Project PXD000534

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Biomedical Dataset
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Summary

Title

Identification of novel biomarker candidates for the immunohistochemical diagnosis of cholangiocellular carcinoma - LC-MS Part

Description

The aim of this study was the identification of biomarkers for the immunohistochemical diagnosis of cholangiocellular carcinoma (CCC). CCC is a primary cancer which arises from the epithelial cells of the bile ducts and is characterised by high mortality rates due to its late clinical presentation and limited treatment options. Tumorous tissue and adjacent non-tumorous liver tissue from eight CCC patients were analysed by two-dimensional differential in-gel electrophoresis (2D-DIGE) and by mass spectrometry-based label-free proteomics. After data analysis and statistical evaluation of the proteins which were found to be differentially regulated between the two experimental groups (fold change ≥ 1.5; p-value ≤ 0.05), 15 candidate proteins were chosen for verification by immunohistochemistry in an independent cohort of 14 patients. This confirmed the significant up-regulation of chloride intracellular channel protein 1 (CLIC1), gelsolin (GSN), pyruvate kinase isozymes M1/M2 (PKM2), serpin H1, 14-3-3 protein sigma (SFN), stress-induced phosphoprotein 1 (STIP1) and tax1-binding protein 3 (Tax1BP3) in tumorous cholangiocytes when compared to normal hepatocytes, whereas fatty acid-binding protein 1 (FABP1) and Betaine-homocysteine S-methyltransferase 1 (BHMT) were significantly down-regulated. Furthermore, STIP1 and SFN were able to differentiate between CCC tumour cells and non-tumorous cholangiocytes with a sensitivity of 100% and 86%, respectively and a specificity of 100% in both cases. We therefore conclude that these proteins should be considered as potential diagnostic biomarkers for CCC in an immunohistochemical application. Additional experiments addressing the validation of these novel biomarker candidates are being performed.

Sample Processing Protocol

See details in reference(s) : 25034945

Data Processing Protocol

See details in reference(s) : 25034945

Contact

Julian Uszkoreit, Ruhr-Universität Bochum, Medizinisches Proteom-Center, Medical Bioinformatics, Algorithmic Proteomics

Submission Date

21/10/2013

Publication Date

21/07/2014

Cell Type

hepatocyte

Quantification

Not available

Experiment Type

Bottom-up proteomics

Assay count

16

Publication

    Padden J, Megger DA, Bracht T, Reis H, Ahrens M, Kohl M, Eisenacher M, Schlaak JO, Canbay AE, Weber F, Hoffmann AC, Kuhlmann K, Meyer HE, Baba HA, Sitek B. Identification of Novel Biomarker Candidates for the Immunohistochemical Diagnosis of Cholangiocellular Carcinoma. Mol Cell Proteomics. 2014 Jul 17. pii: mcp.M113.034942 PubMed: 25034945

Assay

Page 1 2
Page size 10
Showing 1 - 10 of 16 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 31753 Control tissue patient 1 2399 13117 6772 30767 10571
2 31754 Tumor tissue patient 1 3390 23176 14099 30817 15031
3 31755 Control tissue patient 2 2544 18350 10278 31755 13145
4 31756 Tumor tissue patient 2 3421 23127 14056 32258 15023
5 31757 Control tissue patient 3 3004 21568 12453 32891 14822
6 31758 Tumor tissue patient 3 3697 24652 15102 33834 15904
7 31759 Control tissue patient 4 2870 22324 12424 32872 15869
8 31760 Tumor tissue patient 4 3722 24844 15459 31451 15546
9 31761 Tumor tissue patient 5 3294 21819 13704 30723 13689
10 31762 Control tissue patient 6 2788 20097 11417 31436 13830