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

[1]  John G Doench,et al.  Targeting Regnase-1 programs long-lived effector T cells for cancer therapy , 2019, Nature.

[2]  S. Horvat,et al.  CRISPRa-mediated FOXP3 gene upregulation in mammalian cells , 2019, Cell & Bioscience.

[3]  Howard Y. Chang,et al.  c-Jun overexpression in CAR T cells induces exhaustion resistance , 2019, Nature.

[4]  C. Mackall,et al.  Clinical lessons learned from the first leg of the CAR T cell journey , 2019, Nature Medicine.

[5]  G. Lucchini,et al.  Enhanced CAR T cell expansion and prolonged persistence in pediatric patients with ALL treated with a low-affinity CD19 CAR , 2019, Nature Medicine.

[6]  S. Planchais,et al.  Proline oxidation fuels mitochondrial respiration during dark-induced leaf senescence in Arabidopsis thaliana , 2019, Journal of experimental botany.

[7]  Ryan D. Chow,et al.  In vivo CRISPR screening in CD8 T cells with AAV-Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma , 2019, Nature Biotechnology.

[8]  Ryan D. Chow,et al.  Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells , 2019, Cell.

[9]  D. Irvine,et al.  Enhanced CAR–T cell activity against solid tumors by vaccine boosting through the chimeric receptor , 2019, Science.

[10]  Vanessa M. Hubbard-Lucey,et al.  The global pipeline of cell therapies for cancer , 2019, Nature Reviews Drug Discovery.

[11]  Haifeng Song,et al.  A safe and potent anti-CD19 CAR T cell therapy , 2019, Nature Medicine.

[12]  John G Doench,et al.  A CRISPR-Cas9 delivery system for in vivo screening of genes in the immune system , 2019, Nature Communications.

[13]  R. Hollingsworth,et al.  Turning the corner on therapeutic cancer vaccines , 2019, npj Vaccines.

[14]  C. Mackall,et al.  CAR T cell therapy: inroads to response and resistance , 2019, Nature Reviews Immunology.

[15]  G. Salles,et al.  Tisagenlecleucel in Adult Relapsed or Refractory Diffuse Large B‐Cell Lymphoma , 2019, The New England journal of medicine.

[16]  Brian D. Weitzner,et al.  De novo design of potent and selective mimics of IL-2 and IL-15 , 2019, Nature.

[17]  J. Greenbaum,et al.  Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression , 2018, Cell.

[18]  Andrew N Lane,et al.  Collagen prolyl 4-hydroxylase 1 is essential for HIF-1α stabilization and TNBC chemoresistance , 2018, Nature Communications.

[19]  Vanessa M. Hubbard-Lucey,et al.  Trends in the global immuno-oncology landscape , 2018, Nature Reviews Drug Discovery.

[20]  John Lamb,et al.  Guide Swap enables genome-scale pooled CRISPR–Cas9 screening in human primary cells , 2018, Nature Methods.

[21]  A. Ashworth,et al.  Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function , 2018, Cell.

[22]  James J. Collins,et al.  Universal Chimeric Antigen Receptors for Multiplexed and Logical Control of T Cell Responses , 2018, Cell.

[23]  David S. Wishart,et al.  MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis , 2018, Nucleic Acids Res..

[24]  E. Pearce,et al.  Unraveling the Complex Interplay Between T Cell Metabolism and Function. , 2018, Annual review of immunology.

[25]  C. June,et al.  CAR T cell immunotherapy for human cancer , 2018, Science.

[26]  Roy S. Herbst,et al.  The biology and management of non-small cell lung cancer , 2018, Nature.

[27]  C. R. Esteban,et al.  In Vivo Target Gene Activation via CRISPR/Cas9-Mediated Trans-epigenetic Modulation , 2017, Cell.

[28]  Ricardo J. Miragaia,et al.  Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation , 2017, Cell.

[29]  Howard Y. Chang,et al.  Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements , 2017, Nature Genetics.

[30]  Howard Y. Chang,et al.  Discovery of stimulation-responsive immune enhancers with CRISPR activation , 2017, Nature.

[31]  Jesse M. Engreitz,et al.  Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood , 2017, Nature.

[32]  David Lindenmayer,et al.  A subcellular map of the human proteome , 2017, Science.

[33]  Michel Sadelain,et al.  Therapeutic T cell engineering , 2017, Nature.

[34]  Wendell A Lim,et al.  Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. , 2017, Annual review of immunology.

[35]  Haiyan Tan,et al.  Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation , 2017, Immunity.

[36]  Mithat Gönen,et al.  Targeting a CAR to the TRAC locus with CRISPR/Cas9 enhances tumour rejection , 2017, Nature.

[37]  W. Lim,et al.  The Principles of Engineering Immune Cells to Treat Cancer , 2017, Cell.

[38]  J. Wargo,et al.  Primary, Adaptive, and Acquired Resistance to Cancer Immunotherapy , 2017, Cell.

[39]  M. Mann,et al.  L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity , 2016, Cell.

[40]  E. Wherry,et al.  Bioenergetic Insufficiencies Due to Metabolic Alterations Regulated by the Inhibitory Receptor PD-1 Are an Early Driver of CD8(+) T Cell Exhaustion. , 2016, Immunity.

[41]  Simon C Watkins,et al.  The Tumor Microenvironment Represses T Cell Mitochondrial Biogenesis to Drive Intratumoral T Cell Metabolic Insufficiency and Dysfunction. , 2016, Immunity.

[42]  J. Rathmell,et al.  A guide to immunometabolism for immunologists , 2016, Nature Reviews Immunology.

[43]  O. Kretz,et al.  Mitochondrial Dynamics Controls T Cell Fate through Metabolic Programming , 2016, Cell.

[44]  Lior Pachter,et al.  Differential analysis of RNA-seq incorporating quantification uncertainty , 2016, Nature Methods.

[45]  Tsippi Iny Stein,et al.  The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses , 2016, Current protocols in bioinformatics.

[46]  J. Marioni,et al.  Pooling across cells to normalize single-cell RNA sequencing data with many zero counts , 2016, Genome Biology.

[47]  Lior Pachter,et al.  Near-optimal probabilistic RNA-seq quantification , 2016, Nature Biotechnology.

[48]  Chih-Hao Chang,et al.  Emerging concepts of T cell metabolism as a target of immunotherapy , 2016, Nature Immunology.

[49]  Brian Keith,et al.  Distinct Signaling of Coreceptors Regulates Specific Metabolism Pathways and Impacts Memory Development in CAR T Cells. , 2016, Immunity.

[50]  A. Weiss,et al.  A CRISPR-Based Toolbox for Studying T Cell Signal Transduction , 2016, BioMed research international.

[51]  Feng Zhang,et al.  Orthogonal gene knock out and activation with a catalytically active Cas9 nuclease , 2015, Nature Biotechnology.

[52]  R. Schreiber,et al.  Metabolic Competition in the Tumor Microenvironment Is a Driver of Cancer Progression , 2015, Cell.

[53]  G. Church,et al.  Cas9 gRNA engineering for genome editing, activation and repression , 2015, Nature Methods.

[54]  David S. Wishart,et al.  MetaboAnalyst 3.0—making metabolomics more meaningful , 2015, Nucleic Acids Res..

[55]  Neville E. Sanjana,et al.  High-throughput functional genomics using CRISPR–Cas9 , 2015, Nature Reviews Genetics.

[56]  S. Rosenberg,et al.  Adoptive cell transfer as personalized immunotherapy for human cancer , 2015, Science.

[57]  W. Lowther,et al.  Proline dehydrogenase 2 (PRODH2) is a hydroxyproline dehydrogenase (HYPDH) and molecular target for treating primary hyperoxaluria. , 2015, The Biochemical journal.

[58]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[59]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[60]  John T. Chang,et al.  Molecular regulation of effector and memory T cell differentiation , 2014, Nature Immunology.

[61]  A. Dejean,et al.  Rho-GTPases as key regulators of T lymphocyte biology , 2014, Small GTPases.

[62]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

[63]  Robert Langer,et al.  CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling , 2014, Cell.

[64]  Bjoern Peters,et al.  In vivo RNA interference screens identify regulators of antiviral CD4(+) and CD8(+) T cell differentiation. , 2014, Immunity.

[65]  J. C. Love,et al.  In vivo discovery of immunotherapy targets in the tumour microenvironment , 2014, Nature.

[66]  Jieqing Zhu,et al.  Prolyl-4-hydroxylase α subunit 2 promotes breast cancer progression and metastasis by regulating collagen deposition , 2014, BMC Cancer.

[67]  S. Spicuglia,et al.  Active STAT5 Regulates T-bet and Eomesodermin Expression in CD8 T Cells and Imprints a T-bet–Dependent Tc1 Program with Repressed IL-6/TGF-β1 Signaling , 2013, The Journal of Immunology.

[68]  B. Faubert,et al.  Posttranscriptional Control of T Cell Effector Function by Aerobic Glycolysis , 2013, Cell.

[69]  A. Weinberg,et al.  The TNFRs OX40, 4-1BB, and CD40 as targets for cancer immunotherapy. , 2013, Current Opinion in Immunology.

[70]  J. Rathmell,et al.  Metabolic regulation of T lymphocytes. , 2013, Annual review of immunology.

[71]  A. Ferrando,et al.  The molecular basis of T cell acute lymphoblastic leukemia. , 2012, The Journal of clinical investigation.

[72]  Antoni Ribas,et al.  Tumor immunotherapy directed at PD-1. , 2012, The New England journal of medicine.

[73]  J. Asara,et al.  A positive/negative ion–switching, targeted mass spectrometry–based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue , 2012, Nature Protocols.

[74]  Drew M. Pardoll,et al.  The blockade of immune checkpoints in cancer immunotherapy , 2012, Nature Reviews Cancer.

[75]  W. Lowther,et al.  Metabolism of [13C5]hydroxyproline in vitro and in vivo: implications for primary hyperoxaluria. , 2012, American journal of physiology. Gastrointestinal and liver physiology.

[76]  G. V. D. van der Windt,et al.  Mitochondrial respiratory capacity is a critical regulator of CD8+ T cell memory development. , 2012, Immunity.

[77]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[78]  Hao Liu,et al.  CD28 costimulation improves expansion and persistence of chimeric antigen receptor-modified T cells in lymphoma patients. , 2011, The Journal of clinical investigation.

[79]  Wei Liu,et al.  Proline metabolism and microenvironmental stress. , 2010, Annual review of nutrition.

[80]  D. Funck,et al.  Non-redundant functions of two proline dehydrogenase isoforms in Arabidopsis , 2010, BMC Plant Biology.

[81]  S. Crotty,et al.  Effectors and memories: Bcl-6 and Blimp-1 in T and B lymphocyte differentiation , 2010, Nature Immunology.

[82]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[83]  B. Hoppe,et al.  The primary hyperoxalurias. , 2009, Kidney international.

[84]  Graziano Pesole,et al.  Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes , 2009, Nucleic Acids Res..

[85]  David S. Wishart,et al.  MetaboAnalyst: a web server for metabolomic data analysis and interpretation , 2009, Nucleic Acids Res..

[86]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[87]  D. Assimos,et al.  Increased protein intake on controlled oxalate diets does not increase urinary oxalate excretion , 2009, Urological Research.

[88]  D. Koller,et al.  The Immunological Genome Project: networks of gene expression in immune cells , 2008, Nature Immunology.

[89]  J. Phang,et al.  A Novel Function for Hydroxyproline Oxidase in Apoptosis through Generation of Reactive Oxygen Species* , 2008, Journal of Biological Chemistry.

[90]  Craig B. Thompson,et al.  Fuel feeds function: energy metabolism and the T-cell response , 2005, Nature Reviews Immunology.

[91]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[92]  Mark J. Smyth,et al.  Functional significance of the perforin/granzyme cell death pathway , 2002, Nature Reviews Immunology.

[93]  Kristin A. Hogquist,et al.  T cell receptor antagonist peptides induce positive selection , 1994, Cell.

[94]  Peter J. Peters Cytotoxic T lymphocyte granules are secretory lysosomes, containing both perforin and granzymes , 1991, The Journal of experimental medicine.

[95]  Simon C Watkins,et al.  The Tumor Microenvironment Represses T Cell Mitochondrial Biogenesis to Drive Intratumoral T Cell Metabolic Insufficiency and Dysfunction. , 2016, Immunity.

[96]  Laurens van der Maaten,et al.  Accelerating t-SNE using tree-based algorithms , 2014, J. Mach. Learn. Res..

[97]  L. Leserman,et al.  Activated STAT5 promotes long-lived cytotoxic CD8+ T cells that induce regression of autochthonous melanoma. , 2012, Cancer research.

[98]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[99]  Susumu Goto,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..