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Protein Microarrays pp 109–122Cite as

Use of Formalin-Fixed and Paraffin-Embedded Tissues for Diagnosis and Therapy in Routine Clinical Settings

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 785))

Abstract

Formalin-fixed and paraffin-embedded (FFPE) tissues are used routinely everyday in hospitals world-wide for histopathological diagnosis of diseases like cancer. Due to formalin-induced cross-linking of proteins, FFPE tissues present a particular challenge for proteomic analysis. Nevertheless, there has been recent progress for extraction-based protein analysis in these tissues. Novel tools developed in the last few years are urgently needed because precise protein biomarker quantification in clinical FFPE tissues will be crucial for treatment decisions and to assess success or failure of current and future personalized molecular therapies. Furthermore, they will help to conceive why only a subset of patients responds to individualized treatments. Reverse phase protein array (RPPA) is a very promising new technology for quick and simultaneous analysis of many patient samples allowing relative and absolute protein quantifications. In this chapter, we show how protein extraction from FFPE tissues might facilitate the implementation of RPPA for therapy decisions and discuss challenges for application of RPPA in clinical trials and routine settings.

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Abbreviations

DTT:

Dithiothreitol

EGFR:

Epidermal growth factor receptor

ELISA:

Enzyme-linked immunosorbent assay

ERK:

Extracellular signal-regulated kinase

FFPE:

Formalin-fixed and paraffin-embedded

FISH:

Fluorescence in situ hybridisation

H&E:

Hematoxylin and Eosin

HER2/neu/ErbB2:

Human epidermal growth factor receptor 2

IHC:

Immunohistochemistry

MAPK:

Mitogen-activated protein kinase

PAI1:

Plasminogen activator inhibitor 1

RPPA:

Reverse phase protein array

SDS-PAGE:

sodium dodecyl sulfate polyacrylamide gel electrophoresis

uPA:

Urokinase-type plasminogen activator

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Acknowledgments

This study is supported by the German Federal Ministry for Education and Research (BMBF), grant no 01GR0805 to Karl-Friedrich Becker. The authors wish to thank Kai Tran, Kerstin Schragner, and Christa Schott for excellent technical assistance.

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Authors and Affiliations

  1. Institut für Pathologie, Technische Universität München, Munich, Germany

    Daniela Berg, Katharina Malinowsky, Bilge Reischauer, Claudia Wolff & Karl-Friedrich Becker

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  1. Daniela Berg
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  2. Katharina Malinowsky
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  3. Bilge Reischauer
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  4. Claudia Wolff
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  5. Karl-Friedrich Becker
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Correspondence to Karl-Friedrich Becker .

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Editors and Affiliations

  1. (DKFZ), Division of Molecular Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, Heidelberg, 69120, Germany

    Ulrike Korf

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Berg, D., Malinowsky, K., Reischauer, B., Wolff, C., Becker, KF. (2011). Use of Formalin-Fixed and Paraffin-Embedded Tissues for Diagnosis and Therapy in Routine Clinical Settings. In: Korf, U. (eds) Protein Microarrays. Methods in Molecular Biology, vol 785. Humana Press. https://doi.org/10.1007/978-1-61779-286-1_8

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  • DOI: https://doi.org/10.1007/978-1-61779-286-1_8

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  • Print ISBN: 978-1-61779-285-4

  • Online ISBN: 978-1-61779-286-1

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