A T cell resilience model associated with response to immunotherapy in multiple tumor types

[1]  F. Marincola,et al.  A human memory T-cell subset with stem cell-like properties , 2011, Nature Medicine.

[2]  M. Kalady,et al.  Cholesterol Induces CD8+ T Cell Exhaustion in the Tumor Microenvironment. , 2019, Cell metabolism.

[3]  T. Graeber,et al.  The sterol regulatory element binding proteins are essential for the metabolic programming of effector T cells and adaptive immunity , 2013, Nature Immunology.

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

[5]  Shao-xiang Xian,et al.  FIBP knockdown attenuates growth and enhances chemotherapy in colorectal cancer via regulating GSK3β-related pathways , 2018, Oncogenesis.

[6]  Trevor Hastie,et al.  An Introduction to Statistical Learning , 2013, Springer Texts in Statistics.

[7]  Manish R. Patel,et al.  PEGylated IL-10 (Pegilodecakin) Induces Systemic Immune Activation, CD8+ T Cell Invigoration and Polyclonal T Cell Expansion in Cancer Patients. , 2018, Cancer cell.

[8]  Haidong Dong,et al.  Immune resilience in response to cancer therapy , 2020, Cancer Immunology, Immunotherapy.

[9]  Graham M Lord,et al.  Cutting Edge: CD8+ T Cell Priming in the Absence of NK Cells Leads to Enhanced Memory Responses , 2011, The Journal of Immunology.

[10]  K. Wucherpfennig,et al.  Regulation of activated CD4+ T cells by NK cells via the Qa-1-NKG2A inhibitory pathway. , 2007, Immunity.

[11]  Chun Jimmie Ye,et al.  CRISPR activation and interference screens decode stimulation responses in primary human T cells , 2022, Science.

[12]  Aaron M. Newman,et al.  The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. , 2021, Cancer cell.

[13]  E. Ruppin,et al.  Systematic Investigation of Cytokine Signaling Activity at the Tissue and Single-Cell Level , 2021, Nature Methods.

[14]  Torsten Haferlach,et al.  An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase , 2008, British journal of haematology.

[15]  P. Agostinis,et al.  Defining the role of the tumor vasculature in antitumor immunity and immunotherapy , 2018, Cell Death & Disease.

[16]  Bo W. Han,et al.  Tumour heterogeneity and intercellular networks of nasopharyngeal carcinoma at single cell resolution , 2021, Nature Communications.

[17]  Itay Tirosh,et al.  Single-Cell RNA Sequencing in Cancer: Lessons Learned and Emerging Challenges. , 2019, Molecular cell.

[18]  S. Ghosh,et al.  Interleukin-4 is effective in restoring cytotoxic T cell activity that declines during in vivo progression of a murine B lymphoma , 1997, Cancer Immunology, Immunotherapy.

[19]  Stephen R. Williams,et al.  A single-cell and spatially resolved atlas of human breast cancers , 2021, Nature Genetics.

[20]  Jedd D. Wolchok,et al.  Cancer immunotherapy using checkpoint blockade , 2018, Science.

[21]  G. Altan-Bonnet,et al.  Stem-like CD8 T cells mediate response of adoptive cell immunotherapy against human cancer , 2020, Science.

[22]  Michael R Hicks,et al.  A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells. , 2020, Cell stem cell.

[23]  M. Llano,et al.  HLA-E is a major ligand for the natural killer inhibitory receptor CD94/NKG2A. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Xiaoyan Zhang,et al.  Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis , 2018, Nucleic Acids Res..

[25]  Bo Yu,et al.  CDD/SPARCLE: functional classification of proteins via subfamily domain architectures , 2016, Nucleic Acids Res..

[26]  Jun S. Liu,et al.  Inference of transcriptional regulation in cancers , 2015, Proceedings of the National Academy of Sciences.

[27]  Paul J. Hoover,et al.  Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma , 2018, Cell.

[28]  W. Wurst,et al.  Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells , 2015, Nature Biotechnology.

[29]  Alyssa R. Richman,et al.  Inhibitory CD161 receptor identified in glioma-infiltrating T cells by single-cell analysis , 2021, Cell.

[30]  Sarah A. Teichmann,et al.  Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors , 2018, Science.

[31]  Neville E. Sanjana,et al.  A genome-scale screen for synthetic drivers of T cell proliferation , 2022, Nature.

[32]  P. Romero,et al.  CART cells are prone to Fas- and DR5-mediated cell death , 2018, Journal of Immunotherapy for Cancer.

[33]  Jie Luo,et al.  Mechanisms and regulation of cholesterol homeostasis , 2019, Nature Reviews Molecular Cell Biology.

[34]  A. Ho,et al.  Atorvastatin Inhibits T Cell Activation through 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase without Decreasing Cholesterol Synthesis1 , 2007, The Journal of Immunology.

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

[36]  E John Wherry,et al.  Network analysis reveals centrally connected genes and pathways involved in CD8+ T cell exhaustion versus memory. , 2012, Immunity.

[37]  David L Rimm,et al.  Comparison of Biomarker Modalities for Predicting Response to PD-1/PD-L1 Checkpoint Blockade: A Systematic Review and Meta-analysis. , 2019, JAMA oncology.

[38]  P. Van Loo,et al.  Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition , 2021, Cell.

[39]  Jonathan M. Hernandez,et al.  Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer. , 2019, Cancer cell.

[40]  Fan Zhang,et al.  Cholesterol inhibits TCR signaling by directly restricting TCR-CD3 core tunnel motility. , 2022, Molecular cell.

[41]  David R. Jones,et al.  Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers , 2021, Nature.

[42]  David J. Duffy,et al.  Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma , 2015, Oncotarget.

[43]  Josef Spidlen,et al.  Preparing a Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) Compliant Manuscript Using the International Society for Advancement of Cytometry (ISAC) FCS File Repository (FlowRepository.org) , 2012, Current protocols in cytometry.

[44]  Henry W. Long,et al.  A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing , 2018, Science.

[45]  P. Carmeliet,et al.  Phenotype molding of stromal cells in the lung tumor microenvironment , 2018, Nature Medicine.

[46]  H. Stenmark,et al.  Cloning of an intracellular protein that binds selectively to mitogenic acidic fibroblast growth factor. , 1998, The Biochemical journal.

[47]  N. Restifo,et al.  An effective mouse model for adoptive cancer immunotherapy targeting neoantigens. , 2019, JCI insight.

[48]  E. Moon,et al.  CAR T Cells for Solid Tumors: New Strategies for Finding, Infiltrating, and Surviving in the Tumor Microenvironment , 2019, Front. Immunol..

[49]  Monika S. Kowalczyk,et al.  A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade , 2018, Cell.

[50]  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.

[51]  Michael A. Durante,et al.  Single-cell analysis reveals new evolutionary complexity in uveal melanoma , 2020, Nature Communications.

[52]  C. June,et al.  Emerging Cellular Therapies for Cancer. , 2019, Annual review of immunology.

[53]  K. Taskén,et al.  Molecular Mechanisms for cAMP-Mediated Immunoregulation in T cells – Role of Anchored Protein Kinase A Signaling Units , 2016, Front. Immunol..

[54]  D. Green,et al.  Activation‐induced cell death in T cells , 2003, Immunological reviews.

[55]  Minoru Kanehisa,et al.  KEGG as a reference resource for gene and protein annotation , 2015, Nucleic Acids Res..

[56]  S. Berger,et al.  An NK-like CAR T cell transition in CAR T cell dysfunction , 2021, Cell.

[57]  Joshua M. Korn,et al.  Next-generation characterization of the Cancer Cell Line Encyclopedia , 2019, Nature.

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

[59]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[60]  M. Ringnér,et al.  Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma , 2017, Nature Communications.

[61]  Shawn M. Gillespie,et al.  Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer , 2017, Cell.

[62]  Xueda Hu,et al.  Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer. , 2021, Cancer cell.

[63]  G. Freeman,et al.  Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response , 2018, Nature Medicine.

[64]  E. Campo,et al.  Interleukin-10 receptor signaling promotes the maintenance of a PD-1int TCF-1+ CD8+ T cell population that sustains anti-tumor immunity. , 2021, Immunity.

[65]  Feng Zhang,et al.  Identification of essential genes for cancer immunotherapy , 2017, Nature.

[66]  C. Caruso-Neves,et al.  IL-4: an important cytokine in determining the fate of T cells , 2014, Biophysical Reviews.

[67]  D. Speiser,et al.  Molecular profiling of CD8 T cells in autochthonous melanoma identifies Maf as driver of exhaustion , 2015, The EMBO journal.

[68]  Xueda Hu,et al.  Pan-cancer single-cell landscape of tumor-infiltrating T cells , 2021, Science.

[69]  Hans Bitter,et al.  Determinants of response and resistance to CD19 chimeric antigen receptor (CAR) T cell therapy of chronic lymphocytic leukemia , 2018, Nature Medicine.

[70]  Ambrose J. Carr,et al.  Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment , 2018, Cell.