Skip to main content
SpringerLink
Log in

MicroRNA Profiling in Ovarian Cancer

  • Protocol
  • First Online:
Ovarian Cancer

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1049))

Abstract

The evaluation of microRNA profiles has represented one of the first approaches to investigate the aberrant microRNA expression in different human cancers, providing the first experimental evidence of the involvement of these small noncoding RNAs in the tumorigenic process. Currently, these and other methods have been applied to the search of new molecular biomarkers of diagnosis, prognosis, and response to therapy prediction.

Here, we described the approach we used for the determination of a miRNA signature unique for human ovarian cancer, first performing a large-scale screening using a custom-made microarray platform, and then validating the obtained data by Northern blot or real-time PCR.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, Croce CM (2004) Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci USA 101:2999–3004

    Article  PubMed  CAS  Google Scholar 

  2. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99:15524–15529

    Article  PubMed  CAS  Google Scholar 

  3. Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6:857–866

    Article  PubMed  CAS  Google Scholar 

  4. Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru CD, Shimizu M, Zupo S, Dono M et al (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci USA 101:9740–9744

    Article  PubMed  CAS  Google Scholar 

  5. 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 (2005) MicroRNA expression profiles classify human cancers. Nature 435:834–838

    Article  PubMed  CAS  Google Scholar 

  6. Creighton CJ, Reid JG, Gunaratne PH (2009) Expression profiling of microRNAs by deep sequencing. Brief Bioinform 10:490–497

    Article  PubMed  CAS  Google Scholar 

  7. Farazi TA, Horlings HM, Ten Hoeve JJ, Mihailovic A, Halfwerk H, Morozov P, Brown M, Hafner M, Reyal F, van Kouwenhove M, Kreike B, Sie D, Hovestadt V, Wessels LF, van de Vijver MJ, Tuschl T (2011) MicroRNA sequence and expression analysis in breast tumors by deep sequencing. Cancer Res 71:4443–4453

    Article  PubMed  CAS  Google Scholar 

  8. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179

    Article  PubMed  Google Scholar 

  9. Raymond CK, Roberts BS, Garrett-Engele P, Lim LP, Johnson JM (2005) Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 11:1737–1744

    Article  PubMed  CAS  Google Scholar 

  10. Obernosterer G, Martinez J, Alenius M (2010) Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat Protoc 2:1508–1514

    Article  Google Scholar 

  11. Pena JT, Sohn-Lee C, Rouhanifard SH, Ludwig J, Hafner M, Mihailovic A, Lim C, Holoch D, Berninger P, Zavolan M, Tuschl T (2009) miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods 6:139–141

    Article  PubMed  CAS  Google Scholar 

  12. Nuovo G, Lee EJ, Lawler S, Godlewski J, Schmittgen T (2009) In situ detection of mature microRNAs by labeled extension on ultramer templates. Biotechniques 46:115–126

    Article  PubMed  CAS  Google Scholar 

  13. de Planell-Saguer M, Rodicio MC, Mourelatos Z (2010) Rapid in situ codetection of noncoding RNAs and proteins in cells and formalin-fixed paraffin-embedded tissue sections without protease treatment. Nat Protoc 5:1061–1073

    Article  PubMed  Google Scholar 

  14. Wyman SK, Parkin RK, Mitchell PS, Fritz BR, O’Briant K, Godwin AK, Urban N, Drescher CW, Knudsen BS, Tewari M (2009) Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PLoS One 4:e5311

    Article  PubMed  Google Scholar 

  15. Xu JZ, Wong CW (2010) Hunting for robust gene signature from cancer profiling data: sources of variability, different interpretations, and recent methodological developments. Cancer Lett 296:9–16

    Article  PubMed  CAS  Google Scholar 

  16. Peltier HJ, Latham GJ (2008) Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 14:844–852

    Article  PubMed  CAS  Google Scholar 

  17. Marsit CJ, Eddy K, Kelsey KT (2006) MicroRNA responses to cellular stress. Cancer Res 66:10843–10848

    Article  PubMed  CAS  Google Scholar 

  18. Kulshreshtha R, Ferracin M, Wojcik SE, Garzon R, Alder H, Agosto-Perez FJ, Davuluri R, Liu CG, Croce CM, Negrini M, Calin GA, Ivan M (2007) A microRNA signature of hypoxia. Mol Cell Biol 27:1859–1867

    Article  PubMed  CAS  Google Scholar 

  19. Rossi S, Shimizu M, Barbarotto E, Nicoloso MS, Dimitri F, Sampath D, Fabbri M, Lerner S, Barron LL, Rassenti LZ et al (2010) microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival. Blood 116:945–952

    Article  PubMed  CAS  Google Scholar 

  20. Dillhoff M, Liu J, Frankel W, Croce C, Bloomston M (2008) MicroRNA-21 is overexpressed in pancreatic cancer and a potential predictor of survival. J Gastrointest Surg 12:2171–2176

    Article  PubMed  Google Scholar 

  21. Schetter AJ, Leung SY, Sohn JJ, Zanetti KA, Bowman ED, Yanaihara N, Yuen ST, Chan TL, Kwong DL, Au GK et al (2008) MicroRNA expression profiles associated with prognosis and therapeutic outcome in colon adenocarcinoma. JAMA 299:425–436

    Article  PubMed  CAS  Google Scholar 

  22. Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, Taccioli C, Volinia S, Liu CG, Alder H, Calin GA, Ménard S, Croce CM (2007) MicroRNA signatures in human ovarian cancer. Cancer Res 67:8699–8707

    Article  PubMed  CAS  Google Scholar 

  23. Zhang L, Huang J, Yang N, Greshock J, Megraw MS, Giannakakis A, Liang S, Naylor TL, Barchetti A, Ward MR, Yao G, Medina A, O’brien-Jenkins A, Katsaros D, Hatzigeorgiou A, Gimotty PA, Weber BL, Coukos G (2006) microRNAs exhibit high frequency genomic alterations in human cancer. Proc Natl Acad Sci USA 103:9136–9141

    Article  PubMed  CAS  Google Scholar 

  24. Zhang L, Volinia S, Bonome T, Calin GA, Greshock J, Yang N, Liu CG, Giannakakis A, Alexiou P, Hasegawa K, Johnstone CN, Megraw MS, Adams S, Lassus H, Huang J, Kaur S, Liang S, Sethupathy P, Leminen A, Simossis VA, Sandaltzopoulos R, Naomoto Y, Katsaros D, Gimotty PA, DeMichele A, Huang Q, Bützow R, Rustgi AK, Weber BL, Birrer MJ, Hatzigeorgiou AG, Croce CM, Coukos G (2008) Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. Proc Natl Acad Sci USA 105:7004–7009

    Article  PubMed  CAS  Google Scholar 

  25. Bagnoli M, De Cecco L, Granata A, Nicoletti R, Marchesi E, Alberti P, Valeri B, Libra M, Barbareschi M, Raspagliesi F, Mezzanzanica D, Canevari S (2011) Identification of a chrXq27.3 microRNA cluster associated with early relapse in advanced stage ovarian cancer patients. Oncotarget 2:1265–1278

    PubMed  Google Scholar 

  26. Zorn KK, Jazaeri AA, Awtrey CS, Gardner GJ, Mok SC, Boyd J, Birrer MJ (2003) Choice of normal ovarian control influences determination of differentially expressed genes in ovarian cancer expression profiling studies. Clin Cancer Res 9:4811–4818

    PubMed  CAS  Google Scholar 

  27. Farley J, Ozbun LL, Birrer MJ (2008) Genomic analysis of epithelial ovarian cancer. Cell Res 18:538–548

    Article  PubMed  CAS  Google Scholar 

  28. Yang N, Kaur S, Volinia S, Greshock J, Lassus H, Hasegawa K, Liang S, Leminen A, Deng S, Smith L, Johnstone CN, Chen XM, Liu CG, Huang Q, Katsaros D, Calin GA, Weber BL, Bützow R, Croce CM, Coukos G, Zhang L (2008) MicroRNA microarray identifies Let-7i as a novel biomarker and therapeutic target in human epithelial ovarian cancer. Cancer Res 68:10307–10314

    Article  PubMed  CAS  Google Scholar 

  29. Peng DX, Luo M, Qiu LW, He YL, Wang XF (2012) Prognostic implications of microRNA-100 and its functional roles in human epithelial ovarian cancer. Oncol Rep 27:1238–1244. doi:10.3892/or.2012.1625

    PubMed  CAS  Google Scholar 

  30. Hu X, Macdonald DM, Huettner PC, Feng Z, El Naqa I, Schwarz JK, Mutch DG, Grigsby PW, Powell SN, Wang X (2009) A miR-200 microRNA cluster as prognostic marker in advanced ovarian cancer. Gynecol Oncol 114:457–464

    Article  PubMed  CAS  Google Scholar 

  31. Marchini S, Cavalieri D, Fruscio R, Calura E, Garavaglia D, Nerini IF, Mangioni C, Cattoretti G, Clivio L, Beltrame L, Katsaros D, Scarampi L, Menato G, Perego P, Chiorino G, Buda A, Romualdi C, D’Incalci M (2011) Association between miR-200c and the survival of patients with stage I epithelial ovarian cancer: a retrospective study of two independent tumour tissue collections. Lancet Oncol 12:273–285

    Article  PubMed  CAS  Google Scholar 

  32. Leskelä S, Leandro-García LJ, Mendiola M, Barriuso J, Inglada-Pérez L, Muñoz I, Martínez-Delgado B, Redondo A, de Santiago J, Robledo M, Hardisson D, Rodríguez-Antona C (2010) The miR-200 family controls beta-tubulin III expression and is associated with paclitaxel-based treatment response and progression-free survival in ovarian cancer patients. Endocr Relat Cancer 18:85–95

    Article  PubMed  Google Scholar 

  33. Wright GW, Simon RM (2003) A random variance model for detection of differential gene expression in small microarray experiments. Bioinformatics 19:2448–2455

    Article  PubMed  CAS  Google Scholar 

  34. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116–5121

    Article  PubMed  CAS  Google Scholar 

  35. Tibshirani R, Hastie T, Narasimhan B, Chu G (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99:6567–6572

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Experimental Oncology, Fondazione IRCCS, Istituto Nazionale Tumori, Milan, Italy

    Marilena V. Iorio

  2. Department of Molecular Virology, Immunology and Medical Genetics and Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA

    Carlo M. Croce

Authors
  1. Marilena V. Iorio
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carlo M. Croce
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Group of Experimental Therapeutics, Federal State Institution N.N.Petrov Res Institute of Oncology, St. Petersburg, Russia

    Anastasia Malek

  2. Labs of Molecular Tumor Pathology & Func, Charité - Universitatsmedizin Berlin, Berlin, Germany

    Oleg Tchernitsa

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media, New York

About this protocol

Cite this protocol

Iorio, M.V., Croce, C.M. (2013). MicroRNA Profiling in Ovarian Cancer. In: Malek, A., Tchernitsa, O. (eds) Ovarian Cancer. Methods in Molecular Biology, vol 1049. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-547-7_14

Download citation

  • DOI: https://doi.org/10.1007/978-1-62703-547-7_14

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-546-0

  • Online ISBN: 978-1-62703-547-7

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation