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Series GSE122630 Query DataSets for GSE122630
Status Public on Jul 02, 2019
Title On-Treatment Biomarkers Improve Prediction of Response to Neoadjuvant Chemotherapy in Breast Cancer
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Background: Neoadjuvant chemotherapy is increasingly being used to preoperatively shrink breast tumours prior to surgery. This approach also provides the opportunity to study the molecular changes associated with treatment and evaluate whether on-treatment sequential samples can improve response and outcome predictions over diagnostic or excision samples alone.
Methods: A total of 95 samples from a cohort of 50 neoadjuvant chemotherapy-treated primary breast cancer patients (aged 29-76, 48% ER+, 20% HER2+) enrolled in the NEO trial taken before, at 2 weeks on-treatment, mid-therapy and at resection were sequenced with Ion Ampliseq transcriptome yielding expression values for 12,635 genes. Differential expression analysis was performed across 16 responders and 34 non-responders defined by pathological complete response and over treatment time to identify significantly differentially expressed genes, pathways and markers indicative of response status. Prediction accuracy was compared with estimations of established gene signatures, for this dataset and validated using data from the I-SPY1 trial.
Results: AAGAB was identified as a novel on-treatment biomarker for pathological complete response, with an accuracy of 100% in the NEO training dataset and 78% accuracy in the I-SPY1 Trial. AAGAB levels on treatment were also significantly predictive of term survival (p = 0.048, p = 0.031) in the two cohorts. This single gene on-treatment biomarker, had greater predictive accuracy than established prognostic tests, Mammaprint and Pam50 risk of recurrence score, although interesting both of these tests performed better in the on-treatment rather than the accepted pre-treatment setting (accuracy improving consistently by 2-8%).
Conclusion: Changes in gene expression measured in sequential samples from breast cancer patients receiving neoadjuvant chemotherapy resulted in the identification of a novel on-treatment biomarker and suggest that established prognostic tests may have greater prediction accuracy on- than before treatment. These results support the potential use and further evaluation of on- treatment testing in breast cancer to improve the accuracy of tumour response prediction.
 
Overall design A cohort of 95 paired sequentially sampled breast cancer patients with known treatment response were pooled. Samples were taken via needle aspiration at T1 (Pre-treatment), T2 (2 weeks on treatment), T3 (mid chemo, usually 6 weeks), and T4 at surgical resection. Samples were fresh frozen after collection. Samples were sequenced on the Ampliseq platform and differential analysis and processing were performed in R.
 
Contributor(s) Bownes RJ, Turnbull AK, Matínez-Pérez C, Cameron DA, Sims AH, Oikonomidou O
Citation(s) 31200764
Submission date Nov 16, 2018
Last update date Jul 02, 2019
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)
GPL17303 Ion Torrent Proton (Homo sapiens)
Samples (95)
GSM3476662 NEO11 [Patient_11_T1]
GSM3476663 NEO11 [Patient_11_T2]
GSM3476664 NEO11 [Patient_11_T3]
Relations
BioProject PRJNA505812
SRA SRP169094

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
GSE122630_Processed_data.txt.gz 2.3 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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