Citations

Our research uncovers a role for ATR in responding to ECM stiffness and promoting epithelial-to-mesenchymal transition (EMT) and metastasis. ATR, when deubiquitinated and upregulated by USP21 under enhanced ECM stiffness conditions, phosphorylates the nuclear protein SUN2, which promotes β-catenin nuclear translocation and EMT. ATM-mediated EMT promotes polymorphonuclear myeloid-derived suppressor cell recruitment and inhibits CD103 + dendritic cells, fostering an immunosuppressive tumor milieu. ATR inhibition disrupts this malignant cascade by promoting mesenchymal-to-epithelial transition to enhance antitumor immunity and mitigate metastases. Consistently, circulating HLA-DR + dendritic cells were also enhanced following treatment with the ATR inhibitor berzosertib in patients with therapeutically resistant early-stage breast cancer. Our data suggest that ATR-targeted therapy may be optimized by considering both DNA damage–dependent and EMT-inducing effects of ATR ATR promotes metastasis and immunosuppression through EMT process

Background Tumor-infiltrating lymphocytes (TILs) are established determinants of clinical outcomes in breast cancer. 1–6 While stromal TILs (sTILs) are commonly evaluated due to easier scoring and higher interobserver reproducibility, intraepithelial TILs may provide additional insights into anti-tumor immunity. 7 We aimed to comprehensively characterize immunotype-associated cellular landscapes in triple-negative breast cancer (TNBC) and identify features associated with clinical outcomes. Methods 212 TNBC tumors were classified into three immunotypes based on immune infiltrate location and density: immune desert (ID), immune excluded (IE), and immune inflamed (IN). 8 Single-cell spatial transcriptomics was performed on 75 tumors to define the cellular composition and functional states of the tumor microenvironment across immunotypes. Findings were validated and integrated with bulk RNA sequencing data and clinical outcome datasets from FinXX, CALGB-40603, I-SPY 2, and Real-World Clinico-Genomic Data (RWCGD) cohorts. Results Patients with IN tumors had significantly improved outcomes compared with ID tumors. Despite high sTILs, IE tumors showed poor outcomes similar to ID tumors. Single-cell spatial analysis revealed that ID and IE tumors exhibited reduced major histocompatibility complex I/II expression and fewer tumor-resident plasmacytoid dendritic cells (pDCs) compared with IN tumors, which were enriched for interferon-alpha (IFNα) and interferon-gamma (IFNγ) responses. High IFN response scores were associated with favorable outcomes across multiple therapy types in independent datasets. Deconvolution of RWCGD bulk RNA-seq data confirmed that pDC abundance correlated with improved outcomes specifically in hormone receptor–negative subtypes. Conclusions Our study highlights pDCs and IFN signaling as hallmarks of effective anti-tumor immunity in TNBC. Immunotype-based profiling underscores the limited prognostic value of sTILs alone in immune-excluded tumors and supports pDCs and IFN pathways as potential biomarkers for prognosis and therapeutic development in TNBC.

TPS655 Background: Early (14-28 day) on-treatment suppression of tumor proliferation during neoadjuvant endocrine therapy (NET) is strongly associated with favorable long-term outcomes in estrogen receptor–positive (ER+) HER2– breast cancer. In premenopausal women, tamoxifen with or without ovarian function suppression (OFS) results in suboptimal Ki-67 suppression compared with aromatase inhibitor + OFS. (Z)-endoxifen (ENDX), the active metabolite of tamoxifen, dually inhibits ER signaling and PKCβ1-mediated AKT activation, supporting its evaluation as an alternative NET strategy in this population. Methods: EVANGELINE (NCT05607004) is an ongoing, multicenter, open-label Phase 2 study evaluating daily 40 mg ENDX plus goserelin administered every 28 days as neoadjuvant therapy in premenopausal women with ER+/HER2–, cT2–3, cN0–1 breast cancer. The primary objective is to determine the proportion of patients with baseline Ki-67 >10% who achieve Ki-67 ≤10% after 4 weeks of therapy. A Simon two-stage design is used to test whether the Week 4 Ki-67 ≤10% rate is at least 65%, with 20 patients enrolled into the first stage and, if promising, another 25 patients enrolled into the second stage (cohort A). A parallel cohort of 20 patients with baseline Ki-67 ≤10% (cohort B) is enrolled to assess objective response rate (ORR) at 24 weeks per RECIST v1.1. Secondary objectives include examining safety and tolerability, residual cancer burden, and PEPI score. Correlative analyses include examining effect of treatment on select tumor and plasma biomarkers. Clinical trial information: NCT05607004 .

Abstract Stromal tumor infiltrating lymphocytes (sTILs), quantified via hematoxylin and eosin (H&E) tumor slides, are associated with improved response to chemotherapy and better overall survival (OS) in triple-negative breast cancer (TNBC). Digitization of H&E slides offers the opportunity for image-based computational approaches to enumerate sTILs. We describe QuTILs, a research-based TIL enumeration approach using a multilayer perceptron-based framework trained on open-source H&E images using the QuPath software and executed on a standard computer. QuTILs was applied to H&E images from two phase III TNBC clinical trials, CALGB 40502 and 40603 (total n = 462 patients). In Cox proportional hazards models, QuTILs showed significant univariate association in CALGB 40502, with higher TIL% associated with reduced hazard (HR: 0.75, 95% CI: 0.63–0.91), which remained significant in multivariable models and validation CALGB 40603 TNBC clinical trial. In summary, QuTILs provides a computationally efficient, open-source workflow for sTIL identification from digital H&E images for research application.

Triple-negative breast cancer (TNBC) is an aggressive breast cancer subtype characterized by lack of estrogen receptor expression, progesterone receptor expression, and human epidermal growth factor 2 overexpression/amplification. Given its generally aggressive biology, current guidelines recommend systemic therapy for most patients, with anthracycline- and taxane-based regimens being historically preferred. However, the clinical outcomes of patients with stage I TNBC and the benefit (or lack thereof) of (neo)adjuvant chemotherapy have not been prospectively evaluated as this population has largely been excluded from prospective randomized clinical trials. As such, management decisions for stage I TNBC are typically extrapolated from trials enrolling patients with stage II or III TNBC or based on retrospective analyses. Currently, the primary factor influencing systemic therapy decisions is the anatomic stage, without other biomarkers clinically used to guide systemic therapy. This review summarizes the existing evidence supporting current and emerging systemic therapy strategies for stage I TNBC, with a special focus on treatment de-escalation and promising biomarkers that can advance personalized treatment selection.

The treatment paradigm of stage II to III triple-negative breast cancer (TNBC) is rapidly evolving, with the recent incorporation of pembrolizumab to neoadjuvant chemotherapy improving disease outcomes. Nevertheless, almost one in five patients with early-stage TNBC will relapse in 5 years, underscoring an urgent need to identify and improve outcomes for those at high risk of recurrence. Novel therapeutic strategies including antibody-drug conjugates, anti-vascular endothelial growth factor therapies, dual immune checkpoint blockade, and locoregional therapies to augment the antitumor immune response are being investigated in clinical trials. Biomarker strategies including tumor infiltrating lymphocytes, immune signatures, and circulating tumor DNA are being explored to identify patients at a high risk of relapse and to predict treatment response. In this article, we review recent advances in the management of stage II to III TNBC, highlight emerging investigational therapies and combinations, and explore novel biomarker strategies aimed at personalizing the care for patients with stage II to III TNBC.

Triple-negative breast cancer (TNBC) is characterized by the lack of estrogen receptor (ER), progesterone receptor, and human epidermal growth factor receptor 2 overexpression. Historically, treatment options for TNBC have been limited, because of the absence of actionable targets. The addition of immune checkpoint inhibitors to chemotherapy improved outcomes for a subset of patients with metastatic PD-L1–positive disease; however, a critical need for more effective therapies remains. Antibody-drug conjugates (ADCs) have been a promising advance in the management of advanced TNBC and are reshaping the landscape as they move earlier into the treatment algorithm. A greater understanding of the molecular heterogeneity of TNBC has enabled the pursuit of more targeted and personalized therapeutic strategies. Despite this, TNBC continues to have the least favorable outcomes compared with other breast cancer subtypes. This review highlights current evidence and future challenges in advanced TNBC, including optimizing therapeutic sequencing and the ongoing need for predictive biomarkers and novel agents.

Abstract Background: MHC class II molecules are normally restricted to professional antigen-presenting cells. Prior TNBC studies have focused on immune-compartment MHC-II. Using spatial transcriptomics, we recently identified aberrant tumor-cell MHC-II expression. Here, we characterized the immune architecture surrounding HLA-DRA-expressing tumor cells. Methods: High-plex single-cell spatial transcriptomics (CosMxTM SMI) was performed on treatment-naïve TNBC (Mayo TMA, n=65) and two neoadjuvant pembrolizumab cohorts (Mayo n=8; Emory n=4). Spatial neighborhoods were mapped relative to HLA-DRA-high tumor cells. Differential expression and adaptive immune gene-set scores were evaluated. Clinical relevance was assessed using FinXX (n=114), I-SPY2 (n=364), and Caris CODEai (n=3,662). Results: HLA-DRA-high tumor regions showed significant enrichment of adaptive immune subsets within ≤50 μm, including B cells, CD8+ T cells, NK cells, macrophages, and plasmacytoid dendritic cells. In pembrolizumab-treated cohorts, responders exhibited higher proportions of HLA-DRA-high tumor cells and greater numbers of B cells, plasmablasts, CD4+ and CD8+ T cells, and macrophages near tumor cells. Responders’ tumors showed upregulation of antigen-presentation machinery, B-cell/plasma-cell programs, CXCL13, and NOTCH3/DLL1. Across I-SPY2 and FinXX, higher HLA-DRA correlated with pathologic complete response and improved survival. In CODEai TNBC, high HLA-DRA expression correlated with higher CXCL13 (median TPM 7.5 vs. 1.1, q<0.05) and longer overall survival (24.2 vs. 18.5 months, HR 0.77, 95% CI 0.71-0.83, p<0.0001). This association was TNBC-specific. High CXCL13 also predicted improved survival (26.6 vs. 16.5 months, HR 0.64, 95% CI 0.59-0.69, p<0.0001). Conclusions: Tumor-cell HLA-DRA expression defines a highly organized adaptive immune niche enriched with B cells and activated T-cell populations in close proximity. Adaptive immune programs—including enhanced antigen presentation and CXCL13-mediated B-cell/plasma-cell pathways—consistently associate with improved outcomes across TNBC cohorts treated with chemotherapy and immune checkpoint blockade. Aberrant tumor-cell MHC-II expression may contribute to antitumor immunity and warrants further investigation as a potential therapeutic target. Citation Format: Yi Liu, Sachin Kumar Deshmukh, Thiti Susiriwatananont, Panuch Eiamprapaporn, Bogang Wu, Heikki Joensuu, Roberto A. Leon-Ferre, David Zahrieh, Judy C. Boughey, James Newell Ingle, Fergus J. Couch, Sharon Wu, Shipra Gandhi, Maryam Lustberg, George W. Sledge, Matthew P. Goetz, Keith L. Knutson, E Aubrey Thompson, Jodi Carter, Saranya Chumsri. Spatially resolved tumor-cell MHC class II shapes adaptive immunity and therapeutic response in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1200.

Abstract Background: Stromal tumor infiltrating lymphocytes (sTILs) are associated with improved response to chemotherapy and better overall survival (OS) in triple-negative breast cancer (TNBC). Quantification of sTILs via hematoxylin and eosin (H&E) tumor slides offers a widely available method to define a simple, effective surrogate for host anti-tumor immunity. Digitization of H&E slides has rapidly gained acceptance for use in diagnostic pathology and research, opening the door for image-based computational approaches to enumerate sTILs, among other features. Methods: We describe QuTILs - a multilayer perceptron-based framework to detect/enumerate TILs trained on >700,000 cells via The Cancer Genome Atlas Program (TCGA) slide images, implemented in the widely used open-source QuPath digital pathology suite. QuTILs was applied to digital H&E images using standard computing in primary breast tumors from phase 3 breast cancer clinical trials - CALGB 40502 (testing), CALGB 40601 and 40603 (validation) - in total 1,729 total images from 962 unique patients. The aims of this investigation were: 1) to assess the relationship between TIL patterns with overall or event-free survival outcomes; 2) to benchmark diverse image-based characteristics of TIL abundance and spatial architecture; and 3) to evaluate the association between image-based TIL levels and RNA-seq-based immune deconvolution metrics (CIBERSORT, EPIC, quanTIseq). Results: QuTILs average processing time was 7.9 minutes for whole-slide total TIL count and area density on a standard laptop workstation. In CALGB 40502, there was positive but modest correlation between pathologist TILs and QuTILs total TILs %, higher in the TNBC subgroup of CALGB 40502 (Pearson r = 0.55). In Cox proportional hazards models, the CALGB 40502 TNBC cohort showed significant univariate association for total TILs % with increasing decile (higher total TIL%) associated with reduced hazard (hazard ratio [HR]: 0.712, 95% CI: 0.559-0.906; P = 0.006), which remained significant in multivariable model incorporating age, race, and treatment arm (HR: 0.713, 95% CI: 0.556-0.915; P = 0.008). In validation TNBC clinical trial CALGB 40603, marginal TILs % was significant in the univariable Cox model (HR: 0.786, 95% CI: 0.639-0.966). Evaluation of TILs % by QuTILs with RNAseq-based deconvolution metrics in cohort-stratified and deconvolution method-stratified multivariable models showed that decile total TILs % by QuTILs was shown to significantly predict outcome in the EPIC (HR: 0.668, 95% CI: 0.466-0.957) and quanTIseq (HR: 0.646, 95% CI: 0.446-0.936) sets, with a similar magnitude as in clinical Cox, suggesting that RNA-based deconvolution estimates may not supplement the prognostic power of image-based TIL estimates. Exploratory analyses of pre- versus post-neoadjuvant therapy H&E images in CALGB 40603 and CALGB 40601 revealed a significant decrease in QuTILs total TIL% in CALGB 40603 for all pairs (n = 118 pairs, pre-median=9.52%, post-median=6.33%; Wilcoxon signed rank P < 0.001) but no significant change in QuTILs total TIL% among all pairs in CALGB 40601 (n = 82 pairs, pre-median=15.92%, post-median=15.10%; P = 0.886). Conclusions: QuTILs provides a computationally efficient open-source workflow for sTIL identification from digital H&E images that can be deployed on a standard laptop. We present the first evaluation of digital sTIL enumeration in CALGB 40502, CALGB 40603, and CALGB 40601 phase III breast cancer clinical trials and demonstrate significant prognostic association with QuTIL total TIL % among TNBCs across studies. Citation Format: M. Vater, R. Salgado, E. Blige, H. Lefebvre, A. Strahan, M. Gatti-Mays, H. Rugo, K. Ballman, M. Watson, Y. Wen, R. Leon-Ferre, K. Niazi, W. Symmans, L. Carey, K. AbdulJabbar, Z. Li, D. Stover. Qutils: open-source image-based infiltrating immune cell detection and outcomes in calgb 40502, calgb 40603, and calgb 40601 phase iii breast cancer clinical trials [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 PS2-07-27.