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Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity
Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliv...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7026647/ https://www.ncbi.nlm.nih.gov/pubmed/31853536 http://dx.doi.org/10.1093/nar/gkz1151 |
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author | Voith von Voithenberg, Lena Fomitcheva Khartchenko, Anna Huber, Deborah Schraml, Peter Kaigala, Govind V |
author_facet | Voith von Voithenberg, Lena Fomitcheva Khartchenko, Anna Huber, Deborah Schraml, Peter Kaigala, Govind V |
author_sort | Voith von Voithenberg, Lena |
collection | PubMed |
description | Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. This spatial multiplexing method can be combined with ISH-approaches based on signal amplification, with bright field detection and with the commonly used format of formalin-fixed paraffin-embedded tissue sections. By using this method, we analyzed the expression of HER2 with internal positive and negative controls (ActB, dapB) as well as predictive biomarker panels (ER, PgR, HER2) in a spatially multiplexed manner on single mammary carcinoma sections. We further demonstrated the applicability of the technique for subtype differentiation in breast cancer. Local analysis of HER2 revealed medium to high spatial heterogeneity of gene expression (Cohen effect size r = 0.4) in equivocally tested tumor tissues. Thereby, we exemplify the importance of using such a complementary approach for the analysis of spatial heterogeneity, in particular for equivocally tested tumor samples. As the method is compatible with a range of ISH approaches and tissue samples, it has the potential to find broad applicability in the context of molecular analysis of human diseases. |
format | Online Article Text |
id | pubmed-7026647 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-70266472020-02-25 Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity Voith von Voithenberg, Lena Fomitcheva Khartchenko, Anna Huber, Deborah Schraml, Peter Kaigala, Govind V Nucleic Acids Res Methods Online Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. This spatial multiplexing method can be combined with ISH-approaches based on signal amplification, with bright field detection and with the commonly used format of formalin-fixed paraffin-embedded tissue sections. By using this method, we analyzed the expression of HER2 with internal positive and negative controls (ActB, dapB) as well as predictive biomarker panels (ER, PgR, HER2) in a spatially multiplexed manner on single mammary carcinoma sections. We further demonstrated the applicability of the technique for subtype differentiation in breast cancer. Local analysis of HER2 revealed medium to high spatial heterogeneity of gene expression (Cohen effect size r = 0.4) in equivocally tested tumor tissues. Thereby, we exemplify the importance of using such a complementary approach for the analysis of spatial heterogeneity, in particular for equivocally tested tumor samples. As the method is compatible with a range of ISH approaches and tissue samples, it has the potential to find broad applicability in the context of molecular analysis of human diseases. Oxford University Press 2020-02-20 2019-12-19 /pmc/articles/PMC7026647/ /pubmed/31853536 http://dx.doi.org/10.1093/nar/gkz1151 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Methods Online Voith von Voithenberg, Lena Fomitcheva Khartchenko, Anna Huber, Deborah Schraml, Peter Kaigala, Govind V Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity |
title | Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity |
title_full | Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity |
title_fullStr | Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity |
title_full_unstemmed | Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity |
title_short | Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity |
title_sort | spatially multiplexed rna in situ hybridization to reveal tumor heterogeneity |
topic | Methods Online |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7026647/ https://www.ncbi.nlm.nih.gov/pubmed/31853536 http://dx.doi.org/10.1093/nar/gkz1151 |
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