Analysis of Glioma Cell Platinum Response by Metacomparison of Two-dimensional Chromatographic Proteome Profiles

Christine Billecke,Imran Malik,Ashley Movsisyan,Syed Sulghani,Azita Sharif,Tom Mikkelsen,Nicholas P Farrell,Oliver Bögler

doi:10.1074/mcp.m500124-mcp200

Abstract

Successful clinical development of cancer treatments is aided by the development of molecular markers that allow the identification of patients likely to respond. In the case of broadly cytotoxic drugs, such as the multinuclear series of platinum chemotherapeutic agents that we are evaluating for the treatment of glioma, one route to marker identification is proteomic profiling. We are using the two-dimensional chromatography system, the ProteomeLab PF2D, to compare proteomic profiles of glioma cells in culture before and after drug treatment. The existing software tools allowed the rapid identification of peaks increased by treatment of a given drug as compared with control untreated cells. To compare across these pairs, we developed new software, called the MetaComparison Tool (MCT). The MCT uses the chromatographic characteristics of peaks as identifiers, an approach that was validated by mass spectrometry of two independent isolations of a peak, from cells that were treated with two different platinum compounds. The MCT made it possible to rapidly query whether a given peak responded to more than one treatment and so allowed the identification of peaks that were specific to a given drug. As a result, this analysis greatly reduced the list of peaks whose isolation and downstream analysis by mass spectrometry is warranted, accelerating the search for protein markers of response.

Highlights

Successful clinical development of cancer treatments is aided by the development of molecular markers that allow the identification of patients likely to respond
We show that proteome displays generated by two-dimensional liquid chromatography can be compared using new computer software, the MetaComparison Tool (MCT),[1] and that this approach can rapidly lead to the identification of peaks worth further analysis as proteins whose expression is responsive to drug treatment
The proteomic profiling platform chosen for this work is the ProteomeLab PF2D (Beckman Coulter, Inc., Fullerton, CA), which is based on recent advances in technology using chromatographic separation of proteins in liquid phase, from the work of Dr David Lubman and colleagues (12, 13)

Summary

Introduction

Successful clinical development of cancer treatments is aided by the development of molecular markers that allow the identification of patients likely to respond. We show that proteome displays generated by two-dimensional liquid chromatography can be compared using new computer software, the MetaComparison Tool (MCT),[1] and that this approach can rapidly lead to the identification of peaks worth further analysis as proteins whose expression is responsive to drug treatment.

Results

Conclusion