Cargando…

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-...

Descripción completa

Detalles Bibliográficos
Autores principales: Kim, Yoon-Seob, Choi, Jinyong, Lee, Sug Hyung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Korean Society of Pathologists/The Korean Society for Cytopathology 2023
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
_version_ 1784871051838095360
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
work_keys_str_mv AT kimyoonseob singlecellandspatialsequencingapplicationinpathology
AT choijinyong singlecellandspatialsequencingapplicationinpathology
AT leesughyung singlecellandspatialsequencingapplicationinpathology