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Anal Biochem. 2018 Apr 15;547:77-83. doi: 10.1016/j.ab.2018.02.001. Epub 2018 Feb 22.

A strategy to analyse activity-based profiling of tyrosine kinase substrates in OCT-embedded lung cancer tissue.

Author information

1
Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland. Electronic address: stephan.arni@usz.ch.
2
PamGene International B.V., 's-Hertogenbosch, The Netherlands.
3
Department of Physiology, Biophysics and Neuroscience, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico.
4
Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland; Center for Public Health Initiatives, University of Pennsylvania, Philadelphia, USA.
5
Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland.

Abstract

The use of optimal cutting temperature (OCT) medium has served to improve the long-term preservation of surgical tissue specimens. Unfortunately, the presence of polymers in OCT has been found to generate signal interference in proteomic-based techniques. Indeed the presence of OCT medium in tissue lysates precludes the analysis of activity based proteomic profiles obtained from lung adenocarcinoma (LuAdCa) resection specimens. In order to probe this question further tissue lysates were prepared from 47 lung non-neoplastic and tumour, node, metastasis (TNM) stage 1 LuAdCa resection specimens embedded with or without OCT, and data of activity based multiplex profiles of protein tyrosine kinase peptide substrates were obtained. We found that changes in overall phosphorylation level coincided with the use of OCT and subsequently developed an OCT per peptide median correcting strategy by performing median centering on the values of each peptide. Application of this post-analytical strategy not only can identify changes in kinase activity but can also assist in identifying novel targets for therapeutic intervention against LuAdCa.

KEYWORDS:

Lung adenocarcinoma; Methodology for proteomics; Optimal cutting temperature medium; Protein activity microarrays; Protein tyrosine kinase

PMID:
29408474
DOI:
10.1016/j.ab.2018.02.001

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