title: Integrative analyses identify modulators of response to neoadjuvant aromatase inhibitors in patients with early breast cancer.
abstract: BACKGROUND
  Aromatase inhibitors (AIs) are a vital component of estrogen receptor positive (ER+) breast cancer treatment. De novo and acquired resistance, however, is common. The aims of this study were to relate patterns of copy number aberrations to molecular and proliferative response to AIs, to study differences in the patterns of copy number aberrations between breast cancer samples pre- and post-AI neoadjuvant therapy, and to identify putative biomarkers for resistance to neoadjuvant AI therapy using an integrative analysis approach.
  
  
  METHODS
  Samples from 84 patients derived from two neoadjuvant AI therapy trials were subjected to copy number profiling by microarray-based comparative genomic hybridisation (aCGH, n=84), gene expression profiling (n=47), matched pre- and post-AI aCGH (n=19 pairs) and Ki67-based AI-response analysis (n=39).
  
  
  RESULTS
  Integrative analysis of these datasets identified a set of nine genes that, when amplified, were associated with a poor response to AIs, and were significantly overexpressed when amplified, including CHKA, LRP5 and SAPS3. Functional validation in vitro, using cell lines with and without amplification of these genes (SUM44, MDA-MB134-VI, T47D and MCF7) and a model of acquired AI-resistance (MCF7-LTED) identified CHKA as a gene that when amplified modulates estrogen receptor (ER)-driven proliferation, ER/estrogen response element (ERE) transactivation, expression of ER-regulated genes and phosphorylation of V-AKT murine thymoma viral oncogene homolog 1 (AKT1).
  
  
  CONCLUSIONS
  These data provide a rationale for investigation of the role of CHKA in further models of de novo and acquired resistance to AIs, and provide proof of concept that integrative genomic analyses can identify biologically relevant modulators of AI response.
authors.affiliation: Royal Marsden Hospital, London, UK. elena.lopez-knowles@icr.ac.uk.|Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. elena.lopez-knowles@icr.ac.uk.
authors.forename: Elena
authors.initials: E
authors.lastname: López-Knowles
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. paul.wilkerson@icr.ac.uk.
authors.forename: Paul M
authors.initials: PM
authors.lastname: Wilkerson
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. ricardo.ribas@icr.ac.uk.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Ribas
authors.affiliation: Royal Marsden Hospital, London, UK. helenlanderson@btinternet.com.|Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. helenlanderson@btinternet.com.
authors.forename: Helen
authors.initials: H
authors.lastname: Anderson
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. alan.mackay@icr.ac.uk.
authors.forename: Alan
authors.initials: A
authors.lastname: Mackay
authors.affiliation: Royal Marsden Hospital, London, UK. zara.ghazoui@astrazeneca.com.|Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. zara.ghazoui@astrazeneca.com.|Current affiliation: AstraZeneca, Alderley Park, Macclesfield, SK10 4TG, UK. zara.ghazoui@astrazeneca.com.
authors.forename: Zara
authors.initials: Z
authors.lastname: Ghazoui
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. aradhana.rani@icr.ac.uk.
authors.forename: Aradhana
authors.initials: A
authors.lastname: Rani
authors.affiliation: Royal Marsden Hospital, London, UK. peter.osin@rmh.nhs.uk.
authors.forename: Peter
authors.initials: P
authors.lastname: Osin
authors.affiliation: Royal Marsden Hospital, London, UK. ashutosh.nerurkar@rmh.nhs.uk.
authors.forename: Ash
authors.initials: A
authors.lastname: Nerurkar
authors.affiliation: University of Edinburgh, Edinburgh, UK. Lorna.Renshaw@luht.scot.nhs.uk.
authors.forename: Lorna
authors.initials: L
authors.lastname: Renshaw
authors.affiliation: University of Edinburgh, Edinburgh, UK. al720@medschl.cam.ac.uk.|Current affiliation: Academic Laboratory of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, UK. al720@medschl.cam.ac.uk.
authors.forename: Alexey
authors.initials: A
authors.lastname: Larionov
authors.affiliation: University of Edinburgh, Edinburgh, UK. bill@aromil.co.uk.
authors.forename: William R
authors.initials: WR
authors.lastname: Miller
authors.affiliation: University of Edinburgh, Edinburgh, UK. mike.dixon@ed.ac.uk.
authors.forename: J Michael
authors.initials: JM
authors.lastname: Dixon
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. reisfilj@mskcc.org.|Current affiliation: Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA. reisfilj@mskcc.org.
authors.forename: Jorge S
authors.initials: JS
authors.lastname: Reis-Filho
authors.affiliation: Royal Marsden Hospital, London, UK. anita.dunbier@otago.ac.nz.|Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. anita.dunbier@otago.ac.nz.|Current affiliation: Department of Biochemistry, University of Otago, Dunedin, New Zealand. anita.dunbier@otago.ac.nz.
authors.forename: Anita K
authors.initials: AK
authors.lastname: Dunbier
authors.affiliation: Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. Lesley-Ann.Martin@icr.ac.uk.
authors.forename: Lesley-Ann
authors.initials: LA
authors.lastname: Martin
authors.affiliation: Royal Marsden Hospital, London, UK. Mitch.dowsett@icr.ac.uk.|Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK. Mitch.dowsett@icr.ac.uk.
authors.forename: Mitch
authors.initials: M
authors.lastname: Dowsett
mesh_terms: D000818:Animals; D018931:Antineoplastic Agents, Hormonal / Q000494:pharmacology / Q000627:therapeutic use*; D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use; D047072:Aromatase Inhibitors / Q000494:pharmacology / Q000627:therapeutic use*; D014408:Biomarkers, Tumor; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics* / Q000378:metabolism / Q000401:mortality / Q000473:pathology; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D002797:Choline Kinase / Q000235:genetics / Q000378:metabolism; D002869:Chromosome Aberrations; D016000:Cluster Analysis; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D051379:Mice; D020360:Neoadjuvant Therapy; D009367:Neoplasm Staging; D011379:Prognosis; D011960:Receptors, Estrogen / Q000378:metabolism; D015203:Reproducibility of Results; D016896:Treatment Outcome
chemical_list: D018931:Antineoplastic Agents, Hormonal; D047072:Aromatase Inhibitors; D014408:Biomarkers, Tumor; D011960:Receptors, Estrogen; C517212:CHKA protein, human; D002797:Choline Kinase