Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation

Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits the ability to profile mRNA expression, we explored factors predicting the success of mRNA expression profiling of FFPE material and investigated an approach to overcome the limitation. Methods: Bladder ( n =140, st...

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Bibliographic Details
Published in:British journal of cancer 2012-08, Vol.107 (4), p.684-694
Main Authors: Hall, J S, Taylor, J, Valentine, H R, Irlam, J J, Eustace, A, Hoskin, P J, Miller, C J, West, C M L
Format: Article
Language:English
Subjects:
631/337/1645/2020
631/337/384/331
631/67/68
692/699/67
Adenocarcinoma
Adenocarcinoma - genetics
Adenylate cyclase
Age
Arrays
Bioinformatics
Biological and medical sciences
Biomedical and Life Sciences
Biomedicine
Bladder
Cancer Research
Carcinoma, Squamous Cell - genetics
Cervix
Drug Resistance
Epidemiology
Exons
Female
Fixatives - pharmacology
Formaldehyde - pharmacology
Gene expression
Gene Expression Profiling - methods
Gene Expression Regulation, Neoplastic
Genomes
Humans
Male
Medical research
Medical sciences
MicroRNAs
MicroRNAs - metabolism
miRNA
Molecular Diagnostics
Molecular Medicine
Nucleoli
Oncology
Paraffin Embedding - methods
Quality control
RNA Stability
RNA, Messenger - metabolism
snoRNA
squamous cell carcinoma
Success
Time Factors
Tissue Preservation
Tumors
Urinary bladder
Urinary Bladder Neoplasms - genetics
Uterine Cervical Neoplasms - genetics
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Summary:Background: As degradation of formalin-fixed paraffin-embedded (FFPE) samples limits the ability to profile mRNA expression, we explored factors predicting the success of mRNA expression profiling of FFPE material and investigated an approach to overcome the limitation. Methods: Bladder ( n =140, stored 3–8 years) and cervix ( n =160, stored 8–23 years) carcinoma FFPE samples were hybridised to Affymetrix Exon 1.0ST arrays. Percentage detection above background (%DABG) measured technical success. Biological signal was assessed by distinguishing cervix squamous cell carcinoma (SCC) and adenocarcinoma (AC) using a gene signature. As miR-205 had been identified as a marker of SCC, precursor mir-205 was measured by Exon array and mature miR-205 by qRT–PCR. Genome-wide microRNA (miRNA) expression (Affymetrix miRNA v2.0 arrays) was compared in eight newer FFPE samples with biological signal and eight older samples without. Results: RNA quality controls (QCs) (e.g., RNA integrity (RIN) number) failed to predict profiling success, but sample age correlated with %DABG in bladder ( R =−0.30, P
ISSN:0007-0920
1532-1827
DOI:10.1038/bjc.2012.294