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

References

• Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004;116:281–97.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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 fine-needle aspirates can classify benign and malignant tissues. Clin Chem 2008;54:1716–24.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 1987;162:156–9.
   PubMed Web of Science ®Google Scholar
• ‘Isolation of RNA using Trizol Reagent’. Available at: https://commerce.invitrogen.com/index.cfm?fuseaction=iProtocol.unitSectionTree&treeNodeId=48EE00F4EFA019A020C63E2B5B3E5399
   Google Scholar
• 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.
   Google Scholar
• Smyth GK. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004;3:Article3.
   PubMedGoogle Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Smyth GK, Speed T. Normalization of cDNA microarray data. Methods 2003;31:265–73.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Peter ME. Let-7 and miR-200 microRNAs: guardians against pluripotency and cancer progression. Cell Cycle 2009;8:843–52.
   PubMed Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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 microRNA expression. RNA 2010;16:991–1006.
   PubMed Web of Science ®Google Scholar