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Single-cell and spatial sequencing application in pathology
Traditionally, diagnostic pathology uses histology representing structural alterations in a disease’s cells and tissues. In many cases, however, it is supplemented by other morphology-based methods such as immunohistochemistry and fluorescent in situ hybridization. Single-cell RNA sequencing (scRNA-...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Korean Society of Pathologists/The Korean Society for Cytopathology
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9846004/ https://www.ncbi.nlm.nih.gov/pubmed/36623813 http://dx.doi.org/10.4132/jptm.2022.12.12 |
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author | Kim, Yoon-Seob Choi, Jinyong Lee, Sug Hyung |
author_facet | Kim, Yoon-Seob Choi, Jinyong Lee, Sug Hyung |
author_sort | Kim, Yoon-Seob |
collection | PubMed |
description | Traditionally, diagnostic pathology uses histology representing structural alterations in a disease’s cells and tissues. In many cases, however, it is supplemented by other morphology-based methods such as immunohistochemistry and fluorescent in situ hybridization. Single-cell RNA sequencing (scRNA-seq) is one of the strategies that may help tackle the heterogeneous cells in a disease, but it does not usually provide histologic information. Spatial sequencing is designed to assign cell types, subtypes, or states according to the mRNA expression on a histological section by RNA sequencing. It can provide mRNA expressions not only of diseased cells, such as cancer cells but also of stromal cells, such as immune cells, fibroblasts, and vascular cells. In this review, we studied current methods of spatial transcriptome sequencing based on their technical backgrounds, tissue preparation, and analytic procedures. With the pathology examples, useful recommendations for pathologists who are just getting started to use spatial sequencing analysis in research are provided here. In addition, leveraging spatial sequencing by integration with scRNA-seq is reviewed. With the advantages of simultaneous histologic and single-cell information, spatial sequencing may give a molecular basis for pathological diagnosis, improve our understanding of diseases, and have potential clinical applications in prognostics and diagnostic pathology. |
format | Online Article Text |
id | pubmed-9846004 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | The Korean Society of Pathologists/The Korean Society for Cytopathology |
record_format | MEDLINE/PubMed |
spelling | pubmed-98460042023-01-31 Single-cell and spatial sequencing application in pathology Kim, Yoon-Seob Choi, Jinyong Lee, Sug Hyung J Pathol Transl Med Review Traditionally, diagnostic pathology uses histology representing structural alterations in a disease’s cells and tissues. In many cases, however, it is supplemented by other morphology-based methods such as immunohistochemistry and fluorescent in situ hybridization. Single-cell RNA sequencing (scRNA-seq) is one of the strategies that may help tackle the heterogeneous cells in a disease, but it does not usually provide histologic information. Spatial sequencing is designed to assign cell types, subtypes, or states according to the mRNA expression on a histological section by RNA sequencing. It can provide mRNA expressions not only of diseased cells, such as cancer cells but also of stromal cells, such as immune cells, fibroblasts, and vascular cells. In this review, we studied current methods of spatial transcriptome sequencing based on their technical backgrounds, tissue preparation, and analytic procedures. With the pathology examples, useful recommendations for pathologists who are just getting started to use spatial sequencing analysis in research are provided here. In addition, leveraging spatial sequencing by integration with scRNA-seq is reviewed. With the advantages of simultaneous histologic and single-cell information, spatial sequencing may give a molecular basis for pathological diagnosis, improve our understanding of diseases, and have potential clinical applications in prognostics and diagnostic pathology. The Korean Society of Pathologists/The Korean Society for Cytopathology 2023-01 2023-01-10 /pmc/articles/PMC9846004/ /pubmed/36623813 http://dx.doi.org/10.4132/jptm.2022.12.12 Text en © 2023 The Korean Society of Pathologists/The Korean Society for Cytopathology https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0 (https://creativecommons.org/licenses/by-nc/4.0/) ) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Kim, Yoon-Seob Choi, Jinyong Lee, Sug Hyung Single-cell and spatial sequencing application in pathology |
title | Single-cell and spatial sequencing application in pathology |
title_full | Single-cell and spatial sequencing application in pathology |
title_fullStr | Single-cell and spatial sequencing application in pathology |
title_full_unstemmed | Single-cell and spatial sequencing application in pathology |
title_short | Single-cell and spatial sequencing application in pathology |
title_sort | single-cell and spatial sequencing application in pathology |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9846004/ https://www.ncbi.nlm.nih.gov/pubmed/36623813 http://dx.doi.org/10.4132/jptm.2022.12.12 |
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