Triple Negative Breast Cancers: An Obsolete Entity?

Triple negative breast cancer is defined on the basis of what it is not. It has served as a useful umbrella entity for management of patients with breast cancer for the last couple of decades. However, during this period a number of novel therapies have become available. These therapies have been documented to be useful in subsets of TNBCs that can be identified on the basis of distinct biologic alterations. Herein we revisit the categorization and usage of the TNBC as an entity to assess its utility in view of the currently available therapies.

Intraoperative assessment of axillary sentinel lymph nodes by telepathology

PURPOSE

Although axillary dissection is no longer indicated for many breast cancer patients with 1-2 positive axillary sentinel lymph nodes (ASLN), intraoperative ASLN assessment is still performed in many institutions for patients undergoing mastectomy or neoadjuvant therapy. With recent advancements in digital pathology, pathologists increasingly evaluate ASLN via remote telepathology. We aimed to compare the performance characteristics of remote telepathology and conventional on-site intraoperative ASLN assessment.

METHODS

Data from ASLN evaluation for breast cancer patients performed at two sites between April 2021 and October 2022 was collated. Remote telepathology consultation was conducted via the Aperio eSlideManager system.

RESULTS

A total of 385 patients were identified during the study period (83 telepathology, 302 on-site evaluations). Although not statistically significant (P = 0.20), the overall discrepancy rate between intraoperative and final diagnoses was slightly higher at 9.6% (8/83) for telepathology compared with 5.3% (16/302) for on-site assessment. Further comparison of performance characteristics of ASLN assessment between telepathology and conventional on-site evaluation revealed no statistically significant differences between deferral rates, discrepancy rates, interpretive or sampling errors, major or minor disagreements, false negative or false positive results as well as clinical impact and turn-around time (P ≥ 0.12).

CONCLUSION

ASLN assessment via telepathology is not significantly different from conventional on-site evaluation, although it shows a slightly higher overall discrepancy rate between intraoperative and final diagnoses (9.6% vs. 5.3%). Further studies are warranted to ensure accuracy of ASLN assessment via telepathology.

Predicting Breast Cancer Events in Ductal Carcinoma In Situ (DCIS) Using Generative Adversarial Network Augmented Deep Learning Model

Standard clinicopathological parameters (age, growth pattern, tumor size, margin status, and grade) have been shown to have limited value in predicting recurrence in ductal carcinoma in situ (DCIS) patients. Early and accurate recurrence prediction would facilitate a more aggressive treatment policy for high-risk patients (mastectomy or adjuvant radiation therapy), and simultaneously reduce over-treatment of low-risk patients. Generative adversarial networks (GAN) are a class of DL models in which two adversarial neural networks, generator and discriminator, compete with each other to generate high quality images. In this work, we have developed a deep learning (DL) classification network that predicts breast cancer events (BCEs) in DCIS patients using hematoxylin and eosin (H & E) images. The DL classification model was trained on 67 patients using image patches from the actual DCIS cores and GAN generated image patches to predict breast cancer events (BCEs). The hold-out validation dataset (n = 66) had an AUC of 0.82. Bayesian analysis further confirmed the independence of the model from classical clinicopathological parameters. DL models of H & E images may be used as a risk stratification strategy for DCIS patients to personalize therapy.

High Interobserver Variability among Pathologists Using Combined Positive Score to Evaluate PD-L1 Expression in Gastric, Gastroesophageal Junction and Esophageal Adenocarcinoma

Reliable, reproducible methods to interpret programmed death ligand-1 (PD-L1) expression on tumor cells (TC) and immune cells (IC) are needed for pathologists to inform decisions associated with checkpoint inhibitor therapies. Our international study compared interpathologist agreement of PD-L1 expression using combined positive score (CPS) under standardized conditions on samples from patients with gastric/gastroesophageal junction/esophageal adenocarcinoma. Tissue sections from 100 adenocarcinoma pre-treatment biopsies were stained in a single laboratory using the PD-L1 IHC 28-8 and 22C3(Agilent) pharmDx immunohistochemical assays. PD-L1 CPS was evaluated by 12 pathologists on scanned whole slide images of these biopsies before and after a 2-hour CPS training session by Agilent. Additionally, pathologists determined PD-L1 positive TC, IC, and total viable TC on a single tissue fragment from 35 of 100 biopsy samples. Scoring agreement among pathologists was assessed using the intraclass correlation coefficient (ICC). Interobserver variability for CPS for 100 biopsies was high with only fair agreement among pathologists both pre- (range 0.45 to 0.55) and post-training (range 0.56 to 0.57) for both assays. For the 35 single biopsy samples, poor/fair agreement was also observed for the total number viable TC (ICC 0.09), number of PD-L1 positive IC (ICC 0.19), number of PD-L1 positive TC (ICC 0.54), and calculated CPS (ICC 0.14), while calculated TC score (positive TC/Total TC) showed excellent agreement (ICC 0.82). Retrospective histologic review of samples with the poorest interpathologist agreement revealed (1) ambiguous identification of positively staining stromal cells, (2) faint or variable intensity of staining, (3) difficulty in distinguishing membranous from cytoplasmic tumor staining, and (4) cautery and crush artifact, as possible confounding factors. These results emphasize the need for objective techniques to standardize the interpretation of PD-L1 expression when using the CPS methodology on gastric/gastroesophageal junction cancer biopsies to accurately identify patients most likely to benefit from immune checkpoint inhibitor therapy.

The Role of ESRP1 in the Regulation of PHGDH in Estrogen Receptor-Positive Breast Cancer

Resistance to hormone therapy leads to a recurrence of estrogen receptor-positive breast cancer. We have demonstrated that the epithelial splicing regulatory protein 1 (ESRP1) significantly affects cell/tumor growth and metabolism and is associated with a poor prognosis in this breast cancer subtype. In this study, we aimed to investigate the ESRP1 protein-messenger RNA (mRNA) interaction in hormone therapy-resistant breast cancer. RNA-binding protein immunoprecipitation (RIP) followed by Clariom D (Applied Biosystems/Thermo Fisher Scientific) transcriptomics microarray (RIP-Chip) was performed to identify mRNA-binding partners of ESRP1. The integration of RIP-Chip and immunoprecipitation-mass spectrometry analyses identified phosphoglycerate dehydrogenase (PHGDH), a key metabolic enzyme, as a binding partner of ESRP1 in hormone-resistant breast cancer. Bioinformatic analysis showed ESRP1 binding to the 5' untranslated region of PHGDH. RNA electrophoresis mobility shift assay and RIP-quantitative reverse transcription-polymerase chain reaction further validated the ESRP1-PHGDH binding. In addition, knockdown of ESRP1 decreased PHGDH mRNA stability significantly, suggesting the posttranscriptional regulation of PHGDH by ESRP1. The presence or absence of ESRP1 levels significantly affected the stability in tamoxifen-resistant LCC2 and fulvestrant-resistant LCC9 cells. PHGDH knockdown in tamoxifen-resistant cells further reduced the oxygen consumption rate (ranging from P = .005 and P = .02), mimicking the effects of ESRP1 knockdown. Glycolytic parameters were also altered (ranging P = .001 and P = .005). ESRP1 levels did not affect the stability of PHGDH in T-47D cells, although knockdown of PHGDH affected the growth of these cells. In conclusion, to our knowledge, this study, for the first time, reports that ESRP1 binds to the 5' untranslated region of PHGDH, increasing its mRNA stability in hormone therapy-resistant estrogen receptor-positive breast cancer. These findings provide evidence for a novel mechanism of action of RNA-binding proteins such as ESRP1. These new insights could assist in developing novel strategies for the treatment of hormone therapy-resistant breast cancer.

Targeting the Tumor-Tumor Microenvironment Crosstalk

INTRODUCTION

Cancer development and progression is a complex process influenced by co-evolution of the cancer cells and their microenvironment. However, traditional anti-cancer therapy is mostly targeted toward cancer cells. To improve the efficacy of cancer drugs, the complex interactions between the tumor (T) and the tumor microenvironment (TME) should be considered while developing therapeutics.

AREAS COVERED

The present review article will discuss the components of T-TME as well as the potential to co-target these two distinct elements. We document that these approaches have resulted in success in preventing tumor progression and metastasis, albeit in animal models in some cases. Lastly, it is important to consider the tissue context and tumor type as these could significantly modify the role of these molecules/pathways and hence the overall likelihood of response. Furthermore, we discuss the potential strategies to target the components of tumor microenvironment in anti-cancer therapy. PubMed and ClinicalTrials.gov was searched through May 2023.

EXPERT OPINION

The tumor-tumor microenvironment cross talk and heterogeneity are major mechanisms conferring resistance to standard of care. Better understanding of the tissue specific T-TME interactions and dual targeting has the promise of improving cancer control and clinical outcomes.

Systematically higher Ki67 scores on core biopsy samples compared to corresponding resection specimen in breast cancer: a multi-operator and multi-institutional study

Ki67 has potential clinical importance in breast cancer but has yet to see broad acceptance due to inter-laboratory variability. Here we tested an open source and calibrated automated digital image analysis (DIA) platform to: (i) investigate the comparability of Ki67 measurement across corresponding core biopsy and resection specimen cases, and (ii) assess section to section differences in Ki67 scoring. Two sets of 60 previously stained slides containing 30 core-cut biopsy and 30 corresponding resection specimens from 30 estrogen receptor-positive breast cancer patients were sent to 17 participating labs for automated assessment of average Ki67 expression. The blocks were centrally cut and immunohistochemically (IHC) stained for Ki67 (MIB-1 antibody). The QuPath platform was used to evaluate tumoral Ki67 expression. Calibration of the DIA method was performed as in published studies. A guideline for building an automated Ki67 scoring algorithm was sent to participating labs. Very high correlation and no systematic error (p = 0.08) was found between consecutive Ki67 IHC sections. Ki67 scores were higher for core biopsy slides compared to paired whole sections from resections (p ≤ 0.001; median difference: 5.31%). The systematic discrepancy between core biopsy and corresponding whole sections was likely due to pre-analytical factors (tissue handling, fixation). Therefore, Ki67 IHC should be tested on core biopsy samples to best reflect the biological status of the tumor.

Spatially variant immune infiltration scoring in human cancer tissues

The Immunoscore is a method to quantify the immune cell infiltration within cancers to predict the disease prognosis. Previous immune profiling approaches relied on limited immune markers to establish patients’ tumor immunity. However, immune cells exhibit a higher-level complexity that is typically not obtained by the conventional immunohistochemistry methods. Herein, we present a spatially variant immune infiltration score, termed as SpatialVizScore, to quantify immune cells infiltration within lung tumor samples using multiplex protein imaging data. Imaging mass cytometry (IMC) was used to target 26 markers in tumors to identify stromal, immune, and cancer cell states within 26 human tissues from lung cancer patients. Unsupervised clustering methods dissected the spatial infiltration of cells in tissue using the high-dimensional analysis of 16 immune markers and other cancer and stroma enriched labels to profile alterations in the tumors’ immune infiltration patterns. Spatially resolved maps of distinct tumors determined the spatial proximity and neighborhoods of immune-cancer cell pairs. These SpatialVizScore maps provided a ranking of patients’ tumors consisting of immune inflamed, immune suppressed, and immune cold states, demonstrating the tumor’s immune continuum assigned to three distinct infiltration score ranges. Several inflammatory and suppressive immune markers were used to establish the cell-based scoring schemes at the single-cell and pixel-level, depicting the cellular spectra in diverse lung tissues. Thus, SpatialVizScore is an emerging quantitative method to deeply study tumor immunology in cancer tissues.

Two Instrument Comparison of Reagents From a US FDA-Approved Assay for the Assessment of Ki-67 in High-Risk Early Breast Cancer

The objective of this study was to measure concordance of results obtained from the US Food and Drug Administration-approved Ki-67 immunohistochemistry MIB-1 pharmDx assay performed on the Dako Omnis automated staining instrument (Omnis) versus results produced from the assay reagents applied using an optimized protocol on the more widely available Autostainer Link 48 (ASL48) platform. Tissue sections obtained from 40 formalin-fixed paraffin-embedded breast carcinoma samples, with available Oncotype DX Breast Recurrence Score (RS) results, were stained. Three certified pathologists scored slides at 3 timepoints, totaling 360 observations for each instrument (N=720 total) using the approved scoring approach. Using the ≥20% cutoff, agreement was calculated with corresponding 2-sided 95% percentile bootstrap confidence intervals (CIs). Pairwise comparisons (N=360) from the interinstrument evaluation, performed with all observers, resulted in 325 (90.3%) concordant outcomes (244 negative and 81 positive) and 35 (9.7%) discordant outcomes. The overall agreement was 90.3% (95% confidence interval, 85.6% to 94.4%). No significant systematic differences were observed between instruments. Specimens scored from the Omnis were on average <1% higher than ASL48, with high correlation and little bias between the continuous Ki-67 scores (concordance correlation coefficient=0.916). Most specimens with a Ki-67 score ≥20% had a RS >25. This study demonstrated that good concordance can be achieved with the reagents run on the ASL48 instrument when using an optimized protocol and standardized scoring.

Tumor Infiltrating Lymphocytes in Multi-National Cohorts of Ductal Carcinoma In Situ (DCIS) of Breast

Tumor-infiltrating lymphocytes (TILs) are prognostic in invasive breast cancer. However, their prognostic significance in ductal carcinoma in situ (DCIS) has been controversial. To investigate the prognostic role of TILs in DCIS outcome, we used different scoring methods for TILs in multi-national cohorts from Asian and European women. Self-described race was genetically confirmed using QC Infinium array combined with radmixture software. Stromal TILs, touching TILs, circumferential TILs, and hotspots were quantified on H&E-stained slides and correlated with the development of second breast cancer events (BCE) and other clinico-pathological variables. In univariate survival analysis, age older than 50 years, hormone receptor positivity and the presence of circumferential TILs were weakly associated with the absence of BCE at the 5-year follow-up in all cohorts (p < 0.03; p < 0.02; and p < 0.02, respectively, adjusted p = 0.11). In the multivariable analysis, circumferential TILs were an independent predictor of a better outcome (Wald test p = 0.01), whereas younger age was associated with BCE. Asian patients were younger with larger, higher grade, HR negative DCIS lesions, and higher TIL variables. The spatial arrangement of TILs may serve as a better prognostic indicator in DCIS cases than stromal TILs alone and may be added in guidelines for TILs evaluation in DCIS.

Deconvolution of gene expression for microenvironmental cell types in thymomas

e20623

Background: Thymomas are rare neoplasms in the anterior mediastinum that account for less than 1% of tumors. The presence of immune cells within the tumor is one of the cardinal features of thymomas. However, the nature of the immune infiltration is not well characterized. Methods: Deconvolution of the gene expression of thymomas in the TCGA-THYM cohort was performed using the CIBERSORT and xCELL programs. Pairwise correlative analyses were performed to study the relationships of cell types and thymoma histological subtypes. Results: The differences in presence of immune cells was better highlighted using xCELL, which identifies 67 categories of cells rather than in the 23 categories identified by CIBERSORT. As expected, there were dramatic differences in the presence of T-cells (almost all subtypes) and B-cells between A/AB and type B (-1, -2, -3) thymomas. A significant difference (P < 0.0001) in different type B thymomas was observed for the presence of monocytes, macrophages, and M1, but not in M2 macrophages. Significant differences in dendritic cells were observed within subtypes of B thymoma. Similarly, statistically significant differences were observed between most subtypes in Immunoscore (except AB/B3) and MicroenvironmentScore (except A/B3; AB/B2 and AB/B3). However, StromalScore differences were observed only in comparisons of type A/AB with B type thymomas (except AB/B3). Interestingly, there also differences in postulated pre-adipocytes, hepatocytes, mesangial cells and osteoblasts in types A vs B, and melanocytes between subtypes of B thymomas. Conclusions: The differences in lymphoid content of the tumor microenvironment is associated with dramatic changes in cell type distribution in subtypes of thymoma. These differences in composition underpin their clinicopathological behavior including incidence of myasthenia and likelihood of recurrence.

Protein Profiling of Breast Cancer for Treatment Decision-Making

The increasing use of neoadjuvant therapy has resulted in therapeutic decisions being made on the basis of diagnostic needle core biopsy. For many patients, this method might yield the only fragment of tumor available for biomarker analysis, necessitating judicious use. Many multiplex protein analytic methods have been developed that employ fluorescence or other tags to overcome the limitations of immunohistochemistry while still retaining the spatial annotation. Interpretation of the data can be difficult because of the limitations of the human eye. Computational deconvolution of the signals may be necessary for some of these methods to enable identification of cell-specific localization and coexpression of biomarkers. Herein, we present the different methods that are coming of age and their application in cancer research, with a focus on breast cancer. We also discuss the limitations, which include high costs and long turnaround times. The methods are also based on the premise that preanalytical factors will have identical impact on all proteins analyzed. There is a need to establish standards to normalize the data and enable cross-sample comparisons. In spite of these limitations, the multiplex technologies are extremely valuable discovery tools and can provide novel insights into the biology of cancer and mechanisms of drug resistance.

Is conservative management of ductal carcinoma in situ risky?

Nonsurgical management of ductal carcinoma in situ is controversial and little is known about the long-term consequences of this approach. In this study, we aimed to determine the risk of (a) upstaging to invasive carcinoma at excision and (b) ipsilateral breast cancer events in patients who might have been eligible for nonsurgical management of DCIS trials. Data from women aged 20 years or older with a biopsy diagnosis of DCIS between January 1, 2010 to December 31, 2014 were collated. The women underwent biopsy and surgical resection (lumpectomy or mastectomy) and were treated with radiation or endocrine therapy as per treating physicians’ choice. The development of ipsilateral breast cancer events (IBEs) was analyzed in patients with at least 5 years of follow-up after standard of care therapy for DCIS. Subset-analysis was undertaken to identify the incidence of IBEs in patients eligible for nonsurgical management trials. The study population consisted of 378 patients with matched cases of biopsy and surgical excision. The overall upstaging rate to IBC was 14.3 and 12.9% for COMET, 8.8% for LORIS, and 10.7% for LORD trial “eligible” patients. At 5 years of follow-up, ~11.5% of overall and trial eligible patients developed IBEs of which approximately half were invasive IBEs. In conclusion, women with DCIS who would have been eligible for nonsurgical management trials have a significantly high risk of developing ipsilateral breast events within 5 years of diagnosis. Better selection criteria are needed to identify DCIS patients who are at very low risk for the development of IBC.

Breast Implant Capsule-Associated Squamous Cell Carcinoma: Report of 2 Patients

Breast implant augmentation is a low-risk procedure with few life-threatening complications. Capsular contracture and rupture/leakage of the implant are the most common complications encountered. Malignant breast implant augmentation-associated lesions are rare, with anaplastic large cell lymphoma being the most common. Squamous cell carcinomas associated with breast implant augmentation are exceedingly rare, with only eight patients reported. Breast implant capsule-associated squamous cell carcinoma occurs in patients with long standing breast implant augmentations (>11 years). We report two additional patients with breast implant capsule-associated squamous cell carcinoma. Review of the literature reveals that invasion beyond the breast implant capsule into the adjacent tissue by the squamous cell carcinoma appears to have negative prognostic implications, and possibly warrants close clinical follow-up.

Abstract P1-08-35: Stromal tumor infiltrating lymphocytes analysis by race and ethnicity in triple negative breast cancers from 2 phase III randomized adjuvant breast cancer trials: ECOG-ACRIN E2197 and E1199

Background: Black patients with triple negative breast cancer (TNBC) have worse survival outcomes, even after adjusting for stage at diagnosis, income, insurance status and other socioeconomic factors. Little is known regarding anti-tumor immune responses in Black patients and how these differences affect responses to treatment in TNBC. Limited data exists regarding the stromal tumor infiltrating lymphocytes (sTILs, which are strongly prognostic in TNBC) distribution based on race and ethnicity. Here we evaluate the prevalence, distribution, and prognostic impact of sTILs in TNBC by race/ethnicity from 2 prospective clinical trials of adjuvant anthracycline/taxane-based chemotherapy (E2197 and E1199). Methods: Full-face hematoxylin and eosin-stained sections of 481 tumors from ECOG-ACRIN trials E2197 and E1199 were previously evaluated for density of sTILs and shown to be associated with disease-free survival (DFS), distant recurrence-free interval (DRFI), and overall survival (OS) (Adams, et al JCO 2014). Further analyses were undertaken to evaluate the impact of race/ethnicity. Results: The majority of the 481 TNBC were from White patients (82.3%, n=403); with 12.3% (n=59) Black patients, 1.6% (n=14) other (9 Hispanic, 3 Asian, 2 Other), and 0.5% (n=5) unknown race. Age distribution (mean 49.2 for White and 49.2 for Black) and node negative disease (White 68/403 (42%), Black 24/59 (41%)) were similar. However, tumor size ≤2cm was seen more commonly in White patients (34%, 137/403) compared with Black patients (20%, 12/59). Black patients had a higher proportion of high sTILs (≥30%) with 23.7% (14/59) compared to White patients (11.4%, 46/403). The association of continuous stromal TILs with DFS (hazard ratio for a 10-point difference) was 0.84 (95% CI 0.72, 0.98) for White patients and 0.94 (95% CI 0.73, 1.20) for Black patients [159 DFS events for Whites, 26 DFS events for Blacks]. Conclusions: This is the first dataset from prospective clinical trials evaluating sTILs in TNBC in Black patients. Prevalence of high sTILs was greater in Black patients compared to White patients. The association between increasing sTILs and improved invasive disease-free survival across racial/ethnic groups must be investigated in larger datasets.

Table 1.Race/EthnicityTotal (n=481)White (n=403)Black (n=59)Other (n=19)Mean age49.049.249.245.6T1 (tumor &lt;=2cm)157(32.6%)137 (34.0%)12 (20.3%)8 (42.1%)T2 (tumor &gt;2 and &lt;=5cm)283(58.8%)232 (57.6%)41 (69.5%)10 (52.6%)T3 and T441 (8.5%)34 (8.4%)6 (10.2%)1 (5.3%)Node negative197 (41.0%)168 (41.7%)24 (40.7%)5 (26.3%)Median sTILs (Quartiles)10 (10, 20)10 (10, 20)10 (10,20)20 (10, 30)sTILs = 095 (19.8%)83 (20.6%)10 (16.9%)2 (10.5%)sTILs 10-29%319 (66.3%)274 (68.0%)35 (59.3%)10 (52.6%)sTILs ≥30%67 (13.9%)46 (11.4%)14 (23.7%)7 (36.8%)—sTIL 30-49%,46 (9.6%)32 (7.9%)11 (18.6%)3 (15.8%)—sTIL 50-74%,17 (3.5%)11 (2.7%)3 (5.1%)3 (15.8%)—sTIL 75-100%4 (0.8%)3 (0.7%)01 (5.2%)iDFS (HR for 10% sTIL increase)0.86 (95% CI 0.76, 0.98)0.84 (95% CI 0.72, 0.98)0.94 (95% CI 0.73, 1.20)0.97 (95% CI 0.68, 1.40)DRFI (HR for 10% sTIL increase)0.82 (95% CI 0.68, 0.99)0.79 (95% CI 0.63, 1.00)1.08 (95% CI 0.82, 1.44)0.54 (95% CI 0.32, 0.90)OS (HR for 10% sTIL increase)0.81 (95% CI 0.69, 0.95)0.76 (95% CI 0.62, 0.94)1.01 (95% CI 0.76, 1.35)0.83 (95% CI 0.54, 1.29)

Citation Format: Natalie Klar, Robert J Gray, Sylvia Adams, Joseph A Sparano, Lori J Goldstein, Angela M DeMichele, Antonio C Wolff, Nancy E Davidson, George W Sledge, Sunil S Badve. Stromal tumor infiltrating lymphocytes analysis by race and ethnicity in triple negative breast cancers from 2 phase III randomized adjuvant breast cancer trials: ECOG-ACRIN E2197 and E1199 [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-08-35.

A Phase II Trial of Adjuvant Durvalumab Following Trimodality Therapy for Locally Advanced Esophageal and Gastroesophageal Junction Adenocarcinoma: A Big Ten Cancer Research Consortium Study

BACKGROUND

Most patients with resectable locally advanced esophageal and gastroesophageal junction (GEJ) adenocarcinoma (AC) receive concurrent chemoradiation (CRT) followed by esophagectomy. The majority of patients do not achieve pathologic complete response (pCR) with neoadjuvant CRT, and the relapse rate is high among these patients.

METHODS

We conducted a phase II study (ClinicalTrials.gov Identifier: NCT02639065) evaluating the efficacy and safety of PD-L1 inhibitor durvalumab in patients with locally advanced esophageal and GEJ AC who have undergone neoadjuvant CRT followed by R0 resection with evidence of persistent residual disease in the surgical specimen. Patients received durvalumab 1500 mg IV every 4 weeks for up to 1 year. The primary endpoint was 1-year relapse free survival (RFS). Secondary endpoint was safety and tolerability of durvalumab following trimodality therapy. Exploratory endpoints included correlation of RFS with PD-L1 expression, HER-2 expression, and tumor immune cell population.

RESULTS

Thirty-seven patients were enrolled. The majority (64.9%) had pathologically positive lymph nodes. The most common treatment related adverse events were fatigue (27%), diarrhea (18.9%), arthralgia (16.2%), nausea (16.2%), pruritus (16.2%), cough (10.8%), and increase in AST/ALT/bilirubin (10.8%). Three (8.1%) patients developed grade 3 immune mediated adverse events. One-year RFS was 73% (95% CI, 56-84%) with median RFS of 21 months (95% CI, 14-40.4 months). Patients with GEJ AC had a trend toward superior 1-year RFS compared to those with esophageal AC (83% vs. 63%, p = 0.1534). There was a numerical trend toward superior 1-year RFS among patients with PD-L1 positive disease compared to those with PD-L1 negative disease, using CPS of ≥10 (100% vs. 66.7%, p = 0.1551) and ≥1 (84.2% vs. 61.1%, p = 0.1510) cutoffs. A higher relative proportion of M2 macrophages and CD4 memory activated T cells was associated with improved RFS (HR = 0.16; 95% CI, 0.05-0.59; p = 0.0053; and HR = 0.37; 95% CI, 0.15-0.93, p = 0.0351, respectively).

CONCLUSIONS

Adjuvant durvalumab in patients with residual disease in the surgical specimen following trimodality therapy for locally advanced esophageal and GEJ AC led to clinically meaningful improvement in 1-year RFS compared to historical control rate. Higher PD-L1 expression may have a correlation with the efficacy of durvalumab in this setting. Higher proportion of M2 macrophages and CD4 memory activated T cells was associated with superior RFS.

Preoperative Breast MRI for Newly Diagnosed Ductal Carcinoma in Situ: Imaging Features and Performance in a Multicenter Setting (ECOG-ACRIN E4112 Trial)

Background There are limited data from clinical trials describing preoperative MRI features and performance in the evaluation of mammographically detected ductal carcinoma in situ (DCIS). Purpose To report qualitative MRI features of DCIS, MRI performance in the identification of additional disease, and associations of imaging features with pathologic, genomic, and surgical outcomes from the Eastern Cooperative Oncology Group-American College of Radiology Imaging Network (ECOG-ACRIN) E4112 trial. Materials and Methods Secondary analyses of a multicenter prospective clinical trial from the ECOG-ACRIN Cancer Research Group included women with DCIS diagnosed with conventional imaging techniques (mammography and US), confirmed via core-needle biopsy (CNB), and enrolled between March 2015 and April 2016 who were candidates for wide local excision (WLE) based on conventional imaging and clinical examination results. DCIS MRI features and pathologic features from CNB and excision were recorded. Each woman without invasive upgrade of the index DCIS at WLE received a 12-gene DCIS score. MRI performance metrics were calculated. Associations of imaging features with invasive upgrade, dichotomized DCIS score (<39 vs ≥39), and single WLE success were estimated in uni- and multivariable analyses. Results Among 339 women (median age, 60 years; interquartile range, 51-66 years), most DCIS cases showed nonmass enhancement (NME) (195 of 339 [58%]) on MRI scans with larger median size than on mammograms (19 mm vs 12 mm; P < .001). Positive predictive value of MRI-prompted CNBs was 32% (21 of 66) (95% CI: 22, 44), yielding an additional cancer detection rate of 6.2% (21 of 339) (95% CI: 4.1, 9.3). MRI false-positive rate was 14.2% (45 of 318) (95% CI: 10.7, 18.4). No imaging features were associated with invasive upgrade or DCIS score (P = .05 to P = .95). Smaller size and focal NME distribution at MRI were linked to single WLE success (P < .001). Conclusion Preoperative MRI depicted ductal carcinoma in situ (DCIS) diagnosed with conventional imaging most commonly as nonmass enhancement, with larger median span than mammography, and additional cancer detection rate of 6.2%. MRI features of this subset of DCIS did not enable prediction of pathologic or genomic outcomes. Clinical trial registration no. NCT02352883 © RSNA, 2021 Online supplemental material is available for this article. See also the editorial by Kuhl in this issue.

Determining PD-L1 Status in Patients with Triple-Negative Breast Cancer: Lessons Learned from IMpassion130

Triple-negative breast cancer (TNBC) accounts for approximately 12% to 17% of all breast cancers and has an aggressive clinical behavior. Increased tumor-infiltrating lymphocyte counts are prognostic for survival in TNBC, making this disease a potential target for cancer immunotherapy (CIT). Research on immunophenotyping of tumor-infiltrating lymphocytes is revealing molecular and structural organization in the tumor microenvironment that may predict patient prognosis. The anti-programmed death-ligand 1 (PD-L1) antibody atezolizumab plus nab-paclitaxel was the first CIT combination to demonstrate progression-free survival benefit and clinically meaningful overall survival benefit in the first-line treatment of metastatic TNBC (mTNBC) in patients with PD-L1-expressing tumor-infiltrating immune cells (IC) in ≥ 1% of the tumor area. This led to its US and EU approval for mTNBC and US approval of the VENTANA PD-L1 (SP142) assay as a companion diagnostic immunohistochemistry (IHC) assay. Subsequently, the anti- programmed death-1 (PD-1) antibody pembrolizumab plus chemotherapy was approved by the FDA for mTNBC based on progression-free survival benefit in patients with a combined positive score ≥10 by its concurrently approved 22C3 companion diagnostic assay. Treatment guidelines now recommend PD-L1 testing for patients with mTNBC, and the testing landscape will likely become increasingly complex as new anti-PD-L1/PD-1 agents and diagnostics are approved for TNBC. Integrating PD-L1 testing into current diagnostic workflows for mTNBC may provide more treatment options for these patients. Therefore, it is critical for medical oncologists and pathologists to understand the available assays and their relevance to therapeutic options to develop an appropriate workflow for IHC testing.

Genomic clustering analysis identifies molecular subtypes of thymic epithelial tumors independent of World Health Organization histologic type

Further characterization of thymic epithelial tumors (TETs) is needed. Genomic information from 102 evaluable TETs from The Cancer Genome Atlas (TCGA) dataset and from the IU-TAB-1 cell line (type AB thymoma) underwent clustering analysis to identify molecular subtypes of TETs. Six novel molecular subtypes (TH1-TH6) of TETs from the TCGA were identified, and there was no association with WHO histologic subtype. The IU-TAB-1 cell line clustered into the TH4 molecular subtype and in vitro testing of candidate therapeutics was performed. The IU-TAB-1 cell line was noted to be resistant to everolimus (mTORC1 inhibitor) and sensitive to nelfinavir (AKT1 inhibitor) across the endpoints measured. Sensitivity to nelfinavir was due to the IU-TAB-1 cell line’s gain-of function (GOF) mutation in PIK3CA and amplification of genes observed from array comparative genomic hybridization (aCGH), including AURKA, ERBB2, KIT, PDGFRA and PDGFB, that are known upregulate AKT, while resistance to everolimus was primarily driven by upregulation of downstream signaling of KIT, PDGFRA and PDGFB in the presence of mTORC1 inhibition. We present a novel molecular classification of TETs independent of WHO histologic subtype, which may be used for preclinical validation studies of potential candidate therapeutics of interest for this rare disease.

Race, Ethnicity, and Clinical Outcomes in Hormone Receptor-Positive, HER2-Negative, Node-Negative Breast Cancer in the Randomized TAILORx Trial

BACKGROUND

Black race is associated with worse outcomes in early breast cancer. We evaluated clinicopathologic characteristics, the 21-gene recurrence score (RS), treatment delivered, and clinical outcomes by race and ethnicity among women who participated in the Trial Assigning Individualized Options for Treatment.

METHODS

The association between clinical outcomes and race (White, Black, Asian, other or unknown) and ethnicity (Hispanic vs non-Hispanic) was examined using proportional hazards models. All P values are 2-sided.

RESULTS

Of 9719 eligible women with hormone receptor-positive, HER2-negative, node-negative breast cancer, there were 8189 (84.3%) Whites, 693 (7.1%) Blacks, 405 (4.2%) Asians, and 432 (4.4%) with other or unknown race. Regarding ethnicity, 889 (9.1%) were Hispanic. There were no substantial differences in RS or ESR1, PGR, or HER2 RNA expression by race or ethnicity. After adjustment for other covariates, compared with White race, Black race was associated with higher distant recurrence rates (hazard ratio [HR] = 1.60, 95% confidence intervals [CI] = 1.07 to 2.41) and worse overall survival in the RS 11-25 cohort (HR = 1.51, 95% CI = 1.06 to 2.15) and entire population (HR = 1.41, 95% CI = 1.05 to 1.90). Hispanic ethnicity and Asian race were associated with better outcomes. There was no evidence of chemotherapy benefit for any racial or ethnic group in those with a RS of 11-25.

CONCLUSIONS

Black women had worse clinical outcomes despite similar 21-gene assay RS results and comparable systemic therapy in the Trial Assigning Individualized Options for Treatment. Similar to Whites, Black women did not benefit from adjuvant chemotherapy if the 21-gene RS was 11-25. Further research is required to elucidate the basis for this racial disparity in prognosis.

Cisplatin +/- rucaparib after preoperative chemotherapy in patients with triple-negative or BRCA mutated breast cancer

Patients with triple-negative breast cancer (TNBC) who have residual disease after neoadjuvant therapy have a high risk of recurrence. We tested the impact of DNA-damaging chemotherapy alone or with PARP inhibition in this high-risk population. Patients with TNBC or deleterious BRCA mutation (TNBC/BRCAmut) who had >2 cm of invasive disease in the breast or persistent lymph node (LN) involvement after neoadjuvant therapy were assigned 1:1 to cisplatin alone or with rucaparib. Germline mutations were identified with BROCA analysis. The primary endpoint was 2-year disease-free survival (DFS) with 80% power to detect an HR 0.5. From Feb 2010 to May 2013, 128 patients were enrolled. Median tumor size at surgery was 1.9 cm (0-11.5 cm) with 1 (0-38) involved LN; median Residual Cancer Burden (RCB) score was 2.6. Six patients had known deleterious BRCA1 or BRCA2 mutations at study entry, but BROCA identified deleterious mutations in 22% of patients with available samples. Toxicity was similar in both arms. Despite frequent dose reductions (21% of patients) and delays (43.8% of patients), 73% of patients completed planned cisplatin. Rucaparib exposure was limited with median concentration 275 (82-4694) ng/mL post-infusion on day 3. The addition of rucaparib to cisplatin did not increase 2-year DFS (54.2% cisplatin vs. 64.1% cisplatin + rucaparib; P = 0.29). In the high-risk post preoperative TNBC/BRCAmut setting, the addition of low-dose rucaparib did not improve 2-year DFS or increase the toxicity of cisplatin. Genetic testing was underutilized in this high-risk population.

Multi-protein spatial signatures in ductal carcinoma in situ (DCIS) of breast

BACKGROUND

There is limited knowledge about DCIS cellular composition and relationship with breast cancer events (BCE).

METHODS

Immunofluorescence multiplexing (MxIF) was used to image and quantify 32 cellular biomarkers in FFPE DCIS tissue microarrays. Over 75,000 DCIS cells from 51 patients (median 9 years follow-up for non-BCE cases) were analysed for profiles predictive of BCE. K-means clustering was used to evaluate cellular co-expression of epithelial markers with ER and HER2.

RESULTS

Only ER, PR and HER2 significantly correlated with BCE. Cluster analysis identified 6 distinct cell groups with different levels of ER, Her2, cMET and SLC7A5. Clusters 1 and 3 were not significant. Clusters 2 and 4 (high ER/low HER2 and SLC7A5/mixed cMET) significantly correlated with low BCE risk (P = 0.001 and P = 0.034), while cluster 6 (high HER2/low ER, cMET and SLC7A5) correlated with increased risk (P = 0.018). Cluster 5 (similar to cluster 6, except high SLC7A5) trended towards significance (P = 0.072). A continuous expression score (Escore) based on these 4 clusters predicted likelihood of BCE (AUC = 0.79, log-rank test P = 5E-05; LOOCV AUC = 0.74, log-rank test P = 0.006).

CONCLUSION

Multiplexed spatial analysis of limited tissue is a novel method for biomarker analysis and predicting BCEs. Further validation of Escore is needed in a larger cohort.

CIBERSORT analysis of TCGA and METABRIC identifies subgroups with better outcomes in triple negative breast cancer

Studies have shown that the presence of tumor infiltrating lymphocytes (TILs) in Triple Negative Breast Cancer (TNBC) is associated with better prognosis. However, the molecular mechanisms underlying these immune cell differences are not well delineated. In this study, analysis of hematoxylin and eosin images from The Cancer Genome Atlas (TCGA) breast cancer cohort failed to show a prognostic benefit of TILs in TNBC, whereas CIBERSORT analysis, which quantifies the proportion of each immune cell type, demonstrated improved overall survival in TCGA TNBC samples with increased CD8 T cells or CD8 plus CD4 memory activated T cells and in Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) TNBC samples with increased gamma delta T cells. Twenty-five genes showed mutational frequency differences between the TCGA high and low T cell groups, and many play important roles in inflammation or immune evasion (ATG2B, HIST1H2BC, PKD1, PIKFYVE, TLR3, NOTCH3, GOLGB1, CREBBP). Identification of these mutations suggests novel mechanisms by which the cancer cells attract immune cells and by which they evade or dampen the immune system during the cancer immunoediting process. This study suggests that integration of mutations with CIBERSORT analysis could provide better prediction of outcomes and novel therapeutic targets in TNBC cases.

Tumour-infiltrating lymphocytes in ductal carcinoma in situ (DCIS)-assessment with three different methodologies and correlation with Oncotype DX DCIS Score

AIMS

Tumour-infiltrating lymphocytes (TILs) are prognostic in invasive breast cancer; however, their prognostic significance in ductal carcinoma in situ (DCIS) has not been established. The Oncotype DX (ODX) Breast DCIS Score test is a genomic assay used to predict the local recurrence risk. The aims of this study were to quantify TILs in DCIS by the use of three methodologies, and correlate them with the ODX DCIS Score.

METHODS AND RESULTS

We studied 97 DCIS cases, all with an ODX DCIS Score. Cases with a low ODX DCIS Score were considered as one group, and those with an intermediate/high ODX Score were considered together. TILs were quantified on haematoxylin and eosin-stained slides. The methodologies used to quantify TILS included assessment of stromal TILs, assessment of touching TILs, and assessment of circumferential TILS. In cases with >5% stromal TILS, the percentage of stromal TILS was considered to be high. In cases with a mean number of more than five touching TILs per DCIS duct, TILs were considered to be present. The ODX DCIS Score was intermediate/high in 27 (28%) cases and low in 70 (72%) cases. There were >5% stromal TILs in 33 (34%) cases, and more than five touching TILs per DCIS duct in 15 (15%) cases; circumferential TILs were present in nine (9%) cases. In univariate analysis, a low ODX DCIS Score showed significant associations with absent touching TILS (P = 0.027), stromal TILs < 5% (P = 0.031), and absent circumferential TILs (P = 0.002). In logistic regression analysis adjusted for necrosis and nuclear grade, touching TILs and circumferential TILs showed significant associations with the ODX DCIS Score, whereas stromal TILs did not.

CONCLUSIONS

Our results suggest that both the presence of TILs and the spatial arrangement of TILs or close proximity of TILs to DCIS, and TILs touching or encircling DCIS, may be predictive of recurrence.

Fibroblastic sarcomas of the mediastinum

Primary mediastinal fibroblastic sarcomas constitute a rare, heterogeneous group of neoplasms, mainly including solitary fibrous tumor (SFT) (benign and malignant), low grade fibromyxoid sarcoma (LGFMS), adult fibrosarcoma (FS), myxofibrosarcoma, sclerosing epithelioid FS, etc. Although morphologically diverse, they frequently have similar clinical and radiological features. Overlapping of histological features among these neoplasms can make it challenging for pathologists to come to an accurate diagnosis. In addition, other mesenchymal neoplasms and spindle cell neoplasms of the epithelial cell origin can occur in the mediastinum. Immunostaining and molecular testing are important ancillary studies to confirm or rule out primary mediastinal fibroblastic neoplasms. SFT and LGFMS occur more often than adult FS in the mediastinum and both have reliable immunostaining markers STAT6 and MUC4, respectively, and unique molecular changes. The incidence of adult FS has decreased dramatically due to recognition of morphologically and genetically distinctive subtypes of fibroblastic sarcoma and better understanding of mesenchymal and non-mesenchymal mimickers. Adult FS is extremely rare and a diagnosis of exclusion. Adult FS can be rendered only after careful histological examination and thorough ancillary studies have ruled out all its mimickers. This article is focused on reviewing clinicopathological features, immunostaining, molecular changes, prognosis and differential diagnosis of SFT, LGFMS, and adult FS. Correct diagnosis is crucial for oncologists to make appropriate clinical management plans.

ColoType: a forty gene signature for consensus molecular subtyping of colorectal cancer tumors using whole-genome assay or targeted RNA-sequencing

Colorectal cancer (CRC) tumors can be partitioned into four biologically distinct consensus molecular subtypes (CMS1-4) using gene expression. Evidence is accumulating that tumors in different subtypes are likely to respond differently to treatments. However, to date, there is no clinical diagnostic test for CMS subtyping. In this study, we used novel methodology in a multi-cohort training domain (n = 1,214) to develop the ColoType scores and classifier to predict CMS1-4 based on expression of 40 genes. In three validation cohorts (n = 1,744, in total) representing three distinct gene-expression measurement technologies, ColoType predicted gold-standard CMS subtypes with accuracies 0.90, 0.91, 0.88, respectively. To accommodate for potential intratumoral heterogeneity and tumors of mixed subtypes, ColoType was designed to report continuous scores measuring the prevalence of each of CMS1-4 in a tumor, in addition to specifying the most prevalent subtype. For analysis of clinical specimens, ColoType was also implemented with targeted RNA-sequencing (Illumina AmpliSeq). In a series of formalin-fixed, paraffin-embedded CRC samples (n = 49), ColoType by targeted RNA-sequencing agreed with subtypes predicted by two independent methods with accuracies 0.92, 0.82, respectively. With further validation, ColoType by targeted RNA-sequencing, may enable clinical application of CMS subtyping with widely-available and cost-effective technology.

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.

Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring.

Clinical Outcomes in Early Breast Cancer With a High 21-Gene Recurrence Score of 26 to 100 Assigned to Adjuvant Chemotherapy Plus Endocrine Therapy: A Secondary Analysis of the TAILORx Randomized Clinical Trial

Importance

A high 21-gene recurrence score (RS) by breast cancer assay is prognostic for distant recurrence of early breast cancer after local therapy and endocrine therapy alone, and for chemotherapy benefit.

Objective

To describe clinical outcomes for women with a high RS who received adjuvant chemotherapy plus endocrine therapy in the TAILORx trial, a population expected to have a high distant recurrence rate with endocrine therapy alone.

Design, Setting, and Participants

In this secondary analysis of data from a multicenter randomized clinical trial, 1389 women with hormone receptor-positive, ERBB2-negative, axillary node-negative breast cancer, and a high RS of 26 to 100 were prospectively assigned to receive adjuvant chemotherapy in addition to endocrine therapy. The analysis was conducted on May 12, 2019.

Interventions

The adjuvant chemotherapy regimen was selected by the treating physician.

Main Outcomes and Measures

Freedom from recurrence of breast cancer at a distant site, and freedom from recurrence, second primary cancer, and death (also known as invasive disease-free survival [IDFS]).

Results

Among the 9719 eligible women, with a mean age of 56 years (range 23-75 years), 1389 (14%) had a recurrence score of 26 to 100, of whom 598 (42%) had an RS of 26 to 30 and 791 (58%) had an RS of 31 to 100. The most common chemotherapy regimens included docetaxel/cyclophosphamide in 589 (42%), an anthracycline without a taxane in 334 (24%), an anthracycline and taxane in 244 (18%), cyclophosphamide/methotrexate/5-fluorouracil in 52 (4%), other regimens in 81 (6%), and no chemotherapy in 89 (6%). At 5 years, the estimated rate of freedom from recurrence of breast cancer at a distant site was 93.0% (standard error [SE], 0.8%), freedom of recurrence of breast cancer at a distant and/or local regional site 91.0% (SE, 0.8%), IDFS 87.6% (SE, 1.0%), and overall survival 95.9% (SE, 0.6%).

Conclusions and Relevance

The estimated rate of freedom from recurrence of breast cancer at a distant site in women with an RS of 26 to 100 treated largely with taxane and/or anthracycline-containing adjuvant chemotherapy regimens plus endocrine therapy in the prospective TAILORx trial was 93% at 5 years, an outcome better than expected with endocrine therapy alone in this population.

Trial Registration

ClinicalTrials.gov identifier: NCT00310180.

Abstract P2-10-06: Ethnicity-dependent alternative RNA splicing variations of estrogen receptor in breast cancer

Background: African-American (AA) women are more likely to have poorer outcomes and die of breast cancer than European Ancestry (EA) women, even among patients with similar stage and tumor subtype. Despite the higher incidence of aggressive triple-negative breast cancer (TNBC) in AA women, the greatest survival disparities are observed within the “good-prognosis” estrogen receptor receptor-positive (ERpos) subtypes. This exists even after correcting for the socioeconomic factors suggesting the distinct biological basis for disparities. Understanding the factors underpinning breast cancer disparities is critical to reduce the disparity-related poor outcomes. We hypothesized that Alternative RNA splicing (ARS) of estrogen receptor could influence the tumor aggressiveness and particularly, response to therapy. To this end, we examined the expression of estrogen receptor (ER) transcripts in AA and EA ethnicity groups in breast cancer. Design: The effect of ethnicity on alternative RNA splicing of ER was explored using BRCA-TCGA data and a web-based tool for splicing variants analysis. The significance of ESR1 transcripts with respect to race, ER, Progesterone receptor (PR) and tumor stage was analyzed using JMP statistical package. Results: Expression of the 27 ESR1 transcripts were analyzed in 838 cases (705 EA and 133 AA). Of these 27 transcripts, 16 were expressed in TCGA-BRCA cohort. The majority of these cases belonged to ERpos/PRpos/HER2neg group (n=339; 308 EA and 31 AA). Differential expression of four transcripts (isoform_uc003qom, P = 0.0047; isoform_uc010kio, P = 0.0345; isoform_uc010kir, P = 0.0492 and isoform_uc011eev, P = 0.0066) were significant in AA compared to EA women; all of these were lower in AA. Similar analyses by Stage in this group demonstrated that overall ESR1 levels were associated with tumor stage but none of the individual transcripts exhibited similar association. In ERpos/PRneg/HER2neg subgroup (n=61; 48 EA and 13 AA), two transcripts (isoform_uc010kir, P = 0.028 and isoform_uc011eey, P = 0.0435) retained significance suggesting the important interaction of PR with race. As expected, most of the ER transcripts were not significant in 112 TNBC (78 EA and 34 AA) patients except for the isoform_uc010eev, P = 0.0354. In ERpos/PRpos/HER2pos cases (n=89; 81 EA and 8 AA), isoform_uc010kir, P = 0.0056 and isoform_uc010kis, P = 0.0365 were significantly differentially expressed by race. There was no difference in transcript expression in HER2pos group (n=29; 22 EA and 7AA). Conclusions: Dramatic variation in ESR1 transcript expression was observed in AA versus EA populations. These variations were further affected by ER and PR status. As variations in transcript expression can have a striking impact on mRNA stability and translation efficacy, better understanding of transcript differences is necessary. The observed results have several important implications for clinical management and could explain some of the differences in responses to endocrine therapy observed in association with ethnicity dependent health disparities.

Citation Format: Yesim Gokmen-Polar, Sunil S Badve. Ethnicity-dependent alternative RNA splicing variations of estrogen receptor in 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 P2-10-06.

Abstract P5-02-01: Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study

Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but has unacceptable between-laboratory variability. Here we tested an open source and calibrated automated digital image analysis (DIA) platform to: (i) Assess inter-laboratory reproducibility of automated Ki67 measurement among 17 participating labs and compare those with standardized pathologist-based visual scoring. (ii) Investigate the comparability of Ki67 measurement across corresponding core biopsy and whole section cases. (iii) Test prognostic potential of the built Ki67 scoring algorithms on an independent cohort.

Methods: Two sets of 60 previously stained slides containing 30 core-cut biopsy and 30 corresponding whole tumor sections from 30 ER+ breast cancer cases were sent to 17 participating labs for automated assessment of average Ki67 expression. The blocks were centrally cut and stained for Ki67 using the Mib-1 antibody. The QuPath (open-source software) DIA platform was used to evaluate tumoral Ki67 expression. Calibration of the DIA method was performed in our previous study (Acs et al, Lab Invest 2019). A detailed guideline for building an automated Ki67 scoring algorithm was sent to the participating labs. Visual scoring of average Ki67 expression was performed by pathologists according to published standardized methods (Leung et al, NPJ Br Cancer 2016; Leung et al, Histopath 2019). Locked down DIA Ki67 scoring algorithms were applied to a validation cohort: 222 breast cancer cases from the Karolinska University Hospital in whole section format. Sufficient reproducibility to declare analytical validity was defined as an Intra Class Correlation (ICC) with lower limit of 95% credible interval (CI) &gt;0.80. Markov Chain Monte Carlo routines for generalized linear mixed models were used to estimate ICCs and calculate corresponding CIs.

Results: The same-section ICC was 0.902 (CI: 0.852-0.949) across 17 labs using calibrated DIA platform on core biopsy slides and 0.845 (CI: 0.778-0.912) on whole sections. The different-section ICC across the 17 labs was 0.873 (CI: 0.806-0.932) scoring on core biopsy slides and 0.777 (CI: 0.670-0.874) on whole sections. The pathologist-based visual Ki67 scoring showed ICC of 0.860 for all comparisons, respectively (CI: 0.795-0.927). Similar to what was observed for visual Ki67 scoring, the DIA scores are higher for core biopsy slides compared to paired whole sections (p≤0.001; median difference: 5.31%; IQR: 11.50%). Ki67 scores of all locked down DIA algorithms correlates significantly (p≤0.023) with outcome on the validation cohort (observed hazard ratios range: 2.518-2.922).

Conclusions: Automated Ki67 evaluation using a calibrated, open-source DIA platform (QuPath) met the pre-specified criterion of success on core biopsies but not on whole sections in the multi-institutional setting. The systematic discrepancy between core biopsy and corresponding whole sections was likely due to pre-analytical factors (tissue handling, fixation) and intratumor heterogeneity. We found that different algorithms built according to calibrated DIA methods had similar prognostic potential. Assessment of clinical utility is planned.

Citation Format: Balazs Acs, Samuel C.Y. Leung, Kelley M. Kidwell, Indu Arun, Renaldas Augulis, Sunil S. Badve, Yalai Bai, Anita L. Bane, John M.S. Bartlett, Jane Bayani, Gilbert Bigras, Annika Blank, Signe Borgquist, Henk Buikema, Martin C. Chang, Robin L. Dietz, Andrew Dodson, Anna Ehinger, Susan Fineberg, Cornelia M. Focke, Dongxia Gao, Allen M. Gown, Carolina Gutierrez, Johan Hartman, Judith C. Hugh, Zuzana Kos, Anne-Vibeke Lænkholm, Arvydas Laurinavicius, Richard M. Levenson, Rustin Mahboubi-Ardakani, Mauro G. Mastropasqua, Takuya Moriya, Sharon Nofech-Mozes, C. Kent Osborne, Liron Pantanowitz, Frédérique M. Penault-Llorca, Tammy Piper, Mary Anne Quintayo, Tilman T. Rau, Stefan Reinhard, Stephanie Robertson, Takashi Sakatani, Roberto Salgado, Melanie Spears, Jane Starczynski, Tomoharu Sugie, Bert van der Vegt, Giuseppe Viale, Shakeel Virk, Lila A. Zabaglo, Daniel F. Hayes, Mitch Dowsett, Torsten O. Nielsen, David L. Rimm, International Ki67 in Breast Cancer Working Group, BIG-NABCG. Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study [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 P5-02-01.

Ductal carcinoma in situ of breast: update 2019

Ductal carcinoma in situ is a non-invasive form of breast cancer. Its incidence is increasing due to widespread use of mammographic screening. It presents several diagnostic and management challenges in part due to its relatively indolent behaviour. Most series analysing biomarkers in these lesions are small (<100 patients) and large clinical trials have not been frequent. Herein, we review the recent progress made in understanding the biology of this entity and the tools available for prognostication.

Independent Validation of EarlyR Gene Signature in BIG 1-98: A Randomized, Double-Blind, Phase III Trial Comparing Letrozole and Tamoxifen as Adjuvant Endocrine Therapy for Postmenopausal Women With Hormone Receptor-Positive, Early Breast Cancer

Background

EarlyR gene signature in estrogen receptor–positive (ER+) breast cancer is computed from the expression values of ESPL1, SPAG5, MKI67, PLK1, and PGR. EarlyR has been validated in multiple cohorts profiled using microarrays. This study sought to verify the prognostic features of EarlyR in a case-cohort sample from BIG 1–98, a randomized clinical trial of ER+ postmenopausal breast cancer patients treated with adjuvant endocrine therapy (letrozole or tamoxifen).

Methods

Expression of EarlyR gene signature was estimated by Illumina cDNA-mediated Annealing, Selection, and Ligation assay of RNA from formalin-fixed, paraffin-embedded primary breast cancer tissues in a case-cohort subset of ER+ women (N = 1174; 216 cases of recurrence within 8 years) from BIG 1–98. EarlyR score and prespecified risk strata (≤25 = low, 26–75 = intermediate, >75 = high) were “blindly” computed. Analysis endpoints included distant recurrence–free interval and breast cancer–free interval at 8 years after randomization. Hazard ratios (HRs) and test statistics were estimated with weighted analysis methods.

Results

The distribution of the EarlyR risk groups was 67% low, 19% intermediate, and 14% high risk in this ER+ cohort. EarlyR was prognostic for distant recurrence–free interval; EarlyR high-risk patients had statistically increased risk of distant recurrence within 8 years (HR = 1.73, 95% confidence interval = 1.14 to 2.64) compared with EarlyR low-risk patients. EarlyR was also prognostic of breast cancer–free interval (HR = 1.74, 95% confidence interval = 1.21 to 2.62).

Conclusions

This study confirmed the prognostic significance of EarlyR using RNA from formalin-fixed, paraffin-embedded tissues from a case-cohort sample of BIG 1–98. EarlyR identifies a set of high-risk patients with relatively poor prognosis who may be considered for additional treatment. Further studies will focus on analyzing the predictive value of EarlyR signature.

Profiling molecular regulators of recurrence in chemorefractory triple-negative breast cancers

Background

Approximately two thirds of patients with localized triple-negative breast cancer (TNBC) harbor residual disease (RD) after neoadjuvant chemotherapy (NAC) and have a high risk-of-recurrence. Targeted therapeutic development for TNBC is of primary significance as no targeted therapies are clinically indicated for this aggressive subset. In view of this, we conducted a comprehensive molecular analysis and correlated molecular features of chemorefractory RD tumors with recurrence for the purpose of guiding downstream therapeutic development.

Methods

We assembled DNA and RNA sequencing data from RD tumors as well as pre-operative biopsies, lymphocytic infiltrate, and survival data as part of a molecular correlative to a phase II post-neoadjuvant clinical trial. Matched somatic mutation, gene expression, and lymphocytic infiltrate were assessed before and after chemotherapy to understand how tumors evolve during chemotherapy. Kaplan-Meier survival analyses were conducted categorizing cancers with TP53 mutations by the degree of loss as well as by the copy number of a locus of 18q corresponding to the SMAD2, SMAD4, and SMAD7 genes.

Results

Analysis of matched somatic genomes pre-/post-NAC revealed chaotic acquisition of copy gains and losses including amplification of prominent oncogenes. In contrast, significant gains in deleterious point mutations and insertion/deletions were not observed. No trends between clonal evolution and recurrence were identified. Gene expression data from paired biopsies revealed enrichment of actionable regulators of stem cell-like behavior and depletion of immune signaling, which was corroborated by total lymphocytic infiltrate, but was not associated with recurrence. Novel characterization of TP53 mutation revealed prognostically relevant subgroups, which were linked to MYC-driven transcriptional amplification. Finally, somatic gains in 18q were associated with poor prognosis, likely driven by putative upregulation of TGFß signaling through the signal transducer SMAD2.

Conclusions

We conclude TNBCs are dynamic during chemotherapy, demonstrating complex plasticity in subclonal diversity, stem-like qualities, and immune depletion, but somatic alterations of TP53/MYC and TGFß signaling in RD samples are prominent drivers of recurrence, representing high-yield targets for additional interrogation.

Electronic supplementary material

The online version of this article (10.1186/s13058-019-1171-7) contains supplementary material, which is available to authorized users.

Analytical validation of a standardised scoring protocol for Ki67 immunohistochemistry on breast cancer excision whole sections: an international multicentre collaboration

AIMS

The nuclear proliferation marker Ki67 assayed by immunohistochemistry has multiple potential uses in breast cancer, but an unacceptable level of interlaboratory variability has hampered its clinical utility. The International Ki67 in Breast Cancer Working Group has undertaken a systematic programme to determine whether Ki67 measurement can be analytically validated and standardised among laboratories. This study addresses whether acceptable scoring reproducibility can be achieved on excision whole sections.

METHODS AND RESULTS

Adjacent sections from 30 primary ER⁺ breast cancers were centrally stained for Ki67 and sections were circulated among 23 pathologists in 12 countries. All pathologists scored Ki67 by two methods: (i) global: four fields of 100 tumour cells each were selected to reflect observed heterogeneity in nuclear staining; (ii) hot-spot: the field with highest apparent Ki67 index was selected and up to 500 cells scored. The intraclass correlation coefficient (ICC) for the global method [confidence interval (CI) = 0.87; 95% CI = 0.799-0.93] marginally met the prespecified success criterion (lower 95% CI ≥ 0.8), while the ICC for the hot-spot method (0.83; 95% CI = 0.74-0.90) did not. Visually, interobserver concordance in location of selected hot-spots varies between cases. The median times for scoring were 9 and 6 min for global and hot-spot methods, respectively.

CONCLUSIONS

The global scoring method demonstrates adequate reproducibility to warrant next steps towards evaluation for technical and clinical validity in appropriate cohorts of cases. The time taken for scoring by either method is practical using counting software we are making publicly available. Establishment of external quality assessment schemes is likely to improve the reproducibility between laboratories further.

Abstract 2109: A novel role for ESRP1 in regulating proliferation in therapy-resistant ER-positive breast cancer

Epithelial Splicing Regulatory Protein 1 (ESRP1) is a key splicing factor that plays an important role in cancer. We have previously demonstrated that ESRP1 is associated with poor prognosis and tamoxifen resistance in human ER-positive (ER+) breast tumors. Knockdown of ESRP1 decreased the tumor growth in ER+ breast cancer models resistant to endocrine therapy. In this study, we explored the upstream/downstream regulatory mechanisms of ESRP1 in tamoxifen-resistant breast cancer using ESRP1 knockdown model. Probe based-Human Transcriptome Array 2.0 (HTA; Applied Biosystems/Thermo Fisher) was performed using RNAs from control and ESRP1 knockdown cells [tamoxifen-resistant LCC2 cells (2-control) versus LCC2 cells with ESRP1 knockdown (2C3)] in ER+ breast cancer. Transcriptome profiling of ESRP1 in 2C3 knockdown model revealed that CEBP gamma, a transcription factor belonging to the CCAAT/enhancer-binding protein (C/EBP) family, was significantly decreased in ESRP1 knockdown cells (p value=2.33E-06). The expression of other related proteins C/EBP family including C/EBP alpha, C/EBP beta, and C/EBP delta that form homodimers and heterodimers with each other was also assessed. In knockdown cells, C/EBP alpha was increased (p value=0.0022), while two different C/EBP beta transcripts were decreased (p values=0.0010 and 0.03, respectively). C/EBP delta expression was not significantly altered. Using a competitive promoter-binding transcription-factor assay, we measured the transcription activity of C/EBP gamma in the absence and presence of ESRP1 promoter DNA fragment. We identified strong binding of C/EBP gamma to ESRP1 promoter region indicating that it is upstream regulator of ESRP1. CEBP transcription factor family members are important regulators of proliferation via cyclin-dependent kinases (CDKs). We further demonstrated that CDK4/CDK6 inhibitor abemaciclib decreases the expression of ESRP1 and C/EBPG levels significantly (p values= 0.0009 and 0.0019, respectively). In conclusion, for the first time, we identify that C/EBP gamma upregulates ESRP1 expression, which further regulates proliferation through control of expression of CDKs.

Citation Format: Yesim Gökmen-Polar, Yuan Gu, Xiaoping Gu, Sunil S. Badve. A novel role for ESRP1 in regulating proliferation in therapy-resistant ER-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2109.

Clinical and Genomic Risk to Guide the Use of Adjuvant Therapy for Breast Cancer

BACKGROUND

The use of adjuvant chemotherapy in patients with breast cancer may be guided by clinicopathological factors and a score based on a 21-gene assay to determine the risk of recurrence. Whether the level of clinical risk of breast cancer recurrence adds prognostic information to the recurrence score is not known.

METHODS

We performed a prospective trial involving 9427 women with hormone-receptor-positive, human epidermal growth factor receptor 2-negative, axillary node-negative breast cancer, in whom an assay of 21 genes had been performed, and we classified the clinical risk of recurrence of breast cancer as low or high on the basis of the tumor size and histologic grade. The effect of clinical risk was evaluated by calculating hazard ratios for distant recurrence with the use of Cox proportional-hazards models. The initial endocrine therapy was tamoxifen alone in the majority of the premenopausal women who were 50 years of age or younger.

RESULTS

The level of clinical risk was prognostic of distant recurrence in women with an intermediate 21-gene recurrence score of 11 to 25 (on a scale of 0 to 100, with higher scores indicating a worse prognosis or a greater potential benefit from chemotherapy) who were randomly assigned to endocrine therapy (hazard ratio for the comparison of high vs. low clinical risk, 2.73; 95% confidence interval [CI], 1.93 to 3.87) or to chemotherapy plus endocrine (chemoendocrine) therapy (hazard ratio, 2.41; 95% CI, 1.66 to 3.48) and in women with a high recurrence score (a score of 26 to 100), all of whom were assigned to chemoendocrine therapy (hazard ratio, 3.17; 95% CI, 1.94 to 5.19). Among women who were 50 years of age or younger who had received endocrine therapy alone, the estimated (±SE) rate of distant recurrence at 9 years was less than 5% (≤1.8±0.9%) with a low recurrence score (a score of 0 to 10), irrespective of clinical risk, and 4.7±1.0% with an intermediate recurrence score and low clinical risk. In this age group, the estimated distant recurrence at 9 years exceeded 10% among women with a high clinical risk and an intermediate recurrence score who received endocrine therapy alone (12.3±2.4%) and among those with a high recurrence score who received chemoendocrine therapy (15.2±3.3%).

CONCLUSIONS

Clinical-risk stratification provided prognostic information that, when added to the 21-gene recurrence score, could be used to identify premenopausal women who could benefit from more effective therapy. (Funded by the National Cancer Institute and others; ClinicalTrials.gov number, NCT00310180.).

Abstract P4-08-17: Expression score (Escore) for the prediction of likelihood of recurrence of DCIS

Background: Ductal carcinoma in situ (DCIS) accounts for at least 20% of breast cancers. Factors associated with recurrence of DCIS or progression to invasive carcinoma are not well delineated. The goals of the current study were to profile the epithelial cells using the GE Cell DIVE™ immuno-fluorescent based analyses. This was coupled with semi-automated algorithms to characterize the inter-relationships between cell populations and likelihood of recurrence.

Patients and Methods: A TMA-based (total 8 TMAs) cohort of cases of DCIS with and without recurrence was obtained from Oxford University. Recurrence in this cohort was defined as ipsilateral DCIS, ipsilateral invasive, contralateral invasive and metastatic. Analysis for 31 epithelial markers (HER4, CK56, ABCG2, PTEN, S6, CKAE1, PR, ER, NaKATPase, CK19, ALDH1, CK PCK26, cMET, CD44v6, HER2, CDCP1, p53, CK15, COX2, VEGFR2, ABCb1, HTF9C, CD10, MRP4, CEACAM5, EGFR, p21, MRP5, SLC7A5, Ki67, DAPI) was performed on a single FFPE TMA section containing cases of DCIS. Briefly, FFPE sections from TMAs containing DCIS were sequentially (cyclically) stained for the markers. Each cycle entailed staining with 2-3 markers followed by imaging, dye inactivation, and re-staining. DAPI was used for nuclear demarcation and for registration of the images, while S6, pan-cadherin, Na+K+ATPase and pan-cytokeratin were used for epithelial segmentation. K-means clustering followed regression analysis was performed to identify inter-relationships between markers and association with likelihood of recurrence. Log-rank analysis was performed and the relapse-free survival data depicted using Kaplan Meier plots. Escore was developed by logistic regression model, classification model on recurrence

Results: Filtering of the expression analysis by the quality, specificity, compartment localization and fields entirely composed of DCIS, in addition to availability of clinical data resulted final analysis of 31 markers in 67 cases. Correlation analyses were performed on each of the markers to identify markers that were significantly correlated in univariate analysis. K-means cluster analysis was performed using a set of 4 markers (ER, HER2, SLC7A5 and cMET) to identify 6 clusters. High cMET (cluster 1; low HER2 and SLC7A5) and High ER (low cMET, HER2, SLC7A5; Cluster 5) were associated with low risk of recurrence (p values 0.014 and &lt;0.0001). In contrast, Cluster 2 (High HER2, high SLC7A5, low ER) and Cluster 3 (High HER2, low ER, SLC7A5and cMET) were associated with increased risk of recurrence (P values 0.038 and 0.076). A regression analysis based algorithm was developed using these markers to calculate a numerical score which could predict likelihood of recurrence. As depicted in the KM plots, the HR for recurrence increases significantly (P-value 2.4E-05; p=0.02 with LOOCV) with increase in expression score (Escore).

Conclusions: We describe the development of an Escore using expression 4 markers to predict likelihood of recurrence. Additional ongoing studies will seek to validate the utility of the Escore in predicting likelihood of recurrence of DCIS and development of invasive carcinomas and comparison with other scoring systems.

Citation Format: Badve SS, Cho S, Gokmen-Polar Y, Zavodszky M, Sui Y, Chadwick C, Tan PH, Gerdes M, Harris AL, Ginty F. Expression score (Escore) for the prediction of likelihood of recurrence of DCIS [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 P4-08-17.

Abstract P5-04-13: Splicing factor ESRP1 controls ER-positive breast cancer progression by altering metabolic pathway genes

Background Epithelial Splicing Regulatory Protein (ESRP1)is a key splicing factor that regulates Epithelial-to-Mesenchymal Transition (EMT) splicing program. Our previous study demonstrated that high levels of ESRP1 are associated with poor prognosis in human ER-positive (ER+) breast tumors in an independent manner of EMT process. We next explored the potential mechanisms that contribute to the role ESRP1 in endocrine therapy-resistant breast cancer.

Methods Probe based-Human Transcriptome Array 2.0 (HTA; Applied Biosystems/Thermo Fisher) was performed using RNAs from control and ESRP1 knockdown cells (LCC2 versus 2C3 ESRP1 and LCC9 versus 9C2 ESRP1) of endocrine resistant breast cancer. Functional enrichment analyses were performed using the DAVID functional annotation tool (http://david.abcc.ncifcrf.gov/). To confirm the functional importance of ESRP1 on regulation of cellular metabolism, we have performed experiments that analyze the metabolic substrate flux in response to ESRP1 knockdown in resistant cells (The Seahorse XFp Cell Energy Phenotype Assay). Differentially expressed genes were validated using Western blotting assay.

Results Transcriptome profiling of ESRP1in 2C3 and 9C2 knockdown models revealed differentially expressed genesusing HTA 2.0 platform. In LCC2 versus 2C3 ESRP1 knockdown, expression of 1186 genes (1263 transcripts) have been altered significantly, while 413 genes (432 transcripts) have been significantly regulated in LCC9 versus 9C2 ESRP1 knockdown with FDR&lt;0.1 Of these significant genes, 34 downregulated and 68 upregulated (102 genes total) were shared by both 2C3 and 9C2 ESRP1 knockdowns. Using the DAVID Functional Annotation Clustering Tool, we identified the biological processes altered significantly in response to ESRP1 knockdown. The most significant annotation clusters downregulated in ESRP1 knockdown consists of fatty acid metabolism/lipid metabolism (SCD, ACACA, FASN, ACAT2, PLCH1, and HPGD), and oxireductase processes (SCD, PHGDH, FASN, DHTKD1 and HPGD. We confirmed the altered metabolic function using the Seahorse analyzer. These analyses confirmed that ESRP1 knockdown altered the glycolysis rate (extracellular acidification rate; ECAR) in both tamoxifen-resistant and fulvestrant-resistant models. In addition, ESRP1 knockdown decreased the mitochondrial respiration in tamoxifen-resistant cells, but not fulvestrant resistant cells. Using Western blotting, we validated the altered levels of fatty acid synthase (FASN) and Stearoyl-CoA desaturase 1 (SCD1), key enzymes in fatty acid metabolism. Phosphoglycerate Dehydrogenase (PHGDH), a poor prognosis marker in cancers including breast cancer, was also downregulated in response to ESRP1 knockdown. Taken together, we have demonstrated a novel functional impact of ESRP1 on the regulation of tumor growth at the functional and molecular level independent of EMT.

Conclusions For the first time, we show the role of ESRP1 in altering the cellular metabolism thereby contributing to tumor growth. The study provides a molecular evidence for the role of altered metabolism in determining adverse prognosis of ER+ breast cancer via the control of ESRP1, a splicing factor. Further studies to determine the therapeutic value are underway.

Citation Format: Gokmen-Polar Y, Gu Y, Gu X, Badve SS. Splicing factor ESRP1 controls ER-positive breast cancer progression by altering metabolic pathway genes [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 P5-04-13.

Abstract GS4-07: Race, ethnicity and clinical outcomes in hormone receptor-positive, HER2-negative, node-negative breast cancer: results from the TAILORx trial

Background: Black race is associated with worse outcomes in localized hormone receptor (HR)-positive breast cancer in population-based and in clinical trial cohorts, whether using self-identified race (Albain et al. JNCI 2009 [PMID: 19584328; Sparano et al. JNCI 2012 [PMID: 22250182) or genetically-identified race (Schneider et al. J Precision Oncol 2017 [PMID: 29333527]). This disparity persists after adjustment for treatment delivery parameters (Hershman et al. JCO 2009 [PMID:19307504]). We evaluated clinicopathologic characteristics, treatment delivered and clinical outcomes in the Trial Assigning Individualized Options for Treatment (TAILORx) by race and ethnicity (Sparano et al. NEJM 2018 [PMID: 29860917]).

Methods: The analysis included 9719 evaluable TAILORx participants. The association between clinical outcomes and race (white, black, Asian, other/unknown) and ethnicity (Hispanic vs. non-Hispanic) was examined, including invasive disease-free survival (iDFS), distant relapse-free interval (DRFI), relapse-free interval (RFI), and overall survival (OS). Proportional hazards models were fit including age (5 categories), tumor size (&gt;2 cm vs. &lt;=2 cm), histologic grade (high vs. medium vs. low vs. unknown), continuous recurrence score (RS), race, and ethnicity in the overall population and randomized treatment arms in the RS 11-25 cohort.

Results: The study population included 8189 (84%) whites, 693 (7%) blacks, 405 (4%) Asians, and 432 (4%) with other/unknown race. Regarding ethnicity, 7635 (79%) were non-Hispanic, 889 (9%) Hispanic, and 1195 (12%) unknown. There was no significant difference in RS distribution (p=0.22) in blacks compared with whites, or in median (17 vs. 17) or mean RS (19.1 vs. 18.2). There was likewise no difference in Hispanic vs. non-Hispanic ethnicity for RS distribution (p=0.72) or median (17 vs. 17) or mean RS (18.5 vs. 18.0). Black race (39% vs. 30%) and Hispanic ethnicity (39% vs. 30%) were both associated with younger age (&lt;/=50 years) at diagnosis. The use and type of adjuvant chemotherapy and endocrine therapy, and duration of endocrine therapy, were similar in black (vs. white) and Hispanic (vs. non-Hispanic) populations. In proportional hazards models, black race (compared with white race) was associated with worse clinical outcomes in the entire population and in those with a RS 11-25 (see table). Hispanic ethnicity was generally associated with better outcomes (compared with non-Hispanic ethnicity). For the cohort with a RS of 11-25, there was no evidence for chemotherapy benefit for any racial or ethnic group.

Race (black vs.white) and clinical outcomes in proportional hazards modelsClinical endpointEntire Population (N=693 black) Hazard ratio for eventRS 11-25 (N=471 black) Hazard ratio for eveniDFS1.33 (p=0.005)1.49 (p=0.001)DRFI1.21 (p=0.28)1.60 (p=0.02)RFI1.39 (p=0.02)1.80 (p&lt;0.001)OS1.52 (p=0.005)1.67 (p=0.003

Conclusions: In patients eligible and selected for participation in TAILORx, black women had worse clinical outcomes despite similar 21-gene assay RS results and comparable systemic therapy. This adds to an emerging body of evidence suggesting a biologic basis or other factors contributing to racial disparities in HR-positive breast cancer that requires further evaluation.

Citation Format: Albain K, Gray RJ, Sparano JA, Makower DF, Pritchard KI, Hayes DF, Geyer, Jr. CE, Dees EC, Goetz MP, Olson, Jr. JA, Lively T, Badve SS, Saphner TJ, Wagner LI, Whelan TJ, Ellis MJ, Paik S, Wood WC, Ravdin PM, Keane MM, Gomez HL, Reddy PS, Goggins TF, Mayer IA, Brufsky AM, Toppmeyer DL, Kaklamani VG, Berenberg JL, Abrams J, Sledge, Jr. GW. Race, ethnicity and clinical outcomes in hormone receptor-positive, HER2-negative, node-negative breast cancer: results from the TAILORx trial [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 GS4-07.

ColotypeR gene signature predicts response to cetuximab in colorectal cancer metastases

599

Background: The consensus molecular subtypes (CMS1-4) partition primary colorectal cancer (CRC) into subgroups with distinct molecular characteristics. We previously reported a 20-genes ColotypeR-CMS signature that accurately defines CMS subtypes for primary CRC tumor samples. The utility of CMS subtyping in defining response to treatment of CRC metastases remains to be established. Here, we report the ability of ColotypeR scores to predict differential response to cetuximab among CMS subtypes in CRC metastases. Methods: The role of ColotypeR-CMS signature scores was assessed in CRC metastasis samples (GSE5851, N = 68, Affymetrix microarray) in predicting response to cetuximab. Progression-free survival (PFS) was the primary endpoint. The predictive significance of ColotypeR-CMS scores relative to KRAS mutation status was also studied using multivariate Cox proportional hazards models. Results: ColotypeR-CMS scores were computed in GSE5851 using the algorithm developed in primary tumor samples. Higher values of ColotypeR-CMS CMS2 score were significantly predictive of longer PFS (p = 5 x 10-5for the score test in Cox proportional hazards model; hazard ratio 0.20 (95%CI 0.09-0.44) in CRC metastases samples (GSE5851, N = 68) treated with cetuximab. PFS was independent of CMS1,3, 4 scores. KRAS wild type tumors had significantly longer PFS (p = 0.01; hazard ratio 0.49 (95%CI 0.28-0.86). In multivariate survival analysis, ColotypeR-CMS CMS2 score added to the significance of KRAS status (p = 0.012) and ColotypeR-CMS CMS2 score was predictive of longer PFS in KRAS wild type tumors (p = 0.009; hazard ratio 0.20 (95%CI 0.06-0.69)). Conclusions: We showed that in CRC metastasis samples, the ColotypeR CMS2 score was highly predictive of sensitivity to cetuximab treatment, while no increase in PFS was observed for higher values of CMS1, 3, 4 scores.

CMS-PDX: A 20-gene genomic panel to predict consensus molecular subtypes in patient-derived xenografts (PDX) of colorectal cancer

598

Background: The consensus molecular subtypes (CMS1-4) partition colorectal cancer (CRC) into subgroups with varying prognoses and treatment responses. We previously reported the ColotypeR-CMS genomic scores (4 scores defined with 5 genes each) that accurately define the CMS subtypes of primary CRC tumors. There is also a critical need to develop an epithelial cell based algorithm for CMS subtyping of PDX models. Methods: To define scores predicting CMS subtypes for PDX models, genes that both predict CMS subtypes in primary CRC tissue and that have linearly correlated expression in primary tumor and tissue-matched PDX models, were identified in GSE35144 (N = 64, Affymetrix microarray). Using the identified genes, a 20-gene CMS-PDX score was developed using multistate gene methodology. ROC curve (AUC) analysis was used to measure the ability of CMS-PDX scores to predict subtypes obtained with CMScaller (473 genes), a preclinical CMS classifier. The ability of CMS subtypes to determine cetuximab response in PDX cohorts was analyzed in GSE78806 (N = 121, Affymetrix microarray) and GSE76402 (N = 529, Illumina beadarray). Results: In GSE78806 (N = 121), CMS1-4 subtypes obtained with CMScaller were predicted by CMS-PDX scores with AUC 0.88, 0.94, 0.81, 0.86, respectively; in GSE78806 CMScaller failed to classify 32% of samples. In CRC-derived PDX models, higher values of the CMS-PDX CMS2 score were predictive of reduced tumor volume following cetuximab treatment (p = 1.7 x 10-5in GSE78806, p < 2.2 x 10-16in GSE76402, by linear regression.) In contrast, higher values of the CMS1 score were predictive of increased tumor volume (p = 3.8 x 10-5in GSE78806, p = 2.9 x 10-10in GSE76402.) Change in tumor volume was independent of the CMS-PDX CMS4 score in both PDX cohorts. Conclusions: We showed that the 20-genes CMS-PDX scores are predictive of CMS subtypes obtained with CMScaller. Moreover, CMS2, by CMS-PDX scores, was highly predictive of sensitivity to cetuximab treatment in CRC PDX models.

EarlyR signature predicts response to neoadjuvant chemotherapy in breast cancer

BACKGROUND

EarlyR gene signature uses ESPL1, SPAG5, MKI67, PLK1 and PGR to classify ER+ breast cancer (ER+ BC) into EarlyR-Low, EarlyR-Int, and EarlyR-High risk strata and is prognostic in patients treated with adjuvant chemotherapy. The ability of EarlyR to predict pathological complete response (pCR) and long-term survival following neoadjuvant chemotherapy (NACT) is evaluated herein.

MATERIALS

The ability of EarlyR gene signature to predict pCR was assessed in publicly available Affymetrix microarray datasets (Cohort A; n = 659; 74 pCR events) derived from NACT-treated ER+ BC patients. Distant relapse-free survival (DRFS) results were analyzed in patients treated with NACT and adjuvant hormone therapy (AHT) (n = 281) and compared with patients treated with AHT alone (n = 455) (Cohort B; n = 736; 142 events).

RESULTS

In cohort A, EarlyR was a significant predictor of pCR (p = 5.8 × 10-11) (EarlyR-Low, n = 400, pCR = 40, 5%; EarlyR-Int, n = 69, pCR = 7, 15% and EarlyR-High, n = 190, pCR = 47, 24%). In EarlyR-Low of Cohort B, the 5-year DRFS was not significantly (p = 0.55) different between NACT + AHT [0.81 (95%CI 0.73-0.90)] and AHT-only [0.85 (95%CI 0.81-0.90)]. In contrast, in EarlyR-High, the 5-year DRFS was higher (p = 0.019) in NACT + AHT [0.81 (95%CI 0.70-0.93)] as compared to AHT-only [0.60 (95%CI 0.51-0.71)].

CONCLUSIONS

High EarlyR is strongly associated with pCR in patients treated with neoadjuvant chemotherapy. EarlyR also predicts poor DRFS outcomes for patients in EarlyR-High not receiving NACT, and improved survival in NACT-treated EarlyR-High patients. EarlyR is not only a prognostic assay but also a predictive assay that identifies patients, who are also likely to respond to chemotherapy.