Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study

BMC Genomics

Research Article

Oscar Rueda¹  Helena M. Earl²  Carlos Caldas²  Mahesh Iddawela³  Jed Cowley⁴  Oleg Eremin⁵  Jenny Eremin⁵ 

[1] Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, CB2 0RE, Cambridge, UK;Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, CB2 0RE, Cambridge, UK;Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, UK;Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK;Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, CB2 0RE, Cambridge, UK;Department of Oncology, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, UK;Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge, UK;Department of Anatomy & Developmental Biology, Monash University, 3800, Clayton, VIC, Australia;School of Clinical Sciences, Monash University, Clayton, Australia;PathLinks, Lincoln County Hospital, Lincoln, UK;Research and Development, Lincoln Breast Unit, Lincoln County Hospital, Lincoln, UK;Nottingham Digestive Disease Centre, Faculty of Medicine and Health Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, UK;

关键词: Gene Expression;    Copy Number;    FFPE;    Genomics;    Breast Cancer;    DASL;    Molecular Inversion Probes Assay;    Oncoscan Array;    Molecular Markers;   

DOI  :  10.1186/s12864-017-3867-3

 received in 2016-12-16, accepted in 2017-06-16,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAn absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples.MethodsThe cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC).ResultsForty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q (55%), 8q (40%) and 17q (40%), whereas 11q11 (37%) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13 (62%), 8q24 (54%) and 20q (47%). Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER– cancers identified over-expression of TTF1, LAF-4 and C-MYB (p ≤ 0.05), and between pCR vs non-pCRs, over-expression of CXCL9, AREG, B-MYB and under-expression of ABCG2.ConclusionThis study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide reliable information and will be a useful tool in molecular marker studies.Trial RegistrationTrial registration number ISRCTN09184069 and registered retrospectively on 02/06/2010.

【 授权许可】

CC BY   
© The Author(s). 2017