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PURPOSE Triple-negative breast cancer (TNBC) is considered aggressive, and therefore, virtually all young patients with TNBC receive (neo)adjuvant chemotherapy. Increased stromal tumor-infiltrating lymphocytes (sTILs) have been associated with a favorable prognosis in TNBC. However, whether this association holds for patients who are node-negative (N0), young (< 40 years), and chemotherapy-naïve, and thus can be used for chemotherapy de-escalation strategies, is unknown. METHODS We selected all patients with N0 TNBC diagnosed between 1989 and 2000 from a Dutch population–based registry. Patients were age < 40 years at diagnosis and had not received (neo)adjuvant systemic therapy, as was standard practice at the time. Formalin-fixed paraffin-embedded blocks were retrieved (PALGA: Dutch Pathology Registry), and a pathology review including sTILs was performed. Patients were categorized according to sTILs (< 30%, 30%-75%, and ≥ 75%). Multivariable Cox regression was performed for overall survival, with or without sTILs as a covariate. Cumulative incidence of distant metastasis or death was analyzed in a competing risk model, with second primary tumors as competing risk. RESULTS sTILs were scored for 441 patients. High sTILs (≥ 75%; 21%) translated into an excellent prognosis with a 15-year cumulative incidence of a distant metastasis or death of only 2.1% (95% CI, 0 to 5.0), whereas low sTILs (< 30%; 52%) had an unfavorable prognosis with a 15-year cumulative incidence of a distant metastasis or death of 38.4% (32.1 to 44.6). In addition, every 10% increment of sTILs decreased the risk of death by 19% (adjusted hazard ratio: 0.81; 95% CI, 0.76 to 0.87), which are an independent predictor adding prognostic information to standard clinicopathologic variables (χ2 = 46.7, P < .001). CONCLUSION Chemotherapy-naïve, young patients with N0 TNBC with high sTILs (≥ 75%) have an excellent long-term prognosis. Therefore, sTILs should be considered for prospective clinical trials investigating (neo)adjuvant chemotherapy de-escalation strategies.

Kaplan-Meier curves of the non-BRCA1-like cohort split by XIST-53BP1 and chemotherapy regimen.

Analysis of genomic loss of the XIST locus by array comparative genomic hybridization

Supplemental Table 1 - Description of the study according to REMARK criteria. Supplemental Table 2 - Survival analysis of XIST and 53BP1 in non-BRCA1-like patients. Supplemental Table 3 - Clinical characteristics of the full trial population for which 53BP1 status was available. Supplemental Table 4 - Cox Proportional Hazards Model for Recurrence Free Survival including prognostic effect of 53BP1 and chemotherapy effect by 53BP1 in the full trial population for which 53BP1 status was available. Supplemental Table 5 - Clinical characteristics of the triple negative trial population for which 53BP1 status was available. Supplemental Table 6 - Cox Proportional Hazards Model for Recurrence Free Survival including prognostic effect of 53BP1 and chemotherapy effect by 53BP1 in triple negative trial population for which 53BP1 status was available. Supplemental Table 7 - Cox Proportional Hazards Model for Recurrence Free Survival including prognostic effect of 53BP1 and chemotherapy effect by 53BP1 in the full trial population for which 53BP1 status was available. Supplemental Table 8 - Cox Proportional Hazards Model for Recurrence Free Survival including prognostic effect of 53BP1 and chemotherapy effect by 53BP1 in triple negative trial population

Supplemental Figure Legends

Analysis of genomic loss of the 53BP1 locus by array comparative genomic hybridization

Supplementary Data from Differential Survival and Therapy Benefit of Patients with Breast Cancer Are Characterized by Distinct Epithelial and Immune Cell Microenvironments

S1: Image of full size blot for figure 1A; S2: Image of full size blot for figure 1B; S3: SRC3-pS543 and SRC3 chromatin binding patterns in MCF7 cells; S4: Venn diagram of SRC1, SRC2 and SRC3-pS543 enriched binding sites; S5: A. ChIP-QPCR validation of differential enriched chromatin binding sites for total SRC3 and SRC3-pS543; S6: Hormone dependence and phospho-specificity of SRC3-pS543 at sites either or not shared with total SRC3; S7: Overlap of ERïƒ¡ï€ and SRC3 with other publically available datasets; S8: Fulvestrant decreases SRC3-pS543/chromatin interactions at sites shared with ER; S9: Venn diagram, showing the overlap of GO pathways enriched for genes proximal to chromatin binding sites for SRC3-pS543 unique, SRC3 unique or shared regions; S10: 2D graph of normalized ChIP-seq data, illustrating signal for ER, total SRC3, H3K4me1, H3K4me2, H3K4me3 and H3K27Ac binding events at genomic regions occupied by SRC3-pS543; S11: Histological analysis of SRC3 and SRC3-pS543 expression in representative tumour sections; S12: Scatterplot analysis for total SRC3 versus SRC3-pS543 signal in the Nottingham Tenovus Primary Breast Carcinoma Series; S13: Disease Free Survival and breast cancer specific survival in breast cancer patients based on SRC3 protein expression; S14: Disease Free Survival and breast cancer specific survival in patients with HER2 positive and SRC3 high breast cancers compared with all other patients.

Purpose:Extensive work in preclinical models has shown that microenvironmental cells influence many aspects of cancer cell behavior, including metastatic potential and their sensitivity to therapeutics. In the human setting, this behavior is mainly correlated with the presence of immune cells. Here, in addition to T cells, B cells, macrophages, and mast cells, we identified the relevance of nonimmune cell types for breast cancer survival and therapy benefit, including fibroblasts, myoepithelial cells, muscle cells, endothelial cells, and seven distinct epithelial cell types.Experimental Design:Using single-cell sequencing data, we generated reference profiles for all these cell types. We used these reference profiles in deconvolution algorithms to optimally detangle the cellular composition of more than 3,500 primary breast tumors of patients that were enrolled in the SCAN-B and MATADOR clinical trials, and for which bulk mRNA sequencing data were available.Results:This large data set enables us to identify and subsequently validate the cellular composition of microenvironments that distinguish differential survival and treatment benefit for different treatment regimens in patients with primary breast cancer. In addition to immune cells, we have identified that survival and therapy benefit are characterized by various contributions of distinct epithelial cell types.Conclusions:From our study, we conclude that differential survival and therapy benefit of patients with breast cancer are characterized by distinct microenvironments that include specific populations of immune and epithelial cells.

QPCR primer sequences for ChIP validations.

Purpose:BRCA1-deficient breast cancers carry a specific DNA copy-number signature (“BRCA1-like”) and are hypersensitive to DNA double-strand break (DSB) inducing compounds. Here, we explored whether (i) EZH2 is overexpressed in human BRCA1-deficient breast tumors and might predict sensitivity to DSB-inducing drugs; (ii) EZH2 inhibition potentiates cisplatin efficacy in Brca1-deficient murine mammary tumors.Experimental Design:EZH2 expression was analyzed in 497 breast cancers using IHC or RNA sequencing. We classified 370 tumors by copy-number profiles as BRCA1-like or non-BRCA1–like and examined its association with EZH2 expression. Additionally, we assessed BRCA1 loss through mutation or promoter methylation status and investigated the predictive value of EZH2 expression in a study population of breast cancer patients treated with adjuvant high-dose platinum-based chemotherapy compared with standard anthracycline-based chemotherapy. To explore whether EZH2 inhibition by GSK126 enhances sensitivity to platinum drugs in EZH2-overexpressing breast cancers we used a Brca1-deficient mouse model.Results:The highest EZH2 expression was found in BRCA1-associated tumors harboring a BRCA1 mutation, BRCA1-promoter methylation or were classified as BRCA1 like. We observed a greater benefit from high-dose platinum-based chemotherapy in BRCA1-like and non-BRCA1–like patients with high EZH2 expression. Combined treatment with the EZH2 inhibitor GSK126 and cisplatin decreased cell proliferation and improved survival in Brca1-deficient mice in comparison with single agents.Conclusions:Our findings demonstrate that EZH2 is expressed at significantly higher levels in BRCA1-deficient breast cancers. EZH2 overexpression can identify patients with breast cancer who benefit significantly from intensified DSB-inducing platinum-based chemotherapy independent of BRCA1-like status. EZH2 inhibition improves the antitumor effect of platinum drugs in Brca1-deficient breast tumors in vivo.

Figure and table legends for supplementary data

Immunohistological stainings of breast tumors for EZH2 (representative examples of used antibodies)

Supplementary Table from Differential Survival and Therapy Benefit of Patients with Breast Cancer Are Characterized by Distinct Epithelial and Immune Cell Microenvironments

Purpose: The steroid receptor coactivator SRC3 is essential for the transcriptional activity of estrogen receptor α (ERα). SRC3 is sufficient to cause mammary tumorigenesis, and has also been implicated in endocrine resistance. SRC3 is posttranslationally modified by phosphorylation, but these events have not been investigated with regard to functionality or disease association. Here, we investigate the spatial selectivity of SRC3-pS543/DNA binding over the human genome and its expression in primary human breast cancer in relation with outcome.Experimental Design: Chromatin immunoprecipitation, coupled with sequencing, was used to determine the chromatin binding patterns of SRC3-pS543 in the breast cancer cell line MCF7 and two untreated primary breast cancers. IHC was used to assess the expression of SRC3 and SRC3-pS543 in 1,650 primary breast cancers. The relationship between the expression of SRC3 and SRC3-pS543, disease-free survival (DFS), and breast cancer specific survival (BCSS) was assessed.Results: Although total SRC3 is selectively found at enhancer regions, SRC3-pS543 is recruited to promoters of ERα responsive genes, both in the MCF7 cell line and primary breast tumor specimens. SRC3-pS543 was associated with both improved DFS (P = 0.003) and BCSS (P = 0.001) in tamoxifen untreated high-risk patients, such a correlation was not seen in tamoxifen-treated cases, the interaction was statistically significant (P = 0.001). Multivariate analysis showed SRC3-pS543 to be an independent prognostic factor.Conclusions: Phosphorylation of SRC3 at S543 affects its genomic interactions on a genome-wide level, where SRC3-pS543 is selectively recruited to promoters of ERα-responsive genes. SRC3-pS543 is a prognostic marker, and a predictive marker of response to endocrine therapy. Clin Cancer Res; 22(2); 479–91. ©2015 AACR.

Supplementary Figure from Differential Survival and Therapy Benefit of Patients with Breast Cancer Are Characterized by Distinct Epithelial and Immune Cell Microenvironments

Primer sequences corresponding with supplemental figure S5.

Kaplan-Meier survival plot of endometrial cancer patients who were not treated with tamoxifen for their breast cancer, categorized as ERalpha+/FOXA1+, ERalpha+/FOXA1-, ERalpha-/FOXA1+ or ERalpha-/FOXA1-.

supplementary methods

Tamoxifen, a small-molecule antagonist of the transcription factor estrogen receptor alpha (ERα) used to treat breast cancer, increases risks of endometrial cancer. However, no parallels of ERα transcriptional action in breast and endometrial tumors have been found that might explain this effect. In this study, we addressed this issue with a genome-wide assessment of ERα-chromatin interactions in surgical specimens obtained from patients with tamoxifen-associated endometrial cancer. ERα was found at active enhancers in endometrial cancer cells as marked by the presence of RNA polymerase II and the histone marker H3K27Ac. These ERα binding sites were highly conserved between breast and endometrial cancer and enriched in binding motifs for the transcription factor FOXA1, which displayed substantial overlap with ERα binding sites proximal to genes involved in classical ERα target genes. Multifactorial ChIP-seq data integration from the endometrial cancer cell line Ishikawa illustrated a functional genomic network involving ERα and FOXA1 together with the enhancer-enriched transcriptional regulators p300, FOXM1, TEAD4, FNFIC, CEBP8, and TCF12. Immunohistochemical analysis of 230 primary endometrial tumor specimens showed that lack of FOXA1 and ERα expression was associated with a longer interval between breast cancer and the emergence of endometrial cancer, exclusively in tamoxifen-treated patients. Our results define conserved sites for a genomic interplay between FOXA1 and ERα in breast cancer and tamoxifen-associated endometrial cancer. In addition, FOXA1 and ERα are associated with the interval time between breast cancer and endometrial cancer only in tamoxifen-treated breast cancer patients. Cancer Res; 76(13); 3773–84. ©2016 AACR.

legends to supplementary tables and figures

BackgroundThe addition of adjuvant capecitabine to standard chemotherapy of early-stage triple-negative breast cancer (TNBC) patients has improved survival in a few randomised trials and in meta-analyses. However, many patients did not benefit. We evaluated theBRCA1-like DNA copy number signature, indicative of homologous recombination deficiency, as a predictive biomarker for capecitabine benefit in the TNBC subgroup of the FinXX trial.MethodsEarly-stage TNBC patients were randomised between adjuvant capecitabine-containing (TX + CEX: capecitabine-docetaxel, followed by cyclophosphamide-epirubicin-capecitabine) and conventional chemotherapy (T + CEF: docetaxel, followed by cyclophosphamide-epirubicin-fluorouracil). TumourBRCA1-like status was determined on low-coverage, whole genome next-generation sequencing data using an established DNA comparative genomic hybridisation algorithm.ResultsFor 129/202 (63.9%) patients theBRCA1-like status could be determined, mostly due to lack of tissue. During a median follow-up of 10.7 years, 35 recurrences and 32 deaths occurred. Addition of capecitabine appears to improve recurrence-free survival more among 61 (47.3%) patients with non-BRCA1-like tumours (HR 0.23, 95% CI 0.08–0.70) compared to 68 (52.7%) patients withBRCA1-like tumours (HR 0.66, 95% CI 0.24–1.81) (P-interaction = 0.17).ConclusionBased on our data, patients with non-BRCA1-like TNBC appear to benefit from the addition of capecitabine to adjuvant chemotherapy. Patients withBRCA1-like TNBC may also benefit. Additional research is needed to define the subgroup withinBRCA1-like TNBC patients who may not benefit from adjuvant capecitabine.

Purpose Everolimus plus exemestane (EVE/EXE) is a registered treatment option for ER-positive, HER2-negative (ER +/HER2-) metastatic breast cancer (MBC), but resistance mechanisms limit efficacy. We aimed to find markers that might help select patients with a higher chance on benefit from EVE/EXE. Methods Immunohistochemistry (IHC) of PTEN, p-AKT(Thr308), p-AKT(Ser473), p-4EBP1, p-p70S6K, p-S6RP(Ser240/244), p-ERK1/2 and p-S6RP (Ser235/236) was performed on primary tumour tissue and on biopsies immediately taken from ER +/HER2- MBC patients before the start of standard EVE/EXE (Eudract 2013-004120-11). Unsupervised hierarchical clustering was executed to create heatmaps to distinguish subgroups of preferentially activated and less-activated PI3K/MAPK proteins. Uni- and multivariate Cox models were used for associations with PFS. Results Primary tumour tissue from 145 patients was retrieved. Median PFS was 5.4 months. Patients without (neo)adjuvant therapy (p = 0.03) or bone only disease (p = 0.04) had longer PFS on EVE/EXE. In primary tumours, neither single proteins nor PI3K/MAPK-associated heatmap subgroups were significantly associated with PFS. In 21 patients a non-osseous biopsy obtained before dosing was useful for continuous scoring, which demonstrated upregulation of several proteins as compared to readings in corresponding primary tumour tissues. These comparisons revealed that increased expression of p-4EBP1 was significantly associated with worse PFS (multivariate HR 3.69, p = 0.05). Conclusions IHC of single proteins or heatmap subgroups of the differentially activated PI3K/MAPK pathways was not able to discriminate patients on EVE/EXE with poor or better PFS. Upregulation of p-4EBP1 in pre-treatment biopsies as compared to levels in primary tumours pointed towards shorter PFS.

Purpose: Extensive work in preclinical models has shown that microenvironmental cells influence many aspects of cancer cell behavior, including metastatic potential and their sensitivity to therapeutics. In the human setting, this behavior is mainly correlated with the presence of immune cells. Here, in addition to T cells, B cells, macrophages, and mast cells, we identified the relevance of nonimmune cell types for breast cancer survival and therapy benefit, including fibroblasts, myoepithelial cells, muscle cells, endothelial cells, and seven distinct epithelial cell types. Experimental Design: Using single-cell sequencing data, we generated reference profiles for all these cell types. We used these reference profiles in deconvolution algorithms to optimally detangle the cellular composition of more than 3,500 primary breast tumors of patients that were enrolled in the SCAN-B and MATADOR clinical trials, and for which bulk mRNA sequencing data were available. Results: This large data set enables us to identify and subsequently validate the cellular composition of microenvironments that distinguish differential survival and treatment benefit for different treatment regimens in patients with primary breast cancer. In addition to immune cells, we have identified that survival and therapy benefit are characterized by various contributions of distinct epithelial cell types. Conclusions: From our study, we conclude that differential survival and therapy benefit of patients with breast cancer are characterized by distinct microenvironments that include specific populations of immune and epithelial cells.

Breast cancer tumor grade is strongly associated with patient survival. In current clinical practice, pathologists assign tumor grade after visual analysis of tissue specimens. However, different studies show significant inter-observer variation in breast cancer grading. Computer-based breast cancer grading methods have been proposed but only work on specifically selected tissue areas and/or require labor-intensive annotations to be applied to new datasets. In this study, we trained and evaluated a deep learning-based breast cancer grading model that works on whole-slide histopathology images. The model was developed using whole-slide images from 706 young (lt; 40 years) invasive breast cancer patients with corresponding tumor grade (low/intermediate vs. high), and its constituents nuclear grade, tubule formation and mitotic rate. The performance of the model was evaluated using Cohen's kappa on an independent test set of 686 patients using annotations by expert pathologists as ground truth. The predicted low/intermediate (n = 327) and high (n = 359) grade groups were used to perform survival analysis. The deep learning system distinguished low/intermediate versus high tumor grade with a Cohen's Kappa of 0.59 (80% accuracy) compared to expert pathologists. In subsequent survival analysis the two groups predicted by the system were found to have a significantly different overall survival (OS) and disease/recurrence-free survival (DRFS/RFS) (p lt; 0.05). Univariate Cox hazard regression analysis showed statistically significant hazard ratios (p lt; 0.05). After adjusting for clinicopathologic features and stratifying for molecular subtype the hazard ratios showed a trend but lost statistical significance for all endpoints. In conclusion, we developed a deep learning-based model for automated grading of breast cancer on whole-slide images. The model distinguishes between low/intermediate and high grade tumors and finds a trend in the survival of the two predicted groups.

Purpose: BRCA1-deficient breast cancers carry a specific DNA copy-number signature (“BRCA1-like”) and are hypersensitive to DNA double-strand break (DSB) inducing compounds. Here, we explored whether (i) EZH2 is overexpressed in human BRCA1-deficient breast tumors and might predict sensitivity to DSB-inducing drugs; (ii) EZH2 inhibition potentiates cisplatin efficacy in Brca1-deficient murine mammary tumors. Experimental Design: EZH2 expression was analyzed in 497 breast cancers using IHC or RNA sequencing. We classified 370 tumors by copy-number profiles as BRCA1-like or non-BRCA1–like and examined its association with EZH2 expression. Additionally, we assessed BRCA1 loss through mutation or promoter methylation status and investigated the predictive value of EZH2 expression in a study population of breast cancer patients treated with adjuvant high-dose platinum-based chemotherapy compared with standard anthracycline-based chemotherapy. To explore whether EZH2 inhibition by GSK126 enhances sensitivity to platinum drugs in EZH2-overexpressing breast cancers we used a Brca1-deficient mouse model. Results: The highest EZH2 expression was found in BRCA1-associated tumors harboring a BRCA1 mutation, BRCA1-promoter methylation or were classified as BRCA1 like. We observed a greater benefit from high-dose platinum-based chemotherapy in BRCA1-like and non-BRCA1–like patients with high EZH2 expression. Combined treatment with the EZH2 inhibitor GSK126 and cisplatin decreased cell proliferation and improved survival in Brca1-deficient mice in comparison with single agents. Conclusions: Our findings demonstrate that EZH2 is expressed at significantly higher levels in BRCA1-deficient breast cancers. EZH2 overexpression can identify patients with breast cancer who benefit significantly from intensified DSB-inducing platinum-based chemotherapy independent of BRCA1-like status. EZH2 inhibition improves the antitumor effect of platinum drugs in Brca1-deficient breast tumors in vivo.

541 Background: The meiotic DNA break regulator HORMAD1 is aberrantly expressed in many cancers and is associated with increased genomic instability. The susceptibility of HORMAD1 expressing tumors to agents targeting DNA damage repair (DDR) pathways is poorly understood since clinical data within the context of a randomized clinical trial (RCT) is lacking. Here, we retrospectively studied HORMAD1 expression as a putative predictive biomarker in an RCT for benefit of adjuvant high-dose platinum-based chemotherapy (HDCT) with autologous stem cell support in patients with high-risk HER2-negative early breast cancer (BC). Methods: Patients with stage III BC participated in an RCT comparing HDCT to conventional chemotherapy (CDCT; Rodenhuis et all, NEJM, 2003; Steenbruggen et all, JAMA Oncol, 2020). We studied the subgroup with HER2-negative BC for whom tumor BRCA1-like classification was previously determined using a validated DNA comparative genomic hybridization algorithm (Vollebergh et all, BCR, 2014). Tumor HORMAD1 expression was determined on FFPE samples using RNAscope, an RNA in situ hybridization method, and classified as negative (no expression) or positive (any expression detected). Results: For 195/246 (79.3%) HER2-negative patients treated according to protocol, HORMAD1 RNAscope status was available; dropout was due to absence or insufficient quality of tumor specimens. HORMAD1 positivity was enriched in triple-negative breast cancer (TNBC) (23/47; 48.9%). Furthermore, in all HER2-negative BCs, HORMAD1 positivity (45/195; 23.1%) was associated with age ≤40 years, histological grade III, 10%. Such association, although not significant, was also observed within TNBC. During a median follow-up of 20.3 years, 124 (63.6%) recurrences and 115 deaths (59.0%) occurred. The prognostic effect of HORMAD1 positivity on overall survival (OS) varied with follow-up time and was borderline significant at 10 years and significant thereafter (10-year: adjusted (adj.) HR 0.47, 95% CI 0.21-1.04; 15-year: adj. HR 0.25, 95% CI 0.07-0.91). Benefit on RFS from HDCT over CDCT was stronger in patients with HORMAD1-positive tumors (adj. HR 0.18, 95% CI 0.06-0.54) than in patients with HORMAD1-negative tumors (adj. HR 0.69, 95% CI 0.46-1.02) (P-interaction = 0.02). Similar results were observed for OS. Conclusions: In this retrospective sub study of 195 patients with high-risk HER2-negative BC participating in an RCT, tumor HORMAD1 expression is predictive for benefit of high-dose platinum-based chemotherapy. Our observations are consistent with the prior observations that HORMAD1 expression is associated with genomic instability and impaired DDR pathways. Further research is warranted to validate our findings. Clinical trial information: NCT03087409.

Background: Recent data demonstrate that patients with early-stage triple negative breast cancer (TNBC) benefit from escalating adjuvant treatment with capecitabine. However, since a substantial proportion of patients does not benefit, predictive biomarkers to select those individuals upfront are needed. Over half of all TNBCs have a BRCA1-like DNA copy number signature similar to the profile found in germline BRCA1-mutated breast cancers and indicative for homologous recombination deficiency. We evaluate this signature as a predictive biomarker for capecitabine benefit in archived specimens of the randomized controlled FinXX trial. Additionally, we compared the concordance of our DNA-based BRCA1-like classifier with the RNA-based NanoString BRCAness signature. Methods: Early-stage TNBC patients were randomized between adjuvant capecitabine-containing chemotherapy (TX+CEX: capecitabine plus docetaxel, followed by cyclophosphamide, epirubicin and capecitabine) and conventional adjuvant chemotherapy (T+CEF: docetaxel, followed by cyclophosphamide, epirubicin, and fluorouracil). Breast tumor BRCA1-like status was determined on low coverage, whole genome next-generation sequencing data using an established DNA comparative genomic hybridization algorithm. We used interaction analysis in proportional hazards models to evaluate whether benefit of adjuvant capecitabine-containing versus conventional chemotherapy differs between BRCA1-like and non-BRCA1-like tumors in early-stage TNBC patients.Results: For 129 (63.9%) of the 202 TNBC patients the BRCA1-like status could be determined. Thirty-five recurrences and 32 deaths occurred during a median follow-up of 10.7 years. The capecitabine effect on recurrence-free survival did not significantly differ between the 68 patients (52.7%) with a BRCA1-like tumor (HR 0.66, 95% CI 0.24-1.81) and others (HR 0.23, 95% CI 0.08-0.70, P interaction = 0.17), also after adjustment for clinico-pathological variables. Conclusions: In the FinXX trial, the BRCA1-like status was not associated with a differential benefit from capecitabine-containing adjuvant chemotherapy compared to conventional chemotherapy in the TNBC subgroup. Based on this study, it is unlikely that the BRCA1-like classifier can be used to distinguish patients who do and do not benefit from capecitabine-enriched standard adjuvant chemotherapy.

The phosphatidylinositol-3-kinase (PI3K) and mitogen-activated protein kinase(MAPK) pathways are frequently activated in breast cancer. We recently demonstrated the importance of analyzing multiple proteins as read-out for pathway activation in ER+/HER2- breast cancer, since single proteins are known to provide insufficient information. Here, we determined pathway activation in other primary breast cancer intrinsic subtypes derived from postmenopausal patients. Tumor blocks were recollected and immunohistochemistry was performed using antibodies against PTEN, p-AKT(Thr308), p-AKT(Ser473), p-p70S6K, p-4EBP1, p-S6RP(Ser235/236) and p-ERK1/2, followed by unsupervised hierarchical clustering. In 32 ER+/HER2+, 37 ER-/HER2+ and 74 triple-negative breast cancer patients, subgroups were identified with preferentially activated (A) and preferentially not activated (N) proteins. These subgroups likely reflect tumors with differences in biological behavior as well as treatment outcome.

Estrogen receptor alpha (ER alpha) is a key transcriptional regulator in the majority of breast cancers. ER alpha-positive patients are frequently treated with tamoxifen, but resistance is common. In this study, we refined a previously identified 111-gene outcome prediction-classifier, revealing FEN1 as the strongest determining factor in ER alpha-positive patient prognostication. FEN1 levels were predictive of outcome in tamoxifen-treated patients, and FEN1 played a causal role in ER alpha-driven cell growth. FEN1 impacted the transcriptional activity of ER alpha by facilitating coactivator recruitment to the ER alpha transcriptional complex. FEN1 blockade induced proteasome-mediated degradation of activated ER alpha, resulting in loss of ER alpha-driven gene expression and eradicated tumor cell proliferation. Finally, a high-throughput 465,195 compound screen identified a novel FEN1 inhibitor, which effectively blocked ER alpha function and inhibited proliferation of tamoxifen-resistant cell lines as well as ex vivo-cultured ER alpha-positive breast tumors. Collectively, these results provide therapeutic proof of principle for FEN1 blockade in tamoxifen-resistant breast cancer. Significance: These findings show that pharmacologic inhibition of FEN1, which is predictive of outcome in tamoxifen-treated patients, effectively blocks ER alpha function and inhibits proliferation of tamoxifen-resistant tumor cells. The authors thank Ron Kerkhoven from the NKI Genomics Core Facility. The authors thank Sheila Stewart (Department of Cell Biology and Physiology, Washington University, St. Louis, MO) for providing pShuttle-FEN1hWT and pShuttle-D181A, Robert Nicholson (Cardiff School of Pharmacy and Pharmaceutical Science, Cardiff University, United Kingdom) for providing the TAM-R cells, Kenneth Nephew (Indiana University, School of Medicine, Bloomington, IN) for providing MCF7-T cells. The authors thank Hongmao Sun and David Maloney (National Center for Advancing Translational Sciences, NIH, Bethesda, MD) for the additional design and analyses of the FEN1 HTS inhibitor screen and synthesis of required protein and reagents. This work was supported by the Dutch Cancer Society KWF, Netherlands Organization for Scientific Research (NWO), A Sister's Hope, the National Center for Advancing Translational Sciences, National Institutes of Health (R03 MH092154-01), National Institute on Aging, the National Health and Medical Research Council of Australia (ID 1084416; ID 20160711 to W.D. Tilley and T.E. Hickey), the Royal Adelaide Hospital Research Foundation and the Cancer Australia/National Breast Cancer Foundation (ID CA1043497). Zwart, W (corresponding author), Netherlands Canc Inst, Div Oncogen, Amsterdam, Netherlands; Netherlands Canc Inst, Plesmanlaan 121, NL-1066 CX Amsterdam, Netherlands. w.zwart@nki.nl

Effective treatment of invasive lobular carcinoma (ILC) of the breast is hampered by late detection, invasive growth, distant metastasis, and poor response to chemotherapy. Phosphoinositide 3-kinase (PI3K) signaling, one of the major druggable oncogenic signaling networks, is frequently activated in ILC. We investigated treatment response and resistance to AZD8055, an inhibitor of mammalian target of rapamycin (mTOR), in the K14-cre;Cdh1Flox/Flox;Trp53Flox/Flox (KEP) mouse model of metastatic ILC. Inhibition of mTOR signaling blocked the growth of primary KEP tumors as well as the progression of metastatic disease. However, primary tumors and distant metastases eventually acquired resistance after long-term AZD8055 treatment, despite continued effective suppression of mTOR signaling in cancer cells. Interestingly, therapeutic responses were associated with increased expression of genes related to antigen presentation. Consistent with this observation, increased numbers of tumor-infiltrating major histocompatibility complex class II-positive (MHCII+) immune cells were observed in treatment-responsive KEP tumors. Acquisition of treatment resistance was associated with loss of MHCII+ cells and reduced expression of genes related to the adaptive immune system. The therapeutic efficacy of mTOR inhibition was reduced in Rag1−/- mice lacking mature T and B lymphocytes, compared to immunocompetent mice. Furthermore, therapy responsiveness could be partially rescued by transplanting AZD8055-resistant KEP tumors into treatment-naïve immunocompetent hosts. Collectively, these data indicate that the PI3K signaling pathway is an attractive therapeutic target in invasive lobular carcinoma, and that part of the therapeutic effect of mTOR inhibition is mediated by the adaptive immune system.

Background IGF-1R is overexpressed in a substantial number of breast cancer cases. When phosphorylated, IGF-1R activates the PI3K and MAPK pathways. In preclinical studies, IGF-1R overexpression has been described to be associated with tamoxifen resistance. Expression of activated IGF-1R has not been established as a marker for endocrine resistance in the clinic. We tested the value of p-IGF-1R to predict adjuvant tamoxifen benefit in IGF-1R-positive tumors from ER+ breast cancer patients and its possible association with PI3K/MAPK activation. We also carried out cell line experiments to illustrate a potential causal link between IGF-1R activation status, PI3K/MAPK pathway activation and tamoxifen resistance. Methods Primary tumor blocks from 563 ER+ (stage I-III) postmenopausal patients previously randomized between tamoxifen (1 to 3 years) vs. no adjuvant therapy (IKA trial 1982-1993; Beelen et al, Breast Cancer Res, 2014) were recollected. Immunohistochemistry scoring on tissue microarrays included PTEN, p-IGF-1R, p-AKT(Thr308), p-AKT(Ser473) and p-p70S6K(Thr389) by cytoplasmic intensity (0-3), of p-4EBP1(Ser65) and p-ERK1/2(Thr202/204) by percentage of tumor cells with positive nuclear staining and of p-S6RP(Ser235/236) by percentage of tumor cells with positive membranous staining. Informative data on p-IGF-1R staining was available for 364 IGF-1R-positive tumors. Multivariate Cox models including standard prognostic factors were used to assess hazard ratios (HR) for recurrence-free interval for tamoxifen treatment, p-IGF-1R status (negative vs. positive) and their interaction. MCF-7 and T47D cell lines were used to validate the clinical findings. IncuCyte cell proliferation experiments were performed with various IGF-1R-related growth stimulating and inhibiting conditions. Western blots were carried out on cells under various growth conditions to analyze whether activation of IGF-1R would be associated with PI3K/MAPK pathway activation. Results Patients having tumors without p-IGF-1R expression derived significant benefit from tamoxifen (HR 0.4290, 95% CI 0.2356 - 0.7813; p = 0.00566), while those having tumors with p-IGF-1R expression had no benefit (HR 0.8051, 95% CI 0.2643 – 2.453; p = 0.70). The p for interaction was not significant (p = 0.32106). Tumors positive for p-IGF-1R had more expression of (phospho)proteins downstream of the PI3K/MAPK pathways. These results were supported by Western blots from the cell lines examined under various growth conditions. In both cell lines, linsitinib (a dual IGF-1R and insulin receptor inhibitor) was able to block IGF-1R signaling, preventing activation of the PI3K and MAPK pathways and abrogating cell proliferation in the presence of tamoxifen. Conclusions Postmenopausal breast cancer patients with p-IGF-1R-positive tumors appear to derive no benefit from adjuvant tamoxifen. Tumors with p-IGF-1R expression were associated with PI3K/MAPK pathway activation. In breast cancer cell lines with activated IGF-1R signaling, addition of linsitinib to endocrine therapy can restore sensitivity. This combination might be an interesting treatment option for tamoxifen-resistant patients. Citation Format: Kruger DT, Alexi X, Opdam M, Schuurman KG, Sanders J, van der Noort V, Boven E, Zwart W, Linn SC. Phosphorylation of insulin-like growth factor-1 receptor (IGF-1R) is associated with tamoxifen resistance by activating the PI3K/MAPK pathway [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-08-06.

Background Several (activated) proteins of the phosphatidylinositol-3-kinase (PI3K) and/or mitogen-activated protein kinase (MAPK) pathway have been analyzed for an association with adjuvant tamoxifen benefit in estrogen receptor-positive (ER+), HER2-negative (HER2-) breast cancer. Currently, no single protein has yielded convincing results allowing clinical implementation. Combining activated proteins could provide more robust predictive potential. We used unsupervised hierarchical clustering of 7 activated proteins downstream in these pathways, discriminated by expression profile, to analyze adjuvant tamoxifen benefit in ER+/HER2- postmenopausal breast cancer patients. Further, we developed a classification tool based on the generated heatmap groups by pathway activation status to categorize future patients into sensitive for or resistant to adjuvant tamoxifen. Methods Primary tumor blocks from 489 ER+/HER2- (stage I-III) postmenopausal patients previously randomized between tamoxifen (1 to 3 years) vs no adjuvant therapy (IKA trial 1982-1993; Beelen et al, Breast Cancer Res, 2014) were used for immunohistochemistry on tissue microarrays. Median follow-up of the patients without a recurrence event was 8.5 years. Scoring of PTEN, p-AKT(Thr308), p-AKT(Ser473) and p-p70S6K(Thr389) was by cytoplasmic intensity (0-3), p-4EBP1(Ser65) and pERK1/2(Thr202/204) by percentage of tumor cells with positive nuclear staining and p-S6RP(Ser235/236) by the percentage of tumor cells with positive membranous staining. Unsupervised hierarchical clustering was performed on tissue from 293 patients with informative data on all 7 proteins. Cox models were used to assess tamoxifen benefit (defined as the Hazard ratio (HR) of tamoxifen treatment vs no adjuvant therapy for recurrence-free interval) and to compare this benefit between subgroups generated by clustering as well as generated by the classification tool. Cox models included covariates (age, histological grade and subtype, tumor size, PR status) and were stratified for lymph node status. Results Two distinct groups were identified based on hierarchical clustering: one with preferentially activated pathway markers (A) and one with relatively no activation (N). Patients in group N derived significant benefit from tamoxifen (multivariable HR 0.28, 95% CI 0.14 − 0.56, p = 0.000324), while patients from group A had no benefit (multivariable HR 1.57, 95% CI 0.44 – 5.56, p = 0.482), p for interaction 0.018. Contradictory, patients in group A had a better prognosis compared to those in group N (multivariable HR 0.17, 95% CI 0.04 − 0.7, p = 0.014). The classification tool was also successful in differentiating ER+/HER2- patients with or without tamoxifen benefit (p for interaction = 0.016). Conclusions Hierarchical clustering of PI3K/MAPK pathway proteins is able to differentiate patients with adjuvant tamoxifen benefit and patients who would potentially need alternative treatment, for instance with inhibitors of the PI3K or MAPK pathway. The classification tool distinguishing patients with and without tamoxifen benefit should be validated in an independent cohort of postmenopausal patients with primary ER+/HER2- breast cancer. Citation Format: Kruger DT, Beelen K, Opdam M, Sanders J, van der Noort V, Boven E, Linn SC. Clustering of activated proteins of the PI3K and MAPK pathways distinguishes ER+/HER2- primary breast cancer patients with preferential tamoxifen benefit [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD4-12.

To this day, targeted treatment options for patients with triple negative metastatic breast cancer (TNBC) are still virtually absent. Previously, we showed that elevated expression of the tyrosine kinase FER is an independent prognosticator that correlates with poor survival of high-grade and basal/TNBC patients. Here, we show that high FER levels are also associated with improved outcome after adjuvant taxane-based combination chemotherapy, in high-risk, HER2-negative patients. In TNBC cells, we observed a causal relation between high FER levels and sensitivity to taxanes. Our proteomics and mechanistic studies demonstrated that FER regulates endosomal recycling, a microtubule-dependent process that underpins breast cancer cell invasion. Using chemical genetics, we identified DCTN2 as a novel FER substrate. Our work indicates that the DCTN2 tyrosine 6 is essential for tubular recycling domains development in early endosomes and subsequent propagation of TNBC cell invasion in 3D. In conclusion, we show that high FER expression promotes endosomal recycling and represents a candidate predictive marker for benefit of adjuvant taxane-containing chemotherapy in high-risk patients, including TNBC patients. Citation Format: Sandra Tavares, Nalan Liv, Milena Pasolli, Mark Opdam, Max Ratze, Manuel Saornil, Lilian Sluimer, Rutger Hengeveld, Robert van Es, Erik van Werkhoven, Harmjan Vos, Holger Rehmann, Boudewijn Burgering, Hendrika Oosterkamp, Susanne Lens, Judith Klumperman, Sabine Linn, Patrick Derksen. FER regulates endosomal recycling and is a candidate predictor for taxane benefit in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB203.

Background: Anthracycline-based adjuvant chemotherapy has substantially improved breast cancer survival. Both the addition of taxanes as well as using a dose dense treatment schedule can further ameliorate outcome, but inter-individual differences exist. Here we present the efficacy and toxicity of dose dense scheduled doxorubicin/cyclophosphamide (ddAC) versus docetaxel/doxorubicin/cyclophosphamide (TAC), which is, to our knowledge, the first direct comparison of these treatment regimens. Methods: In this Dutch, multicenter phase III trial (ISRCTN61893718), patients with pT1-3, pN0-3, M0 breast cancer were randomized between six cycles of either A60C600 every 2 weeks or T75A50C500 every 3 weeks. All patients received pegfilgrastim. Patients were evaluated for recurrence-free survival (RFS) and overall survival (OS). Survival was compared in a Cox regression analysis and adjusted for known prognostic factors. These factors include age, type of surgery, tumor size, histological grade, ER/PR status, HER2 status, and lymph node status. Adverse events were reported according to the common toxicity criteria (CTCAE version 3.0). Results: Between 2004 and 2012, 664 patients were enrolled of whom 531 (80%) had node positive disease. At a median follow up of 5 years, OS was 92% in the ddAC treated subgroup and 93% in the TAC treated subgroup (adjusted hazard ratio [HR] 0.75, 95% confidence interval [CI] 0.42-1.34, intention to treat population). Forty-two breast-cancer specific deaths were equally divided over both treatment arms. Similarly, no significant difference in RFS was observed between both treatment groups (adjusted HR 0.85, 95% CI 0.55-1.32). Molecular subtypes were defined by St. Gallen criteria: 548 patients (83%) had estrogen receptor positive disease and 102 patients (15%) triple negative disease. No heterogeneity regarding treatment efficacy was observed in these subtypes. In particular, there was no survival benefit for ddAC or TAC in the triple negative subtype. Both treatment regimens were well tolerated. Whereas anemia was more frequent in ddAC treated patients (19% vs 4.7%; p Conclusions: At a median follow up of 5 years no significant survival differences were observed between adjuvant ddAC and TAC, in all patients and in molecular subgroups, including triple negative. Our findings are in line with the Oxford overview, which reported no significant differences between taxane-based chemotherapy and more, non-taxane based chemotherapy given in a dose dense schedule. ddAC could be a reasonable alternative for patients with a contra-indication for TAC. Citation Format: van Rossum AGH, Oosterkamp HM, van Werkhoven E, Opdam M, Mandjes IAM, van Leeuwen-Stok E, van Tinteren H, Kok M, Imholz ALT, Portielje JEA, Bos MMEM, van Bochove A, Wesseling J, Rutgers EJ, Rodenhuis S, Linn SC. Adjuvant dose dense doxorubicin-cyclophosphamide (ddAC) or docetaxel-AC (TAC) for high-risk breast cancer: First results of the randomized MATADOR trial (BOOG-2004-04) [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P5-14-03.

This abstract was withdrawn by the authors.

The prognostic value of tumour-infiltrating lymphocytes (TILs) differs by breast cancer (BC) subtype. The aim of this study was to evaluate TILs in stage III BC in the context of BRCA1/2-like phenotypes and association with outcome and benefit of intensified platinum-based chemotherapy.Patients participated in a randomised controlled trial of adjuvant intensified platinum-based chemotherapy versus conventional anthracycline-based chemotherapy carried out between 1993 and 1999 in stage III BC. Stromal TILs were scored according to International guidelines in these human epidermal growth factor receptor 2 (HER2)-negative tumours. BRCA-profiles were determined using Comparative Genomic Hybridization.TIL levels were evaluated in 248 BCs. High TILs were associated with Triple Negative BC (TNBC). BRCA-like tumours harboured higher TILs compared to non-BRCA-like tumours (median TILs of 20% versus 10%, p 0.01). TIL levels in BRCA1-like tumours were higher compared to BRCA2-like tumours (median TILs of 20% versus 10%, p 0.001). These correlations remained significant within the oestrogen (ER)-positive subgroup, however not within the TNBC subgroup. In this stage III BC cohort, high TIL level was associated with favourable outcome (TILs per 10% increment, recurrence-free survival (RFS): multivariate hazard ratio (HR) 0.82, 95% confidence interval (CI) 0.71-0.94, p = 0.01; overall survival (OS): multivariate HR 0.80, 95% CI 0.68-0.94, p = 0.01). There was no significant interaction between TILs and benefit of intensified platinum-based chemotherapy.In this high-risk breast cancer cohort, high TILs were associated with TNBC and BRCA1-like status. Within the ER-positive subgroup, TIL levels were higher in BRCA1-like compared to BRCA2-like tumours. When adjusted for clinical characteristics, TILs were significantly associated with a more favourable outcome in stage III BC patients.

Purpose The prognostic and predictive values of the MAPK/AKT/ERα phosphorylation axis (pT202/T204MAPK, pT308AKT, pS473AKT, pS118ERα and pS167ERα) in primary tumours were assessed to determine whether these markers can differentiate between patient responses for switching adjuvant endocrine therapy after 2–3 years from tamoxifen to exemestane and continued tamoxifen monotherapy in the Intergroup Exemestane Study (IES). Methods Of the 4724 patients in IES, 1506 were managed in a subset of centres (N = 89) participating in PathIES. These centres recruited 1282 (85%, 1282/1506) women into PathIES of whom 1036 had phospho-marker data. All phospho-markers were analysed by immunohistochemistry staining. Multivariable Cox proportional hazards models of the phospho-markers for disease-free survival (DFS) and overall survival (OS) were adjusted for clinicopathological factors. Treatment effects on the biomarker expression were determined by interaction tests. Benjamini–Hochberg adjustment for multiple testing with a false discovery rate of 10% was applied (pBH). Results Phospho-T202/T204MAPK, pS118ERα and pS167ERα were all found to be correlated (pBH = 0.0002). These markers were not associated with either DFS or OS when controlling for the established clinicopathological factors. Interaction terms between the phospho-markers and treatment strategies for either DFS or OS were not statistically significant (pBH > 0.05 for all). Conclusions This PathIES study confirmed previously described associations between the phosphorylation site markers of AKT, MAPK and ERα activity in postmenopausal breast cancer patients. No prognostic correlations between the phosphorylation markers and clinical outcome were found, nor were they predictive for clinical outcomes among patients who switched therapy over those treated with tamoxifen alone. Electronic supplementary material The online version of this article (10.1007/s10549-018-05110-x) contains supplementary material, which is available to authorized users.