Proteomics

Dataset Information

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Proteomic analysis of distal cholangiocarcinoma


ABSTRACT: Distal cholangiocarcinoma is an aggressive malignancy with a dismal prognosis. There is a lack of diagnostic and prognostic biomarkers. An improved understanding of proteomic changes associated with malignancy and identification of potential biomarkers can help improve the survival of patients. A workflow utilizing discovery mass spectrometry and verification by parallel-reaction monitoring was used to analyze surgically resected formalin-fixed paraffin embedded samples from distal cholangiocarcinoma patients and normal bile ducts in order to identify differentially expressed proteins. 20 tumors and 6 controls were successfully analyzed in the discovery experiment and 16 tumors and 9 controls in the PRM analysis. In the discovery experiment a total of 3057 proteins were identified. 87 proteins were found to be differentially expressed between the conditions (q<0.05 and fold change ≥2 or ≤0.5). 31 proteins were upregulated in the distal cholangiocarcinoma samples as compared to controls and 56 downregulated. Bioinformatic analysis revealed an abundance of the differentially expressed proteins to be associated with the tumor reactive stroma. Parallel-reaction monitoring verified 28 proteins as upregulated and 18 as downregulated. In conclusion several proteins without prior association with cholangiocarcinoma biology were identified and verified as differentially expressed between distal cholangiocarcinoma samples and normal bile ducts. These proteins can be further evaluated to elucidate their biomarker potential and role in distal cholangiocarcinoma carcinogenesis.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Bile Duct

SUBMITTER: Johannes Byrling  

LAB HEAD: Bodil Andersson

PROVIDER: PXD017906 | Pride | 2020-09-09

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
PRMpeptideselection.sky Other
PRMpeptideselection.sky.view Other
PRMpeptideselection.skyd Other
control_FFPE_Sample21_R1.raw Raw
control_FFPE_Sample21_R2.raw Raw
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Publications

Mass spectrometry-based analysis of formalin-fixed, paraffin-embedded distal cholangiocarcinoma identifies stromal thrombospondin-2 as a potential prognostic marker.

Byrling Johannes J   Kristl Theresa T   Hu Dingyuan D   Pla Indira I   Sanchez Aniel A   Sasor Agata A   Andersson Roland R   Marko-Varga György G   Andersson Bodil B  

Journal of translational medicine 20200904 1


<h4>Background</h4>Distal cholangiocarcinoma is an aggressive malignancy with a dismal prognosis. Diagnostic and prognostic biomarkers for distal cholangiocarcinoma are lacking. The aim of the present study was to identify differentially expressed proteins between distal cholangiocarcinoma and normal bile duct samples.<h4>Methods</h4>A workflow utilizing discovery mass spectrometry and verification by parallel reaction monitoring was used to analyze surgically resected formalin-fixed, paraffin-e  ...[more]

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