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Pre-fractionation of Noncirculating Biological Fluids to Improve Discovery of Clinically Relevant Protein Biomarkers

  • Annarita FarinaEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1959)

Abstract

Nowadays, significant difficulties remain in the diagnosis and/or prognosis of many diseases, leading to an unsatisfactory patient management and a counterproductive increase in time and costs. It is therefore crucial to bridge the gap between basic and applied research by complying with clinical requirements, notably from the design stage of the experimental workflow. In this chapter we provide key suggestions for selecting appropriate biological samples and reducing pre-analytical and analytical variabilities to improve the discovery of clinically relevant protein biomarkers.

Key words

Differential centrifugation Extracellular Vesicles Exosomes Microvesicles Body fluids Differential diagnosis Translational medicine 

Notes

Acknowledgment

The author sincerely thanks all the coworkers who, over the years, have substantially contributed in the acquisition of the know-how required for the development of the present protocols, notably: Dr. Yohann Couté (Exploring the Dynamics of Proteomes laboratory at the CEA, Grenoble, France) for the methodological advices about each phase of protein identification and quantitation; Dr. Valeria Severino (Digestive Cancers Biomarkers Group of the Medicine Faculty at the Geneva University, Geneva, Switzerland) for the improvement of protein sub-fractionation protocols; The Proteomic Core Facility (Medicine Faculty at the Geneva University, Geneva, Switzerland) for the adaptation of peptide cleanup methods; Dr. Pierre Lescuyer, (Department of Genetic, Laboratory and Pathology Medicine at the Geneva University Hospitals, Geneva, Switzerland) for crucial knowledge in clinical laboratory requirements; Dr. Jean-Marc Dumonceau (Gedyt Center, Argentina, Buenos Aires) for essential expertise in sample inclusion and collection; Prof. Jean-Louis Frossard (Gastroenterology and Hepatology Service at the Geneva University Hospitals, Geneva, Switzerland) for strong competences in digestive pathologies, constructive criticisms, and continuous help and support; all the trainee students involved in the analyses that allowed assembling and validating the protocols.

References

  1. 1.
    Fuzery AK, Levin J, Chan MM et al (2013) Translation of proteomic biomarkers into FDA approved cancer diagnostics: issues and challenges. Clin Proteomics 10(1):13. https://doi.org/10.1186/1559-0275-10-13Google Scholar
  2. 2.
    Pepe MS, Li CI, Feng Z (2015) Improving the quality of biomarker discovery research: the right samples and enough of them. Cancer Epidemiol Biomark Prev 24(6):944–950. https://doi.org/10.1158/1055-9965.EPI-14-1227Google Scholar
  3. 3.
    Farina A (2014) Proximal fluid proteomics for the discovery of digestive cancer biomarkers. Biochim Biophys Acta 1844(5):988–1002. https://doi.org/10.1016/j.bbapap.2013.10.011Google Scholar
  4. 4.
    Dakappagari N, Zhang H, Stephen L et al (2017) Recommendations for clinical biomarker specimen preservation and stability assessments. Bioanalysis 9(8):643–653. https://doi.org/10.4155/bio-2017-0009Google Scholar
  5. 5.
    Percy AJ, Parker CE, Borchers CH (2013) Pre-analytical and analytical variability in absolute quantitative MRM-based plasma proteomic studies. Bioanalysis 5(22):2837–2856. https://doi.org/10.4155/bio.13.245Google Scholar
  6. 6.
    Baek R, Sondergaard EKL, Varming K et al (2016) The impact of various preanalytical treatments on the phenotype of small extracellular vesicles in blood analyzed by protein microarray. J Immunol Methods 438:11–20. https://doi.org/10.1016/j.jim.2016.08.007Google Scholar
  7. 7.
    Yuana Y, Bertina RM, Osanto S (2011) Pre-analytical and analytical issues in the analysis of blood microparticles. Thromb Haemost 105(3):396–408. https://doi.org/10.1160/Th10-09-0595Google Scholar
  8. 8.
    Jambunathan K, Galande AK (2014) Sample collection in clinical proteomics-Proteolytic activity profile of serum and plasma. Proteomics Clin Appl 8(5–6):299–307. https://doi.org/10.1002/prca.201300037Google Scholar
  9. 9.
    Chutipongtanate S, Chatchen S, Svasti J (2017) Plasma prefractionation methods for proteomic analysis and perspectives in clinical applications. Proteomics Clin Appl 11(7–8). https://doi.org/10.1002/prca.201600135
  10. 10.
    Ivanov AR, Lazarev A (eds) (2011) Sample preparation in biological mass spectrometry. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0828-0Google Scholar
  11. 11.
    Wisniewski JR, Wegler C, Artursson P (2016) Subcellular fractionation of human liver reveals limits in global proteomic quantification from isolated fractions. Anal Biochem 509:82–88. https://doi.org/10.1016/j.ab.2016.06.006Google Scholar
  12. 12.
    Lukic N, Visentin R, Delhaye M et al (2014) An integrated approach for comparative proteomic analysis of human bile reveals overexpressed cancer-associated proteins in malignant biliary stenosis. Biochim Biophys Acta 1844(5):1026–1033. https://doi.org/10.1016/j.bbapap.2013.06.023Google Scholar
  13. 13.
    Farina A, Dumonceau JM, Delhaye M et al (2011) A step further in the analysis of human bile proteome. J Proteome Res 10(4):2047–2063. https://doi.org/10.1021/pr200011bGoogle Scholar
  14. 14.
    Choksawangkarn W, Edwards N, Wang Y et al (2012) Comparative study of workflows optimized for in-gel, in-solution, and on-filter proteolysis in the analysis of plasma membrane proteins. J Proteome Res 11(5):3030–3034. https://doi.org/10.1021/pr300188bGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Digestive Cancers Biomarkers Group, Department of Internal Medicine, Faculty of MedicineUniversity of GenevaGenevaSwitzerland

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