HER2 Subtype Research Articles

MicroRNAome profiling of breast cancer unveils hsa-miR-5683 as a tumor suppressor microRNA predicting favorable clinical outcome.

Breast cancer is a heterogeneous disease with diverse molecular subtypes, underscoring a better understanding of its molecular features and underlying regulatory mechanisms. Therefore, identifying novel prognostic biomarkers and therapeutic targets is crucial for advancing the current standard of care for breast cancer patients. Ninety-six formalin-fixed paraffin-embedded (FFPE) breast cancer samples underwent miRNAome profiling using QIAseq microRNA library kit and sequencing on Illumina platform. Mature miRNA quantification was conducted using CLC Genomics Workbench v21.0.5, while Relapse-free survival (RFS) analysis was conducted using RStudio 2023.09.1. Gain-of-function studies were conducted using miRNA mimics, while the effects of miRNA exogenous expression on cancer hallmark were assessed using 2-dimentional (2D) proliferation assay, three-dimensional (3D) organotypic culture, and live-dead staining. TargetScan database and Ingenuity Pathway Analysis (IPA) were used for miRNA target identification. Hierarchical clustering based on miRNA expression revealed distinct patterns in relation to PAM50 classification and identified miRNAs panels associated with luminal, HER2, and basal subtypes. hsa-miR-5683 emerged as a potential prognostic biomarker, showing a favorable correlation with RFS and suppressing tumorigenicity under 2D and 3D conditions in triple-negative breast cancer (TNBC) models. Findings were further extended to the MCF7 hormone receptor positive (HR+) model. Transcriptomic profiling of hsa-miR-5683 overexpressing TNBC cells revealed its potential role in key oncogenic pathways. Integration of downregulated genes and CRISPR-Cas9 perturbational effects identified ACLY, RACGAP1, AK4, MRPL51, CYB5B, MKRN1, TMEM230, NUP54, ANAPC13, PGAM1, and SOD1 as bona fide gene targets for hsa-miR-5683. Our data provides comprehensive miRNA expression atlas in breast cancer subtypes and underscores the prognostic and therapeutic significance of numerous miRNAs, including hsa-miR-5683 in TNBC. The identified gene targets unravel the intricate regulatory network in TNBC progression, suggesting promising avenues for further research and targeted therapeutic interventions.

7862 The Paradoxical Role Of ERFFI1 In Breast Cancer Progression Is Supported By Its Dynamic Protein Interactome

Abstract Disclosure: A. Ocampo: None. P.D. Bagamasbad: None. In breast cancer (BCa), glucocorticoid (GC) therapy is used in anti-emetic and palliative care. However, the effects of GC therapy in BCa are conflicting as it is beneficial for hormone-responsive luminal subtypes while it promotes tumor progression in more aggressive triple-negative BCa (TNBCs). A factor implicated in this paradoxical shift is the feedback inhibitor of epidermal growth factor receptor (EGFR) signaling, ERBB receptor feedback inhibitor 1 (ERRFI1). In BCa cell lines, ERRFI1 expression is directly regulated by GC receptor (GR). More interestingly, ERRFI1 was found to restrict the GC-enhanced proliferation in normal breast epithelia but enhances the GC-mediated pro-tumorigenic effects in highly aggressive TNBC. To identify the mechanism behind the shift in ERFFI1 function through BCa progression, ERRFI1 protein interactions in the luminal, HER2, and TNBC subtypes were analyzed by identifying differentially expressed proteins from each subtype using available proteome and interactome datasets from Integrated Interactions Database and followed by network and clustering analyses through STRING. The ERRFI1 interactome varied across the subtypes, and gene ontology analysis of the protein networks revealed progressive tumorigenic effects from the least aggressive luminal subtype to the most aggressive TNBC. The luminal BCa-ERRFI1 interactome showed metastatic potential that is countered by negative regulation of receptor tyrosine kinase (RTK) signaling. The HER2-ERRFI1 interactome highlighted the amplification of RTK signaling and its possible modulation through SRC while the TNBC-ERRFI1 interactome presents pro-oncogenic proteins implicated in drug resistance, angiogenesis, and EMT. Interestingly, the interactome also revealed a link between EGFR signaling and GR signaling possibly through ERRFI1, EGFR, and SFN. To determine the function of ERFFI1 in EGFR signaling in BCa, we generated stable ERRFI1 knockdown in different breast epithelial cell models through lentiviral transduction. Cells were then treated with EGF followed by gene expression analysis of known EGF-upregulated genes such as MYC, GSK3B, MCL1, and MMP9. We found that ERRFI1 knockdown enhanced the EGF-dependent induction of MYC and MMP9 in normal MCF10A cells and this effect was not observed in the TNBC MDA-MB-468 line, suggesting the loss of ERRFI1-mediated inhibition of EGFR signaling with BCa tumorigenic potential. Taken together, our findings suggest that the progressive loss of anti-tumorigenic function of ERRFI1 may be explained by its changing interactome in BCa molecular subtypes. Presentation: 6/3/2024

7862 The Paradoxical Role of ERFFI1 in Breast Cancer Progression Is Supported by Its Dynamic Protein Interactome

Abstract Disclosure: A. Ocampo: None. P.D. Bagamasbad: None. In breast cancer (BCa), glucocorticoid (GC) therapy is used in anti-emetic and palliative care. However, the effects of GC therapy in BCa are conflicting as it is beneficial for hormone-responsive luminal subtypes while it promotes tumor progression in more aggressive triple-negative BCa (TNBCs). A factor implicated in this paradoxical shift is the feedback inhibitor of epidermal growth factor receptor (EGFR) signaling, ERBB receptor feedback inhibitor 1 (ERRFI1). In BCa cell lines, ERRFI1 expression is directly regulated by GC receptor (GR). More interestingly, ERRFI1 was found to restrict the GC-enhanced proliferation in normal breast epithelia but enhances the GC-mediated pro-tumorigenic effects in highly aggressive TNBC. To identify the mechanism behind the shift in ERFFI1 function through BCa progression, ERRFI1 protein interactions in the luminal, HER2, and TNBC subtypes were analyzed by identifying differentially expressed proteins from each subtype using available proteome and interactome datasets from Integrated Interactions Database and followed by network and clustering analyses through STRING. The ERRFI1 interactome varied across the subtypes, and gene ontology analysis of the protein networks revealed progressive tumorigenic effects from the least aggressive luminal subtype to the most aggressive TNBC. The luminal BCa-ERRFI1 interactome showed metastatic potential that is countered by negative regulation of receptor tyrosine kinase (RTK) signaling. The HER2-ERRFI1 interactome highlighted the amplification of RTK signaling and its possible modulation through SRC while the TNBC-ERRFI1 interactome presents pro-oncogenic proteins implicated in drug resistance, angiogenesis, and EMT. Interestingly, the interactome also revealed a link between EGFR signaling and GR signaling possibly through ERRFI1, EGFR, and SFN. To determine the function of ERFFI1 in EGFR signaling in BCa, we generated stable ERRFI1 knockdown in different breast epithelial cell models through lentiviral transduction. Cells were then treated with EGF followed by gene expression analysis of known EGF-upregulated genes such as MYC, GSK3B, MCL1, and MMP9. We found that ERRFI1 knockdown enhanced the EGF-dependent induction of MYC and MMP9 in normal MCF10A cells and this effect was not observed in the TNBC MDA-MB-468 line, suggesting the loss of ERRFI1-mediated inhibition of EGFR signaling with BCa tumorigenic potential. Taken together, our findings suggest that the progressive loss of anti-tumorigenic function of ERRFI1 may be explained by its changing interactome in BCa molecular subtypes. Presentation: 6/3/2024

Effect of Breast Cancer Receptor Subtypes and CSF Cytology Status on Survival of Patients With Leptomeningeal Disease

BackgroundIt is unclear whether breast cancer (BC) subtypes or CSF cytology results are associated with overall survival (OS) among patients with BC leptomeningeal disease (LMD). This single-institution retrospective study compares OS among BC patients with LMD across various breast cancer subtypes and CSF cytology results. MethodologyThe study enrolled BC patients diagnosed with LMD between 2010 and 2023. Breast cancer subtypes were classified as A. ER+/HER2-, HER2+, or triple-negative BC (TNBC); B. HER2+, HER2-Low, HER2-Zero. CSF cytology subtypes included CSF+, CSF-, or CSF not tested (NT). OS was summarized via Kaplan-Meier analysis and compared using log-rank test. Cox models were used for multivariate analyses. ResultsOut of 69 patients registered, median OS (95% CI) for ER+/HER2- (n = 33), HER2+ (n = 12) and TNBC (n = 24) subtypes were 8.0 (3.02, 24.8), 5.71 (1.61, not estimated) and 3.2 (1.11, 4.95) months (P = .17). In multivariate analysis, TNBC was associated with worse OS versus ER+/HER2- [Hazard Ratio (HR), 95% CI: 2.64, 1.23-5.80, P = .04]. HER2 subtypes (HER2-Zero, n = 21; HER2-Low, n = 32; HER2+, n = 12) showed no significant differences in OS. Median OS (95% CI) for CSF+ (n = 16), CSF- (n = 18), and CSF NT (n = 35) groups were 3.54 (1.61, 12.72), 13.41 (4.95, 61.93) and 3.28 (1.44, 6.92) months (P = .04). Multivariate analysis showed both CSF+ and CSF NT were associated with shorter OS compared to CSF- group [HR (95% CI) 4.50 (1.75, 12.11) for CSF+ vs. CSF-; 2.91 (1.45, 6.26) for CSF NT vs. CSF-; P = .002]. ConclusionTNBC LMD group was associated with worse OS than ER+/HER2- BC LMD when adjusting for other prognostic factors. CSF- LMD patients had better OS than CSF+ or CSF NT LMD.

Abstract C145: EPHA4 correlates with different functions and clinical outcomes in different breast cancer subtypes

Abstract Ephrin receptor A4, or EPHA4, is a receptor tyrosine kinase that regulates neuronal stem cell maintenance and is implicated in multiple neuronal diseases. Accumulating studies have shown that EPHA4 may also play important roles in cancer progression, and pharmacological EPHA4 modulators have been tested in preclinical models as potential therapies. In breast cancer, EPHA4 is shown to regulate cancer cell invasion, stemness, and immune response. However, as breast cancer is a heterogenous disease, it is unclear whether and to what extend EPHA4 regulates these functions across different breast cancer subtypes and patient populations. To determine EPHA4 functions and potential benefit of targeting EPHA4 in different patient populations, we analyzed clinical and gene expression data from three patient cohorts: TGCA Firehose, I-SPY2 and SCAN-B. Our results show EPHA4 may be involved in angiogenesis and cell migration across all subtypes. While EPHA4 most strongly correlates with immune response in the Her2 subtype, its correlation with stemness and therapeutic resistance is more prominent in the triple negative/basal subtype. We conclude that EPHA4 inhibition maybe most beneficial for triple negative/basal patients. Citation Format: Wenchao Liu, Marsha Rosner. EPHA4 correlates with different functions and clinical outcomes in different breast cancer subtypes [abstract]. In: Proceedings of the 17th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2024 Sep 21-24; Los Angeles, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2024;33(9 Suppl):Abstract nr C145.

Androgen receptor expression and clinical characteristics in breast cancer

ObjectiveTo investigate the relationship between the expression of androgen receptor (AR) and clinical characteristics in breast cancer.Patients and methodsThe clinical records of all 432 patients tested for AR in our institution between January 2020 and May 2023 were reviewed. Clinical characteristics, age, menopausal status, tumor node metastasis (TNM) stage, distant metastasis, pathological complete response (pCR), histopathological features histological grade, estrogen receptor (ER), progesterone receptor, Her-2, Ki-67, and molecular subtype were registered for all patients.ResultsAbout 377 (87.27%) of the 432 patients had AR expression.No significant difference in AR expression was found with age, menopausal status, TNM stage of primary tumor, or pCR. AR was positively and significantly associated with the histological grade, and recurrence. The AR expression was significantly related with molecular subtypes, including ER, PR Her-2, Ki67 and molecular subtype. ER (OR = 10.489, 95%CI: 5.470–21.569), PR (OR = 7.690, 95%CI: 3.974–16.129, Her-2 (OR = 10.489, 95%CI: 2.779–23.490 and tumor recurrence (OR = 0.110, 95%CI: 0.031–0.377 were significant independent risk factors affecting AR expression.ConclusionsAR expression can serve as a reliable basis for judging the clinical molecular types and poor prognosis for breast cancer. AR may be a novel biomarker and target in AR-positive breast cancer depending on significant difference in AR expression among different molecular types of breast cancer.

Insights Into Benzothiazolyl‐Coupled Azetidinone Moieties Toward EGFR Binding and Stability Analysis—Evidence From Molecular Docking and Dynamics Simulation

ABSTRACTBreast cancer, a formidable threat to women's health, mainly manifests in the HER2 subtype, affecting approximately one in five women. Thus, this study endeavors to pioneer novel approaches by exploring the efficacy of benzothiazole‐coupled azetidinone derivatives against EGFR. We aimed to elucidate their potential by employing a comprehensive array of in silico methodologies, including molecular docking, pharmacokinetics profiling, pharmacophore mapping, molecular dynamic simulations, and MMPBSA analysis. Remarkably, our results demonstrate that our designed molecules adhere to Lipinski's rule and comply with essential physiochemical and druggable properties, affirming the promise of these compounds. Ligand MS60 emerges as a lead, showcasing the most substantial interaction with the EGFR receptor, underscored by its impressive docking score of −8.199 kcal/mol. Furthermore, molecular dynamics simulations conducted via GROMACS corroborate the stability of the MS60‐EGFR complex, portraying minimal fluctuations. This assertion is further validated through MMPBSA, PCA analysis, DCCM, and FEL studies, underscoring the robustness of our findings. We have designed the pharmacophore model to unravel critical steric and electronic attributes essential for effective supramolecular interactions with the EGFR receptor. Notably, the presence of the R10, R11, and A4 groups within the ligands underscores their pivotal role in eliciting pharmacological activity, offering valuable insights for further exploration and development.

Radiologic-Pathologic Correlation: Is There an Association Between Contrast-Enhanced Mammography Imaging Features and Molecular Subtypes of Breast Cancer?

This study aims to assess the correlation between imaging features of contrast-enhanced mammography (CEM) and molecular subtypes of breast cancer. This is a retrospective single-institution study of patients who underwent CEM from December 2019 to August 2023. Each patient had at least one histologically proven invasive breast cancer with a core biopsy performed. Patients with a history of breast cancer treatment and lesions not entirely included in the CEM images were excluded. The images were interpreted using the American College of Radiology Breast Imaging Reporting and Data System (ACR BI-RADS) lexicon for CEM, published in 2022. Different imaging features, including the presence of calcifications, architectural distortion, non-mass enhancement, mass morphology, internal enhancement pattern, the extent of enhancement, and lesion conspicuity, were analyzed. The molecular subtypes were studied as dichotomous variables, including luminal A, luminal B, HER2, and basal-like. The association between the imaging features and molecular subtypes was analyzed with a Fisher's exact test. Statistical significance was assumed when the p-value was <0.05. A total of 31 patients with 36 malignant lesions were included in this study. Sixteen lesions (44.4%) were luminal A, four lesions (11.1%) were luminal B, 10 lesions (27.8%) were HER2, and six (16.7%) were basal-like subtypes. The presence of calcifications was associated with the HER2 subtype (p=0.024). Rim-enhancement on recombined images was associated with a basal-like subtype (p=0.001). Heterogeneous enhancement on recombined images was associated with non-basal-like breast cancer (p=0.027). No statistically significant correlation was found between other analyzed CEM imaging features and molecular subtypes. CEM imaging features, including the presence of calcifications and certain internal enhancement patterns, were correlated with distinguishing breast cancer molecular subtypes and thus may further expand the role of CEM.

Identifying miRNA as biomarker for breast cancer subtyping using association rule

— This paper presents a comprehensive study focused on breast cancer subtyping, utilizing a multifaceted approach that integrates feature selection, machine learning classifiers, and miRNA regulatory networks. The feature selection process begins with the CFS algorithm, followed by the Apriori algorithm for association rule generation, resulting in the identification of significant features tailored to Luminal A, Luminal B, HER-2 enriched, and Basal-like subtypes. The subsequent application of Random Forest (RF) and Support Vector Machine (SVM) classifiers yielded promising results, with the SVM model achieving an overall accuracy of 76.60 % and the RF model demonstrating robust performance at 80.85 %. Detailed accuracy metrics revealed strengths and areas for refinement, emphasizing the potential for optimizing subtype-specific recall. To explore the regulatory landscape in depth, an analysis of selected miRNAs was conducted using MIENTURNET, a tool for visualizing miRNA-target interactions. While FDR analysis raised concerns for HER-2 and Basal-like subtypes, Luminal A and Luminal B subtypes showcased significant miRNA-gene interactions. Functional enrichment analysis for Luminal A highlighted the role of Ovarian steroidogenesis, implicating specific miRNAs such as hsa-let-7c-5p and hsa-miR-125b-5p as potential diagnostic biomarkers and regulators of Luminal A breast cancer. Luminal B analysis uncovered associations with the MAPK signaling pathway, with miRNAs like hsa-miR-203a-3p and hsa-miR-19a-3p exhibiting potential diagnostic and therapeutic significance. In conclusion, this integrative approach combines machine learning techniques with miRNA analysis to provide a holistic understanding of breast cancer subtypes. The identified miRNAs and associated pathways offer insights into potential diagnostic biomarkers and therapeutic targets, contributing to the ongoing efforts to improve breast cancer diagnostics and personalized treatment strategies.

Studying on correlation between Ki-67 index and histopathological and immunohistochemical characteristics in invasive breast carcinoma

Background: Breast cancer is the most common cancer and the leading cause of cancer death in women. Molecular subtyping of breast cancer is based on the expression of biomarkers such as ER, PR, HER2/neu and Ki-67. Among them, Ki-67 is a biomarker expressing the proliferation level of breast cancer cells, directly related to disease progression, treatment response and prognosis. Our study aims to evaluate the Ki-67 index and its relationship with histopathological and immunohistochemical characteristics in invasive breast carcinoma. Methods: A cross-sectional descriptive study in 101 paraffin-embedded specimens of patients with invasive breast carcinoma who underwent surgery at Hue University of Medicine and Pharmacy Hospital from October 2019 to June 2021. Results: Tumors with Ki-67 index ≥ 14% account for 65.3%. Breast cancer tumors with tumor size ≤ 2 cm occupy for 50.5%. Histological grade II accounts for 53.1%. The most common disease stage is stage II (40.6%). The rate of axillary lymph node metastasis is 48.5%; The ER(+) and PR(+) rates are 64.4% and 47.5%, respectively. Tumors with HER2(+) account for 32.7%. The Luminal B accounts for the highest proportion (39.4%). The Ki-67 index has a statistically significant relationship with disease stage, histological grade, axillary lymph node metastasis, ER, PR, HER2 and molecular subtypes. There is no relationship between Ki 67 and age, tumor size and histopathological type. Conclusion: Tumors with Ki-67 ≥ 14% account for a high proportion (65.3%). The Ki-67 index has a statistically significant relationship with histopathological and immunohistochemical features: stage of disease, histological grade, axillary lymph node metastasis, ER/PR hormone receptors, and other factors. HER2-positive endodermal growth and molecular subtypes. There is no significant relationship between Ki-67 and age, tumor size and histopathological type. Key words: breast carcinoma; Ki-67; histopathology; immunohistochemistry.

Identifying mutations in ctDNA to predict antibody-drug conjugate response in breast cancer.

e13074 Background: Metastatic breast cancer (mBC) is a complex disease, and outcomes remain poor because new therapies are needed. A new class of drugs, antibody-drug conjugate (ADC), has shown effectiveness across all breast cancer subtypes. Yet FDA- approval for these therapies is restricted only to HER2 and triple-negative subtypes. Therefore, we urgently need to identify which patients, regardless of subtype, will respond to ADCs. The advent of circulating tumor DNA (ctDNA) offers a unique noninvasive method to capture breast cancer (BC) heterogeneity. Recently, ctDNA testing has been employed in clinical practice to guide targeted therapies for mBC, particularly in cases of hormone receptor positive (HR+) disease with mutations in PIK3CA and ESR1. The clinical implications to predict response to ADC therapy in BC remains unclear. Here we test the hypothesis that ctDNA can detect mutations that predict response to novel ADCs. Methods: We analyzed a subset of patients from the Dallas Metastatic Breast Cancer Study comprised of patients with mBC who underwent ctDNA testing using the Tempus xF liquid biopsy ctDNA sequencing panel. The data was analyzed from a single academic medical center between the initial year of ctDNA collection in 2019 to 2023. We identified detectable mutations from patients and addressed a relationship by using Metascape. Relevant signaling pathways were identified: APOBEC, ErbB signaling, p53 and Ras-MAPK pathway. Patients with triple negative, HER2, and HR BC were examined for ADC response and associated mutations. Survival analyses were estimated using Kaplan-Meier and Gehan Breslow Wilcoxon test for statistical analysis. Results: We identified 43 patients with HR+ mBC who had at least one mutation within the Ras-MAPK pathway and 10 of 43 received ADC therapy. Median survival of patients who received ADC therapy 58 months (n=10) vs not receiving ADC therapy 33 months (n=33) (p &lt; 0.05). Of the ten patients who received ADC treatment, 60% had 1+ HER2 staining on tissue biopsy. 70% of patients received Trastuzumab deruxtecan (T-DXd) and 30% received Sacituzumab govitecan (SG). SG was given to patients with negative HER2 staining on biopsy. Patients with at least one mutation within ABOBEC, ErbB signaling, and p53 pathways did not have statistically significant differences in mOS. Conclusions: In HR+ mBC, detection of mutated genes associated with the Ras-MAPK pathway by ctDNA was associated with a more favorable response when treated with ADCs. These findings are exciting because HR+ BCs are being targeted with ADCs regardless of HER2 or TROP2 expression, highlighting the need for new biomarkers to distinguish which HR+ patients to treat. Our retrospective analysis findings are limited by the number of patients with ctDNA testing and also timing of testing. Further studies are needed to solidify the observed correlation between Ras-MAPK pathway mutations and favorable response to ADC treatment.

Mutational landscape of HSP family on human breast cancer

Breast cancer (BRCA) is a prevalent malignancy with the highest incidence among females. BRCA can be categorized into five intrinsic molecular subtypes (LumA, LumB, HER2, Basal, and Normal), each characterized by varying molecular and clinical features determined by the expression of intrinsic genes (PAM50). The Heat Shock Protein (HSP) family is composed of 95 genes evolutionary conservated, they have critical roles in proteostasis in both normal and cancerous processes. Many studies have linked HSP to the development and spread of cancer. They modulate the activity of multiple proteins expressed by oncogenes and anti-oncogenes through a range of interactions. In this study, we evaluate the mutational changes that HSP undergoes in BRCA mainly from the TCGA database. We observe that Copy Number Variations (CNV) are the more frequent events analyzed surpassing the occurrence of point mutations, indels, and translation start site mutations. The Basal subtype showcased the highest count of amplified CNV, including subtype-specific changes, whereas the Luminals tumors accumulated the greatest number of deletion CNV. Meanwhile, the HER2 subtype exhibited a comparatively lower frequency of CNV alterations when compared to the other subtypes. This study integrates CNV and expression data, finding associations between these two variables and the influence of CNV on the deregulation of HSP expression. To enhance the role of HSP as a risk predictor in BRCA, we succeeded in identifying CNV profiles as a prognostic marker. We included Artificial Intelligence to improve the clustering of patients, and we achieved a molecular CNV signature as a significant risk factor independent of known classic markers, including molecular subtypes PAM50. This research enhances the comprehension of HSP DNA alterations in BRCA and its relation with predicting the risk of affected individuals providing insights to develop guide personalized treatment strategies.

Abstract PO1-23-01: A novel nomogram for predicting the possibility of omitting axillary lymph node dissection after neoadjuvant chemotherapy for clinical node-positive breast cancer

Abstract Purpose: Currently, there is no validated strategy established for omitting axillary lymph node dissection (ALND), when axillary node metastases are expected to disappear with neoadjuvant chemotherapy (NAC) for clinical node-positive (cN+) breast cancers. In contrast, it was reported that the axillary pathological complete response (pCR) rate to NAC for cN+ breast cancer is approximately 40%. Therefore, it is necessary to develop a more accurate method for predicting nodal pCR (ypN0) to select patients who can omit ALND after NAC for cN+ breast cancer. Methods: This is a single-centered, retrospective clinical study conducted in 128 patients with cN+ primary breast cancer who underwent ALND after NAC between January 2014 and July 2021 at Saitama Medical Center. Clinical complete response (cCR) was defined as the disappearance of the primary tumor or axillary node metastasis, as confirmed by the findings of imaging. The pCR was defined as the absence of microscopic evidence of residual invasive carcinoma in primary breast tumor or axillary nodes. Clinicopathological variables were compared using Fisher’s exact test or logistic regression, as appropriate. Statistical significance was set at p&amp;lt; 0.05. Results: The median age of the patients was 52 years; 48.4% were premenopausal, 38.3% had cT3 or higher, 22.7% had cN2 or higher, and 50% had stage III disease. Estrogen receptor (ER), progesterone receptor (PgR), and human epidermal growth factor receptor 2 (HER2) positivity accounted for the patients were 58.6%, 50%, and 31.3%, respectively. NAC included sequential taxanes and anthracyclines in 47.7% of the patients, and anti-HER2 therapy was used in all patients of HER2-positive breast cancer. Breast primary tumor cCR (ypT0) was 29.7% and ypN0 was 44.5%. The ypN0 rate was 19.5% higher than the ypT0 rate in all patients (p &amp;lt; 0.001); it was 4.8% higher in the luminal subtype (p=0.009), 25.5% higher in the triple-negative subtype (p &amp;lt; 0.001), and 29.3% higher in the HER2 subtype (p=0.015). Additionally, the ypN0 rate was 3.9% higher than the axillary node cCR (ycN0) rate in all patients (p &amp;lt; 0.001), 7.6% lower in luminal type (p &amp;lt; 0.001), 13.6% higher in triple-negative type (p &amp;lt; 0.001), and 5% higher in the HER2 subtype (p=0.006). When ycN0 was predicted to be ypN0, the negative predictive value (NPV) was 77.2% and the false negative rate (FNR) was 19.7% (Table 1). In the association between ypN0 and preoperative clinico-pathological factors in cN+ breast cancer treated with NAC, univariate analysis showed significant differences in ER negativity (ER-) [hazard ratio (HR): 0.186, 95% confidence interval (CI): 0.086–0.401, p&amp;lt; 0.001], PgR negativity (HR: 0.360, 95% CI: 0.176–0.736, p=0.005), HER2 positivity (HER2+) (HR: 4.394, 95% CI: 1.941–9.949, p&amp;lt; 0.001), ycT0 (HR: 10.667, 95% CI: 4.020–28.304, p&amp;lt; 0.001), and ycN0 (HR: 9.966, 95% CI: 4.399–922.576, p&amp;lt; 0.001). The multivariate analysis revealed that ER, ycT0, and ycN0 were independent predictive factors for ypN0 after NAC in the patients with cN+ breast cancer (Table 2). These independent factors in multivariate analysis were used to create a nomogram for ypN0 prediction. The points added were 82 if the patient was ER-, 56 if the patient was ycT0, and 100 if the patient was ycN0, and the total of these scores was used to predict whether the patient had ypN0. When the Receiver Operating Characteristic curve was used to determine the cut-off value of the total points, 119 or more points were predicted to be ypN0, the NPV was 92.9%, and the FNR was 4.5%, which demonstrated an approximately 15% improvement over the prediction of ypN0 by ycN0 alone (Table 3). Conclusion: ER, ycT0, and ycN0 are independent predictive factors of ypN0 in cN+ breast cancer, suggesting that ypN0 prediction using a nomogram may contribute to individualized axillary treatment. Table 1. Accuracy of ypN0 prediction with ycN0 after NAC for clinical node-positive breast cancer Table2. Univariate and multivariate analyses of the relationship between preoperative clinicopathological factors and pathologically axillary node-negative after neoadjuvant chemotherapy in clinical node-positive breast cancer Table 3. Accuracy of ypN0 prediction after NAC for clinical node-positive breast cancer using Nomogram Citation Format: Hirohito Seki, Yuki Ishiguro, Ken Shimizu, Akitsugu Makino, Yoshiharu Ishizaka, Ai Tsuchiya, Hirotsugu Isaka, Shigeru Imoto. A novel nomogram for predicting the possibility of omitting axillary lymph node dissection after neoadjuvant chemotherapy for clinical node-positive breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-23-01.

Abstract PO4-03-04: Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy

Abstract Objective: The gut microbiome (GM) has been identified as one of the major environmental factors that can regulate the development and maintenance of the immune system. In oncology, while the importance of GM has been evaluated in more immunogenic tumors such as melanoma, lung carcinoma and clear cell carcinoma, its importance in early-stage breast cancer (eBC) is underexplored. The aim of this study was to characterize the GM of patients with eBC who underwent neoadjuvant chemotherapy (NACT) and to evaluate its association with clinicopathologic prognostic factors and outcomes. Methods: This was a prospective study conducted at two Brazilian institutions. Fecal samples were collected at baseline (time 1) and prior to surgery (time 2) from 55 patients who received NACT with anthracycline/taxane. Gut microbiome was analyzed by 16S rRNA amplicon sequencing to characterize the α (InvSimpson index) and β (weighted UniFrac distance metric) diversity, as well as taxonomic composition. Clinicopathologic prognostic factors were retrieved from medical records. Pathological complete response (pCR) was defined as the absence of invasive carcinoma in breast and axillary nodes (ypT0/Tis ypN0). Stromal tumor-infiltrating lymphocytes (sTIL) were reported according to the TIL working group criteria. Information about prior use (&amp;lt; 60 days before stating on NACT) of antibiotic (ATB) was obtained directly from patients. Statistical significance was set at P ≤ 0.05 and analysis of composition of microbiomes (ANCOM-BC2) was used to identify enriched genera with p-values adjusted using FDR correction ≤ 0.25. Results: Median age was 49 years (range 31-73). Eleven patients (20%) reported prior antibiotic use at baseline. About 34.5% of patients had HR+/HER2- tumors, 45.4% had triple negative breast cancer (TNBC), and 20% had HER2-positive breast cancer. Fourteen (25%) patients achieved a pCR. Out of 55, 47 (85.4%) had sTIL information. There was no significant difference in alpha diversity (p = 0.6) or beta-diversity (p = 0.8) between the pCR and residual disease group nor within clinical pathologic factors (age, staging, histological tumor grade, subtype of breast cancer based on IHC, sTIL). The most abundant taxon in both time 1 and time 2 were the same (Blautia at genus level, Lachnospiraceae at family level, and Lachnospirales at order level), and longitudinal samples collected during NACT showed no significant changes in GM composition. At baseline, we found an enrichment for Clostridia sp. among patients who did not use ATB (p &amp;lt; 0.05, pFDR ≤ 0.25). Additionally, we found enrichment for Bifidobacterium (p &amp;lt; 0.05, pFDR ≤ 0.25) among patients with HER2 subtype who presented residual disease. Conclusions: Gut microbiome analysis in early breast cancer is feasible and to our knowledge, this is the first study to evaluate the intestinal microbiota of Brazilian patients with breast cancer. We did not observe any significant association between GM diversity and taxonomic composition with clinical pathologic factors and pCR in this study, nor did we observe changes in the ecological balance of the GM following NACT in breast cancer. Further studies are needed to explore the potential influence of the gut microbial ecosystem on tumor biology and response to neoadjuvant chemo-immunotherapy. Citation Format: Ludmila Thommen, Vitor Heidrich, Rosângela Vieira de Andrade, Luiza Nardin Weis, Maria Sueli Soares Felipe, Melissa Lole Da Cas Vita, Thiago David Alves Pinto, Anamaria Camargo, Romualdo Barroso-Sousa. Characterization of Gut Microbiome of patients with early-stage breast cancer treated with neoadjuvant chemotherapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-03-04.

Abstract PO1-24-07: LYSOSOMAL-ASSOCIATED TRANSMENBRANE 4B (LAPTM4B) AS POTENTIAL BIOMARKER IN BREAST CANCER

Abstract LAPTM4B is a transmembrane that promotes autophagy and renders tumor cells resistant to metabolic and genotoxic stress. Increased expression of LAPTM4B has been found in breast, liver, lung, ovarian, uterine and gastric cancers. Overexpression of LAPTM4B contributes to chemotherapy resistance, proliferation and metastases. We analyze the expression of LAPTM4B in serum by ELISA method in a series of breast cancer patients in different clinical situations to assess its possible potential as a biomarker. A total of 135 patients were analyzed, 95 patients were in early breast cancer and 50 in metastatic disease. Of the 95 patients with early disease, 52 had a luminal A phenotype, 19 luminal B, 15 HER2 positive and 9 triple negative. And of the other 50 they were luminal in 34, HER2 positive in 11 and triple negative in 5. The attached table specifies the values of the LAPTM4B expression in the different clinical situations. GLOBAL LUMINAL A LUMNAL B HER2 TRIPLE NEGATIVE SITUATIONS Laptm4b n Laptm4b n Laptm4b n Laptm4b n Laptm4b n EARLY 9,6 ng/ml 95 7,7 ng/ml 52 12,8 ng/ml 19 13,4 ng/ml 15 7,1 ng/ml 9 METASTATIC 16,8 ng/ml 50 13,7 ng/ml 34 7,2 ng/ml 11 58,9 ng/ml 5 We found a statistic difference in the expression of LAPTM4B in patients with early and metastatic disease (ANOVA test p:0,028 ). LAPTM4B was higher in the luminal B and HER2 subtypes in early breast cancer while in metastatic disease was overexpressed in triple negative. An interesting finding was that in metastatic disease, LAPTM4B was overexpressed in patients with progression compared to patients in response. 30 ng/ml vs 10 ng/ml (ANOVA test p:0,011) LAPTM4B expression may be a potential biomarker in breast cancer since its expression is statistically different in early and metastatic disease (9,6 vs 16,8 ng/ml).In addition, patients with metastatic breast cancer who re in response also have lower levels of LAPTM4B compared with patients in progression. Monitoring the levels of LAPTM4B in serum can help us to predict the treatment response. Citation Format: Serafin Morales Murillo, Ariadna Gasol Cudós, Noemí Tuset Der-Abrain, Izaskun Urdanibia, Ana Velasco Sánchez. LYSOSOMAL-ASSOCIATED TRANSMENBRANE 4B (LAPTM4B) AS POTENTIAL BIOMARKER IN BREAST CANCER [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-24-07.

Abstract PO2-08-05: ERBB2 mutated breast cancer detected by next generation sequencing: integrated analysis based on real-world data and The Cancer Genome Atlas

Abstract Background ERBB2 mutation has been recognized as an actionable target for pan-HER tyrosine kinase inhibitors in the era of precision medicine for solid tumors. In our real-world cohort utilizing next-generation sequencing (NGS), we successfully identified cases of ERBB2-mutated breast cancer. Furthermore, we investigated the clinical and pathological characteristics of these cases by integrating our data with The Cancer Genome Atlas (TCGA). Methods Our real-world cohort with NGS included 423 breast cancer patients treated at Gangnam Severance Hospital in Seoul, Republic of Korea, between April 2017 and January 2023. Among these patients, 13 were confirmed to have ERBB2 mutation through NGS analysis. We also incorporated data from TCGA database, which included 818 cases with ERBB2 sequencing. We compared the clinical characteristics (age, sex, stage, and ER, PR, and HER2 status) between the two groups. Furthermore, we examined the frequency of two of the most common mutations, PIK3CA and TP53, in both groups. Additionally, we investigated the distribution of PAM50 subtypes in the TCGA cohort. Results This study analyzed a total of 1,244 cases with NGS data. Among these cases, 31 (2.5%) exhibited ERBB2 mutation, with 13 patients identified in our dataset and 18 in the TCGA data. Among the 31 cases with ERBB2 mutation, 21 (67.7%) had HER2-negative disease. No significant differences were observed in other clinical characteristics based on ERBB2 status. Within the group of 31 ERBB2-mutated cases, TP53 mutations were found in 12 cases (38.7%), while PIK3CA mutations were found in 12 cases (38.7%). In the TCGA dataset, 4 cases (22.2%) with ERBB2 mutation were classified as HER2-E subtype, and the rate of HER2-E subtype was significantly higher in the ERBB2-mutated group compared to the ERBB2-wild group (22.2% vs. 7.6%, p=0.024). Conversely, 14 cases (77.8%) with ERBB2 mutation exhibited a non-HER2 enriched subtype. Conclusions Consistent with previous knowledge, ERBB2 mutations can be detected in HER2-negative breast cancer, despite their rarity. Furthermore, a considerable proportion of ERBB2-mutated breast cancer may depend on various oncogenic signaling pathways other than the HER2 pathway. Further studies are warranted to optimize therapeutic strategies for ERBB2-mutated breast cancer. Citation Format: Junghyun Kim, Yoonwon Kook, Seung Ho Baek, Min Ji Kim, Sohyun Moon, Seung Eun Lee, Jee Hung Kim, Soong June Bae, Joon Jeong, Sung Gwe Ahn. ERBB2 mutated breast cancer detected by next generation sequencing: integrated analysis based on real-world data and The Cancer Genome Atlas [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-08-05.

Abstract PO5-02-12: Comparison of survival outcomes according to axillary ultrasonography findings and cytology results in early-stage breast cancer patients

Abstract Purpose: Axillary lymph node dissection and sentinel lymph node biopsy are associated with increased risk of post-surgical complications including lymphedema and recent trials have raised questions about the therapeutic benefit of axillary operation in early-stage breast cancer patients. While treatment options for lymph nodes with negative findings on axillary ultrasonography (AUS) or positive findings on fine needle aspiration biopsy (FNAB) are evident, data regarding lymph nodes that are suspicious on AUS but negative by FNAB are limited. Thus, we aimed to compare clinicopathological characteristics of AUS positive and FNAB negative patients with those of AUS negative or FNAB positive patients. Materials and Methods: Medical records of patients who underwent breast cancer surgery between January 2010 and December 2017 were reviewed. Patients were grouped into the following three groups: (a) negative findings on AUS, (b) suspicious findings on AUS but negative on FNAB, (c) and FNAB positive. A total of 4,506 patients were included for analysis, with 3,771 patients with no suspicious lymph nodes on AUS, 557 patients who had suspicious AUS findings but were negative on FNAB, and 178 patients with positive findings on both AUS and FNAB. Primary endpoints were disease free survival (DFS) and recurrence free survival (RFS), and secondary endpoint was overall survival (OS). Results: At a median follow-up period of 92 months, DFS and RFS was significantly higher in the AUS negative group compared to the other two groups (10-year-DFS: 91.6% vs 87.5% vs 75.7%, 10-year-RFS: 95.0% vs 89.9% vs 77.1%, p &amp;lt; 0.001). In terms of OS, AUS negative group and the AUS positive and FNAB negative group did not show statistically significant survival difference (10-year-OS: 94.5% vs 92.8%, p = 0.061), while the FNAB positive group showed significantly lower survival rates (10-year-OS: 81.8%, p &amp;lt; 0.001). Multivariable analysis revealed that not AUS positive and FANB negative but positive FNAB was significantly associated with poor RFS. Moreover, hormone receptor (HR) positive and HER2 negative subtype showed poor DFS and RFS in subgroup analysis. Conclusion: Early breast cancer patients with suspicious findings on AUS but negative FNAB results had similar OS but inferior DFS and RFS compared to those with negative features on AUS, especially in HR(+)HER2(-) subtype. While further prospective trials are warranted to determine whether additional treatment is necessary, close surveillance is recommended for this subgroup of patients. Figure1. Overall survial and Disease free survival according to axillay US and FNAB status Table1. patients' characteristics Table2. prognostic factors for overall survival and disease free survival related to axillary US and FNAB status Citation Format: Suk Jun Lee. Comparison of survival outcomes according to axillary ultrasonography findings and cytology results in early-stage breast cancer patients [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-02-12.

Abstract PO4-25-10: Towards personalized medicine for DCIS - the role of hormone receptors, HER2, and Ki67 status in high-grade DCIS

Abstract Objective: This study aimed to investigate the molecular details in breast ductal carcinoma in situ (DCIS). Expression status of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and Ki67 were investigated among luminal A (LumA), luminal B HER2-negative (LumB HER2-), luminal B HER2-positive (LumB HER2+), HER2-enriched, and triple-negative (TPN), subtypes of DCIS. Materials &amp; Methods: The study comprised formalin-fixed paraffin-embedded (FFPE) specimens of 357 DCIS grade 3 cases diagnosed between 1996 – 2018. Routine diagnostic immunohistochemical (IHC) staining were performed. DCIS cases were classified as LumA, LumB HER2-, LumB HER2+, HER2-enriched or TPN, according to the 2013 St. Gallen guidelines, which is used for molecular subtyping of invasive breast carcinoma (IBC). Each subtype was sorted into three subcategories: “pure” meaning those without an invasive component; “w/invasive” meaning those with an invasive component; and “all” meaning the entire group of the given subtype. Furthermore, ER and PR-receptor expression was registered for LumA, LumB HER2- and LumB HER2+ cases as intervals. The distribution of Ki67 was analyzed within each subtype. For some analyses, we combined the LumA and LumB HER2- subtypes into one entire group. The inter-observer variability of Ki67 was calculated by setting a cut-off value of 20% (2013 St. Gallen). A cohort (n = 47) of DCIS cases with a median Ki67 value of 18% was selected. Ki67 was calculated by analyzing 200 DCIS cells in two separate hotspots. Cohen's Kappa coefficient was calculated based on these data. HER2 (IHC) was scored based on ASCO/CAP guidelines established for routine diagnostic work-up for IBC. 16 equivocal cases (2+) were further investigated using dual SISH. Results: 98% of “all” cases of the LumA subtype showed an ER ≥ 50%. PR expression ≥ 50% was found in 91% of cases in this subtype. The incidence of ER-receptor at a cut-off ≥ 50% in the LumA subtype was significantly higher than that in the LumB HER2- and LumB HER2+ subtypes (p &amp;lt; 0.0001, Chi-square). In contrast, there was a statistically significant reduction in ER-receptor expression at a cut-off &amp;lt; 10% in LumA compared to the latter subtypes. The proportion of cases with PR-receptors with a cut-off of &amp;lt; 20% showed significant differences between LumA, LumB HER2- and LumB HER2+ subtypes (1.6%; 47% and 37%, respectively). There was also a significantly higher proportion of PR-receptor ≥ 50% cases among the LumA subtype. We found a significant association between PR &amp;lt; 20% and HER2 (3+) in luminal subtypes (p &amp;lt; 0.0004, Fisher's exact). There was no significant difference in ER/PR expression in “pure” cases of luminal subtypes of DCIS versus those with an invasive component (p = 0.1831, Chi-square). The Ki67 in the entire population (n = 357) varied from &amp;lt; 1% to &amp;gt; 80%. The mean and median were around 20% in those subtypes whose classifications were not depended on Ki67. There was a significant difference in the distribution of Ki67 when cases of LumA “all” and those of LumB HER2- “all” were combined as one entire group and were compared to LumB HER2+ “all” and HER2-enriched “all” (p-adjusted &amp;lt; 0.0001, Kruskal Wallis). The assessment of Ki67 among different observers showed a Cohen's kappa coefficient of 0.29 – 0.31 (fair agreement). We compared the HER2 (IHC) 0, 1+ and 2+ score among LumA and LumB HER2- subtypes and did not find a statically significant difference, when the “pure” and “w/invasive” were compared (p = 0.603, Chi-square). Conclusions: Ki67 was highly variable in DCIS grade 3. Inter-observer agreement was (as expected) suboptimal, and the cut-off at 20% defined by the 2013 St Gallen guidelines for IBC is not reliable for the distinction of LumA and LumB HER2 subtypes of DCIS. The LumB subtype of DCIS is heterogeneous with considerable variability among the four IHC markers used in the present study. A low PR is strongly associated with HER2 (3+), in luminal subtypes (p &amp;lt; 0.0004, Fisher's exact). Citation Format: Hossein Schandiz, Lorant Farkas, Daehoon Park, Solveig Norheim Andersen, Jürgen Geisler, Torill Sauer. Towards personalized medicine for DCIS - the role of hormone receptors, HER2, and Ki67 status in high-grade DCIS [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-25-10.

Abstract 6698: Tumor microbiota associated with immune enrichment in breast tumor

Abstract Asian cancer patients have enriched immune profiles when compared to Caucasians. This is associated with improved overall survival and potentially better response to immunotherapy. Yet the reason behind enriched Asian immune profiles is unclear. This study investigated microbes found in Malaysian breast tumors in association with immune profiles. We used an existing dataset of RNA-seq data from fresh frozen breast tumor tissue (n=978). Sequencing reads were trimmed and filtered to remove human reads. Non-human reads were mapped to Kraken2 and relative abundance was estimated using Bracken. Microbiome analysis was conducted on R following Microbiome OMA guidebook. The top five genera found in the Malaysian Breast Cancer (MyBrCa) cohort were Pseudomonas, Siphoviridae, Bacillus, Escherichia and Klebsiella. Alpha diversity of basal subtype microbiota was significantly higher than Her2 subtype (Shannon index, p=0.027) whilst the other subtypes were more homogenous. MyBrCa patients with low immune scores were significantly different from high immune scores while controlling for age, stage, grade, ethnicity and PAM50 subtype (PERMANOVA, F-statistic = 1.656, p=0.05). Differential abundance analysis revealed Sulfidibacter and Priestia to be significantly different in abundance between high vs low IFNg groups (FDR-adjusted p-value &amp;lt; 0.05) using ALDEx2, ANCOM-BC2 and ZicoSeq and LinDA algorithms. Sulfidibacter was significantly different between high vs low immune group for Bindea combined immune score and ESTIMATE score groups (FDR-adjusted p-value &amp;lt;0.05). An independent breast cancer cohort (n=419) was used as validation where Sulfidibacter and Priestia were also significantly different in abundance for immune high vs low groups. Machine learning using Random Forest model predicted immune group with an AUC of 0.79 (CI = 0.74, 0.83; p-value &amp;lt; 0.01). The top five most important features contributing to the random forest model were Sulfidibacter, Prestia, Cutibacterium, Acinetobacter and Rhizobium. This study is the largest to date that characterize the tumor microbiota of an Asian cohort of breast cancers, where Sulfidibacter and Priestia, both relatively new and uncharacterized bacteria, were differentially abundant among patients with high vs low immune scores. Citation Format: Li-Fang Yeo, Bernard KB Lim, Tania Islam, Li-Ying Teoh, Suniza Jamaris, Mee-Hoong See, Lai-Meng Looi, Nur Aishah Mohd Taib, Cheng-Har Yip, Pathmanathan Rajadurai, Soo-Hwang Teo, Jia Wern Pan. Tumor microbiota associated with immune enrichment in breast tumor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6698.

Exemestane plus everolimus and palbociclib in metastatic breast cancer: clinical response and genomic/transcriptomic determinants of resistance in a phase I/II trial

The landscape of cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) resistance is still being elucidated and the optimal subsequent therapy to overcome resistance remains uncertain. Here we present the final results of a phase Ib/IIa, open-label trial (NCT02871791) of exemestane plus everolimus and palbociclib for CDK4/6i-resistant metastatic breast cancer. The primary objective of phase Ib was to evaluate safety and tolerability and determine the maximum tolerated dose/recommended phase II dose (100 mg palbociclib, 5 mg everolimus, 25 mg exemestane). The primary objective of phase IIa was to determine the clinical benefit rate (18.8%, n = 6/32), which did not meet the predefined endpoint (65%). Secondary objectives included pharmacokinetic profiling (phase Ib), objective response rate, disease control rate, duration of response, and progression free survival (phase IIa), and correlative multi-omics analysis to investigate biomarkers of resistance to CDK4/6i. All participants were female. Multi-omics data from the phase IIa patients (n = 24 tumor/17 blood biopsy exomes; n = 27 tumor transcriptomes) showed potential mechanisms of resistance (convergent evolution of HER2 activation, BRAFV600E), identified joint genomic/transcriptomic resistance features (ESR1 mutations, high estrogen receptor pathway activity, and a Luminal A/B subtype; ERBB2/BRAF mutations, high RTK/MAPK pathway activity, and a HER2-E subtype), and provided hypothesis-generating results suggesting that mTOR pathway activation correlates with response to the trial’s therapy. Our results illustrate how genome and transcriptome sequencing may help better identify patients likely to respond to CDK4/6i therapies.