CRISPR screening reveals control by Fli1 in infection and cancer

(2021) Zeyu Chen et al.   CELL

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

Recruiting T cells in cancer immunotherapy

(2021) Kathryn E. Yost et al.   SCIENCE

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Identification of a T-bethi Quiescent Exhausted CD8 T Cell Subpopulation That Can Differentiate into TIM3+CX3CR1+ Effectors and Memory-like Cells

(2021) Saravanan Raju et al.   JOURNAL OF IMMUNOLOGY

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

(2021) Hyungseok Seo et al.   NATURE IMMUNOLOGY

Not-so-opposite ends of the spectrum: CD8+ T cell dysfunction across chronic infection, cancer and autoimmunity

(2021) Jenna L. Collier et al.   NATURE IMMUNOLOGY

ARID1A determines luminal identity and therapeutic response in estrogen-receptor-positive breast cancer

(2020) Guotai Xu et al.   NATURE GENETICS

Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies

(2020) Theodore L. Roth 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

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

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

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

BATF3 programs CD8+ T cell memory

(2020) Marco A. Ataide et al.   NATURE IMMUNOLOGY

Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation

(2019) Johan Henriksson et al.   CELL

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

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

NR4A transcription factors limit CAR T cell function in solid tumours

(2019) Joyce Chen et al.   NATURE

CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer

(2019) Laura M. McLane et al.   Annual Review of Immunology

A CRISPR-Cas9 delivery system for in vivo screening of genes in the immune system

(2019) Martin W. LaFleur et al.   Nature Communications

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

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

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

Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells

(2019) Matthew B. Dong et al.   CELL

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

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

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

c-Jun overexpression in CAR T cells induces exhaustion resistance

(2019) Rachel C. Lynn et al.   NATURE

Targeting REGNASE-1 programs long-lived effector T cells for cancer therapy

(2019) Jun Wei et al.   NATURE

OUP accepted manuscript

(2018)   BIOINFORMATICS

Determinants of response and resistance to CD19 chimeric antigen receptor (CAR) T cell therapy of chronic lymphocytic leukemia

(2018) Joseph A. Fraietta et al.   NATURE MEDICINE

Cancer immunotherapy using checkpoint blockade

(2018) Antoni Ribas et al.   SCIENCE

Disruption of TET2 promotes the therapeutic efficacy of CD19-targeted T cells

(2018) Joseph A. Fraietta et al.   NATURE

TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells

(2018) Sanjeev Mariathasan et al.   NATURE

Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function

(2018) Eric Shifrut et al.   CELL

Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

(2018) Nazar Mashtalir et al.   CELL

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection

(2017) Thomas Vierbuchen et al.   MOLECULAR CELL

Chromatin states define tumour-specific T cell dysfunction and reprogramming

(2017) Mary Philip et al.   NATURE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

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

(2017) M Ryan Corces et al.   NATURE METHODS

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

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

(2016) Meromit Singer et al.   CELL

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

(2016) Andrea Schietinger et al.   IMMUNITY

Dynamic Changes in Chromatin Accessibility Occur in CD8 + T Cells Responding to Viral Infection

(2016) James P. Scott-Browne et al.   IMMUNITY

Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes

(2016) David W Morgens et al.   NATURE BIOTECHNOLOGY

ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice

(2016) Radhika Mathur et al.   NATURE GENETICS

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

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

(2016) K. E. Pauken et al.   SCIENCE

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

(2015) Oren Parnas et al.   CELL

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

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

T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection

(2015) Eoin F. McKinney et al.   NATURE

4-1BB costimulation ameliorates T cell exhaustion induced by tonic signaling of chimeric antigen receptors

(2015) Adrienne H Long et al.   NATURE MEDICINE

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Progenitor and Terminal Subsets of CD8+ T Cells Cooperate to Contain Chronic Viral Infection

(2012) M. A. Paley et al.   SCIENCE

ATP-dependent chromatin remodeling: genetics, genomics and mechanisms

(2011) Diana C Hargreaves et al.   CELL RESEARCH

Targeting Tim-3 and PD-1 pathways to reverse T cell exhaustion and restore anti-tumor immunity

(2010) Kaori Sakuishi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY