Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma

Ayako Negishi, Mari Masuda, Masaya Ono, Kazufumi Honda, Miki Shitashige, Reiko Satow, Tomohiro Sakuma, Hideya Kuwabara, Yukihiro Nakanishi, Yae Kanai, Ken Omura, Setsuo Hirohashi, Tesshi Yamada

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

Clinical proteomics using a large archive of formalin-fixed paraffin-embedded (FFPE) tissue blocks has long been a challenge. Recently, a method for extracting proteins from FFPE tissue in the form of tryptic peptides was developed. Here we report the application of a highly sensitive mass spectrometry (MS)-based quantitative proteome method to a small amount of samples obtained by laser microdissection from FFPE tissues. Cancerous and adjacent normal epithelia were micro-dissected from FFPE tissue blocks of 10 squamous cell carcinomas of the tongue. Proteins were extracted in the form of tryptic peptides and analyzed by 2-dimensional image-converted analysis of liquid chromatography and mass spectrometry (2DICAL), a label-free quan-titative proteomics method developed in our laboratory. From a total of 25 018 peaks we selected 72 mass peaks whose expression differed significantly between cancer and normal tissues (P < 0.001, paired t-test). The expression of transglutaminase 3 (TGM3) was significantly down-regulated in cancer and correlated with loss of histological differentiation. Hypermethylation of TGM3 gene CpG islands was observed in 12 oral squamous cell carcinoma (OSCC) cell lines with reduced TGM3 expression. These results suggest that epigenetic silencing of TGM3 plays certain roles in the process of oral carcino-genesis. The method for quantitative proteomic analysis of FFPE tissue described here offers new opportunities to identify disease-specific biomarkers and therapeutic targets using widely available archival samples with corresponding detailed pathological and clinical records.

Original languageEnglish
Pages (from-to)1605-1611
Number of pages7
JournalCancer Science
Volume100
Issue number9
DOIs
Publication statusPublished - 2009 Sep
Externally publishedYes

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Paraffin
Proteomics
Formaldehyde
Squamous Cell Carcinoma
Transglutaminases
Mass Spectrometry
Microdissection
Peptides
CpG Islands
Proteome
Tongue
Epigenomics
Liquid Chromatography
Neoplasms
Proteins
Lasers
Epithelium
Biomarkers
Cell Line
Genes

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Negishi, A., Masuda, M., Ono, M., Honda, K., Shitashige, M., Satow, R., ... Yamada, T. (2009). Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. Cancer Science, 100(9), 1605-1611. https://doi.org/10.1111/j.1349-7006.2009.01227.x

Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. / Negishi, Ayako; Masuda, Mari; Ono, Masaya; Honda, Kazufumi; Shitashige, Miki; Satow, Reiko; Sakuma, Tomohiro; Kuwabara, Hideya; Nakanishi, Yukihiro; Kanai, Yae; Omura, Ken; Hirohashi, Setsuo; Yamada, Tesshi.

In: Cancer Science, Vol. 100, No. 9, 09.2009, p. 1605-1611.

Research output: Contribution to journalArticle

Negishi, A, Masuda, M, Ono, M, Honda, K, Shitashige, M, Satow, R, Sakuma, T, Kuwabara, H, Nakanishi, Y, Kanai, Y, Omura, K, Hirohashi, S & Yamada, T 2009, 'Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma', Cancer Science, vol. 100, no. 9, pp. 1605-1611. https://doi.org/10.1111/j.1349-7006.2009.01227.x
Negishi, Ayako ; Masuda, Mari ; Ono, Masaya ; Honda, Kazufumi ; Shitashige, Miki ; Satow, Reiko ; Sakuma, Tomohiro ; Kuwabara, Hideya ; Nakanishi, Yukihiro ; Kanai, Yae ; Omura, Ken ; Hirohashi, Setsuo ; Yamada, Tesshi. / Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma. In: Cancer Science. 2009 ; Vol. 100, No. 9. pp. 1605-1611.
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