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A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens

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Abstract

We present a novel approach for microarray analysis of RNA derived from microdissected cells of routinely formalin-fixed and paraffin-embedded (FFPE) cancer resection specimens. Subsequent to RNA sample preparation and hybridization to standard GeneChips (Affymetrix), RNA samples yielded 36.43 ± 9.60% (FFPE), 49.90 ± 4.43% (fresh-frozen), and 53.9% (cell line) present calls. Quality control parameters and Q-RT-PCR validation demonstrated reliability of results. Microarray datasets of FFPE samples were informative and comparable to those of fresh-frozen samples. A systematic measurement difference of differentially processed tissues was eliminated by a correction step for comparative unsupervised data analysis of fresh-frozen and FFPE samples. Within FFPE samples, unsupervised clustering analyses clearly distinguished between normal and malignant tissues as well as to further separate tumor samples according to histological World Health Organization (WHO) subtypes. In summary, our approach represents a major step towards integration of microarrays into retrospective studies and enables further investigation of the relevance of microarray analysis for clinico-pathological diagnostics.

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Acknowledgements

The study would not have been possible without the long-term substantial research support to SL and MW by the Mushett Family Foundation, Chester, NJ, USA. The study has been funded in parts (in vitro experiments) by a grant to SL and MW from the German Research Foundation (DFG). SL and MW also acknowledge their collaborators Drs. Laura Tang and David Klimstra at the Memorial Sloan Kettering Cancer Center, New York. CK and JT acknowledge financial support by the BMBF-grant 0313921 FRIYSY.

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Authors and Affiliations

  1. Institute of Pathology, University Hospital, Albert-Ludwigs University, Breisacherstr. 115a, 79106, Freiburg, Germany

    Silke Lassmann, Anja Schoepflin & Martin Werner

  2. Center for Biosystems Analysis (ZBSA), Freiburg Center for Data Analysis and Modeling (FDM), Albert-Ludwigs University, Freiburg, Germany

    Clemens Kreutz & Jens Timmer

  3. Department of Surgery, University Hospital, Albert-Ludwigs University, Freiburg, Germany

    Ulrich Hopt

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  1. Silke Lassmann
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  2. Clemens Kreutz
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  4. Ulrich Hopt
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  6. Martin Werner
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Correspondence to Silke Lassmann.

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Lassmann, S., Kreutz, C., Schoepflin, A. et al. A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens. J Mol Med 87, 211–224 (2009). https://doi.org/10.1007/s00109-008-0419-y

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  • DOI: https://doi.org/10.1007/s00109-008-0419-y

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