Biased detection of guanine-rich microRNAs by array profiling: Systematic error or biological phenomenon?

Journal of Computational Science

Volumn 5, Issue 3, 2014, Pages 351-356

  Mitiushkina, Natalia V ^a   Iyevleva, Aglaya G ^a,b   Kuligina, Ekatherina Sh ^a   Togo, Alexandr V ^a   Miki, Yoshio ^c   Imyanitov, Evgeny N ^a,b,d  

^a N N PETROV RESEARCH INSTITUTE OF ONCOLOGY   (Russian Federation)

^b SAINT PETERSBURG STATE PEDIATRIC MEDICAL UNIVERSITY   (Russian Federation)

^c TOKYO MEDICAL AND DENTAL UNIVERSITY   (Japan)

^d NORTH WESTERN STATE MEDICAL UNIVERSITY NAMED AFTER I I MECHNIKOV   (Russian Federation)

Author keywords

Agilent; Breast cancer; Guanine rich; MicroRNA; MicroRNA array

Indexed keywords

POSITIVE IONS;

AGILENT; BIOLOGICAL PHENOMENA; BREAST CANCER; EXPRESSION PATTERNS; GUANINE-RICH; HIER-ARCHICAL CLUSTERING; MICRORNA EXPRESSION; MICRORNAS;

RNA;

EID: 84901260263     PISSN: 18777503     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jocs.2013.09.002     Document Type: Article

References (23)

1. Ach R.A., Wang H., Curry B. Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol. 2008, 8:69.
2. Anders C., Carey L.A. Understanding and treating triple-negative breast cancer. Oncology (Williston Park) 2008, 22:1233-1239.
3. Blenkiron C., Goldstein L.D., Thorne N.P., Spiteri I., Chin S.F., Dunning M.J., Barbosa-Morais N.L., Teschendorff A.E., Green A.R., Ellis I.O., Tavaré S., Caldas C., Miska E.A. MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol. 2007, 8:R214.
4. Borgan E., Navon R., Vollan H.K., Schlichting E., Sauer T., Yakhini Z., Lingjærde O.C., Sørlie T., Børresen-Dale A.L. Ischemia caused by time to freezing induces systematic microRNA and mRNA responses in cancer tissue. Mol. Oncol. 2011, 5:564-576.
5. Borze I., Guled M., Musse S., Raunio A., Elonen E., Saarinen-Pihkala U., Karjalainen-Lindsberg M.L., Lahti L., Knuutila S. MicroRNA microarrays on archive bone marrow core biopsies of leukemias - method validation. Leuk. Res. 2011, 35:188-195.
6. Callari M., Dugo M., Musella V., Marchesi E., Chiorino G., Grand M.M., Pierotti M.A., Daidone M.G., Canevari S., De Cecco L. Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues. PLoS ONE 2012, 7:e45105.
7. Castellano L., Giamas G., Jacob J., Coombes R.C., Lucchesi W., Thiruchelvam P., Barton G., Jiao L.R., Wait R., Waxman J., Hannon G.J., Stebbing J. The estrogen receptor-alpha-induced microRNA signature regulates itself and its transcriptional response. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:15732-15737.
8. Celton M., Malpertuy A., Lelandais G., de Brevern A.G. Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments. BMC Genom. 2010, 11:15.
9. Chugh P., Dittmer D.P. Potential pitfalls in microRNA profiling. Wiley Interdiscip. Rev. RNA 2012, 3:601-616.
10. Enerly E., Steinfeld I., Kleivi K., Leivonen S.K., Aure M.R., Russnes H.G., Rønneberg J.A., Johnsen H., Navon R., Rødland E., Mäkelä R., Naume B., Perälä M., Kallioniemi O., Kristensen V.N., Yakhini Z., Børresen-Dale A.L. miRNA-mRNA integrated analysis reveals roles for miRNAs in primary breast tumors. PLoS ONE 2011, 6:e16915.
11. Feng Y., Zhang X., Song Q., Li T., Zeng Y. Drosha processing controls the specificity and efficiency of global microRNA expression. Biochim. Biophys. Acta 2011, 1809:700-707.
12. 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.
13. Iyevleva A.G., Kuligina E.Sh., Mitiushkina N.V., Togo A.V., Miki Y., Imyanitov E.N. High level of miR-21, miR-10b, and miR-31 expression in bilateral vs. unilateral breast carcinomas. Breast Cancer Res. Treat. 2012, 131:1049-1059.
14. Janssen E.A., Slewa A., Gudlaugsson E., Jonsdottir K., Skaland I., Søiland H., Baak J.P. Biologic profiling of lymph node negative breast cancers by means of microRNA expression. Mod. Pathol. 2010, 23:1567-1576.
15. Meyer S.U., Pfaffl M.W., Ulbrich S.E. Normalization strategies for microRNA profiling experiments: a 'normal' way to a hidden layer of complexity. Biotechnol. Lett. 2010, 32:1777-1788.
16. Millevoi S., Moine H., Vagner S. G-quadruplexes in RNA biology. Wiley Interdiscip. Rev. RNA 2012, 3:495-507.
17. Oh H.K., Tan A.L., Das K., Ooi C.H., Deng N.T., Tan I.B., Beillard E., Lee J., Ramnarayanan K., Rha S.Y., Palanisamy N., Voorhoeve P.M., Tan P. Genomic loss of miR-486 regulates tumor progression and the OLFM4 antiapoptotic factor in gastric cancer. Clin. Cancer Res. 2011, 17:2657-2667.
18. Pradervand S., Weber J., Lemoine F., Consales F., Paillusson A., Dupasquier M., Thomas J., Richter H., Kaessmann H., Beaudoing E., Hagenbüchle O., Harshman K. Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. Biotechniques 2010, 48:219-222.
19. R Development Core Team R: A Language and Environment for Statistical Computing 2011, R Foundation for Statistical Computing, Vienna, Austria, ISBN: 3-900051-07-0. http://www.r-project.org/.
20. Sah S., McCall M.N., Eveleigh D., Wilson M., Irizarry R.A. Performance evaluation of commercial miRNA expression array platforms. BMC Res. Notes 2010, 3:80.
21. Shafer R.H., Smirnov I. Biological aspects of DNA/RNA quadruplexes. Biopolymers 2000-2001, 56:209-227.
22. Wang H., Ach R.A., Curry B. Direct and sensitive miRNA profiling from low-input total RNA. RNA 2007, 13:151-159.
23. Zhou L., Li X., Liu Q., Zhao F., Wu J. Small RNA transcriptome investigation based on next-generation sequencing technology. J. Genet. Genom. 2011, 38:505-513.