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Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets
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 clinica...
Autores principales: | , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966770/ https://www.ncbi.nlm.nih.gov/pubmed/24670416 http://dx.doi.org/10.1371/journal.pone.0090948 |
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author | Britton, David Zen, Yoh Quaglia, Alberto Selzer, Stefan Mitra, Vikram Lößner, Christopher Jung, Stephan Böhm, Gitte Schmid, Peter Prefot, Petra Hoehle, Claudia Koncarevic, Sasa Gee, Julia Nicholson, Robert Ward, Malcolm Castellano, Leandro Stebbing, Justin Zucht, Hans Dieter Sarker, Debashis Heaton, Nigel Pike, Ian |
author_facet | Britton, David Zen, Yoh Quaglia, Alberto Selzer, Stefan Mitra, Vikram Lößner, Christopher Jung, Stephan Böhm, Gitte Schmid, Peter Prefot, Petra Hoehle, Claudia Koncarevic, Sasa Gee, Julia Nicholson, Robert Ward, Malcolm Castellano, Leandro Stebbing, Justin Zucht, Hans Dieter Sarker, Debashis Heaton, Nigel Pike, Ian |
author_sort | Britton, David |
collection | PubMed |
description | 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. 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 TiO(2), prior to analysis. In-house, commercial and freeware bioinformatic platforms were used to identify relevant biological events from the complex dataset. 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. 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. |
format | Online Article Text |
id | pubmed-3966770 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-39667702014-03-31 Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets Britton, David Zen, Yoh Quaglia, Alberto Selzer, Stefan Mitra, Vikram Lößner, Christopher Jung, Stephan Böhm, Gitte Schmid, Peter Prefot, Petra Hoehle, Claudia Koncarevic, Sasa Gee, Julia Nicholson, Robert Ward, Malcolm Castellano, Leandro Stebbing, Justin Zucht, Hans Dieter Sarker, Debashis Heaton, Nigel Pike, Ian PLoS One Research Article 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. 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 TiO(2), prior to analysis. In-house, commercial and freeware bioinformatic platforms were used to identify relevant biological events from the complex dataset. 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. 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. Public Library of Science 2014-03-26 /pmc/articles/PMC3966770/ /pubmed/24670416 http://dx.doi.org/10.1371/journal.pone.0090948 Text en © 2014 Britton et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Britton, David Zen, Yoh Quaglia, Alberto Selzer, Stefan Mitra, Vikram Lößner, Christopher Jung, Stephan Böhm, Gitte Schmid, Peter Prefot, Petra Hoehle, Claudia Koncarevic, Sasa Gee, Julia Nicholson, Robert Ward, Malcolm Castellano, Leandro Stebbing, Justin Zucht, Hans Dieter Sarker, Debashis Heaton, Nigel Pike, Ian Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets |
title | Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets |
title_full | Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets |
title_fullStr | Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets |
title_full_unstemmed | Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets |
title_short | Quantification of Pancreatic Cancer Proteome and Phosphorylome: Indicates Molecular Events Likely Contributing to Cancer and Activity of Drug Targets |
title_sort | quantification of pancreatic cancer proteome and phosphorylome: indicates molecular events likely contributing to cancer and activity of drug targets |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966770/ https://www.ncbi.nlm.nih.gov/pubmed/24670416 http://dx.doi.org/10.1371/journal.pone.0090948 |
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