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

// Huili Li 1,* , Katherine B. Chiappinelli 1,* , Angela A. Guzzetta 1,* , Hariharan Easwaran 1 , Ray-Whay Chiu Yen 1 , Rajita Vatapalli 1 , Michael J. Topper 1 , Jianjun Luo 1 , Roisin M. Connolly 1,2 , Nilofer S. Azad 1 , Vered Stearns 1,2 , Drew M. Pardoll 1 , Nancy Davidson 3 , Peter A. Jones 4 , Dennis J. Slamon 5 , Stephen B. Baylin 1 , Cynthia A. Zahnow 1 , Nita Ahuja 1,6 1 Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA 2 Breast Cancer Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD, USA 3 Department of Medicine, University of Pittsburgh Cancer Institute and UPMC CancerCenter, Pittsburgh, PA 4 Departments of Urology and Biochemistry and Molecular Biology, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 5 The Jonsson Comprehensive Cancer Center, University of California-Los Angeles 6 Department of Surgery, School of Medicine, Johns Hopkins University, Baltimore, MD, USA * These authors contributed equally to the work Correspondence: Nita Ahuja, email: // Cynthia A. Zahnow, email: // Keywords : Epigenetics, immune, cancers, DNA methyltransferase inhibitor, interferon, methylation, antigen processing Received : February 4, 2014 Accepted : February 16, 2014 Published : February 16, 2014 Abstract 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.