Species-specific gene expression profiling of PDX tumors and humanized mice by RNAscope® ISH

Simultaneous detection of human and mouse EGFR in CRC PDX tissue, RNA in situ hybridization (ISH) using RNAscope<sup>®</sup> LS duplex assay.

Simultaneous detection of human and mouse EGFR in CRC PDX tissue, RNA in situ hybridization (ISH) using RNAscope® LS duplex assay.

Expression of human TGFB1 in LIV PDX mouse tumor sections, RNA in situ hybridization (ISH) using RNAscope<sup>®</sup> 2.5 HD Assay – Brown.

Expression of human TGFB1 in LIV PDX mouse tumor sections, RNA in situ hybridization (ISH) using RNAscope® 2.5 HD Assay – Brown.

Expression of human FGFR4 in LIV PDX mouse tumor sections, RNA in situ hybridization (ISH) using RNAscope<sup>®</sup> 2.5 HD Assay – Brown.

Expression of human FGFR4 in LIV PDX mouse tumor sections, RNA in situ hybridization (ISH) using RNAscope® 2.5 HD Assay – Brown.

Expression of human FGFR4 in LIV PDX tissue, RNA in situ hybridization (ISH) using RNAscope<sup>®</sup> 2.5 HD Assay – Brown

Expression of human FGFR4 in LIV PDX tissue, RNA in situ hybridization (ISH) using RNAscope® 2.5 HD Assay – Brown

Patient-derived xenograft (PDX) tumor models contain human tumor cells growing in a mouse stromal environment. PDX mice not only carry human tumors with their original genotype, but also build up the murine tumor stroma to support tumor cell growth and metastasis. For these reasons PDX mice are widely used animal models for cancer research and drug discovery. Therefore, it is critical to accurately identify and quantify human- and mouse-derived gene transcripts in PDX mice, as well as humanized mice. The RNAscope® assay can be applied to discern human and mouse gene expression in PDX tumor models:

  • Develop species-specific probes for known cancer biomarkers
  • Evaluate human tumor and mouse stromal gene expression profiles in PDX models
  • Simultaneously detect human- and mouse-specific targets in PDX tumors with morphological context
  • Quickly screen of a large number of samples in a single TMA slide
  • The RNAscope® technology can also be applied to characterize humanized mouse models

Current detection methods for species-specific genes in PDX mice often have limited specificity and sensitivity or lack spatial and morphological resolution. Multiple gene profiling methods such as microarray and RNAseq have been applied to investigate human and murine gene expression in humanized mice and PDX tumor models. While these assays may identify the species of origin for the PDX transcriptome, it is difficult to reconstruct the spatial distribution and heterogeneity of the transcripts of interest. Immunohistochemistry (IHC) analysis can provide morphological insights, however, the availability of antibodies as well as the unknown specificity and sensitivity of IHC antibodies hinder accurate interpretation of biomarker localization in the tumor microenvironment. Therefore, there is a strong need to establish an accurate, specific and widely accepted in situ method to identify species-specific RNAs in humanized mice and PDX tumor models. 

The RNAscope® assay is an innovative RNA in situ hybridization (ISH) method that provides single cell gene expression resolution with spatial and morphological context by detecting mRNA and long non-coding RNAs in fresh frozen, fresh fixed or formalin-fixed paraffin-embedded tissues. The signal amplification method and double Z probe design provide high sensitivity and specificity, resulting in a high signal-to-noise ratio in many tissues. This allows for visualization of target RNA as a single dot, where each dot is an individual RNA molecule. 

Application note

In our application note "Species-specific gene expression profiling of patient-derived xenograft tumors by the RNAscope® in situ hybridization assay" we used the RNAscope® technology to visualize gene expression in the human tumor and mouse stroma of two types of PDX mouse models with specially-designed species-specific probes, allowing for the specific detection and visualization of human- and mouse-specific gene targets with morphological context in the same FFPE sample.

Species-specific gene expression profiling of patient-derived xenograft tumors by the RNAscope® in situ hybridization assay

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