Skip to main content
SpringerLink
Log in

Blood-Based miRNA Preparation for Noninvasive Biomarker Development

  • Protocol
  • First Online:
Next-Generation MicroRNA Expression Profiling Technology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 822))

Abstract

This chapter describes several methods for the isolation of miRNAs from peripheral whole blood samples or constituent fractions thereof, such as peripheral blood mononuclear cells, plasma, and serum. The methods described here are recently introduced protocols dedicated to the isolation of total RNAs including small RNAs, e.g., miRNeasy Kit and PAXgene Blood miRNA Kit, or alternatively for the enrichment of low-molecular-weight RNA (LMW RNA) fractions including small RNAs, e.g., using the miRNeasy Kit. Furthermore, modifications of classical RNA purification protocols to facilitate the recovery of small RNAs are highlighted.

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. Boldrick, J. C., Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. L., Belcher, C. E., et al (2002) Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Proc Natl Acad Sci USA 99, 972–7.

    Article  PubMed  CAS  Google Scholar 

  2. Chaussabel, D., Allman, W., Mejias, A., Chung, W., Bennett, L., Ramilo, O., et al (2005) Analysis of significance patterns identifies ubiquitous and disease-specific gene-expression signatures in patient peripheral blood leukocytes. Annals New York Acad Sci 1062, 146–54.

    Article  CAS  Google Scholar 

  3. Horwitz, P. A., Tsai, E. J., Putt, M. E., Gilmore, J. M., Lepore, J. J., Parmacek, M. S., et al (2004) Detection of cardiac allograft rejection and response to immunosuppressive therapy with peripheral blood gene expression. Circulation 110, 3815–21.

    Article  PubMed  CAS  Google Scholar 

  4. Kittleson, M. M., Ye, S. Q., Irizarry, R. A., Minhas, K. M., Edness, G., Conte, J. V., et al (2004) Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation 110, 3444–51.

    Article  PubMed  CAS  Google Scholar 

  5. Chaussabel, D., Quinn, C., Shen, J., Patel, P., Glaser, C., Baldwin, N., et al (2008) A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29, 150–64.

    Article  PubMed  CAS  Google Scholar 

  6. Burczynski, M. E., and Dorner, A. J. (2006) Transcriptional profiling of peripheral blood cells in clinical pharmacogenomic studies. Pharmacogenomics 7, 187–202.

    Article  PubMed  CAS  Google Scholar 

  7. Lonneborg, A., Aaroe, J., Dumeaux, V., and Borresen-Dale, A. L. (2009) Found in transcription: gene expression and other novel blood biomarkers for the early detection of breast cancer. Expert Rev Anticancer Ther 9, 1115–23.

    Article  PubMed  Google Scholar 

  8. Chaussabel, D., Pascual, V., and Banchereau, J. (2010) Assessing the human immune system through blood transcriptomics. BMC Biol 8, 84.

    Article  PubMed  Google Scholar 

  9. Staratschek-Jox, A., Classen, S., Gaarz, A., Debey-Pascher, S., and Schultze, J. L. (2009) Blood-based transcriptomics: leukemias and beyond. Expert Rev Mol Diagn 9, 271–80.

    Article  PubMed  CAS  Google Scholar 

  10. Chitwood, D. H., and Timmermans, M. C. Small RNAs are on the move. Nature 467, 415–9.

    Google Scholar 

  11. Ghildiyal, M., and Zamore, P. D. (2009) Small silencing RNAs: an expanding universe. Nat Rev 10, 94–108.

    Article  CAS  Google Scholar 

  12. Visone, R., and Croce, C. M. (2009) MiRNAs and cancer. Am J Pathol 174, 1131–8.

    Article  PubMed  CAS  Google Scholar 

  13. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs. Science 294, 853–8.

    Article  PubMed  CAS  Google Scholar 

  14. Bartel, D. P. (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–97.

    Article  PubMed  CAS  Google Scholar 

  15. Valencia-Sanchez, M. A., Liu, J., Hannon, G. J., and Parker, R. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20, 515–24.

    Article  PubMed  CAS  Google Scholar 

  16. Iorio, M. V., Ferracin, M., Liu, C. G., Veronese, A., Spizzo, R., Sabbioni, S., et al (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65, 7065–70.

    Article  PubMed  CAS  Google Scholar 

  17. Subramanian, S., Lui, W. O., Lee, C. H., Espinosa, I., Nielsen, T. O., Heinrich, M. C., et al (2008) MicroRNA expression signature of human sarcomas. Oncogene 27, 2015–26.

    Article  PubMed  CAS  Google Scholar 

  18. Calin, G. A., Ferracin, M., Cimmino, A., Di Leva, G., Shimizu, M., Wojcik, S. E., et al (2005) A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 353, 1793–801.

    Article  PubMed  CAS  Google Scholar 

  19. Calin, G. A., Liu, C. G., Sevignani, C., Ferracin, M., Felli, N., Dumitru, C. D., et al (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci USA 101, 11755–60.

    Article  PubMed  CAS  Google Scholar 

  20. Lawrie, C. H., Soneji, S., Marafioti, T., Cooper, C. D., Palazzo, S., Paterson, J. C., et al (2007) MicroRNA expression distinguishes between germinal center B cell-like and activated B cell-like subtypes of diffuse large B cell lymphoma. Int J Cancer 121, 1156–61.

    Article  PubMed  CAS  Google Scholar 

  21. Mattie, M. D., Benz, C. C., Bowers, J., Sensinger, K., Wong, L., Scott, G. K., et al (2006) Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5, 24.

    Article  PubMed  Google Scholar 

  22. Dai, Y., Huang, Y. S., Tang, M., Lv, T. Y., Hu, C. X., Tan, Y. H., et al (2007) Microarray analysis of microRNA expression in peripheral blood cells of systemic lupus erythematosus patients. Lupus 16, 939–46.

    Article  PubMed  CAS  Google Scholar 

  23. Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., Macdonald, P. E., et al (2004) A pancreatic islet-specific microRNA regulates insulin secretion. Nature 432, 226–230.

    Article  PubMed  CAS  Google Scholar 

  24. Sarnow, P., Jopling, C. L., Norman, K. L., Schutz, S., and Wehner, K. A. (2006) MicroRNAs: expression, avoidance and subversion by vertebrate viruses. Nat Rev Microbiol 4, 651–9.

    Article  PubMed  CAS  Google Scholar 

  25. Skog, J., Wurdinger, T., van Rijn, S., Meijer, D. H., Gainche, L., Sena-Esteves, M., et al (2008) Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nat Cell Biol 10, 1470–6.

    Article  PubMed  CAS  Google Scholar 

  26. Valadi, H., Ekstrom, K., Bossios, A., Sjostrand, M., Lee, J. J., and Lotvall, J. O. (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9, 654–9.

    Article  PubMed  CAS  Google Scholar 

  27. Cortez, M. A., and Calin, G. A. (2009) MicroRNA identification in plasma and serum: a new tool to diagnose and monitor diseases. Expert Opin Biol Ther 9, 703–11.

    Article  PubMed  CAS  Google Scholar 

  28. Keller, A., Leidinger, P., Lange, J., Borries, A., Schroers, H., Scheffler, M., et al (2009) Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PLoS One 4, e7440.

    Article  PubMed  Google Scholar 

  29. Murata, K., Yoshitomi, H., Tanida, S., Ishikawa, M., Nishitani, K., Ito, H., et al (2010) Plasma and synovial fluid microRNAs as potential biomarkers of rheumatoid arthritis and osteoarthritis. Arthritis Res Ther 12, R86.

    Article  PubMed  Google Scholar 

  30. Tan, K. S., Armugam, A., Sepramaniam, S., Lim, K. Y., Setyowati, K. D., Wang, C. W., et al (2009) Expression profile of MicroRNAs in young stroke patients. PLoS One 4, e7689.

    Article  PubMed  Google Scholar 

  31. Hoekstra, M., van der Lans, C. A., Halvorsen, B., Gullestad, L., Kuiper, J., Aukrust, P., et al (2010) The peripheral blood mononuclear cell microRNA signature of coronary artery disease. Biochem Biophys Res Commun. 394, 792–7.

    Article  PubMed  CAS  Google Scholar 

  32. Chen, X., Ba, Y., Ma, L., Cai, X., Yin, Y., Wang, K., et al (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18, 997–1006.

    Article  PubMed  CAS  Google Scholar 

  33. Hausler, S. F., Keller, A., Chandran, P. A., Ziegler, K., Zipp, K., Heuer, S., et al (2010) Whole blood-derived miRNA profiles as potential new tools for ovarian cancer screening. Br J Cancer 103, 693–700.

    Article  PubMed  CAS  Google Scholar 

  34. Keller, A., Leidinger, P., Borries, A., Wendschlag, A., Wucherpfennig, F., Scheffler, M., et al (2009) miRNAs in lung cancer - studying complex fingerprints in patient’s blood cells by microarray experiments. BMC Cancer 9, 353.

    Article  PubMed  Google Scholar 

  35. Leidinger, P., Keller, A., Borries, A., Reichrath, J., Rass, K., Jager, S. U., et al (2010) High-throughput miRNA profiling of human melanoma blood samples. BMC Cancer 10, 262.

    Article  PubMed  Google Scholar 

  36. Resnick, K. E., Alder, H., Hagan, J. P., Richardson, D. L., Croce, C. M., and Cohn, D. E. (2009) The detection of differentially expressed microRNAs from the serum of ovarian cancer patients using a novel real-time PCR platform. Gynecol Oncol 112, 55–9.

    Article  PubMed  CAS  Google Scholar 

  37. Chen, J., Lozach, J., Garcia, E. W., Barnes, B., Luo, S., Mikoulitch, I., et al (2008) Highly sensitive and specific microRNA expression profiling using BeadArray technology. Nucleic Acids Res 36, e87.

    Article  PubMed  Google Scholar 

  38. Gaarz, A., Debey-Pascher, S., Classen, S., Eggle, D., Gathof, B., Chen, J., et al (2010) Bead array-based microrna expression profiling of peripheral blood and the impact of different RNA isolation approaches, J Mol Diagn 12, 335–44.

    Article  PubMed  CAS  Google Scholar 

  39. Kruhoffer, M., Dyrskjot, L., Voss, T., Lindberg, R. L., Wyrich, R., Thykjaer, T., et al (2007) Isolation of microarray-grade total RNA, microRNA, and DNA from a single PAXgene blood RNA tube. J Mol Diagn 9, 452–8.

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

Protocols referring to the PAXgene Blood miRNA Kit, PAXgene Blood RNA Kit, QIAamp Criculating Nucleic Acid Kit, miRNeasy Mini Kit, RNeasy Mini kit, RNeasy MinElute Cleanup Kit are established by QIAGEN and were mainly cited literally. We are grateful to receive copyright permission.

Author information

Authors and Affiliations

  1. Life and Medical Sciences (LIMES), Genomics and Immunoregulation, University of Bonn, Bonn, Germany

    Svenja Debey-Pascher & Andrea Staratschek-Jox

  2. Illumina, Inc., San Diego, CA, USA

    Jing Chen

  3. QIAGEN GmbH, Diagnostic Sample Preparation and Stabilization, R&D Department, QIAGEN, Hilden, Germany

    Thorsten Voss

Authors
  1. Svenja Debey-Pascher
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jing Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Thorsten Voss
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Andrea Staratschek-Jox
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Andrea Staratschek-Jox .

Editor information

Editors and Affiliations

  1. Illumina, Inc., Towne Centre Drive 9885, San Diego, 92121, California, USA

    Jian-Bing Fan

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Debey-Pascher, S., Chen, J., Voss, T., Staratschek-Jox, A. (2012). Blood-Based miRNA Preparation for Noninvasive Biomarker Development. In: Fan, JB. (eds) Next-Generation MicroRNA Expression Profiling Technology. Methods in Molecular Biology, vol 822. Humana Press. https://doi.org/10.1007/978-1-61779-427-8_22

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-427-8_22

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-426-1

  • Online ISBN: 978-1-61779-427-8

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation