DOI: 10.6084/m9.figshare.13234520
title: Data and metadata supporting the article: MCM3 upregulation confers endocrine resistance in breast cancer and is a predictive marker of diminished tamoxifen benefit

description: Resistance to endocrine therapy in estrogen receptor-positive (ER+) breast cancer is a major clinical problem with poorly understood mechanisms. In this study, the authors evaluated the mechanism by which minichromosome maintenance protein 3 (MCM3) influences endocrine resistance and its predictive/prognostic potential in ER+ breast cancer.<br><b>Data access</b>: The mass spectrometry proteomics data generated during the study, are publicly available in the PRIDE repository, under the accession number <b>https://identifiers.org/pride.project:PXD001087</b>. The effect of MCM3 knockdown on gene expression in TamR cell lines data, are publicly available in Gene Expression Omnibus, under the accession number: <b>https://identifiers.org/geo:GSE148878</b>. The three microarray gene datasets analysed during the study, are publicly available in Gene Expression Omnibus, under the following accession numbers: <b>https://identifiers.org/geo:GSE20361</b>, <b>https://identifiers.org/geo:GSE38829</b> and <b>https://identifiers.org/geo:GSE50820</b>. Microarray data from 2555 breast cancer patients (cohort 3), analysed during the study, were obtained from the kmplot.com database (<b>www.kmplot.com</b>). Survival analyses datasets supporting figures 2 and 3, are not publicly available to protect patient privacy, but will be made available to authorized researchers who have an approved Institutional Review Board application and have obtained approval from The Regional Committees on Health Research Ethics for Southern Denmark. Please contact the corresponding author with data access requests. All other datasets generated during the study (including immunohistochemistry data and phospho-specific cell cycle antibody microarray analysis data) will be made available upon reasonable request from the corresponding author, Dr. Henrik Ditzel, email address: <b>hditzel@health.sdu.dk</b>. Supplementary tables 1 and 4 are available in the figshare repository, as part of this data record. Uncropped western blots are part of the supplementary files.<br><b>Study approval</b>: All tissue samples were collected in compliance with informed consent policy. The study was approved by the local ethical committee at Karolinska Institute, Stockholm, Sweden.<br><b>Study aims and methodology</b>: Approximately 80% of breast cancers express the estrogen-receptor (ER+), rendering them suitable for adjuvant anti-estrogen treatment. Although tamoxifen is of great benefit for many ER+ breast cancer patients, recurrence occurs in approximately 30% over 15-years of follow-up. Tamoxifen is a selective estrogen receptor modulator (SERM) with both antagonistic and agonistic tissue-dependent effects. In vitro, tamoxifen acts as a partial estrogen antagonist, by antagonizing the estrogen regulation of the transcription of most ER-regulated genes and inhibiting growth of estrogen receptor-dependent breast cancer cells.The minichromosome maintenance 3 protein (MCM3) protein belongs to a family of 6 highly conserved minichromosome maintenance proteins (MCM2-MCM7) that are essential to ensure eukaryotic DNA is replicated only once per cell cycle, and additionally acts as a helicase to drive replication elongation. In this study, the authors used a quantitative proteomic approach combined with systems biology analyses, to gain insight into the biology of endocrine resistance in breast cancer, and to identify potential predictive or prognostic markers.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, were evaluated.Cohort 1: ER+ primary breast cancer tissues from 79 patients collected from Herlev and Roskilde Hospitals, Denmark.Cohort 2: Retrospective cohort of 589 patients from the Danish Breast Cancer Co-operative Group (DBCG) 89C randomized study.Cohort 3: 2555 breast cancer patients of which 2051 were ER+ (1802 were endocrine treated and 503 did not receive any systemic treatment). All data for cohort 3 were obtained from www.kmplot.com database.Cohort 4: Stockholm Breast Cancer Study Group randomised tamoxifen STO-3 trial 1976-1990. A cohort of 1,780 postmenopausal women with breast cancer was randomised to adjuvant tamoxifen for 2 or 5 years (n = 886), or no adjuvant endocrine therapy (n = 894).<br>The human breast cancer cell line MCF-7 was originally received from The Breast Cancer Task Force Cell Culture Bank, Mason Research Institute. Cell lines including tamoxifen-sensitive subline MCF-7/S0.5, tamoxifen-resistant cell lines MCF-7/TAMR-1 (TamR-1), MCF-7/TAMR-4 (TamR-4), MCF-7/TAMR-7 (TamR-7) and fulvestrant-resistant cell line FulvR-1, were derived from the MCF-7 cells.<br>The following techniques and assays are described in more detail in the published article, and its supplementary methods: mass spectrometry-based proteomic analysis, descriptions of the characteristics of patient cohorts, xenograft tumor models, immunohistochemical staining, targeted gene knockdown using siRNA, and statistical analyses.<br><b>Datasets supporting the findings reported in the article:</b> All the datasets supporting the findings of this study are listed in the data file <b>Løkkegaard, S. et al.xlsx</b>.Supplementary table 1 (<b>List of proteins with increased expression in TAMR-1 vs. MCF-7S0.5 cells.xlsx</b>), provides a list of the 275 proteins showing increased expression, and 264 showed reduced expression in TAMR-1 vs. MCF-7/S0.5 cells defined as ≥1.5-fold differential expression.Supplementary table 4 (<b>MCM3 gene knockdown on gene expression profile of tamoxifen-resistant breast cancer cell lines.xlsx</b>), includes data on genes exhibiting altered expression in TamR cells following MCM3 knockdown (transfected with MCM3-specific siRNAs) versus cells transfected with siControl (FDR &lt; 0.05 and ≥ 1.5 fold altered expression).<br><b>Software needed to access data</b>: Files in. dta format can be accessed using the STATA statistical software.