A simple procedure for routine RNA extraction and miRNA array analyses from a single thyroid in vivo fine needle aspirate

Scandinavian Journal of Clinical and Laboratory Investigation

Volumn 70, Issue 8, 2010, Pages 529-534

  Rossing, Maria ^a,b   Kaczkowski, Bogumil ^c   Futoma Kazmierczak, Ewa ^a   Glud, Martin ^a   Klausen, Mikkel ^a   Faber, Jens ^b   Nygaard, Birte ^b   Kiss, Katalin ^b   Sørensen, Christian H ^b   Nielsen, Finn C ^a   Bennedbæk, Finn N ^b   Friis Hansen, Lennart ^a  

^a University of Copenhagen   (Denmark)

^b GENTOFTE UNIVERSITY HOSPITAL   (Denmark)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

Fine needle aspirate; MiRNA microarray; RNA preservation; RNAlater; Thyroid nodules

Indexed keywords

LIQUID NITROGEN; MICRORNA;

ARTICLE; ASPIRATION BIOPSY; CENTRIFUGATION; CLINICAL ARTICLE; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION; HUMAN; HUMAN TISSUE; IN VIVO STUDY; OUTCOME ASSESSMENT; PRIORITY JOURNAL; RNA ANALYSIS; RNA EXTRACTION; THYROID GLAND; THYROID NODULE; TISSUE PRESERVATION; VALIDITY;

BIOPSY, FINE-NEEDLE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; MICRORNAS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; THYROID GLAND;

EID: 78649268746     PISSN: 00365513     EISSN: 15027686     Source Type: Journal    
DOI: 10.3109/00365513.2010.522250     Document Type: Article

References (34)

1. Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281-97.
2. Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, Benjamin H, Shabes N, Tabak S, Levy A, Lebanony D, Goren Y, Silberschein E, Targan N, Ben-Ari A, Gilad S, Sion-Vardy N, Tobar A, Feinmesser M, Kharenko O, Nativ O, Nass D, Perelman M, Yosepovich A, Shalmon B, Polak-Charcon S, Fridman E, Avniel A, Bentwich I, Bentwich Z, Cohen D, Chajut A, Barshack I. MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol 2008;26:462-9.
3. Lu J, Getz G, Miska EA, varez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. MicroRNA expression profiles classify human cancers. Nature 2005;435:834-8.
4. Yu SL, Chen HY, Chang GC, Chen CY, Chen HW, Singh S, Cheng CL, Yu CJ, Lee YC, Chen HS, Su TJ, Chiang CC, Li HN, Hong QS, Su HY, Chen CC, Chen WJ, Liu CC, Chan WK, Chen WJ, Li KC, Chen JJ, Yang PC. MicroRNA signature predicts survival and relapse in lung cancer. Cancer Cell 2008;13:48-57.
5. Chen YT, Kitabayashi N, Zhou XK, Fahey TJ, III, Scognamiglio T. MicroRNA analysis as a potential diagnostic tool for papillary thyroid carcinoma. Mod Pathol 2008;21:1139-46.
6. Nikiforova MN, Tseng GC, Steward D, Diorio D, Nikiforov YE. MicroRNA expression profiling of thyroid tumors: biological significance and diagnostic utility. J Clin Endocrinol Metab 2008;93:1600-8.
7. Weber F, Shen L, Aldred MA, Morrison CD, Frilling A, Saji M, Schuppert F, Broelsch CE, Ringel MD, Eng C. Genetic classification of benign and malignant thyroid follicular neoplasia based on a three-gene combination. J Clin Endocrinol Metab 2005;90:2512-21.
8. Weber F, Teresi RE, Broelsch CE, Frilling A, Eng C. A limited set of human microRNA is deregulated in follicular thyroid carcinoma. J Clin Endocrinol Metab 2006;91:3584-91.
9. Pallante P, Visone R, Ferracin M, Ferraro A, Berlingieri MT, Troncone G, Chiappetta G, Liu CG, Santoro M, Negrini M, Croce CM, Fusco A. MicroRNA deregulation in human thyroid papillary carcinomas. Endocr Relat Cancer 2006;13:497-508.
10. He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, Volinia S, Calin GA, Liu CG, Franssila K, Suster S, Kloos RT, Croce CM, de la CA. The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A 2005;102:19075-80.
11. Eszlinger M, Krohn K, Hauptmann S, Dralle H, Giordano TJ, Paschke R. Perspectives for improved and more accurate classification of thyroid epithelial tumors. J Clin Endocrinol Metab 2008;93:3286-94.
12. Bloomston M, Frankel WL, Petrocca F, Volinia S, Alder H, Hagan JP, Liu CG, Bhatt D, Taccioli C, Croce CM. MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis. JAMA 2007;297:1901-8.
13. Lui PC, Lau PP, Tse GM, Tan PH, Lo RC, Tang VW, Ng WK, Somali A, Mak KL, Thomas TM, Chan NH, Hiang TT, Chan NH. Fine needle aspiration cytology of invasive micropapillary carcinoma of the breast. Pathology 2007;39:401-5.
14. Kandil D, Leiman G, Allegretta M, Trotman W, Pantanowitz L, Goulart R, Evans M. Glypican-3 immunocytochemistry in liver fine-needle aspirates: a novel stain to assist in the differentiation of benign and malignant liver lesions. Cancer 2007;111:316-22.
15. Szafranska AE, Doleshal M, Edmunds HS, Gordon S, Luttges J, Munding JB, Barth RJ, Jr., Gutmann EJ, Suriawinata AA, Pipas JM, Tannapfel A, Korc M, Hahn SA, Labourier E, Tsongalis GJ. Analysis of micrornas in pancreatic fineneedle aspirates can classify benign and malignant tissues. Clin Chem 2008;54:1716-24.
16. Yassa L, Cibas ES, Benson CB, Frates MC, Doubilet PM, Gawande AA, Moore FD, Jr., Kim BW, Nose V, Marqusee E, Larsen PR, Alexander EK. Long-term assessment of a multidisciplinary approach to thyroid nodule diagnostic evaluation. Cancer 2007;111:508-16.
17. Ustun M, Risberg B, Davidson B, Berner A. Cystic change in metastatic lymph nodes: a common diagnostic pitfall in fine-needle aspiration cytology. Diagn Cytopathol 2002;27:387-92.
18. Lubitz CC, Ugras SK, Kazam JJ, Zhu B, Scognamiglio T, Chen YT, Fahey TJ, III. Microarray analysis of thyroid nodule fine-needle aspirates accurately classifies benign and malignant lesions. J Mol Diagn 2006;8:490-8.
19. Catrina RF, Schlette EJ, Stewart JM, Keating MJ, Katz RL, Caraway NP. Fine-needle aspiration biopsy findings in patients with small lymphocytic lymphoma transformed to Hodgkin lymphoma. Am J Clin Pathol 2007;128:571-8.
20. Dunmire V, Wu C, Symmans WF, Zhang W. Increased yield of total RNA from fine-needle aspirates for use in expression microarray analysis. Biotechniques 2002;33:890-2, 894, 896.
21. Sotiriou C, Powles TJ, Dowsett M, Jazaeri AA, Feldman AL, Assersohn L, Gadisetti C, Libutti SK, Liu ET. Gene expression profiles derived from fine needle aspiration correlate with response to systemic chemotherapy in breast cancer. Breast Cancer Res 2002;4: R3.
22. Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987;162:156-9.
23. 'Isolation of RNA using Trizol Reagent '. Available at: https://commerce.invitrogen.com/index.cfm?fuseaction=iProtocol. unitSectionTree&treeNodeId=48EE00F4EFA019A020C6 3E2B5B3E5399.
24. R Development Core Team. R: a language and environment for statistical computing, R foundation for statistical computing, Vienna, Austria, ISBN 3-900051-07-0, 2007.
25. Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004;3: Article3.
26. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004;5: R80.
27. Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth GK. A comparison of background correction methods for two-colour microarrays. Bioinformatics 2007;23:2700-7.
28. Smyth GK, Speed T. Normalization of cDNA microarray data. Methods 2003;31:265-73.
29. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005;33:2697-706.
30. Yu J, Wang F, Yang GH, Wang FL, Ma YN, Du ZW, Zhang JW. Human microRNA clusters: genomic organization and expression profile in leukemia cell lines. Biochem Biophys Res Commun 2006;349:59-68.
31. Hayashita Y, Osada H, Tatematsu Y, Yamada H, Yanagisawa K, Tomida S, Yatabe Y, Kawahara K, Sekido Y, Takahashi T. A polycistronic microRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 2005;65:9628-32.
32. Peter ME. Let-7 and miR-200 microRNAs: guardians against pluripotency and cancer progression. Cell Cycle 2009;8:843-52.
33. Morrison C, Palatini J, Riggenbach J, Radmacher M, Porcu P. Fine-needle aspiration biopsy of non-Hodgkin lymphoma for use in expression microarray analysis. Cancer 2006;108:311-8.
34. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential micro-RNA expression. RNA 2010;16:991-1006.