Epigenetic activation of the interferon response to sensitize cancers to immune therapy

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 DESCRIPTION (provided by applicant): Cancer is the second most common cause of mortality in the United States, causing nearly one out of four deaths. Therapies that activate the host immune system have shown tremendous promise for a wide variety of solid tumors, with patients exhibiting vigorous and durable responses. However, fewer than half of patients respond to these immune therapies. We have shown that epigenetic therapy using DNA methyltransferase inhibitors (DNMTis) can "boost" immune signaling from tumors, through activation of double-stranded RNA including endogenous retroviruses (ERVs), and sensitize tumors to immune therapy. The goals of the mentored phase of this proposal are to further characterize ERV epigenetic regulation and determine the exact mechanism of DNMTi-induced tumor signaling to the host immune system. During the K99 phase, I will 1) use whole-genome sequencing to map epigenetic modifications at ERVs; 2) determine which epigenetic modifying drugs activate ERVs, and 3) characterize cytosolic sensors and cytokines necessary for epigenetic sensitization to immune therapy. Building on the bioinformatics and immunology training from the K99 phase, the goal of the R00 phase is to expand the genomic analysis to investigate other dsRNAs that may contribute to the DNMTi-induced immune response. In addition, I will examine the role of RNA editing, central to the cellular response to viral RNA, in this immune response. Overall, these studies will characterize the role of epigenetics in the innate immune response and determine the mechanism(s) for epigenetic sensitization to immune therapy. The candidate, Dr. Katherine Chiappinelli, has a longstanding interest in epigenetic changes in cancer. The main focus of her independent academic laboratory will be epigenetic regulation of immune signaling in cancer. This K99/R00 proposal is designed to complement Dr. Chiappinelli's previous research and provide her with additional scientific training in bioinformatics and immunology to allow her to succeed as an independent investigator. In addition, this proposal includes a detailed career development plan and an advisory committee that will assist Dr. Chiappinelli through the transition to becoming an independent investigator. Members of her advisory committee will provide her with scientific training in immunology (Drew Pardoll, Cynthia Zahnow) and bioinformatics (Gordon Mills, Ting Wang) as well as guidance as she transitions to independence (Stephen Baylin, Luis Garza). This K99/R00 proposal will provide Dr. Chiappinelli with the training needed to extend the findings from her postdoctoral work and begin her own independent and successful research laboratory.