Chromatin states define tumor-specific T cell dysfunction and reprogramming

Tumour-specific CD8 T cells in solid tumours are dysfunctional, allowing tumours to progress. The epigenetic regulation of T cell dysfunction and therapeutic reprogrammability (for example, to immune checkpoint blockade) is not well understood. Here we show that T cells in mouse tumours differentiate through two discrete chromatin states: a plastic dysfunctional state from which T cells can be rescued, and a fixed dysfunctional state in which the cells are resistant to reprogramming. We identified surface markers associated with each chromatin state that distinguished reprogrammable from non-reprogrammable PD1hi dysfunctional T cells within heterogeneous T cell populations from tumours in mice; these surface markers were also expressed on human PD1hi tumour-infiltrating CD8 T cells. Our study has important implications for cancer immunotherapy as we define key transcription factors and epigenetic programs underlying T cell dysfunction and surface markers that predict therapeutic reprogrammability.

[1]  P. Muranski,et al.  Wnt signaling arrests effector T cell differentiation and generates CD8+ memory stem cells , 2009, Nature Medicine.

[2]  Andrew C. Adey,et al.  Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition , 2010, Genome Biology.

[3]  G. Hämmerling,et al.  Tumor agonist peptides break tolerance and elicit effective CTL responses in an inducible mouse model of hepatocellular carcinoma. , 2009, Immunology letters.

[4]  Anthony A. Hyman,et al.  Ki-67 acts as a biological surfactant to disperse mitotic chromosomes , 2016, Nature.

[5]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[6]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[7]  Mikael Bodén,et al.  MEME Suite: tools for motif discovery and searching , 2009, Nucleic Acids Res..

[8]  P. Doherty,et al.  Differentiation-dependent functional and epigenetic landscapes for cytokine genes in virus-specific CD8+ T cells , 2011, Proceedings of the National Academy of Sciences.

[9]  Jedd D. Wolchok,et al.  The future of cancer treatment: immunomodulation, CARs and combination immunotherapy , 2016, Nature Reviews Clinical Oncology.

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

[11]  A. Rao,et al.  Dynamic Changes in Chromatin Accessibility Occur in CD8+ T Cells Responding to Viral Infection. , 2016, Immunity.

[12]  Todd M. Allen,et al.  The epigenetic landscape of T cell exhaustion , 2016, Science.

[13]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[14]  G. Crabtree,et al.  Nuclear association of a T-cell transcription factor blocked by FK-506 and cyclosporin A , 1991, Nature.

[15]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[16]  S. Leach,et al.  Molecular Profile of Tumor-Specific CD8+ T Cell Hypofunction in a Transplantable Murine Cancer Model , 2016, The Journal of Immunology.

[17]  P. Hwu,et al.  MART-1–Specific Melanoma Tumor-Infiltrating Lymphocytes Maintaining CD28 Expression Have Improved Survival and Expansion Capability Following Antigenic Restimulation In Vitro , 2009, The Journal of Immunology.

[18]  T. Speed,et al.  Distinct epigenetic signatures delineate transcriptional programs during virus-specific CD8(+) T cell differentiation. , 2014, Immunity.

[19]  Cory Y. McLean,et al.  GREAT improves functional interpretation of cis-regulatory regions , 2010, Nature Biotechnology.

[20]  T. Speed,et al.  Distinct Epigenetic Signatures Delineate Transcriptional Programs during Virus-Specific CD8 T Cell Differentiation , 2014 .

[21]  H. Lähdesmäki,et al.  The transcription factor NFAT promotes exhaustion of activated CD8⁺ T cells. , 2015, Immunity.

[22]  Susan M. Kaech,et al.  Transcriptional control of effector and memory CD8+ T cell differentiation , 2012, Nature Reviews Immunology.

[23]  K. Hellström,et al.  Cellular and Humoral immunity to Different Types of Human Neoplasms , 1968, Nature.

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

[25]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[26]  Terrence S. Furey,et al.  The UCSC Genome Browser Database: update 2006 , 2005, Nucleic Acids Res..

[27]  Kate B. Cook,et al.  Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity , 2014, Cell.

[28]  E. Yang,et al.  Transcriptional insights into the CD8+ T cell response to infection and memory T cell formation , 2013, Nature Immunology.

[29]  J. Wolchok,et al.  Genetic Basis for Clinical Response to CTLA-4 Blockade in Melanoma. , 2015, The New England journal of medicine.

[30]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[31]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[32]  J. Delrow,et al.  Rescued Tolerant CD8 T Cells Are Preprogrammed to Reestablish the Tolerant State , 2012, Science.

[33]  T. Schumacher,et al.  Acquired and intrinsic resistance in cancer immunotherapy , 2014, Molecular oncology.

[34]  M. Cooke,et al.  Interleukin-15 rescues tolerant CD8+ T cells for use in adoptive immunotherapy of established tumors , 2006, Nature Medicine.

[35]  R. Ahmed,et al.  Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function , 2013, The Journal of Immunology.

[36]  M. J. Tevethia,et al.  In Vivo Ligation of CD40 Enhances Priming Against the Endogenous Tumor Antigen and Promotes CD8+ T Cell Effector Function in SV40 T Antigen Transgenic Mice1 , 2003, The Journal of Immunology.

[37]  J. Wolchok,et al.  Genetic basis for clinical response to CTLA-4 blockade in melanoma. , 2014, The New England journal of medicine.

[38]  Kathryn Beal,et al.  Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution , 2014, BMC Genomics.

[39]  A. Secord,et al.  Priming and Activation of Human Ovarian and Breast Cancer-specific CD8+ T Cells by Polyvalent Listeria monocytogenes-based Vaccines , 2009, Journal of immunotherapy.

[40]  B. Williams,et al.  Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity , 2012, Cell.

[41]  Martin L. Miller,et al.  Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer , 2015, Science.

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

[43]  Corwin M Zigler,et al.  THE POTENTIAL FOR BIAS IN PRINCIPAL CAUSAL EFFECT ESTIMATION WHEN TREATMENT RECEIVED DEPENDS ON A KEY COVARIATE. , 2011, The annals of applied statistics.

[44]  T. Curran,et al.  The T-cell transcription factor NFATp is a substrate for calcineurin and interacts with Fos and Jun , 1993, Nature.

[45]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[46]  R. Wersto,et al.  Histone Acetylation Facilitates Rapid and Robust Memory CD8 T Cell Response through Differential Expression of Effector Molecules (Eomesodermin and Its Targets: Perforin and Granzyme B)1 , 2008, The Journal of Immunology.

[47]  John Sidney,et al.  Relapse or eradication of cancer is predicted by peptide-major histocompatibility complex affinity. , 2013, Cancer cell.

[48]  J. O’Shea,et al.  Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality , 2016, Cell.

[49]  Robert Gentleman,et al.  Software for Computing and Annotating Genomic Ranges , 2013, PLoS Comput. Biol..

[50]  C. Leslie,et al.  Aerobic glycolysis promotes T helper 1 cell differentiation through an epigenetic mechanism , 2016, Science.

[51]  F. Macian,et al.  NFAT proteins: key regulators of T-cell development and function , 2005, Nature Reviews Immunology.

[52]  M. Giedlin,et al.  Listeria-based cancer vaccines that segregate immunogenicity from toxicity. , 2004, Proceedings of the National Academy of Sciences of the United States of America.