Carey, L. A.

Abstract Background: While there are abundant data on the surgical management of BC after neoadjuvant chemotherapy (NAC), there is less guidance regarding surgical management of BC after NET, particularly with respect to lymph node (LN) surgery. While pathologic complete response (pCR) is common with NAC, it is a rare event with NET. In this analysis we assess the surgeons’ approach in the context of NET. Methods: The ALTERNATE trial is a phase III study that randomized postmenopausal patients (pts) with clinical stage II/III ER+ HER2- BC to receive neoadjuvant anastrozole (A), fulvestrant (F), or both for 6 mos. before surgery. The primary objective was to determine if neoadjuvant F or A+F increases the rate of pCR or ypT1-2N0/N1mic/Ki67 <2.7% residual disease over A alone. Breast surgery was per standard of care. Sentinel lymph node biopsy (SLNB) with or without axillary lymph node dissection (ALND) was required to determine preoperative endocrine prognostic index PEPI score and residual cancer burden (RCB). Surgeons were required to indicate if the patient would be eligible for breast- conserving surgery (BCS) prior to NET. Patient accrual occurred from 2014-2018. The surgical outcomes are reported for the entire group. Results: Among the 3 treatment arms, 933 patients completed 6 cycles of NET. The clinical T stage at diagnosis was 73.6% T2, 22.6% T3and 3.8% T4. Initial tumor size was assessed by mammogram and ultrasound. Primary tumor histology was ductal in 64.8% and lobular in 25.4%.568 pts (60.9%) were clinically node negative (cN0), 36.2% cN1, 2.6% cN2 with 0.3% cN3. LNs were palpable in 25.2%. 383 had LN needle biopsy pre NET, of which 80.9% were positive. The surgeons’ initial impression of the patient’s eligibility for BCS was 74% while 0.6% were considered inoperable.75.5% of pts had post-NET imaging performed. Of those with tumor size recorded, 52.9% were T1 or not visible. Overall, 69.9% of the 933 patients had BCS. Of those 330 pts without post-NET imaging or who had post-NET imaging without a size noted, 64.8% underwent BCS. For pts undergoing BCS, 80.2% required only one surgery for margin clearance. Of the 690 pts deemed eligible for BCS pre NET, 79% had BCS. Of the 240 pts deemed ineligible for BCS pre-NET, 43.8% had BCS. Of the pre-NET cT2 tumors, 79% had BCS while only 45.5% of T3 tumors and 37.1% of T4 tumors had BCS. On surgical pathology, 474 (50.8%) pts were LN+ compared to pre-NET cN+ 39.1% and needle biopsy-proven 33.2%. For pts with pN0, 93.3% had SLNB alone. 6.7 % of pN0 had ALND alone or SLNB+ALND. For those with pN1-3 , 36.3% had SLN only; 37.3% SLN+ ALND; 26.4% ALND alone. Only 0.8% of the patients had no ALND or SLNB performed. Pts undergoing BCS were more likely to have SLNB alone for a +SLN compared to mastectomy pts (62.9% vs. 37.6%; chi-square p<0.0001). For pts with pre-NET +LN on needle biopsy, only 26.8% underwent SLNB alone, while 37.4% underwent ALND alone. Of the 204 LN-positive pts having SLNB alone, 55.9% had only 1 + LN and 27% had only 2+ LNs. For pN+ pts who underwent SLNB +ALND, 42.1% had 1-2 + LNs. Conclusion: With NET, 69.9% of pts achieved BCS, including 43.8% deemed ineligible pre-NET. Given the low rate of pCR to NET, there should not be the expectation of pCR in +LNs. Based on the procedures performed in pts with +SLNs, it appears that surgeons were applying ACOSOG Z0011 criteria for pts having BCS, but were less likely to omit ALND for +LN in pts having mastectomy. The finding of only 1-2 +LNs in many of the LN+ pts suggests that omission of ALND may be a reasonable approach post-NET. Longer follow-up is required to assess local-regional recurrence. Support: U10CA180821, U10CA180882; https://acknowledgments.alliancefound.org. Clinical Trials.gov Identifier: NCT01953588 Citation Format: A. M. Leitch, T. Dockter, V. suman, A. Weiss, G. W. Unzeitig, J. Guenther, S. Sanati, K. Vij, J. Hoog, A. Caudle, A. Tiersten, M. Mita, W. Razaq, T. J. Hieken, Y. Wang, M. Rimawi, M. J. Ellis, E. Winer, K. K. Hunt, A. H. Partridge, L. A. Carey. Surgical outcomes in the ALTERNATE trial (Alliance A011106) -a randomized phase 3 neoadjuvant endocrine therapy (NET) trial in postmenopausal women with clinical stage II/III estrogen receptor positive (ER+) and HER2 negative (HER2-) breast cancer (BC) [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 RF1-02.

Abstract Background: Microtubule inhibitors remain a standard chemotherapy in the management of HER2-negative metastatic breast cancer (MBC). CALGB (Alliance) 40502 was a phase 3 randomized study involving 799 patients with MBC receiving first-line chemotherapy, to determine the optimal chemotherapeutic agent among paclitaxel, nab-paclitaxel, or ixabepilone (with or without bevacizumab). Secondary analysis suggested inferior PFS with nab-paclitaxel specifically among patients with hormone receptor positive (HR+)/HER2-negative breast cancer. Correlative analysis demonstrated significant association of stromal tumor infiltrating lymphocytes (sTILs) with improved progression-free (PFS) and overall survival (OS) in CALGB40502. We hypothesized that immune activation would be associated with differential benefit among distinct microtubule agents. To address this, we evaluated the sTILs and RNA-based immune features association with clinical outcomes, including evaluation of nab-paclitaxel versus paclitaxel. Methods: To limit heterogeneity, analyses focused on pre-treatment primary tumor breast samples with central review/pathologist-enumerated sTILs in accordance with International TILs Working Group methods and RNAseq (n = 280). PAM50 molecular subtypes were assigned based on transcriptomic features. RNAseq data were used to generate immune deconvolution estimates from 5 distinct algorithms (CIBERSORT, xCell, ABIS, ConsensusTME, ImmuCellAI). 1,018 curated breast cancer gene expression signatures GES) were derived from previously published studies. Associations between sTILs and GES were evaluated with sTILs being a categorical variable with the thresholds <5% (low) and (≥5%) high. Results: In the evaluable population, basal-like PAM50 subtype was enriched for high sTILs category (p=1e-4), as anticipated. T-cell and B-cell immune signatures and immune deconvolution estimates were among most highly associated with sTILs. In addition to the expected prognostic association of high T-cell GES, high B-cell-related IgG signature score was also significantly associated with improved overall survival (OS) among triple-negative breast cancer (TNBC) in CALGB 40502 (HR = 0.50,95% CI:0.30-0.86, log-rank p=0.01) but not in HR+/HER2-. In an exploratory analysis of young patients (age at study entry <50 years), high sTILs were associated with improved OS among TNBC patients but worse OS among those with HR+/HER2- MBC (HR = 2.19, 95% CI:1.10-4.36, log-rank p=0.022). High (above median) RNA-based Xcell total immune score was significantly associated with worse OS in both CALGB 40502 and a validation dataset of primary breast cancers, METABRIC (OS HR = 2.12, 95% CI:1.01-4.45, log-rank p=0.042). To further investigate the clinical trial finding of inferior PFS for nab-paclitaxel compared with paclitaxel in patients with HR+/HER2- MBC, there was a significant enrichment of T-cell signatures associated with poor outcome in patients receiving nab-paclitaxel (Fisher exact p<0.001). Conclusion: In this translational analysis of sTILs and RNAseq from a large phase III clinical trial, sTILs and immune signatures were not uniformly associated with better outcome. Rather, high sTILs or immune signatures were associated with worse OS in young patients with HR+/HER2- breast cancer and higher T-cell signatures were associated with inferior PFS with nab-paclitaxel among HR+/HER2- MBC patients. These data reinforce the importance of context/subtype-specific interrogation of the tumor-immune microenvironment Support: U10CA180821, U10CA180882; https://acknowledgments.alliancefound.org. Bristol Myers Squibb (BMS); Clinicaltrials.gov Identifier: NCT00785291 Citation Format: E. K. Blige, K. V. Ballman, A. Michmerhuizen, M. Vater, L. A. Carey, A. H. Partridge, W. F. Symmans, M. A. Watson, C. M. Perou, D. G. Stover, H. S. Rugo. Rna-based immune features associated with benefit from distinct microtubule inhibitor therapy for metastatic her2-negative breast cancer: a post hoc analysis of the calgb 40502 (alliance) phase iii randomized clinical 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 PS1-13-17.

Abstract Introduction: With emerging antibody drug conjugates (ADC) as treatment of metastatic breast cancer (mBC), it is key to understand the mechanisms that drive resistance to inform optimal ADC selection and sequencing. The AURORA (AUR) US Network was established to characterize paired primary and metastatic (met) samples via multiplatform profiling, with a prospective phase of met tissue collection that included pre and post-ADC samples. Methods: Fresh frozen or FFPE met and archival primary tumors were analyzed across 3 platforms: DNA low pass whole genome and exome sequencing (WES), DNA methylation arrays (Methyl) and RNA sequencing (RNA seq). The molecular cohort included pts with data from ≥1 platform. Pairwise gene expression comparisons were performed in R using t-tests, and pathway analysis with GSEA. Results: A total of 168 pts comprised the molecular cohort: WES, 168; Methyl, 163; RNA seq, 168. Median age at mBC diagnosis was 56 (28-88). 21 pts (12.5%) had known germline BRCA1/2 mutations; 37 (22.0%) presented with de novo mBC. Subtype at mBC (if not available, at primary) diagnosis was: 108 (64.3%) HR+/HER2-, 22 (13.1%) HER2+, 33 (19.6%) TNBC and 5 (3.0%) unknown. Among 139 pts with known subtype in the first AUR met collected, 95 (68.3%) were HR+/HER2-, 17 (12.2%) HER2+ and 27 (19.4%) TNBC. 72 pts received ≥1 ADC with 1 (0-4) median line of chemotherapy for mBC prior to ADC1. As ADC1, 42 pts received HER2 ADC (35 trastuzumab deruxtecan, T-DXd; 7 trastuzumab emtansine), 29 TROP2 ADC (28 sacituzumab govitecan, SG; 1 datopotamab deruxtecan) and 1 NECTIN4 ADC. 22 pts received ≥2 ADC (16 immediate sequence; 6 intervening therapy); 11 T-DXd and 11 SG as ADC2. Median duration of ADC1 was 141 days (6-522); 81 (7-425) for ADC2. Progressive disease was the most common reason for ADC discontinuation, denoting resistance in post-ADC samples. 99 samples were collected pre-ADC1 and 24 post-ADC1, of which 5 were pre-ADC2. ERBB2 expression did not differ between samples after HER2 (n=9) vs non-HER2 ADC (n=8) (p=0.55), nor did TACSTD2 after TROP2 (n=8) vs non-TROP2 ADC (n=9) (p=0.16). In pts with HER2+ subtype at mBC diagnosis or AUR collection who received HER2 ADC, ERBB2 expression significantly decreased in post (n=4) vs pre-treatment (n=7) samples (p=0.043). ERBB2 downregulation was observed in 5 pts with paired pre vs post-HER2 ADC samples. In pts who received TROP2 ADC, TACSTD2 expression did not differ in post (n=10) vs pre-treatment (n=47) samples (p=0.63). GSEA of post-ADC samples revealed significant pathway differences by payload, including actin cytoskeleton in post-microtubule inhibitor (MTi) vs non-MTi ADC samples (p=0.001) and ATM-dependent DNA damage response after topoisomerase I inhibitor (TOP1i) vs non-TOP1i ADCs (p=0.043). Lysosomal vesicle biogenesis (p=0.014) and calcium release (p=0.05) pathways significantly differed between ADC naïve vs treated metastases. ERBB2 hypermethylation was not detected in the cohort. TACST2 promoter methylation was observed in 10 samples (β value >0.3) without association with TROP2 ADC exposure. ERBB2 or TACSTD2 mutations were not identified in the ADC-treated cohort. A novel loss-of-function (LOF) mutation in MED12 was detected in one pt immediately post-T-DXd. MED12 LOF has been reported to promote PARP inhibitor and platinum resistance in BRCA-deficient tumors and may represent a novel resistance mechanism to TOP1i. Conclusions: Multiplatform molecular characterization of mBC treated with ADC revealed potential mechanisms of resistance related to downregulation of target expression, payload (e.g., microtubule formation, DNA damage repair) and lysosomal processing. Additional analyses integrating these multimodal data are ongoing. Strategies to overcome resistance, e.g. modifying ADC target, are being evaluated in clinical trials. Citation Format: A. C. Garrido-Castro, W. C. Nenad, J. M. Balko, T. Hinoue, G. L. Wheeler, B. J. Kelly, M. Singha, B. M. Felsheim, A. R. Michmerhuizen, U. Chandran, A. V. Lee, L. A. Carey, T. A. King, E. Mardis, P. W. Laird, K. V. Giridhar, K. A. Hoadley, C. M. Perou. Molecular characterization of resistance to antibody drug conjugates in metastatic breast cancer: a prospective analysis from the AURORA US Network [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 PD3-09.

Abstract Background: Patients with metastatic breast cancer (MBC) often have short survival, and clinical disease management is challenging due to tumor heterogeneity, treatment resistance, and unique contributions of organ-specific metastatic microenvironments. Methods: The retrospective and prospective phases of the AURORA US Metastasis Project have profiled samples from 220 MBC patients using RNA-seq, DNA-seq, and DNA methylation arrays. RNA-seq has been performed on 392 specimens from 143 primary tumors and 249 metastases. In total, there are 162 primary-metastasis pairs from 134 patients (13 patients have 2+ metastases profiled). The 249 metastatic samples include 116 liver, 29 lymph node, 17 lung, 14 bone, 10 brain, and 8 skin metastases. Each specimen was assayed to determine its clinical and molecular subtypes. Here we investigate the molecular causes of clinical and PAM50 subtype switching in primary tumor-metastasis pairs using multi-platform data. Results: Of the patients with paired data in the AURORA dataset, 38/134 (28%) had clinical subtype (HR+/HER2+, HR-/HER2+, HR+/HER2-, TNBC) switches between the primary tumor and paired metastasis. The most common clinical subtype switch was loss of hormone receptor expression (16/38 patients) in the metastatic tumor. Many of these observations have been confirmed by concomitant RNA and/or DNA changes. In addition, 59/134 (44%) patients had PAM50 molecular subtype switches. 26/59 (44%) patients had a Luminal A primary tumor which switched either into Luminal B (16/26) or HER2-Enriched (7/26) subtypes, suggesting recurrent progression mechanisms during metastasis. For example, patient ARRP had a Luminal A primary tumor and a HER2-Enriched bone metastasis. Using DNA clonality data, we identified a clonal mutation in the DNA binding domain of FOXA1 (H247L) as well as mutations in CDH1 (frameshift) and NLRC3 (Q650H) that originated in the primary tumor. A distinct, dominant clone arose in the metastasis, harboring oncogenic activating mutations in PIK3CA (H1047R) and ERBB2 (L869R). There was also an increase in RNA expression of ERBB2 and FGFR4 but no change in ERBB2 copy number. This is in alignment with previous publications demonstrating a shift to the HER2-Enriched subtype, often without gain of HER2 amplification. Interestingly, there were 21 patients that had both clinical and PAM50 subtype switches. Patient ANFC had a HR+/HER2- primary tumor (Luminal A) and a TNBC liver metastasis (HER2-Enriched). Notably, the metastasis lost clinical expression of ER and PR (by IHC), and this was also observed through a decrease in ESR1 and PGR mRNA expression. Using DNA clonality data, we identified 5 new clones in the metastasis that were not present in the primary tumor. Finally, we observed that basal-like primary tumors with a PAM50 subtype switch in the paired metastasis had a significantly lower correlation to the basal-like centroid compared to primary tumors with a basal-like paired metastasis (p=0.0053). This suggests that either these tumors had significant intra-tumoral heterogeneity in the primary tumor and the metastasis originated from a non-basal-like portion of the tumor, or the switches from a basal-like primary tumor are a byproduct of the PAM50 bioinformatics algorithm (i.e. the tumor is very close to 2 subtype centroids). Ongoing analyses will precisely determine which subtype switches can be attributed to genetic or epigenetic causes, organ site biases, and/or bioinformatic methodologies. Conclusions: Using multi-platform molecular analyses, we identified cases of clinical and molecular subtype switching in primary-metastasis pairs. These findings begin to elucidate the underlying molecular drivers of tumor progression and subtype switching in patients with MBC, which may have implications for clinical treatment. Citation Format: A. R. Michmerhuizen, B. M. Felsheim, G. L. Wheeler, B. J. Kelly, M. Singha, T. Hinoue, W. C. Nenad, A. C. Garrido-Castro, J. M. Balko, K. Giridhar, U. Chandran, A. V. Lee, L. A. Carey, T. A. King, K. A. Hoadley, P. W. Laird, E. R. Mardis, C. M. Perou, AURORA US Metastasis Network. Molecular causes of subtype switching in primary and metastatic breast tumor pairs from the AURORA US Project [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 PD2-06.

Abstract Background: Despite its widespread adoption, there is a lack of data as to whether breast MRI for local staging and surgical planning of newly diagnosed breast cancer patients improves oncologic outcomes. The Alliance A011104 phase III trial was designed to test the hypothesis that MRI detection of mammographically occult disease helps to tailor surgical intervention thereby reducing local recurrence and improving local regional control. Here we report on the primary outcome of 5-year local regional recurrence. Methods: Patients with newly diagnosed clinical stage I-II, ER/PR- and HER2- negative (triple- negative) or ER/PR-negative and HER2-positive breast cancer, deemed eligible for breast- conserving surgery (BCS) based on clinical exam, mammography +/- ultrasound were randomized to undergo staging breast MRI or no further local staging. Patients with multifocal tumors that could be encompassed in a single operative resection were eligible. Patients who were carriers of gBRCA 1/2, or who had bilateral breast cancer, or a prior history of breast cancer were excluded. Initial eligibility was limited to patients not scheduled to receive neoadjuvant chemotherapy; however, a subsequent amendment allowed for enrollment after completion of neoadjuvant chemotherapy. Categorical variables were compared between arms with a chi-square or Fisher’s exact test. LRR, distant recurrence and overall survival (OS) were estimated with Kaplan-Meier point estimates and 95% confidence intervals (CIs). Hazard ratios (HRs) and 95% CIs were obtained from Cox proportional hazards models. Results: Of 319 patients enrolled from 2/2014-12/2019,161 were randomized to undergo breast MRI and 158 to no breast MRI evaluation. The mean age at enrollment was 58.9 years (range 29-85). Most patients (72.1%) had T1 tumors, 93.4% were cN0 and 19.7% were HER2 positive. Systemic chemotherapy was utilized in 85% with 17.6% receiving treatment neoadjuvantly; receipt of systemic therapy was unknown for 15 patients (4.7%). Two hundred and ninety-eight patients (93.4%) underwent surgical intervention; 91.9% underwent BCS as initial surgical procedure with no significant differences noted between groups (92.7% in the no MRI group and 91.9% in the MRI group [p=0.62]). Of patients who underwent breast surgery, 293 underwent axillary evaluation with the majority (270 patients, 92%) undergoing sentinel lymph node biopsy as the only axillary intervention. Among patients who received neoadjuvant chemotherapy, the overall pathologic complete response rate was 39.3%, 29.0%in the MRI arm vs. 52.0% no MRI arm (p=0.10). Receipt of adjuvant radiation was comparable between arms, 85.4% and 85.0% receiving radiation in the no MRI and MRI arms, respectively. Among 298 patients evaluable for the primary endpoint, with median follow-up of 61.1 months (0.2, 68.1), there were no differences in rates of LRR; 5-year local regional control was 93.2% (89.0-97.6%) in the MRI group and 95.7% (92.3-99.1%) in the no MRI group (HR: 1.1, 95% CI: 0.3, 3.9). For the entire cohort, 5-year distant recurrence-free rate and OS were 94.3% (91.7, 97.1) and 92.2% (89.1, 95.4), respectively, with no differences between groups. Conclusions: With multimodality therapy, rates of 5-year LRR in patients with early stage triple- negative and HER2-positive breast cancer are very low. Breast MRI for local staging and surgical planning in this setting does not result in improved local regional control. Support: U10CA180821, U10CA180882; UG1CA189823; U10CA180868 (NRG Oncology); ClinicalTrials.gov Identifier: NCT01805076; https://acknowledgments.alliancefound.org Citation Format: I. Bedrosian, K. Ballman, L. M. McCall, C. E. Comstock, G. W. Unzeitig, T. Yen, A. Weiss, B. G. Haffty, J. M. Bensenhaver, S. M. DeSnyder, J. J. Liu, A. H. Partridge, L. A. Carey, K. K. Hunt.Effect of Preoperative Breast MRI Staging on Local Regional Recurrence (LRR) in Early Stage Breast cancer: Alliance A011104/ACRIN 6694 [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 GS2-07.