Abstract 4473: DNMT and PARP inhibitor combination therapy induces an interferon-driven homologous recombination defect in triple-negative breast cancers and acute myeloid leukemia
Authors: McLaughlin Lena J. , Kogan Aksinija A. , Choi Eun Yong , Lapidus Rena S. , Zou Ying , Li Huili , Baylin Stephen B. , Topper Michael J. , Rassool Feyruz V. 
Published: August 2019

Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) are effective in a subset of triple negative breast cancers (TNBC) with BRCA gene mutations, which generates homologous recombination deficiencies (HRD), through synthetic lethality. However, PARPis fail for the majority of sporadic TNBC with intact BRCA1/2 genes and other BRCA-proficient cancers, including acute myeloid leukemia (AML). PARPi, Talazoparib (TAL), has potent PARP trapping ability, in both BRCA mutant and proficient TNBCs and AML. We reported that a combination of TAL with low doses of DNA methyl transferase inhibitor (DNMTi) azacytidine (AZA) or decitabine (DAC), increased PARP trapping even further, leading to increased levels of cytotoxic double strand breaks in vitro and decreased tumor burden in vivo. Low doses of DNMTis have been shown previously to reprogram genome wide cancer signaling, including immune and DNA damage/repair pathways. We now tie these two signaling pathways together for events through which DNMTis plus TAL drive HRD.
BRCA proficient TNBC (N=2) and AML (cell lines (N=2) and primary cells (N=4)) treated with low doses of DNMTis (DAC 10nM and AZA 250-500nM), significantly downregulate expression of genes in HR and Fanconi Anemia (FA) pathways, decreasing HR activity, thus generating HRD. HR is further decreased when DNMTis are combined with TAL. We now link DNMTi/TAL induced HRD to a coupled interferon (IFN) response in both TNBC and AML. In these systems, we elucidate DNMTi/TAL potentiated cGAS-Sting and type 1 IFN signaling, culminating in the induction of IFN responsive genes and inflammatory cytokine production. Importantly, in DNMTi/TAL treated cells, increased expression of IFN signaling genes is strongly linked to downregulation of FA/HR genes through protein interaction network mapping. This inverse association between IFN and HR related genes, was further validated in TCGA data sets for AML and invasive BC, suggesting broad applicability of this observed transcriptional program. The acquisition of HRD from IFN signaling specifically, is verified by the observation of reduced HR gene expression and activity in the presence of exogenous double stranded RNA (Poly(I:C)) or IFNβ treatment in both TNBC and AML cell lines. Finally, knockdown of a key connectivity node between IFN and HR related genes, interferon sensitive gene 15 (ISG15), abrogates downregulation of FA gene expression when treated with IFNβ, suggesting mediation of HRD through ISG15. In conclusion, we have identified a novel mechanism through which IFN-sensitive genes can create an HRD phenotype in BRCA proficient TNBC and AML, suggesting that innate immunity and inflammatory processes may be intrinsically linked to DNA repair in cancer. These studies suggest that immune therapies and/or epigenetic therapy are likely to enhance responses to PARPis in BRCA proficient cancers.
Citation Format: Lena J. McLaughlin, Aksinija A. Kogan, Eun Yong Choi, Rena S. Lapidus, Ying Zou, Huili Li, Stephen B. Baylin, Michael J. Topper, Feyruz V. Rassool. DNMT and PARP inhibitor combination therapy induces an interferon-driven homologous recombination defect in triple-negative breast cancers and acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4473.