Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity

Abstract 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...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research 2020-02, Vol.48 (3), p.e17-e17
Main Authors: Voith von Voithenberg, Lena, Fomitcheva Khartchenko, Anna, Huber, Deborah, Schraml, Peter, Kaigala, Govind V
Format: Article
Language:English
Subjects:
Biomarkers, Tumor - analysis
Biomarkers, Tumor - genetics
Breast Neoplasms - chemistry
Breast Neoplasms - classification
Cell Line
Female
Humans
In Situ Hybridization - methods
Lab-On-A-Chip Devices
Methods Online
Microfluidic Analytical Techniques - methods
Receptor, ErbB-2 - genetics
Receptor, ErbB-2 - metabolism
RNA, Neoplasm - analysis
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract 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.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkz1151