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-...
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| Format: | Article |
| Language: | English |
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Korean Society of Pathologists & the Korean Society for Cytopathology
2023-01-01
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| Series: | Journal of Pathology and Translational Medicine |
| Subjects: | |
| Online Access: | http://www.jpatholtm.org/upload/pdf/jptm-2022-12-12.pdf |
| _version_ | 1797951384657592320 |
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| author | Yoon-Seob Kim Jinyong Choi Sug Hyung Lee |
| author_facet | Yoon-Seob Kim Jinyong Choi Sug Hyung Lee |
| author_sort | Yoon-Seob Kim |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-10T22:29:45Z |
| format | Article |
| id | doaj.art-8568436fe1db421f9db8cbdf62e09fbf |
| institution | Directory Open Access Journal |
| issn | 2383-7837 2383-7845 |
| language | English |
| last_indexed | 2024-04-10T22:29:45Z |
| publishDate | 2023-01-01 |
| publisher | Korean Society of Pathologists & the Korean Society for Cytopathology |
| record_format | Article |
| series | Journal of Pathology and Translational Medicine |
| spelling | doaj.art-8568436fe1db421f9db8cbdf62e09fbf2023-01-17T06:08:50ZengKorean Society of Pathologists & the Korean Society for CytopathologyJournal of Pathology and Translational Medicine2383-78372383-78452023-01-01571435110.4132/jptm.2022.12.1217057Single-cell and spatial sequencing application in pathologyYoon-Seob Kim0Jinyong Choi1Sug Hyung Lee2 Department of Microbiology, The Catholic University of Korea, Seoul, Korea Department of Microbiology, The Catholic University of Korea, Seoul, Korea Biomedicine & Health Sciences, The Catholic University of Korea, Seoul, KoreaTraditionally, 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.http://www.jpatholtm.org/upload/pdf/jptm-2022-12-12.pdfsingle-cell sequencingspatial sequencingpathologyhistologytranscriptomediseases |
| spellingShingle | Yoon-Seob Kim Jinyong Choi Sug Hyung Lee Single-cell and spatial sequencing application in pathology Journal of Pathology and Translational Medicine single-cell sequencing spatial sequencing pathology histology transcriptome diseases |
| 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 | single-cell sequencing spatial sequencing pathology histology transcriptome diseases |
| url | http://www.jpatholtm.org/upload/pdf/jptm-2022-12-12.pdf |
| work_keys_str_mv | AT yoonseobkim singlecellandspatialsequencingapplicationinpathology AT jinyongchoi singlecellandspatialsequencingapplicationinpathology AT sughyunglee singlecellandspatialsequencingapplicationinpathology |