RNAscope® ISH

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RNAscope® ISH Technology - an Advanced Platform for in situ RNA Detection

Interpace Pharma Solutions recognizes the significant need for improved assay technology to evaluate target gene expression in tissues, particularly for preclinical studies. Unfortunately, most in situ RNA detection techniques lack the robustness and sensitivity to reliably detect expression of many target genes in a variety of species and tissue types.

RNAscope® in situ hybridization (ISH) is an Interpace Pharma Solutions offering that can visualize, localize, and quantify gene expression within a single assay, to help advance RNA biomarker analysis for gene and cell-based therapies.

Melissa Sanchez

Melissa Sanchez

Technical Lead

“RNAscope is an excellent addition to our extensive immuno-oncology assay portfolio and helps to unlock the full potential of RNA biomarkers.

RNAscope technology can predict target organ toxicity in preclinical models, confirm correct target site and on-target activity, and allow the ability to rapidly screen target nominees—across virtually any gene, species, tissue, and laboratory workflow.”

Learn More About RNAscope Technology

Widely used immunohistochemistry (IHC) techniques rely on the availability of antibodies which can be expensive and time-consuming to develop. In some cases, it may not be feasible to develop reliable antibodies.

Techniques including microarrays and PCR provide useful molecular profiles, but clinically relevant cell and tissue context information is often lost along with the spatial variation of gene expression patterns. RNAscope ISH benefits

RNAscope is a novel RNA ISH technology with a unique probe design strategy that allows simultaneous signal amplification and background suppression to achieve single-molecule visualization while preserving tissue morphology. The technology enables RNA target expression analysis within intact cells and tissues with high sensitivity and specificity.

Based on a proprietary double Z probe design, RNAscope ISH enables the detection of almost any RNA biomarker with single-molecule sensitivity and high specificity in tissues. It provides a universal solution to characterize tissue distribution of drug targets and biomarkers in a highly specific, sensitive manner.

RNAscope Helps Unlock the full potential of RNA Biomarkers

  • Double-Z probe design provides superior background control
  • Unique hybridization-based signal amplification system yields high signal:noise ratio
  • Single-RNA-molecule detection—possible even in partially degraded samples
RNAscope technology

Hybridization requires Double Z binding – providing simultaneous signal amplification and background noise control

The RNAscope approach to ISH allows multiplex detection for up to four target genes and up to 12 RNA targets per slide when using the HiPlex workflow.

The ability to analyze gene expression in situ, compounded with the high sensitivity and specificity, make RNAscope a preferred platform for translating RNA biomarkers into clinical use.

The unique “double Z” probes simultaneously provide signal amplification and background noise control, resulting in high sensitivity and specificity. Single-molecule visualization of the assay yields quantitative RNA and cell-specific expression within intact tissue architecture.

rnascope ish applications

RNAscope ISH can streamline immune checkpoint target identification; visualize in vivo delivery of CAR-T therapeutic products; and differentiate therapeutic gene sequence from endogenous transcripts selection, even when there is no known or validated antibody. RNAscope unlocks the full potential of RNA biomarkers and is an excellent addition to Interpace’s extensive immuno-oncology assay portfolio.

RNAscope technology can help predict target organ toxicity in preclinical models, confirm correct target sites and on-target activity, and allows the ability to rapidly screen target nominees.

Interpace combines RNAscope with other technologies to provide an unparalleled level of service for our clients and is proud to be a provider of RNAscope technology.
Learn How Our RNAscope Services Can Boost Your Development Program

At Interpace Pharma Solutions, we use RNAscope to support our clients with:

  • Pre-clinical assessment of efficacy and toxicity
  • Region of Interest selection for spatial profiling
  • Visualizing the expression of target(s) across multiple tissues
  • Validating mechanisms of action of novel targets within disease models in tissue samples
  • Assessing tumor heterogeneity and the tumor micro-environment
  • Studying targets where there is limited availability of reliable antibodies

RNAscope is a tool for biomarker and companion diagnostic identification. By detecting biomarker targets in situ, our clients can combine molecular information with histopathology for easier disease classification.

Examples of RNAscope Use

Streamline target identification and selection

  • Distinguish between neoplastic and normal cells that may also be expressing the same antigen
  • Quantitatively measure RNA expression in situ with high sensitivity

EXAMPLE USE: Region of interest (ROI) selection in spatial profiling

Visualize in vivo delivery of therapeutic gene expression and vector sequences (viral or non-viral) to identify:

  • Specific tissue and/or cell type
  • Subcellular localization

EXAMPLE USE: Confirm trafficking of CAR-T therapy to correct target site and on-target activity

Overcome the limitations of IHC

  • Unique “double Z” probe design and signal amplification methodology provides superior background control
  • Custom RNA probes can be designed and validated in a fraction of the time required for antibodies

EXAMPLE USE: Application when antibodies are unavailable, or antibody performance is not ideal

Talk With Us About Your RNAscope Use Case and Learn How We Can Help!

RNAscope Technology Features

Unlock the full potential of RNA biomarkers. RNAscope® ISH Provides High Sensitivity and Specificity

  • Unique hybridization-based signal amplification system yields high signal:noise ratio
  • Single-RNA-molecule detection—possible even in partially degraded samples

Quantitative RNA Expression

  • Single-molecule visualization allows quantification of RNA expression levels for each single cell across heterogeneous cell populations

Morphological Context

  • Cell-specific expression information within intact tissue architecture

Universal Application

  • Virtually any gene, species, and tissue can be assessed
  • Compatible with clinical sample types (FFPE, fresh or fixed-frozen tissues, PBMCs, cultured cells) and laboratory workflows


RNAscope provides the benefits of in situ analysis for RNA biomarkers and can enable rapid development of RNA ISH-based molecular diagnostic assays.

Biomarkers based on DNA, RNA, and proteins are used for cancer diagnosis, prognosis, and therapy guidance, boosting the emergence of personalized medicine. RNA biomarkers or gene expression signatures have emerged as a major class of cancer biomarkers, thanks to widespread use of genome-wide gene expression profiling technologies.

Existing RNA extraction processes destroy the tissue context of gene expression measurements, making it impossible to map the observed signals to individual cells. Single-molecule visualization in individual cells is achieved through RNAscope’s novel probe design strategy and a hybridization-based signal amplification.

Catalog and Made-to-Order Probes

Interpace Pharma Solutions provides access to a library of double "Z" oligo probes designed to hybridize to your specific RNA target of interest. We have availability of over 13,000 RNA targets in over 140 species including human, mouse, rat, dog, cow, zebrafish, rabbit, pig, chicken, monkeys and over 100 viruses.

Our experts will work with you to design in situ hybridization RNA probes for virtually ANY gene in ANY genome for visualization in ANY tissue or Cell

RNAscope ISH is one of the SpatialPlex™ services provided by Interpace Pharma Solutions

SpatialPlex services can:

  • Aid target molecule discovery via ADME studies, Phase I/II trials, and Companion Diagnostic development
  • Quantify RNA and protein expression within context of the tissue
  • Reserve precious tissue for use in other assays
  • Generate, integrate and interpret high-dimensional data from preclinical models or patient samples
  • Detect protein and RNA targets within a dynamic range significantly greater than traditional IHC
  • Explore banked samples with multiplexing platforms to retrospectively analyze clinical studies

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