Non-basal Subtypes Research Articles

Non-basal subtype defined by FOXC1 expression as an independent predictor of capecitabine efficacy in the triple negative breast cancer GEICAM/2003-11_CIBOMA/2004-01 trial.

516 Background: In a prespecified correlative analysis of the GEICAM/2003-11_CIBOMA/2004-01 phase III clinical trial (CIBOMA trial), PAM50 non-basal status identified triple-negative breast cancer (TNBC) patients (pts) most likely to benefit from adjuvant capecitabine (cap). FOXC1 cell plasticity/metastasis transcriptional driver assessment by standardized Veresca FOXC1 Immunohistochemistry (IHC) BC test (Veresca) has shown rigorous capacity to identify basal-like breast cancer (BLBC) subtype throughout TNBC cohorts. We sought to explore the concordance of BLBC identification by FOXC1 with PAM50 molecular subtyping and its prognostic/predictive value in the CIBOMA trial (NCT00130533). Methods: We analyzed FOXC1 expression (Veresca, Onconostic Technologies) and the Ki-67 Antigen MIB-1 (Dako) by IHC on tumors from 705 TNBC pts randomized to maintenance with cap (357, 51%) vs observation (obs) (348, 49%) after standard (neo)adjuvant chemotherapy (CT). Veresca score (VFOXC1) was defined as % of tumor cells with positive nuclear staining (Proportion Score 0-5) plus staining intensity (Intensity Score 0-3). BLBC subtyping by Veresca (cutoff ≥4) and PAM50 signature (Nanostring) were compared using ROC analysis and Kappa index (KI). Ki67 ≥20% cutoff was applied. Cox regression models were assessed to predict DRFS (primary endpoint), DFS and OS (secondary endpoints). Results: VFOXC1≥4 identified 460 (65%) BLBC pts in this CIBOMA trial cohort (229 (49.8%) treated with cap, and 231 (50.2%) in obs). VFOXC1 detection was not associated with any clinicopathological characteristic. VFOXC1 expression significantly correlated with PAM50 BLBC subtyping (ROC analysis AUC 0.874, KI 0.43) but moderately with IHC subtyping (AUC 0.548). VFOXC1 BLBC subtype was not associated with DRFS (HR=0.94; 95%CI 0.68-1.30; p=0.713) in the entire cohort. However, VFOXC1 non-BLBC subtype was a strong independent predictor of cap benefit for DRFS (univariate analysis, interaction p-value p=0.117; HR=0.53; 95%CI 0.31-0.90; p=0.019; multivariate analysis, HR=0.44; 95%CI 0.25–0.76; p=0.003). This predictive effect of VFOXC1 non-BLBC on cap benefit was also confirmed at DFS (HR=0.47; 95%CI 0.28–0.78; p=0.003) and OS (HR=0.48; 95%CI 0.24–0.96; p=0.038), and was independent of Ki67 proliferation status (multivariate DRFS; Ki67<20%, HR=0.41; 95%CI 0.20-0.82; p=0.012; Ki67≥20%, HR=0.31; 95%CI 0.10-0.97; p=0.045). VFOXC1 non-BLBC subtype had no association with clinical outcome in obs arm. Conclusions: In the CIBOMA TNBC trial, the non-BLBC definition by a single biomarker (FOXC1 Veresca) provided prognostic and predictive value of cap benefit after (neo)adjuvant CT, corroborating our previous findings by PAM50 and IHC non-BLBC subtyping. This is a pragmatic option to effectively apply findings from this trial in the real-world setting. Clinical trial information: NCT00130533 .

Abstract PO5-24-03: Breast cancer intrinsic subtypes predict outcomes in primary and metastatic samples

Abstract Background: The prognostic and predictive value of the PAM50 intrinsic subtypes, namely Luminal A, Luminal B, Her2, and Basal-like subtypes, is well-studied in primary as well as metastatic breast cancer settings. Prosigna has emerged as a rapid PAM50 subtype predictor based on the NanoString nCounter assay. However, assay reproducibility across various RNASeq or qRT-PCR platforms can be challenging, especially when applying the predictor on metastatic breast cancer tumors. Here, we used SpinAdapt to create an intrinsic subtype predictor that works on RNA sequencing data, and validates on multiple tumor-sites. We evaluate real-world outcomes for our intrinsic subtype predictions across various immunohistochemical (IHC) labels and metastatic sites. Methods: We trained the subtype predictor on a cohort of 2,497 breast cancer patients using the PAM50 genes, profiled using Nanostring RNA nCounter assay (GSE148426). Approximately 5,423 de-identified records of breast cancer patients sequenced using whole-exome capture RNA-seq were included in our reference dataset. The reference dataset contained samples collected from various sites including breast (n=2440), liver (n=936), lymph node (n=577), lung (n=540), and bone (n=304). For subtype classification, we first batch-corrected the external dataset to Tempus RNA-seq reference dataset using SpinAdapt, then trained a Support-Vector Classifier (SVC) on the corrected data. A 10-fold CV experiment was performed on the corrected dataset to analytically validate the intrinsic subtype predictions. We retrospectively analyzed 7,021 de-identified breast cancer patients with known hormone receptor (HR) or HER2 status and a matched RNASeq sample. The concordance between HR/HER2 status and PAM50 prediction was analyzed, and these patients were excluded from training. Real-world overall survival (rwOS) was evaluated from the time of first diagnosis. The outcomes across intrinsic subtypes were further assessed according to tumor collection site and HR/HER2 IHC status. Results: The 10-fold CV experiment on the Tempus-adapted GSE148426 dataset achieved F-1 scores of 0.97, 0.86, 0.94, and 0.87 on Basal, HER2-like, Luminal A, and Luminal B PAM50 subtypes, respectively. On the Tempus evaluation dataset, 85.3% of HR+/HER2- patients (n=4,366), 65.4% of HR-/HER2+ patients (n=240), and 75.4% of HR-/HER2- patients (n=1,930) were classified as Luminal, HER2-like, and Basal, respectively. Evaluating outcomes on Tempus patients for each PAM50 group, the rwOS for the basal group was significantly shorter than patients not predicted to be basal (n=5,845, p< 2e-90). The rwOS for the predicted PAM50 basal patients remained significantly shorter than non-basal patients even when stratified by site of metastasis: breast (n=2,405; p< 1e-27), lymph node (n=577, p< 1e-7), liver (n=936; p< 1e-25), lung (n=540, p< 1e-13), and bone (n=304, p< 1e-3). Interestingly, within both HR+/HER2- (n=3,653) and HR-/HER2- (n=1,664) IHC cohorts with available outcomes data, the predicted PAM50 basal subtype could further stratify each of these populations with basal-subtype showing significantly worse prognosis than the non-basal subtype (p< 1e-27 and p< 1e-7, respectively). Conclusions: We retrospectively analyzed Tempus multimodal RWD to validate an in-house breast intrinsic subtype predictor that is agnostic to the site of metastasis. The prognostic value of the basal subtype was significant for breast cancer patients across various sites of metastasis including lymph node, liver, lung, and bones and IHC groups. For patients in each of the HR+/HER2- and triple negative IHC groups, the intrinsic molecular subtypes provided an additional level of prognostic detail with statistical significance. These data emphasize the importance of combining molecular subtypes with IHC-based diagnostics to fully characterize clinically relevant subpopulations and risk. Citation Format: Talal Ahmed, Mark Carty, Kaveri Nadhamuni, Raphael Pelossof. Breast cancer intrinsic subtypes predict outcomes in primary and metastatic samples [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-24-03.

Prognostic Value Of Basal Markers (Epidermal Growth Factor Receptor "EGFR" And Cytokeratin 5/6) Expression In Triple-Negative Invasive Breast Cancer.

The To distinguish between basal and non-basal subtypes of triple-negative breast cancers based on epidermal growth factor receptor and cytokeratin 5/6, and to establish the association of the diagnosis with clinicopathological parameters and survival rates. The retrospective study was conducted at the Clinical Oncology and Nuclear Medicine Department of Kafrelsheikh University Hospital and Tanta University Hospital, Egypt, and comprised medical records from January 2014 to December 2018 related to cases with histopathologically proven triple-negative breast cancer who had been treated and followed up for at least 5 years. The cases had been evaluated using immunohistochemistry for epidermal growth factor receptor and Cytokeratin 5/6 expression. Data related to prognostic factors, overallsurvival and disease free survival was retrieved. Data was analysed using SPSS 21. There were 100 patients with median age 50 years (inter-quartile range: 35-55.25 years; range: 22-69 years). There were 58(58%) pre-menopausal subjects, 15(15%) had positive family history, and 68(68%) had tumour size T2. Basal markers were noted in 74(74%) patients. Basal subtype was significantly more common in patients aged <50 years at diagnosis, premenopausal women, patients with positive nodal status, those with grade III tumours, and patients with Ki67 proliferation marker >20% (p<0.05). Tumour size, histological subtypes and lympho-vascular invasion were not significantly different between the groups (p>0.05). The basal subtype had worse disease-free survival and overall survival rates (p<0.05). Triple-negative breast cancer patients who expressed epidermal growth factor receptor and/or cytokeratin 5/6 were found to have poor findings, with worse disease-free survival and overall survival.

Abstract 5271: Correlative analysis of RNA biomarkers for adjuvant capecitabine benefit in the CIBOMA/2004-01phase III clinical trial of triple negative breast cancer patients

Abstract Introduction: Predictive biomarkers for capecitabine benefit in triple negative breast cancer (TNBC) have been recently identified using samples from phase III clinical trials, including immunohistochemical (IHC) non-basal phenotype and RNA biomarkers related to angiogenesis, stroma and capecitabine activation genes. We aimed to validate these findings on the larger phase III CIBOMA clinical trial. Experimental Design: Tumor tissues from TNBC patients randomized to standard (neo)adjuvant chemotherapy with capecitabine vs. observation were analyzed using a 164 gene NanoString custom nCounter codeset. A prespecified statistical plan sought to verify the predictive capacity of PAM50 non-basal molecular subtype previously found by IHC, and tested the hypotheses that breast tumors with increased expression of (meta)genes for cytotoxic T cells, mast cells, endothelial cells, PDL2 and 38 individual genes benefit from adjuvant capecitabine for distant recurrence free survival (DRFS, primary endpoint) and overall survival. Exploratory analyses investigated (a) predictive capacity of categorical expression of biomarkers, and continuous expression of additional genes included in the codeset; (b) the prognostic capacity of continuous biomarker expression. Results: Of the 876 women enrolled in the CIBOMA trial, 658 (75%) were evaluable for analysis (337 with capecitabine and 321 without) with similar baseline characteristics relative to the intention-to-treat population. 553 (84%) cases were profiled as PAM50 basal-like while 105 (16%) were PAM50 non-basal. PAM50 non-basal subtype was the most significant predictor for capecitabine benefit (HRcapecitabine=0.19; 95%CI, 0.07-0.54; p=0&amp;lt;0.001) when compared to PAM50 basal-like (HRcapecitabine=0.9; 95%CI, 0.63-1.28; p=0.55) (p-interaction&amp;lt;0.001, adjusted p-value=0.01). Analysis of biological processes related to PAM50 non-basal subtype revealed its enrichment for mast cells, extracellular matrix, angiogenesis and features of the mesenchymal stem-like TNBC subtype. Multivariate analysis showed a significantly lower DRFS on the observation arm for the mast cell metagene (HRobservation=1.35; 95%CI, 1.12-1.62; p=0.002, adjusted p-value=0.006), particularly among PAM50 non-basal tumors (HRobservation=2.70; 95%CI, 0.99-7.35; p=0.01, p-interaction=0.08). Tumors above the median for genes involved in immune response (PDL2, CCR5), capecitabine metabolism (CES1) and angiogenesis (STC1) were significantly associated with favorable survival rates on the capecitabine arm (HRcapecitabine ranged between 0.51-0.60; p=0&amp;lt;0.05). Conclusions: In this prespecified correlative analysis of the CIBOMA trial, PAM50 non-basal status and the mast cell metagene identified early-stage TNBC patients most likely to benefit from adjuvant capecitabine. Citation Format: Karama Asleh, Ana Lluch, Angela Goytain, Carlos Barrios, Xue Q. Wang, Jesus Herranz, Dongxia Gao, Rosalia Caballero, Samuel Leung, Federico Rojo, Torsten O. Nielsen, Miguel Martin. Correlative analysis of RNA biomarkers for adjuvant capecitabine benefit in the CIBOMA/2004-01phase III clinical trial of triple negative breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5271.

Triple-negative breast cancer - a retrospective audit of 151 cases seen at the Charlotte Maxeke Johannesburg Academic Hospital Breast Unit

BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive, rapidly lethal subgroup of breast cancer which disproportionately affects women of African descent. Lacking hormone receptor expression and human epidermal growth factor receptor 2 (HER2) overexpression, it is difficult to treat. Despite an initial good response to chemotherapy, relapse is common and survival short. The aim of this study of treatment-naive women with TNBC was examination of clinicopathological characteristics and any association of these with patient demographics. METHODS: Demographic data was captured together with the clinical, pathological and histological features of the cancers. Statistical analysis was performed. RESULTS: Of the 960 patients entered in the database of the Charlotte Maxeke Johannesburg Academic Hospital (CMJAH) Breast Unit (BU) over a 3-year period, 151 (15.7%) had TNBC. All patients were female aged 25 to 98 years, and 60.3% were postmenopausal (mean age 64 years). The majority (80.2%) self-identified as black African. Most patients had clinical stage 3 disease, and 17.2% had distant metastases. One hundred women were HIV negative, 35 positive and 20 untested. Tumour biology revealed high-grade morphology in 70% of cases with a mean Ki-67 value of 60%. Forty patients died within 18 months of entry in the database. CONCLUSION: In this series, most patients with TNBC were older, postmenopausal women. This patient cohort may represent a non-basal subtype of TNBC but gene expression profiling was not available. Tumours were locally advanced, rapidly proliferative but not associated with HIV status. The short survival times emphasise the importance of neoadjuvant chemotherapy as soon as the diagnosis of TNBC is made.

Alpha-crystallin B chains enhance cell migration in basal-like 2 triple-negative breast cancer cells.

Triple-negative breast cancer (TNBC) can be divided into six subtypes. Among these subtypes, the basal-like 2 (BL2) subtype shows the lowest five-year survival rate and highest risk of metastasis. Alpha-crystallin B chains (αB-crystallin), a small heat shock protein that is known to be involved in breast cancer metastasis, is highly expressed in the basal-like subtype but not in the other non-basal subtypes. Thus, we hypothesized that αB-crystallin may be an important factor involved in the worse prognosis of the BL2 subtype compared with those of the other TNBC subtypes. Here, we examined the role of αB-crystallin in cell motility in two TNBC cell lines: HCC1806 (BL2 subtype) and, as control, MDA-MB-436 (mesenchymal stem-like subtype). HCC1806 showed greater cell migration capacity and a higher expression level of the gene encoding αB-crystallin (CRYAB) than did MDA-MB-436. Short interfering RNA-mediated silencing of CRYAB expression significantly reduced the cell migration capacity of HCC1806 cells, whereas it had no effect in MDA-MB-436 cells, indicating that αB-crystallin is essential for the migration of HCC1806 cells. Thus, high αB-crystallin expression may be a contributing factor to the poor prognosis of BL2 TNBC.

Mutant Phenotype p53 Immunohistochemical Expression Is Associated With Poor Prognostic Parameters and Disease-Free Survival in Triple-Negative Metaplastic Breast Carcinoma.

IntroductionMetaplastic breast carcinoma (MBC) is a special type of breast cancer that is most commonly triple-negative and has the worst outcome compared to other breast tumors. p53 is a tumor suppressor gene that is frequently mutated in many human cancers. The association of mutant p53 immunohistochemical expression with clinical and prognostic parameters has not been widely studied in triple-negative MBC. Therefore, in this study, we evaluated the expression patterns of p53 in triple-negative MBC and its association with clinical and prognostic parameters.MethodsA retrospective observational study was conducted in the Department of Histopathology at Liaquat National Hospital and Medical College, Pakistan, for a duration of 11 years. A total of 101 cases of triple-negative MBCs were included in the study. p53 immunohistochemistry was performed on the representative tissue blocks. Cases with diffuse strong positive p53 expression were labeled mutant phenotype, while cases with weak patchy p53 expression were termed wild-type.ResultsThe mean age of the patients was 48.33±11.47 years, and the mean tumor size was 3.98±2.07 cm. The mean Ki67 index was 48.98±22.97%. The median disease-free survival of the patients was 24 (three to 68) months, with a median follow-up of 37 (13 to 77) months. Most of the cases were tumor (T)-stage II (51.5%). Axillary metastasis was present in 36.6% of cases, with the perinodal extension in 16.8% of cases. Most cases were non-basal subtype (91.1%), and the majority of cases were grade III (85.1%). Recurrence was observed in 17.8% of cases. Among 101 cases, 52.5% cases showed mutant phenotype p53 expression. A significant association of p53 expression was noted with tumor grade, Ki67 index and disease-free survival. Cases with mutant phenotype p53 expression had a higher tumor grade, higher Ki67 index, and poorer disease-free survival than cases with wild-type p53 expression.ConclusionA substantial proportion of triple-negative MBC expressed diffuse strong expression (mutant phenotype) of p53 in our study, signifying a potential role of p53 as a therapeutic target in triple-negative MBC. Moreover, association of p53 with poor prognostic parameters, such as higher tumor grade and Ki67, and poor disease-free survival underscores the prognostic significance of p53 in triple-negative MBC.

Abstract PS4-12: Potential value of FOXA1 expression as genomic predictor of response to docetaxel and carboplatin neoadjuvant (NA) chemotherapy in patients with triple negative breast cancer (TNBC)

Abstract Background: TNBC is a particularly aggressive subtype with high recurrence rates and poor long-term survival. Anthracycline-free regimens based on docetaxel plus carboplatin (TCb) achieve around 50-55% pathologic complete responses (pCR) which correlates with better survival outcomes. Identification of genomic predictors of response is key to individualize therapies for this heterogeneous breast cancer (BC) subgroup. FOXA1 is a pioneer factor for androgen (AR) and estrogen receptors (ER). Its under-expression has been linked to cancer stemness in TNBC and better prognosis in ER-positive BC. The differential expression of AR, FOXA1 and BRCA1 is associated with sensitivity to chemotherapy in TNBC patients. Data support the plasticity role of FOXA1 driving basal to luminal BC cells by inducing luminal genes but also by repressing the basal phenotype and thus, tumor aggressiveness, although its role as a biomarker in TNBC is still controversial. We have analyzed RNAseq data of FOXA1 and AR in a series of TNBC tumors homogenously treated with neoadjuvant TCb to study their correlation with survival and response. Methodology: 300 TNBC patients have been included in a multicenter, prospective, non-randomized trial aimed to identify predictors of response to TCb in the neoadjuvant setting (NCT01560663). 278/300 patients were evaluable. PAM50 subtypes (NanoString nCounter) and RNAseq (HiSeq2500) were analyzed for those patients with both available samples and evaluable pathological response (n=208). Correlations were studied by the Kendall method. Linear or logistic regressions were adjusted for univariant analysis depending on numerical or categorical response variables, respectively. Results: FOXA1 and AR were differentially expressed between basal and non-basal tumor subtypes (PAM50), being overexpressed in non-basal (p&amp;lt;0.001 for both FOXA1 and AR). FOXA1 and AR were significantly overexpressed in non-basal subtypes from the Vanderbilt TNBC-type classification (36/208) as well. Both genes expression showed a significant correlation with several luminal marker genes. AR was significantly associated with ANXA9 (p=0,008), GATA3 (p=0,00002) and XBP1 (p&amp;lt;0.001), while FOXA1 expression was positively associated with ANXA9 (p=0,03), ESR1 (p&amp;lt;0.001),GATA3 (p&amp;lt;0.001) and XBP1 (p&amp;lt;0.001). In terms of response, significant differences in FOXA1 expression levels were found between responders and non-responders by Residual Disease Burden (RCB) classification taking response as binary variable of PCR vs RCB-I/II/III (p=0.003) as well as pCR/RCB-I vs RCB-II/III (p=0.008) with responders showing a lower FOXA1 expression level. The same analysis for AR expression did not show statistically significant differences. Within the PAM50 basal subgroup, neither AR nor FOXA1 individual gene expression (172/208) showed association with response. For survival, with a median follow-up of 36 months, neither FOXA1 nor AR showed significant impact on EFS or OS per univariate Cox regression analysis (EFS: HRFOXA1 1.076; p=0.307; HRAR 1.156, p=0.084 and OS: HRFOXA11.120, p=0.140; HRAR 1.152, p=0.121). Conclusions: Within our cohort, FOXA1 expression is a better predictor of response to NA chemotherapy than AR. FOXA1 is overexpressed in TNBC tumors who do not achieve pCR with neoadjuvant TCb chemotherapy, correlating with non-basal tumor subtypes. This suggests that measuring FOXA1 expression levels in patients with TNBC could be useful to predict response to TCb regimen enabling physicians to select more effective alternative NA schemes in this population. Citation Format: Sara López-Tarruella, María del Monte-Millán, Enrique Alvarez, Yolanda Jerez, José Ángel García Saenz, Isabel Echavarria, Fernando Moreno, Ivan Márquez-Rodas, Coralia Bueno-Muiño, Blanca Herrero, Maria Cebollero, Rocío Ramos-Medina, Nerea Lobato, Ricardo González del Val, Maria Isabel Palomero, Santiago Lizarraga, Uriel Bohn, Ana Isabel Ballesteros, Patricia Rincón, Tatiana Massarrah, Inmaculada Ocaña, Lucía Villarejo, Charles M Perou, Miguel Martin. Potential value of FOXA1 expression as genomic predictor of response to docetaxel and carboplatin neoadjuvant (NA) chemotherapy in patients with triple negative breast cancer (TNBC) [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 PS4-12.

FOXA1 Gene Expression for Defining Molecular Subtypes of Muscle-Invasive Bladder Cancer after Radical Cystectomy.

It remains unclear how to implement the recently revealed basal and luminal subtypes of muscle-invasive bladder cancer (MIBC) into daily clinical routine and whether molecular marker panels can be reduced. The mRNA expression of basal (KRT5) and luminal (FOXA1, GATA3, KRT20) markers was measured by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and correlated to clinicopathological features, recurrence-free survival (RFS), disease-free survival (DFS), and overall survival (OS) in 80 patients with MIBC who underwent radical cystectomy. Additionally, the correlation of single markers with the basal and non-basal subtypes defined by a 36-gene panel was examined and then validated in the TCGA (The Cancer Genome Atlas) cohort. High expression of FOXA1 (p = 0.0048) and KRT20 (p = 0.0317) was associated with reduced RFS. In the multivariable analysis, only FOXA1 remained an independent prognostic marker for DFS (p = 0.0333) and RFS (p = 0.0310). FOXA1 expression (AUC = 0.79; p = 0.0007) was closest to the combined marker expression (AUC = 0.79; p = 0.0015) in resembling the non-basal subtype defined by the 36-gene panel. FOXA1 in combination with KRT5 may be used to distinguish the basal and non-basal subtypes of MIBC.

Abstract P4-05-02: Machine learning predicts rapid relapse in triple negative breast cancer

Abstract Purpose: Cancers with short interval between diagnosis and metastasis are associated with aggressive clinical course. Specifically, metastatic relapse of triple-negative breast cancer (TNBC) within 2 years of initial primary diagnosis is associated with marked chemoresistance, rapid progression, and poor prognosis. We hypothesized that rapid relapse TNBCs (rrTNBC; distant metastatic relapse or death &amp;lt;2 years) reflect distinct clinical and genomic features vs. late relapse (lrTNBC; &amp;gt;2 years) or no relapse (nrTNBC; no distant relapse or death with at least 5 years follow-up). Patients and Methods: We identified 453 primary TNBCs from three publicly-available datasets and characterized each as rrTNBC, lrTNBC, or nrTNBC. We compiled primary tumor clinical and multi-omic data, including transcriptome (n=453), copy number alterations (CNAs; n=317), and mutations in 171 cancer-related genes (n=317), then calculated expression and immune signatures. Results: Patients with rrTNBC were higher stage at diagnosis (Chi-square p&amp;lt;0.0001) while lrTNBC were more likely to be non-basal PAM50 subtype (Chi-square p=0.03). Among 125 expression signatures, rrTNBC and lrTNBC had significantly lower immune signatures relative to nrTNBC suggesting an immune suppressed microenvironment. lrTNBCs were enriched for eight estrogen/luminal signatures (all FDR p&amp;lt;0.05). There was no significant difference in tumor mutation burden or percent genome altered across the groups. Among mutations, only TP53 mutations were significantly more frequent in rrTNBC compared to lrTNBC (Fisher exact FDR p=0.009). To develop an optimal classifier, we used 77 significant clinical and ‘omic features for training (n=214 patients) using six modeling approaches encompassing simple, machine learning, and artificial neural network (ANN), then evaluated performance to predict rrTNBc vs. lrTNBC vs. nrTNBC in validation cohort (n=90 patients) and independent testing cohort (n=81 patients). Among modeling approaches, support vector machine had the highest average receiver-operator characteristic area under curve (AUC) in both validation (AUC=0.79) and independent testing (AUC=0.72) cohorts. Conclusions: We provide a new approach to define TNBCs based on timing of relapse. We identify distinct clinical and genomic features that can be incorporated into machine learning models to predict rrTNBC. Citation Format: Yiqing Zhang, William Nock, Meghan Wyse, Zachary Weber, Elizabeth J Adams, Asad Sarah, Sinclair Stockard, David Tallman, Jasneet Singh, Junu Bae, Eric P Winer, Nancy U Lin, Yi-Zhou Jiang, Ding Ma, Peng Wang, Leming Shi, Wei Huang, Zhi-Ming Shao, Claire Verschraegen, Mathew Cherian, Maryam B Lustberg, Bhuvana Ramaswamy, Sagar Sardesai, Jeffrey VanDeusen, Nicole Williams, Wesolowski Robert, Daniel G Stover. Machine learning predicts rapid relapse in triple negative breast cancer [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 P4-05-02.

MRPS23 amplification and gene expression in breast cancer; association with proliferation and the non-basal subtypes

PurposeMRPS23 is recognized as a driver of proliferation in luminal breast cancer. The aims of the present study were to describe MRPS23 copy number change in breast cancer, and to assess associations between MRPS23 copy number change and molecular subtype, proliferation and prognosis, and between MRPS23 gene expression and molecular subtype and prognosis.MethodsUsing fluorescence in situ hybridization (FISH), we examined MRPS23 and centromere 17 copy number in 590 formalin-fixed, paraffin-embedded primary tumours and 144 corresponding lymph node metastases from a cohort of Norwegian breast cancer patients. Furthermore, we analysed MRPS23 gene expression data in 1971 primary breast cancer tumours from the METABRIC dataset. We used Pearson’s χ2 test to assess associations between MRPS23 copy number and molecular subtype and proliferation, and between MRPS23 expression and molecular subtype. We studied prognosis by estimating hazard ratios and cumulative incidence of death from breast cancer according to MRPS23 copy number and MRPS23 expression status.ResultsWe found MRPS23 amplification (mean MRPS23 copy number ≥ 6 and/or MRPS23/chromosome 17 ratio ≥ 2) in 8% of primary tumours. Copy number increase associated with non-basal subtypes and higher tumour cell proliferation (Ki67). Higher MRPS23 expression associated with the Luminal B subtype. We found no significant association between MRPS23 amplification or MRSP23 gene expression, and prognosis.ConclusionAmplification of MRPS23 is associated with higher proliferation and non-basal subtypes in breast cancer. High MRPS23 expression is associated with the Luminal B subtype.

Abstract P1-09-05: Clinical and genomic characteristics of borderline ER-positive breast cancers

Abstract Background: Though current guidelines classify breast tumors with ≥1% estrogen receptor (ER) positivity by immunohistochemistry as ER positive, “borderline” tumors expressing ≥1 – &amp;lt;10% positivity have biological similarities to ER negative tumors in prior studies. We sought to describe molecular features of ER-borderline breast cancer in a diverse cohort of incident cases and identify characteristics associated with high-risk borderline tumors. Methods: We used the Carolina Breast Cancer Study, a large population-based study that oversampled young and black women in 44 counties of North Carolina, to study characteristics of ER-borderline cases compared to other ER-positive and ER-negative tumors. Gene expression of ESR1, PAM50 subtype, and risk of recurrence score (ROR-PT, calculated from subtype, proliferation level, and tumor size; categorized as low, medium, high) were quantified using RNA counting methods, with finite mixture modeling to establish a cutoff for ESR1-high vs. -low tumors. The relative frequency differences of clinical and genomic features of borderline vs. positive/negative tumors were estimated using linear regression, adjusted for age and race. Recurrence risk was evaluated by ER status, with and without receipt of endocrine therapy using Kaplan-Meier curves and Cox proportional hazards models. Results: Of 2,859 eligible patients, 8% (n=217) were ER borderline, 26% (n=757) were ER negative and 66% were ER positive. Compared to other ER positive tumors (which were 5% basal-like, 89% luminal, 8% high ROR-PT, 16% ESR1-low), borderlines (40% basal-like, 42% luminal, 26% high ROR-PT, 71% ESR1-low) had a higher relative frequency of basal-like subtype (+37.7%, 95% CI 27.1, 48.4), high ROR-PT (+52.4%, 95% CI 36.8, 68.0), and ESR1-low status (+26.3%, 95% CI 20.2, 32.5). In log-rank analysis, recurrence risk in borderlines was not significantly different from ER negatives. However, after adjusting for patient and tumor factors, recurrence risk in borderlines treated without endocrine therapy was the highest of all subtypes (HR 2.9, 95% CI 1.6, 5.0) and persisted after further adjusting for ROR-PT. Results are summarized in Table 1. Frequency of high ROR-PT was 22% among white women with borderline tumors but was significantly more common among black women with borderline tumors (+26.0%, 95% CI 7.1, 45.0). Among borderlines, high grade was associated with basal-like subtype (+43.4%, 95% CI 18.7, 68.0; reference = non-basal subtype, 52% high grade). Table 1:Recurrence-free survival by ER subtype and endocrine therapy receipt Hazard Ratio (HR) Model 1HR Model 2ER PositiveREFREFER Borderline, no endocrine therapy2.9 (1.6, 5.0)2.3 (1.1, 4.9)ER Borderline, endocrine therapy1.5 (0.7, 3.2)1.5 (0.6, 3.7)ER Negative1.8 (1.3, 2.6)1.5 (0.9, 2.4)Adjusted for (1) age, race, stage, grade, year of diagnosis, (2) variables in (1) and ROR-PT Conclusion: Consistent with prior studies, borderline tumors demonstrated characteristics that were intermediate between other ER positive and negative tumors, with heterogeneity of genomic features. Given the higher recurrence risk among borderlines, identifying aggressive borderline tumors is important. Black women and those with high tumor grade may benefit from further genomic assessment to guide treatment decisions. Citation Format: Benefield HC, Allott EH, Sun X, Reeder-Hayes KE, Troester MA. Clinical and genomic characteristics of borderline ER-positive breast cancers [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 P1-09-05.

Abstract P3-07-08: Multi-omic predictor of rapid and late relapse in primary triple negative breast cancer

Abstract Background: Triple-negative breast cancer (TNBC) is a heterogeneous disease. Clinically, we observe three distinct TNBC outcomes: 1) rapid relapse (rrTNBC) characterized by aggressive drug resistant disease; 2) late relapse (lrTNBC) characterized by indolent or treatment responsive disease; and 3) no relapse (NoRTNBC). We hypothesized that distinct clinical and genomic features of primary tumors define rapid versus late relapse in TNBC. Approach: Using three publicly-available datasets (METABRIC, TCGA, and a prior gene expression meta-analysis), we identified 455 patients diagnosed with primary TNBC with adequate follow-up to be characterized as rrTNBC (relapse or death within 2 years of diagnosis), lrTNBC (relapse or death more than 2 years after diagnosis), or NoRTNBC (no relapse/death with at least 5 years follow-up). We compiled basic clinical (n=455 patients) and primary tumor multi-omic data, including whole transcriptome (n=455), whole genome copy number (n=317), and mutation data for 171 cancer-related genes (n=317). We evaluated intrinsic subtypes (PAM50, TNBCtype), 125 gene expression signatures, CIBERSORT immune subsets, copy number, and mutation frequency. Results: We first evaluated patients with relapse (rrTNBC+lrTNBC) vs. NoRTNBC. There was no significant difference in age, grade, stage at diagnosis, or PAM50 or TNBC subtype proportion between relapse and NoRTNBC. Among 125 expression signatures, five immune signatures were significantly higher in NoRTNBCs (FDR p&amp;lt;0.05) suggesting increased immune activity in patients who do not relapse. Using CIBERSORT inferred immune subsets, anti-tumor CD8 T-cell, M1 macrophage, and gamma-delta T-cell subsets were all highly correlated to these immune signatures (all Pearson's r &amp;gt;= 0.3, all p&amp;lt;1.2e-8). Among genomic features, patients who relapsed were significantly more likely to harbor a mutation in PIK3CA (Fisher exact FDR p=0.02) but there was no significant difference in tumor mutation burden or percent genome altered (Student's t-test p=0.83 and p=0.99, respectively). We then evaluated primary TNBC genomic data in patients who ultimately developed rapid vs. late relapse. Patients with rrTNBC were more likely to be higher stage (p&amp;lt;0.0001) while lrTNBC were more likely to be non-basal PAM50 subtype (p=0.03). Among 11 significantly altered gene expression signatures (FDR p&amp;lt;0.05), 6 estrogen/luminal signatures were significantly higher in lrTNBC. Mutations in DNAH11 and PIK3CA were more common in lrTNBC (Fisher exact FDR p=0.04 and p=0.05, respectively) but there were no significant differences in tumor mutation burden or copy number burden (Student's t-test p=0.13 and p=0.45, respectively). Using 317 cases with full genomic data divided into training and validation datasets, we will report a comparison of machine learning models for predicting relapse versus no relapse and rapid versus late relapse. Conclusions: Primary TNBC tumors destined for rapid, late, or no relapse reflect distinct genomic features. Anti-tumor immune signatures and subsets are enriched in patients who do not relapse yet no difference in mutational or copy number burden. Relative to rapid relapse TNBCs, late relapse TNBCs are enriched for non-basal tumors, estrogen/luminal expression signatures, and mutations in DNAH11 and PIK3CA. Citation Format: Zhang Y, Nock W, Asad S, Adams E, Singh J, Damicis A, Lustberg MB, Noonan A, Reinbolt R, Sardesai S, VanDeusen J, Wesolowski R, Williams N, Ramaswamy B, Stover DG. Multi-omic predictor of rapid and late relapse in primary triple negative 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 P3-07-08.

Abstract P5-16-04: A randomized phase II neoadjuvant study comparing docetaxel and cyclophosphamide (TC) with 5-fluorouracil, epirubicin, and cyclophosphamide followed by docetaxel (FEC-D) for hormone receptor-negative breast cancer: The Kanagawa breast oncology group (KBOG) 1101 study

Abstract Purpose: This study aimed to evaluate response to neoadjuvant chemotherapy (NAC) for patients with hormone receptor-negative (HR-negative) breast cancer (BC) to identify subtypes that require anthracycline treatment. Methods: In total, 103 patients with operable HR-negative BC were registered. They were randomely assigned to administration of 6 cycles of docetaxel (75mg/m2) and cyclophosphamide (600 mg/m2) (TC6) or 3 cycles of 5-fluorouracil (500 mg/m2), epirubicin (100mg/m2), and cyclophosphamide (500mg/m2) followed by 3 cycles of docetaxel (100mg/m2) (FEC-D). Cytokeratin (CK) 5/6 and EGFR expression were used to identify basal and non-basal triple-negative (TN) BC. The primary endpoint was pathological complete response (pCR); secondary endpoints were safety, breast-conserving surgery, disease-free survival, and overall survival. Predictive factors of pCR for each regimen were also evaluated. Results: The pCR rate was 36% for FEC-D and 25.5% for TC6, which did not differ significantly (P=0.265). When TN BC was subdivided into basal and non-basal subtypes, the pCR rate in the basal subtype was significantly lower for TC6 (13.6%) than for FEC-D (42.9%) (P=0.033), but did not significantly differ in the non-basal (TC6, 36.4%; FEC-D, 25.0%) and HER2-positive (TC6, 41.7%; FEC-D, 35.7%) cases. The relative dose intensities of epirubicin and docetaxel in FEC-D and docetaxel in TC6 were 96.3±13.0%, 93.5±14.6%, and 93.9±16.3% (mean±SD), respectively. Occurrence of grade ≥2 adverse events was significant in FEC-D-treated patients. Poor appetite (P&amp;lt;0.001), nausea (P&amp;lt;0.001), vomiting (P&amp;lt;0.001), dysgeusia (P=0.03), and fatigue (P=0.05) were significantly more common for FEC-D than TC6. Patients treated with FEC-D experienced significantly more febrile neutropenia and anemia (P=0.016 and 0.017, respectively). The rates of breast-conserving surgery were 68.0 and 72.3% for FEC-D and TC6, respectively (P=0.641). Patients achieved pCR had better DFS (log rank test, P = 0.287) and OS (log rank test, P = 0.069), though not significant. Patients treated with FEC-D had better DFS (log rank test, P = 0.107) and OS (log rank test, P = 0.159), though not significant. Among patients with TN BC, those treated with FEC-D had significantly better DFS (log rank test, P = 0.016) and OS (log rank test, P = 0.034) than treated with TC6. Low ALDH1 expression and high topo IIα protein expression were strongly correlated with pCR in FEC-D, with odds ratios (ORs) of 4.33 [95% CI, 1.02–18.38] and 4.08 [0.97–17.2], respectively. ALDH1 was also associated with pCR in TC, OR=3.50 [0.84–14.6]. Other factors, including age, tumor size, nodal status, tumor grade, Ki67, p53, and TOP 2A status were not associated with pCR in either regimen. Conclusions:We found that TC6 was less effective than FEC-D for treating HR-negative BC because it was insufficient for TNBC, particularly for basal BC. This suggests that anthracycline is more important than taxane for basal BC. Additionally, ALDH1 could be a marker for resistance to conventional chemotherapy. Citation Format: Narui K, Ishikawa T, Shimizu D, Tanabe M, Sasaki T, Oba MS, Morita S, Nawata S, Kida K, Mogaki M, Doi T, Tsugawa K, Ogata H, Ota T, Kosaka Y, Sengoku N, Kuranami M, Saito Y, Suzuki Y, Suto A, Arioka H, Chishima T, Ichikawa Y, Endo I, Tokuda Y. A randomized phase II neoadjuvant study comparing docetaxel and cyclophosphamide (TC) with 5-fluorouracil, epirubicin, and cyclophosphamide followed by docetaxel (FEC-D) for hormone receptor-negative breast cancer: The Kanagawa breast oncology group (KBOG) 1101 study [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-16-04.

Effect of Basal Subtype in Survival in Metastatic Breast Cancer Patients who Received First-Line Gemcitabine-Carboplatin after Receiving Anthracyclines and Taxanes in Adjuvant Phase

To assess the effect of basal subtype in survival in patients with metastatic breast cancer who received first-line gemcitabine\carboplatin. Patients & Methods: The basal subtype status was determined by using the basal cytokeratin markers CK5/6. Eligible metastatic tripe negative breast cancer (MTNBC) women with prior adjuvant treatment by anthracyclines and taxanes were enrolled to receive carboplatin AUC 5 in day1 and gemcitabine 1gm/m2 on day1 and 8 for up to 6 cycles, until disease progression or unacceptable toxicity. End points were progression-free survival and overall survival in patients with basal and non-basal subtype. Results: Thirty-three patients of MTNBC presented in a period from February 2013 to March 2015 were treated with gemcitabine\carboplatin. Patients had a median age of 43.6years (range, 24-71 years, S.D: 11.161)23 patients were premenopausal (69.7%) & 10 patients were postmenopausal (30.3%). Approximately 81% of patients had a good PS (0-1). 12 patients were basal subtype (positive ck5/6) from twenty patients who had accessible specimens for examination of cytokeratin (12out of 20=60%), Mean overall survival (OS) in patients has basal subtype were 12 months, while in patients has non-basal subtype were 12.96 months (95% CI-3.53-5.45) P<0.242). Median progression-free survival (PFS) in basal subtype were 5.857 months while in non-basal subtype were 6.15 months (95% CI-1.79738-2.39079) P<0.456). Conclusion: Post metastatic presentation, the OS and PFS was slightly lower among patients with basal subtypes compared to non-basal subtypes; however this difference in PFS and OS between the two groups did not reach statistical significance.

Methylation of the SEPT9_v2 promoter as a novel marker for the detection of circulating tumor DNA in breast cancer patients.

The aim of the present study was to evaluate the promoter methylation status of SEPT9_v2 in breast cancer and to detect this methylated gene in circulating tumor DNA (ctDNA) in plasma. Bisulfite sequencing was performed with a next generation sequencer. Methylation of the SEPT9_v2 promoter was found in 67%(8/12) of breast cancer cell lines and 53% (10/19) of breast tumor tissue, but not in normal breast tissue (0/19). A clear inverse correlation was observed between the expression of SEPT9_v2 mRNA and the methylation index (MI) both in cell lines and breast cancer tissues. The MI of SEPT9_v2 was significantly higher in non-basal subtype of breast cancer (13.0%, n=84) than in basal subtype (3.0%, n=23) (P<0.0001). Methylated SEPT9_v2 ctDNA in plasma was detected in 11% (9/82) of primary breast cancer patients and 52% (26/50) of metastatic breast cancer patients, but not in the healthy controls (0/51). These results indicate that SEPT9_v2 promoter hypermethylation, which silences the expression of SEPT9_v2 mRNA, is observed in a significant proportion of breast tumors, and that methylated SEPT9_v2 may serve as a novel tumor marker for breast cancer.

Abstract P3-06-27: BRCAness is important to identify TNBC subtype resistant to taxanes

Abstract BACKGROUND: Triple negative breast cancer (TNBC) is heterogeneous and consists of tumors associated with basal like, BRCA related and cancer stem cell (CSC) phenotypes. Although anti-cancer agents are substantial for treating TNBC, existing ones do not work in some subpopulation in TNBC at all. However, it has not been reported that subdivision of TNBC is useful for choosing ant-cancer agents. AIM: To examine whether subdividing TNBC is beneficial for tailored chemotherapy and to identify predictive factors for existing anti-cancer agents in TNBC. METHODS: Sixty-six TNBC cases from a randomized phase II trial comparing TCx6 (TC6) with FEC followed by docetaxel (FEC-D) as neoadjuvant chemotherapy for hormone receptor-negative breast cancer (Kanagawa Breast Oncology Group 1101 Study). TNBC was subdivided by 1) IHC of CK 5/6 and EGFR into basal- and non-basal subtypes, and 2) MLPA of BRCA1 into BRCA1 and non-BRCA1 subtypes. The pCR rates were examined according to each regimen and subtype. 3) The association of grade 3 pCR was examined with Ki-67, p53, aldehyde dehydrogenase (ALDH) 1 and topoisomerase 2A (topoIIα) by IHC and TOP2A by FISH for each regimen. RESULTS: 1) In basal subtype, the pCR rate was significantly higher for FEC-D (42.9%) compared with TC6 (13.6%) (p=0.033), but it was equivalent in non-basal subtype (FEC-D vs TC: 25.0% vs 36.4%, p=0.554). 2) In BRCA1 subtype, it was more significant (FEC-D vs TC: 53.8 % vs 13.3%, p=0.022). 3) An association between pCR and low ALDH1 expression was found in both FEC-D and TC6 (OR: 3.75 and 2.73). High topo IIα protein expression was associated with pCR in FEC-D (OR: 3.5). DISCUSSION: TC6 was less effective than FEC-D in basal subtype and BRCA1 subtype, showing that taxanes cannot exert their anticancer role in tumors with BRCA1 dysfunction. Although basal subtype may contain more BRCA1-defective tumors than non-basal subtype, MLPA of BRCA1 was better to identify subtype resistant to taxanes than CK5/6 and EGFR. ALDH1 predicted treatment efficacy, and could therefore represent a marker of resistance to conventional chemotherapy. Citation Format: Takashi Ishikawa, Kazutaka Narui, Kazuhiro Shimada, Kumiko Kida, Mari S Oba, Mikiko Tanabe, Yasushi Ichikawa, Sadatoshi Sugae, Itaru Endo. BRCAness is important to identify TNBC subtype resistant to taxanes [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-06-27.

Abstract P6-16-03: Intrinsic subtypes and MRI patterns in brain metastasis associated with breast cancer

Abstract Background: Breast cancer is the 2nd most common cancer to metastasize to the brain. The development of brain metastasis (BM) is associated with a lower median survival compared with other locations of metastasis and carries with it high morbidity and reduced quality of life. There are limited treatment options and virtually no approved targeted therapies for this disease. We have previously reported specific pathways enriched in BM compared to primary tumors and now further this study to examine pathways by intrinsic subtype and location of and number of BM. Methods: Archival FFPE material was obtained from BM using pathology records; clinical data, including MRI images, was retrieved from medical records and institutional tumor registry under an IRB protocol. Tumor DNA/RNA was extracted from 2 mm cores macrodissected from the FFPE tissue blocks using the Qiagen AllPrep DNA/RNA FFPE kit. Gene expression profiling was performed using Affymetrix Human Transcriptome Array 2.0 microarray on BM samples for which sufficient RNA was available. Gene-level expression quantification was derived after RMA normalization using the Affymetrix Transcriptome Analysis Console. PAM50 subtypes were assigned by clustering samples using median-subtracted PAM50 gene expression levels. Differential gene expression was estimated using the non-parametric Mann-Whitney test, followed by assessment of false discovery rate using the Banjamini-Hochberg FDR methodology. Pathway enrichment analysis was performed using the NCI Pathway Interaction Database. Results: Gene expression profiling showed the following intrinsic subtype distribution among all BM: luminal A 32% (19/59), luminal B 31% (18/59), HER2 enriched 7% (4/59), and basal subtype 31% (18/59). At time of development of BM 64% (38/59) of patients presented with a single lesion compared to 36% (21/59) of patients who presented with multiple lesions (p=0.12). Thirty-nine percent (7/18) of patients with basal subtypes were observed to present with multiple BM compared to 61% (11/18) non-basal subtypes (p=0.25). In addition, 12% (13/59) of BM were found to be exclusively dural-based lesions. They appeared more frequently in the luminal subtypes [11/13 vs 2/13; p=0.06]. A total of 314 genes were differentially expressed (Wilcox pval &amp;lt; 0.05; FDR &amp;lt; 0.01) between the basal and luminal subtypes. As expected, we found that the FOXA transcription factor network was up-regulated in luminal when compared to the basal subtype, whereas the FOXM1 transcription factor network was up-regulated in the basals. We also found a total of 28 genes to be significantly differentially expressed (Wilcox pval &amp;lt; 0.05; FDR &amp;lt; 0.01) between the dural and non-dural BM. The beta1 integrin and syndecan-1 pathways were significantly enriched, along with angiogenesis and lymphatic endothelium pathways. Key genes in these pathways (COL1A1, COL1A2, COL3A1, CDH11, were found to be at least 2-fold up-regulated in the dural BM compared to non-dural BM. Conclusion: Identifying pathways that are differentially expressed between intrinsic subtypes may help us develop new targeted therapies to provide more treatment options for breast cancer patients with brain metastasis. Citation Format: Nicole Williams, Vinay Varadan, Aditi Vadodkar, Kristy Miskimen, Stephanie Kim, Shaveta Vinayak, Paula Silverman, Jill Barnholtz-Sloan, Andrew Sloan, Cheryl Thompson, Lisa Rogers, Hannah Gilmore, Lyndsay Harris. Intrinsic subtypes and MRI patterns in brain metastasis associated with breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-16-03.

Hypermethylation of BRCA1 gene: implication for prognostic biomarker and therapeutic target in sporadic primary triple-negative breast cancer.

Paraffin sections from 239 cases of surgical resected mammary gland carcinomas were assessed to determine the role of BRCA1 gene methylation in sporadic triple-negative breast cancer and to evaluate the relationship between BRCA1 gene methylation and clinicopathologic features of triple-negative breast cancer in the National Cancer Center, China. Diagnostic tissues collected from patients received mastectomy in the National Cancer Center from January 1, 1999 to December 31, 2008 were reviewed. Tissue microarrays were constructed using 239 triple-negative breast cancer cases and stained with estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, cytokeratin 5/6, and epidermal growth factor receptor. Methylation status of the BRCA1 promoter was measured by methylation-specific PCR and analyzed against clinicopathologic characteristics, subtypes, and prognosis using standard statistical methods. Among the 239 triple-negative breast cancer cases, 137 (57.3 %) showed methylation of the BRCA1. According to the immunohistochemistry results, triple-negative breast cancer cases were classified into basal-like breast cancer (60.7 %) and non-basal-like breast cancer (39.3 %). The frequency of BRCA1 methylation was significantly higher in basal-like breast cancer subtype (71.7 %) than the non-basal subtype (35.1 %). Thus, BRCA1 methylation is statistically significantly correlated with basal-like breast cancer subtype (p < 0.001). Multivariate analyses further showed that BRCA1 promoter methylation is an independently predictor of overall survival (p = 0.023; HR 2.32; 95 % CI 1.12-4.81) and disease-free survival (p = 0.022; HR 2.36; 95 % CI 1.13-4.90) in triple-negative breast cancer. Here we demonstrated that epigenetic alteration of key tumor suppressor gene can be a promising biomarker for the prognosis of triple-negative breast cancer/basal-like breast cancer. Specifically our finding revealed that BRCA1 methylation is closely associated with a significant decrease in overall survival and disease-free survival, highlighting BRCA1 promoter methylation as promising and powerful biomarkers for effect and better prognosis of DNA damaging agents for triple-negative breast cancer/basal-like breast cancer.

Abstract 1899: Predictive factors of anthracycline or taxan based chemotherapy: Analysis from a randomized phase II trial comparing docetaxel plus cyclophosphamide with epirubicin plus cyclophosphamide followed by docetaxel as neoadjuvant chemotherapy for hormone receptor-negative breast cancer

Abstract Background: Taxane-based regimens have been developed and used widely to treat breast cancer. It has therefore become important to identify subgroups of patients in which anthracyclines are indispensable. Thus, we had conducted a randomized phase II NAC study to compare a taxane with and without an anthracycline in hormone receptor (HR) negative breast-cancer subtypes and examined predictive factors for each regimen. Aim: To examine the predictive factors for six cycles of docetaxel and cyclophosphamide (TC6) compared with 5-fluorouracil, epirubicin, and cyclophosphamide followed by docetaxel (FEC-D). Methods: Eligibility criteria were operable HR-negative breast cancer, age younger than 75 years and ECOG PS0-1. According to HER2 status, 103 patients were randomly assigned to TC (75/600 mg/m2) every 3 weeks ×6 or FEC (500/100/500 mg/m2) every 3 weeks ×3 followed by D (100 mg/m2) every 3 weeks ×3. Triple-negative (TN) breast cancer was subdivided by cytokeratin 5/6 and epidermal growth factor receptor into basal- and non-basal subtypes. The association of grade 3 pathological complete response (pCR) was examined with Ki-67, p53, aldehyde dehydrogenase (ALDH) 1 and topoisomerase 2A (TOP2A) by immunohistochemistry and TOP2A by fluorescence in situ hybridization) for each regimen. Results: Ninety-seven of 103 patients were analyzed successfully (50 for FEC-D and 47 for TC6). The pCR rate tended to be higher in FEC-D-treated patients compared with TC6-treated patients (pCR: 36.0 vs. 25.5%, n.s.). FEC-D treatment was significantly more effective than TC6 in basal-type (p=0.033) but not in non-basal and HER2 subtypes. ALDH1 was associated with resistance to both regimens (FEC-D: p=0.047, TC6: p=0.085) Conclusions: TC6 was not more effective than FEC-D in HR negative breast cancer. TC6 was significantly less active than FEC-D in basal subtype, and equivalent to FEC-D in HER2 and non-basal subtypes. ALDH1 could provide a marker for novel strategies such as stem cell-based therapies for breast cancer. The association of BRCAness with pCR is being investigated and will be presented at the meeting. Citation Format: Takashi Ishikawa, Kazutaka Narui, Kazuhiro Shimada, Kumiko Kida, Sadatoshi Sugae, Yasushi Ichikawa, Mikiko Tanabe, Itaru Endo, Mari S. Oba. Predictive factors of anthracycline or taxan based chemotherapy: Analysis from a randomized phase II trial comparing docetaxel plus cyclophosphamide with epirubicin plus cyclophosphamide followed by docetaxel as neoadjuvant chemotherapy for hormone receptor-negative breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1899. doi:10.1158/1538-7445.AM2014-1899