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Series GSE119262 Query DataSets for GSE119262
Status Public on Aug 30, 2018
Title Gene expression profiling of pre-operative mTOR inhibitor everolimus treatment in breast cancer
Organism Homo sapiens
Experiment type Expression profiling by array
Summary There is growing evidence that uncontrolled activation of the PI3K/Akt/mTOR pathway contributes to the development and progression of breast cancer. Inhibition of this pathway has antitumour effects in preclinical studies and efficacy in combination with other agents in breast cancer patients. The aim of this study is to characterise the effects of pre-operative everolimus treatment in primary breast cancer patients and to identify potential molecular predictors of response. Twenty-seven patients with oestrogen receptor (ER)-positive breast cancer completed 11ā€“14 days of neoadjuvant treatment with 5-mg everolimus. Core biopsies were taken before and after treatment and analysed using Illumina HumanRef-8 v2 Expression BeadChips. Changes in proliferation (Ki67) and phospho-AKT were measured on diagnostic core biopsies/resection samples embedded in paraffin by immunohistochemistry to determine response to treatment. Patients that responded to everolimus treatment with significant reductions in proliferation (fall in % Ki67 positive cells) also had significant decreases in the expression of genes involved in cell cycle (P = 8.70Eāˆ’09) and p53 signalling (P = 0.01) pathways. Highly proliferating tumours that have a poor prognosis exhibited dramatic reductions in the expression of cell cycle genes following everolimus treatment. The genes that most clearly separated responding from non-responding pre-treatment tumours were those involved with protein modification and dephosphorylation, including DYNLRB2, ERBB4, PTPN13, ULK2 and DUSP16. The majority of ER-positive breast tumours treated with everolimus showed a significant reduction in genes involved with proliferation, these may serve as markers of response and predict which patients will derive most benefit from mTOR inhibition.
 
Overall design Primary biopsy and resection breast tumour samples, collected pre and post everolimus treatment for 2 weeks. Note that the are 21 pairs and 2 pre-treatment only samples.
 
Contributor(s) Sims AH
Citation(s) 20480226
Submission date Aug 30, 2018
Last update date Aug 30, 2018
Contact name Andrew H Sims
E-mail(s) andrew.sims@ed.ac.uk
Organization name University of Edinburgh
Department Institute of Genetics and Molecular Medicine
Lab Applied Bioinformatics of Cancer
Street address Systems Medicine Building
City Carrington Crescent
State/province Edinburgh
ZIP/Postal code EH4 2XR
Country United Kingdom
 
Platforms (1)
GPL6104 Illumina humanRef-8 v2.0 expression beadchip
Samples (88)
GSM3362421 SAMPLE 1: Patient1.Pre_Replicate1
GSM3362422 SAMPLE 2: Patient1.Pre_Replicate2
GSM3362423 SAMPLE 3: Patient4.Post_Replicate1
Relations
BioProject PRJNA488625

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE119262_RAW.tar 3.4 Mb (http)(custom) TAR
GSE119262_non-normalized.txt.gz 11.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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