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To assess the long-term (20-year) endocrine therapy benefit in premenopausal patients with breast cancer.Secondary analysis of the Stockholm trial (STO-5, 1990-1997) randomly assigning 924 premenopausal patients to 2 years of goserelin (3.6 mg subcutaneously once every 28 days), tamoxifen (40 mg orally once daily), combined goserelin and tamoxifen, or no adjuvant endocrine therapy (control) is performed. Random assignment was stratified by lymph node status; lymph node-positive patients (n = 459) were allocated to standard chemotherapy (cyclophosphamide, methotrexate, and fluorouracil). Primary tumor immunohistochemistry (n = 731) and gene expression profiling (n = 586) were conducted in 2020. The 70-gene signature identified genomic low-risk and high-risk patients. Kaplan-Meier analysis, multivariable Cox proportional hazard regression, and multivariable time-varying flexible parametric modeling assessed the long-term distant recurrence-free interval (DRFI). Swedish high-quality registries allowed a complete follow-up of 20 years.In estrogen receptor-positive patients (n = 584, median age 47 years), goserelin, tamoxifen, and the combination significantly improved long-term distant recurrence-free interval compared with control (multivariable hazard ratio [HR], 0.49; 95% CI, 0.32 to 0.75, HR, 0.57; 95% CI, 0.38 to 0.87, and HR, 0.63; 95% CI, 0.42 to 0.94, respectively). Significant goserelin-tamoxifen interaction was observed (This study shows 20-year benefit from 2 years of adjuvant endocrine therapy in estrogen receptor-positive premenopausal patients and suggests differential treatment benefit on the basis of tumor genomic characteristics. Combined goserelin and tamoxifen therapy showed no benefit over single treatment. Long-term follow-up to assess treatment benefit is critical.

Background: Women with estrogen receptor (ER)-positive disease have a long-term risk of distant recurrence. The poor survival of premenopausal women diagnosed with breast cancer combined with the otherwise long life expectancy makes it especially important to identify tumor characteristics associated with long-term survival. Intra-tumor heterogeneity, having cancer cells of varying characteristics across the tumor, may promote therapeutic resistance and metastatic capacity. We have previously shown that high intra-tumor heterogeneity of ER increases the risk of fatal breast cancer. To our knowledge, the relation between intra-tumor heterogeneity of progesterone receptor (PR) expression and long-term survival is not known. We aimed to study the association between intra-tumor heterogeneity of PR and long-term survival of premenopausal women in the Stockholm tamoxifen trial (STO-5), with 20-years complete follow-up. Methods: This study was a secondary analysis of 504 ER-positive/PR-positive premenopausal women from the STO-5 trial (1990-1997). 451 women had human epidermal growth factor receptor 2 (HER2)-negative tumors. Patients were randomized to receive either 2 years of endocrine treatment (tamoxifen and/or goserelin) or no endocrine treatment. Lymph node-positive patients (n=251) also received standard chemotherapy (CMF). Immunohistochemical analysis, including estimating the proportion of tumor cells for each PR intensity level (0, 1+, 2+, or 3+), was completed in 2020. Intra-tumor heterogeneity of PR was calculated using Rao’s quadratic entropy and then categorized into low and high intra-tumor heterogeneity groups, using a predefined cutoff at the second tertile. Complete long-term (20 year) follow-up was obtained from high-quality Swedish registries. Long-term distant recurrence-free interval (DRFI) was assessed using univariate Kaplan-Meier analysis and multivariable Cox proportional hazard modeling, adjusting for patient and tumor characteristics. Results: A statistically significant difference in 20-year DRFI was seen between patients with high and low intra-tumor heterogeneity of PR in the univariate Kaplan-Meier analysis (log-rank P< 0.01). Survival proportions for DRFI at 20 years were 60.2% (95% CI, 53.2%-68.1%) and 73.3% (95% CI, 68.6%-78.3%) for patients with high and low PR intra-tumor heterogeneity, respectively. Analysis in patients with HER2-negative tumors yielded similar results. In the multivariable analysis, women with high intra-tumor heterogeneity of PR had a significantly increased long-term risk of distant recurrence, compared to women with low intra-tumor heterogeneity, hazard ratio (HR)=1.49 (95% CI, 1.08-2.06). The same pattern was seen in HER2-negative women, HR=1.50 (95% CI, 1.06-2.12), see Table. Conclusions: This study suggests an increased long-term risk of distant recurrences in ER-positive/PR-positive premenopausal women with high intra-tumor heterogeneity of PR as compared to women with low intra-tumor heterogeneity of PR, independent of HER2 status. Ongoing analyses include using deep learning for image analysis of breast cancer tumors to examine intra-tumor heterogeneity at higher resolution and for various tumor characteristics. Better understanding of tumor characteristics associated with long-term risk in premenopausal women is needed, given the poor prognosis and early onset of the disease. Long-term risk of distant recurrence by PR intra-tumor heterogeneity and HER2 status Multivariable Cox proportional hazard regression modeling of 20-year distant recurrence-free interval (DRFI) by high and low PR intra-tumor heterogeneity. ER-positive/PR-positive and ER-positive/PR-positive/HER2-negative premenopausal women were analyzed separately. The crude model was adjusted for age, randomization year, lymph node status, and endocrine treatment. The full model was adjusted for age, randomization year, lymph node status, endocrine treatment, tumor size, Ki-67 status, and HER2 status. Citation Format: Oscar Danielsson, Huma Dar, Gizeh Perez-Tenorio, Anna Nordenskjöld, Christina Yau, Christopher C. Benz, Laura J. Esserman, Bo Nordenskjöld, Olle Stål, Tommy Fornander, Annelie Johansson, Linda S. Lindström. Long-term survival and intra-tumor heterogeneity of progesterone receptor expression in estrogen receptor-positive/progesterone receptor-positive premenopausal women with breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-05-03.

Background Risk assessment is important for breast cancer prevention and early detection. We aimed to examine whether common risk factors, mammographic features and breast cancer risk prediction scores of a woman were associated with breast cancer risk for her sisters. Methods We included 53,051 women from the KARMA study. Established risk factors were derived using self-reported questionnaires, mammograms, and SNP genotyping. Using the Swedish Multi-Generation Register, we identified 32,198 sisters of the KARMA women (including 5,352 KARMA participants and 26,846 non-participants). Cox models were used to estimate the hazard ratios of breast cancer for both women and their sisters, respectively. Results A higher breast cancer polygenic risk score, a history of benign breast disease, and higher breast density in women were associated with an increased risk of breast cancer for both women and their sisters. No statistically significant association was observed between breast microcalcifications and masses in women and breast cancer risk for their sisters. Furthermore, higher breast cancer risk scores in women were associated with an increased risk of breast cancer for their sisters. Specifically, the hazard ratios for breast cancer per 1 standard deviation increase in age-adjusted KARMA, BOADICEA, and Tyrer-Cuzick risk scores were 1.16 (95% CI = 1.07 to 1.27), 1.23 (95% CI = 1.12 to 1.35) and 1.21 (95% CI = 1.11 to 1.32), respectively. Conclusion A woman’s breast cancer risk factors are associated with her sister's breast cancer risk. However, the clinical utility of these findings requires further investigation.

Multivariable analysis of prognostic markers in endocrine-treated patients

Supplementary Figure 1 CONSORT diagram, TEX cohort Supplementary Figure 2 Long term post-relapse BCSS for gene expression signatures Supplementary Figure 3 Short term post-relapse BCSS for gene expression signatures Supplementary Figure 4 Long and short term post-relapse BCSS Kaplan-Meier curves for PAM50 at specific metastatic sites

(A) ROC and (B) Kaplan-Meier analysis of our training dataset in patient subgroups (i) All, (ii) Untreated, (iii) Untreated ER positive and (iv) Endocrine treated patients.

Supplementary Table 1. Primary tumour characteristics of patients included in the translational TEX trial Supplementary Table 2. Metastatic signature subtype split by primary tumour PR status and adjuvant therapy (N = 109) Supplementary Table 3. Long and short-term univariate Cox regression analysis for all signatures, post-relapse BCSS as clinical endpoint Supplementary Table 4. Long and short-term Likelihood ratios for all signatures in metastases from All, lymph nodes and other sites combined groups

Purpose: Transcriptional pathway activity and the molecular subtypes of breast cancer metastases have been shown to significantly influence patient postrelapse survival. Here, we further determine the relevance of clinically employed gene signatures in the advanced breast cancer (ABC) setting.Experimental Design: Sufficient RNA for expression profiling was obtained from distant metastatic or inoperable loco-regional relapse tissue by fine-needle aspiration from 109 patients of the Swedish TEX clinical trial. Gene signatures (GGI, 70 gene, recurrence score, cell-cycle score, risk of recurrence score, and PAM50) were applied to all metastases, and their relationship to long- (5-year) and short-term (1.5-year) postrelapse survival at all and locoregional lymph nodes (n = 40) versus other metastatic sites (n = 69) combined was assessed using Kaplan–Meier and/or multivariate Cox regression analyses.Results: The majority of metastases were classified into intermediate or high-risk groups by all signatures, and a significant association was found between metastatic signature subgroups and primary tumor estrogen receptor status and histologic grade (P < 0.05). When considering all sites of metastasis, only PAM50 was statistically significant in Kaplan–Meier analysis (Log-rank P = 0.008 and 0.008 for long- and short-term postrelapse breast cancer–specific survival, respectively). This significance remained in both uni- and multivariate models when restricting analyses to lymph node metastases only, and a similar trend was observed in other metastatic sites combined, but did not reach formal significance.Conclusions: Our findings are the first to demonstrate that the PAM50 signature can provide prognostic information from the lymph node metastases of ABC patients. Clin Cancer Res; 23(23); 7225–31. ©2017 AACR.

Supplementary figure S1: Survival analysis (Kaplan-Meier estimates) with Breast cancer specific survival (BCSS) as end point for All patients of Cohort 1. Supplementary figure S2: Flowchart showing simplified results from Cohort 1. Supplementary figure S3: Additional prognostic value of gene expression signatures beyond Ki67/IHC, Cohort 1. Supplementary figure S4: Additional prognostic value of Ki67/IHC beyond gene expression signatures, Cohort 1. Supplementary figure S5: Additional prognostic value of gene expression signatures beyond Ki67/IHC, Cohort 2. Supplementary figure S6: Additional prognostic value of Ki67/IHC beyond gene expression signatures, Cohort 2.

All supplementary materials and methods

Correlations between the MV score and 22 gene modules in (A) Uppsala dataset, (B) Stockholm dataset, (C) NKI dataset and (D) Rotterdam dataset.

Supplementary table S1. Cell cycle genes Supplementary table S2. Cross-table of concordance between Ki67 immunohistochemical staining and gene expression signature classifications in Cohorts 1 and 2 Supplementary table S3. Clinico-pathological characteristics of patient subgroups in cohort 1 Supplementary table S4. Change in C-index when adding gene expression signatures to Ki67/IHC for All, ER+/LN-, ER+/LN-, ER- patients in Cohorts 1 and 2. Supplementary Table S5. Clinico-pathological characteristics of patient subgroups in cohort 2

Purpose: Gene signatures and Ki67 stratify the same breast tumor into opposing good/poor prognosis groups in approximately 20% of patients. Given this discrepancy, we hypothesized that the combination of a clinically relevant signature and IHC markers may provide more prognostic information than either classifier alone.Experimental Design: We assessed Ki67 alone or combined with ER, PR and HER2 (forming IHC subtypes), and the research versions of the Genomic Grade Index, 70-gene, cell-cycle score, recurrence score (RS), and PAM50 signatures on matching TMA/whole tumor sections and microarray data in two Swedish breast cancer cohorts of 379 and 209 patients, with median follow-up of 12.4 and 12.5 years, respectively. First, we fit Cox proportional hazards models and used the change in likelihood ratio (Δ LR) to determine the additional prognostic information provided by signatures beyond that of (i) Ki67 and (ii) IHC subtypes. Second and uniquely, we then assessed whether signatures could compete well with pathology-based IHC classifiers by calculating the additional prognostic information of Ki67/IHC subtypes beyond signatures.Results: In cohort 1, only RS and PAM50 provided additional prognostic information beyond Ki67 and IHC subtypes (Δ LR-χ2 Ki67: RS = 12.8, PAM50 = 20.7, IHC subtypes: RS = 12.9, PAM50 = 11.7). Conversely, IHC subtypes added prognostic information beyond all signatures except PAM50. Similar results were observed in cohort 2.Conclusions: RS and PAM50 provided more prognostic information than the IHC subtypes in all breast cancer patients; however, the IHC subtypes did not add any prognostic information to PAM50. Clin Cancer Res; 23(24); 7512–20. ©2017 AACR.

The concordance index of the PAM50 and GGI signatures alone or in combination with the MV score in four independent datasets

Purpose: The ability of vascular genes to provide treatment predictive information in breast cancer patients remains unclear. As such, we assessed the expression of genes representative of normal endothelial microvasculature (MV) in relation to treatment-specific patient subgroups.Experimental Design: We used expression data from 993 breast tumors to assess 57 MV genes (summarized to yield an MV score) as well as the genomic grade index (GGI) and PAM50 signatures. MV score was compared with CD31 staining by correlation and gene ontology (GO) analysis, along with clinicopathologic characteristics and PAM50 subtypes. Uni-, multivariate, and/or t-test analyses were performed in all and treatment-specific subgroups, along with a clinical trial cohort of patients with metastatic breast cancer, seven of whom received antiangiogenic therapy.Results: MV score did not correlate with microvessel density (correlation = 0.096), but displayed enrichment for angiogenic GO terms, and was lower in Luminal B tumors. In endocrine-treated patients, a high MV score was associated with decreased risk of metastasis [HR 0.58; 95% confidence interval (CI), 0.38–0.89], even after adjusting for histologic grade, but not GGI or PAM50. Subgroup analysis showed the prognostic strength of the MV score resided in low genomic grade tumors and MV score was significantly increased in metastatic breast tumors after treatment with sunitinib + docetaxel (P = 0.031).Conclusions: MV score identifies two groups of better and worse survival in low-risk endocrine-treated breast cancer patients. We also show normalization of tumor vasculature on a transcriptional level in response to an angiogenic inhibitor in human breast cancer samples. Clin Cancer Res; 22(10); 2417–26. ©2016 AACR.

PurposeGene signatures have been shown to add prognostic information beyond that of routine clinico-pathological factors, however their utility in older breast cancer patients remains unclear. As such, the aim of this study was to determine if gene signatures can provide prognostic information that may aid treatment decisions for older breast cancer patients.Experimental designResearch versions of the genomic grade index (GGI), 70-gene recurrence score (RS), cell cycle score (CCS), PAM50 Risk of Recurrence score - Proliferation (ROR-P), and PAM50 signatures were applied to 39 breast cancer datasets totalling 9583 patients. After filtering based on age ≥ 70 years, the presence of Estrogen Receptor (ER) and survival information availability 871 patients remained. The prognostic capacity of signatures was tested in all (n=871), ER-positive/lymph node-positive (ER+/LN+, n=335) and ER-positive/lymph node-negative (ER+/LN-, n=374) patients using Kaplan-Meier and multivariable Cox proportional hazard modeling.ResultsAll gene signatures were statistically significant in Kaplan-Meier analysis of all and ER+/LN+ patients (Log-rankP< 0.001). This significance remained in multivariable analysis (Cox proportional hazards,P≤ 0.05). In ER+/LN-patients the GGI, 70-gene, CCS, ROR-P, and PAM50 signatures were significant in Kaplan-Meier analysis (Log-rankP≤ 0.05) but only the 70-gene, CCS, ROR-P, and PAM50 signatures remained so in multivariable analysis (Cox proportional hazards,P≤ 0.05).ConclusionsIn general, we found that gene signatures provide prognostic information in survival analyses of all, ER+/LN+ and ER+/LN-older (≥70 years) breast cancer patients, suggesting a potential role in aiding treatment decision in older patients.Translational RelevanceThe utility of gene expression signatures in breast cancer patients has been most clearly demonstrated in the TAILORx, RxPONDER and MINDACT randomised clinical trials. However, few older patients (≥70 years) were included in these trials meaning that signature utility in this patient group remains unclear. As such, we performed the first comprehensive study comparing the prognostic performance of multiple clinically relevant gene expression signatures in a single older breast cancer patient cohort. We show that in general gene signatures provide independent prognostic information in All, ER+/LN+ and ER+/LN-patients who are over the age of 70 years. These results support a potential role for signatures in aiding treatment decisions in older breast cancer patients and indicate that further investigation is warranted in prospective clinical study to elucidate their treatment predictive value.

The clinical impact of tumor-infiltrating lymphocytes (TILs) is less known for breast cancer patients with the estrogen receptor-positive (ER+)/human epidermal growth factor receptor-negative (HER−) subtype. Here, we explored the prognostic and predictive value of TILs regarding distant recurrence-free interval (DRFI) and breast cancer-specific survival (BCSS) in 763 postmenopausal patients randomized to receive tamoxifen vs. no systemic treatment. TILs were assessed in whole section tumor samples stained with H&E and divided into low (

Background: Tamoxifen is a standard endocrine therapy for both pre- and postmenopausal ER-positive breast cancer patients. Patients with ER-positive disease have a long-term risk of distant recurrence, thus, long-term follow-up studies are essential to understand true treatment benefit. Clinically used tumor characteristics are prognostic 5-10 years after primary diagnosis, however, whether these characteristics are predictive of long-term tamoxifen benefit is largely unexplored. Therefore, we aimed to determine the long-term tamoxifen therapy benefit by the clinically used tumor characteristics in pre- vs postmenopausal patients in the Stockholm tamoxifen (STO)-trials with 20-years complete follow-up. Methods: Secondary analysis of 1242 ER-positive/HER2-negative patients from the STO-trials, randomized to at least 2 years of 40 mg tamoxifen vs no endocrine therapy (control). Premenopausal lymph node-positive patients were allocated to chemotherapy as standard of care and postmenopausal high-risk patients were further randomized to chemotherapy vs radiotherapy. Tumor immunohistochemical analysis was recently conducted. Complete 20-year follow-up was obtained from Swedish high-quality registries. Long-term distant recurrence-free interval (DRFI) was assessed by multivariable Cox proportional hazard regression and time-varying analysis using flexible parametric modelling. Results: Premenopausal patients showed significantly improved long-term DRFI from tamoxifen vs control if they were lymph node-negative (Hazard Ratio [HR]=0.46; 95% CI, 0.24-0.87), PR-positive (HR=0.61; 95% CI, 0.41-0.91), or of genomic low risk (HR=0.47; 95% CI, 0.26-0.85), see Table. In postmenopausal patients, significantly improved long-term DRFI from tamoxifen vs control was seen for all good prognosis tumor characteristics, i.e. small tumor size (pT≤20mm: HR=0.55; 95% CI, 0.39-0.77), tumor grade 1-2 (HR=0.55; 95% CI, 0.41-0.73), lymph node-negative (HR=0.44; 95% CI, 0.30-0.64), PR-positive (HR=0.60; 95% CI, 0.44-0.80), Ki-67-low (< 15%: HR=0.51; 95% CI, 0.38-0.68), and genomic low risk (HR=0.53; 95% CI, 0.37-0.74), see Table. Also, postmenopausal patients with large tumor size (pT>20mm: HR=0.64; 95% CI, 0.44-0.94) and PR-negative tumors (HR=0.51; 95% CI, 0.32-0.81) showed significant long-term tamoxifen benefit. Time-varying analysis in premenopausal patients indicated that tamoxifen therapy benefit diminished over time. Significant tamoxifen benefit until year 5, 10, and 15 after primary diagnosis was observed for PR-positive, lymph node-negative, and genomic low-risk patients, respectively. Postmenopausal patients had a significant long-term tamoxifen benefit if they had tumors of small or large tumor size, tumor grade 1-2, lymph node-negative status, PR-positive status, low Ki-67 levels, or genomic low risk. Conclusions: This study suggests a differential long-term tamoxifen therapy benefit in pre- vs postmenopausal patients. Clinically defined low-risk postmenopausal patients have long-term tamoxifen benefit, whereas the benefit is absent or diminish over time for premenopausal patients. Improved long-term prognostic and endocrine therapy predictive markers in premenopausal breast cancer patients with poor prognosis and long life-expectancy is needed, which could involve molecular tools. Long-term tamoxifen benefit in premenopausal and postmenopausal breast cancer patients by the clinically used tumor characteristics. Table Multivariable Cox proportional hazard regression analysis of 20-year distant recurrence-free interval (DRFI) for patients with ER-positive/HER2-negative tumors, comparing patients randomized to tamoxifen vs patients randomized to no endocrine therapy (control). Adjusted for age, randomization year, tumor size, tumor grade, lymph node status, PR status, Ki-67 status, chemotherapy, radiotherapy, and type of surgery. Citation Format: Annelie Johansson, Huma Dar, Anna Nordenskjöld, Gizeh Perez-Tenorio, Christina Yau, Christopher C. Benz, Laura J. Esserman, Laura Van’t Veer, Bo Nordenskjöld, Olle Stål, Tommy Fornander, Linda S. Lindström. Differential Long-Term Benefit from Adjuvant Tamoxifen Therapy in Estrogen Receptor (ER)-Positive/Human Epidermal Growth Factor Receptor 2 (HER2)-Negative Premenopausal and Postmenopausal Breast Cancer Patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-03-11.

Background: The risk for patients with estrogen receptor (ER)-positive breast cancer remains stable decades after primary diagnosis, with a large proportion of distant metastatic events occurring late. Thus, long-term follow-up studies are essential to understand true treatment benefit. Tamoxifen (TAM) therapy is a fundamental endocrine treatment for ER-positive breast cancer. We have previously shown a long-term tamoxifen therapy benefit for patients with less aggressive tumor characteristics in ER-positive/HER2-negative patients. However, ER-positive breast cancer is highly heterogenous and can be separated into different molecular subpopulations that behave differently during extended follow-up. The long-term tamoxifen benefit by molecular subtype is largely unexplored. We therefore aimed to investigate the long-term benefit from tamoxifen by clinically used tumor characteristics in Luminal A vs Luminal B patients in the Stockholm tamoxifen (STO)-trials with complete 20-years follow-up. Methods: Secondary analysis of ER-positive/HER2-negative patients with Luminal A or B molecular subtype (n=952) from the STO-trials (1976-1997) randomized to TAM (40 mg) vs no endocrine therapy (control). Gene expression data was generated using custom designed Agilent arrays from FFPE breast cancer tumor tissue and was used to define PAM50 molecular subtypes. The clinically used markers were reannotated in 2014 and 2020. Complete 20-year follow-up was obtained from Swedish high-qualitative registries. The long-term distant recurrence-free interval (DRFI) was assessed by Kaplan-Meier, multivariable Cox proportional hazard regression and time-varying analysis, using flexible parametric modelling. Results: Multivariable analysis showed significantly improved long-term DRFI from TAM vs control for both Luminal A (HR=0.59; 95% CI, 0.44-0.81) and Luminal B (HR=0.67; 95% CI, 0.46-0.99) patients. Time-varying analysis showed that patients with Luminal A subtype significantly benefitted from TAM for 15 years (HR=0.60, 95% CI, 0.39-0.94 at year 15), whereas patients with Luminal B subtype had a significant TAM benefit for 5 years (HR=0.64, 95% CI, 0.42-0.98 at year 5), see Table. Furthermore, a significant long-term TAM benefit for patients with large tumor size (pT>20mm: HR=0.46; 95% CI, 0.25-0.84), tumor grade 1-2 (HR=0.55; 95% CI, 0.40-0.77), lymph node-negative (HR=0.51, 95% CI, 0.34-0.78), PR-positive (HR=0.57, 95% CI, 0.40-0.81) and Ki-67-low tumors (HR=0.55, 95% CI, 0.39-0.77) was seen for Luminal A patients. In Luminal B patients, significantly improved long-term DRFI from TAM vs control was seen for small tumor size (pT≤20mm: HR=0.44; 95% CI, 0.24-0.80), tumor grade 1-2 (HR=0.51; 95% CI, 0.29-0.90), lymph node-negative (HR=0.40, 95% CI, 0.19-0.83), PR-positive (HR=0.59, 95% CI, 0.38-0.93) and Ki-67-low tumors (HR=0.45, 95% CI, 0.25-0.84). Conclusions: This study suggests a 15 years tamoxifen benefit for patients with Luminal A subtype tumors, whereas the benefit for patients with Luminal B tumors is up to five years after diagnosis. Furthermore, our study suggests a long-term tamoxifen benefit for patients with less aggressive tumor characteristics regardless of tumor subtype, except for tumor size in Luminal A patients. ER-positive breast cancer is a heterogeneous disease and long-term follow-up studies in molecular subtypes are essential to understand differences in treatment benefit. Table. Time-varying analysis of long-term tamoxifen therapy benefit by PAM50 molecular subtype. Time-varying analysis of distant recurrence-free interval (DRFI) to assess how tamoxifen benefit varied over the 20 year of follow-up using flexible parametric survival modelling. Patients included in analyses with no missing values. Estimated hazard ratios (HR) at year 5, 10, 15 and 20 for patients with Luminal A or Luminal B molecular subtype tumors randomized to tamoxifen therapy, as compared with patients randomized to no endocrine therapy (control). Adjusted for age, period of primary breast cancer diagnosis, tumor size, tumor grade, lymph node status, PR status, Ki-67 status, chemotherapy, radiotherapy, type of surgery, and menopausal status. *indicates significant findings P Citation Format: Huma Dar, Annelie Johansson, Anna Nordenskjöld, Gizeh Perez-Tenorio, Christina Yau, Christopher C. Benz, Laura J. Esserman, Bo Nordenskjöld, Olle Stål, Tommy Fornander, Linda S. Lindström. Long-Term Benefit from Adjuvant Tamoxifen in Luminal A and Luminal B Breast Cancer Patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-03-04.

The clinical impact of tumor-infiltrating lymphocytes (TILs) is less known for breast cancer patients with the estrogen receptor-positive (ER+)/human epidermal growth factor receptor-negative (HER-) subtype. Here, we explored the prognostic and predictive value of TILs regarding distant recurrence-free interval (DRFI) and breast cancer-specific survival (BCSS) in 763 postmenopausal patients randomized to receive tamoxifen vs. no systemic treatment. TILs were assessed in whole section tumor samples stained with HE and divided into low (lt;10%), intermediate (10-39%), or high (≥40%). High TILs were associated with poor prognostic variables and good prognoses for all patients, but not within the ER+/HER2- group. Within the ER+/HER2- group, high gene expression of CD19 and PD-L1 and high IMMUNE1 score indicated good prognosis in multivariable analysis while high CD8 and CD19 gene expression and high IMMUNE1 score were associated with less tamoxifen benefit. These results indicate that within the ER+/HER2- subtype there could be subsets of patients where expression of specific TIL markers might be used to reveal candidates for immune therapy interventions upon failure of the endocrine therapy.

Background: Elderly breast cancer patients (≥70 years old) are under-represented in clinical trials and remain an undertreated population. Gene expression signatures have been shown to add additional prognostic information beyond that of routine clinicopathological factors, however their utility in elderly breast cancer patients remains unclear. As such, the main aim of this study is to determine if gene signatures can provide prognostic information that may help to aid treatment decisions for elderly breast cancer patients. Material and methods: Research versions of the genomic grade index (GGI), 70-gene, 21-gene recurrence score (RS), cell cycle score (CCS), PAM50 and PAM50 Risk of Relapse score - Proliferation (ROR-P) signatures were applied to 39 open access breast cancer datasets totalling 9583 patients. After filtering based on age ≥ 70 years old, the presence of Estrogen Receptor (ER) and survival information availability 871 patients remained. The prognostic capacity of signatures was tested in all (N=871), Estrogen Receptor positive/Lymph node positive (ER+/LN+, N=335) and Estrogen Receptor positive/Lymph node negative (ER+/LN-, N=374) patients using Kaplan-Meier and multi-variable Cox proportional hazard modeling. Models were adjusted for tumor size, grade, ER and lymph node status in all patients, and tumor size and grade in the ER+/LN+ and ER+/LN- subgroup analyses. Recurrence Free Survival (RFS) censored at 10 years was used as clinical endpoint and defined as the time from date of curative surgery to the time of recurrence or death. Both loco-regional recurrences and distant metastatic events were included in this endpoint. Results: Tumours from patients ≥ 70 years of age showed high levels of ER (87%), were large (69% ≥ 20 mm) and were of intermediate or high grade (82%). All gene signatures were statistically significant in Kaplan-Meier analysis of all and ER+/LN+ patients (Logrank P < 0.001). This significance remained in multi-variable analysis (Cox proportional hazards, P ≤ 0.05) with the exception of PAM50 which showed a trend (P ≤ 0.1) in ER+/LN+ patients. In ER+/LN- patients the GGI, 70-gene, PAM50, ROR-P, and CCS signatures were significant in Kaplan-Meier analysis (Logrank P ≤ 0.05) but only the 70-gene, PAM50, ROR-P, and CCS signatures remained so in multi-variable analysis (Cox proportional hazards, P ≤ 0.05). Conclusions: In general, we found that gene signatures provide statistically significant prognostic information in Kaplan-Meier and multi-variable analyses of all, ER+/LN+ and ER+/LN- breast patients over the age of 70. Table 1: Multivariable proportional hazard (Cox) analyses for all gene signatures for patients above age of 70. NOTE: Bold values indicate P < 0.05. aAdjusted for tumor size, tumor grade, estrogen receptor status, and lymph node status. bAdjusted for tumor size and tumor grade. Citation Format: Miguel Castresana Aguirre, Annelie Johansson, Linda S. Lindström, Nick Tobin. Gene signatures provide independent prognostic information in elderly breast cancer patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-01-08.

The PIK3CA gene, encoding the p110α catalytic subunit of PI 3-kinase (PI3K), is mutated in more than 30% of breast cancers. Most mutations concentrate to the hotspots E542K and E545K and H1047R and are associated with hyperactivation of the phosphatidylinositol 3′-kinase/Akt pathway in vitro. The estrogen receptor-positive (ER+)/human epidermal growth factor receptor 2-negative (HER2-) (ER+/HER2-) breast cancers stand for more than 40% of the PIK3CA mutations where these constitute a new therapeutic target for endocrine-treatment resistant advanced breast cancers. Although PIK3CA is an oncogene, its mutations are associated with good prognosis. Here, we explored the prognostic and predictive role of PIK3CA hotspot mutations for low-risk postmenopausal breast cancer patients randomized to receive tamoxifen vs. no systemic treatment, followed for over 25 years and with extensive clinical records. Mutation analysis was performed using formalin-fixed paraffin-embedded tumors with digital droplet PCR (ddPCR). PIK3CA mutations were present in 35,6% of patients, predominantly within the ER+/HER2- subtype (49,8%) compared with the HER2+ and TNBC subtypes. The most frequent mutation found in all patients was H1047R (18%) followed by E545K (14%) and E542K (6%). Significant associations were found between all hotspot mutations and low grade, positive progesterone receptor (PR) expression, HER2 negative status, low Ki-67 (proliferation marker), and high expression score of a PIK3CA-mutation-associated gene module. Moreover, PIK3CA mutations were often found in patients with ultralow risk to develop distant recurrences according to the 70-gene signature. All PIK3CA mutations were coupled with longer distant recurrence-free interval (DRFI) in all patients in univariate and multivariable analysis after adjusting for tumor size, receptor status (ER, PR, HER2), tumor grade, Ki-67 and tamoxifen: HR multivariable (95% CI)=0.53 (0.28-0.98). In agreement with our previous results, PIK3CA mutations indicated good prognosis for patients with highly proliferative tumors (Ki-67>15%): H.R multivariable (95% CI)=0.15 (0.03-0.69) and high risk by the 70-gene signature: HR multivariable (95% CI)=0.14 (0.03-0.61) but not for low proliferative tumors (Ki-67 Citation Format: Carolin Jönsson, Zeinab Alkashaf, Josefine Sandström, Annelie Johansson, Tommy Fornander, Linda S. Lindström, Gizeh Perez Tenorio. PIK3CA hotspot mutations as biomarkers for prognosis and treatment prediction in low-risk postmenopausal breast cancer patients [abstract]. In: Proceedings of the AACR Special Conference: Cancer Metastasis; 2022 Nov 14-17; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_2):Abstract nr B027.

Genomic alterations resulting in loss of control over the cell cycle is a fundamental hallmark of human malignancies. Whilst pan-cancer studies have broadly assessed tumour genomics and their impact on oncogenic pathways, analyses taking the baseline signalling levels in normal tissue into account are lacking. To this end, we aimed to reclassify the cell cycle activity of tumours in terms of their tissue of origin and determine the DNA mutations, chromosome arm-level changes and signalling pathways driving cell cycle activity. Combining normal tissue and pan-cancer data from over 13,000 samples we demonstrate that tumours of gynaecological origin show the highest levels of baseline corrected cell cycle activity, partially owing to hormonal signalling and gene expression changes. We also show that normal and tumour tissues can be separated into groups (quadrants) of low/high cell cycle activity and propose the novel hypothesis of an upper limit on these activity levels in tumours.

The metastatic potential of estrogen receptor (ER)-positive breast cancers is heterogeneous and distant recurrences occur months to decades after primary diagnosis. We have previously shown that patients with tumors classified as ultralow risk by the 70-gene signature have a minimal long-term risk of fatal breast cancer. Here, we evaluate the previously unexplored underlying clinical and molecular characteristics of ultralow risk tumors in 538 ER-positive patients from the Stockholm tamoxifen randomized trial (STO-3). Out of the 98 ultralow risk tumors, 89% were luminal A molecular subtype, whereas 26% of luminal A tumors were of ultralow risk. Compared to other ER-positive tumors, ultralow risk tumors were significantly (Fishers test, P < .05) more likely to be of smaller tumor size, lower grade, progesterone receptor (PR)-positive, human epidermal growth factor 2 (HER2)-negative and have low Ki-67 levels (proliferation-marker). Moreover, ultralow risk tumors showed significantly lower expression scores of multi-gene modules associated with the AKT/mTOR-pathway, proliferation (AURKA), HER2/ERBB2-signaling, IGF1-pathway, PTEN-loss and immune response (IMMUNE1 and IMMUNE2) and higher expression scores of the PIK3CA-mutation-associated module. Furthermore, 706 genes were significantly (FDR < 0.001) differentially expressed in ultralow risk tumors, including lower expression of genes involved in immune response, PI3K/Akt/mTOR-pathway, histones, cell cycle, DNA repair, apoptosis and higher expression of genes coding for epithelial-to-mesenchymal transition and homeobox proteins, among others. In conclusion, ultralow risk tumors, associated with minimal long-term risk of fatal disease, differ from other ER-positive tumors, including luminal A molecular subtype tumors. Identification of these characteristics is important to improve our prediction of nonfatal vs fatal breast cancer. Funding Agencies|Swedish Research Council (Vetenskapsradet)Swedish Research Council [2020-02466]; Swedish Research Council for Health, Working life and Welfare (FORTE) [2019-00477]; Gosta Milton Donation Fund (Stiftelsen Gosta Miltons donationsfond); Swedish Cancer SocietySwedish Cancer Society [180385, 190140]; Stockholm Cancer Society (Cancerforeningen i Stockholm); California Breast Cancer Research Program (CBCRP) [180B-0065]; National Institutes of Health (NIH)United States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [U01-CA196406]

BackgroundPan-cancer genomic analyses based on the magnitude of pathway activity are currently lacking. Focusing on the cell cycle, we examined the DNA mutations and chromosome arm-level aneuploidy within tumours with low, intermediate and high cell cycle activity.Patients and methodsMatching mRNA, gene mutational status, chromosomal arm-level aberrations and clinico-pathological data was assembled from pan-cancer studies of 9,515 patients with 32 different cancers. Cell cycle activity was estimated from mRNA data using the cell cycle score (CCS) signature. Barplots were used to visualise mutation and chromosomal aberration frequency within CCS subgroups. Kaplan-Meier and multivariable Cox-regression analyses were used to determine survival differences between CCS subgroups.ResultsCell cycle activity varied broadly across and within all cancers. TP53 and PIK3CA mutations were common in all CCS subgroups but with increasing frequency as cell cycle activity levels increased (P < 0.001). Mutations in BRAF and gains in 16p were less frequent CCS high tumours (P < 0.001). In Kaplan-Meier analysis, patients whose tumours were CCS Low had a longer PFI relative to intermediate or high (P < 0.001) and this significance remained in multivariable analysis (CCS intermediate: HR = 1.37; 95% CI 1.17 – 1.60, CCS high: 1.54; 1.29 – 1.84, CCS Low = Ref).ConclusionsCell cycle activity varies across and within cancers and whilst similar DNA alterations can be found at all activity levels, some notable exceptions exist. These data also demonstrate that independent prognostic information can be derived on a pan-cancer level from a simple measure of cell cycle activity.

The aggressive nature of breast cancers detected between planned mammographic screens, so-called interval cancers, remains elusive. Here, we aim to characterise underlying molecular features of interval cancer.From 672 patients with invasive breast cancer, we analysed gene expression differences between 90 'true' interval cancer cases (i.e. women with low-dense breasts defined as per cent mammographic density25%) and 310 screen-detected tumours while accounting for PAM50 subtypes and thus overall tumour aggressiveness. We computed an interval cancer gene expression profile (IC-Gx) in a total of 2270 breast tumours (regardless of interval cancer status) and tested for association with expression-based immune subtypes in breast cancer. In addition, we investigated the contribution of inherited and somatic genetic variants in distinct features of interval cancer.We identified 8331 genes nominally associated with interval cancer (P-value 0.05, fold-change 1.5). Gene set enrichment analysis showed immune-related pathways as key processes altered in interval cancer. Our IC-Gx, based on 47 genes with the strongest associations (false discovery rate 0.05), was found to be associated mainly with immune subtypes involving interferon response. We isolated an interaction network of interval cancer and interferon genes for which a significant load of somatic and germline variants in class I interferon genes was observed.We identified novel molecular features of interval breast cancer highlighting interferon pathways as a potential target for prevention or treatment.

Clinically used breast cancer markers, such as tumor size, tumor grade, progesterone receptor (PR) status, and Ki-67 status, are known to be associated with short-term survival, but the association of these markers with long-term (25-year) survival is unclear.To assess the association of clinically used breast cancer markers with long-term survival and treatment benefit among postmenopausal women with lymph node-negative, estrogen receptor [ER]-positive and ERBB2-negative breast cancer who received tamoxifen therapy.This study was a secondary analysis of data from a subset of 565 women with ER-positive/ERBB2-negative breast cancer who participated in the Stockholm tamoxifen (STO-3) randomized clinical trial. The STO-3 clinical trial was conducted from 1976 to 1990 and comprised 1780 postmenopausal women with lymph node-negative breast cancer who were randomized to receive adjuvant tamoxifen therapy or no endocrine therapy. Complete 25-year follow-up data through December 31, 2016, were obtained from Swedish national registers. Immunohistochemical markers were reannotated in 2014. Data were analyzed from April to December 2020.Patients in the original STO-3 clinical trial were randomized to receive 2 years of tamoxifen therapy vs no endocrine therapy. In 1983, patients who received tamoxifen therapy without cancer recurrence during the 2-year treatment and who consented to continued participation in the STO-3 study were further randomized to receive 3 additional years of tamoxifen therapy or no endocrine therapy.Distant recurrence-free interval (DRFI) by clinically used breast cancer markers was assessed using Kaplan-Meier and multivariable Cox proportional hazards analyses adjusted for age, period of primary diagnosis, tumor size (T1a and T1b [T1a/b], T1c, and T2), tumor grade (1-3), PR status (positive vs negative), Ki-67 status (low vs medium to high), and STO-3 clinical trial arm (tamoxifen treatment vs no adjuvant treatment). A recursive partitioning analysis was performed to evaluate which markers were able to best estimate long-term DRFI.The study population comprised 565 postmenopausal women (mean [SD] age, 62.0 [5.3] years) with lymph node-negative, ER-positive/ERBB2-negative breast cancer. A statistically significant difference in long-term DRFI was observed by tumor size (88% for T1a/b vs 76% for T1c vs 63% for T2 tumors; log-rank P .001) and tumor grade (81% for grade 1 vs 77% for grade 2 vs 65% for grade 3 tumors; log-rank P = .02) but not by PR status or Ki-67 status. Patients with smaller tumors (hazard ratio [HR], 0.31 [95% CI, 0.17-0.55] for T1a/b tumors and 0.58 [95% CI, 0.38-0.88] for T1c tumors) and grade 1 tumors (HR, 0.48; 95% CI, 0.24-0.95) experienced a significant reduction in the long-term risk of distant recurrence compared with patients with larger (T2) tumors and grade 3 tumors, respectively. A significant tamoxifen treatment benefit was observed among patients with larger tumors (HR, 0.53 [95% CI, 0.32-0.89] for T1c tumors and 0.34 [95% CI, 0.16-0.73] for T2 tumors), lower tumor grades (HR, 0.24 [95% CI, 0.07-0.82] for grade 1 tumors and 0.50 [95% CI, 0.31-0.80] for grade 2 tumors), and PR-positive status (HR, 0.38; 95% CI, 0.24-0.62). The recursive partitioning analysis revealed that tumor size was the most important characteristic associated with long-term survival, followed by clinical trial arm among patients with larger tumors.This secondary analysis of data from the STO-3 clinical trial indicated that, among the selected subgroup of patients, tumor size followed by tumor grade were the markers most significantly associated with long-term survival. Furthermore, a significant long-term tamoxifen treatment benefit was observed among patients with larger tumors, lower tumor grades, and PR-positive tumors.

Key Points Question What is the risk of benign breast diseases (BBDs) and how are they associated with age, hormonal breast cancer risk factors, and family history of breast cancer? Findings In this cohort study of 61 617 women in Sweden, incidence rates for distinct BBD subtypes in individuals 25 to 69 years of age were estimated. The study found that the risk of the most common BBDs by hormonal factors was influenced by age and that family history of breast cancer was associated with the risk of proliferative and nonproliferative BBDs. Meaning These results indicate that age and hormonal factors influence the risk of BBDs and that a better understanding of BBDs is important to improve our understanding of breast diseases as a whole., Importance Benign breast diseases (BBDs) are common and associated with breast cancer risk, yet the etiology and risk of BBDs have not been extensively studied. Objective To investigate the risk of BBDs by age, hormonal factors, and family history of breast cancer. Design, Setting, and Participants This retrospective cohort study assessed 70 877 women from the population-based Karolinska Mammography Project for Risk Prediction of Breast Cancer (KARMA) who attended mammographic screening or underwent clinical mammography from January 1, 2011, to March 31, 2013, at 4 Swedish hospitals. Participants took part in a comprehensive questionnaire on recruitment. All participants had complete follow-up through high-quality Swedish national registers until December 31, 2015. Pathology medical records on breast biopsies were obtained for the participants, and BBD subtypes were classified according to the latest European guidelines. Analyses were conducted from January 1 to July 31, 2020. Exposures Hormonal risk factors and family history of breast cancer. Main Outcomes and Measures For each BBD subtype, incidence rates (events per 100 000 person-years) and multivariable Cox proportional hazards ratios (HRs) with time-varying covariates were estimated between the ages of 25 and 69 years. Results A total of 61 617 women within the mammographic screening age of 40 to 69 years (median age, 53 years) at recruitment with available questionnaire data were included in the study. Incidence rates and risk estimates varied by age and BBD subtype. At premenopausal ages, nulliparity (compared with parity ≥3) was associated with reduced risk of epithelial proliferation without atypia (EP; HR, 0.62; 95% CI, 0.46-0.85) but increased risk of cysts (HR, 1.38; 95% CI, 1.03-1.85). Current and long (≥8 years) oral contraceptive use was associated with reduced premenopausal risk of fibroadenoma (HR, 0.65; 95% CI, 0.47-0.90), whereas hormone replacement therapy was associated with increased postmenopausal risks of epithelial proliferation with atypia (EPA; HR, 1.81; 95% CI, 1.07-3.07), fibrocystic changes (HR, 1.60; 95% CI, 1.03-2.48), and cysts (HR, 1.98; 95% CI, 1.40-2.81). Furthermore, predominantly at premenopausal ages, obesity was associated with reduced risk of several BBDs (eg, EPA: HR, 0.31; 95% CI, 0.17-0.56), whereas family history of breast cancer was associated with increased risk (eg, EPA: HR, 2.11; 95% CI, 1.48-3.00). Conclusions and Relevance These results suggest that the risk of BBDs varies by subtype, hormonal factors, and family history of breast cancer and is influenced by age. Better understanding of BBDs is important to improve the understanding of benign and malignant breast diseases., This cohort study investigates the risk of benign breast diseases in women by age, hormonal breast cancer risk factors, and family history of breast cancer.

Background Use of cyclin D1 (CCND1) gene amplification as a breast cancer biomarker has been hampered by conflicting assessments of the relationship between cyclin D1 protein levels and patient survival. Here, we aimed to clarify its prognostic and treatment predictive potential through comprehensive long-term survival analyses. Methods CCND1 amplification was assessed using SNP arrays from two cohorts of 1965 and 340 patients with matching gene expression array and clinical follow-up data of over 15 years. Kaplan-Meier and multivariable Cox regression analyses were used to determine survival differences between CCND1 amplified vs. non-amplified tumours in clinically relevant patient sets, within PAM50 subtypes and within treatment-specific subgroups. Boxplots and differential gene expression analyses were performed to assess differences between amplified vs. non-amplified tumours within PAM50 subtypes. Results When combining both cohorts, worse survival was found for patients with CCND1-amplified tumours in luminal A (HR = 1.68; 95% CI, 1.15–2.46), luminal B (1.37; 1.01–1.86) and ER+/LN−/HER2− (1.66; 1.14–2.41) subgroups. In gene expression analysis, CCND1-amplified luminal A tumours showed increased proliferation (P

Resistance to endocrine therapy in estrogen receptor-positive (ER+) breast cancer is a major clinical problem with poorly understood mechanisms. There is an unmet need for prognostic and predictive biomarkers to allow appropriate therapeutic targeting. We evaluated the mechanism by which minichromosome maintenance protein 3 (MCM3) influences endocrine resistance and its predictive/prognostic potential in ER+ breast cancer. We discovered that ER+ breast cancer cells survive tamoxifen and letrozole treatments through upregulation of minichromosome maintenance proteins (MCMs), including MCM3, which are key molecules in the cell cycle and DNA replication. Lowering MCM3 expression in endocrine-resistant cells restored drug sensitivity and altered phosphorylation of cell cycle regulators, including p53(Ser(315,33)), CHK1(Ser(317)), and cdc25b(Ser(323)), suggesting that the interaction of MCM3 with cell cycle proteins is an important mechanism of overcoming replicative stress and anti-proliferative effects of endocrine treatments. Interestingly, the MCM3 levels did not affect the efficacy of growth inhibitory by CDK4/6 inhibitors. Evaluation of MCM3 levels in primary tumors from four independent cohorts of breast cancer patients receiving adjuvant tamoxifen mono-therapy or no adjuvant treatment, including the Stockholm tamoxifen (STO-3) trial, showed MCM3 to be an independent prognostic marker adding information beyond Ki67. In addition, MCM3 was shown to be a predictive marker of response to endocrine treatment. Our study reveals a coordinated signaling network centered around MCM3 that limits response to endocrine therapy in ER+ breast cancer and identifies MCM3 as a clinically useful prognostic and predictive biomarker that allows personalized treatment of ER+ breast cancer patients. Funding Agencies|Danish Cancer SocietyDanish Cancer Society; Danish Cancer Research Foundation; Danish Research CouncilDet Frie Forskningsrad (DFF); Danish Strategic Research CouncilDanske Strategiske Forskningsrad (DSF); A Race Against Breast Cancer; Region of Southern Denmark Research Foundation; Odense University Hospital Research Council

BackgroundBreast cancer tumors are heterogenous, including their metastatic potential and time to distant metastasis. Patients with estrogen receptor (ER)-positive tumors have a continuous long-term risk of fatal disease decades after diagnosis. Recently, ER-positive breast cancer patients classified as having ultralow risk tumors by the 70-gene expression signature (MammaPrint) were associated with a minimal risk of fatal disease. However, the underlying tumor characteristics of ultralow risk tumors are unknown.MethodsSecondary analysis of the Stockholm tamoxifen randomized trial (STO-3, 1976-1990) enrolling postmenopausal lymph node-negative breast cancer patients. Immunohistochemistry of the clinically used breast cancer markers (n=727 patients) and gene expression profiling by Agilent microarrays (n=652 patients) were performed in 2014. Ultralow risk tumors, identified by the 70-gene signature, were compared to other ER-positive tumors (of low/high risk) and Luminal A and B PAM50 subtype tumors (ER-positive, low/high risk) by the clinical markers and multi-gene modules, representative of specific biological processes and pathways, using Fisher’s exact test. Furthermore, differential gene expression analysis was performed contrasting ultralow risk tumors to other ER-positive tumors (of low/high risk) using t-statistics and false discovery rate (FDR).ResultsUltralow risk tumors were significantly (P

Purpose: Gene signatures and Ki67 stratify the same breast tumor into opposing good/poor prognosis groups in approximately 20% of patients. Given this discrepancy, we hypothesized that the combination of a clinically relevant signature and IHC markers may provide more prognostic information than either classifier alone. Experimental Design: We assessed Ki67 alone or combined with ER, PR and HER2 (forming IHC subtypes), and the research versions of the Genomic Grade Index, 70-gene, cell-cycle score, recurrence score (RS), and PAM50 signatures on matching TMA/whole tumor sections and microarray data in two Swedish breast cancer cohorts of 379 and 209 patients, with median follow-up of 12.4 and 12.5 years, respectively. First, we fit Cox proportional hazards models and used the change in likelihood ratio (Δ LR) to determine the additional prognostic information provided by signatures beyond that of (i) Ki67 and (ii) IHC subtypes. Second and uniquely, we then assessed whether signatures could compete well with pathology-based IHC classifiers by calculating the additional prognostic information of Ki67/IHC subtypes beyond signatures. Results: In cohort 1, only RS and PAM50 provided additional prognostic information beyond Ki67 and IHC subtypes (Δ LR-χ2 Ki67: RS = 12.8, PAM50 = 20.7, IHC subtypes: RS = 12.9, PAM50 = 11.7). Conversely, IHC subtypes added prognostic information beyond all signatures except PAM50. Similar results were observed in cohort 2. Conclusions: RS and PAM50 provided more prognostic information than the IHC subtypes in all breast cancer patients; however, the IHC subtypes did not add any prognostic information to PAM50. Clin Cancer Res; 23(24); 7512–20. ©2017 AACR.

The vast majority of head and neck cancers (HNCs) are sporadic squamous cell carcinomas, smoking and heavy drinking being the main risk factors. However, little is known about the possible role of family history and the importance of inherited factors versus shared environment. We used Swedish population-based registries to study the family history of HNC. In order to estimate the risk for family members to get the same cancer, and the risk for cancer-specific death in patients with a family history of HNC compared with patients without a family history, multivariate Cox proportional hazards analyses were performed. A 1.43-fold increased risk for developing HNC in the first-degree relatives (FDRs) of HNC patients [hazard ratio (HR), 1.43; 95% CI, 1.28-1.61] was found, when compared with relatives of healthy controls. In spouses of patients with HNC, the risk for developing any HNC was moderately increased (HR, 1.25; 95% CI, 1.01-1.53), compared with spouses of healthy controls. In addition, a 1.34-fold increased risk for death of HNC was found in HNC patients with a family history of HNC (HR, 1.34; 95% CI, (1.03-1.73) compared with HNC patients without a family history. We found an increased risk for HNC in relatives and spouses of HNC patients, when compared with family members of healthy controls. This suggests that in addition to inherited factors, shared environmental factors have a significant role in the development of the cancer. Family history of HNC was associated with worse survival in a newly diagnosed HNC patient.

Purpose: Interval breast cancer is of clinical interest, as it exhibits an aggressive phenotype and evades detection by screening mammography. A comprehensive picture of somatic changes that drive tumors to become symptomatic in the screening interval can improve understanding of the biology underlying these aggressive tumors.Experimental Design: Initiated in April 2013, Clinical Sequencing of Cancer in Sweden (Clinseq) is a scientific and clinical platform for the genomic profiling of cancer. The breast cancer pilot study consisted of women diagnosed with breast cancer between 2001 and 2012 in the Stockholm/Gotland regions. A subset of 307 breast tumors was successfully sequenced, of which 113 were screen-detected and 60 were interval cancers. We applied targeted deep sequencing of cancer-related genes; low-pass, whole-genome sequencing; and RNA sequencing technology to characterize somatic differences in the genomic and transcriptomic architecture by interval cancer status. Mammographic density and PAM50 molecular subtypes were considered.Results: In the univariate analyses, TP53, PPP1R3A, and KMT2B were significantly more frequently mutated in interval cancers than in screen-detected cancers. Acquired somatic copy number aberrations with a frequency difference of at least 15% between the two groups included gains in 17q23-q25.3 and losses in 16q24.2. Gene expression analysis identified 447 significantly differentially expressed genes, of which 120 were replicated in an independent microarray dataset. After adjusting for PAM50, most differences were no longer significant.Conclusions: Molecular differences by interval cancer status were observed, but they were largely explained by PAM50 subtypes. This work offers new insights into the biological differences between the two tumor groups. Clin Cancer Res; 23(10); 2584–92. ©2016 AACR.

Background: We have previously demonstrated that gene expression signatures and Ki67 stratify the same breast tumour into opposing good/poor prognosis groups in approximately 20% of cases. Given this, we hypothesized that the combination of a clinically relevant gene signature and IHC markers may provide more prognostic information than either classifier alone. We tested this hypothesis in a large independent cohort of Swedish breast cancer patients with long-term follow-up data. Methods: We assessed Ki67, ER, PR, HER2 and the research versions of the Genomic Grade Index (GGI), Mammaprint, cell-cycle score (CCS), Recurrence Score (RS) and PAM50 gene expression classifiers on matching TMA and microarray data in a Swedish breast cancer cohort of 623 patients. Change in likelihood-ratio (Δ LR-χ2) was used to first determine the additional prognostic information provided by gene expression signatures beyond that provided by 1) Ki67 alone and 2) Ki67 plus ER, PR and HER2, grouped to form the IHC molecular subtypes. Secondly and conversely, we then determined the additional prognostic information provided by Ki67/IHC subtypes beyond gene expression signatures. Results: Representative images from Ki67/gene signature contrast groups show tumours with high levels of Ki67 expression that are classified as good prognosis by gene signatures and conversely, tumours with low Ki67 that are classified into poor prognosis groups by gene signatures. In all patients (n=623), the majority of signatures provided statistically significant information beyond that of Ki67 alone, however only RS and PAM50 remained significant in the presence of the IHC subtypes (Δ LR-χ2 RS= 11.7 and PAM50 = 15.4; P = 0.002 and 0.004, respectively). Conversely, IHC subtypes added prognostic information beyond gene signatures whilst Ki67 alone did not, a notable exception to this was PAM50. Conclusions: In general, a combination of the IHC subtypes with gene signatures provides more prognostic information than either classifier alone when considering all breast cancer patients. Subsequent analyses will focus on patient subgroups including ER positive, node positive and ER positive, node negative groups, along with validation of our work in a second dataset of 253 patients. Change in likelhood ratio with the addition of gene expression signatures to Ki67/IHC subgroups and vice-versa All Patients All PatientsSig. added to Ki67:Sig. Δ LRχ2P-valueSig. added to IHC subtypesSig. Δ LRχ2P-valueGGI6.00.014GGI2.50.108Mammaprint6.30.011Mammaprint1.10.279RS20.8< 0.001RS11.70.002CCS1.70.409CCS2.00.360PAM5025.0< 0.001PAM5015.40.004 Ki67 added to sig.:Ki67 Δ LRχ2P-valueIHC added to sig.:IHC Δ LRχ2P-valueGGI1.60.205GGI14.90.001Mammaprint1.60.199Mammaprint15.30.001RS0.50.477RS12.60.005CCS4.10.041CCS16.10.001PAM502.30.13PAM506.10.107Sig.: Gene expression signature; GGI: Genomic grade index; RS: Recurrence score; CCS: Cell cycle score. Citation Format: Lundberg A, Lindström LS, Falato C, Carlson JW, Foukakis T, Czene K, Bergh J, Tobin NP. Gene expression signatures and immunohistochemical subtypes add prognostic value to each other [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 P1-07-07.

Background: We have previously demonstrated how transcriptional pathway activity and the molecular subtypes of breast cancer metastases significantly influence patient post-relapse survival. Here we extend our analysis to determine whether the prognostic information provided by gene expression signatures in primary breast tumours is also relevant in the metastatic setting. Specifically, we test the research versions of the Genomic Grade Index (GGI), Mammaprint, Recurrence score (RS) and PAM50 gene signatures along with our own cell-cycle based classifier (CCS). Methods: 287 patients with morphologically confirmed loco-regional or distant breast cancer relapse were enrolled in the Swedish multicenter TEX trial from December 2002 until June 2007. Of these, sufficient tumour RNA for gene expression profiling was obtained from metastatic tissue by fine needle aspiration from 111 patients (totalling 120 relapse biopsies). Gene signatures were applied as described in the original research articles and their relationship to short (1.5 year) and long-term (5 year) post-relapse survival was assessed using likelihood ratio, Kaplan-Meier and Cox regression analysis. Results: As anticipated from an aggressive metastatic cohort, the majority of samples (> 70%) were classified into intermediate or high risk groups by all signatures. In both short and long-term survival analysis only PAM50 provided statistically significant prognostic information (short: LRχ2 = 14.7, p = 0.005 and long: LRχ2 = 13.2, p = 0.010), with the cell cycle score signature displaying a prognostic trend in long-term survival only (LRχ2 = 5.2, p = 0.074). Kaplan-Meier curves and Cox regression analysis suggest that the strength of both signatures resides in their ability to select a group of low-risk patients with better long-term survival. Conclusions: Our findings demonstrate the prognostic utility of the multi-level PAM50 and to a lesser extent, cell cycle score signatures in predicting survival of patients with metastatic breast cancer. Simpler binary gene expression signatures (GGI and Mammaprint) do not appear to capture the same prognostic information and as such may have limited utility in a metastatic setting. Short and long term survival Likehood Ratios for five gene expression signatures in metastatic breast cancer Short term survival (1.5 year)Long term survival (5 year)Gene SignatureLRχ2P-valueLRχ2P-valueGGI1.30.2510.50.500Mammaprint1.70.1900.60.427RS3.90.1434.40.110CCS2.80.2425.20.074PAM5014.70.00513.20.010GGI: Genomic grade index; RS: Recurrence score; CCS: Cell cycle score Citation Format: Tobin NP, Lundberg A, Lindström LS, Harrell JC, Egyhazi Brage S, Frostvik Stolt M, Einbeigi Z, Loman N, Malmberg M, Perou CM, Bergh J, Hatschek T. Multi-level gene expression signatures provide significant prognostic information in metastatic breast cancer patients [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 P1-07-16.

Background We and others have shown that the clinically used breast cancer markers alter their expression throughout tumor progression, influencing patient survival (Lindström et al, JCO 2012). What are the likely explanations to our findings? Here, we aimed to determine whether breast cancer intra-tumor heterogeneity of the estrogen receptor (ER) is a marker of tumor aggressiveness and benefit of tamoxifen therapy in a large randomized trial. Material and methods The Stockholm Tamoxifen (STO-3) trial enrolled postmenopausal lymph node negative breast cancer patients with a tumor size of less than 30 mm, between 1976 and 1990, to be randomized to receive adjuvant tamoxifen versus not. From the original randomized trial cohort approximately half of the patients (778 patients) had primary tumor formalin-fixed paraffin-embedded blocks available and were included in our study. No significant differences in age and period of diagnosis, type of surgery received, receptor status, tumor grade and size were observed between the treatment arms. All tumor slides were immunostained in a central laboratory using the SP1 antibody. ER slides were scored by two independent breast cancer pathologists assessing the fraction of cancer cells for each ER intensity level (0, +1, +2 or +3) compared to established standards. The resulting distribution of ER stained tumor cells defines intra-tumor heterogeneity of ER (Rao's quadratic entropy (QE),Potts et al, Lab Invest 2012). Intra-tumor heterogeneity was categorized using the third tertile as cut-off for high heterogeneity (726 patients). Analyses of long-term breast cancer specific survival (25 years) by intra-tumor heterogeneity of ER were performed using univariate Kaplan-Meier and multivariate Cox proportional hazard modeling adjusting for treatment arm, age and period of diagnoses, ER, progesterone receptor (PR), HER2, Ki-67, tumor grade, and tumor size. Further, a test of correlation was performed to investigate whether intra-tumor heterogeneity of ER was correlated to the percentage of ER positive cells, the H-Score or the Luminal A and B subtype (PAM50). Results In the univariate Kaplan-Meier analyses, a statistically significant difference in long-term survival by intra-tumor heterogeneity of ER was seen for all patients (log rank, P=0.018), tamoxifen treated arm (log rank, P=0.0033), but not untreated arm (log rank, P=0.19). However in the multivariate analysis, patients with high intra-tumor heterogeneity of ER in the treated arm as well as in the untreated arm had an almost two-fold increased long-term risk of fatal breast cancer disease as compared to patients with low or intermediate heterogeneity (Treated arm: HR, 2.06; 95% CI, 1.04-4.07 and Untreated arm: HR, 1.71; 95% CI, 1.01-2.87). No significant correlation of intra-tumor heterogeneity to the tested variables was seen. Conclusions Patients with high intra-tumor heterogeneity of ER had less benefit from tamoxifen therapy and an increased long-term risk of fatal breast cancer disease. Our findings should be clinically relevant since therapy benefit was evaluated in a randomized trial with long-term follow-up. Citation Format: Lindström LS, Yau C, Czene K, Thompson CK, van't Veer LJ, Nordenskjöld B, Stål O, Fornander T, Benz CC, Borowsky AD, Esserman LJ. Intra-tumor heterogeneity of the estrogen receptor predicts less benefit from tamoxifen therapy and poor long-term breast cancer patient survival – Retrospective analyses of the STO-3 randomized trial [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 P2-05-03.

Background To understand which breast cancer (BC) risk factors also increase the risk of fibroadenoma and investigate whether these factors have the same effect in BC patients with previous fibroadenoma. Methods Using multistate survival analysis on a large dataset (n = 58 322), we examined the effects of BC risk factors on transitions between three states: event-free, biopsy-confirmed fibroadenoma, and BC. Hazard ratios and corresponding 95% confidence intervals associated with covariate effects were estimated. Median follow-up time was 25.3 years. Results The mean ages at diagnosis of fibroadenoma and BC were 42.6 and 48.3 years, respectively. Participant characteristics known to increase the risk of BC were found to increase the risk of fibroadenoma (family history of BC and higher education). Participant characteristics known to confer protective effects for BC (older age at menarche, more children, and larger childhood body size) were found to reduce fibroadenoma risk. The effect sizes associated with the direct transitions from event-free to fibroadenoma and BC were generally not different for the covariates tested. Age at fibroadenoma diagnosis was associated with the transition from fibroadenoma to BC (hazard ratioper year increase = 1.07 [95% confidence interval = 1.03 to 1.12]). Conclusion We showed that biopsy-confirmed fibroadenomas shared many risk factors with BC. More work is needed to understand the relationships between fibroadenoma and BC to identify women who are at high risk of developing BC after a fibroadenoma diagnosis.

The long-term mortality remains unknown in women diagnosed with breast cancer in situ (BCIS). Here we assessed the cause-specific mortality in BCIS patients. This population-based cohort study included 12 243 women diagnosed with BCIS in Sweden between 1980 and 2011. Patients were followed until death, emigration, or 31 December 2013, whichever came first. The 30-year cumulative incidence of breast cancer-specific mortality was 6.3%, which is considerably lower than 49.7% observed for other-cause mortality. Women diagnosed with BCIS were more likely to die from breast cancer (standardize mortality ratio [SMR], 3.85; 95%CI, 3.47-4.27) but less likely to die from cardiovascular disease (SMR, 0.88; 95% CI, 0.82-0.95) than women in the general population. Specifically, the SMRs for breast cancer-specific mortality decreased over time from 5.17 (95%CI, 3.95-6.81) among BCIS diagnosed during 1980-1989 to 3.03 (95%CI, 2.35-3.91) among those diagnosed during 2000-2011. Furthermore, higher risk of death from other causes was seen among those with older age at BCIS diagnosis, lower levels of education, nulliparity, higher Charlson Comorbidity Index, and being hospitalized before BCIS diagnosis; whereas lower risk of death from breast cancer was seen among BCIS diagnosed in the later time period and those with younger age at first birth. We conclude that most women diagnosed with BCIS die from causes other than breast cancer, which highlights the need for actions not only to reduce non-breast cancer mortality but also to identify patient where extensive curative BCIS treatment is not adding to survival. This article is protected by copyright. All rights reserved.

Background Better tools are needed to identify breast cancer patients at very low risk of dying from their disease. We applied a previously specified 'Ultralow risk' threshold for the FDA-cleared MammaPrint 70-gene expression score to predict long-term absence of breast cancer-specific mortality in a Swedish randomized trial of breast cancer patients treated with tamoxifen (Tam) versus not and followed for more than 25 years. Methods Between 1976-1990 the Stockholm Tamoxifen (STO) trial enrolled and randomized node negative breast cancer patients with tumor size less than 30 mm to receive 2 years of Tam versus not, without regard to hormone receptor status. In the Tam-treated arm, patients without relapse at 2 years were further randomized to receive 3 additional years of Tam versus no additional endocrine therapy. From the original STO randomized trial cohort, about half (778 cases) had remaining formalin-fixed paraffin-embedded primary tumor blocks for additional tumor characterization and MammaPrint analysis. In this validation dataset, which now has >25 years follow-up, breast cancer-specific survival was assessed between MammaPrint scored 'Ultralow risk', 'Low risk' or 'High risk' categories by Kaplan-Meier analyses and multivariate Cox proportional hazard modeling, adjusting for treatment, age, period of diagnosis, tumor size, grade, receptor (ER, PR, HER2) and Ki-67 status. Results: In this unscreened patient population MammaPrint scored 15% of patients as 'Ultra-low risk', 43% as 'Low risk' and 42% as 'High risk'. At 20 years, a statistically significant difference in survival between risk categories was seen for all patients (log rank, P=0.0001), the Tam treated arm (log rank, P=0.0088) and the untreated arm (log rank, P=0.014). Ultra-low risk patients have significantly lower risk of disease-specific death relative to Low and High risk patients in our multivariate Cox analysis. Among Ultra-low risk patients there were no deaths out to 15 years in the Tam-treated arm; by 20 years, disease-specific survival in Tam-treated and untreated arms were 94% and 90%. The majority of Tam-treated patients received only 2 years of treatment, with ∼35% going on to receive 5 years of treatment. All Ultra-low risk cases were HR+HER2-. 78% were luminal A by PAM50; but only 31% of luminal A were Ultra-low risk. Invasive ductal (no-special-type) carcinomas were the most frequent, but lobular, tubular, invasive papillary and invasive cribriform subtypes were enriched and mucinous types were absent. Conclusions: Node-negative, T15 y) metastatic recurrence risk exists if left untreated, 'Ultralow risk' status could identify women for whom lumpectomy alone and a short course of adjuvant endocrine therapy is sufficient. Given the high frequency (∼50%) of such 'Ultralow risk' tumors detected in modern screening cohorts (e.g. MINDACT), a substantial fraction of newly diagnosed women could benefit from more targeted and less aggressive local and adjuvant therapy. Citation Format: Esserman LJ, Thompson CK, Yau C, van 't Veer LJ, Borowsky AD, Tobin NP, Nordenskjöld B, Fornander T, Stål O, Benz CC, Lindström LS. Identification of tumors with an indolent disease course: MammaPrint ultralow signature validation in a retrospective analysis of a Swedish randomized tamoxifen trial. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-09-01.

Breast cancer molecular prognostic tools that predict recurrence risk have mainly been established on endocrine-treated patients and thus are not optimal for the evaluation of benefit from endocrine therapy. The Stockholm tamoxifen (STO-3) trial which randomized postmenopausal node-negative patients to 2-year tamoxifen (followed by an optional randomization for an additional 3-year tamoxifen vs nil), versus no adjuvant treatment, provides a unique opportunity to evaluate long-term 20-year benefit of endocrine therapy within prognostic risk classes of the 70-gene prognosis signature that was developed on adjuvantly untreated patients. We assessed by Kaplan-Meier analysis 20-year breast cancer-specific survival (BCSS) and 10-year distant metastasis-free survival (DMFS) for 538 estrogen receptor (ER)-positive, STO-3 trial patients with retrospectively ascertained 70-gene prognosis classification. Multivariable analysis of long-term (20 years) BCSS by STO-3 trial arm in the 70-gene high-risk and low-risk subgroups was performed using Cox proportional hazard modeling adjusting for classical patient and tumor characteristics. Tamoxifen-treated, 70-gene low- and high-risk patients had 20-year BCSS of 90 and 83%, as compared to 80 and 65% for untreated patients, respectively (log-rank p amp;lt; 0.0001). Notably, there is equivalent tamoxifen benefit in both high (HR 0.42 (0.21-0.86), p = 0.018) and low (HR 0.46 (0.25-0.85), p = 0.013) 70-gene risk categories even after adjusting for clinico-pathological factors for BCSS. Limited tamoxifen exposure as given in the STO-3 trial provides persistent benefit for 10-15 years after diagnosis in a time-varying analysis. 10-year DMFS was 93 and 85% for low- and high-risk tamoxifen-treated, versus 83 and 70% for low- and high-risk untreated patients, respectively (log-rank p amp;lt; 0.0001). Patients with ER-positive breast cancer, regardless of high or low 70-gene risk classification, receive significant survival benefit lasting over 10 years from adjuvant tamoxifen therapy, even when given for a relatively short duration. Funding Agencies|California Breast Cancer Research Program BCRP award [180B-0065]; Breast Cancer Research Foundation [BCRF]; Swedish Research Council [521-2014-2057]; FORTE [2014-1962]; Stiftelsen Gosta Miltons Donationsfond [The Gosta Milton Donation Fund]; Cancerforeningen i Stockholm [Stockholm Cancer Society]