Spatiotemporal co-dependency between macrophages and exhausted CD8+ T cells in cancer

T cell exhaustion is a major impediment to anti-tumor immunity. However, it remains elusive how other immune cells in the tumor microenvironment (TME) contribute to this dysfunctional state. Here we show that the biology of tumor-associated macrophages (TAM) and exhausted T cells (Tex) in the TME is extensively linked. We demonstrate that in vivo depletion of TAM reduces exhaustion programs in tumor-infiltrating CD8+ T cells and reinvigorates their effector potential. Reciprocally, transcriptional and epigenetic profiling reveals that Tex express factors that actively recruit monocytes to the TME and shape their differentiation. Using lattice light sheet microscopy, we show that TAM and CD8+ T cells engage in unique long-lasting antigen-specific synaptic interactions that fail to activate T cells, but prime them for exhaustion, which is then accelerated in hypoxic conditions. Spatially resolved sequencing supports a spatiotemporal self-enforcing positive feedback circuit that is aligned to protect rather than destroy a tumor. Graphical Abstract

[1]  Shuqiang Li,et al.  Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma , 2021, Nature.

[2]  David M. Schauder,et al.  BATF regulates progenitor to cytolytic effector CD8+ T cell transition during chronic viral infection , 2021, Nature Immunology.

[3]  M. Krummel,et al.  Holistic Characterization of Tumor Monocyte-to-Macrophage Differentiation Integrates Distinct Immune Phenotypes in Kidney Cancer , 2021, bioRxiv.

[4]  T. Cheng,et al.  Single-Cell Analysis of the Pan-Cancer Immune Microenvironment and scTIME Portal , 2021, Cancer Immunology Research.

[5]  S. Turley,et al.  Fibroblast-macrophage reciprocal interactions in health, fibrosis, and cancer. , 2021, Immunity.

[6]  P. Hogan,et al.  BATF and IRF4 cooperate to counter exhaustion in tumor-infiltrating CAR T cells , 2021, Nature Immunology.

[7]  A. Olshen,et al.  A Pan-Cancer Census of Dominant Tumor Immune Archetypes , 2021, bioRxiv.

[8]  D. Pe’er,et al.  A unified atlas of CD8 T cell dysfunctional states in cancer and infection. , 2021, Molecular cell.

[9]  Howard Y. Chang,et al.  Transient “rest” restores functionality in exhausted CAR-T cells via epigenetic remodeling , 2021, Science.

[10]  Steven L. Chang,et al.  Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma , 2021, Cancer cell.

[11]  Steven L. Chang,et al.  Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. , 2021, Cancer cell.

[12]  Xueda Hu,et al.  A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells , 2021, Cell.

[13]  Greg M. Delgoffe,et al.  Mitochondrial stress induced by continuous stimulation under hypoxia rapidly drives T cell exhaustion , 2021, Nature immunology.

[14]  Lihua Zhang,et al.  Inference and analysis of cell-cell communication using CellChat , 2020, Nature Communications.

[15]  M. Philip,et al.  CD8+ T cell differentiation and dysfunction in cancer , 2016, Nature Reviews Immunology.

[16]  D. Figarella-Branger,et al.  SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution. , 2020, Cell metabolism.

[17]  José Alquicira-Hernández,et al.  Nebulosa recovers single cell gene expression signals by kernel density estimation , 2020, bioRxiv.

[18]  A. Amalfitano,et al.  SLAMF7 Signaling Reprograms T Cells Towards Exhaustion in the Tumor Microenvironment , 2020, SSRN Electronic Journal.

[19]  David Chisanga,et al.  Early precursor T cells establish and propagate T cell exhaustion in chronic infection , 2020, Nature Immunology.

[20]  Maxim N. Artyomov,et al.  TREM2 Modulation Remodels the Tumor Myeloid Landscape Enhancing Anti-PD-1 Immunotherapy , 2020, Cell.

[21]  I. Amit,et al.  Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer , 2020, Cell.

[22]  D. Pe’er,et al.  A unified atlas of CD8 T cell dysfunctional states in cancer and infection , 2020, bioRxiv.

[23]  Christopher S. McGinnis,et al.  ZipSeq: barcoding for real-time mapping of single cell transcriptomes , 2020, Nature Methods.

[24]  Howard Y. Chang,et al.  Impaired mitochondrial oxidative phosphorylation limits the self-renewal of T cells exposed to persistent antigen , 2020, Nature Immunology.

[25]  E. Wherry,et al.  Developmental Relationships of Four Exhausted CD8+ T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms. , 2020, Immunity.

[26]  A. Kamphorst,et al.  An intra-tumoral niche maintains and differentiates stem-like CD8 T cells , 2019, Nature.

[27]  Elisabeth F. Heuston,et al.  Single-Cell RNA-Seq Reveals TOX as a Key Regulator of CD8+ T cell Persistence in Chronic Infection , 2019, Nature Immunology.

[28]  M. Delorenzi,et al.  TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection , 2019, Nature.

[29]  Yong Liu,et al.  TOX is a critical regulator of tumour-specific T cell differentiation , 2019, Nature.

[30]  S. Berger,et al.  TOX transcriptionally and epigenetically programs CD8+ T cell exhaustion , 2019, Nature.

[31]  Maria Anna Rapsomaniki,et al.  A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer , 2019, Cell.

[32]  Howard Y. Chang,et al.  Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion , 2019, Nature Biotechnology.

[33]  Chun Jimmie Ye,et al.  Unleashing Type-2 Dendritic Cells to Drive Protective Antitumor CD4+ T Cell Immunity , 2019, Cell.

[34]  R. Satija,et al.  Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression , 2019, Genome Biology.

[35]  Andrew J. Hill,et al.  The single cell transcriptional landscape of mammalian organogenesis , 2019, Nature.

[36]  F. Hodi,et al.  Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade , 2019, Nature Immunology.

[37]  Brian Ruffell,et al.  Macrophages as regulators of tumour immunity and immunotherapy , 2019, Nature Reviews Immunology.

[38]  Daniel E. Speiser,et al.  Intratumoral Tcf1+PD‐1+CD8+ T Cells with Stem‐like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy , 2019, Immunity.

[39]  Mark Gerstein,et al.  GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..

[40]  Jennifer L. Guerriero Macrophages: Their Untold Story in T Cell Activation and Function. , 2019, International review of cell and molecular biology.

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

[42]  Mauro A. A. Castro,et al.  The chromatin accessibility landscape of primary human cancers , 2018, Science.

[43]  C. Klein,et al.  A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small cell lung cancer treated with PD-1 blockade , 2018, Nature Medicine.

[44]  S. Asthana,et al.  A natural killer–dendritic cell axis defines checkpoint therapy–responsive tumor microenvironments , 2018, Nature Medicine.

[45]  N. Bercovici,et al.  Macrophages impede CD8 T cells from reaching tumor cells and limit the efficacy of anti–PD-1 treatment , 2018, Proceedings of the National Academy of Sciences.

[46]  R. Weinberg,et al.  Understanding the tumor immune microenvironment (TIME) for effective therapy , 2018, Nature Medicine.

[47]  Jia Gu,et al.  fastp: an ultra-fast all-in-one FASTQ preprocessor , 2018, bioRxiv.

[48]  W. Shi,et al.  Transcription Factor IRF4 Promotes CD8+ T Cell Exhaustion and Limits the Development of Memory‐like T Cells during Chronic Infection , 2017, Immunity.

[49]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[50]  Christina S. Leslie,et al.  Chromatin states define tumor-specific T cell dysfunction and reprogramming , 2017, Nature.

[51]  Frederic Bartumeus,et al.  Visualizing dynamic microvillar search and stabilization during ligand detection by T cells , 2017, Science.

[52]  T. Gajewski,et al.  Tumor-Residing Batf3 Dendritic Cells Are Required for Effector T Cell Trafficking and Adoptive T Cell Therapy. , 2017, Cancer cell.

[53]  M. Krummel,et al.  Tumor-infiltrating lymphocytes are dynamically desensitized to antigen but are maintained by homeostatic cytokine. , 2016, JCI insight.

[54]  S. Berger,et al.  Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade , 2016, Science.

[55]  Matheus C. Bürger,et al.  Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy , 2016, Nature.

[56]  M. Delorenzi,et al.  High antigen levels induce an exhausted phenotype in a chronic infection without impairing T cell expansion and survival , 2016, The Journal of experimental medicine.

[57]  Jeffrey J Delrow,et al.  Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis. , 2016, Immunity.

[58]  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.

[59]  T. Kaisho,et al.  Critical Role for CD103(+)/CD141(+) Dendritic Cells Bearing CCR7 for Tumor Antigen Trafficking and Priming of T Cell Immunity in Melanoma. , 2016, Cancer cell.

[60]  F. Ginhoux,et al.  Expansion and Activation of CD103(+) Dendritic Cell Progenitors at the Tumor Site Enhances Tumor Responses to Therapeutic PD-L1 and BRAF Inhibition. , 2016, Immunity.

[61]  Ash A. Alizadeh,et al.  Abstract PR09: The prognostic landscape of genes and infiltrating immune cells across human cancers , 2015 .

[62]  A. Regev,et al.  Spatial reconstruction of single-cell gene expression , 2015, Nature Biotechnology.

[63]  Sebastian Amigorena,et al.  Dissecting the tumor myeloid compartment reveals rare activating antigen-presenting cells critical for T cell immunity. , 2014, Cancer cell.

[64]  R. Emerson,et al.  PD-1 blockade induces responses by inhibiting adaptive immune resistance , 2014, Nature.

[65]  Sebastian Amigorena,et al.  Dissecting the Tumor Myeloid Compartment Reveals Rare Activating Antigen-Presenting Cells Critical for T Cell Immunity. , 2014, Cancer cell.

[66]  Charity W. Law,et al.  voom: precision weights unlock linear model analysis tools for RNA-seq read counts , 2014, Genome Biology.

[67]  K. Schäkel,et al.  Low-dose irradiation programs macrophage differentiation to an iNOS⁺/M1 phenotype that orchestrates effective T cell immunotherapy. , 2013, Cancer cell.

[68]  C. Lewis,et al.  Macrophage regulation of tumor responses to anticancer therapies. , 2013, Cancer cell.

[69]  Clotilde Théry,et al.  CD8+ tumor-infiltrating T cells are trapped in the tumor-dendritic cell network. , 2013, Neoplasia.

[70]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[71]  Yuquan Wei,et al.  Prognostic Significance of Tumor-Associated Macrophages in Solid Tumor: A Meta-Analysis of the Literature , 2012, PloS one.

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

[73]  Mikala Egeblad,et al.  Marginating dendritic cells of the tumor microenvironment cross-present tumor antigens and stably engage tumor-specific T cells. , 2012, Cancer cell.

[74]  Laura J. Esserman,et al.  Leukocyte composition of human breast cancer , 2011, Proceedings of the National Academy of Sciences.

[75]  Karin Jirström,et al.  Leukocyte complexity predicts breast cancer survival and functionally regulates response to chemotherapy. , 2011, Cancer discovery.

[76]  Drew A. Torigian,et al.  CD40 Agonists Alter Tumor Stroma and Show Efficacy Against Pancreatic Carcinoma in Mice and Humans , 2011, Science.

[77]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[78]  E. Wherry,et al.  Molecular signature of CD8+ T cell exhaustion during chronic viral infection. , 2007, Immunity.

[79]  Z. Trajanoski,et al.  Type, Density, and Location of Immune Cells Within Human Colorectal Tumors Predict Clinical Outcome , 2006, Science.

[80]  Gordon K. Smyth,et al.  limma: Linear Models for Microarray Data , 2005 .