Regulation of repetitive elements in cancer by P53 and epigenetic mechanisms

Despite focused research efforts, the five year survival for ovarian cancer (OC) has remained unchanged for decades and novel therapies are urgently needed for this deadly disease. Therapies that activate the immune system to kill cancer cells, including anti-PD-1 checkpoint blockade therapy, have shown

vigorous and durable responses, but the majority of patients, including those with OC, fail to respond. The underlying mechanism remains unclear. Repetitive elements (REs) comprise the majority (45%) of the human genome. In most somatic tissues, REs are silenced by DNA methylation and other epigenetic modifications to

prevent their transcription. We demonstrated that treating OC cells with DNA methylation inhibitors (DNMTis) and histone deacetylase inhibitors (HDACis) increases immune signaling from tumors through demethylation of REs and production of RE double-stranded RNA to activate the interferon response. This signaling recruits

CD8+ T cells to sensitize tumors to anti-PD-1 immunotherapy. REs translate proteins that can be targeted as tumor-associated antigens. Thus RE activation both promotes interferon signaling to reverse the immune- suppressive tumor microenvironment and presents potential tumor-specific antigens as T cell targets.

The premise of this proposal is that P53 and epigenetic mechanisms regulate REs in cancer and thus mutant TP53 will affect immune signaling and response to epigenetic and immune therapy. Approximately half of all cancers have mutations in TP53, the gene encoding the P53 protein, 90% of which are “hotspot”

mutations located in the DNA binding domain. These missense mutations encode functional proteins with reduced transcriptional activity at canonical cell cycle target genes that may also exhibit oncogenic gain of function transcriptional activity at new targets. High grade serous OC makes up about 70% of all cases and is

characterized by nearly 100% mutant TP53. While the critical role of P53 in cell cycle regulation and apoptosis is known, P53 regulation of REs in cancer remains poorly defined. Approximately 30% of P53 binding sites are found in REs and our preliminary data show that P53 binds directly to REs. Further, we show that P53 hotspot

mutant cell lines treated with DNMTi/HDACi exhibit significantly increased chromatin accessibility at REs and transcription of REs compared to TP53 wild type cell lines. We hypothesize that mutant P53 aberrantly activates REs, amplifying the RE-induced immune response. We will test this hypothesis via the following aims: In Aim 1, we will determine how wild type and mutant

TP53 regulate REs to affect the DNMTi/HDACi-induced interferon response. In Aim 2, we will determine how p53 status affects the DNMTi/HDACi-induced T cell response and sensitization to immune therapy in a mouse model of OC and a clinical trial of OC patients treated with immunotherapy. In Aim 3, we will evaluate REs as

tumor antigens in different P53 backgrounds. Results of this innovative work will answer novel basic science questions about REs and P53 and open new directions for epigenetic and immune therapy in OC.