High-throughput miRNA profiling of human melanoma blood samples

BMC Cancer

Volumn 10, Issue , 2010, Pages

  Leidinger, Petra ^a   Keller, Andreas ^b,c   Borries, Anne ^b   Reichrath, Jörg ^a   Rass, Knuth ^a   Jager, Sven U ^d   Lenhof, Hans Peter ^e   Meese, Eckart ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b Febit Biomed Gmbh   (Germany)

^c Biomarker Discovery Center Heidelberg   (Germany)

^d Medical School Saarland University ^*  (Germany)

^e SAARLAND UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; TUMOR MARKER;

ACCURACY; ARTICLE; BLOOD ANALYSIS; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE EXPRESSION REGULATION; HIGH THROUGHPUT SCREENING; HUMAN; MELANOMA; MELANOMA CELL; MICROARRAY ANALYSIS; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SENSITIVITY AND SPECIFICITY; BLOOD; CANCER STAGING; CASE CONTROL STUDY; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; PATHOLOGY; PREDICTION AND FORECASTING; PRINCIPAL COMPONENT ANALYSIS; REPRODUCIBILITY; VALIDATION STUDY;

CASE-CONTROL STUDIES; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MELANOMA; MICRORNAS; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PREDICTIVE VALUE OF TESTS; PRINCIPAL COMPONENT ANALYSIS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TUMOR MARKERS, BIOLOGICAL;

EID: 77953029993     PISSN: None     EISSN: 14712407     Source Type: Journal    
DOI: 10.1186/1471-2407-10-262     Document Type: Article

References (42)

1. Sawyers CL. The cancer biomarker problem. Nature 2008, 452(7187):548-552. 10.1038/nature06913, 18385728.
2. Cho WC. MicroRNAs in cancer - from research to therapy. Biochim Biophys Acta 2009, 1805(2):209-17.
3. Cho WC. MicroRNAs: Potential biomarkers for cancer diagnosis, prognosis and targets for therapy. Int J Biochem Cell Biol 2009,
4. Croce CM, Calin GA. miRNAs, cancer, and stem cell division. Cell 2005, 122(1):6-7. 10.1016/j.cell.2005.06.036, 16009126.
5. Wang QZ, Xu W, Habib N, Xu R. Potential uses of microRNA in lung cancer diagnosis, prognosis, and therapy. Curr Cancer Drug Targets 2009, 9(4):572-594. 10.2174/156800909788486731, 19519323.
6. Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ. Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci USA 2009, 106(11):4402-4407. 10.1073/pnas.0813371106, 2657429, 19246379.
7. Cortez MA, Calin GA. MicroRNA identification in plasma and serum: a new tool to diagnose and monitor diseases. Expert Opin Biol Ther 2009, 9(6):703-711. 10.1517/14712590902932889, 19426115.
8. Chin LJ, Slack FJ. A truth serum for cancer--microRNAs have major potential as cancer biomarkers. Cell Res 2008, 18(10):983-984. 10.1038/cr.2008.290, 18833286.
9. Gilad S, Meiri E, Yogev Y, Benjamin S, Lebanony D, Yerushalmi N, Benjamin H, Kushnir M, Cholakh H, Melamed N, et al. Serum microRNAs are promising novel biomarkers. PLoS One 2008, 3(9):e3148. 10.1371/journal.pone.0003148, 2519789, 18773077.
10. Keller A, Leidinger P, Borries A, Wendschlag A, Wucherpfennig F, Scheffler M, Huwer H, Lenhof HP, Meese E. miRNAs in lung cancer - studying complex fingerprints in patient's blood cells by microarray experiments. BMC Cancer 2009, 9:353. 10.1186/1471-2407-9-353, 2764731, 19807914.
11. Keller A, Leidinger P, Lange J, Borries A, Schroers H, Scheffler M, Lenhof HP, Ruprecht K, Meese E. Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PLoS One 2009, 4(10):e7440. 10.1371/journal.pone.0007440, 2757919, 19823682.
12. Mueller DW, Bosserhoff AK. Role of miRNAs in the progression of malignant melanoma. Br J Cancer 2009, 101(4):551-556. 10.1038/sj.bjc.6605204, 19638982.
13. Liu A, Tetzlaff MT, Vanbelle P, Elder D, Feldman M, Tobias JW, Sepulveda AR, Xu X. MicroRNA Expression Profiling Outperforms mRNA Expression Profiling in Formalin-fixed Paraffin-embedded Tissues. Int J Clin Exp Pathol 2009, 2(6):519-527. 2713447, 19636399.
14. Ma Z, Lui WO, Fire A, Dadras SS. Profiling and discovery of novel miRNAs from formalin-fixed, paraffin-embedded melanoma and nodal specimens. J Mol Diagn 2009, 11(5):420-429.
15. Glud M, Klausen M, Gniadecki R, Rossing M, Hastrup N, Nielsen FC, Drzewiecki KT. MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling. J Invest Dermatol 2009, 129(5):1219-1224. 10.1038/jid.2008.347, 19005486.
16. Mueller DW, Rehli M, Bosserhoff AK. miRNA expression profiling in melanocytes and melanoma cell lines reveals miRNAs associated with formation and progression of malignant melanoma. J Invest Dermatol 2009, 129(7):1740-1751. 10.1038/jid.2008.452, 19212343.
17. Gaur A, Jewell DA, Liang Y, Ridzon D, Moore JH, Chen C, Ambros VR, Israel MA. Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 2007, 67(6):2456-2468. 10.1158/0008-5472.CAN-06-2698, 17363563.
18. Worley LA, Long MD, Onken MD, Harbour JW. Micro-RNAs associated with metastasis in uveal melanoma identified by multiplexed microarray profiling. Melanoma Res 2008, 18(3):184-190. 10.1097/CMR.0b013e3282feeac6, 18477892.
19. Griffiths-Jones S. miRBase: the microRNA sequence database. Methods Mol Biol 2006, 342:129-138.
20. Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res 2006, (34 Database):D140-144. 10.1093/nar/gkj112, 1347474, 16381832.
21. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, (36 Database):D154-158. 2238936, 17991681.
22. Smyth GK, Yang YH, Speed T. Statistical issues in cDNA microarray data analysis. Methods Mol Biol 2003, 224:111-136.
23. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article3.
24. Vapnik V. The nature of statistical learning theory. 2000, New York: Spinger, 2.
25. Vorwerk S, Ganter K, Cheng Y, Hoheisel J, Stahler PF, Beier M. Microfluidic-based enzymatic on-chip labeling of miRNAs. N Biotechnol 2008, 25(2-3):142-149. 10.1016/j.nbt.2008.08.005, 18786664.
26. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.
27. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001, 125(1-2):279-284. 10.1016/S0166-4328(01)00297-2, 11682119.
28. Hochberg Y. A sharper bonferroni procedure for multiple tests of significance. Biometrica 1988, 75:185-193.
29. Pearson K. On Lines and Planes of Closest Fit to Systems of Points in Space. Philosophical Magazine 1901, 2(6):559-572.
30. Shaw P. Multivariate statistics for the Environmental Sciences. 2003, London: Hodder-Arnold.
31. Team R. R: A Language and Environment for Statistical Computing. 2008, Vienna: R Foundation for Statistical Computing.
32. McCarthy DJ, Smyth GK. Testing significance relative to a fold-change threshold is a TREAT. Bioinformatics 2009, 25(6):765-771. 10.1093/bioinformatics/btp053, 2654802, 19176553.
33. Lu M, Zhang Q, Deng M, Miao J, Guo Y, Gao W, Cui Q. An analysis of human microRNA and disease associations. PLoS One 2008, 3(10):e3420. 10.1371/journal.pone.0003420, 2559869, 18923704.
34. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 2006, 9(3):189-198. 10.1016/j.ccr.2006.01.025, 16530703.
35. Zhang Y, Li M, Wang H, Fisher WE, Lin PH, Yao Q, Chen C. Profiling of 95 microRNAs in pancreatic cancer cell lines and surgical specimens by real-time PCR analysis. World J Surg 2009, 33(4):698-709. 10.1007/s00268-008-9833-0, 19030927.
36. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, et al. microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci USA 2006, 103(24):9136-9141. 10.1073/pnas.0508889103, 1474008, 16754881.
37. Sonkoly E, Stahle M, Pivarcsi A. MicroRNAs: novel regulators in skin inflammation. Clin Exp Dermatol 2008, 33(3):312-315. 10.1111/j.1365-2230.2008.02804.x, 18419608.
38. Dai Y, Sui W, Lan H, Yan Q, Huang H, Huang Y. Comprehensive analysis of microRNA expression patterns in renal biopsies of lupus nephritis patients. Rheumatol Int 2009, 29(7):749-754. 10.1007/s00296-008-0758-6, 18998140.
39. Sonkoly E, Wei T, Janson PC, Saaf A, Lundeberg L, Tengvall-Linder M, Norstedt G, Alenius H, Homey B, Scheynius A, et al. MicroRNAs: novel regulators involved in the pathogenesis of Psoriasis?. PLoS One 2007, 2(7):e610. 10.1371/journal.pone.0000610, 1905940, 17622355.
40. Williams AE. Functional aspects of animal microRNAs. Cell Mol Life Sci 2008, 65(4):545-562. 10.1007/s00018-007-7355-9, 17965831.
41. Tang Y, Luo X, Cui H, Ni X, Yuan M, Guo Y, Huang X, Zhou H, de Vries N, Tak PP, et al. MicroRNA-146A contributes to abnormal activation of the type I interferon pathway in human lupus by targeting the key signaling proteins. Arthritis Rheum 2009, 60(4):1065-1075. 10.1002/art.24436, 19333922.
42. Chen X, Ba Y, Ma L, Cai X, Yin Y, Wang K, Guo J, Zhang Y, Chen J, Guo X, et al. Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 2008, 18(10):997-1006. 10.1038/cr.2008.282, 18766170.