Limits...
Prognostic significance of promyelocytic leukemia expression in gastrointestinal stromal tumor; integrated proteomic and transcriptomic analysis.

Ichikawa H, Yoshida A, Kanda T, Kosugi S, Ishikawa T, Hanyu T, Taguchi T, Sakumoto M, Katai H, Kawai A, Wakai T, Kondo T - Cancer Sci. (2014)

Bottom Line: 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).Immunohistochemistry of 254 additional cases from multiple clinical facilities showed that PML-negative cases were significantly frequent in the I-GIST group (P < 0.001).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).

View Article: PubMed Central - PubMed

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

Related in: MedlinePlus

Integrated proteomic and transcriptomic analysis shows promyelocytic leukemia (PML) downregulation in gastrointestinal stromal tumors (GIST) of the small intestine (I-GIST), and its potential as a prognostic biomarker. Workflow of the proteomic and transcriptomic analysis (a). Heat-map of the genes differentially expressed at the protein level (b). Venn diagrams showing the numbers of commonly upregulated and downregulated genes at both the protein and mRNA levels (c). Western blotting shows the differences in PML expression between the samples used for proteomic analysis (d). Kaplan–Meier analysis of recurrence-free survival according to the expression of PML mRNA in S-GIST of GSE8167 (e).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4317774&req=5

fig01: Integrated proteomic and transcriptomic analysis shows promyelocytic leukemia (PML) downregulation in gastrointestinal stromal tumors (GIST) of the small intestine (I-GIST), and its potential as a prognostic biomarker. Workflow of the proteomic and transcriptomic analysis (a). Heat-map of the genes differentially expressed at the protein level (b). Venn diagrams showing the numbers of commonly upregulated and downregulated genes at both the protein and mRNA levels (c). Western blotting shows the differences in PML expression between the samples used for proteomic analysis (d). Kaplan–Meier analysis of recurrence-free survival according to the expression of PML mRNA in S-GIST of GSE8167 (e).

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.


Prognostic significance of promyelocytic leukemia expression in gastrointestinal stromal tumor; integrated proteomic and transcriptomic analysis.

Ichikawa H, Yoshida A, Kanda T, Kosugi S, Ishikawa T, Hanyu T, Taguchi T, Sakumoto M, Katai H, Kawai A, Wakai T, Kondo T - Cancer Sci. (2014)

Integrated proteomic and transcriptomic analysis shows promyelocytic leukemia (PML) downregulation in gastrointestinal stromal tumors (GIST) of the small intestine (I-GIST), and its potential as a prognostic biomarker. Workflow of the proteomic and transcriptomic analysis (a). Heat-map of the genes differentially expressed at the protein level (b). Venn diagrams showing the numbers of commonly upregulated and downregulated genes at both the protein and mRNA levels (c). Western blotting shows the differences in PML expression between the samples used for proteomic analysis (d). Kaplan–Meier analysis of recurrence-free survival according to the expression of PML mRNA in S-GIST of GSE8167 (e).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4317774&req=5

fig01: Integrated proteomic and transcriptomic analysis shows promyelocytic leukemia (PML) downregulation in gastrointestinal stromal tumors (GIST) of the small intestine (I-GIST), and its potential as a prognostic biomarker. Workflow of the proteomic and transcriptomic analysis (a). Heat-map of the genes differentially expressed at the protein level (b). Venn diagrams showing the numbers of commonly upregulated and downregulated genes at both the protein and mRNA levels (c). Western blotting shows the differences in PML expression between the samples used for proteomic analysis (d). Kaplan–Meier analysis of recurrence-free survival according to the expression of PML mRNA in S-GIST of GSE8167 (e).
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.

Bottom Line: 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).Immunohistochemistry of 254 additional cases from multiple clinical facilities showed that PML-negative cases were significantly frequent in the I-GIST group (P < 0.001).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).

View Article: PubMed Central - PubMed

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
Related in: MedlinePlus