Ballman, K.

Abstract Background: The Breast Cancer Index (BCI) is clinically validated to stratify patients with hormone receptor-positive (HR+), early-stage BC based on the risk of overall (0-10 years [y]) and late (5-10 y) distant recurrence (DR) with N0/N1 lymph node involvement. Validation of BCI in patients with HR+ HER2+ BC has been limited, especially in patients treated with adjuvant trastuzumab-based chemotherapy. The HOXB13 and IL17BR genes constitute the predictive component of BCI and are known to exhibit an ER-dependent correlation pattern with HER2. We evaluated the prognostic performance of BCI in patients with HR+ HER2+ disease enrolled in the NCCTG N9831 (Alliance) trial treated with the combination of chemotherapy and trastuzumab. Methods: All available tumor specimens from patients with HR+ HER2+ N0/N1 BC in arms B (sequential trastuzumab) and C (concurrent trastuzumab) of the trial were included. BCI testing was performed blinded to clinical outcomes. The primary endpoint was distant recurrence-free interval (DRFI). BCI (N0) and BCIN+ (N1) risk groups were calculated based on prespecified cut points. Kaplan-Meier analysis and log-rank testing were used to assess the prognostic significance of BCI/BCIN+ risk groups based on DR. Cox proportional hazard models with and without clinical covariates were used to estimate hazard ratios (HRs), and the associated 95% confidence intervals (CIs). Results: A total of 454 HR+ patients (234 arm B, 220 arm C), including 69 N0 and 385 N1 patients, were analyzed (median age was 47 y, 85% N1, 55% T2, 63% G3). BCIN+ scores were available for 378 of the 385 N1 patients due to missing tumor grade for 7 patients. The median follow-up was 12.7 years. In the overall cohort, BCI/BCIN+ stratified 51 (11%), 24 (5%) and 372 (83%) patients as low-, intermediate- and high-risk with 10-y DRFI rates of 96% (95% CI: 84-99%), 100% (100-100%) and 89% (86-92%), respectively. Since the low and intermediate risk groups had few patients and a similar risk of 10-y DRFI, they are combined into a single low-risk group hereafter. Thus, for overall 10-y DR, 75 (17%) and 372 (83%) of patients were classified by BCI/BCIN+ as low and high risk with 10-y DRFI rates of 97% (95% CI: 89-99%) and 89% (95% CI: 86-92%), respectively (HR=4.50, 95% CI: 1.09-18.61; p = 0.038). BCI/BCIN+ remained statistically significant in the multivariable analysis, adjusting for age, treatment, and nodal status (HR=7.54, 95% CI: 1.34-42.64; p = 0.022). For 69 N0 patients, BCI stratified 54 (78%) and 15 (22%) patients as low and high risk with 10-y DRFI rates of 100% (95% CI, 100-100%) and 77% (95% CI, 44-92%), respectively (p = 0.012). For 378 N1 patients, BCIN+ stratified 21 (6%) and 357 (94%) of patients as low and high risk with 10-y DRFI of 90% (95% CI, 66-97%) and 90% (95% CI, 86-93%), respectively (p = 0.07). Of the 21 patients classified as BCIN+ low-risk, two had BCIN+ scores of 6.75 and 6.73 in close proximity to the cut point (6.93) and experienced DR after 5 years, resulting in the same 10-y DRFI for both BCIN+ low- and high-risk patients. Conclusions: BCI is significantly prognostic for the risk of overall DR (0-10 y) in patients with HR+ HER2+ disease treated with adjuvant trastuzumab-based chemotherapy. Optimization of BCI cut points may further improve prognostic performance in HR+ HER2+. Additional validation in other HR+ HER2+ cohorts treated in the modern setting with anti-HER2-based therapy is warranted, given the small sample size of N0 patients and relatively low DR rate in the late recurrence cohort. In summary, these results provide further evidence of BCI’s utility to support clinical decision-making for adjuvant endocrine therapies for HR+ HER2+ BC. Support: U10CA180821, U10CA180882, U24CA196171, Genentech; Clinicaltrials.gov Id: NCT00005970; https://acknowledgments.alliancefound.org. Citation Format: S. Chumsri, E. Liu, K. Edwards, Y. Wen, Y. Zhang, A. K. Anderson, A. H. Partridge, L. Carey, K. Ballman, E. Perez, K. Treuner, M. Goetz, E. Thompson. Prognostic performance of Breast Cancer Index in patients with early-stage HR+ HER2+ breast cancer (BC) treated with adjuvant trastuzumab: NCCTG N9831 (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 PS3-08-08.

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.

Abstract Background: PALLAS (PALbociclib CoLlaborative Adjuvant Study, NCT02513394) is a randomized phase III trial comparing two years of the CDK4/6 inhibitor palbociclib combined with the physician’s choice of adjuvant endocrine therapy, versus endocrine therapy alone for patients with Stage II-III hormone receptor-positive, HER2-negative (HR+/HER2-) breast cancer. Molecular residual disease (MRD) detection via circulating tumor DNA (ctDNA) testing was a predefined biomarker analysis to identify patients at highest risk of recurrence. Methods: PALLAS participants with available tumor block, at least a baseline (pre-study treatment) plasma sample, and either whole blood or buffy coat were randomly selected from the overall study population. Plasma samples on cycle 1 day 1 (C1D1), cycle 6 day 1 (C6D1), and at the end of treatment (EOT) were collected, processed, and stored. Nucleic acids were extracted from primary tumor tissue or, when primary tissue was insufficient, from post-neoadjuvant tumor tissue, provided the sample had sufficient material and tumor cellularity (>25 mm2 tissue area with ≥20% tumor nuclei). Data from next generation sequencing of tumor tissue and matched normal DNA were used to create a personalized ctDNA SignateraTM assay (Natera, Inc.) for MRD assessment in the peripheral blood. ctDNA was reported as mean tumor molecules/mL (MTM/mL) of plasma. The primary endpoint was distant recurrence-free interval (DRFI) based on ctDNA status. Cox Proportional Hazards models were used to evaluate prognosis and predictive interactions. To minimize bias, the biorepository and laboratory teams were blinded to participant identity. Results: In total, 1280 participants were randomly selected for inclusion in this preplanned ctDNA sub-study. WES and WGS are being conducted on tissue, and Signatera results will be generated. Results for association of MRD status (positive/negative) and MTM/mL with DRFI in the context of 7 year median follow up of this study cohort will be reported. Conclusions: The planned analysis is ongoing and the presented work will provide data from the first randomized phase 3 adjuvant study in HR+/HER2- breast cancer to report MRD status by treatment arm. Citation Format: H. A. Parsons, K. Ballman, E. Heitzer, M. Watson, M. Balic, D. Hlauschek, D. Renner, E. Kalashnikova, G. Steger, J. M. Balko, Y. Novik, M. Martin, A. A. Rodriguez, Z. Dayao, A. Chan, E. Nili Gal-Yam, M. C. Liu, C. Isaacs, M. Los, M. Gil Gil, B. Felder, C. Denkert, P. Fasching, F. Liu, T. O'Donnell, E. L. Mayer, M. Gnant, W. F. Symmans, A. DeMichele. Tumor-informed circulating tumor DNA analysis to assess molecular residual disease for prognosis and prediction of benefit from palbociclib in the PALLAS trial [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 RF3-04.