title: Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues.
abstract: Global micro-RNA (miR) profiling of human malignancies is increasingly performed, but to date, the majority of such analyses have used frozen tissues. However, formalin fixation is the standard and routine histological practice for optimal preservation of cellular morphology. To determine whether miR analysis of formalin-fixed tissues is feasible, quantitative real-time PCR (qRT-PCR) profiling of miR expression in 40 archival formalin-fixed paraffin-embedded (FFPE) breast lumpectomy specimens were performed. Taqman Low Density Arrays (TLDAs) were used to assess the expression level of 365 miRs in 34 invasive ductal carcinomas and in 6 normal comparators derived from reduction mammoplasties. Its technical reproducibility was high, with intra-sample correlations above 0.9 and with 92.8% accuracy in differential expression comparisons, indicating such global profiling studies to be technically and biologically robust. The TLDA data were confirmed using conventional single-well qRT-PCR analysis, showing a strong and statistically significant concordance between these two methods. Paired frozen and FFPE breast cancer samples from the same patients showed a similar level of robust correlation of at least 0.94. Compared with normal breast samples, a panel of miRs was consistently dysregulated in breast cancer, including earlier-reported breast cancer-related miRs, such as upregulated miR-21, miR-155, miR-191, and miR-196a, and downregulated miR-125b and miR-221. Additional novel miR sequences of potential biological relevance were also uncovered. These results show the validity and utility of conducting global miR profiling using FFPE samples, thereby offering enormous opportunities to evaluate archival banks of such materials, linked to clinical databases, to rapidly acquire greater insight into the clinically relevant role for miRs in human malignancies.
authors.affiliation: Division of Applied Molecular Oncology, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.
authors.forename: Angela B Y
authors.initials: AB
authors.lastname: Hui
authors.forename: Wei
authors.initials: W
authors.lastname: Shi
authors.forename: Paul C
authors.initials: PC
authors.lastname: Boutros
authors.forename: Naomi
authors.initials: N
authors.lastname: Miller
authors.forename: Melania
authors.initials: M
authors.lastname: Pintilie
authors.forename: Tony
authors.initials: T
authors.lastname: Fyles
authors.forename: David
authors.initials: D
authors.lastname: McCready
authors.forename: Derek
authors.initials: D
authors.lastname: Wong
authors.forename: Kate
authors.initials: K
authors.lastname: Gerster
authors.forename: Levi
authors.initials: L
authors.lastname: Waldron
authors.forename: Igor
authors.initials: I
authors.lastname: Jurisica
authors.forename: Linda Z
authors.initials: LZ
authors.lastname: Penn
authors.forename: Fei-Fei
authors.initials: FF
authors.lastname: Liu
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D001943:Breast Neoplasms / Q000378:metabolism*; D018270:Carcinoma, Ductal, Breast / Q000378:metabolism*; D016022:Case-Control Studies; D005260:Female; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D046228:Microarray Analysis / Q000592:standards*; D008875:Middle Aged; D016612:Paraffin Embedding; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D035683:MicroRNAs