Reductive carboxylation epigenetically instructs T cell differentiation

Orthogonal cytokine engineering enables novel synthetic effector states escaping canonical exhaustion in tumor-rejecting CD8+ T cells

(2023) Jesus Corria-Osorio et al.   NATURE IMMUNOLOGY

A genome-scale gain-of-function CRISPR screen in CD8 T cells identifies proline metabolism as a means to enhance CAR-T therapy

(2022) Lupeng Ye et al.   Cell Metabolism

Both APRIL and antibody-fragment-based CAR T cells for myeloma induce BCMA downmodulation by trogocytosis and internalization

(2022) Nicolas Camviel et al.   Journal for ImmunoTherapy of Cancer

Integrative bulk and single-cell profiling of pre-manufacture T-cell populations reveals factors mediating long-term persistence of CAR T-cell therapy

(2021) Gregory M Chen et al.   Cancer Discovery

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

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

GTRD: an integrated view of transcription regulation

(2020) Semyon Kolmykov et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Metabolic Profiling Using Stable Isotope Tracing Reveals Distinct Patterns of Glucose Utilization by Physiologically Activated CD8+ T Cells

(2019) Eric H. Ma et al.   IMMUNITY

Early TCR Signaling Induces Rapid Aerobic Glycolysis Enabling Distinct Acute T Cell Effector Functions

(2018) Ashley V. Menk et al.   Cell Reports

CART cells are prone to Fas- and DR5-mediated cell death

(2018) Benjamin O. Tschumi et al.   Journal for ImmunoTherapy of Cancer

Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids

(2018) Michael D. Neinast et al.   Cell Metabolism

Polycomb Repressive Complex 2-Mediated Chromatin Repression Guides Effector CD8 + T Cell Terminal Differentiation and Loss of Multipotency

(2017) Simon M. Gray et al.   IMMUNITY

Studies on the Interaction of the Histone Demethylase KDM5B with Tricarboxylic Acid Cycle Intermediates

(2017) Hanna Tarhonskaya et al.   JOURNAL OF MOLECULAR BIOLOGY

Origin and differentiation of human memory CD8 T cells after vaccination

(2017) Rama S. Akondy et al.   NATURE

AG-221, a First-in-Class Therapy Targeting Acute Myeloid Leukemia Harboring Oncogenic IDH2 Mutations

(2017) Katharine Yen et al.   Cancer Discovery

Atropos: specific, sensitive, and speedy trimming of sequencing reads

(2017) John P. Didion et al.   PeerJ

CD8 + T Cells Utilize Highly Dynamic Enhancer Repertoires and Regulatory Circuitry in Response to Infections

(2016) Bing He et al.   IMMUNITY

Reductive carboxylation supports redox homeostasis during anchorage-independent growth

(2016) Lei Jiang et al.   NATURE

S-2-hydroxyglutarate regulates CD8+ T-lymphocyte fate

(2016) Petros A. Tyrakis et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

(2016) René Dreos et al.   NUCLEIC ACIDS RESEARCH

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

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

Production of retroviral constructs for effective transfer and expression of T-cell receptor genes using Golden Gate cloning

(2015) Lori V. Coren et al.   BIOTECHNIQUES

Acetyl Coenzyme A: A Central Metabolite and Second Messenger

(2015) Federico Pietrocola et al.   Cell Metabolism

The interplay of histone modifications - writers that read

(2015) T. Zhang et al.   EMBO REPORTS

The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection

(2015) Claudia X. Dominguez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

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

Adoptive transfer of activated marrow-infiltrating lymphocytes induces measurable antitumor immunity in the bone marrow in multiple myeloma

(2015) Kimberly A. Noonan et al.   Science Translational Medicine

Metformin Antagonizes Cancer Cell Proliferation by Suppressing Mitochondrial-Dependent Biosynthesis

(2015) Takla Griss et al.   PLOS BIOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Distinct Epigenetic Signatures Delineate Transcriptional Programs during Virus-Specific CD8+ T Cell Differentiation

(2014) Brendan E. Russ et al.   IMMUNITY

Mitochondria Are Required for Antigen-Specific T Cell Activation through Reactive Oxygen Species Signaling

(2013) Laura A. Sena et al.   IMMUNITY

Glutamine-driven oxidative phosphorylation is a major ATP source in transformed mammalian cells in both normoxia and hypoxia

(2013) J. Fan et al.   Molecular Systems Biology

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Fueling Immunity: Insights into Metabolism and Lymphocyte Function

(2013) E. L. Pearce et al.   SCIENCE

Targeted Inhibition of Mutant IDH2 in Leukemia Cells Induces Cellular Differentiation

(2013) F. Wang et al.   SCIENCE

Mitochondrial Reactive Oxygen Species Promote Epidermal Differentiation and Hair Follicle Development

(2013) R. B. Hamanaka et al.   Science Signaling

Reductive glutamine metabolism is a function of the α-ketoglutarate to citrate ratio in cells

(2013) Sarah-Maria Fendt et al.   Nature Communications

Inhibition of  -KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors

(2012) M. Xiao et al.   GENES & DEVELOPMENT

PDK1 regulation of mTOR and hypoxia-inducible factor 1 integrate metabolism and migration of CD8+T cells

(2012) David K. Finlay et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

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

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

The Transcription Factor Myc Controls Metabolic Reprogramming upon T Lymphocyte Activation

(2011) Ruoning Wang et al.   IMMUNITY

Reductive carboxylation supports growth in tumour cells with defective mitochondria

(2011) Andrew R. Mullen et al.   NATURE

Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia

(2011) Christian M. Metallo et al.   NATURE

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

(2010) Lihua J Zhu et al.   BMC BIOINFORMATICS

Isocitrate Dehydrogenase 1 and 2 Mutations in Cancer: Alterations at a Crossroads of Cellular Metabolism

(2010) Z. J. Reitman et al.   JNCI-Journal of the National Cancer Institute

Differential12C-/13C-Isotope Dansylation Labeling and Fast Liquid Chromatography/Mass Spectrometry for Absolute and Relative Quantification of the Metabolome

(2009) Kevin Guo et al.   ANALYTICAL CHEMISTRY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Genome-wide Analysis of Histone Methylation Reveals Chromatin State-Based Regulation of Gene Transcription and Function of Memory CD8+ T Cells

(2009) Yasuto Araki et al.   IMMUNITY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation

(2009) K. E. Wellen et al.   SCIENCE