Microarray comparative analysis of melanoma microRNA depending on the tissue fixation method

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Cutaneous melanoma is the most aggressive form of skin cancer characterized by rapid progression, invasiveness and low survival rates. This explains the importance of optimization of early detection of this tumor. At the present time molecular and genetic methods of cancer investigation are broadly used. One of such methods is microarray that allows to analyze the expression of thousands genes in the single cell. However, this method makes high demands on the quality of samples and research procedure. Today the most common approach for tumor tissue preservation is formalin fixation followed paraffin embedding. This procedure is broadly used in clinical medicine but may affect the structure and availability of nucleic acids of the study sample. The present investigation was done to evaluate the effect of melanoma tissue fixation on the result of microRNA expression analysis by microarray. In this regard, we made comparative study of microRNA expression in melanoma samples fixed in formaldehyde and RNase inhibitor reagent based on ammonium sulfate solution. It has been shown that fixation by formalin as compared to ammonium salts based RNase inhibiting fixator alters the level of 454 microRNAs. Some miRNAs among them are playing an important role in the melanoma progression. Thus, molecular studies of skin tissues by microarray requires more thorough standardization of sample fixation methods or using of special RNA stabilizing solutions. The application of the formalin fixation method to preserve tissue for miRNA expression analysis requires further study.

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About the authors

A. V Komina

Krasnoyarsk State Medical University n.a. prof. V.F. Voyno-Yasenetsky

660022, Krasnoyarsk, Russia

N. V Palkina

Krasnoyarsk State Medical University n.a. prof. V.F. Voyno-Yasenetsky

660022, Krasnoyarsk, Russia

M. B Aksenenko

Krasnoyarsk State Medical University n.a. prof. V.F. Voyno-Yasenetsky

660022, Krasnoyarsk, Russia

Tatyana G. Ruksha

Krasnoyarsk State Medical University n.a. prof. V.F. Voyno-Yasenetsky

Email: tatyana_ruksha@mail.ru
660022, Krasnoyarsk, Russia
MD, PhD, DSc., Head of Department of pathophysiology, KGMU n.a. prof. V.F. Voyno-Yasenetsky


  1. Имянитов Е.Н. Эпидемиология и биология опухолей кожи. Практическая онкология. 2012; 13(2): 61-8.
  2. Ascierto P.A., Kirkwood J.M., Grob J.J., Simeone E., Grimaldi A.M., Maio M., et al. The role of BRAF V600 mutation in melanoma. J. Transl. Med. 2012; 10: 85. doi: 10.1186/1479-5876-10-85.
  3. Woodman S.E., Trent J.C., Stemke-Hale K., Lazar A.J., Pricl S., Pavan G.M., et al. Activity of dasatinib against L576P KIT mutant melanoma: molecular, cellular, and clinical correlates. Mol. Cancer Ther. 2009; 8(8): 2079-85.
  4. Fadiel A., Naftolin F. Microarray applications and challenges: a vast array of possibilities. Int. Arch. Biosci. 2003; 2003: 1111-21.
  5. Snijders A.M., Meijer G.A., Brakenhoff R.H., van den Brule A.J., van Diest P.J. Microarray techniques in pathology: tool or toy? Mol. Pathol. 2000; 53(6): 289-94.
  6. Ambros V. The functions of animal microRNAs. Nature. 2004; 431(7006): 350-5.
  7. Berg D., Malinowsky K., Reischauer B., Wolff C., Becker K.F. Use of formalin-fixed and paraffin-embedded tissues for diagnosis and therapy in routine clinical settings. Methods Mol. Biol. 2011; 785: 109-22. doi: 10.1007/978-1-61779-286-1-8.
  8. Evers D.L., Fowler C.B., Cunningham B.R., Mason J.T., O’Leary T.J. The effect of formaldehyde fixation on RNA. J. Mol. Diagn. 2011; 13(3): 282-8.
  9. Sengüven B., Baris E., Oygur T., Berktas M. Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues. Int. J. Med. Sci. 2014; 11(5): 494-9.
  10. Masuda N. Ohnishi T., Kawamoto Sh., Monden M. and Okubo K. Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples. Nucl. Acids Res. 1999; 27(22): 4436-43.
  11. Ji L., Chen X. Regulation of small RNA stability: methylation and beyond. Cell Res. 2012; 22(4): 624-36. doi: 10.1038/cr.2012.36.
  12. Matsuda Y., Fujii T., Suzuki T., Yamahatsu K., Kawahara K., Teduka K., et al. Comparison of fixation methods for preservation of morphology, RNAs, and proteins from paraffin-embedded human cancer cell-implanted mouse models. J. Histochem. Cytochem. 2011; 59(1): 68-75.
  13. Van Eijsden R.G., Stassen C., Daenen L., Van Mulders S.E., Bapat P.M., Siewers V., et al. A universal fixation method based on quaternary ammonium salts (RNAlater) for omics-technologies: Saccharomyces cerevisiae as a case study. Biotechnol. Lett. 2013; 35(6): 891-900.
  14. Sand M., Skrygan M., Sand D., Georgas D., Gambichler T., Hahn S.A., et al. Comparative microarray analysis of microRNA expression profiles in primary cutaneous malignant melanoma, cutaneous malignant melanoma metastases, and benign melanocytic nevi. Cell Tissue Res. 2013; 351(1): 85-98. doi: 10.1007/s00441-012-1514-5.
  15. Melnik B.C. MiR-21: an environmental driver of malignant melanoma? J. Transl. Med. 2015; 13: 202. doi: 10.1186/s12967-015-0570-5.
  16. Forloni M., Dogra S.K., Dong Y., Conte D. Jr., Ou J., Zhu L.J., et al. miR-146a promotes the initiation and progression of melanoma by activating Notch signaling. Elife. 2014; 3: e01460.
  17. Liu S., Tetzlaff M.T., Cui R., Xu X. miR-200c inhibits melanoma progression and drug resistance through down-regulation of BMI-1. Am. J. Pathol. 2012; 181(5): 1823-35.
  18. Kozubek J., Altaf F., Dadras S.S. MicroRNA biomarkers in melanoma. In: Murphy M.J., ed. Diagnostic and Prognostic Biomarkers and Therapeutic Targets in Melanoma. New York: Springer; 2012: 113-26.
  19. Wei Y., Du Y., Chen X., Li P., Wang Y., Zang W., et al. Expression patterns of microRNA-218 and its potential functions by targeting CIP2A and BMI1 genes in melanoma. Tumour Biol. 2014; 35(8): 8007-15.
  20. Bennett P.E., Bemis L., Norris D.A., Shellman Y.G. miR in melanoma development: miRNAs and acquired hallmarks of cancer in melanoma. Physiol. Genomics. 2013; 45(22): 1049-59.
  21. Penna E., Orso F., Cimino D., Tenaglia E., Lembo A., Quaglino E., et al. MicroRNA-214 contributes to melanoma tumour progression through suppression of TFAP2C. EMBO J. 2011; 30(10): 1990-2007. doi: 10.1038/emboj.201 1.102.
  22. Mazar J., Qi F., Lee B., Marchica J., Govindarajan S., Shelley J., et al. MicroRNA 211 functions as a metabolic switch in human melanoma cells. Mol. Cell. Biol. 2016; 36(7): 1090-108. doi: 10.1128/MCB.00762-15.
  23. Glud M., Klausen M., Gniadecki R., Rossing M., Hastrup N., Nielsen F.C., et al. MicroRNA expression in melanocytic nevi: the usefulness of formalin-fixed, paraffin-embedded material for miRNA microarray profiling. J. Invest. Dermatol. 2009; 129(5): 1219-24.
  24. Kashofer K., Viertler Ch., Pichler M., Zatloukal K. Quality control of RNA preservation and extraction from paraffin-embedded tissue: implications for RT-PCR and microarray analysis. PLoS ONE. 2013; 8(7): e70714.
  25. Li J., Smyth P., Flavin R., Cahill S., Denning K., Aherne S., et al. Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffinembedded (FFPE) cells and snap frozen cells. BMC Biotechnol. 2007; 7: 36.
  26. Flores O., Kennedy E.M., Skalsky R.L., Cullen B.R. Differential RISC association of endogenous human microRNAs predicts their inhibitory potential. Nucleic Acids Res. 2014; 42(7): 1-11.
  27. Bail S., Swerdel M., Liu H., Jiao X., Goff L.A., Hart R.P., et al. Differential regulation of microRNA stability. RNA. 2010; 16(5): 1032-9. doi: 10.1261/rna.1851510.
  28. Davoren P.A., McNeill R.E., Lowery A.J., Kerin M.J., Miller N. Identification of suitable endogenous control genes for micro-RNA gene expression analysis in human breast cancer. BMC Mol. Biol. 2008; 9: 76. doi: 10.1186/1471-2199-9-76.
  29. Carlsson J., Helenius G., Karlsson M., Lubovac Z., Andrén O., Olsson B., et al. Validation of suitable endogenous control genes for expression studies of miRNA in prostate cancer tissues. Cancer Genet. Cytogenet. 2010; 202(2): 71-5.
  30. Srinivasan M., Sedmak D., Jewell S. Effect of fixatives and tissue processing on the content and integrity of nucleic acids. Am. J. Pathol. 2002; 161(6): 1961-71.



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Copyright (c) 2016 Komina A.V., Palkina N.V., Aksenenko M.B., Ruksha T.G.

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