HER2/ERBB2 copy number analysis by targeted next-generation sequencing in breast cancer

OBJECTIVES

A combination of immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) is the current standard of care for HER2 evaluation in breast cancer. Here, we investigate the potential clinical utility of next-generation sequencing (NGS)-derived HER2/ERBB2 copy number (CN) data for predicting HER2 status as defined by American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) guidelines.

METHODS

In total, 294 locally recurrent and metastatic breast cancers previously tested by targeted hybrid capture-based NGS and by HER2 IHC/FISH were included. Analyses focused on the ERBB2 median log2 ratios and start-end genomic coordinates from NGS, average HER2 CN and HER2/CEP17 ratios from FISH, and the HER2 IHC scores. We also determined a more stringent log2 ratio cutoff to predict HER2-positive status with 100% specificity.

RESULTS

Sixty-four (22%) cases were HER2 positive and 230 (78%) were HER2 negative by ASCO/CAP guidelines. The ERBB2 median log2 ratios from NGS strongly correlated with HER2 status by IHC/FISH (area under receiver operator characteristic curve = 0.951). ERBB2 log2 ratio more than 1.7 was 100% specific for HER2-positive results by IHC/FISH. Start and end genomic coordinates for regions of gain near ERBB2 by NGS also predicted HER2 status.

CONCLUSIONS

Copy number data from our NGS panel strongly correlate with HER2 status. Using a stringent cutoff, ERBB2 log2 ratio accurately predicts HER2 positivity with high specificity. The NGS CN assessment may have utility in determining HER2 status in certain clinical settings.

Qualification of a multiplexed tissue imaging assay and detection of novel patterns of HER2 heterogeneity in breast cancer

Emerging data suggests that HER2 intratumoral heterogeneity (ITH) is associated with therapy resistance, highlighting the need for new strategies to assess HER2 ITH. A promising approach is leveraging multiplexed tissue analysis techniques such as cyclic immunofluorescence (CyCIF), which enable visualization and quantification of 10-60 antigens at single-cell resolution from individual tissue sections. In this study, we qualified a breast cancer-specific antibody panel, including HER2, ER, and PR, for multiplexed tissue imaging. We then compared the performance of these antibodies against established clinical standards using pixel-, cell- and tissue-level analyses, utilizing 866 tissue cores (representing 294 patients). To ensure reliability, the CyCIF antibodies were qualified against HER2 immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) data from the same samples. Our findings demonstrate the successful qualification of a breast cancer antibody panel for CyCIF, showing high concordance with established clinical antibodies. Subsequently, we employed the qualified antibodies, along with antibodies for CD45, CD68, PD-L1, p53, Ki67, pRB, and AR, to characterize 567 HER2+ invasive breast cancer samples from 189 patients. Through single-cell analysis, we identified four distinct cell clusters within HER2+ breast cancer exhibiting heterogeneous HER2 expression. Furthermore, these clusters displayed variations in ER, PR, p53, AR, and PD-L1 expression. To quantify the extent of heterogeneity, we calculated heterogeneity scores based on the diversity among these clusters. Our analysis revealed expression patterns that are relevant to breast cancer biology, with correlations to HER2 ITH and potential relevance to clinical outcomes.

Implantation of engineered adipocytes that outcompete tumors for resources suppresses cancer progression

Tumors acquire an increased ability to obtain and metabolize nutrients. Here, we engineered and implanted adipocytes to outcompete tumors for nutrients and show that they can substantially reduce cancer progression. Growing cells or xenografts from several cancers (breast, colon, pancreas, prostate) alongside engineered human adipocytes or adipose organoids significantly suppresses cancer progression and reduces hypoxia and angiogenesis. Transplanting modulated adipocyte organoids in pancreatic or breast cancer mouse models nearby or distal from the tumor significantly suppresses its growth. To further showcase therapeutic potential, we demonstrate that co-culturing tumor organoids derived from human breast cancers with engineered patient-derived adipocytes significantly reduces cancer growth. Combined, our results introduce a novel cancer therapeutic approach, termed adipose modulation transplantation (AMT), that can be utilized for a broad range of cancers.

Abstract P4-09-04: Correlation between histology and molecular subtypes in triple negative breast cancer

Correlation between histology and molecular subtypes in triple negative breast cancer Authors: Tabata Alves Domingos, MD; 1* Roberto Bonfim Pimenta Peixoto, MD; 1* Ashka Patel, BS1,2; Krishan Taneja, PhD; 1 Wendy Y. Chen, MD, MPH; 4,5,6 Elizabeth A. Mittendorf, MD, PhD; 5,6,7 Alexa Zimbalist, MS; 3 Elizabeth M. Cespedes Feliciano, ScD SM; 3 Deborah A. Dillon, MD 1,2 *equal contribution Author Affiliations 1. Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115 2. Breast Oncology, Dana-Farber Brigham Cancer Center, Boston, MA 02215 3. Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612 4. Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115 5. Department of Medical Oncology Dana Farber Cancer Institute, Boston, MA 02215 6. Harvard Medical School, Boston, MA 02215 7. Division of Breast Surgery, Brigham and Women’s Hospital, Boston, MA 02215 Background Recently defined molecular subtypes of triple negative breast cancer (TNBC) show distinct clinical outcomes and suggest new therapeutic targets but have not been integrated into current pathologic classification systems. Here, we describe the histopathologic features of TNBC according to four molecular subtypes: basal-like immune activated (BLIA), basal-like immune suppressed (BLIS), luminal androgen receptor (LAR) and mesenchymal (MES), classified using the NanoString BC360 gene expression assay. Methods Stage II and III invasive breast cancers were identified in the Kaiser Permanente (KP) clinical pathology archives (2005-2015) and triple negative status was determined from the KP Northern California Cancer Registry data on immunohistochemistry. Selected slides were reviewed by two pathologists who recorded key histopathologic features [histologic subtype, presence of apocrine, metaplastic or micropapillary features, nuclear grade, mitotic score, and Tumor Infiltrating Lymphocytes (TILs)] and marked the best tumor areas for molecular analysis. TILs were evaluated according to the guidelines of the International TILs Working Group. Cases were macrodissected and evaluated using the NanoString BC360 gene expression assay. Histologic features were then summarized according to molecular subtype. Results Of 72 TNBCs, 60 were classified as Basal-like (83.3%), 7 as HER2-enriched (9.7%) and 5 as Luminal A (6.9%). 41 cases were classified as BLIA (56.9%), 14 as BLIS (19.4%), 13 as LAR (18.0%) and 4 as MES (5.5%). Both BLIA and BLIS tumors showed uniformly high nuclear grade and high mitotic score but differed significantly in TILs (BLIA average 32% vs BLIS average 9%; p value< 0.001, t-test for mean difference in TILs). The majority of LAR cases (69%) showed apocrine differentiation, not present in any other molecular subtype (p value< 0.001, chi-square test for presence of apocrine differentiation). LAR cases showed high nuclear grade but a lower average mitotic score (average score of 2) compared with the basal-like subtypes. TILs in LAR tumors were intermediate (17%) between BLIA and BLIS tumors. Of the 4 MES cases, all showed high nuclear grade. TILs in the MES cases were also intermediate (14%) between BLIA and BLIS tumors. Other histologic features, including lobular subtype, metaplastic and micropapillary features were not associated with specific triple negative molecular subtypes. Conclusion TILs are high in the BLIA molecular subtype (average 32%), low in the BLIS subtype (average 9%) and intermediate in LAR (average 17%) and MES (average 14%) subtypes. Apocrine features, if present in a TNBC, are a strong predictor of LAR molecular subtype. The inclusion of TILs and apocrine features (both easily derived from H&E slides) in routine pathology reporting could improve the classification of TNBC and aid in the identification of patients more likely to respond to specific therapies for the BLIA, BLIS and LAR subtypes, especially in resource-limited settings.

Citation Format: Tabata Alves Domingos, Roberto Bonfim Pimenta Peixoto, Ashka Patel, Krishan Taneja, Wendy Y. Chen, Elizabeth A. Mittendorf, Alexa Zimbalist, Elizabeth M. Cespedes Feliciano, Deborah A. Dillon. Correlation between histology and molecular subtypes 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 P4-09-04.

Abstract PD7-07: Somatic alterations in primary tumors of patients (pts) with metastatic breast cancer (MBC) may predict likelihood of brain metastasis

Background: Despite advances in treatment options, outcomes remain poor for many pts with breast cancer brain metastases (BCBMs). Identifying genomic predictors of brain metastasis from primary tumors could lead to better stratification of pts at risk and drive the development of preventative strategies. The objective of this study was to describe the landscape of genomic alterations in primary tumors from pts with MBC who subsequently did or did not develop BCBMs.

Methods: We performed a case control study to identify somatic alterations in primary tumors associated with a higher incidence of brain metastases. We reviewed outcomes for 2562 unique MBC patients from a single institution who underwent targeted next-generation DNA sequencing of > 280 cancer-related genes (OncoPanel) from their tumor between July 1, 2013 and December 31, 2020. Pts were included in this analysis if they had at least 2 years of follow-up from date of metastatic diagnosis and OncoPanel testing on a primary breast tumor. We compared single nucleotide variants (oncogenic or likely oncogenic), copy number variation (amplification and deep deletions) and tumor mutation burden in the primary tumors of pts in this cohort. Copy number variation was corrected for Panel version and tumor purity. Wilcoxon rank sum test and Fisher exact test was used to compare genomic differences between groups. False discovery rate was used to correct for multiple hypothesis testing and q < 0.1 was considered significant

Results: A total of 369 pts were included in the final analytic cohort. Of these, 115 were diagnosed with brain mets (cases, BM group) and 224 were not (controls, nBM group). The BM group was enriched for patients with HER2-positive breast cancer (33 vs 12.5%), consistent with previous work. In the whole cohort, the most common and clinically significant somatic alterations (oncogenic single nucleotide variants or copy number high amplification or two copy deletion) are shown in Table 1. When adjusting for subtype there were no significantly enriched SNVs in BM vs nBM group. When adjusting for subtype, FGFR1 amplification was significantly enriched in hormone receptor positive HER2 negative (HR+ HER2-) patients with BM (log2 odds ratio 1.22, q < 0.1). Tumor mutation burden was not significantly different in primary tumors between the BM and nBM groups (median TMB 7.3 vs 6.1, Wilcoxon p = 0.08).

Pathway analysis combining all subtypes revealed that RTK_RAS pathway (log2 odds ratio 1.64, q value < 0.1) and TP53 pathway (log2 odds ratio 1.15, q value < 0.1) gene sets were significantly enriched in the BM group. When controlling for subtype, pathway analysis revealed that RTK_RAS pathway gene set was significantly enriched in HR+ HER2- BM group (log2 odds ratio 1.36 q < 0.1).

Conclusions: In this case control series of patients with metastatic breast cancer with or without brain metastases, we found that primary tumors that are enriched for somatic alterations in the RTK_RAS and TP53 pathway may be associated with higher risk of developing brain metastases. Further validation in larger cohorts is warranted.

Table 1. Frequency of somatic alterations in primary tumor by brain metastasis outcome.

Citation Format: Sheheryar Kabraji, Yvonne Y. Li, Melissa E. Hughes, Hersh V. Gupta, Lauren Buckley, Janet L. Files, Ayesha Mohammed-Abreu, Anne-Marie Feeney, Greg Kirkner, Ashka Patel, Ana C. Garrido-Castro, Romualdo Barroso-Sousa, Brittany Bychkovsky, Matthew Meyerson, Sara Tolaney, Deborah A. Dillon, Bruce Johnson, Eric Winer, Andrew Cherniack, Nancy U. Lin. Somatic alterations in primary tumors of patients (pts) with metastatic breast cancer (MBC) may predict likelihood of brain metastasis [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 PD7-07.

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

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.

Abstract P5-03-02: Adiposity and immune-related gene expression in the breast tumor microenvironment

Background: Extreme adiposity has been associated with tumor progression and increased mortality after a breast cancer diagnosis, but the underlying mechanisms remain unclear. Pre-clinical and in vitro analyses suggest that higher levels of adiposity impair anti-tumor immunity, but studies in human breast cancer patients are lacking. Previously, we found that higher levels of subcutaneous adiposity had stronger associations with breast cancer outcomes than did higher levels of visceral adiposity or overall obesity measured by BMI, underscoring the importance of measuring adipose tissue distribution as well as overall body size to understand the adiposity-cancer link.

Methods: We identified women with a first-primary, stage 2 or 3 invasive breast cancer diagnosed and treated at Kaiser Permanente Northern California between 2005 and 2015. Using diagnostic computed tomography scans collected as part of routine clinical care, we measured subcutaneous (SAT) and visceral adipose tissue (VAT) areas in cm2 at the third lumbar vertebra. We calculated body mass index (BMI) from clinically-collected height and weight. We isolated RNA from 251 FFPE breast tumors collected at biopsy or excision; these were a preliminary, random sample within each immunohistochemical subtype groups from an ongoing study that will analyze 1400 breast tumors. We verified RNA quality prior to performing NanoString BC 360™ assays to calculate the PAM50 molecular intrinsic subtype and measure the expression levels of genes related to immune cell abundance and anti-tumor immune activity. Using linear regression models, we examined the mean change in log2 gene expression (dependent variables) associated with each adiposity exposure (BMI, SAT and VAT as independent variables).

Results: Mean (SD) age at diagnosis was 56 (13); a majority of women were either overweight (BMI 25- < 30-kg/m2: 30%) or obese (BMI>30-kg/m2: 35%), and most were diagnosed with stage 2 (61%) vs. stage 3 (39%) breast cancer with representation from each PAM50 subtype: n (%) Luminal A, 46 (18%) Luminal B, 56 (22%), HER2-overexpressing 26 (27%), and 82 (33%) basal-like. In unadjusted analyses, expression of genes related to macrophages, PD-1 and TIGIT increased with increasing subcutaneous adiposity, whereas expression of genes related to mast cells decreased (see Table 1). We found a similar (though non-significant) pattern for BMI. Associations with increasing visceral adiposity were closer to the null. After adjusting for PAM50 subtype, age and stage at diagnosis, only the association of increasing subcutaneous adiposity with increasing PD-1 expression remained statistically significant.

Conclusion: Excess subcutaneous adiposity was associated with increased PD-1 expression, whereas excess visceral adiposity or obesity defined by BMI were not. These results from the first 251 samples of an ongoing study of 1400 tumors provide evidence from human breast cancer patients to demonstrate the importance of measuring body composition to assess adipose tissue distribution and support the hypothesis that excess adiposity impairs anti-tumor immunity.

Association of Adiposity Measures with Immune-Related Gene Expression in the Breast Tumor Microenvironment (n=251 patients with stage 2-3 breast cancer at Kaiser Permanente Northern California) 195% Confidence Interval 2A 1-unit increase represents a doubling in the log expression level of the genes in the signature

Citation Format: Deborah A. Dillon, Elizabeth M. Cespedes Feliciano, Alexa Zimbalist, En Cheng, Bette J. Caan, Wendy Y. Chen, Elizabeth A. Mittendorf, Roberto Bonfim Pimenta Peixoto, Tabata Alves Domingos, Krishan Taneja, Ashka Patel. Adiposity and immune-related gene expression in the breast tumor microenvironment [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 P5-03-02.

Abstract HER2-05: HER2-05 Comprehensive genomic characterization of HER2-low breast cancer

Background: About half of all breast cancers exhibit low HER2 expression. Despite lack of ERBB2 amplification, HER2-low tumors respond to trastuzumab deruxtecan (T-DXd), leading to the NCCN recommendation of T-DXd both for patients with HER2+ and HER2-low metastatic breast cancer (MBC). It remains however unclear if HER2-low represents a distinct molecular entity, as compared to HER2-0 MBC. Here, we compare the genomic landscape of HER2-low versus HER2-0 breast cancers in a large, single institution cohort. Methods: We identified consecutive patients with MBC seen at Dana-Farber Cancer Institute between 07/2013 and 12/2020. Patients were included if they had HER2-negative MBC per ASCO/CAP Guidelines and had undergone next generation sequencing (NGS) testing with a targeted, tumor-only platform (OncoPanel). Based on the HER2 status of the specimen tested by NGS, patients were divided into 2 groups: (i) HER2-low if immunohistochemistry (IHC) 1+ or 2+ non-amplified, or (ii) HER2-0 if IHC 0. Mutations of interest detected on NGS were classified as oncogenic using the OncoKB tool and additional annotation. Genomic profiles of HER2-low and HER2-0 tumors were compared using Chi-Square and Kruskal-Wallis tests. To determine genomic event enrichment between the two HER2 groups, logistic regression models were used, accounting for background rate and estrogen receptor (ER) expression. ERBB2 copy counts were calculated for tumors with recorded histology-estimated purities and copy-number segmentation using a simple model of allelic gain/loss. Results: Among 1847 patients with HER2-negative MBC, 1043 underwent NGS testing on a HER2-low (n=489, 47%) or HER2-0 sample (n=554, 53%). Most samples were metastatic (71%, n=743) while 29% (n=300) were from primary tumors. 73% had ductal histology, 13% were lobular and 14% had mixed or other histology. ER expression was enriched among HER2-low vs. HER2-0 tumors (76% vs. 60%; p< 0.001). Focusing on the most commonly occurring genetic mutations, no major differences were observed in HER2-low vs. HER2-0 tumors, after correcting for ER status (Table 1). Among all mutational events, any mutation in MPL, CYLD, and MAP3K and oncogenic mutations in TP53 and NF1 were more common in HER2-0, while any mutation in MTOR, RAD21, DNMT3A, and PDGFRA were enriched in HER2-low patients, when controlling for ER status and background mutational rate (p< 0.05). However, no mutation reached significance after accounting for multiple hypothesis testing. Similarly, no deep deletion or high amplification CNV events reached significance for either group. Analysis of tumor mutational burden in HER2-low vs. HER-0 tumors revealed no significant differences (median: 7.26 muts/Mb vs. 7.60 muts/Mb, p=1.00), including when accounting for ER status. Finally, among tumors with sufficient tumor purity for ERBB2 copy count analysis (n=374 and 419 for HER2-low and HER2-0, respectively), HER2-low tumors had a significantly higher number of ERBB2 alleles as compared to HER2-0 (< 2 copies, 15.0% vs. 30.9%, 2 copies 67.4% vs. 60.5%, and >2 copies, 17.6% vs. 8.6%; p< 0.001 by Kruskal-Wallis). Conclusions: To our knowledge, this is the largest comprehensive genomic analysis of HER2-low MBC to date. In our cohort of patients with HER2-negative MBC, the genomic landscape of HER2-low and HER2-0 tumors did not differ significantly, apart from a higher number of ERBB2 alleles. These data further support the notion that HER2-low, as currently defined, is not a distinct molecular subtype of breast cancer.

Citation Format: Paolo Tarantino, Hersh V. Gupta, Melissa E. Hughes, Janet L. Files, Sarah Strauss, Gregory Kirkner, Anne-Marie Feeney, Yvonne Y. Li, Ana C. Garrido-Castro, Romualdo Barroso-Sousa, Brittany Bychkovsky, Laura MacConaill, Neal Lindeman, Bruce Johnson, Matthew Meyerson, Sheheryar Kabraji, Rinath Jeselsohn, Xintao Qiu, Rong Li, Henry W. Long, Eric Winer, Deborah A. Dillon, Giuseppe Curigliano, Andrew Cherniack, Sara Tolaney, Nancy U. Lin. HER2-05 Comprehensive genomic characterization of HER2-low 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 HER2-05.

Abstract OT1-12-02: Preliminary report of the PRECISION Trial (Profiling Early Breast Cancer for Radiotherapy Omission): A Phase II Study of Breast-Conserving Surgery Without Adjuvant Radiotherapy for Favorable-Risk Breast Cancer

Background: Breast conserving surgery (BCS) is typically followed by adjuvant radiotherapy (RT) based on several landmark trials demonstrating improvements in disease control and survival. Since completion of these historical trials, the advent of molecular subtyping has revealed that breast cancer is not a single disease entity, but rather a class of cancers with differential risk profiles. We evaluated whether RT could be safely omitted following BCS for patients with the most favorable subtype as defined by the Prosigna PAM50 assay. Methods: We conducted a multicenter prospective single-arm cohort study with IRB approval and an FDA investigational device exemption (IDE). Eligible patients were women 50 to 75 years of age (inclusive) who had undergone BCS revealing tumors ≤2cm in size, that were estrogen or progesterone receptor positive (HR+), HER2 negative, grade 1-2, node negative (N0), with negative excision margins (no ink on tumor). Intent to take endocrine therapy was required. Upon registration, tumors were submitted for central Prosigna testing and those with Risk of Recurrence (ROR) score ≤40 were deemed eligible for the investigational omission of RT. The primary endpoint was the 5-year locoregional recurrence rate (LRR). Anticipating a total of 345 RT-omitting patients to enroll over 3.5 years, the study was designed with 90% power to exclude a 5-year LRR of 5% using a one-sample exponential test with one-sided type I error of 0.025. Results: From 2016 to 2020, 671 patients were registered from 13 centers, inclusive of affiliated regional network sites. Of these, 382 patients had a ROR Score ≤40 and opted to forego RT, comprising the main intention-to-treat (ITT) study population. Median age was 65 years (range 50 to 75), and median tumor size was 0.9 cm (range 0.1 to 2.0 cm). At a median follow-up of 26.9 months, 12 events were observed: 4 patients had ipsilateral in-breast recurrences, 7 had contralateral breast cancers, and 1 developed an unrelated melanoma. There were no regional-nodal or distant recurrences. The 2-year cumulative rate of LRR was 0.3% (95% CI: 0 – 1.0%). Of the 4 ipsilateral breast recurrences, 2 were in the same quadrant as the original primary tumor. Conclusion: In this preliminary report of the PRECISION trial, patients 50-75 years of age undergoing BCS and endocrine therapy for pT1N0 HR+ HER2-negative breast cancer with ROR score ≤40 had exceedingly low rates of LRR in the absence of adjuvant RT at a median follow-up of 26.9 months. Additional follow-up is required to determine whether these favorable results are durable.

Citation Format: Lior Z. Braunstein, Julia Wong, Deborah A. Dillon, Yu-Hui Chen, Paul Catalano, Oren Cahlon, Mahmoud B. El-Tamer, Rachel Jimenez, Atif Khan, Carmen Perez, Rinaa Punglia, Ron Shiloh, Laura Warren, David Wazer, Jean Wright, Elizabeth Buckley, Tari King, Simon Powell, Eric Winer, Jennifer Bellon. Preliminary report of the PRECISION Trial (Profiling Early Breast Cancer for Radiotherapy Omission): A Phase II Study of Breast-Conserving Surgery Without Adjuvant Radiotherapy for Favorable-Risk 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 OT1-12-02.

Abstract P5-14-06: Tumor Genomic Landscape in Older Women with Metastatic Breast Cancer (MBC)

Background. Patients (pts) who develop MBC at older ages are underrepresented in clinical trials, are less likely to be included in comprehensive biomarker characterization studies, and experience worse breast cancer-specific survival than their younger counterparts. Elucidating genomic underpinnings of MBC and possible therapeutic targets for older breast cancer patients are critical priorities. Methods. We identified pts age >70 years at MBC diagnosis and a younger cohort (ages 50-69; age < 50), who were treated for MBC at a single center and who had their metastatic (or if not available, the primary) tumor, assessed by a targeted, tumor-only next generation sequencing (NGS) platform (OncoPanel) between 2013-2020. The NGS panel included mutations, copy number variation, tumor mutational burden (TMB), and hypermutation (HM) status, with mutations classified as oncogenic using the OncoKB tool and additional annotation. Copy number events were selected as being “oncogenic” if a high amplification was called for an oncogene or a deep deletion for a tumor suppressor. We compared findings for older (age >70) vs. younger (age < 50 and ages 50-69) MBC pts using Chi-Square and Kruskal-Wallis tests. To determine genomic event enrichment, logistic regression (LR) models were used, controlling for age (continuous), background rate, and tumor subtype (those with unknown subtype [n=27] were excluded from models). False discovery rate (FDR) was used to correct for multiple hypothesis testing. Results. The final analytic cohort included 2,380 pts. The median age at MBC diagnosis was 54.1 years overall (range 18.5- 91.9) and 73.6 years for those age >70. A total of 137 metastatic and 76 primary tumors were sequenced in pts age >70; in those age < 70, 1383 metastatic and 784 primary tumors were sequenced (for age < 50 [n=857] and 50-69 [n=1310]). Older pts were more likely to present with HR+/HER2- tumors (70.9% v. 62.4% v. 52.4%), and less likely to present with HER2+ (9.4% v. 14.4% v. 22.8%) or triple-negative breast cancer (TNBC) (18.8% v. 21.9% vs. 24.0%) at MBC diagnosis (listed >70, 50-69, < 50; P=1e-7). Older pts had higher average TMB vs. younger pts (9.57 in pts > 70, 8.56 in ages 50-69, 7.34 in ages < 50; P=3.5e-5). This was due to older pts having a higher incidence of hypermutation status as defined as TMB >10: 26.3% in age >70, 23.2% in ages 50-69, 16.8% in age < 50. Using q=0.1 as the threshold of significance, the presence of CDH1, PIK3CA, MAP3K1, TET2, and AKT oncogenic mutations were also enriched in older pts, while the presence of oncogenic GATA3, BRCA2, and TP53 mutations, as well as any mutation in BRCA1 were enriched in younger pts (too few oncogenic BRCA1 mutations were present for accurate modeling). The frequency of oncogenic PIK3CA mutations in HR+/HER2- tumors was highest in the oldest pts (44.4% in pts age >70 v. 31.6% in age 50-69 v. 26.7% in age < 50). Of pts who had oncogenic BRCA1/2 mutations identified on tumor-only NGS testing and underwent clinical germline testing (n=7 v. 60 v. 67, oldest to youngest), older pts had the lowest incidence of germline BRCA pathogenic variants (14.3% vs. 47.2.% vs. 67.2%; p=0.01); most BRCA mutations identified on NGS testing in older patients were considered likely somatic. When assessing enrichment in copy number events, ERBB2, RAD21, and BRIP1 amplifications were all significantly less frequent in older pts (q< 0.1), even when accounting for tumor subtype. Conclusions. In a large cohort of pts with MBC, the mutational and copy number landscape for older pts differs from that in younger pts, even after controlling for tumor subtype. Key actionable findings include a higher proportion of high TMB and PIK3CA-mutated tumors, emphasizing the importance of genomic profile testing in this pt population and further exploration of efficacy and tolerability of relevant therapies in those age >70 years.

Citation Format: Hersh V. Gupta, Rachel Freedman, Melissa E. Hughes, Yvonne Y. Li, Gregory Kirkner, Janet L. Files, Sarah Strauss, Ana C. Garrido-Castro, Lauren Buckley, Romualdo Barroso-Sousa, Brittany Bychkovsky, Sara Tolaney, Laura MacConaill, Neal Lindeman, Bruce Johnson, Matthew Meyerson, Eric Winer, Deborah A. Dillon, Andrew Cherniack, Nancy U. Lin. Tumor Genomic Landscape in Older Women with Metastatic Breast Cancer (MBC) [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 P5-14-06.

Invasive lobular carcinoma with extracellular mucin (ILCEM): clinicopathologic and molecular characterization of a rare entity

Invasive lobular carcinoma with extracellular mucin (ILCEM) is a rare histologic subtype of breast cancer. Little is known about the pathologic or genomic signatures that distinguish ILCEM from classic invasive lobular carcinoma (ILC) or mucinous carcinoma. We studied 17 breast cancers with lobular morphology and extracellular mucin. Thirteen tumors with sufficient tissue for DNA extraction were analyzed by a next generation sequencing (NGS) assay that interrogates 447 genes for mutations and copy number variations (CNVs). Median patient age was 66 yrs (range: 31-77 yrs). Sixteen patients presented with masses, 7 of which were >2 cm. Seven patients had lymph node metastases. The cases of ILCEM were moderately (n = 13) or poorly differentiated (n = 4), frequently exhibiting variant morphology that has not been previously described or emphasized, including grade 3 nuclei (n = 11), diffuse signet ring cells (n = 10), solid growth (n = 4), tumor necrosis (n = 3) or apocrine features (n = 2). All tumors showed absent or reduced membranous E-cadherin expression. Concurrent lobular carcinoma in situ (LCIS) was seen in 11/17 cases, 1 of which was a striking example of signet ring cell LCIS with extracellular mucin. Receptor profiles were ER+/HER2- (n = 15) and ER+/HER2+ (n = 2). With a median follow-up of 83.5 months (range: 3-171 months) in 12 patients with available information, 8 patients had recurrences resulting in 4 cancer-related deaths. The most common CNVs were 16q loss (n = 11) and 1q gain (n = 9). CDH1 gene-level alterations were detected in all but one case, including frameshift (n = 7), nonsense (n = 2), and donor splice site (n = 1) mutations and indels (n = 2). Recurrent mutations were also seen in PIK3CA (n = 3), POLQ (n = 3), TP53 (n = 3), ERBB3 (n = 3), ERBB2 (n = 2), and RUNX1 (n = 2). Genes with recurrent amplifications included GATA3 (n = 4), FOXA1 (n = 3), CCND1 (n = 2). Our data highlights ILCEM as a distinct variant of ILC that often presents with higher-grade and variant morphologic features and is associated with an aggressive clinical course. NGS data support an overall lobular-type molecular profile and reveal potentially targetable alterations in a subset of cases with recurrence.

Multidimensional Molecular Profiling of Metastatic Triple-Negative Breast Cancer and Immune Checkpoint Inhibitor Benefit

PURPOSE

In metastatic triple-negative breast cancer (mTNBC), consistent biomarkers of immune checkpoint inhibitor (ICI) therapy benefit remain elusive. We evaluated the immune, genomic, and transcriptomic landscape of mTNBC in patients treated with ICIs.

METHODS

We identified 29 patients with mTNBC treated with pembrolizumab or atezolizumab, either alone (n = 9) or in combination with chemotherapy (n = 14) or targeted therapy (n = 6), who had tumor tissue and/or blood available before ICI therapy for whole-exome sequencing. RNA sequencing and CIBERSORTx-inferred immune population analyses were performed (n = 20). Immune cell populations and programmed death-ligand 1 expression were assessed using multiplexed immunofluorescence (n = 18). Clonal trajectories were evaluated via serial tumor/circulating tumor DNA whole-exome sequencing (n = 4). Association of biomarkers with progression-free survival and overall survival (OS) was assessed.

RESULTS

Progression-free survival and OS were longer in patients with high programmed death-ligand 1 expression and tumor mutational burden. Patients with longer survival also had a higher relative inferred fraction of CD8+ T cells, activated CD4+ memory T cells, M1 macrophages, and follicular helper T cells and enrichment of inflammatory gene expression pathways. A mutational signature of defective repair of DNA damage by homologous recombination was enriched in patients with both shorter OS and primary resistance. Exploratory analysis of clonal evolution among four patients treated with programmed cell death protein 1 blockade and a tyrosine kinase inhibitor suggested that clonal stability post-treatment was associated with short time to progression.

CONCLUSION

This study identified potential biomarkers of response to ICIs among patients with mTNBC: high tumor mutational burden; presence of CD8+, CD4 memory T cells, follicular helper T cells, and M1 macrophages; and inflammatory gene expression pathways. Pretreatment deficiencies in the homologous recombination DNA damage repair pathway and the absence of or minimal clonal evolution post-treatment may be associated with worse outcomes.

Insights into Immune Escape During Tumor Evolution and Response to Immunotherapy Using a Rat Model of Breast Cancer

Animal models are critical for the preclinical validation of cancer immunotherapies. Unfortunately, mouse breast cancer models do not faithfully reproduce the molecular subtypes and immune environment of the human disease. In particular, there are no good murine models of estrogen receptor-positive (ER+) breast cancer, the predominant subtype in patients. Here, we show that Nitroso-N-methylurea-induced mammary tumors in outbred Sprague-Dawley rats recapitulate the heterogeneity for mutational profiles, ER expression, and immune evasive mechanisms observed in human breast cancer. We demonstrate the utility of this model for preclinical studies by dissecting mechanisms of response to immunotherapy using combination TGFBR inhibition and PD-L1 blockade. Short-term treatment of early-stage tumors induced durable responses. Gene expression profiling and spatial mapping classified tumors as inflammatory and noninflammatory, and identified IFNγ, T-cell receptor (TCR), and B-cell receptor (BCR) signaling, CD74/MHC II, and epithelium-interacting CD8+ T cells as markers of response, whereas the complement system, M2 macrophage phenotype, and translation in mitochondria were associated with resistance. We found that the expression of CD74 correlated with leukocyte fraction and TCR diversity in human breast cancer. We identified a subset of rat ER+ tumors marked by expression of antigen-processing genes that had an active immune environment and responded to treatment. A gene signature characteristic of these tumors predicted disease-free survival in patients with ER+ Luminal A breast cancer and overall survival in patients with metastatic breast cancer receiving anti-PD-L1 therapy. We demonstrate the usefulness of this preclinical model for immunotherapy and suggest examination to expand immunotherapy to a subset of patients with ER+ disease. See related Spotlight by Roussos Torres, p. 672.

STING agonism reprograms tumor-associated macrophages and overcomes resistance to PARP inhibition in BRCA1-deficient models of breast cancer

PARP inhibitors (PARPi) have drastically changed the treatment landscape of advanced ovarian tumors with BRCA mutations. However, the impact of this class of inhibitors in patients with advanced BRCA-mutant breast cancer is relatively modest. Using a syngeneic genetically-engineered mouse model of breast tumor driven by Brca1 deficiency, we show that tumor-associated macrophages (TAMs) blunt PARPi efficacy both in vivo and in vitro. Mechanistically, BRCA1-deficient breast tumor cells induce pro-tumor polarization of TAMs, which in turn suppress PARPi-elicited DNA damage in tumor cells, leading to reduced production of dsDNA fragments and synthetic lethality, hence impairing STING-dependent anti-tumor immunity. STING agonists reprogram M2-like pro-tumor macrophages into an M1-like anti-tumor state in a macrophage STING-dependent manner. Systemic administration of a STING agonist breaches multiple layers of tumor cell-mediated suppression of immune cells, and synergizes with PARPi to suppress tumor growth. The therapeutic benefits of this combination require host STING and are mediated by a type I IFN response and CD8+ T cells, but do not rely on tumor cell-intrinsic STING. Our data illustrate the importance of targeting innate immune suppression to facilitate PARPi-mediated engagement of anti-tumor immunity in breast cancer.

A human breast atlas integrating single-cell proteomics and transcriptomics

The breast is a dynamic organ whose response to physiological and pathophysiological conditions alters its disease susceptibility, yet the specific effects of these clinical variables on cell state remain poorly annotated. We present a unified, high-resolution breast atlas by integrating single-cell RNA-seq, mass cytometry, and cyclic immunofluorescence, encompassing a myriad of states. We define cell subtypes within the alveolar, hormone-sensing, and basal epithelial lineages, delineating associations of several subtypes with cancer risk factors, including age, parity, and BRCA2 germline mutation. Of particular interest is a subset of alveolar cells termed basal-luminal (BL) cells, which exhibit poor transcriptional lineage fidelity, accumulate with age, and carry a gene signature associated with basal-like breast cancer. We further utilize a medium-depletion approach to identify molecular factors regulating cell-subtype proportion in organoids. Together, these data are a rich resource to elucidate diverse mammary cell states.

Temporal and spatial topography of cell proliferation in cancer

Proliferation is a fundamental trait of cancer cells, but its properties and spatial organization in tumours are poorly characterized. Here we use highly multiplexed tissue imaging to perform single-cell quantification of cell cycle regulators and then develop robust, multivariate, proliferation metrics. Across diverse cancers, proliferative architecture is organized at two spatial scales: large domains, and smaller niches enriched for specific immune lineages. Some tumour cells express cell cycle regulators in the (canonical) patterns expected of freely growing cells, a phenomenon we refer to as 'cell cycle coherence'. By contrast, the cell cycles of other tumour cell populations are skewed towards specific phases or exhibit non-canonical (incoherent) marker combinations. Coherence varies across space, with changes in oncogene activity and therapeutic intervention, and is associated with aggressive tumour behaviour. Thus, multivariate measures from high-plex tissue images capture clinically significant features of cancer proliferation, a fundamental step in enabling more precise use of anti-cancer therapies.

Integrative multiomics-histopathology analysis for breast cancer classification

Histopathologic evaluation of biopsy slides is a critical step in diagnosing and subtyping breast cancers. However, the connections between histology and multi-omics status have never been systematically explored or interpreted. We developed weakly supervised deep learning models over hematoxylin-and-eosin-stained slides to examine the relations between visual morphological signal, clinical subtyping, gene expression, and mutation status in breast cancer. We first designed fully automated models for tumor detection and pathology subtype classification, with the results validated in independent cohorts (area under the receiver operating characteristic curve ≥ 0.950). Using only visual information, our models achieved strong predictive performance in estrogen/progesterone/HER2 receptor status, PAM50 status, and TP53 mutation status. We demonstrated that these models learned lymphocyte-specific morphological signals to identify estrogen receptor status. Examination of the PAM50 cohort revealed a subset of PAM50 genes whose expression reflects cancer morphology. This work demonstrates the utility of deep learning-based image models in both clinical and research regimes, through its ability to uncover connections between visual morphology and genetic statuses.

Interim clinical trial analysis of intraoperative mass spectrometry for breast cancer surgery

Optimal resection of breast tumors requires removing cancer with a rim of normal tissue while preserving uninvolved regions of the breast. Surgical and pathological techniques that permit rapid molecular characterization of tissue could facilitate such resections. Mass spectrometry (MS) is increasingly used in the research setting to detect and classify tumors and has the potential to detect cancer at surgical margins. Here, we describe the ex vivo intraoperative clinical application of MS using a liquid micro-junction surface sample probe (LMJ-SSP) to assess breast cancer margins. In a midpoint analysis of a registered clinical trial, surgical specimens from 21 women with treatment naïve invasive breast cancer were prospectively collected and analyzed at the time of surgery with subsequent histopathological determination. Normal and tumor breast specimens from the lumpectomy resected by the surgeon were smeared onto glass slides for rapid analysis. Lipidomic profiles were acquired from these specimens using LMJ-SSP MS in negative ionization mode within the operating suite and post-surgery analysis of the data revealed five candidate ions separating tumor from healthy tissue in this limited dataset. More data is required before considering the ions as candidate markers. Here, we present an application of ambient MS within the operating room to analyze breast cancer tissue and surgical margins. Lessons learned from these initial promising studies are being used to further evaluate the five candidate biomarkers and to further refine and optimize intraoperative MS as a tool for surgical guidance in breast cancer.

Histopathologic features of breast cancer in Li-Fraumeni syndrome

Breast cancer is the most common malignancy in female patients with Li-Fraumeni syndrome (LFS), a rare autosomal dominant hereditary syndrome characterized by germline TP53 mutations. Recent studies have shown that the majority of these tumors are estrogen receptor (ER) positive with frequent HER2 co-expression. However, the morphologic features of these tumors have not been as well studied as other germline-associated breast cancers. We evaluated the pathologic features of 27 invasive and in situ carcinomas from patients with known germline TP53 mutations collected through the Li-Fraumeni Consortium. Overall, 60% of cases were HER2 positive and 44% showed ER co-expression. Most DCIS was high nuclear grade with central necrosis and associated periductal fibrosis and lymphocytic response. Invasive carcinomas were mostly of ductal type (NOS), modified Scarff-Bloom-Richardson (mSBR) high grade, with marked nuclear atypia and high mitotic rate. Prominent tumor infiltrating lymphocytes, syncytial growth pattern, or pushing borders were not seen in these tumors. High p53 IHC expression was seen in tumors from individuals with germline TP53 missense mutations whereas little or no protein expression (<1% nuclear expression, null pattern) was seen in tumors from carriers of non-missense mutations. In this study, we report in detail the morphologic features of invasive and in situ carcinomas in LFS. We found that these tumors share features with cancers harboring somatic TP53 mutations but are distinct from BRCA-associated breast cancers.

Abstract PS18-02: Highly multiplexed tissue-based cyclic immunofluorescence (t-CyCIF) for precision oncology identifies novel patterns of HER2 heterogeneity in breast cancer

Background

Immunohistochemical (IHC) evaluation has shown that human epidermal growth factor receptor 2 (HER2) may not be expressed homogeneously among all cancer cells within a given tumor. The clinical significance of intratumoral HER2 heterogeneity is unclear. Exploration of tumor heterogeneity is facilitated by tissue imaging technologies such as t-CyCIF, a highly multiplexed immunofluorescence microscopy technique that permits visualization of up to 60 antigens and analysis on a single cell level from formalin-fixed, paraffin-embedded tissue. To utilize t-CyCIF for the evaluation of breast tumors, this study was undertaken to: 1) validate antibodies to be used against the clinically relevant markers HER2, estrogen receptor (ER) and progesterone receptor (PR), and 2) use these antibodies along with other validated antibodies to define the tumor microenvironment (TME) to interrogate breast tumors at a single cell level.

Methods

T-CyCIF is an iterative whole-slide imaging process, in which successive four-channel images, each involving different antibodies, are collected from the same sample and then merged to generate a high-dimensional representation used for visualization and analysis. In phase one of this study, 948 tissue cores (representing 295 patients in triplicate) were used to validate HER2, ER, and PR antibodies against a single antibody commonly used in clinical practice as a reference. Analyses were performed at the level of tissue cores, cells and pixels. Inter-assay analyses were performed comparing: t-CyCIF vs. IHC, the latter assessed by digital pathology and two pathologists; and also, t-CyCIF vs. fluorescence in situ hybridization (FISH) for HER2. In the second phase, following selection of validated HER2, ER and PR antibodies, expression of CD45, CD68, PD-L1, p53, Ki67, pRB and the androgen receptor (AR) were evaluated at a single cell level in 312 HER2+ invasive breast cancer samples, representing 104 patients, to better understand the TME, cancer cell heterogeneity and the cell identities/states present in breast carcinomas.

Results

In the first phase of the study, 13 different ER, PR or HER2 antibodies were analyzed. The pixel-to-pixel evaluation, which evaluates concordance in staining, resulted in r scores of 0.86 (ER; Pearson correlation), 0.93 (PR) and 0.94 (HER2) and correlation scores in single-cell comparisons ranged from 0.76 to 0.81. Correlation scores on the tissue core level were high in the inter-assay analyses, i.e. t-CyCIF vs. IHC (e.g. r scores up to 0.87 and 0.91 for ER and HER2, respectively, on t-CyCIF vs. Aperio; and 0.85 to 0.94 by pathology review) and t-CyCIF vs. HER2 FISH (r scores up to 0.71). This resulted in validated fluorophore-conjugated antibody panels for use in t-CyCIF that correspond well to established standards. In the second phase, single cell analysis of HER2+ breast cancer was performed. Cancer cells were defined as keratin positive and using t-Distributed Stochastic Neighbor Embedding (t-SNE) seven cancer cell clusters were identified including two HER2hi clusters differing in ER, p53, AR and PD-L1 expression, two HER2lo clusters differing in PR, Ki67, pRB, p53 and AR and three HER2neg clusters differing in PR, Ki67, ER, PD-L1 and AR. Heterogeneity scores were calculated based on diversity among clusters.

Conclusion

This study is the first to evaluate the performance of breast cancer-specific antibodies in a highly multiplexed imaging platform such as t-CyCIF. Using the validated antibody panel, we uncovered patterns of expression of markers relevant to breast cancer biology that correlate with HER2 high, low and negative states. Ongoing studies are looking at correlations between HER2 heterogeneity, responses to therapy and clinical outcomes.

Citation Format: Jennifer L Guerriero, Jia-Ren Lin, Ricardo G Pastorello, Ziming Du, Shaolin Mei, Krishan Taneja, Stuart J Schnitt, Deborah A Dillon, Peter K Sorger, Sandro Santagata, Elizabeth A Mittendorf. Highly multiplexed tissue-based cyclic immunofluorescence (t-CyCIF) for precision oncology identifies novel patterns of HER2 heterogeneity in breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-02.

Abstract PS4-25: Comprehensive genomic analysis reveals molecular correlates of response to immune checkpoint inhibitors (ICI) in metastatic triple-negative breast cancer (mTNBC)

Background: Genomic mechanisms associated with response to ICI in mTNBC are largely unknown. The aim of this work is to assess the genomic and immune profiles of mTNBC samples collected from patients (pts) treated with ICI. Methods: We identified 31 women with mTNBC treated with ICI (pembrolizumab, n=6, NCT02447003; atezolizumab, n=4, NCT01375842; nivolumab + cabozantinib, n = 6, NCT03316586; pembrolizumab + eribulin, n=8, NCT02513472; atezolizumab + nab-paclitaxel, n=7, NCT01633970) who had tumor tissue or blood available for sequencing obtained before and after ICI. Clinical benefit (CB), here defined as any objective response or stable disease (SD) for &gt; 24 weeks, was observed in 20 pts (65%). An extraordinary responder was defined as having CB ≥ 2 yrs; 5 pts were considered extraordinary responders (range 26-60months). Whole exome sequencing (WES) was done on each tumor and on germline DNA from blood (23 pts had successful WES performed on samples collected before ICI; 5 of these had WES on samples taken after disease progression). RNA sequencing (RNAseq) was successfully performed in 18 of the tumors with WES performed on samples before ICI; and 3 of these had RNAseq on samples taken after disease progression. 18 pts had tumors assessed by multiplex immunofluorescence (mIF) panels encompassing CD4, CD8, PD-1, PD-L1, and cytokeratin on samples collected before ICI. WES, deep targeted panel and low coverage whole genome sequencing were performed on serially collected plasma samples from 22 pts to evaluate tumor fraction and specific mutations. The association between biomarkers and clinical benefit to ICI was assessed. Results: 21 of 31 pts (67%) had received ≥1 prior lines of systemic therapy in the metastatic setting before starting ICI. Among the most frequently mutated genes at baseline are: TP53 (57%); PIK3CA (18%); DNAH5, MYH8 (both 13%); KMT2C, AKT1, LAMA2 (all 9%). Pts with CB had a higher tumor mutational burden (TMB) than pts with no CB (p=0.018). Differential expression analysis of RNAseq data revealed an upregulation of several immune-related genes in pts with CB, indicating increased immune infiltration in that group. Gene set enrichment analysis of this expression data using hallmark and canonical pathway gene sets from MSigDB (nominal p-val &lt; 0.05) showed that, compared to samples from pts without CB, extraordinary responders had elevated transcriptional signatures of several cancer-related pathways associated with cell survival, proliferation and metabolism, as well as genes associated with increased immune infiltration and upregulation of inflammatory response programs. The mIF showed that the tumor microenvironment (TME) of pts with CB were enriched in Cytokeratin-negative/PD-L1-positive cells compared to those without CB (p=0.014). Expression of CD4, CD8 and PD-1 was not significantly different between pts with and without CB. Genomic analysis of circulating tumor DNA, and tumor evolutionary analysis for pts with both pre- and post-ICI samples (acquired resistance) will be presented. Conclusions: Clinical benefit to ICI in mTNBC was associated with upregulation of immune-related pathways, enrichment of non-tumoral PD-L1-positive cells in TME, and high TMB.

Citation Format: Romualdo Barroso-Sousa, Juliet Forman, Zachary T. Weber, Katherine Collier, Katrina Z. Kao, Edward T. Richardson, III, Tanya Keenan, Ofir Cohen, Michael P. Manos, Ryan C. Brennick, Patrick Ott, F. Steve Hodi, Deborah A. Dillon, Nancy U. Lin, Eliezer E. Van Allen, Scott Rodig, Eric P. Winer, Elizabeth A. Mittendorf, Catherine J. Wu, Daniel Stover, Nikhil Wagle, Sachet Shukla, Sara Tolaney. Comprehensive genomic analysis reveals molecular correlates of response to immune checkpoint inhibitors (ICI) in metastatic triple-negative breast cancer (mTNBC) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS4-25.

Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer

Despite objective responses to PARP inhibition and improvements in progression-free survival compared to standard chemotherapy in patients with BRCA-associated triple-negative breast cancer (TNBC), benefits are transitory. Using high dimensional single-cell profiling of human TNBC, here we demonstrate that macrophages are the predominant infiltrating immune cell type in BRCA-associated TNBC. Through multi-omics profiling we show that PARP inhibitors enhance both anti- and pro-tumor features of macrophages through glucose and lipid metabolic reprogramming driven by the sterol regulatory element-binding protein 1 (SREBP-1) pathway. Combined PARP inhibitor therapy with CSF-1R blocking antibodies significantly enhanced innate and adaptive anti-tumor immunity and extends survival in BRCA-deficient tumors in vivo and is mediated by CD8+ T-cells. Collectively, our results uncover macrophage-mediated immune suppression as a liability of PARP inhibitor treatment and demonstrate combined PARP inhibition and macrophage targeting therapy induces a durable reprogramming of the tumor microenvironment, thus constituting a promising therapeutic strategy for TNBC.

Genomic Characterization of de novo Metastatic Breast Cancer

PURPOSE

In contrast to recurrence after initial diagnosis of stage I-III breast cancer [recurrent metastatic breast cancer (rMBC)], de novo metastatic breast cancer (dnMBC) represents a unique setting to elucidate metastatic drivers in the absence of treatment selection. We present the genomic landscape of dnMBC and association with overall survival (OS).

EXPERIMENTAL DESIGN

Targeted DNA sequencing (OncoPanel) was prospectively performed on either primary or metastatic tumors from 926 patients (212 dnMBC and 714 rMBC). Single-nucleotide variants, copy-number variations, and tumor mutational burden (TMB) in treatment-naïve dnMBC primary tumors were compared with primary tumors in patients who ultimately developed rMBC, and correlated with OS across all dnMBC.

RESULTS

When comparing primary tumors by subtype, MYB amplification was enriched in triple-negative dnMBC versus rMBC (21.1% vs. 0%, P = 0.0005, q = 0.111). Mutations in KMTD2, SETD2, and PIK3CA were more prevalent, and TP53 and BRCA1 less prevalent, in primary HR⁺/HER2^- tumors of dnMBC versus rMBC, though not significant after multiple comparison adjustment. Alterations associated with shorter OS in dnMBC included TP53 (wild-type: 79.7 months; altered: 44.2 months; P = 0.008, q = 0.107), MYC (79.7 vs. 23.3 months; P = 0.0003, q = 0.011), and cell-cycle (122.7 vs. 54.9 months; P = 0.034, q = 0.245) pathway genes. High TMB correlated with better OS in triple-negative dnMBC (P = 0.041).

CONCLUSIONS

Genomic differences between treatment-naïve dnMBC and primary tumors of patients who developed rMBC may provide insight into mechanisms underlying metastatic potential and differential therapeutic sensitivity in dnMBC. Alterations associated with poor OS in dnMBC highlight the need for novel approaches to overcome potential intrinsic resistance to current treatments.

Navitoclax enhances the effectiveness of EGFR-targeted antibody-drug conjugates in PDX models of EGFR-expressing triple-negative breast cancer

BACKGROUND

Targeted therapies for triple-negative breast cancer (TNBC) are limited; however, the epidermal growth factor receptor (EGFR) represents a potential target, as the majority of TNBC express EGFR. The purpose of these studies was to evaluate the effectiveness of two EGFR-targeted antibody-drug conjugates (ADC: ABT-414; ABBV-321) in combination with navitoclax, an antagonist of the anti-apoptotic BCL-2 and BCL-XL proteins, in order to assess the translational relevance of these combinations for TNBC.

METHODS

The pre-clinical efficacy of combined treatments was evaluated in multiple patient-derived xenograft (PDX) models of TNBC. Microscopy-based dynamic BH3 profiling (DBP) was used to assess mitochondrial apoptotic signaling induced by navitoclax and/or ADC treatments, and the expression of EGFR and BCL-2/XL was analyzed in 46 triple-negative patient tumors.

RESULTS

Treatment with navitoclax plus ABT-414 caused a significant reduction in tumor growth in five of seven PDXs and significant tumor regression in the highest EGFR-expressing PDX. Navitoclax plus ABBV-321, an EGFR-targeted ADC that displays more effective wild-type EGFR-targeting, elicited more significant tumor growth inhibition and regressions in the two highest EGFR-expressing models evaluated. The level of mitochondrial apoptotic signaling induced by single or combined drug treatments, as measured by DBP, correlated with the treatment responses observed in vivo. Lastly, the majority of triple-negative patient tumors were found to express EGFR and co-express BCL-XL and/or BCL-2.

CONCLUSIONS

The dramatic tumor regressions achieved using combined agents in pre-clinical TNBC models underscore the abilities of BCL-2/XL antagonists to enhance the effectiveness of EGFR-targeted ADCs and highlight the clinical potential for usage of such targeted ADCs to alleviate toxicities associated with combinations of BCL-2/XL inhibitors and systemic chemotherapies.

Identifying ERBB2 Activating Mutations in HER2-Negative Breast Cancer: Clinical Impact of Institute-Wide Genomic Testing and Enrollment in Matched Therapy Trials

PURPOSE

The yield of comprehensive genomic profiling in recruiting patients to molecular-based trials designed for small subgroups has not been fully evaluated. We evaluated the likelihood of enrollment in a clinical trial that required the identification of a specific genomic change based on our institute-wide genomic tumor profiling.

PATIENTS AND METHODS

Using genomic profiling from archived tissue samples derived from patients with metastatic breast cancer treated between 2011 and 2017, we assessed the impact of systematic genomic characterization on enrollment in an ongoing phase II trial (ClinicalTrials.gov identifier: NCT01670877). Our primary aim was to describe the proportion of patients with a qualifying ERBB2 mutation identified by our institutional genomic panel (OncoMap or OncoPanel) who enrolled in the trial. Secondary objectives included median time from testing result to trial registration, description of the spectrum of ERBB2 mutations, and survival. Associations were calculated using Fisher's exact test.

RESULTS

We identified a total of 1,045 patients with metastatic breast cancer without ERBB2 amplification who had available genomic testing results. Of these, 42 patients were found to have ERBB2 mutation and 19 patients (1.8%) were eligible for the trial on the basis of the presence of an activating mutation, 18 of which were identified by OncoPanel testing. Fifty-eight percent of potentially eligible patients were approached, and 33.3% of eligible patients enrolled in the trial guided exclusively by OncoPanel testing.

CONCLUSION

More than one half of eligible patients were approached for trial participation and, significantly, one third of those were enrolled in NCT01670877. Our data illustrate the ability to enroll patients in trials of rare subsets in routine clinical practice and highlight the need for these broadly based approaches to effectively support the success of these studies.

Abstract CT271: PRECISION (Profiling early breast cancer for radiotherapy omission): A phase II study of breast-conserving surgery without adjuvant radiotherapy for favorable-risk breast cancer

Background: Radiation therapy (RT) following breast conserving surgery (BCS) is known to improve locoregional and distant control in women with invasive breast cancer; however, RT does pose significant cost and potential risk, including concern for cardiopulmonary toxicity and secondary malignancy. Randomized trials show that the omission of RT among older women with otherwise favorable-risk breast cancer does not affect overall survival (OS) at 10 years, and modestly increases the risk of local recurrence (LR). Nevertheless, there is little prospective support for RT omission in younger women. Moreover, risk stratification in the randomized prospective studies to date relies on limited methods with potentially low fidelity at distinguishing luminal subtypes. Enhanced molecular profiling techniques could better discern tumor biology and, in turn, more precisely assess risk. PAM-50 is an expression profile of 50 genes used to classify breast cancer intrinsic subtype with consequent prognostic implications. The goal of this study is to identify low-risk breast cancer patients with luminal A subtype who may feasibly omit RT from their therapeutic regimen. Methods: This is a phase II prospective cohort study (NCT02653755) designed to assess the safety of treatment de-escalation (omission of RT) in women with favorable-risk invasive breast cancer following BCS. Eligibility criteria include female patients with invasive breast cancer, age 50-75, with tumors less than or equal to 2cm, negative surgical margins, ER+ or PR+ and HER2- disease, grade 1 or 2, no lymph node involvement, and no plans for chemotherapy or biologic therapy, who are eligible for and willing to receive endocrine therapy. Tumor samples from eligible patients will undergo PAM-50 transcriptional profiling using the Nanostring Prosigna assay. A low Risk of Recurrence (ROR) score, corresponding to the luminal A subtype, will permit patients to forego radiotherapy should they so choose. The primary endpoint is 5-year risk of local or regional recurrence of invasive or in situ breast carcinoma within the ipsilateral breast or regional lymph nodes. Study enrollment began in May 2016.

Citation Format: Mira A. Patel, Deborah A. Dillon, Giulia Digiovanni, Yu-Hui Chen, Paul Catalano, Carmen Perez, David Wazer, Jean Wright, Rachel Jimenez, Eric Winer, Julia Wong, Jennifer Bellon, Lior Z. Braunstein. PRECISION (Profiling early breast cancer for radiotherapy omission): A phase II study of breast-conserving surgery without adjuvant radiotherapy for favorable-risk breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT271.

Fibroblast-tumor cell signaling limits HER2 kinase therapy response via activation of MTOR and antiapoptotic pathways

Despite the implementation of multiple HER2-targeted therapies, patients with advanced HER2+ breast cancer ultimately develop drug resistance. Stromal fibroblasts represent an abundant cell type in the tumor microenvironment and have been linked to poor outcomes and drug resistance. Here, we show that fibroblasts counteract the cytotoxic effects of HER2 kinase-targeted therapy in a subset of HER2+ breast cancer cell lines and allow cancer cells to proliferate in the presence of the HER2 kinase inhibitor lapatinib. Fibroblasts from primary breast tumors, normal breast tissue, and lung tissue have similar protective effects on tumor cells via paracrine factors. This fibroblast-mediated reduction in drug sensitivity involves increased expression of antiapoptotic proteins and sustained activation of the PI3K/AKT/MTOR pathway, despite inhibition of the HER2 and the RAS-ERK pathways in tumor cells. HER2 therapy sensitivity is restored in the fibroblast cocultures by combination treatment with inhibitors of MTOR or the antiapoptotic proteins BCL-XL and MCL-1. Expression of activated AKT in tumor cells recapitulates the effects of fibroblasts resulting in sustained MTOR signaling and poor lapatinib response. Lapatinib sensitivity was not altered by fibroblasts in tumor cells that exhibited sustained MTOR signaling due to a strong gain-of-function PI3KCA mutation. These findings indicate that in addition to tumor cell-intrinsic mechanisms that cause constitutive PI3K/AKT/MTOR pathway activation, secreted factors from fibroblasts can maintain this pathway in the context of HER2 inhibition. Our integrated proteomic-phenotypic approach presents a strategy for the discovery of protective mechanisms in fibroblast-rich tumors and the design of rational combination therapies to restore drug sensitivity.

Genomic profiling of pleomorphic and florid lobular carcinoma in situ reveals highly recurrent ERBB2 and ERRB3 alterations

Pleomorphic LCIS (P-LCIS) and florid LCIS (F-LCIS) are morphologic variants distinguished from classic LCIS by marked nuclear pleomorphism and/or an expansile growth pattern with or without necrosis. Given the rarity of these LCIS variants, little data exist regarding their molecular pathogenesis, natural history, and optimal management. The purpose of this study was to genomically profile LCIS variants to gain further insight into their biology. Nineteen cases of pure LCIS variants (17 P-LCIS, 2 F-LCIS) diagnosed on core needle biopsy at our institution from 2006 to 2017 were included, five of which were upgraded to invasive cancer at excision. Macrodissected lesions were analyzed by a hybrid-capture next generation sequencing assay that surveyed exonic sequences of 447 genes for mutations and copy number variations (CNVs) and 191 regions across 60 genes for structural rearrangements. LCIS variants were all confirmed as E-cadherin negative by immunohistochemistry. Receptor profiles among the 17 P-LCIS cases included HR+/HER2- (nine cases), HR+/HER2+ (three cases), HR-/HER2+ (two cases), and HR-/HER2- (three cases). The two F-LCIS cases were HR+/HER2- and HR+/HER2+. All LCIS variants had genetic alterations consistent with a lobular phenotype including 1q gain (16 cases), 16q loss (18 cases), and CDH1 mutations (18 cases). Highly recurrent ERBB2 alterations were noted including mutations (13 cases) and amplifications (six cases). Other significant alterations included mutations in PIK3CA (six cases), RUNX1 (four cases), ERBB3 (four cases), and CBFB (three cases), as well as amplification of CCND1 (five cases). A TP53 mutation was identified in one case of HR-/HER2+ P-LCIS with signet ring cell features that lacked 1q gain and 16q loss. P-LCIS and F-LCIS contain genetic alterations characteristic of lobular neoplasia; however, these LCIS variants are distinguished from classical LCIS reported in the literature by their highly recurrent ERBB2 alterations.

Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls.

Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting.

The path to a better biomarker: application of a risk management framework for the implementation of PD-L1 and TILs as immuno-oncology biomarkers in breast cancer clinical trials and daily practice

Immune checkpoint inhibitor therapies targeting PD-1/PD-L1 are now the standard of care in oncology across several hematologic and solid tumor types, including triple negative breast cancer (TNBC). Patients with metastatic or locally advanced TNBC with PD-L1 expression on immune cells occupying ≥1% of tumor area demonstrated survival benefit with the addition of atezolizumab to nab-paclitaxel. However, concerns regarding variability between immunohistochemical PD-L1 assay performance and inter-reader reproducibility have been raised. High tumor-infiltrating lymphocytes (TILs) have also been associated with response to PD-1/PD-L1 inhibitors in patients with breast cancer (BC). TILs can be easily assessed on hematoxylin and eosin-stained slides and have shown reliable inter-reader reproducibility. As an established prognostic factor in early stage TNBC, TILs are soon anticipated to be reported in daily practice in many pathology laboratories worldwide. Because TILs and PD-L1 are parts of an immunological spectrum in BC, we propose the systematic implementation of combined PD-L1 and TIL analyses as a more comprehensive immuno-oncological biomarker for patient selection for PD-1/PD-L1 inhibition-based therapy in patients with BC. Although practical and regulatory considerations differ by jurisdiction, the pathology community has the responsibility to patients to implement assays that lead to optimal patient selection. We propose herewith a risk-management framework that may help mitigate the risks of suboptimal patient selection for immuno-therapeutic approaches in clinical trials and daily practice based on combined TILs/PD-L1 assessment in BC. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Abstract A105: PARP inhibition modulates the infiltration, phenotype, and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the antitumor potential of TAMs

Patients with BRCA-associated triple-negative breast cancer (TNBC) have few effective treatment options. PARP inhibitors are promising, and we recently showed they induce an influx of white blood cells, including CD8+ T cells and macrophages into the tumor. The influx of CD8+ cells, mediated by activation of the STING pathway in tumor cells, contributes substantially to efficacy of PARP inhibition in mice. Strikingly, in these studies the greatest infiltration of immune cells into the tumor was macrophages. Given that objective responses to PARP inhibition have been observed in clinical trials but the benefits are transitory, we hypothesized that this was due to a suppressive tumor microenvironment, driven by tumor macrophages. To better understand the molecular basis of resistance to PARP inhibitors, we used high-dimensional single-cell immune profiling on human TNBC. We observed a ≥10-fold increase in TAMs in BRCA-associated TNBC compared to BRCA-wild-type TNBC. Using a preclinical model of BRCA1-deficient triple-negative breast cancer, we found that PARP inhibitors not only further increased TAM abundance but also induced functional and phenotypic changes associated with STING pathway activation, antigen presentation, and chemokine and cytokine signaling. PARP inhibitors increased the frequency of TAMs expressing costimulatory molecules CD80 and CD86 as well as the activation and maturation marker CD40, which are indicative of an antitumor phenotype. We also identified a novel negative feedback mechanism that limits the functionality of the anti-tumor TAMs and is consistent with induction of an immune-suppressive macrophage population. Utilizing transcriptomic, proteomic, and metabolic profiling of ex vivo cultured human myeloid cells, we identified multiple biologic processes associated with PARP inhibition, showing that these drugs directly affect macrophage states and phenotypes. Remarkably, in the preclinical BRCA1-deficient TNBC model, the novel combination of PARP inhibition with macrophage modulation significantly extended remissions obtained with PARP inhibitor therapy only, and this advantage persisted when treatment was discontinued, suggestive of a durable reprogramming of the tumor microenvironment. Moreover, CD8+ cells were required for the extension of PARP inhibitor-induced remissions, suggesting that targeting macrophages lifted the constraints imposed by protumor macrophages on CD8+ T cell-mediated tumor cell killing. We identify mechanisms related to macrophage and T-cell activation that increase PFS and provide evidence that TAMs may serve as targets for new therapeutic interventions designed to overcome PARP inhibitor resistance in BRCA-associated TNBC.

Citation Format: Anita K. Mehta, Emily M. Cheney, Jessica A. Castrillon, Jia-Ren Lin, Mateus de Oliveira Taveira, Christina A. Hartl, Nathan T. Johnson, William M. Oldham, Marian Kalocsay, Sarah A. Boswell, Olmo Sonzogni, Constantia Pantelidou, Brett P. Gross, Shawn Johnson, Deborah A. Dillon, Sandro Santagata, Judy E. Garber, Nadine Tung, Elizabeth A. Mittendorf, Gerburg M. Wulf, Geoffrey I. Shapiro, Peter K. Sorger, Jennifer L. Guerriero. PARP inhibition modulates the infiltration, phenotype, and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the antitumor potential of TAMs [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A105.

Abstract P5-04-01: PARP inhibition modulates the infiltration, phenotype and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the anti-tumor potential of TAMs

Patients with BRCA-associated triple negative breast cancer (TNBC) have few effective treatment options. PARP inhibitors are promising, and we recently showed they induce an influx of white blood cells, including CD8+ T-cells and macrophages into the tumor. The influx of CD8+ cells, mediated by activation of the STING pathway in tumor cells, contributes substantially to efficacy of PARP inhibition in mice. Strikingly, in these studies, the greatest infiltration of immune cells into the tumor was macrophages. Given objective responses to PARP inhibition have been observed in clinical trials but the benefits are transitory, we hypothesized that this was presumably due to a suppressive tumor microenvironment, driven by tumor macrophages. To better understand the molecular basis of resistance to PARP inhibitors, we used high dimensional single-cell immune profiling on human TNBC. We observed a ≥10-fold increase in TAMs in BRCA-associated TNBC compared to BRCA-wildtype TNBC. Using a pre-clinical model of BRCA1-deficient triple-negative breast cancer, we found that PARP inhibitors not only further increased TAM abundance but also induced functional and phenotypic changes associated with STING pathway activation, antigen presentation, and chemokine and cytokine signaling. PARP inhibitors increased the frequency of TAMs expressing co-stimulatory molecules CD80 and CD86 as well as the activation and maturation marker CD40, which are indicative of an anti-tumor phenotype. We also identified a novel negative feedback mechanism which limits the functionality of the anti-tumor TAMs, and is consistent with induction of an immune suppressive macrophage population. Utilizing transcriptomic, proteomic and metabolic profiling of ex vivo cultured human myeloid cells, we identified multiple biological processes associate with PARP inhibition, showing that these drugs directly affect macrophage states and phenotypes. Remarkably, in the pre-clinical BRCA1-deficient TNBC model, the novel combination of PARP inhibition with macrophage modulation significantly extended remissions obtained with PARP inhibitor therapy only, and this advantage persisted when treatment was discontinued, suggestive of a durable reprogramming of the tumor microenvironment. Moreover, CD8+ cells were required for the extension of PARP inhibitor-induced remissions, suggesting that targeting macrophages lifted the constraints imposed by pro-tumor macrophages on CD8+ T cell-mediated tumor cell killing. We identify mechanisms related to macrophage and T-cell activation that increase PFS and provide evidence that TAMs may serve as targets for new therapeutic interventions designed to overcome PARP inhibitor resistance in BRCA-associated TNBC.

Citation Format: Jennifer L Guerriero, Anita K Mehta, Emily M Cheney, Jessica A. Castrillon, Jia-Ren Lin, Mateus de Oliveira Taveira, Olmo Sonzogni, Constantia Pantelidou, Christina A Hartl, William M Oldham, Nathan T Johnson, Sarah A Boswell, Marian Kalocsay, Matthew J Berberich, Sholin Mei, Dan Wang, Shawn Johnson, Brett Gross, Deborah A Dillon, Mikel Lipschitz, Evisa Gjini, Scott Rodig, Sandro Santagata, Judy E Garber, Nadine Tung, Peter Sorger, Geoffrey I Shapiro, Gerburg M Wulf, Elizabeth A Mittendorf. PARP inhibition modulates the infiltration, phenotype and function of tumor-associated macrophages (TAMs) in BRCA-associated breast cancer and can be augmented by harnessing the anti-tumor potential of TAMs [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-04-01.

Abstract P3-11-06: Pre-clinical assessment of combined ABT-263/Navitoclax and ABT-414 or ABBV-321 treatment for EGFR-expressing TNBC

Despite a notable incidence of EGFR1 copy number alterations and/or enrichment of EGFR protein in a significant fraction of TNBCs, clinical application of classical EGFR-targeted therapeutics has been discouraging. Tumor specific EGFR-targeted antibodies (ABT-806) and their antibody-drug conjugates (ADC:414;321), which eliminate side effects associated with systemic anti-EGFR treatments, represent promising alternative therapeutic approaches. 414, comprised of 806 conjugated to the powerful cytotoxic MMAF, has demonstrated notable effectiveness within EGFR1-amplified/mutated tumors. However, since TNBCs are often enriched for EGFR expression in the absence of EGFR1 amplification or mutation, we explored whether neutralization of BCL-2/XL via ABT-263/Navitoclax would enhance the effectiveness of 414. Here, we evaluated 414+263 in a panel of seven EGFR-expressing patient-derived xenograft (PDX) models of TNBC. Tumor-bearing mice were randomized into one of two groups, either 414+263 or placebos. Tumor volumes were calculated via caliper-based measurements pre- and post-treatment. 14 days post-treatment, tumor growth inhibition was observed in five out of seven combination-treated tumor models; however, consistent tumor regressions were only observed in one of these models (HCI-010). Compared to the other PDX models, HCI-010 tumors were distinguished by EGFR1 low polysomy and the highest EGFR expression levels. To further explore combined treatment within HCI-010, we evaluated single-agents. To determine EGFR relevance, we also included a non-tumor targeted ADC (095-MMAF) as a single agent or in combination with 263. Tumor growth inhibition & regressions were observed in either 263 or 414+263 treated tumors. These responses were most significant under combined treatment conditions (avg. regression=40%). Tumor growth was unaffected by 414 or 095-MMAF single agents. Tumors treated with 095-MMAF+263 were comparable to single agent 263. Based upon these results, we considered an alternative EGFR-targeted ADC (321). 321, comprised of an affinity-matured version of 806 conjugated to the powerful cytotoxic PBD, exhibits enhanced EGFR affinities and has demonstrated notable effectiveness within EGFR-overexpressing tumors. To evaluate 321 combined treatment within HCI-010, tumor-bearing mice were randomized into six groups: placebos; 263; 321; 263+321; 095-PBD; 263+095-PBD. Tumor growth inhibition & tumor regressions were maintained under 263 and, unlike 414, also observed under 321 treatments. 321 resulted in dramatic tumor regressions (avg. regression=66%). Notably, 263 enhanced the effectiveness of 321 as evidenced by even more dramatic and near complete tumor regressions (avg. regression=88%). We extended these studies to include HCI-025, an additional PDX characterized by EGFR1 low polysomy and EGFR expression levels comparable to HCI-010. To evaluate 321 combined treatment within HCI-025; we performed a similar six-group study. HCI-025 tumors were also sensitive to single agent 321 (avg. regression=36%). Similar to HCI-010 and as evidenced by dramatic tumor regressions, 263 also enhanced the effectiveness of 321 within HCI-025 (avg. regression=68%). 095-PBD and 263+095-PBD also resulted in HCI-010 and HCI-025 tumor growth inhibition & regressions; however supportive of EGFR-mediated effects, 321 responses were greater than 095-PBD and 263+321 responses were greater than 263+095-PBD. These results underscore the significant potential of BCL-2/XL-inhibitors to enhance the effectiveness of cytotoxic agents delivered via ADCs. Notably, this strategy avoids the toxicities associated with systemic chemotherapy and BCL-2/XL-inhibitors. These results also highlight the translational relevance of 321+263, within the context of EGFR-expressing TNBC.

Citation Format: Jason J Zoeller, Aleksandr Vagodny, Veerle W. Daniels, Krishan Taneja, Benjamin Y. Tan, Yoko S. DeRose, Maihi Fujita, Alana L. Welm, Anthony Letai, Joel D. Leverson, Vincent Blot, Roderick T. Bronson, Deborah A. Dillon, Joan S. Brugge. Pre-clinical assessment of combined ABT-263/Navitoclax and ABT-414 or ABBV-321 treatment for EGFR-expressing TNBC [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-11-06.

Abstract P5-02-03: Highly multiplexed tissue-based cyclic immunofluorescence in breast cancer for precision oncology

Background: Tissue-based cyclic immunofluorescence (t-CyCIF) is a recently described technique for highly multiplexed immunofluorescence microscopy of formalin-fixed, paraffin-embedded (FFPE) specimens. Via an iterative process, successive four-channel images are collected from the same sample and then registered to each other to generate a high-dimensional representation that is used for visualization and analysis. This technique can be used to capture up to 60 different antigens on a single FFPE tumor section and permits quantification of cell lineage and state markers, intracellular signaling proteins, drug targets and immune cell antigens, thereby promoting biomarker discovery efforts that are fundamental to precision oncology. As with most technologies that utilize immunostaining, proper antibody validation is key to reliable performance. In this study we used t-CyCIF to evaluate multiple antibodies directed against proteins commonly used to characterize breast carcinomas and their associated microenvironment. Our goal was to validate these antibodies on the t-CyCIF platform prior to the more widespread use of this technology to propel novel discoveries on breast cancer initiation, progression and treatment.

Methods: To choose the optimal antibody candidate for each biomarker in t-CyCIF, we compared multiple fluorophore-conjugated antibodies for each of the following three proteins routinely evaluated in breast carcinomas: estrogen receptor (ER), progesterone receptor (PR) and HER2. For each of these, a single antibody commonly used in clinical practice was used as a reference. Analyses were performed at the level of pixels, cells and tissue cores. In addition, inter-assay analyses were performed comparing: (1) t-CyCIF vs. immunohistochemistry (IHC), the latter assessed both by digital pathology and by two independent pathologists; and (2) t-CyCIF vs. fluorescence in situ hybridization (FISH) for HER2. Following validation of these antibodies, we evaluated the expression of CD45, CD68, PD-L1, p53, Ki67 and androgen receptor along with ER, PR and HER2, to better understand both the tumor microenvironment and the cell identities/states in breast carcinomas.

Results: A total of 948 tissue cores were included in the study. In the first phase, 13 different antibodies were analyzed: three raised against ER and five each against PR and HER2. The pixel-to-pixel evaluation resulted in r scores using Pearson correlation equal to 0.86 for both ER markers tested; ranging from 0.88 to 0.93 for PR; and from 0.56 to 0.94 for HER2. The correlation scores in single-cell comparisons ranged from 0.76 to 0.88 for ER, 0.54 to 0.81 for PR, and from 0.56 to 0.76 for HER2. Comparisons were then performed at the tissue core level. In light of the data generated through these multiple levels of analyses, we identified fluorophore-conjugated candidates for use in t-CyCIF. Correlation scores on the tissue core level were high in the inter-assay analyses, i.e. t-CyCIF vs. IHC (e.g. r scores up to 0.91 for HER2 on t-CyCIF vs. IHC) and t-CyCIF vs. HER2 FISH (r scores up to 0.71). In the second phase, we characterized the tumor microenvironment and cell identities present in 260 breast carcinomas. With a qualified panel of antibodies, we performed single-cell analyses of 589,343 cells and identified unexpected patterns of PD-L1 expression in distinct populations of tumor cells.

Conclusion: This study is the first to evaluate the performance of breast cancer-specific antibodies in a highly multiplexed imaging platform such as t-CyCIF. This work demonstrates a step-by-step approach for qualifying reagents to be used in a multiplexed, spatially resolved tissue imaging modality. This validation study will facilitate the use of t-CyCIF for additional studies in breast cancer to evaluate both tumor elements and components of the microenvironment.

Citation Format: Ricardo G Pastorello, Jia-Ren Lin, Ziming Du, Shaolin Mei, Krishan Taneja, Deborah A Dillon, Stuart J Schnitt, Peter K Sorger, Elizabeth A Mittendorf, Sandro Santagata, Jennifer L Guerriero. Highly multiplexed tissue-based cyclic immunofluorescence in breast cancer for precision oncology [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-02-03.

Loss of SMAD4 protein expression in gastrointestinal and extra-gastrointestinal carcinomas

AIMS

SMAD4 (DPC4) is a tumour suppressor gene that is dysregulated in various tumour types, particularly pancreaticobiliary and gastrointestinal carcinomas. Corresponding loss of protein expression has been reported in approximately 50% of pancreatic and 25% of colonic adenocarcinomas. In the evaluation of carcinoma of unknown primary site, immunohistochemical loss of SMAD4 expression is often used to suggest pancreaticobiliary origin, but there are limited data on the spectrum of SMAD4 expression in carcinomas of other sites. This study evaluates the frequency of SMAD4 loss in a large cohort of carcinomas from diverse anatomical sites.

METHODS AND RESULTS

Immunohistochemistry for SMAD4 was performed on tissue microarrays or whole tissue sections of 1210 carcinomas from various organs: gastrointestinal tract, liver, pancreas/biliary tract, lung, breast, thyroid, kidney, ovary and uterus. Expression was considered lost when there was complete absence of staining in tumour cell nuclei, in the presence of intact staining in non-neoplastic cells. SMAD4 loss was seen in 58% of pancreatic adenocarcinomas, 27% of appendiceal adenocarcinomas, 19% of colorectal adenocarcinomas, 16% of cholangiocarcinomas, 10% of lung adenocarcinomas and <5% of oesophageal, breast, gastric and mucinous ovarian adenocarcinomas. All papillary thyroid, hepatocellular, non-mucinous ovarian, endometrial and renal cell carcinomas showed intact SMAD4 nuclear expression.

CONCLUSION

In addition to pancreaticobiliary, appendiceal and colonic tumours, SMAD4 loss is also seen in a small subset of other carcinomas, specifically breast, lung, oesophageal and gastric adenocarcinomas, all of which are typically CK7-positive, similar to pancreaticobiliary carcinoma. Awareness of SMAD4 loss in these other carcinoma types is helpful in the evaluation of carcinomas of unknown or uncertain primary site.

Neutralization of BCL-2/XL Enhances the Cytotoxicity of T-DM1 In Vivo

One of the most recent advances in the treatment of HER2+ breast cancer is the development of the antibody-drug conjugate, T-DM1. T-DM1 has proven clinical benefits for patients with advanced and/or metastatic breast cancer who have progressed on prior HER2-targeted therapies. However, T-DM1 resistance ultimately occurs and represents a major obstacle in the effective treatment of this disease. Because anti-apoptotic BCL-2 family proteins can affect the threshold for induction of apoptosis and thus limit the effectiveness of the chemotherapeutic payload, we examined whether inhibition of BCL-2/XL would enhance the efficacy of T-DM1 in five HER2-expressing patient-derived breast cancer xenograft models. Inhibition of BCL-2/XL via navitoclax/ABT-263 significantly enhanced the cytotoxicity of T-DM1 in two of three models derived from advanced and treatment-exposed metastatic breast tumors. No additive effects of combined treatment were observed in the third metastatic tumor model, which was highly sensitive to T-DM1, as well as a primary treatment-exposed tumor, which was refractory to T-DM1. A fifth model, derived from a treatment naïve primary breast tumor, was sensitive to T-DM1 but markedly benefited from combination treatment. Notably, both PDXs that were highly responsive to the combination therapy expressed low HER2 protein levels and lacked ERBB2 amplification, suggesting that BCL-2/XL inhibition can enhance sensitivity of tumors with low HER2 expression. Toxicities associated with combined treatments were significantly ameliorated with intermittent ABT-263 dosing. Taken together, these studies provide evidence that T-DM1 cytotoxicity could be significantly enhanced via BCL-2/XL blockade and support clinical investigation of this combination beyond ERBB2-amplified and/or HER2-overexpressed tumors.

Seven-Year Follow-Up Analysis of Adjuvant Paclitaxel and Trastuzumab Trial for Node-Negative, Human Epidermal Growth Factor Receptor 2-Positive Breast Cancer

PURPOSE

The Adjuvant Paclitaxel and Trastuzumab trial was designed to address treatment of patients with small human epidermal growth factor receptor 2 (HER2)-positive breast cancer. The primary analysis of the Adjuvant Paclitaxel and Trastuzumab trial demonstrated a 3-year disease-free survival (DFS) of 98.7%. In this planned secondary analysis, we report longer-term outcomes and exploratory results to characterize the biology of small HER2-positive tumors and genetic factors that may predispose to paclitaxel-induced peripheral neuropathy (TIPN).

PATIENTS AND METHODS

In this phase II study, patients with HER2-positive breast cancer with tumors 3 cm or smaller and negative nodes received paclitaxel (80 mg/m²) with trastuzumab for 12 weeks, followed by trastuzumab for 9 months. The primary end point was DFS. Recurrence-free interval (RFI), breast cancer-specific survival, and overall survival (OS) were also analyzed. In an exploratory analysis, intrinsic subtyping by PAM50 (Prosigna) and calculation of the risk of recurrence score were performed on the nCounter analysis system on archival tissue. Genotyping was performed to investigate TIPN.

RESULTS

A total of 410 patients were enrolled from October 2007 to September 2010. After a median follow-up of 6.5 years, there were 23 DFS events. The 7-year DFS was 93% (95% CI, 90.4 to 96.2) with four (1.0%) distant recurrences, 7-year OS was 95% (95% CI, 92.4 to 97.7), and 7-year RFI was 97.5% (95% CI, 95.9 to 99.1). PAM50 analyses (n = 278) showed that most tumors were HER2-enriched (66%), followed by luminal B (14%), luminal A (13%), and basal-like (8%). Genotyping (n = 230) identified one single-nucleotide polymorphism, rs3012437, associated with an increased risk of TIPN in patients with grade 2 or greater TIPN (10.4%).

CONCLUSION

With longer follow-up, adjuvant paclitaxel and trastuzumab is associated with excellent long-term outcomes. Distribution of PAM50 intrinsic subtypes in small HER2-positive tumors is similar to that previously reported for larger tumors.

Abstract PD9-01: Genomic alterations associated with loss of HR expression in metastatic breast cancer

Background: Discordance in hormone receptor (HR) status between primary (p) tumors and metastatic (m) recurrences has been widely described. Loss of estrogen and progesterone receptor expression occurs in ˜12% of asynchronous recurrences, leading to triple-negative (TN) status in the metastasis. Genomic mechanisms driving HR loss and its prognostic and therapeutic implications have not been fully elucidated.

Methods: Targeted NGS (Oncopanel, OP) at Dana-Farber Cancer Institute using multiplexed copy number variation and mutation (mut) detection across the full coding regions of 300 genes and selected intronic regions of 35 genes was prospectively performed on either archival primary or metastatic samples collected in patients (pts) with metastatic breast cancer (MBC). Receptor status at initial diagnosis and recurrence were reviewed using a 1% cutoff to define HR-positivity and excluding HER2+ cases. Fisher´s exact test was used to compare frequency of alterations. Tumor mut burden (TMB) was computed normalizing the sum of reported exon mut in each pt by the exonic-bait-set size of the panel.

Results: Between 8/2013-9/2016, 929 pts with MBC underwent OP testing. Of 517 pts diagnosed with primary HR+/HER2- breast cancer, at time of recurrence 388 remained HR+/HER2- (pHR+/mHR+), 39 switched to HR-/HER2- (pHR+/mTN, of which 23 (59%) had initial HR expression &gt;10%), 10 switched to HER2+ and 80 had unknown metastatic receptor status. Comparison between primary samples in pHR+/mHR+ (n=245) and pHR+/mTN (n=24) showed that pHR+/mTN was significantly more likely to harbor mut in TP53, STK11 and MSH6, amplifications (amp) in CCNE1 and FGFR2, and less likely to have PIK3CA mut or CCND1 amp. Median TMB in primary pHR+/mHR+ was 6.05 mut/Mb (0-37.5) and 5.68 mut/Mb (1.2-10.9) in pHR+/mTN (p=0.45). Metastatic samples in pHR+/mTN (n=15) were enriched in ARID1A, CRTC2 and CDH1 mut compared to metastases (n=40) in pts who remained TN (pTN/mTN). Deletions in CDKN2A/2B and RB1, and mut in TP53, NOTCH2 and ERCC2 were more prevalent in recurrent tumors of pHR+/mTN than pHR+/mHR+. In metastases, TMB was higher in pHR+/mTN than pTN/mTN or pHR+/mHR+ (10.9 vs. 7.0 vs. 7.3 mut/Mb, respectively; p=0.002). Median OS from initial diagnosis was 9.4 yrs in pHR+/mTN, less than pHR+/mHR+ (15.9 yrs; p=0.009) and greater than pTN/mTN (4.3 yrs; p=0.008). Median OS from MBC diagnosis was 1.8 yrs in pHR+/mTN, less than pHR+/mHR+ (6.4 yrs; p=0.001) but not significantly different than pTN/mTN (1.5 yrs, p=0.3).

 pHR+/mHR+ (n=245)pHR+/mTN (n=24)p value NFreq (%)NFreq (%) MutTP536325.72083.3&lt;0.00001PIK3CA9438.4000GATA33514.3000.053STK1152.0312.50.026MSH641.6312.50.017AmpFGFR20028.30.008CCNE10028.30.008CCND14418.0000.018

Conclusion: Targeted NGS shows that alterations in DNA damage and cell-cycle regulation pathways in primary HR+ tumors are associated with HR loss in the metastatic setting. Primary tumors that lose HR appear more similar to basal-like than luminal tumors, despite &gt;10% baseline HR expression in most pts, and once metastatic, survival is comparable to pTN/mTN. Metastases with HR loss have higher TMB than those that remain HR+ or TN throughout the course of the disease. These findings, if confirmed, may influence treatment and pt selection for clinical trials.

Citation Format: Garrido-Castro AC, Hughes ME, Cherniack A, Barroso-Sousa R, Bychkovsky BL, Di Lascio S, Berger A, Mittendorf EA, Files JL, Guo H, Kumari P, Cerami E, Krop IE, Wagle N, Lindeman NI, MacConaill LE, Dillon DA, Winer EP, Lin NU. Genomic alterations associated with loss of HR expression in metastatic breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-01.

Abstract P4-04-02: Identifying ERBB-2 activating mutations (mts) in HER2 negative tumors for clinical trials – Impact of institute-wide genomic testing and trial matching on trial enrollment in clinical practice

Introduction

Tailored treatment trials with biomarker-driven hypotheses are becoming an important strategy in drug development. Umbrella, basket and enrichment trials with eligibility predicated upon results of tumor sequencing are increasingly common. Several institutional and commercial genomic assays have been developed. However, the value of broad-based testing in recruiting patients (pts) to molecular-based clinical trials designed for small subgroups has not been fully evaluated and has been challenging to assess in a real-world setting. We evaluated the likelihood of trial enrollment based upon an institute-wide genomic test.

Methods

Since 2013, all pts with metastatic breast cancer (MBC) seen at least once at Dana-Farber Cancer Institute have been offered the option of tumor sequencing using multiplexed copy number variation (CNV) and mts detection across the full coding regions of a total of 447 cancer genes and 191 regions across 60 genes for rearrangement detection (Oncopanel; OP). For our primary analysis, we selected the ongoing multi-center phase II trial (NCT01670877) activated at our site on Sep 30, 2013, evaluating neratinib in ERBB-2 mutated pts, as the study provided a clear delineation of eligible mts, and timing of slot availability was retrievable retrospectively over an extended time frame. Our primary aim was to describe the proportion of pts with a qualifying ERBB-2 mt detected by OP who enrolled on the selected trial. Secondary objectives included median time from OP result to trial registration and description of ERBB-2 mts spectrum within each subtype. Associations were calculated by Fisher's test.

Results

We identified a total of 1,046 pts with HER-2 negative MBC and who had OP results between Sep 1, 2013 and Jun 1, 2017. A total of 43 pts (4.1%) were found to have ERBB-2 mts. Of these, 20 (1.9%) had activating eligible mts. The proportion of these pts who enrolled in the trial was 30% (6/20). Of the remaining 14 pts, 5 screen-failed and 2 were enrolled with known ERBB-2 mt through other testing modalities. Seven of 20 (35%) molecularly eligible pts were not approached (3 pts lost to follow-up, 3 enrolled in other clinical trials and 1 pt chose standard treatment). The median time from OP result to trial enrollment was 85 days (34-554). A significantly higher frequency of ERBB2 activating mts was found in ER+ compared to ER- primary tumors (2.5% vs. 0.3%, p =0.036), and in lobular tumors compared with ductal (5.5% vs. 1.25%, p=0.003). Frequency of eligible mts in primary tumors were similar to metastatic site (1.9% and 1.8%, respectively p=1.0)

Discussion

In this cohort, activating ERBB-2 mts were present in 20 of 1046 (1.9%) pts tested. Although over half of pts with eligible mts on OP testing were approached for NCT01670877, only 0.5% of the total tested population were enrolled (6/1046). Our data illustrate the substantial challenges in screening and enrolling to trials of rare subsets, even within a large academic institution, and point to the need for creative and novel approaches to leverage pts and community- and academic-based providers to more effectively support the success of such studies.

Citation Format: Exman P, Garrido-Castro A, Hughes ME, Freedman RA, Ma C, Bose R, Cerami E, Wagle N, Barroso-Sousa R, Fitz CD, Lindeman NI, MacConaill L, Bychkovsky BL, Lloyd MR, Mackichan CR, Kumari P, Tolaney SM, Krop IE, Winer EP, Dillon DA, Lin NU. Identifying ERBB-2 activating mutations (mts) in HER2 negative tumors for clinical trials – Impact of institute-wide genomic testing and trial matching on trial enrollment in clinical practice [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-04-02.

Mixed Invasive Ductal and Lobular Carcinoma of the Breast: Prognosis and the Importance of Histologic Grade

BACKGROUND

The diagnosis of mixed invasive ductal and lobular carcinoma (IDC-L) in clinical practice is often associated with uncertainty related to its prognosis and response to systemic therapies. With the increasing recognition of invasive lobular carcinoma (ILC) as a distinct disease subtype, questions surrounding IDC-L become even more relevant. In this study, we took advantage of a detailed clinical database to compare IDC-L and ILC regarding clinicopathologic and treatment characteristics, prognostic power of histologic grade, and survival outcomes.

MATERIALS AND METHODS

In this retrospective cohort study, we identified 811 patients diagnosed with early-stage breast cancer with IDC-L or ILC. Descriptive statistics were performed to compare baseline clinicopathologic characteristics and treatments. Survival rates were subsequently analyzed using the Kaplan-Meier method and compared using the Cox proportional hazards model.

RESULTS

Patients with ILC had more commonly multifocal disease, low to intermediate histologic grade, and HER2-negative disease. Histologic grade was prognostic for patients with IDC-L but had no significant discriminatory power in patients with ILC. Among postmenopausal women, those with IDC-L had significantly better outcomes when compared with those with ILC: disease-free survival (DFS) and overall survival (OS; adjusted hazard ratio [HR], 0.54; 95% confidence interval [CI] 0.31-0.95). Finally, postmenopausal women treated with an aromatase inhibitor had more favorable DFS and OS than those treated with tamoxifen only (OS adjusted HR, 0.50; 95% CI, 0.29-0.87), which was similar for both histologic types (p = .212).

CONCLUSION

IDC-L tumors have a better prognosis than ILC tumors, particularly among postmenopausal women. Histologic grade is an important prognostic factor in IDC-L but not in ILC.

IMPLICATIONS FOR PRACTICE

This study compared mixed invasive ductal and lobular carcinoma (IDC-L) with invasive lobular carcinomas (ILCs) to assess the overall prognosis, the prognostic role of histologic grade, and response to systemic therapy. It was found that patients with IDC-L tumors have a better prognosis than ILC, particularly among postmenopausal women, which may impact follow-up strategies. Moreover, although histologic grade failed to stratify the risk of ILC, it showed an important prognostic power in IDC-L, thus highlighting its clinical utility to guide treatment decisions of IDC-L. Finally, the disease-free survival advantage of adjuvant aromatase inhibitors over tamoxifen in ILC was consistent in IDC-L.

Abstract 4564: The immune microenvironment in hormone receptor-positive breast cancer and treatment outcome following preoperative chemotherapy plus bevacizumab

Background: Hormone receptor-positive (HR+) breast cancers (BC) have fewer tumor-infiltrating lymphocytes (TILs) and lower response rates to immune checkpoint inhibitors in early phase studies than other breast cancer subtypes. Immune biomarkers that accurately reflect the immune microenvironment have important clinical implications in HR+ BC patients. Prior evidence suggests that macrophage-related immune pathways may be relevant to the pathophysiology of HR+ BC.

Methods: Patients identified from a prospective trial of preoperative bevacizumab (preop bev) followed by bev with adriamycin/cyclophosphamide/paclitaxel dose-dense chemotherapy (chemo). Tumor samples were collected at diagnosis and surgery (pre-tx and post-tx). TILs and immunohistochemical staining for PD-L1, CD8, and CD68 were scored. Whole transcriptome sequencing (RNAseq) and Nanostring PanCancer Immune Profiling Panel were performed. Pathologic response at surgery was assessed by Miller-Payne (MP) and residual cancer burden (RCB) scores. An immune score was calculated for each pre-tx specimen by integrating 10 published immune signatures. Immune cell subsets were inferred from bulk transcriptional data using CIBERSORT.

Results: 55 patients had at least 1 evaluable specimen and were included for analysis. 18% of pre-tx tumors had ‘high' (≥10%) TILs and ‘high' TILs were associated with significantly higher immune signature score (p=0.004). Immune score correlated highly with proportion of CIBERSORT anti-tumor M1 macrophage and CD8 T-cell signatures (r&gt;0.65 and p&lt;0.001) and was significantly associated with RCB. Higher pre-tx TILs, tPD-L1, sPD-L1, CD8, and CD68 were associated with favorable RCB significantly associated with more favorable RCB after adjustment for tumor size and grade. Pathologic complete response occurred in 4 pts; all 4 had high pre-tx TILs, pre-tx tPD-L1, or both. Among patients with residual disease, there were significantly fewer TILs and CD8 cells after chemotherapy (Wilcoxon signed rank p=0.037 and p=0.002, respectively), however tPD-L1 and CD68 were not significantly different. Nanostring analyses demonstrated that chemokines and complement pathway components were among most significantly enriched post-tx relative to pre-tx.

Conclusions: Most HR+/HER2- breast tumors demonstrate low levels of anti-tumor immune activity; however, those with higher levels have a more favorable response to chemo plus bev. Assessment of immune activity based on RNA signatures is consistent with histology and immune-related protein expression. T-cell- and checkpoint-related biomarkers tend to decrease following preoperative chemo plus bev in HR+/HER2- breast cancer. Following treatment with chemotherapy/bevacizumab, we observe increased expression of chemokines and complement pathway genes.

Citation Format: Adrienne G. Waks, Daniel G. Stover, William T. Barry, Deborah A. Dillon, Evisa Gjini, Scott J. Rodig, Jane E. Brock, Michele Baltay, Jennifer Savoie, Eric P. Winer, Ian E. Krop, Sara M. Tolaney. The immune microenvironment in hormone receptor-positive breast cancer and treatment outcome following preoperative chemotherapy plus bevacizumab [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4564.

Abstract 1611: High quality next generation sequencing results for breast cancer using dual-mode biopsy tissue preservation

Introduction: Formalin-fixed paraffin-embedded (FFPE) tissue is commonly used for molecular analysis, including for next generation sequencing (NGS). In an effort to improve the quality of molecular results in small tissue samples, we developed a novel biopsy transport device that splits the biopsy sample longitudinally for dual-mode preservation by freezing (for biomolecular analysis) and formalin (for the evaluation of histologic features without freezing artifact). In this feasibility study we compared NGS results from samples acquired by the new device with those obtained using standard biopsy handling procedures.

Methods: Following informed consent, biopsy samples were obtained ex-vivo by a breast imaging radiologist under ultrasound guidance from invasive cancers in two mastectomy specimens using a standard biopsy needle (Mission 14G, CR Bard). A reference sample (REF) was placed directly into 10% neutral buffered formalin. An experimental sample (EXP) was placed in the new device, ink marked on one end for orientation and sectioned longitudinally. After sectioning, one half-sample was formalin fixed and one half was frozen and then stored at -80 degrees until further processing. The REF samples and one half of the EXP samples were fixed for 24 hours then processed routinely into FFPE blocks. DNA was extracted from the REF sample and the frozen EXP half-sample and evaluated using NGS Oncopanel (targeted exome sequencing, Illumina) at 25ng, 50ng and 100ng input template.

Results: The formalin-fixed EXP halves maintained high quality of tissue histology with minimal artifacts. The number of unique, aligned, high-quality reads was on average 1.85-fold greater in the EXP specimens relative to the paired REF samples for all three template amounts in both tumors that were analyzed (range 1.58-fold to 2.29-fold; p=0.0016). More than twice as many high-quality reads were present in the EXP specimens for Tier 2 and Tier 3 mutations (TP53, PIK3CA and GATA3) at the lowest template amounts (average 2.40-fold at 25ng). Copy number reads showed lower cutoff scores (a measure of signal variability across segments) in EXP samples than in REF samples (p=0.0052).

Conclusions: Dual-mode preservation of core biopsy samples by freezing and formalin can be done with the new device and it provides equivalent quality of histology sections. Preservation of biopsy samples by freezing rather than formalin improved the quality of NGS evaluation in all samples down to 25ng input template, both for single variant analysis and for copy number detection. Longitudinal sectioning of the tissue samples allows for assessment of tumor purity and for macrodissection of the oriented frozen half-sample as needed. These improvements allow for greater confidence in variant and copy number calls with lower input template amounts.

Citation Format: Deborah A. Dillon, Elizabeth P. Garcia, Michele Baltay, Krishan Taneja, Teri Bowman, Eva C. Gombos, Tom Gal, Stuart G. Silverman, Erez Nevo, Shoshan Nevo. High quality next generation sequencing results for breast cancer using dual-mode biopsy tissue preservation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1611.

In Vitro Liquid Extraction Surface Analysis Mass Spectrometry (ivLESA-MS) for Direct Metabolic Analysis of Adherent Cells in Culture

Conventional metabolomic methods include extensive sample preparation steps and long analytical run times, increasing the likelihood of processing artifacts and limiting high throughput applications. We present here in vitro liquid extraction surface analysis mass spectrometry (ivLESA-MS), a variation on LESA-MS, performed directly on adherent cells grown in 96-well cell culture plates. To accomplish this, culture medium was aspirated immediately prior to analysis, and metabolites were extracted using LESA from the cell monolayer surface, followed by nano-electrospray ionization and MS analysis in negative ion mode. We applied this platform to characterize and compare lipidomic profiles of multiple breast cancer cell lines growing in culture (MCF-7, ZR-75-1, MDA-MB-453, and MDA-MB-231) and revealed distinct and reproducible lipidomic signatures between the cell lines. Additionally, we demonstrated time-dependent processing artifacts, underscoring the importance of immediate analysis. ivLESA-MS represents a rapid in vitro metabolomic method, which precludes the need for quenching, cell harvesting, sample preparation, and chromatography, significantly shortening preparation and analysis time while minimizing processing artifacts. This method could be further adapted to test drugs in vitro in a high throughput manner.

Recurrent EML4-NTRK3 fusions in infantile fibrosarcoma and congenital mesoblastic nephroma suggest a revised testing strategy

Infantile fibrosarcoma and congenital mesoblastic nephroma are tumors of infancy traditionally associated with the ETV6-NTRK3 gene fusion. However, a number of case reports have identified variant fusions in these tumors. In order to assess the frequency of variant NTRK3 fusions, and in particular whether the recently identified EML4-NTRK3 fusion is recurrent, 63 archival cases of infantile fibrosarcoma, congenital mesoblastic nephroma, mammary analog secretory carcinoma and secretory breast carcinoma (tumor types that are known to carry recurrent ETV6-NTRK3 fusions) were tested with NTRK3 break-apart FISH, EML4-NTRK3 dual fusion FISH, and targeted RNA sequencing. The EML4-NTRK3 fusion was identified in two cases of infantile fibrosarcoma (one of which was previously described), and in one case of congenital mesoblastic nephroma, demonstrating that the EML4-NTRK3 fusion is a recurrent genetic event in these related tumors. The growing spectrum of gene fusions associated with infantile fibrosarcoma and congenital mesoblastic nephroma along with the recent availability of targeted therapies directed toward inhibition of NTRK signaling argue for alternate testing strategies beyond ETV6 break-apart FISH. The use of either NTRK3 FISH or next-generation sequencing will expand the number of cases in which an oncogenic fusion is identified and facilitate optimal diagnosis and treatment for patients.

Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer

Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.

Abstract GS3-07: Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA

Introduction:

Triple-negative breast cancer (TNBC) is a poor prognosis breast cancer subset characterized by relatively few mutations but extensive copy number alterations (CNAs). Cell-free DNA (cfDNA) offers the potential to overcome infrequent tumor biopsies in metastatic TNBC (mTNBC) and interrogate the genomics of chemotherapy resistance.

Methods:

506 archival or fresh plasma samples were identified from 164 patients with mTNBC who had previously received chemotherapy. We performed low coverage whole genome sequencing to determine genome-wide copy number and estimate 'tumor fraction' of cfDNA (TFx) using our recently-developed approach, ichorCNA. In patient samples with TFx &gt;10%, we identified regions that were significantly gained or lost using GISTIC2.0. We compared CNAs of 20 paired primary-metastatic samples and also mTNBCs from cfDNA versus primary TNBCs from TCGA and METABRIC.

Results:

We successfully obtained high quality, low coverage whole genome sequencing data for 478 (94.5%) plasma samples from 158 patients, with 1 to 14 samples per patient. TFx and copy number profiles were highly concordant with paired metastatic biopsy (n=10, range 0-7 days from biopsy to blood draw) with sensitivity of 0.86 and specificity of 0.90 and reproducible in independently-processed blood draws (TFx intraclass correlation coefficient 0.984). Median overall survival from time of first blood draw was 8 months, and TFx was highly correlated independent of primary stage, primary receptor status, age at primary diagnosis, BRCA status, and metastatic line of therapy: adjusted hazard ratio between 4th and 1st quartiles = 2.14 (95% CI 1.40-3.28; p=0.00049). 101/158 patients (63.9%) had at least one sample with TFx &gt;10%, our threshold for high confidence CNA calls. Copy number profiles and percent genome altered were remarkably similar between mTNBCs and primary TNBCs in TCGA and METABRIC (n=433), suggesting that large-scale chromosomal events are infrequent in TNBC metastatic progression. We identified chromosomal gains that demonstrated significant enrichment in mTNBCs relative to paired primary TNBCs (n=20) and also TCGA/METABRIC, including driver genes (NOTCH2, AKT2, AKT3) and putative antibody-drug conjugate targets. Finally, we identify a novel association of gains of 18q11 and/or 19p13 with poor metastatic prognosis, independent of clinicopathologic factors and TFx.

Conclusions:

Here, we present the first large-scale genomic characterization of metastatic TNBC to our knowledge, derived exclusively from cfDNA. 'Tumor fraction' of cfDNA is an independent prognostic marker in mTNBC. Primary and metastatic TNBC have remarkably similar copy number profiles yet we identify alterations enriched and prognostic in mTNBC. Collectively, these data have potential implications in the understanding of metastasis, therapeutic resistance, and novel therapeutic targets.

Citation Format: Stover DG, Parsons HA, Ha G, Freeman S, Barry B, Guo H, Choudhury A, Gydush G, Reed S, Rhoades J, Rotem D, Hughes ME, Dillon DA, Partridge AH, Wagle N, Krop IE, Getz G, Golub TA, Love JC, Winer EP, Tolaney SM, Lin NU, Adalsteinsson VA. Genome-wide copy number analysis of chemotherapy-resistant metastatic triple-negative breast cancer from cell-free DNA [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS3-07.

Nipple-Invasive Primary Carcinomas: Clinical, Imaging, and Pathologic Features of Breast Carcinomas Originating in the Nipple

Context Patients choosing to retain the nipple when undergoing therapeutic or prophylactic mastectomy are at risk for cancers arising at that site. Objective To identify cases of invasive carcinoma arising within the nipple and to investigate their clinical, imaging, biologic, and staging features. Design Carcinomas were identified by prospective review of surgical and consult cases at 4 hospitals. Results The 24 patients identified presented with symptoms related to the nipple. Mammography did not detect the cancer in most cases. Ten patients (42%) had skin changes from ductal carcinoma in situ involving nipple skin (Paget disease), with small foci of invasion into the dermis, and 6 of those 10 carcinomas (60%) stained positive for human epidermal growth factor receptor 2 (HER2). The remaining 14 patients (58%) presented with a nipple mass or with skin changes. These were larger invasive carcinomas of both ductal and lobular types. Only 2 of those 14 carcinomas (14%) were HER2⁺. Three of 15 patients (20%) undergoing lymph node biopsy had a single metastasis. No patients have had recurrent disease. Conclusions Rare, invasive, primary nipple carcinomas typically present as subtle nipple thickening or an exudative crust on the skin. Imaging studies are often nonrevealing. A variety of histologic and biologic types of carcinomas occur, similar to cancers arising deeper in the breast. Although the carcinomas invaded into the dermis, some with skin ulceration, the likelihood of lymph node metastasis was no higher than carcinomas of similar sizes. Patients who choose to preserve their nipple(s) should be aware of the possibility of breast cancer arising at that site and to bring any observed changes to the attention of their health care providers.

An Update of Mucinous Lesions of the Breast

Mucinous lesions of the breast include a variety of benign and malignant epithelial processes that display intracytoplasmic or extracellular mucin, including mucocelelike lesions, mucinous carcinoma, solid papillary carcinoma, and other rare subtypes of mucin-producing carcinoma. The most important diagnostic challenge is the finding of free-floating or stromal mucin accumulations for which the significance depends on the clinical, radiologic, and pathologic context. This article emphasizes the differential diagnosis between mucocelelike lesions and mucinous carcinoma, with a brief consideration of potential mimics, such as biphasic and mesenchymal lesions with myxoid stroma ("stromal mucin") and foreign material.