Cell Therapy

CAR-T and TCR-T cell, as well as NK cell and macrophage therapies are being developed for treatment of solid tumor. RNAscope in situ hybridization is the only method that enables specific detection of these viral vector-based cell therapies in intact human tumor biopsies. Techniques such as immunohistochemistry (IHC) are unable to differentiate therapeutic cells from endogenous untransduced cells. However, by using RNAscope probes that target the viral untranslated regions (UTRs) present in all CAR and TCR mRNAs, engineered therapeutic cells can be specifically detected and quantified in the tumor microenvironment (TME). RNAscope UTR probes can be combined easily with other probes to assess activation state, e.g., IFNG and GZMB, as well as with immunohistochemical (IHC) and immunofluorescent (IF) detection of CD3, CD4, CD8-positive T cells. These assays are used to monitor cell therapies in post-treatment patient biopsies and in preclinical animal models for safety and efficacy.


Key features of the RNAscope assay for cell therapy applications:

  • Measure target gene expression across all normal tissues in animal models and human samples with limits of detection below IHC
  • Visualize and quantify CAR/TCR T cell infiltration and activation in tumor and off-tumor tissues
  • Simultaneously detect CAR/TCR vector and cytokines, T cell markers, or other cell-type markers


Fig. 1 CAR and TCR cell therapy probes consisting of pooled (“ZZ”) oligos targeting viral untranslated regions (UTRs) of CAR and TCR mRNA


Fig. 2 RNAscope assay of CAR-T and TCR-T cells. (Left) ROR1-targeted CAR-T cells infiltration and activation in ROR1-positive mouse lung and liver. RNAscope CAR 3’UTR probe and GZMB probe detect activated CAR+ T cell; Mm-Ror1 probe signal in mouse liver and lung. (Middle) BCMA-targeted CAR-T cell infiltration and activation in BCMA-positive xenograft tumor. RNAscope CAR 3’UTR and IFNG probe with CD3 immunofluorescence. (Right) NY-ESO-1 TCR-T cells infiltrating and recruiting CD3-positive T cells in post-treatment liposarcoma patient biopsy. RNAscope Duplex assay with TCR UTR (red) and CD3E (green) probes



Catalog Probes (Ex: WPRE, UTR, IFNG, etc.)

Search Catalog Control & Target Probes

If your gene of interest in not listed in our catalog, ACD can design and manufacture new in situ hybridization probes for you, To order or get more info on Made-to-Order New Targets Probes, please fill in the form below and an ACD Account Executive will contact you.

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Professional Assay Services

  • Unparalleled expertise in RNAscope and BaseScope ISH
  • High capacity and high throughput, delivering more than 10,000 slides per year
  • Supporting dozens of cell and gene therapy companies for research studies enabling pre-IND submission
  • Team of specialists perform quantitative image analysis using HALO® Software (Indica Labs)
  • Board-certified pathologist review
  • Actionable results delivered in weeks rather than months
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Recorded Webinar

RNAscope in situ Assays of Cell Therapy in Solid Tumors, Tumor Infiltration and Activation

Chimeric antigen receptor T (CAR-T) cells are promising treatments for hematologic and solid malignancies. CAR-T cells can recognize and eliminate neoplastic cells expressing specific protein antigens. However, the current generation of CAR-T cells cannot distinguish between neoplastic and normal cells that may also be expressing the same antigen, thus potentially resulting in “on-target/off-tumor” toxicity. In this GEN webinar, we will review the RNAscope in situ hybridization (ISH) method and show applications of the technology in the CAR-T cell and immuno-oncology fields. We will demonstrate how RNAscope ISH can be utilized to identify novel CAR-T cell targets and subsequently qualify monoclonal antibodies directed against those targets for immunohistochemistry. We will show how ISH can be used to predict CAR-T cell target organ toxicity in preclinical models. Finally, we will discuss optimal preparation of tissues, cell pellets, and cytospin slides for evaluation by ISH. You Will Learn - How RNAscope ISH technology can streamline your target identification and selection workflows - The advantages of using ISH for immunotherapeutic target cell selection - How ISH evaluation of target expression in normal tissues can be used to predict CAR-T cell induced toxicity - Optimal tissue, cell pellet, and cytospin slide preparation for RNAscope ISH

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Application Note

Application note "Preclinical CAR-T cell target safety, biodistribution, and tumor infiltration analysis using the RNAscope ISH assay'

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Flyer "T-Cell Therapy and Trafficking and Activation Analysis Using RNAscope in situ Hybridization"

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Advanced Cell Diagnostics

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