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Gene expression profiling in single cells within tissue

Nature Methods volume 2, pages 663–665 (2005)Cite this article

Abstract

We developed a robust multiplex fluorescent in situ hybridization (FISH) technique in archival formalin-fixed, paraffin-embedded (FFPE) human tissue sections while preserving the microanatomical context. This identifies single-cell gene expression patterns by probing multiple, unique nascent RNA transcripts and yields predictive quantitative gene expression signatures.

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Figure 1: Detection of nascent RNA (transcription sites) in paraffin-embedded tissue.
Figure 2: Correlation of single-cell multigene expression profiles with diagnostic pathology.
Figure 3: A combinatorial analysis of five genes provides a gene expression signature for each state.

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Acknowledgements

This work was supported in part by US National Institutes of Health CA-R33-083208 and by Aureon Laboratories.

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Authors and Affiliations

  1. Aureon Laboratories, 28 Wells Avenue, Yonkers, 10701, New York, USA

    Paola Capodieci, Michael Donovan, Heidi Buchinsky, Yusuf Jeffers & Jon Edelson

  2. Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, 10021, New York, USA

    Carlos Cordon-Cardo & William Gerald

  3. Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, 10461, New York, USA

    Shailesh M Shenoy & Robert H Singer

Authors
  1. Paola Capodieci
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  2. Michael Donovan
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  3. Heidi Buchinsky
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  4. Yusuf Jeffers
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  5. Carlos Cordon-Cardo
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  6. William Gerald
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  7. Jon Edelson
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  8. Shailesh M Shenoy
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  9. Robert H Singer
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Corresponding authors

Correspondence to Paola Capodieci or Robert H Singer.

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Competing interests

R.H.S. and C.C.-C. are scientific cofounders of Aureon Laboratories.

Supplementary information

Supplementary Table 1

Sequences used to generate probes. (PDF 46 kb)

Supplementary Table 2

Mean Number of Transcription Sites (with Standard Error of the Mean) per 100 Cells for each Diagnosis. (PDF 47 kb)

Supplementary Table 3

Diagnostic importance of gene expression profiling. (PDF 52 kb)

Supplementary Methods (PDF 84 kb)

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Capodieci, P., Donovan, M., Buchinsky, H. et al. Gene expression profiling in single cells within tissue. Nat Methods 2, 663–665 (2005). https://doi.org/10.1038/nmeth786

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