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

Journal of Molecular Diagnostics

Volumn 10, Issue 6, 2008, Pages 513-519

  Zhang, Xiao ^a   Chen, Jiamin ^a   Radcliffe, Tom ^a,c   LeBrun, Dave P ^a,b   Tron, Victor A ^a,b   Feilotter, Harriet ^a,b  

^a QUEEN S UNIVERSITY   (Canada)

^b QUEEN S UNIVERSITY   (Canada)

^c Predictive Patterns Software Inc   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; PARAFFIN;

ARTICLE; CONTROLLED STUDY; CORRELATION COEFFICIENT; GENE EXPRESSION; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; RNA EXTRACTION; RNA HYBRIDIZATION;

EID: 55949095602     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.2353/jmoldx.2008.080077     Document Type: Article

References (29)

1. Xi Y, Nakajima G, Gavin E, Morris CG, Kudo K, Hayashi K, Ju J: Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples. RNA 2007, 13:1668-1674
2. Lee RC, Feinbaum RL, Ambros V: The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854
3. Jay C, Nemunaitis J, Chen P, Fulgham P, Tong AW: miRNA profiling for diagnosis and prognosis of human cancer. DNA Cell Biol 2007, 26:293-300
4. Hsu PW, Huang HD, Hsu SD, Lin LZ, Tsou AP, Tseng CP. Stadler PF, Washietl S, Hofacker IL: miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. Nucleic Acids Res 2006, 34:D135-D139
5. Yu Z, Jian Z, Shen SH, Purisima E, Wang E: Global analysis of microRNA target gene expression reveals that miRNA targets are lower expressed in mature mouse and Drosophila tissues than in the embryos. Nucleic Acids Res 2007, 35:152-164
6. Ambros V: MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell 2003, 113:673-676
7. Chen JF, Murchison EP, Tang R, Callis TE, Tatsuguchi M, Deng Z, Rojas M, Hammond SM, Schneider MD, Selzman CH, Meissner G, Patterson C, Hannon GJ, Wang DZ: Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure. Proc Natl Acad Sci USA 2008, 105:2111-2116
8. Yang H, Kong W, He L, Zhao JJ, O'Donnell JD, Wang J, Wenham RM, Coppola D, Kruk PA, Nicosia SV, Cheng JQ: MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res 2008, 68:425-433
9. Mitomo S, Maesawa C, Ogasawara S, Iwaya T, Shibazaki M, Yashima-Abo A, Kotani K, Oikawa H, Sakurai E, Izutsu N, Kato K, Komatsu H, Ikeda K, Wakabayashi G, Masuda T: Downregulation of miR-138 is associated with overexpression of human telomerase reverse transcriptase protein in human anaplastic thyroid carcinoma cell lines. Cancer Sci 2008, 99:280-286
10. Caldas C, Brenton JD: Sizing up miRNAs as cancer genes. Nat Med 2005, 11:712-714
11. Castoldi M, Schmidt S, Benes V, Noerholm M, Kulozik AE, Hentze MW, Muckenthaler MU: A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 2006, 12:913-920
12. Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, Sjoblom T, Barad O, Bentwich Z, Szafranska AE, Labourier E, Raymond CK, Roberts BS, Juhl H, Kinzler KW, Vogelstein B, Velculescu VE: The colorectal microRNAome. Proc Natl Acad Sci USA 2006, 103:3687-3692
13. Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z: Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 2004, 1:155-161
14. Nelson PT, Baldwin DA, Kloosterman WP, Kauppinen S, Plasterk RH, Mourelatos Z: RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA 2006, 12:187-191
15. Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K: Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 1999, 27:4436-4443
16. Hamatani K, Eguchi H, Takahashi K, Koyama K, Mukai M, Ito R, Taga M, Yasui W, Nakachi K: Improved RT-PCR amplification for molecular analyses with long-term preserved formalin-fixed, paraffin-embedded tissue specimens. J Histochem Cytochem 2006, 54:773-780
17. Wang WX, Rajeev BW, Stromberg AJ, Ren N, Tang G, Huang Q, Rigoutsos I, Nelson PT: The expression of microRNA miR-107 decreases early in Alzheimer's disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J Neurosci 2008, 28:1213-1223
18. Calame K: MicroRNA-155 function in B Cells. Immunity 2007, 27:825-827
19. Lee DY, Deng Z, Wang CH, Yang BB: MicroRNA-378 promotes cell survival, tumor growth, and angiogenesis by targeting SuFu and Fus-1 expression. Proc Natl Acad Sci USA 2007, 104:20350-20355
20. Latronico MV, Catalucci D, Condorelli G: Emerging role of microRNAs in cardiovascular biology. Circ Res 2007, 101:1225-1236
21. Yang M, Mattes J: Discovery, biology and therapeutic potential of RNA interference, microRNA and antagomirs. Pharmacol Ther 2008, 117:94-104
22. Shell S, Park SM, Radjabi AR, Schickel R, Kistner EO, Jewell DA, Feig C, Lengyel E, Peter ME: Let-7 expression defines two differentiation stages of cancer. Proc Natl Acad Sci USA 2007, 104:11400-11405
23. Nicoloso MS, Calin GA: MicroRNA involvement in brain tumors: from bench to bedside. Brain Pathol 2008, 18:122-129
24. Lowery AJ, Miller N, McNeill RE, Kerin MJ: MicroRNAs as prognostic indicators and therapeutic targets: potential effect on breast cancer management. Clin Cancer Res 2008, 14:360-365
25. Nuovo GJ: In situ detection of precursor and mature microRNAs in paraffin embedded, formalin fixed tissues and cell preparations. Methods 2008, 44:39-46
26. Nakajima G, Hayashi K, Xi Y, Kudo K, Uchida K, Takasaki K, Yamamoto M, Ju J: Non-coding MicroRNAs hsa-let-7g and hsa-miR-181b are associated with chemoresponse to S-1 in colon cancer. Cancer Genomics Proteomics 2006, 3:317-324
27. Wang H, Ach RA, Curry B: Direct and sensitive miRNA profiling from low-input total RNA. RNA 2007, 13:151-159
28. Mc Sherry EA, Mc Goldrick A, Kay EW, Hopkins AM, Gallagher WM, Dervan PA: Formalin-fixed paraffin-embedded clinical tissues show spurious copy number changes in array-CGH profiles. Clin Genet 2007, 72:441-447
29. von Ahlfen S, Missel A, Bendrat K, Schlumpberger M: Determinants of RNA quality from FFPE samples. PLoS ONE 2007, 2:e1261