Abstract C051: Emerging Novel Targets to treat non-responding HER2-negative breast cancer patients: The neoadjuvant I-SPY2 TRIAL 2300 patient Omics data and organoid studies

Abstract Introduction Treatment options for early-stage aggressive breast cancer are improving, particularly with the introduction of neoadjuvant PARP inhibitors, immune oncology agents (IO), and dual HER2 targeting. In the neoadjuvant trial I-SPY2 we previously established a schema of molecular ‘Response Predictive Subtypes’ (RPS), where for 4 out of 6 subtypes optimal tumor biology-treatment matching is predicted to result in 60-90% pathologic complete response (pCR), associated with long-term survival benefit (PMID:35623341), which also includes the prospectively validated immune-sensitive subtype (PMID:39277672). However, one third of 2300 I-SPY2 patients treated 2010-2024 across 28 treatments had very low pathologic complete response (pCR) rates in all arms (∼10% on average). These patients have HER2-negative tumors with low expression of immune genes and low DNA repair deficiency (DRD) (HER2-/Immune-/DRD- subtype). Here, we characterized the tumor biology of I-SPY patients with non-responding subtypes to identify novel targets of vulnerability, which we tested for efficacy in patient-derived organoids. Methods We analyzed pre-treatment gene expression (GE) and phospho-protein (RPPA) data of 1628 HER2-patients across 20 treatment arms in I-SPY2 for canonical metabolic, signaling, and regulatory pathways from the Molecular Signatures Database (n=2274). We compared 1) HR+HER2-/Immune-/DRD- (RPS1;n=617) vs other (Immune+ and/or DRD+) HR+HER2- tumors (n=272) and 2) TN/Immune-/DRD- (RPS2;n=177) vs other (Immune+ and/or DRD+) TN tumors (n=562) using Wilcoxon rank-sum tests with Benjamini-Hochberg adjustment, ‘adjusted p-values’ <0.05 were considered significant. Organoids derived from HR+HER2- and triple-negative (TN) breast cancers grown in 3D cultures were used to perform drug screens with inhibitors of candidate targets from the Omics analyses. Results GE and RPPA data from the RPS HER2-/Immune-/DRD- subtypes RPS1(HR+) and RPS2(TN) tumors infer that they are characterized by a dormant-like, low proliferation state with significantly altered epigenetic modulator activity, WNT-signaling, and various metabolic pathways. Concomitantly, there is an observed increase of potential targets such as CyclinD1, Androgen Receptor, PI3K/AKT/mTOR, HDAC5, bcl2, and low HER2, potentially mediated in part by RUNX3. Our organoid studies on a set of chemo-resistant TN organoids show that pro-apoptotic agents, including bcl-2 inhibitors and IAP inhibitors, as well as HDAC inhibitors, can overcome resistance to cisplatin, as assessed by both chemical cell viability assays and imaging-based assays. Conclusion The dormant-like state of HER2-/Immune-/DRD- non-responding subtypes (RPS1/RPS2) combined with our organoid treatment studies suggests that senolytics and HDAC inhibitors may be potential therapeutic strategies. The I-SPY2 neoadjuvant trial provides the opportunity to test these new concepts in the upfront treatment block where new therapies are tested without standard chemotherapy. Citation Format: Laura van t Veer, Tam Binh V. Bui, Denise Wolf, Emanuel Petricoin, Julia Wulfkuhle, Jean-Philippe Coppé, Renée van Amerongen, Nadine Goldhammer, Annuska Glas, Douglas Yee, Jane Perlmutter, Rosalyn Sayaman, Christina Yau, Lajos Pusztai, Paula Pohlmann, Laura Esserman, Jennifer Rosenbluth. Emerging Novel Targets to treat non-responding HER2-negative breast cancer patients: The neoadjuvant I-SPY2 TRIAL 2300 patient Omics data and organoid studies [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2025 Oct 22-26; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2025;24(10 Suppl):Abstract nr C051.