title: Integrative analysis of miRNA and gene expression reveals regulatory networks in tamoxifen-resistant breast cancer.
abstract: Tamoxifen is an effective anti-estrogen treatment for patients with estrogen receptor-positive (ER+) breast cancer, however, tamoxifen resistance is frequently observed. To elucidate the underlying molecular mechanisms of tamoxifen resistance, we performed a systematic analysis of miRNA-mediated gene regulation in three clinically-relevant tamoxifen-resistant breast cancer cell lines (TamRs) compared to their parental tamoxifen-sensitive cell line. Alterations in the expression of 131 miRNAs in tamoxifen-resistant vs. parental cell lines were identified, 22 of which were common to all TamRs using both sequencing and LNA-based quantitative PCR technologies. Although the target genes affected by the altered miRNA in the three TamRs differed, good agreement in terms of affected molecular pathways was observed. Moreover, we found evidence of miRNA-mediated regulation of ESR1, PGR1, FOXM1 and 14-3-3 family genes. Integrating the inferred miRNA-target relationships, we investigated the functional importance of 2 central genes, SNAI2 and FYN, which showed increased expression in TamR cells, while their corresponding regulatory miRNA were downregulated. Using specific chemical inhibitors and siRNA-mediated gene knockdown, we showed that both SNAI2 and FYN significantly affect the growth of TamR cell lines. Finally, we show that a combination of 2 miRNAs (miR-190b and miR-516a-5p) exhibiting altered expression in TamR cell lines were predictive of treatment outcome in a cohort of ER+ breast cancer patients receiving adjuvant tamoxifen mono-therapy. Our results provide new insight into the molecular mechanisms of tamoxifen resistance and may form the basis for future medical intervention for the large number of women with tamoxifen-resistant ER+ breast cancer.
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Tejal
authors.initials: T
authors.lastname: Joshi
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.
authors.forename: Daniel
authors.initials: D
authors.lastname: Elias
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Section of Molecular Disease Biology, Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Jan
authors.initials: J
authors.lastname: Stenvang
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.
authors.forename: Carla L
authors.initials: CL
authors.lastname: Alves
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|BGI (Beijing Genomics Institute), Beishan Industrial Zone, Shenzhen, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Teng
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.
authors.forename: Maria B
authors.initials: MB
authors.lastname: Lyng
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Breast Cancer Group, Cell Death and Metabolism, Danish Cancer Society Research Center, Copenhagen, Denmark.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Lykkesfeldt
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Section of Molecular Disease Biology, Department of Veterinary Disease Biology, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Nils
authors.initials: N
authors.lastname: Brünner
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|BGI (Beijing Genomics Institute), Beishan Industrial Zone, Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Ramneek
authors.initials: R
authors.lastname: Gupta
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Workman
authors.affiliation: Sino-Danish Breast Cancer Research Centre, University of Copenhagen, Copenhagen, Denmark.|Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark.|Department of Oncology, Odense University Hospital, Odense, Denmark.
authors.forename: Henrik J
authors.initials: HJ
authors.lastname: Ditzel
mesh_terms: D048948:14-3-3 Proteins / Q000378:metabolism; D018931:Antineoplastic Agents, Hormonal / Q000494:pharmacology; D001940:Breast / Q000378:metabolism; D001943:Breast Neoplasms / Q000188:drug therapy*; D045744:Cell Line, Tumor; D015331:Cohort Studies; D019008:Drug Resistance, Neoplasm; D047628:Estrogen Receptor alpha / Q000378:metabolism; D005260:Female; D000072278:Forkhead Box Protein M1 / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D047908:Intracellular Signaling Peptides and Proteins / Q000378:metabolism; D061986:MCF-7 Cells; D035683:MicroRNAs / Q000378:metabolism*; D009687:Nuclear Proteins / Q000378:metabolism; D034741:RNA, Small Interfering / Q000494:pharmacology; D000071250:Snail Family Transcription Factors / Q000378:metabolism; D013629:Tamoxifen / Q000494:pharmacology*
chemical_list: D048948:14-3-3 Proteins; D018931:Antineoplastic Agents, Hormonal; C506487:ESR1 protein, human; D047628:Estrogen Receptor alpha; C107585:FOXM1 protein, human; D000072278:Forkhead Box Protein M1; D047908:Intracellular Signaling Peptides and Proteins; C439067:MRFAP1 protein, human; D035683:MicroRNAs; D009687:Nuclear Proteins; D034741:RNA, Small Interfering; C000604408:SNAI2 protein, human; D000071250:Snail Family Transcription Factors; C000610447:YWHAG protein, human; C572235:YWHAZ protein, human; D013629:Tamoxifen
keywords: antihormonal therapy; breast cancer; endocrine resistance; miRNA-mediated gene regulation; miRNAs