Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

BMC Cancer

Research Article

Bruce J Youngson¹  Naomi Miller¹  Scott Boerner¹  Al Muktafi Sadi²  Dong-Yu Wang²  Susan J Done³  Wey L Leong⁴ 

[1] Laboratory Medicine Program, Princess Margaret Hospital, University Health Network, 610 University Avenue, M5G 2M9, Toronto, Ontario, Canada;Ontario Cancer Institute and Campbell Family Institute for Breast Cancer Research, Princess Margaret Hospital, University Health Network, 610 University Avenue, M5G 2M9, Toronto, Ontario, Canada;Ontario Cancer Institute and Campbell Family Institute for Breast Cancer Research, Princess Margaret Hospital, University Health Network, 610 University Avenue, M5G 2M9, Toronto, Ontario, Canada;Laboratory Medicine Program, Princess Margaret Hospital, University Health Network, 610 University Avenue, M5G 2M9, Toronto, Ontario, Canada;Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, 1 King's College Circle, M5S 1A8, Toronto, Ontario, Canada;Department of Medical Biophysics, University of Toronto, Ontario Cancer Institute, Princess Margaret Hospital, 610 University Avenue, M5G 2M9, Toronto, Ontario, Canada;Ontario Cancer Institute and Campbell Family Institute for Breast Cancer Research, Princess Margaret Hospital, University Health Network, 610 University Avenue, M5G 2M9, Toronto, Ontario, Canada;Surgical Oncology, Princess Margaret Hospital, University Health Network, 610 University Avenue, M5G 2M9, Toronto, Ontario, Canada;

关键词: Breast Cancer;    Gene Profile;    Fine Needle Aspiration Biopsy;    FFPE Sample;    FFPE Specimen;   

DOI  :  10.1186/1471-2407-11-253

 received in 2010-12-22, accepted in 2011-06-16,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe ability of gene profiling to predict treatment response and prognosis in breast cancers has been demonstrated in many studies using DNA microarray analyses on RNA from fresh frozen tumor specimens. In certain clinical and research situations, performing such analyses on archival formalin fixed paraffin-embedded (FFPE) surgical specimens would be advantageous as large libraries of such specimens with long-term follow-up data are widely available. However, FFPE tissue processing can cause fragmentation and chemical modifications of the RNA. A number of recent technical advances have been reported to overcome these issues. Our current study evaluates whether or not the technology is ready for clinical applications.MethodsA modified RNA extraction method and a recent DNA microarray technique, cDNA-mediated annealing, selection, extension and ligation (DASL, Illumina Inc) were evaluated. The gene profiles generated from FFPE specimens were compared to those obtained from paired fresh fine needle aspiration biopsies (FNAB) of 25 breast cancers of different clinical subtypes (based on ER and Her2/neu status). Selected RNA levels were validated using RT-qPCR, and two public databases were used to demonstrate the prognostic significance of the gene profiles generated from FFPE specimens.ResultsCompared to FNAB, RNA isolated from FFPE samples was relatively more degraded, nonetheless, over 80% of the RNA samples were deemed suitable for subsequent DASL assay. Despite a higher noise level, a set of genes from FFPE specimens correlated very well with the gene profiles obtained from FNAB, and could differentiate breast cancer subtypes. Expression levels of these genes were validated using RT-qPCR. Finally, for the first time we correlated gene expression profiles from FFPE samples to survival using two independent microarray databases. Specifically, over-expression of ANLN and KIF2C, and under-expression of MAPT strongly correlated with poor outcomes in breast cancer patients.ConclusionWe demonstrated that FFPE specimens retained important prognostic information that could be identified using a recent gene profiling technology. Our study supports the use of FFPE specimens for the development and refinement of prognostic gene signatures for breast cancer. Clinical applications of such prognostic gene profiles await future large-scale validation studies.

【 授权许可】

Unknown   
© Sadi et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.