Abstract PD2-03: Basal-like residual disease after neoadjuvant chemotherapy is immunologically cold and associated with poor prognosis in triple negative breast cancer CALGB 40603 (Alliance)

Abstract Background: Despite therapeutic advances in the early-stage triple-negative breast cancer (TNBC) setting, residual disease (RD) following neoadjuvant therapy remains a key predictor of poor prognosis. In this study, we performed transcriptomic profiling on 340 pre-treatment and 70 matched post-treatment RD samples from the CALGB 40603 Phase II trial, which evaluated the effects of adding carboplatin or bevacizumab to a neoadjuvant chemotherapy (NACT) regimen of weekly paclitaxel, followed by dose-dense doxorubicin and cyclophosphamide, in patients with stage II/III TNBC. RNAseq data from these samples were used to assess 959 gene expression signatures and their association with outcomes. Results: The prognostic gene expression signatures identified in RD specimens differed substantially from those in pre-treatment samples for both event-free survival (EFS) and overall survival (OS), including features that are predictors of outcome in the pre-treatment setting. These include immune expression signatures that are prognostic in the pre-treatment setting but lack prognostic value when measured in RD specimens. Conversely, PAM50 molecular subtype and proliferation signatures, which are not prognostic in the pre-treatment setting, were prognostic when measured in RD. The RD specimens were further classified based on their residual cancer burden (RCB), which we observed to be a strong prognostic feature of OS. Supervised analysis comparing paired pre- and post-treatment samples show that RCB-I RD specimens had high fibroblast signatures and low tumor/proliferation signatures. We therefore focused on comparing pre-treatment vs. RCB II+III RD, where tumor cell content remains high. TNBC patients whose tumors were basal-like both pre- and post-treatment by PAM50 subtyping, showed the worst OS compared to other RD subtypes (Univariate Cox; HR = 3.51; 95% CI: 1.72 to 7.15, p 0.001). Comparing the pre-treatment samples of these “basal-basal” tumors (n=21) to the other pre-treatment tumors (n = 102), we identified elevated chromosomal amplifications of oncogenic drivers (i.e., MYC, CDK6, and CCND1) and lower B-cell and T-cell gene expression. Moreover, we show that adding RD basal-like status to a Cox model of RCB significantly improves prognostic value for OS (HR = 3.46; 95% CI: 1.50 to 7.97; p = 0.004). Paired analyses of basal-like RD and matched pre-treatment specimens revealed even lower lymphocyte levels following NACT, along with downregulation of MHC Class I and interferon signaling gene signatures, indicating an immune-cold environment in basal-like RD. We next explored potential drug targets in these immune-cold, basal-like RD tumors and found moderate to high mRNA expression of TROP2 and/or HER2 (i.e., HER2-low). We therefore tested the antibody-drug conjugates (ADCs) sacituzumab govitecan and trastuzumab deruxtecan on a basal-like patient-derived xenograft model established from a pre-treatment biopsy of a “basal-basal” TNBC patient who ultimately had RD following conventional NACT. Both ADCs demonstrated activity in this chemo refractory model, suggesting we may see a benefit of ADCs in ongoing studies of TNBC patients with RD following standard NACT. Conclusion: We show that in early-stage TNBC, prognostic features measured in RD specimens following NACT may be different from those in the pre-treatment setting, providing a rationale for prognostic biomarker development in the RD setting. Substantial immune depletion in basal-like RD may have implications for treatments with immune checkpoint inhibition. However, our preclinical data suggests that this high-risk group of “basal-basal” patients may benefit from use of ADCs. Support: U10CA180821, U24CA196171; https://acknowledgments.alliancefound.org. Citation Format: P. D. Rädler, B. M. Felsheim, A. Fernandez-Martinez, A. D. Pfefferle, M. C. Hayward, W. Sikov, L. A. Carey, C. M. Perou. Basal-like residual disease after neoadjuvant chemotherapy is immunologically cold and associated with poor prognosis in triple negative breast cancer CALGB 40603 (Alliance) abstract. In: Proceedings of the San Antonio Breast Cancer Symposium 2025; 2025 Dec 9-12; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(4 Suppl):Abstract nr PD2-03.