Inducing DNA Repair Deficiencies in Triple Negative Breast Cancers Through Pharmacologic Stimulation of Innate Immune Signaling

Abstract

Poly (ADP-ribose) polymerase inhibitors (PARPi) are FDA approved in a subset of patients with ovarian cancer or metastatic breast cancers who harbor BRCA gene mutations. These mutations generate homologous recombination deficiencies (HRD) and are the main predictor to PARPi sensitivity. Unfortunately, responses to therapy have not been durable and have failed for the majority of sporadic triple negative breast cancers (TNBC). We previously reported that DNA methyltransferase inhibitor (DNMTi) azacytidine (Aza) improves the efficacy of a new generation of PARPi, Talazoparib (Tal), through increased trapping of cytotoxic PARP-DNA complexes in both BRCA-mutant and -proficient TNBC. These trapped complexes lead to increased and persistent levels of lethal double strand breaks (DSBs), suggesting that DSB repair may also be impaired with this treatment. In the present study, we show that Aza/Tal treatment in BRCA-proficient TNBC cell lines significantly downregulates expression of HR and Fanconi Anemia (FA) genes, notably FANCD2, and decreases HR activity, thus generating HRD. DNMTi have also been established to induce a viral mimicry response which upregulate Type I interferon (IFN) signaling and production of inflammatory cytokines. We now link Aza/Tal facilitated HRD and induction of innate immune and inflammatory related genes, mediated in part through a STING dependent mechanism. Gene set enrichment analysis of RNA-Seq data derived from mono- and combination-treatments, reveal enrichment of innate immune and cytosolic DNA sensing pathways with significant increases of TNFα/NF-κB and IFNαβ gene sets. Overlap between HRD and immune related signaling was evaluated using the STRING database, which reveals a significant interaction specifically between FA pathway and TNFα/NF-κB and IFNαβ pathway genes. This inverse relationship was also validated in both METABRIC TNBC dataset and other TCGA data sets suggesting broad applicability of this observed transcriptional program independent of pharmacologic intervention. Additionally, Tal driven cytosolic DNA as well as an Aza augmentation in STING protein expression, emerges as the key node in Aza/Tal induced innate immune signaling to drive HRD. Induction of what we define as a pathogen mimicry response to drive HRD mechanism suggests that DNMTi-PARPi therapy strategies can expand the therapeutic scope of PARPi to encompass treatment of BRCA-proficient cancers.