Tissue Sample Preparation for Biomarker Discovery

  • Yoshiyuki Suehara
  • Daisuke Kubota
  • Tsuyoshi Saito
Part of the Methods in Molecular Biology book series (MIMB, volume 1002)


Global protein expression studies, an approach known as “proteomics,” can offer important clues for understanding tumor biology that cannot be obtained by other approaches. Proteomic studies have provided protein expression profiles of tumors that can be used to develop novel diagnostic and therapeutic biomarkers. In this chapter, we describe the strategy and design of proteomic studies, as well as the protocols for tissue sample collection and preparation for biomarker discovery, especially tumor biomarkers, followed by a few examples of our recent proteomic studies.

Key words

Proteomics 2D-DIGE Tissue samples preparation Soft tissue sarcomas 



This work was supported by a grant from the Japan Society for the Promotion of Science (JSPS), a science Grant-in-Aid for Young Scientists B, No-22791405. The authors appreciate critical comments and support from Dr. Makoto Endo and Dr. Eisuke Kobayashi.


  1. 1.
    Suehara Y (2011) Proteomic analysis of soft ­tissue sarcoma. Int J Clin Oncol 16:92–100CrossRefGoogle Scholar
  2. 2.
    Kondo T, Hirohashi S (2006) Application of highly sensitive fluorescent dyes (CyDye DIGE Fluor saturation dyes) to laser microdissection and two-dimensional gel electrophoresis (2D-DIGE) for cancer proteomics. Nat Protoc 1:2940–2956PubMedCrossRefGoogle Scholar
  3. 3.
    Suehara Y, Kondo T, Fujii K et al (2006) Proteomic signatures corresponding to histological classification and grading of soft-tissue sarcomas. Proteomics 6:4402–4409PubMedCrossRefGoogle Scholar
  4. 4.
    Kawai A, Kondo T, Suehara Y, Kikuta K, Hirohashi S (2008) Global protein-expression analysis of bone and soft tissue sarcomas. Clin Orthop Relat Res 466:2099–2106PubMedCrossRefGoogle Scholar
  5. 5.
    Suehara Y, Kikuta K, Nakayama R et al (2009) Anatomic site-specific proteomic signatures of gastrointestinal stromal tumors. Proteomics Clin Appl 3:584–596CrossRefGoogle Scholar
  6. 6.
    Suehara Y, Kikuta K, Nakayama R et al (2009) GST-P1 as a histological biomarker of synovial sarcoma revealed by proteomics. Proteomics Clin Appl 3:623–634CrossRefGoogle Scholar
  7. 7.
    Suehara Y, Kondo T, Seki K et al (2008) Pfetin as a prognostic biomarker of gastrointestinal stromal tumors revealed by proteomics. Clin Cancer Res 14:1707–1717PubMedCrossRefGoogle Scholar
  8. 8.
    Kikuta K, Tochigi N, Shimoda T et al (2009) Nucleophosmin as a candidate prognostic biomarker of Ewing’s sarcoma revealed by proteomics. Clin Cancer Res 15:2885–2894PubMedCrossRefGoogle Scholar
  9. 9.
    Suehara Y, Tochigi N, Kubota D et al (2011) Secernin-1 as a novel prognostic biomarker candidate of synovial sarcoma revealed by proteomics. J Proteomics 74:829–842PubMedCrossRefGoogle Scholar
  10. 10.
    Kikuta K, Tochigi N, Saito S et al (2010) Peroxiredoxin 2 as a chemotherapy responsiveness biomarker candidate in osteosarcoma revealed by proteomics. Proteomics Clin Appl 4:560–567PubMedGoogle Scholar
  11. 11.
    Kikuta K, Kubota D, Saito T et al (2012) Clinical proteomics identified ATP-dependent RNA helicase DDX39 as a novel biomarker to predict poor prognosis of patients with gastrointestinal stromal tumor. J Proteomics 75:1089–1098PubMedCrossRefGoogle Scholar
  12. 12.
    Ericsson C, Nister M (2011) Protein extraction from solid tissue. Methods Mol Biol 675:307–312PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Yoshiyuki Suehara
    • 1
  • Daisuke Kubota
    • 1
  • Tsuyoshi Saito
    • 2
  1. 1.Department of Orthopedic SurgeryJuntendo University School of MedicineTokyoJapan
  2. 2.Department of Human PathologyJuntendo University School of MedicineTokyoJapan

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