title: Multimodal Assessment of Estrogen Receptor mRNA Profiles to Quantify Estrogen Pathway Activity in Breast Tumors.
abstract: BACKGROUND
  Molecular markers have transformed our understanding of the heterogeneity of breast cancer and have allowed the identification of genomic profiles of estrogen receptor (ER)-α signaling. However, our understanding of the transcriptional profiles of ER signaling remains inadequate. Therefore, we sought to identify the genomic indicators of ER pathway activity that could supplement traditional immunohistochemical (IHC) assessments of ER status to better understand ER signaling in the breast tumors of individual patients.
  
  
  METHODS
  We reduced ESR1 (gene encoding the ER-α protein) mRNA levels using small interfering RNA in ER+MCF7 breast cancer cells and assayed for transcriptional changes using Affymetrix HG U133 Plus 2.0 arrays. We also compared 1034 ER+and ER-breast tumors from publicly available microarray data. The principal components of ER activity generated from these analyses and from other published estrogen signatures were compared with ESR1 expression, ER-α IHC, and patient survival.
  
  
  RESULTS
  Genes differentially expressed in both analyses were associated with ER-α IHC and ESR1 mRNA expression. They were also significantly enriched for estrogen-driven molecular pathways associated with ESR1, cyclin D1 (CCND1), MYC (v-myc avian myelocytomatosis viral oncogene homolog), and NFKB (nuclear factor kappa B). Despite their differing constituent genes, the principal components generated from these new analyses and from previously published ER-associated gene lists were all associated with each other and with the survival of patients with breast cancer treated with endocrine therapies.
  
  
  CONCLUSIONS
  A biomarker of ER-α pathway activity, generated using ESR1-responsive mRNAs in MCF7 cells, when used alongside ER-α IHC and ESR1 mRNA expression, could provide a method for further stratification of patients and add insight into ER pathway activity in these patients.
authors.affiliation: Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand. Electronic address: a.muthukaruppan@auckland.ac.nz.
authors.forename: Anita
authors.initials: A
authors.lastname: Muthukaruppan
authors.affiliation: Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
authors.forename: Annette
authors.initials: A
authors.lastname: Lasham
authors.affiliation: Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
authors.forename: Kathryn J
authors.initials: KJ
authors.lastname: Woad
authors.affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Black
authors.affiliation: Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
authors.forename: Cherie
authors.initials: C
authors.lastname: Blenkiron
authors.affiliation: Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC.
authors.forename: Lance D
authors.initials: LD
authors.lastname: Miller
authors.affiliation: Canterbury Health Laboratories, Christchurch, New Zealand.
authors.forename: Gavin
authors.initials: G
authors.lastname: Harris
authors.affiliation: Discipline of Oncology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
authors.forename: Nicole
authors.initials: N
authors.lastname: McCarthy
authors.affiliation: Discipline of Oncology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Findlay
authors.affiliation: Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
authors.forename: Andrew N
authors.initials: AN
authors.lastname: Shelling
authors.affiliation: Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand; New Zealand Bioinformatics Institute, The University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.
authors.forename: Cristin G
authors.initials: CG
authors.lastname: Print
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism*; D002352:Carrier Proteins; D047628:Estrogen Receptor alpha / Q000235:genetics / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007150:Immunohistochemistry; D061986:MCF-7 Cells; D017410:Practice Guidelines as Topic; D034622:RNA Interference; D012333:RNA, Messenger / Q000378:metabolism; D034741:RNA, Small Interfering; D011960:Receptors, Estrogen; D015398:Signal Transduction; D046888:Tissue Array Analysis
chemical_list: D014408:Biomarkers, Tumor; D002352:Carrier Proteins; C506487:ESR1 protein, human; D047628:Estrogen Receptor alpha; D012333:RNA, Messenger; D034741:RNA, Small Interfering; D011960:Receptors, Estrogen; C010140:estrophilin
keywords: Breast cancer; ER; ESR1; Gene expression; MCF7; Principal component analysis; RNA