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Identification of hypoxia-regulated proteins using MALDI-mass spectrometry imaging combined with quantitative proteomics

Djidja, M and Chang, J and Hadjiprocopis, A and Schmich, F and Sinclair, J and Mrsnik, M and Schoof, EM and Barker, HE and Linding, R and Jorgensen, C and Erler, JT (2014) Identification of hypoxia-regulated proteins using MALDI-mass spectrometry imaging combined with quantitative proteomics. Journal of Proteome Research. pp. 2297-2313.

Abstract

Hypoxia is present in most solid tumors and is clinically correlated with increased metastasis and poor patient survival. While studies have demonstrated the role of hypoxia and hypoxia-regulated proteins in cancer progression, no attempts have been made to identify hypoxia-regulated proteins using quantitative proteomics combined with MALDI-mass spectrometry imaging (MALDI-MSI). Here we present a comprehensive hypoxic proteome study and are the first to investigate changes in situ using tumor samples. In vitro quantitative mass spectrometry analysis of the hypoxic proteome was performed on breast cancer cells using stable isotope labeling with amino acids in cell culture (SILAC). MS analyses were performed on laser-capture microdissected samples isolated from normoxic and hypoxic regions from tumors derived from the same cells used in vitro. MALDI-MSI was used in combination to investigate hypoxia-regulated protein localization within tumor sections. Here we identified more than 100 proteins, both novel and previously reported, that were associated with hypoxia. Several proteins were localized in hypoxic regions, as identified by MALDI-MSI. Visualization and data extrapolation methods for the in vitro SILAC data were also developed, and computational mapping of MALDI-MSI data to IHC results was applied for data validation. The results and limitations of the methodologies described are discussed. 2014 American Chemical Society

Item Type: Article
Additional Information: NIBR author: Djidja, M institute: NIBR- address only contributor address: (Djidja, Chang, Hadjiprocopis, Schmich, Mrsnik, Barker, Erler) Hypoxia and Metastasis Team, Cancer Research U.K. Tumour Cell Signalling Unit, Institute of Cancer Research, London, United Kingdom (Sinclair, Jorgensen) Division of Cancer Biology, Cancer Research U.K. Tumour Cell Signalling Unit, Institute of Cancer Research, London, United Kingdom (Schoof, Linding) Department of Systems Biology, Centre for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Lyngby, Denmark (Chang, Erler) Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaloes Vej 5, Copenhagen 2200, Denmark (Djidja) Novartis Pharma, Biologics Process Research and Development - Analytical Development, Klybeckstrasse 141, CH-4057 Basel, Switzerland (Schmich) ETH Zurich, D-BSSE, Computational Biology Group (CBG), Mattenstrasse 26, CH-4058 Basel, Switzerland (Mrsnik) European Organization for Research and Treatment of Cancer (EORTC), Avenue Mounier, 83/11, 1200 Brussels, Belgium
Date Deposited: 13 Oct 2015 13:12
Last Modified: 13 Oct 2015 13:12
URI: https://oak.novartis.com/id/eprint/22660

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