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Quantification of pancreatic cancer proteome and phosphorylome: indicates molecular events likely contributing to cancer and activity of drug targets.
- Source :
-
PloS one [PLoS One] 2014 Mar 26; Vol. 9 (3), pp. e90948. Date of Electronic Publication: 2014 Mar 26 (Print Publication: 2014). - Publication Year :
- 2014
-
Abstract
- Objective: LC-MS/MS phospho-proteomics is an essential technology to help unravel the complex molecular events that lead to and propagate cancer. We have developed a global phospho-proteomic workflow to determine activity of signaling pathways and drug targets in pancreatic cancer tissue for clinical application.<br />Methods: Peptides resulting from tryptic digestion of proteins extracted from frozen tissue of pancreatic ductal adenocarcinoma and background pancreas (n = 12), were labelled with tandem mass tags (TMT 8-plex), separated by strong cation exchange chromatography, then were analysed by LC-MS/MS directly or first enriched for phosphopeptides using IMAC and TiO2, prior to analysis. In-house, commercial and freeware bioinformatic platforms were used to identify relevant biological events from the complex dataset.<br />Results: Of 2,101 proteins identified, 152 demonstrated significant difference in abundance between tumor and non-tumor tissue. They included proteins that are known to be up-regulated in pancreatic cancer (e.g. Mucin-1), but the majority were new candidate markers such as HIPK1 & MLCK. Of the 6,543 unique phosphopeptides identified (6,284 unique phosphorylation sites), 635 showed significant regulation, particularly those from proteins involved in cell migration (Rho guanine nucleotide exchange factors & MRCKα) and formation of focal adhesions. Activator phosphorylation sites on FYN, AKT1, ERK2, HDAC1 and other drug targets were found to be highly modulated (≥2 fold) in different cases highlighting their predictive power.<br />Conclusion: Here we provided critical information enabling us to identify the common and unique molecular events likely contributing to cancer in each case. Such information may be used to help predict more bespoke therapy suitable for an individual case.
- Subjects :
- Amino Acid Sequence
Biomarkers metabolism
DNA Damage
DNA Repair
Discriminant Analysis
Extracellular Matrix metabolism
Focal Adhesions metabolism
Gene Ontology
Humans
Least-Squares Analysis
Phosphopeptides metabolism
Phosphorylation
Protein Kinases metabolism
Pseudopodia metabolism
Signal Transduction
Up-Regulation
Antineoplastic Agents therapeutic use
Neoplasm Proteins metabolism
Pancreatic Neoplasms drug therapy
Pancreatic Neoplasms metabolism
Proteome metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1932-6203
- Volume :
- 9
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- PloS one
- Publication Type :
- Academic Journal
- Accession number :
- 24670416
- Full Text :
- https://doi.org/10.1371/journal.pone.0090948