Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers

Epigenetic therapy is emerging as a potential therapy for solid tumors. To investigate its mechanism of action, we performed integrative expression and methylation analysis of 63 cancer cell lines (breast, colorectal, and ovarian) after treatment with the DNA methyltransferase inhibitor 5-azacitidine (AZA). Gene Set Enrichment Analysis demonstrated significant enrichment for immunomodulatory pathways in all three cancers (14.4-31.3%) including interferon signaling, antigen processing and presentation, and cytokines/chemokines. Strong upregulation of cancer testis antigens was also observed. An AZA IMmune gene set (AIMs) derived from the union of these immunomodulatory pathway genes classified primary tumors from all three types into “high” and “low” AIM gene expression subsets in tumor expression data from both TCGA and GEO. Samples from selected patient biopsies showed upregulation of AIM genes after treatment with epigenetic therapy. These results point to a broad immune stimulatory role for DNA demethylating drugs in multiple cancers.

[1]  S. Baylin,et al.  Harnessing the potential of epigenetic therapy to target solid tumors. , 2014, The Journal of clinical investigation.

[2]  Andreas Schlicker,et al.  Colorectal cancer intrinsic subtypes predict chemotherapy benefit, deficient mismatch repair and epithelial-to-mesenchymal transition , 2013, International journal of cancer.

[3]  C. Zahnow,et al.  Alterations of immune response of non-small cell lung cancer with Azacytidine , 2013, Oncotarget.

[4]  J. Mohler,et al.  DNA methylation and nucleosome occupancy regulate the cancer germline antigen gene MAGEA11 , 2013, Epigenetics.

[5]  Mira Ayadi,et al.  Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic Value , 2013, PLoS medicine.

[6]  C. Zahnow,et al.  Abstract 4666: A phase 2 study investigating the safety, efficacy and surrogate biomarkers of response of 5-azacitidine (5-AZA) andentinostat (MS-275) in patients with triple-negative advanced breast cancer. , 2013 .

[7]  K. Cibulskis,et al.  Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. , 2012, The Journal of clinical investigation.

[8]  Paul J Hertzog,et al.  Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape , 2012, Nature Medicine.

[9]  L. Cope,et al.  Biomarkers for detection and prognosis of breast cancer identified by a functional hypermethylome screen , 2012, Epigenetics.

[10]  D. Matei,et al.  Epigenetic resensitization to platinum in ovarian cancer. , 2012, Cancer research.

[11]  Nita Ahuja,et al.  Transient low doses of DNA-demethylating agents exert durable antitumor effects on hematological and epithelial tumor cells. , 2012, Cancer cell.

[12]  Brian C. Haynes,et al.  Reduced DICER1 Elicits an Interferon Response in Endometrial Cancer Cells , 2012, Molecular Cancer Research.

[13]  George Coukos,et al.  Cancer immunotherapy comes of age , 2011, Nature.

[14]  J. Herman,et al.  Combination epigenetic therapy has efficacy in patients with refractory advanced non-small cell lung cancer. , 2011, Cancer discovery.

[15]  Olufunmilayo I. Olopade,et al.  Basal-like Breast cancer DNA copy number losses identify genes involved in genomic instability, response to therapy, and patient survival , 2011, Breast Cancer Research and Treatment.

[16]  Peter A. Jones,et al.  A decade of exploring the cancer epigenome — biological and translational implications , 2011, Nature Reviews Cancer.

[17]  X. Chen,et al.  Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. , 2011, The Journal of clinical investigation.

[18]  Martin J. Aryee,et al.  A DNA hypermethylation module for the stem/progenitor cell signature of cancer , 2011, Genome research.

[19]  R. Schreiber,et al.  Cancer Immunoediting: Integrating Immunity’s Roles in Cancer Suppression and Promotion , 2011, Science.

[20]  K. Odunsi,et al.  Regulation of cancer germline antigen gene expression: implications for cancer immunotherapy. , 2010, Future oncology.

[21]  Kelly M. McGarvey,et al.  Polycomb CBX7 promotes initiation of heritable repression of genes frequently silenced with cancer-specific DNA hypermethylation. , 2009, Cancer research.

[22]  J. Mohler,et al.  Increased Expression of Androgen Receptor Coregulator MAGE-11 in Prostate Cancer by DNA Hypomethylation and Cyclic AMP , 2009, Molecular Cancer Research.

[23]  Andrew J. G. Simpson,et al.  CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens , 2008, Nucleic Acids Res..

[24]  Laurent Ozbun,et al.  A gene signature predicting for survival in suboptimally debulked patients with ovarian cancer. , 2008, Cancer research.

[25]  H. Verheul,et al.  Synergistic In vivo Antitumor Effect of the Histone Deacetylase Inhibitor MS-275 in Combination with Interleukin 2 in a Murine Model of Renal Cell Carcinoma , 2007, Clinical Cancer Research.

[26]  Wei Chen,et al.  Comparing the DNA Hypermethylome with Gene Mutations in Human Colorectal Cancer , 2007, PLoS genetics.

[27]  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.

[28]  Rafael A. Irizarry,et al.  Bioinformatics and Computational Biology Solutions using R and Bioconductor , 2005 .

[29]  R. Pazdur,et al.  Approval Summary: Azacitidine for Treatment of Myelodysplastic Syndrome Subtypes , 2005, Clinical Cancer Research.

[30]  L. Platanias.  Mechanisms of type-I- and type-II-interferon-mediated signalling , 2005, Nature Reviews Immunology.

[31]  J. Herman,et al.  CpG island methylator phenotype in colorectal cancer. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[32]  S. Pestka,et al.  Enhanced expression of surface tumor-associated antigens on human breast and colon tumor cells after recombinant human leukocyte alpha-interferon treatment. , 1984, Cancer research.

[33]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

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

[35]  David A Jones,et al.  Limited gene activation in tumor and normal epithelial cells treated with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine. , 2004, Molecular pharmacology.

[36]  T. Haaf,et al.  The effects of 5-azacytidine and 5-azadeoxycytidine on chromosome structure and function: implications for methylation-associated cellular processes. , 1995, Pharmacology & therapeutics.

[37]  A. Čihák.  Biological effects of 5-azacytidine in eukaryotes. , 1974, Oncology.

[38]  H. Pitot,et al.  Effects of 5-azacytidine on hepatic polyribosomes and maturation of ribosomal RNA. , 1974, Acta biologica et medica Germanica.