An array-based analysis of microRNA expression comparing matched frozen and formalin-fixed paraffin-embedded human tissue samples.

MicroRNAs (miRNAs) are small, noncoding RNAs that suppress gene expression at the posttranscriptional level via an antisense RNA-RNA interaction. miRNAs used for array-based profiling are generally purified from either snap-frozen or fresh samples. Because tissues found in most pathology departments are available only in formalin-fixed and paraffin-embedded (FFPE) states, we sought to evaluate miRNA derived from FFPE samples for microarray analysis. In this study, miRNAs extracted from matched snap-frozen and FFPE samples were profiled using the Agilent miRNA array platform (Agilent, Santa Clara, CA). Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. Seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling, and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results; technical replicates showed high correlations with one another (Kendall tau, 0.722 to 0.853; Spearman rank correlation coefficient, 0.891 to 0.954). Our results showed consistent high correlations between matched frozen and FFPE samples (Kendall tau, 0.669 to 0.815; Spearman rank correlation coefficient, 0.847 to 0.948), supporting the use of FFPE-derived miRNAs for array-based, gene expression profiling.

[1]  G. Tonini,et al.  Transcribed-ultra conserved region expression profiling from low-input total RNA , 2010, BMC Genomics.

[2]  Michael D. Schneider,et al.  Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure , 2008, Proceedings of the National Academy of Sciences.

[3]  G. Wakabayashi,et al.  Downregulation of miR‐138 is associated with overexpression of human telomerase reverse transcriptase protein in human anaplastic thyroid carcinoma cell lines , 2008, Cancer science.

[4]  Guiliang Tang,et al.  The Expression of MicroRNA miR-107 Decreases Early in Alzheimer's Disease and May Accelerate Disease Progression through Regulation of β-Site Amyloid Precursor Protein-Cleaving Enzyme 1 , 2008, The Journal of Neuroscience.

[5]  Michael J Kerin,et al.  MicroRNAs as Prognostic Indicators and Therapeutic Targets: Potential Effect on Breast Cancer Management , 2008, Clinical Cancer Research.

[6]  Huan Yang,et al.  MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. , 2008, Cancer research.

[7]  G. Calin,et al.  MicroRNA Involvement in Brain Tumors: From Bench to Bedside , 2008, Brain pathology.

[8]  K. Calame.  MicroRNA-155 function in B Cells. , 2007, Immunity.

[9]  Burton B. Yang,et al.  MicroRNA-378 promotes cell survival, tumor growth, and angiogenesis by targeting SuFu and Fus-1 expression , 2007, Proceedings of the National Academy of Sciences.

[10]  M. Latronico,et al.  Emerging role of microRNAs in cardiovascular biology. , 2007, Circulation research.

[11]  Silke von Ahlfen,et al.  Determinants of RNA Quality from FFPE Samples , 2007, PloS one.

[12]  E. Kay,et al.  Formalin‐fixed paraffin‐embedded clinical tissues show spurious copy number changes in array‐CGH profiles , 2007, Clinical genetics.

[13]  Kazuhiko Hayashi,et al.  Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples. , 2007, RNA.

[14]  E. Kistner,et al.  Let-7 expression defines two differentiation stages of cancer , 2007, Proceedings of the National Academy of Sciences.

[15]  Chris Jay,et al.  miRNA profiling for diagnosis and prognosis of human cancer. , 2007, DNA and cell biology.

[16]  Edwin Wang,et al.  Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos , 2006, Nucleic acids research.

[17]  R. Ach,et al.  Direct and sensitive miRNA profiling from low-input total RNA. , 2006, RNA.

[18]  Masakazu Yamamoto,et al.  Non-coding MicroRNAs hsa-let-7g and hsa-miR-181b are Associated with Chemoresponse to S-1 in Colon Cancer. , 2006, Cancer genomics & proteomics.

[19]  W. Yasui,et al.  Improved RT-PCR Amplification for Molecular Analyses with Long-term Preserved Formalin-fixed, Paraffin-embedded Tissue Specimens , 2006, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[20]  Vladimir Benes,et al.  A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). , 2006, RNA.

[21]  Brian S. Roberts,et al.  The colorectal microRNAome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Hsien-Da Huang,et al.  miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes , 2005, Nucleic Acids Res..

[23]  R. Plasterk,et al.  RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. , 2005, RNA.

[24]  Carlos Caldas,et al.  Sizing up miRNAs as cancer genes , 2005, Nature Medicine.

[25]  Zissimos Mourelatos,et al.  Microarray-based, high-throughput gene expression profiling of microRNAs , 2004, Nature Methods.

[26]  V. Ambros.  MicroRNA Pathways in Flies and Worms Growth, Death, Fat, Stress, and Timing , 2003, Cell.

[27]  M. Monden,et al.  Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. , 1999, Nucleic acids research.

[28]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[29]  J. Mattes,et al.  Discovery, biology and therapeutic potential of RNA interference, microRNA and antagomirs. , 2008, Pharmacology & therapeutics.

[30]  G. Nuovo.  In situ detection of precursor and mature microRNAs in paraffin embedded, formalin fixed tissues and cell preparations. , 2008, Methods.