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Automated analysis of protein expression and gene amplification within the same cells of paraffin-embedded tumour tissue

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Cellular Oncology Aims and scope Submit manuscript

An Erratum to this article was published on 20 August 2011

Abstract

Background

The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC) and Fluorescence in situ Hybridization (FISH) negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell.

Methods

Paraffin-embedded tissue sections of colorectal cancers were stained for CD133 expression. IHC images were acquired and image coordinates recorded. Slides were subsequently hybridized with fluorescently labeled DNA probes. FISH images were taken at the previously recorded positions allowing for direct comparison of protein expression and gene copy number signals within the same cells/tissue areas. Relocation, acquisition of the IHC and FISH images, and enumeration of FISH signals in the immunophenotyped tumour areas were done in an automated fashion.

Results

Automated FISH analysis was performed on 13 different colon cancer samples that had been stained for CD133; each sample was scored for MYC, ZNF217 and Chromosome 6 in CD133 positive and negative glands. From the 13 cases four (31%) showed amplification for the MYC oncogene and seven of 13 (54%) cases were amplified for ZNF217. There was no significant difference between CD133 positive tumour and CD133 negative tumour cells.

Conclusion

The technique and algorithm presented here enables an easy and reproducible combination of IHC and FISH based on a novel automated algorithm using relocation and automated spot counting.

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Acknowledgments

The classifiers for this algorithm are available from Metasystems Group Inc. at support@metasystems.org.

The authors thank Buddy Chen for preparing figures and IT related support.

Timo Gaiser is supported by a fellowship within the post doctorate program of the Mildred Scheel Foundation. The study was supported by the Intramural Research Program by the NIH, National Cancer Institute.

Conflict of interest

Aparajita Dutta is employed as Client Services Manager and Application Scientist with MetaSystems Company. All others authors declare no conflict of interest. No conflict exists for materials or devices used in this study.

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Authors and Affiliations

  1. Section of Cancer Genomics, National Cancer Institute, National Institutes of Health, Building 50, Room 1408, 50 South Drive, Bethesda, MD, 20892, USA

    Timo Gaiser, Lissa Berroa-Garcia, Thomas Ried & Kerstin Heselmeyer-Haddad

  2. Institute for Pathology, Paracelsus Medical University, 5020, Salzburg, Austria

    Ralf Kemmerling

  3. MetaSystems, 300 Bear Hill Rd, Waltham, MA, 02451, USA

    Aparajita Dutta

Authors
  1. Timo Gaiser
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  2. Lissa Berroa-Garcia
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  3. Ralf Kemmerling
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  4. Aparajita Dutta
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  5. Thomas Ried
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  6. Kerstin Heselmeyer-Haddad
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Corresponding author

Correspondence to Thomas Ried.

Additional information

This is a reprint from ‘Automated analysis of protein expression and gene amplification within the same cells of paraffin-embedded tumour tissue, Timo Gaiser, Lissa Berroa-Garcia, Ralf Kemmerling, Aparajita Dutta, Thomas Ried, Kerstin Heselmeyer-Haddad’ originally published in Analytical Cellular Pathology/Cellular Oncology, Volume 33, number 2, 2010, pp. 105–112, IOS Press.

An erratum to this article can be found at http://dx.doi.org/10.1007/s13402-011-0057-1

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Gaiser, T., Berroa-Garcia, L., Kemmerling, R. et al. Automated analysis of protein expression and gene amplification within the same cells of paraffin-embedded tumour tissue. Cell Oncol. 34, 337–342 (2011). https://doi.org/10.1007/s13402-011-0032-x

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