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Ariotta V, Azzalini E, Canzonieri V, Hautaniemi S, Bonin S. Comparative Analysis of Gene Expression Analysis Methods for RNA in Situ Hybridization Images. J Mol Diagn 2024; 26:931-942. [PMID: 39068989 DOI: 10.1016/j.jmoldx.2024.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/27/2024] [Accepted: 06/26/2024] [Indexed: 07/30/2024] Open
Abstract
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. The methods were compared using high-grade serous ovarian carcinoma samples, focusing on CCNE1, WFDC2, and PPIB genes. The findings demonstrate good concordance between automated methods and RNAscope, with RT-droplet digital PCR showing less concordance. Additionally, QuantISH exhibits robust performance, even for low-expressed genes like CCNE1, showcasing its modular design and enhancing accessibility as a viable alternative for gene expression analysis.
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Affiliation(s)
- Valeria Ariotta
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eros Azzalini
- Department of Medical Sciences, University of Trieste, Trieste, Italy
| | - Vincenzo Canzonieri
- Department of Medical Sciences, University of Trieste, Trieste, Italy; Pathology Unit, Centro di Riferimento Oncologico IRCCS, Aviano-National Cancer Institute, Pordenone, Italy
| | - Sampsa Hautaniemi
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Serena Bonin
- Department of Medical Sciences, University of Trieste, Trieste, Italy.
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Spencer-Dene B, Mukherjee P, Alex A, Bera K, Tseng WJ, Shi J, Chaney EJ, Spillman DR, Marjanovic M, Miranda E, Boppart SA, Hood SR. Localization of unlabeled bepirovirsen antisense oligonucleotide in murine tissues using in situ hybridization and CARS imaging. RNA (NEW YORK, N.Y.) 2023; 29:1575-1590. [PMID: 37460153 PMCID: PMC10578491 DOI: 10.1261/rna.079699.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/29/2023] [Indexed: 09/20/2023]
Abstract
Current methods for detecting unlabeled antisense oligonucleotide (ASO) drugs rely on immunohistochemistry (IHC) and/or conjugated molecules, which lack sufficient sensitivity, specificity, and resolution to fully investigate their biodistribution. Our aim was to demonstrate the qualitative and quantitative distribution of unlabeled bepirovirsen, a clinical stage ASO, in livers and kidneys of dosed mice using novel staining and imaging technologies at subcellular resolution. ASOs were detected in formalin-fixed paraffin-embedded (FFPE) and frozen tissues using an automated chromogenic in situ hybridization (ISH) assay: miRNAscope. This was then combined with immunohistochemical detection of cell lineage markers. ASO distribution in hepatocytes versus nonparenchymal cell lineages was quantified using HALO AI image analysis. To complement this, hyperspectral coherent anti-Stokes Raman scattering (HS-CARS) imaging microscopy was used to specifically detect the unique cellular Raman spectral signatures following ASO treatment. Bepirovirsen was localized primarily in nonparenchymal liver cells and proximal renal tubules. Codetection of ASO with distinct cell lineage markers of liver and kidney populations aided target cell identity facilitating quantification. Positive liver signal was quantified using HALO AI, with 12.9% of the ASO localized to the hepatocytes and 87.1% in nonparenchymal cells. HS-CARS imaging specifically detected ASO fingerprints based on the unique vibrational signatures following unlabeled ASO treatment in a totally nonperturbative manner at subcellular resolution. Together, these novel detection and imaging modalities represent a significant increase in our ability to detect unlabeled ASOs in tissues, demonstrating improved levels of specificity and resolution. These methods help us understand their underlying mechanisms of action and ultimately improve the therapeutic potential of these important drugs for treating globally significant human diseases.
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Affiliation(s)
- Bradley Spencer-Dene
- In Vitro/In Vivo Translation, BioImaging, GSK, Stevenage SG1 2NY, United Kingdom
| | - Prabuddha Mukherjee
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Aneesh Alex
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- In Vitro/In Vivo Translation, BioImaging, GSK, Upper Providence, Pennsylvania 19426, USA
| | - Kajari Bera
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Wei-Ju Tseng
- In Vitro/In Vivo Translation, BioImaging, GSK, Upper Providence, Pennsylvania 19426, USA
| | - Jindou Shi
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Eric J Chaney
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Darold R Spillman
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Marina Marjanovic
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Elena Miranda
- In Vitro/In Vivo Translation, BioImaging, GSK, Stevenage SG1 2NY, United Kingdom
| | - Stephen A Boppart
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Steve R Hood
- In Vitro/In Vivo Translation, BioImaging, GSK, Stevenage SG1 2NY, United Kingdom
- GSK Center for Optical Molecular Imaging, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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Atout S, Shurrab S, Loveridge C. Evaluation of the Suitability of RNAscope as a Technique to Measure Gene Expression in Clinical Diagnostics: A Systematic Review. Mol Diagn Ther 2021; 26:19-37. [PMID: 34957535 PMCID: PMC8710359 DOI: 10.1007/s40291-021-00570-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2021] [Indexed: 01/01/2023]
Abstract
Objective To evaluate the application of RNAscope in the clinical diagnostic field compared to the current ‘gold standard’ methods employed for testing gene expression levels, including immunohistochemistry (IHC), quantitative real time PCR (qPCR), and quantitative reverse transcriptase PCR (qRT-PCR), and to detect genes, including DNA in situ hybridisation (DNA ISH). Methods This systematic review searched CINAHL, Medline, Embase and Web of Science databases for studies that were conducted after 2012 and that compared RNAscope with one or more of the ‘gold standard’ techniques in human samples. QUADAS-2 test was used for the evaluation of the articles’ risk of bias. The results were reviewed narratively and analysed qualitatively. Results A total of 27 articles (all retrospective studies) were obtained and reviewed. The 27 articles showed a range of low to middle risk of bias scores, as assessed by QUADAS-2 test. 26 articles studied RNAscope within cancer samples. RNAscope was compared to different techniques throughout the included studies (IHC, qPCR, qRT-PCR and DNA ISH). The results confirmed that RNAscope is a highly sensitive and specific method that has a high concordance rate (CR) with qPCR, qRT-PCR, and DNA ISH (81.8–100%). However, the CR with IHC was lower than expected (58.7–95.3%), which is mostly due to the different products that each technique measures (RNA vs. protein). Discussion This is the first systematic review to be conducted on the use of RNAscope in the clinical diagnostic field. RNAscope was found to be a reliable and robust method that could complement gold standard techniques currently used in clinical diagnostics to measure gene expression levels or for gene detection. However, there were not enough data to suggest that RNAscope could stand alone in the clinical diagnostic setting, indicating further prospective studies to validate diagnostic accuracy values, in keeping with relevant regulations, followed by cost evaluation are required. Supplementary Information The online version contains supplementary material available at 10.1007/s40291-021-00570-2.
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Affiliation(s)
- Sameeha Atout
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Room 202, Sir James Black Building, Glasgow, G128QQ, UK
| | - Shaymaa Shurrab
- Division of Biochemical Diseases, Department of Paediatrics, School of Medicine, BC Children's Hospital, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Carolyn Loveridge
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Room 202, Sir James Black Building, Glasgow, G128QQ, UK.
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Brodie C. Overcoming Autofluorescence (AF) and Tissue Variation in Image Analysis of In Situ Hybridization. Methods Mol Biol 2020; 2148:19-32. [PMID: 32394373 DOI: 10.1007/978-1-0716-0623-0_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fluorescent detection of nucleic acid sequences such as DNA or RNA allows for multiplexing and visualization of an increased number of targets compared with chromogenic methods. This is due to the number of chromogens available as well as the ability of image analysis software platforms to distinguish between colors. Autofluorescence (AF) can be problematic during fluorescent imaging because the AF interferes with the detection of the specific fluorescent signals especially when the target signals are weak. AF has a broad emission spectrum leading to difficulty when performing image analysis due to masking of the specific signal across multiple wavelengths. Tissue sample variation can also affect levels of AF. In this chapter we share a method for overcoming the issues caused by sample variation and AF using HALO software on RNAscope in situ hybridization images.
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Affiliation(s)
- Cara Brodie
- Histopathology and ISH Core Facility, Cancer Research UK/Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.
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