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Biomarkers such as DNA, RNA, and protein are powerful tools in clinical diagnostics and therapeutic development for many diseases. Identifying RNA expression at the single cell level within the morphological context by RNA in situ hybridization provides a great deal of information on gene expression changes over conventional techniques that analyze bulk tissue, yet widespread use of this technique in the clinical setting has been hampered by the dearth of automated RNA ISH assays. Here we present an automated version of the RNA ISH technology RNAscope that is adaptable to multiple automation platforms. The automated RNAscope assay yields a high signal-to-noise ratio with little to no background staining and results comparable to the manual assay. In addition, the automated duplex RNAscope assay was able to detect two biomarkers simultaneously. Lastly, assay consistency and reproducibility were confirmed by quantification of TATA-box binding protein (TBP) mRNA signals across multiple lots and multiple experiments. Taken together, the data presented in this study demonstrate that the automated RNAscope technology is a high performance RNA ISH assay with broad applicability in biomarker research and diagnostic assay development. J. Cell. Biochem. 117: 2201-2208, 2016. © 2016 Wiley Periodicals, Inc.
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http://dx.doi.org/10.1002/jcb.25606 | DOI Listing |
Front Vet Sci
August 2025
Unitat mixta d'investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain.
Introduction: Detection of porcine circovirus 2 (PCV2) in lymphoid tissues is essential for diagnostic and research purposes. hybridisation (ISH) enables the localisation of viral genomes in tissue sections but is traditionally assessed visually, which may introduce subjectivity.
Methods: This study developed an automated pixel classifier to quantify the PCV2 genome using RNAscope ISH technology.
STAR Protoc
June 2025
Research Laboratory Section, Offices of Health Science Research, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand. Electronic address:
Here, we present a protocol for quantifying the expression of genes detected by fluorescence insitu hybridization at single-cell spatial resolution using an imaging analysis pipeline developed based on CellProfiler software. We describe steps for comparing gene expression between cancer samples with and without metastasis. We detail procedures for detecting target transcripts using RNAscope multiplex fluorescent assays and visualization using Vectra Polaris Automated Quantitative Pathology Imaging.
View Article and Find Full Text PDFGenome Biol
June 2025
Division of Chromatin Networks, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Background: Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid development of spatial transcriptomics methods, each with unique characteristics, makes it challenging to select the most suitable technology for specific research objectives. Here, we compare four imaging-based approaches-RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium-alongside Visium, a sequencing-based method.
View Article and Find Full Text PDFJ Imaging Inform Med
June 2025
Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.
RNAscope staining of breast cancer tissue allows pathologists to deduce genetic characteristics of the cancer by inspection at the microscopic level, which can lead to better diagnosis and treatment. Chromogenic RNAscope staining is easy to fit into existing pathology workflows, but manually analyzing the resulting tissue samples is time consuming. There is also a lack of peer-reviewed, performant solutions for automated analysis of chromogenic RNAscope staining.
View Article and Find Full Text PDFJ Mol Diagn
October 2024
Department of Medical Sciences, University of Trieste, Trieste, Italy. Electronic address:
Gene expression analysis is pivotal in cancer research and clinical practice. Although traditional methods lack spatial context, RNA in situ hybridization (RNA-ISH) is a powerful technique that retains spatial tissue information. Here, RNAscope score, RT-droplet digital PCR, and automated QuantISH and QuPath were used for quantifying RNA-ISH expression values from formalin-fixed, paraffin-embedded samples.
View Article and Find Full Text PDF