Longitudinal single cell profiling of regulatory T cells identifies IL-33 as a driver of tumor immunosuppression

Regulatory T cells (Tregs) can impair anti-tumor immune responses and are associated with poor prognosis in multiple cancer types. Tregs in human tumors span diverse transcriptional states distinct from those of peripheral Tregs, but their contribution to tumor development remains unknown. Here, we used single cell RNA-Seq to longitudinally profile conventional CD4+ T cells (Tconv) and Tregs in a genetic mouse model of lung adenocarcinoma. Tissue-infiltrating and peripheral CD4+ T cells differed, highlighting divergent pathways of activation during tumorigenesis. Longitudinal shifts in Treg heterogeneity suggested increased terminal differentiation and stabilization of an effector phenotype over time. In particular, effector Tregs had enhanced expression of the interleukin 33 receptor ST2. Treg-specific deletion of ST2 reduced effector Tregs, increased infiltration of CD8+ T cells into tumors, and decreased tumor burden. Our study shows that ST2 plays a critical role in Treg-mediated immunosuppression in cancer, highlighting new potential paths for therapeutic intervention.

[1]  R. Weissleder,et al.  Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types , 2018, Proceedings of the National Academy of Sciences.

[2]  Boxi Kang,et al.  Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing , 2018, Nature Medicine.

[3]  D. Hanahan,et al.  GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth , 2018, Cancer cell.

[4]  A. McKenzie,et al.  TH2 cell development and function , 2017, Nature Reviews Immunology.

[5]  A. Rudensky,et al.  A nonimmune function of T cells in promoting lung tumor progression , 2017, The Journal of experimental medicine.

[6]  Ricardo J. Miragaia,et al.  Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation , 2019, Immunity.

[7]  Le Cong,et al.  A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells , 2017, Cell.

[8]  Nipun A. Mistry,et al.  Generation of RORγt+ Antigen-Specific T Regulatory 17 Cells from Foxp3+ Precursors in Autoimmunity. , 2017, Cell reports.

[9]  S. Shan,et al.  IL-33 blockade suppresses tumor growth of human lung cancer through direct and indirect pathways in a preclinical model , 2017, Oncotarget.

[10]  R. Lechler,et al.  An Atlas of Human Regulatory T Helper-like Cells Reveals Features of Th2-like Tregs that Support a Tumorigenic Environment , 2017, Cell reports.

[11]  Boxi Kang,et al.  Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing , 2017, Cell.

[12]  J. Kirkwood,et al.  Interferon-γ Drives Treg Fragility to Promote Anti-tumor Immunity , 2017, Cell.

[13]  I. Sagap,et al.  Molecular Signatures of Human Regulatory T Cells in Colorectal Cancer and Polyps , 2017, Front. Immunol..

[14]  A. Rudensky,et al.  Stability and function of regulatory T cells expressing the transcription factor T-bet , 2017, Nature.

[15]  Peter Bankhead,et al.  QuPath: Open source software for digital pathology image analysis , 2017, Scientific Reports.

[16]  S. Sakaguchi,et al.  Regulatory T cells in cancer immunotherapy , 2016, Cell Research.

[17]  H. Stunnenberg,et al.  Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells , 2016, Immunity.

[18]  G. Plitas,et al.  Regulatory T Cells Exhibit Distinct Features in Human Breast Cancer. , 2016, Immunity.

[19]  S. Shan,et al.  IL-33 signaling fuels outgrowth and metastasis of human lung cancer. , 2016, Biochemical and biophysical research communications.

[20]  C. Leslie,et al.  Memory of Inflammation in Regulatory T Cells , 2016, Cell.

[21]  D. Mock,et al.  Innate-like functions of natural killer T cell subsets result from highly divergent gene programs , 2016, Nature Immunology.

[22]  M. Hattori,et al.  Two FOXP3+CD4+ T cell subpopulations distinctly control the prognosis of colorectal cancers , 2016, Nature Medicine.

[23]  A. Rudensky,et al.  T cell receptor signalling in the control of regulatory T cell differentiation and function , 2016, Nature Reviews Immunology.

[24]  Anneliese O. Speak,et al.  T cell fate and clonality inference from single cell transcriptomes , 2016, Nature Methods.

[25]  Nikhil S. Joshi,et al.  A Modular Assembly Platform for Rapid Generation of DNA Constructs , 2016, Scientific Reports.

[26]  C. Benoist,et al.  Poor Repair of Skeletal Muscle in Aging Mice Reflects a Defect in Local, Interleukin-33-Dependent Accumulation of Regulatory T Cells. , 2016, Immunity.

[27]  Joseph L. Herman,et al.  Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis , 2015, Nature Methods.

[28]  Mikhail Pogorelyy,et al.  VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires , 2015, PLoS Comput. Biol..

[29]  Bin Shang,et al.  Prognostic value of tumor-infiltrating FoxP3+ regulatory T cells in cancers: a systematic review and meta-analysis , 2015, Scientific Reports.

[30]  D. Campbell Control of Regulatory T Cell Migration, Function, and Homeostasis , 2015, The Journal of Immunology.

[31]  Nikhil S. Joshi,et al.  Regulatory T Cells in Tumor-Associated Tertiary Lymphoid Structures Suppress Anti-tumor T Cell Responses. , 2015, Immunity.

[32]  A. Rudensky,et al.  A Distinct Function of Regulatory T Cells in Tissue Protection , 2015, Cell.

[33]  Fabian J. Theis,et al.  destiny: diffusion maps for large-scale single-cell data in R , 2015, Bioinform..

[34]  Aurélien Marabelle,et al.  Immune Checkpoint Modulation for Non–Small Cell Lung Cancer , 2015, Clinical Cancer Research.

[35]  Richard T. Lee,et al.  Myocardial pressure overload induces systemic inflammation through endothelial cell IL-33 , 2015, Proceedings of the National Academy of Sciences.

[36]  Christine M. Miller,et al.  Antigen- and cytokine-driven accumulation of regulatory T cells in visceral adipose tissue of lean mice. , 2015, Cell metabolism.

[37]  W. Shi,et al.  The transcriptional regulators IRF4, BATF and IL-33 orchestrate development and maintenance of adipose tissue–resident regulatory T cells , 2015, Nature Immunology.

[38]  F. Végran,et al.  Th9 Cells: a Novel Cd4 T-cell Subset in the Immune War against Cancer the Role of Cd4 T-cell Polarization in Cancer the Biology of Th9 Cells the Mechanism of the Antitumor Effects of Th9 Future Direction and Concluding Remarks , 2022 .

[39]  G. Weiner,et al.  Cancer immunotherapy and breaking immune tolerance: new approaches to an old challenge. , 2015, Cancer research.

[40]  Li Zhang,et al.  IL-33 promotes ST2-dependent lung fibrosis by the induction of alternatively activated macrophages and innate lymphoid cells in mice , 2014, The Journal of allergy and clinical immunology.

[41]  J. Girard,et al.  IL-33: an alarmin cytokine with crucial roles in innate immunity, inflammation and allergy. , 2014, Current opinion in immunology.

[42]  P. Gestraud,et al.  Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes. , 2014, Cell reports.

[43]  Francisco J. Sánchez-Rivera,et al.  Rapid modeling of cooperating genetic events in cancer through somatic genome editing , 2014, Nature.

[44]  Yasmine Belkaid,et al.  The Alarmin IL-33 Promotes Regulatory T Cell Function in the Intestine , 2014, Nature.

[45]  N. Arsenijević,et al.  Interleukin‐33/ST2 axis promotes breast cancer growth and metastases by facilitating intratumoral accumulation of immunosuppressive and innate lymphoid cells , 2014, International journal of cancer.

[46]  Kairong Cui,et al.  The transcription factors T-bet and Runx are required for the ontogeny of pathogenic interferon-γ-producing T helper 17 cells. , 2014, Immunity.

[47]  C. Benoist,et al.  A Special Population of Regulatory T Cells Potentiates Muscle Repair , 2013, Cell.

[48]  Åsa K. Björklund,et al.  Smart-seq2 for sensitive full-length transcriptome profiling in single cells , 2013, Nature Methods.

[49]  G. Plitas,et al.  Transient regulatory T cell ablation deters oncogene-driven breast cancer and enhances radiotherapy , 2013, The Journal of experimental medicine.

[50]  R. Ribeiro,et al.  Mechanisms Underlying CD4+ Treg Immune Regulation in the Adult: From Experiments to Models , 2013, Front. Immunol..

[51]  J. Wolchok,et al.  Fc-dependent depletion of tumor-infiltrating regulatory T cells co-defines the efficacy of anti–CTLA-4 therapy against melanoma , 2013, The Journal of experimental medicine.

[52]  Michael R. Green,et al.  Depleting tumor-specific Tregs at a single site eradicates disseminated tumors. , 2013, The Journal of clinical investigation.

[53]  Rona S. Gertner,et al.  Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells , 2013, Nature.

[54]  C. Sima,et al.  Clinical impact of immune microenvironment in stage I lung adenocarcinoma: tumor interleukin-12 receptor β2 (IL-12Rβ2), IL-7R, and stromal FoxP3/CD3 ratio are independent predictors of recurrence. , 2013, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[55]  Sven Malchow,et al.  Basic principles of tumor-associated regulatory T cell biology. , 2013, Trends in immunology.

[56]  D. Jouan-Rimbaud Bouveresse,et al.  Independent components analysis with the JADE algorithm , 2012 .

[57]  D. Roos,et al.  The cytokines interleukin 27 and interferon-γ promote distinct Treg cell populations required to limit infection-induced pathology. , 2012, Immunity.

[58]  H. Sung,et al.  Cutting Edge: Intravascular Staining Redefines Lung CD8 T Cell Responses , 2012, The Journal of Immunology.

[59]  D. Campbell,et al.  T-bet+ Treg Cells Undergo Abortive Th1 Cell Differentiation due to Impaired Expression of IL-12 Receptor β2 , 2012, Immunity.

[60]  K. Odunsi,et al.  CXCR3+ T regulatory cells selectively accumulate in human ovarian carcinomas to limit type I immunity. , 2012, Cancer research.

[61]  T. Malek,et al.  IL-2 Receptor Signaling Is Essential for the Development of Klrg1+ Terminally Differentiated T Regulatory Cells , 2012, The Journal of Immunology.

[62]  A. Regev,et al.  Induction and molecular signature of pathogenic TH17 cells , 2012, Nature Immunology.

[63]  C. Benoist,et al.  PPARγ is a major driver of the accumulation and phenotype of adipose-tissue Treg cells , 2012, Nature.

[64]  C. Sautès-Fridman,et al.  The immune contexture in human tumours: impact on clinical outcome , 2012, Nature Reviews Cancer.

[65]  A. Rudensky,et al.  Regulatory T cells: mechanisms of differentiation and function. , 2012, Annual review of immunology.

[66]  G. Dranoff,et al.  Experimental mouse tumour models: what can be learnt about human cancer immunology? , 2011, Nature Reviews Immunology.

[67]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[68]  T. Jacks,et al.  Uncoupling cancer mutations reveals critical timing of p53 loss in sarcomagenesis. , 2011, Cancer research.

[69]  T. Jacks,et al.  Endogenous T cell responses to antigens expressed in lung adenocarcinomas delay malignant tumor progression. , 2011, Cancer cell.

[70]  S. Sakaguchi Regulatory T cells: history and perspective. , 2011, Methods in molecular biology.

[71]  K. Shimizu,et al.  Tumor-Infiltrating Foxp3+ Regulatory T Cells are Correlated with Cyclooxygenase-2 Expression and are Associated with Recurrence in Resected Non-small Cell Lung Cancer , 2010, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[72]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[73]  J. Christensen,et al.  CXCR3 Directs Antigen-Specific Effector CD4+ T Cell Migration to the Lung During Parainfluenza Virus Infection1 , 2009, The Journal of Immunology.

[74]  Christophe Benoist,et al.  Lean, but not obese, fat is enriched for a unique population of regulatory T cells that affect metabolic parameters , 2009, Nature Medicine.

[75]  T. Jacks,et al.  Conditional mouse lung cancer models using adenoviral or lentiviral delivery of Cre recombinase , 2009, Nature Protocols.

[76]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[77]  Daniel J. Campbell,et al.  T-bet controls regulatory T cell homeostasis and function during type-1 inflammation , 2009, Nature Immunology.

[78]  C. Elson,et al.  Late developmental plasticity in the T helper 17 lineage. , 2009, Immunity.

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

[80]  Chen Dong,et al.  CCR6 Regulates the Migration of Inflammatory and Regulatory T Cells1 , 2008, The Journal of Immunology.

[81]  D. Vignali,et al.  How regulatory T cells work , 2008, Nature Reviews Immunology.

[82]  J. Fujimoto,et al.  Administration of IL-33 induces airway hyperresponsiveness and goblet cell hyperplasia in the lungs in the absence of adaptive immune system. , 2008, International immunology.

[83]  T. Hanke,et al.  Characterization of mouse CD4 T cell subsets defined by expression of KLRG1 , 2007, European journal of immunology.

[84]  A. Rudensky,et al.  Altering the distribution of Foxp3+ regulatory T cells results in tissue-specific inflammatory disease , 2007, The Journal of experimental medicine.

[85]  A. Rudensky,et al.  Regulatory T cells prevent catastrophic autoimmunity throughout the lifespan of mice , 2007, Nature Immunology.

[86]  M. Joshi,et al.  Tumor infiltrating Foxp3+ regulatory T‐cells are associated with recurrence in pathologic stage I NSCLC patients , 2006, Cancer.

[87]  H. Weiner,et al.  Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells , 2006, Nature.

[88]  T. Jacks,et al.  The differential effects of mutant p53 alleles on advanced murine lung cancer. , 2005, Cancer research.

[89]  J Fernando Bazan,et al.  IL-33, an interleukin-1-like cytokine that signals via the IL-1 receptor-related protein ST2 and induces T helper type 2-associated cytokines. , 2005, Immunity.

[90]  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.

[91]  Y. Wan,et al.  Identifying Foxp3-expressing suppressor T cells with a bicistronic reporter. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[92]  J. Buer,et al.  Developmental Stage, Phenotype, and Migration Distinguish Naive- and Effector/Memory-like CD4+ Regulatory T Cells , 2004, The Journal of experimental medicine.

[93]  Alf Hamann,et al.  Expression of the integrin αEβ7 identifies unique subsets of CD25+ as well as CD25− regulatory T cells , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[94]  A. Scheffold,et al.  Expression of the integrin alpha Ebeta 7 identifies unique subsets of CD25+ as well as CD25- regulatory T cells. , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[95]  Erkki Oja,et al.  Independent component analysis: algorithms and applications , 2000, Neural Networks.

[96]  D. J. Matthews,et al.  T1/St2-Deficient Mice Demonstrate the Importance of T1/St2 in Developing Primary T Helper Cell Type 2 Responses , 2000, The Journal of experimental medicine.

[97]  B. Williams,et al.  Identification of genes differentially regulated by interferon α, β, or γ using oligonucleotide arrays , 1998 .

[98]  B. Williams,et al.  Identification of genes differentially regulated by interferon alpha, beta, or gamma using oligonucleotide arrays. , 1998, Proceedings of the National Academy of Sciences of the United States of America.