Response In Triple-negative Breast Cancer Research Articles

Abstract 397: The role of heparan sulfate in enhancing the chemotherapeutic response in triple-negative breast cancer

Abstract Among women worldwide, breast cancer has the highest incidence and is the leading cause of cancer-related death. Patients with the triple-negative breast cancer (TNBC) subtype have an inferior prognosis in comparison to other breast cancers because the current therapies do not facilitate long-lasting responses. Thus, there is a critical need for novel therapeutic strategies that induce stronger responses. In our previous research, we discovered that augmenting the concentration of extracellular ATP (eATP) greatly enhances the chemotherapeutic response of TNBC cell lines by activating purinergic receptors (P2RXs), leading to cell death through the induction of non-selective membrane permeability. However, eATP levels are limited by several classes of extracellular ATPases. One endogenous molecule of interest that can inhibit multiple classes of extracellular ATPases is heparan sulfate. Heparan sulfate itself is degraded by heparanase, an enzyme that is known to be highly expressed in various cancers, including breast cancer. Heparan sulfate has previously been shown to regulate several cancer-related processes such as fibroblast growth factor signaling, neoangiogenesis by sequestering vascular endothelial growth factors in the extracellular matrix, hedgehog signaling and cell adhesion. In this project, we identified an additional mechanism for a tumor suppressor role of heparan sulfate: inhibition of extracellular ATPases, leading to augmented levels of eATP. Several heparanase inhibitors have been previously identified, including OGT 2115, suramin, PI-88, and PG 545. We hypothesized that heparanase inhibitors would augment eATP concentrations in TNBC by increasing heparan sulfate in the tumor microenvironment, resulting in increased cell death in response to chemotherapy. We treated TNBC cell lines MDA-MB 231, Hs 578t, and MDA-MB 468 and non-tumorigenic immortal mammary epithelial MCF-10A cells with increasing concentrations of the chemotherapeutic agent paclitaxel in the presence of heparan sulfate and/or OGT 2115 with eATP content and cell viability being assessed. Moreover, to confirm that the effects of OGT 2115 are mediated through eATP, we utilized specific antagonists to the purinergic receptors P2RX4 and P2RX7. In addition, the protein expression of heparanase was compared in all the examined cell lines via Western blot analysis. We also evaluated the effects of this combination on the breast cancer-initiating cell population in the treated cells using flow cytometry and tumorsphere formation efficiency assays. These results demonstrate that inhibiting the degradation of heparan sulfate in the tumor microenvironment enhances the susceptibility of TNBC cell lines to chemotherapy by augmenting extracellular ATP concentrations. This strategy could potentially be used to induce deeper and more durable responses in triple-negative breast cancer patients. Citation Format: Jasmine M. Manouchehri, Jharna Datta, Mathew A. Cherian. The role of heparan sulfate in enhancing the chemotherapeutic response in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 397.

Abstract 5569: Quantification of tumor-associated vasculature as an imaging biomarker for monitoring the response of triple-negative breast cancer to neoadjuvant chemotherapy

Abstract Introduction: Patients with locally advanced, triple-negative breast cancer (TNBC) typically receive neoadjuvant systemic therapy (NAST). However, the response of TNBC to NAST is varied and a prognostic marker is still lacking. Since angiogenesis plays an important role in cancer progression, the quantification of changes in the tumor vasculature during treatment has the potential to provide useful information for characterizing the treatment response. We have recently developed a method to quantify changes in tumor-associated vasculature through a novel analysis of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). In this study, we investigated its ability to monitor the response of TNBC to NAST. Methods: Dynamic contrast-enhanced (DCE) MRI was acquired in TNBC patients (N = 50; 25 pathological complete response (pCR), 25 non-pCR) before, after 2 and 4 cycles of Adriamycin/Cyclophosphamide (A/C), as part of the ARTEMIS trial (NCT02276433). Using DCE-MRI, we identified the tumor-associated vessels via a breast vasculature analysis. Specifically, the difference between pre- and post-contrast DCE-MRI images was enhanced by a histogram-based intensity transfer function. The 3D vasculature in the breast was then segmented by applying a Hessian filter. Given the vasculature segmented by the algorithms and the tumor masks segmented by radiologists, a lowest-cost tracking algorithm was used to automatically detect the vessels that are most likely to contact the tumor. These vessels are defined as tumor-associated vessels (TAV). The number of TAVs per patient was tabulated and the Wilcoxon rank sum test compared the TAV values before (V1), after 2 cycles (V2), and after 4 cycles of NAST (V3). Additionally, we compared the percent change of TAV from V1 to V3 between the pCR patients and non-pCR patients. Statistical significance was defined as P < 0.05. Results: A significant decrease in the number of TAVs was observed during the NAST. In particular, the number of TAVs has a median (interquartile range) of 15 (7 - 24), 7 (3 - 14), and 2 (0 - 8) at V1, V2, V3, respectively, which are (pair-wise) significantly different (P < 0.01). Moreover, pCR patients showed a significantly greater decrease in the number of TAVs as compared to non-pCR patients. The percent changes in the number of TAVs from V1 to V3 have a median (range) of -88.89% (-100.00% - -60.00%) and -66.67% (-87.85% - -40.88%) in the pCR and non-pCR patients, respectively (P < 0.05). Conclusion: These preliminary results demonstrate that tumor-associated vasculature may be a valuable imaging biomarker for monitoring the response of TNBC to NAST. Ongoing efforts include additional investigation of the TAVs beyond their number, as well as applying the analysis to more patients. Citation Format: Chengyue Wu, Casey E. Stowers, Zhan Xu, Ernesto A. B. F. Lima, Clinton Yam, Jong Bum Son, Jingfei Ma, Gaiane M. Rauch, Thomas E. Yankeelov. Quantification of tumor-associated vasculature as an imaging biomarker for monitoring the response of triple-negative breast cancer to neoadjuvant chemotherapy. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5569.

Abstract 398: The inhibition of sulfation of heparan sulfate augments the chemotherapeutic response in triple-negative breast cancer

Abstract The leading cause of cancer-related death among women worldwide is breast cancer. The triple-negative breast cancer (TNBC) subtype has limited therapeutic options that produce durable responses. As a result, it is associated with an especially poor prognosis compared to other breast cancer subtypes. Hence, the development of innovative therapeutic strategies that produce deeper and more durable responses is critically needed. We found that increasing extracellular ATP (eATP) can enhance the susceptibility of TNBC cell lines to chemotherapy through the activation of purinergic receptors (P2RXs) P2RX4 and P2RX7. However, eATP levels are limited by several different classes of eATPases, making the design of a single molecule that effectively inhibits all classes of eATPase complicated. Heparan sulfate, a carbohydrate moiety that is covalently linked to several cell surface and extracellular matrix proteins has previously been identified as an endogenous inhibitor of several classes of eATPases. Heparan sulfate is desulfated by sulfatases 1 and 2 at the 6-O-hydroxyl groups of glucosamine residues in heparan sulfate. Sulfatase 2 has been determined to be highly expressed in a variety of cancers including breast cancer, whereas sulfatase 1 is not. Several sulfatase inhibitors have been previously developed, such as OKN-007, which is a specific inhibitor of sulfatase 2. We hypothesized that OKN-007 would augment eATP levels in TNBC cell lines exposed to chemotherapy by increasing levels of heparan sulfate in the tumor microenvironment, leading to intensified cell death. TNBC cell lines MDA-MB 231, Hs 578t, and MDA-MB 468 and non-tumorigenic immortal mammary epithelial MCF-10A cells were treated with increasing concentrations of the chemotherapeutic agent paclitaxel in the presence of heparan sulfate and/or OKN-007, and eATP content and cell viability were evaluated. Inhibitors to the purinergic receptors P2RX4 and P2RX7 were used to further confirm that the mechanism of enhanced cell death induced by OKN-007 was through these receptors. In addition, basal protein and cell surface expression of sulfatases 1 and 2 were determined in all the examined cell lines via ELISA, Western blot, and flow cytometry analysis. To assess the effects on cancer-initiating cell properties, TNBC cell lines were treated with paclitaxel in the presence of heparan sulfate and/or OKN-007, and the tumorsphere formation efficiency assay used to assess for cancer-initiating cells. In parallel, we assessed for effects on cancer-initiating cells in treated cells using flow cytometry. Our results showed that inhibiting the 6-O desulfation of heparan sulfate increases eATP accumulation, thereby, enhancing TNBC cell lines’ response to chemotherapy. These findings may lead to therapies for TNBC based on sulfatase 2 inhibition that results in more effective responses with fewer side effects. Citation Format: Jasmine M. Manouchehri, Jharna Datta, Mathew A. Cherian. The inhibition of sulfation of heparan sulfate augments the chemotherapeutic response in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 398.

Abstract 845: Developing MRI-based digital-twins via mathematical modeling and deep learning to predict the response of triple-negative breast cancer to neoadjuvant therapy

Abstract More than 50% of triple negative breast cancer (TNBC) patients do not respond well to the standard-of-care neoadjuvant therapy (NAT). Therefore, methods capable of predicting treatment response will be highly useful to optimize intervention and outcomes for TNBC patients. To address this problem, we aim to integrate quantitative magnetic resonance imaging (MRI) with biology-based mathematical modeling and deep learning to make patient-specific predictions of TNBC response to NAT using only pretreatment data. TNBC patients (n = 150) enrolled in the ARTEMIS trial (NCT02276443) received doxorubicin/cyclophosphamide (A/C) followed by paclitaxel. MRI exams were acquired for each patient at the following timepoints: (1) before initiation of NAT, (2) after two A/C cycles, (3) after four A/C cycles, and (4) at the conclusion of NAT. Using patient-specific MRI data from the first two exams, we calibrated a biology-based mathematical model to characterize migration, proliferation, and treatment-induced death of tumor cells. We then used this model as a digital twin to predict spatiotemporal tumor response. While effective, this approach requires the patient to have completed at least part of their NAT regime before we are able to predict therapeutic response. To relax this requirement, we have developed an approach that combines deep learning and biology-based mathematical modeling to predict the response of TNBC to NAT before treatment initiation. Specifically, we integrated a U-Net-based convolutional neural network with our mathematical model to regress between pre-treatment data and the model parameters obtained from a training set. Using parameters from learning a network with a subset of 68 patients, our mathematical model yielded concordance correlation coefficients between the predicted and measured patient-specific changes in tumor cellularity and volume at the third imaging point of 0.95 and 0.92, respectively. Spatially, we obtain the median difference between predicted and measured percent change in cellularity from visit one to visit three for each patient, giving a mean (95% confidence interval) of -6.51% (-7.13%, -5.90%) across all patients. These encouraging results may be further improved using methods such as expanding to a spatially-resolved proliferation rate, including genetic and/or histological data, and extending the deep learning framework to the end of the treatment course to predict pathological response. This approach allows us to obtain patient-specific predictions of response before NAT commences, thereby providing the opportunity to optimize interventions and patient outcomes. Citation Format: Casey E. Stowers, Chengyue Wu, Sidharth Kumar, Ernesto A.B.F. Lima, Xhan Zu, Clinton Yam, Jong Bum Son, Jingfei Ma, Jonathan I. Tamir, Gaiane M. Rauch, Thomas E. Yankeelov. Developing MRI-based digital-twins via mathematical modeling and deep learning to predict the response of triple-negative breast cancer to neoadjuvant therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 845.

Abstract 1762: MALT1 is activated by doxorubicin and mediates therapy resistance in triple-negative breast cancer

Abstract Background: Breast cancer is the most commonly diagnosed malignancy in American women. The triple-negative breast cancer (TNBC) subtype has among the worst prognosis due to high rates of recurrence and metastasis. Since TNBC lacks targetable receptor proteins, treatment relies upon non-specific chemotherapy, which can become ineffective upon onset of resistance. One potential driver of TNBC treatment resistance is MALT1, the effector component of the CARMA-BCL10-MALT1 signaling complex, which activates NF-κB in multiple cancer cell types, including TNBC. Notably, breast cancer cells demonstrate increased sensitivity to chemotherapies such as doxorubicin and cisplatin when MALT1 is depleted. NF-κB activation has been suggested to promote DNA repair and the MALT1-NF-κB inducible factor, IL-6 has been shown to repress the immunogenic effects of doxorubicin. Hence, we hypothesize that MALT1 is a pharmaceutically targetable driver of TNBC treatment resistance. Mechanistically, we hypothesize that MALT1 promotes chemotherapy resistance by enhancing DNA repair and suppressing immunogenic cell death. Methods/Results: We analyzed RNAseq and proteomic data from TCGA and CPTAC, respectively, and found that MALT1 is highly expressed in basal breast cancer (a subtype largely composed of TNBC) and its expression level in this context is associated with reduced pathological complete response and survival. With the purpose of evaluating the effect of MALT1 protease inhibition on chemotherapy sensitivity, we first sought to identify TNBC cell lines that were most resistant to doxorubicin using GDSC and CTRP databases. Results indicated that MDA-MB-231, BT20 and HCC1143 were highly resistant. We then performed western blots to assess MALT1 expression and CellTiter-Glo assays to determine the doxorubicin IC50s for these cell lines. Results indicate that MALT1 expression correlates with the degree of doxorubicin resistance among these cell lines. To determine if MALT1 blockade, via siRNA-knockdown or MALT1 protease inhibitor treatment (JNJ-67856633 or MLT-748), increased doxorubicin sensitivity, CellTiter-Glo and Incucyte Caspase-3/7 assays were performed. Findings indicated that MALT1 blockade results in decreased cell viability and increased apoptosis in response to doxorubicin. Mechanistically, MALT1 protease is activated by doxorubicin and MALT1 inhibition increases expression of the immunogenic cell death protein, calreticulin (CRT) in response to doxorubicin. Conclusions and Future Directions: Initial studies suggest that targeting MALT1 enhances TNBC sensitivity to doxorubicin. We will next assess the effect of MALT1 blockade on DNA repair mechanisms in doxorubicin-treated TNBC cells. Additionally, we will test the role of MALT1 in suppressing immunogenic cell death. Through these studies, we hope to inform new approaches for improving treatment response in TNBC. Citation Format: Maria Beecher, Dong Hu, Linda Klei, Jack Little, Linda M. McAllister-Lucas, Peter C. Lucas. MALT1 is activated by doxorubicin and mediates therapy resistance in triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1762.

Abstract 6190: Polymerase theta inhibition activates the cGAS-STING pathway and cooperates with immune checkpoint blockade in BRCA-deficient cancers

Abstract Cancers deficient in homologous recombination (HR) repair secondary to mutations in genes such as BRCA1 or BRCA2, are dependent on alternative DNA damage response (DDR) pathways to maintain genomic integrity, rendering them susceptible to synthetic lethal targeting of these pathways. Recently, inhibitors of polymerase theta (POLθ, encoded by POLQ), the critical enzyme in microhomology-mediated end-joining (MMEJ), have been shown to be synthetic lethal with HR repair deficiency (Zhou et al. Nature Cancer 2021). Both HR and MMEJ require nucleolytic DNA end-resection to allow for DSB repair, and we have previously shown that MMEJ acts as a barrier to DNA end-resection at DSBs (Patterson-Fortin et al. Cancer Research 2022). Given the synthetic lethality between HR and MMEJ leads to unrestrained DNA end-resection generating chromosomal abnormalities and the release of nuclear DNA into the cytoplasm, we hypothesized that POLθ inhibition in HR-deficient cancers would activate the cGAS/STING innate immune response pathway and facilitate immunotherapy. To investigate the interactions of POLθ inhibition with the immune microenvironment in HR-deficient cancers, we used human cell lines and genetically modified mouse models representative of BRCA1-deficient triple-negative breast cancer (TNBC) and BRCA2-deficient pancreatic ductal adenocarcinoma (PDAC). Genetic or pharmacological inhibition of POLθ using novobiocin, a first-in-class inhibitor of the POLθ ATPase domain, induced significantly increased cytosolic dsDNA contained in micronuclei. This free DNA was sensed by the cytosolic DNA sensor cyclic GMP-AMP (cGAMP) synthetase (cGAS), increasing synthesis of cGAMP, in HR-deficient tumor cells but not in HR-proficient tumor cells. Increased cGAMP bound to and activated stimulator of interferon genes (STING), triggering phosphorylation of TBK1 and ultimately of IRF3. Activation of the cGAS/STING pathway by POLθ inhibition drove the expression of type I interferon response elements, including PD-L1. Depletion of STING by siRNA or by CRISPR abrogated this pro-inflammatory signaling and abolished the anti-tumor efficacy of novobiocin-mediated POLθ inhibition. Pharmacologic inhibition of POLθ enhanced Granzyme B+ CD8+ T-cell tumor infiltration. Importantly, antibody-mediated depletion of CD8+ T-cell severely compromised the anti-tumor efficacy of novobiocin-mediated POLθ inhibition, whereas anti-tumor activity of POLθ inhibition was augmented with the addition of either anti-PD-1 or anti-CTLA-4 antibodies. These results demonstrate that POLθ inhibition in HR-deficient cancers mediates a pro-inflammatory response in HR-deficient TNBC or PDAC tumor microenvironments, and that immune checkpoint blockade inhibition enhances the therapeutic efficacy of POLθ inhibition. Citation Format: Jeffrey Patterson-Fortin, Heta Jadhav, Constantia Pantelidou, Tin Phan, Carter Grochala, Anita K. Mehta, Jennifer L. Guerriero, Gerburg M. Wulf, Brian M. Wolpin, Ben Z. Stanger, Andrew J. Aguirre, James M. Cleary, Alan D. D'Andrea, Geoffrey I. Shapiro. Polymerase theta inhibition activates the cGAS-STING pathway and cooperates with immune checkpoint blockade in BRCA-deficient cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6190.

Abstract 3160: A rapid, non-invasive test to determine HER2-low status in triple negative breast cancer (TNBC) patients

Abstract Background: TNBC is defined as a HER2-negative disease, as assessed via immunohistochemistry (IHC). An IHC 3+ score is considered positive and 2+ (with a negative ISH), 1+, and zero scores are considered negative. Recently, HER2-low (1+, 2+) breast cancer has been proposed as a targetable disease distinct from TNBC. Indeed, use of an anti-HER2 antibody drug conjugate (ADC) in HER2-low metastatic patients resulted in improved progression free and overall survival (DESTINY-Breast04), and remarkably generated a response in HER2-zero cases. The potential to expand the current treatment for HER2-low and -zero patients, highlights the limitations of traditional HER2 assessment, including HER2 intra-tumoral heterogeneity, differential IHC pathology staining, and inter-reader variability. We therefore sought to address how to optimally identify HER2-low TNBC patients that may benefit from HER2 ADCs. Methods: We developed a rapid, non-invasive test to determine HER2-low status in TNBC tumors. Our test uses radiological imaging (DCE-MRIs) coupled with the biophysical simulation platform TumorScope and is informed by single cell RNA-sequencing data to connect molecular regulation to the tumor microenvironment in individual patients. We leveraged these relationships to design a rapid, non-invasive test, HER2Scope, that captures the fraction of each TNBC tumor likely to express significant levels of HER2 (a “HER2 score”). We then characterized the HER2 score in a cohort of TNBC patients from our Virtual Tumor Bank, leading us to identify 3 distinct cohorts: HER2-negative, -low, and -moderate tumors. Results: Using our platform, we identified that HER2 expression is associated with less proliferation and lower nutrient use. Interestingly, we found that there was significant overlap in HER2 expression between HER2+ and TNBC tumors. HER2Scope-identified HER2-low and- moderate tumors were associated with a lower likelihood of pCR in response to chemotherapy compared to HER2-zero tumors (25.3% in HER2-moderate vs. 40% in HER2-zero), suggesting a more aggressive and less drug-responsive phenotype in HER2-low and -moderate tumors. We then tested the expected rate of HER2-low and -moderate tumors within TNBC tumors using our Virtual Tumor Bank (n=264) and found a HER2-low and -moderate response rate of 56% (95% CI = 49-62%), which is strikingly similar to the TNBC response rate to trastuzumab deruxtecan (TDXd) reported in the DAISY trial (42%). HER2Scope may therefore be an effective test to identify TNBC patients for HER2 ADC therapies. Conclusion: We present a novel test to identify HER2-nonzero TNBC patients rapidly and non-invasively. HER2Scope relies on radiological imaging, and therefore does not depend on an inherently variable score derived from biopsy-driven pathologic staining. Additionally, by evaluating the entire tumor, it addresses the challenge of HER2 intra-tumoral heterogeneity. Citation Format: Daniel Cook, Snehal Patel, John Whitman, Nicole Hobbs, Dorys A. Lopez-Ramos, John Pfeiffer, Joseph Peterson, Tushar Pandey, Anuja K. Antony, John Cole. A rapid, non-invasive test to determine HER2-low status in triple negative breast cancer (TNBC) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3160.

The Response of Triple-Negative Breast Cancer to Neoadjuvant Chemotherapy and the Epithelial–Mesenchymal Transition

It would be highly desirable to find prognostic and predictive markers for triple-negative breast cancer (TNBC), a strongly heterogeneous and invasive breast cancer subtype often characterized by a high recurrence rate and a poor outcome. Here, we investigated the prognostic and predictive capabilities of ARIADNE, a recently developed transcriptomic test focusing on the epithelial-mesenchymal transition. We first compared the stratification of TNBC patients obtained by ARIADNE with that based on other common pathological indicators, such as grade, stage and nodal status, and found that ARIADNE was more effective than the other methods in dividing patients into groups with different disease-free survival statistics. Next, we considered the response to neoadjuvant chemotherapy and found that the classification provided by ARIADNE led to statistically significant differences in the rates of pathological complete response within the groups.

TP53 Signature Score Predicts Prognosis and Immune Response in Triple-negative Breast Cancer.

Triple-negative breast cancer (TNBC) is considered a heterogeneous disease and achieving a pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) is considered a surrogate biomarker of a favorable prognosis. Previously, the TP53 signature (TP53sig)-score, the expression profile of 33 genes, has been reported to predict the prognosis of all types of early-stage breast cancer. Herein, we analyzed whether the TP53sig-score can be used to subclassify a TNBC cohort and investigated the molecular biological characteristics of the higher TP53sig-score. Publicly available data from TCGA (RNA-sequence) and METABRIC (microarray) and expression data from real clinical specimens (NanoString Technologies) were used to explore the prognosis and molecular features of TNBC. The high TP53sig-score group in the present study and the cohort in METABRIC tended to have a worse prognosis than the low TP53sig-score group (p=0.583 and 0.196, respectively). In both the pCR and non-pCR groups, the high TP53sig-score patients tended to have a poor prognosis (p=0.0739). Moreover, when the NAC response and TP53sig-score were combined, the five-year breast cancer-free rate among the four groups differed significantly (p=0.043). In addition, high TP53sig-score was related to gene ontology terms, such as "cell differentiation" and "innate immune response". Notably, this group had the potential to respond favorably to immunotherapy according to the tumor immune dysfunction and exclusion model. The combination of the response to NAC and the TP53sig-score in TNBC was able to predict an unfavorable prognosis. Furthermore, patients with a high TP53sig-score showed a favorable response to immunotherapy.

Abstract P1-13-11: YES1 is a targetable vulnerability for improving taxane response in triple-negative breast cancer

Abstract Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype. Due to the lack of receptor expression, there are limited targeted therapies available for TNBC. As a result, TNBC patients are primarily treated with chemotherapies such as taxanes. Although TNBCs initially regress in response to taxane treatment, resistance is common. One mechanism of taxol unresponsiveness/resistance is an increase in chromosomal instability (CIN). Increased CIN can confer survival advantages to cancer cells and increase their aggressiveness. However, CIN levels can be leveraged using drugs that inhibit proteins important for chromosomal stability. Combining CIN-inducing drugs, such as taxanes, can improve treatment efficacy or re-sensitize tumor cells to certain drugs by shifting cells towards a state of maladaptive CIN that is incompatible with cell viability. We have found that the non-receptor SRC family kinase YES1 is crucial for chromosomal stability. YES1 is important for cell division, motility, adhesion, and survival in both normal and TNBC cells. Since taxol and YES1 silencing independently increase chromosomal instability, I hypothesized that combining a YES1 inhibitor (YES1i) with taxanes would shift cells toward an irreversible state of maladaptive CIN, decreasing their survival. I found that YES1 mRNA and protein are upregulated in taxane-resistant cells and that YES1 protein expression correlates with the paclitaxel IC50 in a panel of TNBC cell lines, suggesting that YES1 may drive taxane resistance. Furthermore, I found that a selective YES1 inhibitor (CH6953755) synergizes with paclitaxel and improves taxane response in both in vitro and in vivo TNBC models. In addition, the combination of YES1i and paclitaxel treatment increases phenotypes associated with chromosomal instability more than either drug alone. These data suggest that YES1 inhibition in combination with taxanes represents an innovative and novel drug treatment regimen that improves TNBC patient outcomes. Citation Format: Natasha Ingles, Katrina Piemonte, Salendra Singh, Kristen Weber-Bonk, Ruth Keri. YES1 is a targetable vulnerability for improving taxane response in triple-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-13-11.

Abstract PD5-02: PD5-02 An Organoid Model System to Study Resistance Mechanisms, Predictive Biomarkers, and New Strategies to Overcome Therapeutic Resistance in Early-Stage Triple-Negative Breast Cancer

Abstract Background: While new treatments and improved subtyping schemas are anticipated to improve treatment response in triple-negative breast cancer (TNBC) patients, therapeutic resistance remains a significant challenge. Moreover, there is an urgent need for additional research model systems to study resistance and residual disease in breast cancer, including aggressive subtypes of breast cancer. Organoid culture is a promising technology used for growing breast cancer cells with high efficiency; however, the extent to which treatment resistance can be modeled using this system is unknown. This research used patient-derived organoid cultures in the context of computational analyses of large molecular and clinical datasets to study resistance mechanisms, biomarkers, and alternative treatment strategies to overcome drug resistance in early-stage TNBC. Methods: Organoid cultures were derived from breast tumor samples (taken from lumpectomy, mastectomy, or core biopsy samples), digested to the organoid level using collagenase, and grown in three dimensional cultures using a basement membrane extract and a fully-defined organoid medium (Dekkers et al. Nat Protoc 2021). An evaluation of all available I-SPY2 biomarker data (Wolf et al. Cancer Cell 2022) was performed focusing on genes, proteins, and pathways associated with resistance. These were then used to study whether resistance biomarkers identified in patient tumors are also present in organoids propagated from breast cancer post-treatment residual disease. To this end, bulk RNA sequencing data of organoids were normalized and merged with the TCGA dataset (Hoadley et al. Cell 2018) to enable analysis in a larger context, and immunofluorescence staining of organoids was performed. A high-throughput 386 anti-cancer drug compound screen and subsequent synergy testing with the most promising compounds were performed to identify and predict alternative treatment strategies. Additional assays to explore kinome activity in this organoid model are in progress. Results: A TNBC organoid biobank was established (n=31), which was enriched for inflammatory breast cancer (IBC; n=15), an aggressive form of breast cancer. Most organoids were derived from residual disease after neoadjuvant therapy. Bulk RNA sequencing analysis performed on 10 TNBC organoids revealed 3 subsets that were characterized predominantly by either normal-like/luminal androgen receptor or basal-like features or expressed distinct gene expression profiles, with IBC cases present in all 3 subsets. Intriguingly, the IBC organoids were characterized by higher expression of a number of immune-related signatures, despite an absence of clear immune cells in culture. A residual disease IBC/TNBC organoid resistant to chemotherapy was used to perform the 386-drug compound screen. The organoid model showed resistance to veliparib-cisplatin, consistent with the expression of gene/protein biomarkers predictive of drug resistance found in I-SPY2 (low PARPi7 levels and high pFOXO1 and pMEK1/2 expression). In addition, the screen identified multiple classes of inhibitors as promising synergistic/additive candidates for overcoming resistance to cisplatin. Conclusion: In this proof-of-principle study, we demonstrated the utility of matching I-SPY2 resistance biomarkers and signatures to residual disease tumor organoid cultures. We show that tumor organoid cultures modeling drug resistance states are a useful complement to existing research models of breast cancer and can be used for compound testing. We have developed a pipeline to propagate residual tumors from patients enrolled in I-SPY2 into organoid cultures to create a broader platform for preclinical drug testing informed by tumor biology with the ultimate goal of enabling faster, more successful translational studies and increased treatment options for resistant disease. Citation Format: Tam Binh V. Bui, Denise M. Wolf, Kaitlin Moore, Isaac S. Harris, Pravin Phadatare, Christina Yau, Lamorna A. Brown Swigart, Laura J. Esserman, Jean-Philippe Coppe, Julia Wulfkuhle, Emanuel F. Petricoin, Michael Campbell, Laura M. Selfors, Deborah A. Dillon, Beth Overmoyer, Filipa Lynce, Laura Van ’t Veer, Jennifer Rosenbluth. PD5-02 An Organoid Model System to Study Resistance Mechanisms, Predictive Biomarkers, and New Strategies to Overcome Therapeutic Resistance in Early-Stage Triple-Negative Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD5-02.

Predicting Response of Triple-Negative Breast Cancer to Neoadjuvant Chemotherapy Using a Deep Convolutional Neural Network-Based Artificial Intelligence Tool.

Achieving a pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) is associated with improved patient outcomes in triple-negative breast cancer (TNBC). Currently, there are no validated predictive biomarkers for the response to NAC in TNBC. We developed and validated a deep convolutional neural network-based artificial intelligence (AI) model to predict the response of TNBC to NAC. Whole-slide images (WSIs) of hematoxylin and eosin-stained core biopsies from 165 (pCR in 60 and non-pCR in 105) and 78 (pCR in 31 and non-pCR in 47) patients with TNBC were used to train and validate the model. The model extracts morphometric features from WSIs in an unsupervised manner, thereby generating clusters of morphologically similar patterns. Downstream ranking of clusters provided regions of interest and morphometric scores; a low score close to zero and a high score close to one represented a high or low probability of response to NAC. The predictive ability of AI score for the entire cohort of 78 patients with TNBC ascertained by receiver operating characteristic analysis demonstrated an area under the curve (AUC) of 0.75. The AUC for stages I, II, and III disease were 0.88, 0.73, and 0.74, respectively. Using a cutoff value of 0.35, the positive predictive value of the AI score for pCR was 73.7%, and the negative predictive value was 76.2% for non-pCR patients. To our knowledge, this study is the first to demonstrate the use of an AI tool on digitized hematoxylin and eosin-stained tissue images to predict the response to NAC in patients with TNBC with high accuracy. If validated in subsequent studies, these results may serve as an ancillary aid for individualized therapeutic decisions in patients with TNBC.

Abstract P1-06-02: The effect of race on pathologic complete response rates and overall survival in patients with triple negative breast cancer

Abstract Introduction: Despite the recent overall improvement in survival for patients with breast cancer, racial disparities in outcomes persist. While studies have demonstrated that socioeconomic factors and access to treatment play a role, differences in tumor biology may also contribute. Black women are significantly more likely to develop triple negative breast cancer (TNBC), the deadliest of the breast cancer subtypes, with more TNBC patients progressing to incurable, metastatic disease than patients with any other breast cancer subtype. Studies have demonstrated that TNBC patients who achieve a pathologic complete response (pCR), defined as no residual invasive cancer in the breast or lymph nodes after neoadjuvant chemotherapy (NAC), have improved survival. We hypothesize that rates of pCR and overall survival (OS) in patients with TNBC may differ by race/ethnicity, which may account in part for the disparities in outcomes observed. Methods: Adult female patients with stage I-III TNBC diagnosed in 2010-2019 who received NAC followed by surgery were identified from the National Cancer Database (NCDB). Race/ethnicity was defined as Hispanic (H), Non-Hispanic White (NHW), Non-Hispanic Black (NHB), Non-Hispanic Asian (NHA), and Non-Hispanic Other (NHO). pCR was defined as no invasive cancer in either the breast or axilla (ypT0/is,N0) at surgery. Logistic regression was used to estimate the association of race/ethnicity with achievement of pCR after adjustment for covariates. Unadjusted OS was estimated using the Kaplan-Meier method, and the log-rank test was used to compare groups. Cox Proportional Hazards models were used to estimate the association of race/ethnicity and achievement of pCR with OS after adjustment for covariates. Additional interaction and subgroup analyses were also conducted. Results: Of the 40,890 patients identified, 29.8% (n=12,173) demonstrated pCR after NAC. The unadjusted 5-year OS rates for those who achieved pCR were significantly higher compared to patients with no pCR (0.917, 95% CI 0.911-0.923 vs 0.667, 95% CI 0.661-0.673, log-rank p< 0.001). Hispanic patients were more likely to achieve pCR (OR 1.19, 95% CI 1.08-1.31, p=0.001), and NHB patients were less likely to achieve pCR (OR 0.89, 95% CI 0.83-0.95, p=0.001) compared to NHW, even after adjustment. Unadjusted OS was also notably lower for NHB patients compared to every other race group (5-year OS rate: NHB 0.709 vs NHW 0.746 vs NHO 0.771 vs H 0.772 vs NHA 0.816, log-rank p< 0.001); however, this difference did not persist after adjustment for patient and disease factors, including achievement of pCR. Interval from diagnosis to start of chemotherapy (OR 0.95, 95% CI 0.94-0.96, p< 0.001) and duration after chemotherapy start to surgery (OR 1.02, 95% CI 1.02-1.03, p< 0.001) were associated with the odds of achieving pCR. Overall, the effect of achieving pCR on OS did not differ by race/ethnicity (interaction p=0.10). Discussion: Achieving pCR after NAC in patients with TNBC is associated with a significant improvement in OS. Yet, rates of pCR appear to differ based on race/ethnicity, with NHB patients demonstrating significantly lower rates of pCR than NHW patients, which may contribute to the disparities in survival outcomes observed. In addition to addressing socioeconomic factors and access to treatment, further research examining whether biological differences exist based on race that influence response of TNBC to current standard therapies is essential for improving survival outcomes for this disproportionately affected patient population. Citation Format: Hannah E. Woriax, Samantha M. Thomas, Jennifer K. Plichta, Laura H. Rosenberger, Astrid Botty van de bruele, Akiko Chiba, Gayle DiLalla, Carolyn Menendez, E Shelley Hwang, Maggie L. DiNome. The effect of race on pathologic complete response rates and overall survival in patients with triple negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P1-06-02.

Systemic immune mediators reflect tumour-infiltrating lymphocyte intensity and predict therapeutic response in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer (BC). Neoadjuvant chemotherapy has proven efficacy in its treatment, and a pathological complete response (pCR) to therapy is predictive of improved long-term survival. The immune response is key to successful neoadjuvant chemotherapy, as indicated by the relation between the percentage of stromal tumour-infiltrating lymphocytes (TILs) in pre-treated tumour tissue samples and the likelihood of achieving pCR. Here we studied systemic immune mediators from volunteer TNBC patients before undergoing neoadjuvant chemotherapy to determine the systemic response association with TIL intensity, treatment response and survival. Patients were classified into pCR responder or non-responder at time of surgery. We found higher levels of immune mediators before treatment began in patients that went on to be pCR responders versus non-pCR, with area under the curve (AUC) values of 0.64-0.80. We also observed a positive correlation between inflammatory systemic immune mediators and the percentage of TILs in pCR responder patients. Combining TILs and systemic immune mediator levels provided stronger AUC values (range of 0.72-0.82). Last, performing a progression-free survival analysis with several of the systemic cytokines that predict pCR, segregated the patients into long- and short-survival groups based on high and low production of the cytokines, respectively. Our study demonstrates that circulating cytokines, before treatment begins, predict pCR in TNBC patients treated with neoadjuvant chemotherapy. Moreover, they may act as a surrogate marker of high TILs or together with TILs to better predict pCR and survival.

Stromal grading predicts pathologic complete response and prognosis in triple-negative breast cancer.

Do traditional prognostic factors fully account for the diversity of clinical behavior in breast cancer? Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer seen to have a poor prognosis, although there is great variation in clinical outcomes. Most recently, novel approaches have targeted the tumoral microenvironment (TME) to determine prognosis and tumor-associated stroma has become increasingly recognized as a potential biomarker to predict treatment response and prognosis in TNBC. The principle aim of this paper is to demonstrate an approach to stromal grading in TNBC, with consideration of its utility for predicting pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) and clinical survival outcomes. We evaluated 152 TNBC cases from the Firehose Legacy TCGA Cohort and validated our findings in a series of 110 patients from our health system. Stromal grading correlated with clinical outcomes related to prognosis and response to NAC, advanced pathologic stage, as well as clinical demographics like age over 50years with good interobserver reliability (83.6-89.1%). Looking forward, the TME could carve out a more precision-based care in TNBC and breast cancer generally.

Assessment of Response to Neoadjuvant Systemic Treatment in Triple-Negative Breast Cancer Using Functional Tumor Volumes from Longitudinal Dynamic Contrast-Enhanced MRI

Early assessment of neoadjuvant systemic therapy (NAST) response for triple-negative breast cancer (TNBC) is critical for patient care in order to avoid the unnecessary toxicity of an ineffective treatment. We assessed functional tumor volumes (FTVs) from dynamic contrast-enhanced (DCE) MRI after 2 cycles (C2) and 4 cycles (C4) of NAST as predictors of response in TNBC. A group of 100 patients with stage I-III TNBC who underwent DCE MRI at baseline, C2, and C4 were included in this study. Tumors were segmented on DCE images of 1 min and 2.5 min post-injection. FTVs were measured using the optimized percentage enhancement (PE) and signal enhancement ratio (SER) thresholds. The Mann-Whitney test was used to compare the performance of the FTVs at C2 and C4. Of the 100 patients, 49 (49%) had a pathologic complete response (pCR) and 51 (51%) had a non-pCR. The maximum area under the receiving operating characteristic curve (AUC) for predicting the treatment response was 0.84 (p < 0.001) for FTV at C4 followed by FTV at C2 (AUC = 0.82, p < 0.001). The FTV measured at baseline was not able to discriminate pCR from non-pCR. FTVs measured on DCE MRI at C2, as well as at C4, of NAST can potentially predict pCR and non-pCR in TNBC patients.

Ethnic disparities in the immune microenvironment of triple negative breast cancer and its role in therapeutic outcomes.

In 2020, newly diagnosed breast cancer (BC) cases surpassed that of lung cancer among women, making it the most common female cancer globally. In spite of recent increases in incidence rates, mortality due to BC has declined since 1989. These declines have been attributed to advancements in treatment modalities as well as increased mammography surveillance. Despite these advances, African American (AA) women are 40% more likely to die from BC than Caucasian women. Multifactorial etiology has been implicated in the disparity of BC mortality rates among AA women. As an example, AA women have a disproportionate incidence of triple negative breast cancer (TNBC), which has a poor prognosis and marginal treatment options. Increasingly, the tumor microenvironment (TME) has gained relevance as it relates to primary tumor progression, metastasis and treatment possibilities. The treatment outcomes or pathological complete response (pCR) in TNBC among AA women are affected by differences in TME. The TME of AA women exhibit several variances in acellular and cellular components associated with pro-tumorigenic effects. For example, increased levels of the adipocyte-related hormone, resistin, the pro-inflammatory cytokine, IL-6, and the CC chemokine, CCL2, within the TME of AA women gives rise to an increased density of M2 macrophages, also known as tumor-associated macrophages. Elevated levels of vascular endothelial growth factor in the TME of AA women increase the vascular density or vascularity, which facilitate aggressive tumor growth and metastasis. Furthermore, a pro-tumorigenic TME is supported by increased levels of the CXC chemokine, CXCL12 that results in the recruitment of regulatory T lymphocytes (Tregs ). Due to these and other differences in the TME of AA women, precision oncology can target specific aspects of the TME that may contribute to a poorer prognosis. In addition to the discrepancies in the TME, AA women face socio-economic barriers that limit their ability to access state-of-the-art, novel therapies against metastatic TNBC. In this review, we will provide a brief overview of the tumor immune microenvironment, immune-based treatment options for TNBC and their potential to decrease health disparities due to ethnicity.

Triple negative breast cancer: Immunogenicity, tumor microenvironment, and immunotherapy.

Triple negative breast cancer (TNBC) is a biologically diverse subtype of breast cancer characterized by genomic and transcriptional heterogeneity and exhibiting aggressive clinical behaviour and poor prognosis. In recent years, emphasis has been placed on the identification of mechanisms underlying the complex genomic and biological profile of TNBC, aiming to tailor treatment strategies. High immunogenicity, specific immune activation signatures, higher expression of immunosuppressive genes and higher levels of stromal Tumor Infiltrating Lymphocytes, constitute some of the key elements of the immune driven landscape associated with TNBC. The unprecedented response of TNBC to immunotherapy has undoubtedly changed the standard of care in this disease both in the early and the metastatic setting. However, the extent of interplay between immune infiltration and mutational signatures in TNBC is yet to be fully unravelled. In the present review, we present clinical evidence on the immunogenicity and tumour microenvironment influence on TNBC progression and the current treatment paradigms in TNBC based on immunotherapy.

Identification of an immune classifier for predicting the prognosis and therapeutic response in triple-negative breast cancer

Identification of an immune classifier for predicting the prognosis and therapeutic response in triple-negative breast cancer

Enzymatic Digestion of Cell-surface Heparan Sulfate Alters the Radiation Response in Triple-negative Breast Cancer Cells

Radiation resistance represents a major challenge in the treatment of breast cancer. As heparan sulfate (HS) chains are known to contribute to tumorigenesis, we aimed to investigate the interplay between HS degradation and radiation response in triple-negative breast cancer (TNBC) cells. HS chains were degraded in vitro as TNBC cells MDA-MB-231 and HCC1806 were treated with heparinase I and III. Subsequently, radioresistance was determined via colony formation assay after doses of 2, 4 and 6 Gy. Cell cycle profile, stem cell characteristics, expression of HS, activation of beta integrins, and apoptosis were determined by flow cytometry. Additionally, cell motility was analyzed via wound-healing assays, and expression and activation of FAK, CDK-6, Src, and Erk1/2 were quantified by western blot pre- and post-irradiation. Finally, the expression of cytokines was analyzed using a cytokine array. Radiation promoted cell cycle changes, while heparinase treatment induced apoptosis in both cell lines. Colony formation assays showed significantly increased radio-resistance for both cell lines after degradation of HS. Cell migration was similarly upregulated after degradation of HS compared to controls. This effect was even more prominent after irradiation. Interestingly, FAK, a marker of radioresistance, was significantly activated in the heparinase-treated group. Additionally, we found Src to be dysregulated in MDA-MB-231 cells. Finally, we observed differential secretion of GRO, CXCL1, IGFBP1, IL8, Angiogenin, and Osteoprotegerin after HS degradation and radiotherapy. Our results suggest an influence of HS chains on the development of radioresistance in TNBC.