Prognostic significance of promyelocytic leukemia expression in gastrointestinal stromal tumor; integrated proteomic and transcriptomic analysis.
Bottom Line: For proteins showing differential expressions, global mRNA expression was compared between 9 I-GIST and 23 S-GIST.Among the 2555 genes analyzed, we found that promyelocytic leukemia (PML), a tumor suppressor gene, was significantly downregulated in I-GIST at both the protein and mRNA levels (P < 0.01; fold difference ≥2.0).The 5-year recurrence-free survival rate was significantly lower in the PML-negative than in the PML-positive cases (60.1% vs 91.7%; P < 0.001).
Affiliation: Division of Pharmacoproteomics, National Cancer Center Research Institute, Tokyo, Japan; Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.Show MeSH
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Mentions: Proteins were extracted from fresh frozen tissues as described previously.24 Sixty microgram protein samples were separated by 12.5% SDS-PAGE. Each gel lane was cut into 24 pieces of equal size using a GridCutter (Gel Company, San Francisco, CA, USA), and each gel piece was subjected to in-gel tryptic digestion as described previously.27 The final trypsin digests were subjected to liquid chromatography coupled with LTQ-Orbitrap XL mass spectrometer (Thermo Fisher Scientific, San Jose, CA, USA) (Fig.1a). Peptide identification and protein quantification were performed using Mascot (version 2.2; Matrix Science, London, UK) and Progenesis LC-MS version 3.4 (Nonlinear Dynamics, Newcastle, UK), respectively. Details of the mass spectrometric analysis are provided in the supporting information (Suppl. Doc. S1). The processed raw data for protein abundance was loaded to Expressionist analyst (GeneData, Basel, Switzerland), and subjected to quantile normalization, hierarchical clustering analysis, principal component analysis and statistical analysis using Welch's t-test.
Affiliation: Division of Pharmacoproteomics, National Cancer Center Research Institute, Tokyo, Japan; Division of Digestive and General Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.