High stability of microRNAs in tissue samples of compromised quality

Virchows Archiv

Volumn 463, Issue 6, 2013, Pages 765-774

  Peiró Chova, Lorena ^a   Peña Chilet, María ^a   López Guerrero, José Antonio ^b   García Giménez, José Luis ^c   Alonso Yuste, Elisa ^a   Burgues, Octavio ^a,d   Lluch, Ana ^a,d   Ferrer Lozano, Jaime ^a   Ribas, Gloria ^a  

^a Biomedical Research Institute Hospital Clinic de Valencia INCLIVA   (Spain)

^b INSTITUTO VALENCIANO DE ONCOLOGÍA   (Spain)

^c UNIVERSITY OF VALENCIA   (Spain)

^d HOSPITAL CLÍNICO UNIVERSITARIO   (Spain)

Author keywords

Biobank; Breast cancer; Compromised quality samples; microRNA

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA 125B; MICRORNA 191; MICRORNA 21; RNA; SNORNA RNU6B; UNCLASSIFIED DRUG; PARAFFIN;

ARTICLE; BIODEGRADATION; BREAST CANCER; CANCER PATIENT; CANCER SURGERY; CONTROLLED STUDY; CRYOPRESERVATION; FORMALIN FIXED PARAFFIN EMBEDDED TISSUE SAMPLE; GAPDH GENE; GENE; HPRT1 GENE; HUMAN; HUMAN TISSUE; PRIORITY JOURNAL; QUALITY CONTROL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA ISOLATION; RNA STABILITY; THAWING; TISSUE AND ORGAN PREPARATION AND CULTURE; BREAST TUMOR; FEMALE; GENETICS; PROCEDURES; REAL TIME POLYMERASE CHAIN REACTION; TISSUE FIXATION;

BREAST NEOPLASMS; CRYOPRESERVATION; FEMALE; HUMANS; PARAFFIN EMBEDDING; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA STABILITY; RNA, MESSENGER; TISSUE FIXATION;

EID: 84890537889     PISSN: 09456317     EISSN: 14322307     Source Type: Journal    
DOI: 10.1007/s00428-013-1485-2     Document Type: Article

References (35)

1. Cambon-Thomsen A, Ducournau P, Gourraud PA, Pontille D (2003) Biobanks for genomics and genomics for biobanks. Comp Funct Genomics 4(6):628-634. doi: 10.1002/cfg.333
2. Bresters D, Schipper ME, Reesink HW, Boeser-Nunnink BD, Cuypers HT (1994) The duration of fixation influences the yield of HCV cDNA-PCR products from formalin-fixed, paraffin-embedded liver tissue. J Virol Methods 48(2-3):267-272
3. Macabeo-Ong M, Ginzinger DG, Dekker N, McMillan A, Regezi JA, Wong DT, Jordan RC (2002) Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses. Mod Pathol 15(9):979-987. doi: 10.1097/01.MP.0000026054.62220.FC
4. Cronin M, Pho M, Dutta D, Stephans JC, Shak S, Kiefer MC, Esteban JM, Baker JB (2004) Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase- polymerase chain reaction assay. Am J Pathol 164(1):35-42. doi: 10.1016/S0002-9440(10)63093-3
5. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5(7):522-531. doi: 10.1038/nrg1379nrg1379
6. Hui AB, Shi W, Boutros PC, Miller N, Pintilie M, Fyles T, McCready D, Wong D, Gerster K, Waldron L, Jurisica I, Penn LZ, Liu FF (2009) Robust global micro-RNA profiling with formalin-fixed paraffin-embedded breast cancer tissues. Lab Invest 89(5):597-606. doi: 10.1038/labinvest.2009.12
7. Nelson PT, Baldwin DA, Scearce LM, Oberholtzer JC, Tobias JW, Mourelatos Z (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1(2):155-161. doi: 10.1038/nmeth717
8. Esquela-Kerscher A, Slack FJ (2006) Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer 6(4):259-269. doi: 10.1038/nrc1840
9. O'Day E, Lal A (2010) MicroRNAs and their target gene networks in breast cancer. Breast Cancer Res 12(2):201. doi: 10.1186/bcr2484
10. Garofalo M, Quintavalle C, Di Leva G, Zanca C, Romano G, Taccioli C, Liu CG, Croce CM, Condorelli G (2008) MicroRNA signatures of TRAIL resistance in human non-small cell lung cancer. Oncogene 27(27):3845-3855. doi: 10.1038/onc.2008.6
11. Lawrie CH (2008) MicroRNA expression in lymphoid malignancies: new hope for diagnosis and therapy? J Cell Mol Med 12(5A):1432-1444. doi: 10.1111/j.1582-4934.2008.00399.x
12. Sandoval J, Peiro-Chova L, Pallardo FV, Garcia-Gimenez JL (2013) Epigenetic biomarkers in laboratory diagnostics: emerging approaches and opportunities. Expert Rev Mol Diagn 13(5):457-471. doi: 10.1586/erm.13.37
13. Li J, Smyth P, Flavin R, Cahill S, Denning K, Aherne S, Guenther SM, O'Leary JJ, Sheils O (2007) Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells. BMC Biotechnol 7:36. doi: 10.1186/1472-6750-7-36
14. Doleshal M, Magotra AA, Choudhury B, Cannon BD, Labourier E, Szafranska AE (2008) Evaluation and validation of total RNA extraction methods for microRNA expression analyses in formalin-fixed, paraffin-embedded tissues. J Mol Diagn 10(3):203-211. doi: 10.2353/jmoldx.2008.070153
15. Zhang X, Chen J, Radcliffe T, Lebrun DP, Tron VA, Feilotter H (2008) An array-based analysis of microRNA expression comparing matched frozen and formalin-fixed paraffin-embedded human tissue samples. J Mol Diagn 10(6):513-519. doi: 10.2353/jmoldx.2008.080077
16. Lovendorf MB, Zibert JR, Hagedorn PH, Glue C, Odum N, Ropke MA, Skov L (2012) Comparison of microRNA expression using different preservation methods of matched psoriatic skin samples. Exp Dermatol 21(4):299-301. doi: 10.1111/j.1600-0625.2012.01445.x
17. Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, Fedele V, Ginzinger D, Getts R, Haqq C (2006) Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5:24. doi: 10.1186/1476-4598-5-24
18. Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F, Visone R, Iorio M, Roldo C, Ferracin M, Prueitt RL, Yanaihara N, Lanza G, Scarpa A, Vecchione A, Negrini M, Harris CC, Croce CM (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A 103(7):2257-2261. doi: 10.1073/pnas.0510565103
19. Si ML, Zhu S, Wu H, Lu Z, Wu F, Mo YY (2007) miR-21-mediated tumor growth. Oncogene 26(19):2799-2803. doi: 10.1038/sj.onc.1210083
20. Gee HE, Buffa FM, Camps C, Ramachandran A, Leek R, Taylor M, Patil M, Sheldon H, Betts G, Homer J, West C, Ragoussis J, Harris AL (2011) The small-nucleolar RNAs commonly used for microRNA normalisation correlate with tumour pathology and prognosis. Br J Cancer 104(7):1168-1177. doi: 10.1038/sj.bjc.6606076
21. de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW, Span PN (2005) Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest 85(1):154-159. doi: 10.1038/labinvest.3700208
22. Klopfleisch R, Weiss AT, Gruber AD (2011) Excavation of a buried treasure - DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues. Histol Histopathol 26(6):797-810
23. Ma Y, Dai H, Kong X (2012) Impact of warm ischemia on gene expression analysis in surgically removed biosamples. Anal Biochem 423(2):229-235. doi: 10.1016/j.ab.2012.02.003
24. von Smolinski D, Leverkoehne I, von Samson-Himmelstjerna G, Gruber AD (2005) Impact of formalin-fixation and paraffin-embedding on the ratio between mRNA copy numbers of differently expressed genes. Histochem Cell Biol 124(2):177-188. doi: 10.1007/s00418-005-0013-0
25. Srinivasan M, Sedmak D, Jewell S (2002) Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am J Pathol 161(6):1961-1971. doi: 10.1016/S0002-9440(10)64472-0
26. Abrahamsen HN, Steiniche T, Nexo E, Hamilton-Dutoit SJ, Sorensen BS (2003) Towards quantitative mRNA analysis in paraffin-embedded tissues using real-time reverse transcriptase-polymerase chain reaction: a methodological study on lymph nodes from melanoma patients. J Mol Diagn 5(1):34-41. doi: 10.1016/S1525-1578(10)60449-7
27. Masuda N, Ohnishi T, Kawamoto S, Monden M, Okubo K (1999) Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucleic Acids Res 27(22):4436-4443
28. Korga A, Wilkolaska K, Korobowicz E (2007) Difficulties in using archival paraffin-embedded tissues for RNA expression analysis. Postepy Hig Med Dosw (Online) 61:151-155
29. Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW (2010) mRNA and microRNA quality control for RT-qPCR analysis. Methods 50(4):237-243. doi: 10.1016/j.ymeth.2010.01.010
30. Ambros V (2001) microRNAs: tiny regulators with great potential. Cell 107(7):823-826
31. Dijkstra JR, Mekenkamp LJ, Teerenstra S, De Krijger I, Nagtegaal ID (2012) MicroRNA expression in formalin-fixed paraffin embedded tissue using real time quantitative PCR: the strengths and pitfalls. J Cell Mol Med 16(4):683-690. doi: 10.1111/j.1582-4934.2011.01467.x
32. Xi Y, Nakajima G, Gavin E, Morris CG, Kudo K, Hayashi K, Ju J (2007) Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples. RNA 13(10):1668-1674. doi: 10.1261/rna.642907
33. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105(30):10513-10518. doi: 10.1073/pnas.0804549105
34. Oliveira IB, Ramos DR, Lopes KL, Souza RM, Heimann JC, Furukawa LN (2012) Isolated total RNA and protein are preserved after thawing for more than twenty-four hours. Clinics (Sao Paulo) 67(3):255-259
35. Thasler WE, Thasler RM, Schelcher C, Jauch KW (2013) Biobanking for research in surgery: are surgeons in charge for advancing translational research or mere assistants in biomaterial and data preservation? Langenbecks Arch Surg 398(4):487-499. doi: 10.1007/s00423-013-1060-y