Quantitative proteomics using formalin-fixed paraffin-embedded tissues of oral squamous cell carcinoma.
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 microdissected 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 quantitative 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 carcinogenesis. 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.
Negishi
Ayako
A
Chemotherapy Division, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan.
Masuda
Mari
M
Ono
Masaya
M
Honda
Kazufumi
K
Shitashige
Miki
M
Satow
Reiko
R
Sakuma
Tomohiro
T
Kuwabara
Hideya
H
Nakanishi
Yukihiro
Y
Kanai
Yae
Y
Omura
Ken
K
Hirohashi
Setsuo
S
Yamada
Tesshi
T
D015153:Blotting, Western; D002294:Carcinoma, Squamous Cell / Q000737:chemistry* / Q000473:pathology; D002853:Chromatography, Liquid; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D005557:Formaldehyde / Q000737:chemistry; D020868:Gene Silencing; D006801:Humans; D015151:Immunoblotting; D007124:Immunoenzyme Techniques; D008297:Male; D042282:Microdissection; D008875:Middle Aged; D009363:Neoplasm Proteins / Q000032:analysis* / Q000235:genetics / Q000378:metabolism; D016612:Paraffin Embedding; D020543:Proteome / Q000032:analysis; D040901:Proteomics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D016707:Tissue Fixation; D014062:Tongue Neoplasms / Q000737:chemistry* / Q000473:pathology; D011503:Transglutaminases / Q000235:genetics / Q000378:metabolism; D014407:Tumor Cells, Cultured
D009363:Neoplasm Proteins; D020543:Proteome; D012333:RNA, Messenger; D005557:Formaldehyde; C498712:TGM3 protein, human; D011503:Transglutaminases