Preclinical and clinical characterization of DNMT inhibitors +/- standard chemoimmunotherapy in TNBC - Given the heterogeneity and aggressiveness of TNBC, it is likely that successful novel targeted therapies will continue to rely on identifying subsets of TNBC patients most likely to respond based on robust predictive biomarkers. Compared to other subtypes, TNBC exhibits extensive epigenomic misregulation. In our preliminary and published data, we identified a subset of TNBC with elevated DNA methyltransferase 3A (DNMT3A) that exhibits unique sensitivity to DNMT inhibitors (DNMTi). We have shown that in TNBC, DNMTi induce degradation of DNMTs through the E3 ligase TRAF6. We developed a DNMT3A IHC clinical assay and found that up to 80% all TNBC tumors express DNMT3A, and ˜30% exhibit moderate-strong staining. DNMT3A+ was associated with poor clinical outcomes independent of tumor stage, nodal metastases and immune infiltration. Building upon our preliminary data, this proposal seeks to evaluate further the preclinical and clinical activity and mechanisms of action of DNMTi + chemoimmunotherapy in DNMT3A+ TNBC, and to clinically evaluate biomarkers with predictive and pharmacodynamic utility, with a focus on DNMT3A IHC and other biomarkers in relevant pathways. Historically, enthusiasm for DNMTi has been hampered by limited efficacy in previous clinical trials, mostly in ER+ breast cancer. There is little clinical information on these agents in TNBC. Emerging evidence and our preclinical data suggest that DNMTi exhibit combinatorial effects with taxanes and immunotherapy. We hypothesized that the addition of DNMTi to chemoimmunotherapy would be beneficial in patients with DNMT3A+ TNBC. At the mechanistic level, although identified as a major mechanism of DNMTi action, how the viral mimicry pathway regulates DNMTi activity in TNBC remains unclear and requires further elucidation. Our preliminary data identified ZNF101 as a new regulator of the viral mimicry pathway to regulate IFN-induced gene expression in TNBC. Our proposed Aims are intended to further evaluate biomarkers and mechanisms of drug action in samples collected from a prospective phase I trial supported through the NCI CTEP (NCT05673200), where we are evaluating an oral DNMTi (ASTX727) in combination with paclitaxel and pembrolizumab in patients with metastatic TNBC, including the subset of DNMT3A high tumors (Aim 1), and to evaluate ZNF101 and viral mimicry pathway involvement in anti-tumor activity (Aim 2) and anti- tumor immunity induced by DNMTis (Aim 3). The results will be further tested in biospecimens collected from a completed trial, NCT02957968, which evaluated IV decitabine + paclitaxel and pembrolizumab. While DNMTi have been evaluated before in unselected breast cancer, the innovation in our project is the biomarker-driven approach based on novel mechanisms of action described by our group. If successful, our finding will significantly impact a large number of TNBC patients, as it may allow us to: (1) Gain novel insights into DNMTi activity in TNBC, (2) repurpose DNMTi in patients most likely to benefit based on biomarkers and (3) enhance the therapeutic efficacy especially in metastatic TNBC patients who have progressed on standard of care.
