Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironment
Abstract Background The tumor microenvironment contributes to tumor initiation, growth, invasion, and metastasis. The tumor microenvironment is heterogeneous in cellular and acellular components, particularly structural features and their gene expression at the inter-and intra-tumor levels. Main tex...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-04-01
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| Series: | Cancer Cell International |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12935-022-02580-4 |
| _version_ | 1828496738658287616 |
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| author | Hailan Yan Jinghua Shi Yi Dai Xiaoyan Li Yushi Wu Jing Zhang Zhiyue Gu Chenyu Zhang Jinhua Leng |
| author_facet | Hailan Yan Jinghua Shi Yi Dai Xiaoyan Li Yushi Wu Jing Zhang Zhiyue Gu Chenyu Zhang Jinhua Leng |
| author_sort | Hailan Yan |
| collection | DOAJ |
| description | Abstract Background The tumor microenvironment contributes to tumor initiation, growth, invasion, and metastasis. The tumor microenvironment is heterogeneous in cellular and acellular components, particularly structural features and their gene expression at the inter-and intra-tumor levels. Main text Single-cell RNA sequencing profiles single-cell transcriptomes to reveal cell proportions and trajectories while spatial information is lacking. Spatially resolved transcriptomics redeems this lack with limited coverage or depth of transcripts. Hence, the integration of single-cell RNA sequencing and spatial data makes the best use of their strengths, having insights into exploring diverse tissue architectures and interactions in a complicated network. We review applications of integrating the two methods, especially in cellular components in the tumor microenvironment, showing each role in cancer initiation and progression, which provides clinical relevance in prognosis, optimal treatment, and potential therapeutic targets. Conclusion The integration of two approaches may break the bottlenecks in the spatial resolution of neighboring cell subpopulations in cancer, and help to describe the signaling circuitry about the intercommunication and its exact mechanisms in producing different types and malignant stages of tumors. |
| first_indexed | 2024-12-11T12:35:02Z |
| format | Article |
| id | doaj.art-96f060ae3eb6483f9817e4e8329baa66 |
| institution | Directory Open Access Journal |
| issn | 1475-2867 |
| language | English |
| last_indexed | 2024-12-11T12:35:02Z |
| publishDate | 2022-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Cancer Cell International |
| spelling | doaj.art-96f060ae3eb6483f9817e4e8329baa662022-12-22T01:07:09ZengBMCCancer Cell International1475-28672022-04-0122111210.1186/s12935-022-02580-4Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironmentHailan Yan0Jinghua Shi1Yi Dai2Xiaoyan Li3Yushi Wu4Jing Zhang5Zhiyue Gu6Chenyu Zhang7Jinhua Leng8Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeDepartment of Obstetrics and Gynecology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical CollegeAbstract Background The tumor microenvironment contributes to tumor initiation, growth, invasion, and metastasis. The tumor microenvironment is heterogeneous in cellular and acellular components, particularly structural features and their gene expression at the inter-and intra-tumor levels. Main text Single-cell RNA sequencing profiles single-cell transcriptomes to reveal cell proportions and trajectories while spatial information is lacking. Spatially resolved transcriptomics redeems this lack with limited coverage or depth of transcripts. Hence, the integration of single-cell RNA sequencing and spatial data makes the best use of their strengths, having insights into exploring diverse tissue architectures and interactions in a complicated network. We review applications of integrating the two methods, especially in cellular components in the tumor microenvironment, showing each role in cancer initiation and progression, which provides clinical relevance in prognosis, optimal treatment, and potential therapeutic targets. Conclusion The integration of two approaches may break the bottlenecks in the spatial resolution of neighboring cell subpopulations in cancer, and help to describe the signaling circuitry about the intercommunication and its exact mechanisms in producing different types and malignant stages of tumors.https://doi.org/10.1186/s12935-022-02580-4IntegrationSingle-cell RNA sequencingSpatially resolved transcriptomicsTumor microenvironment |
| spellingShingle | Hailan Yan Jinghua Shi Yi Dai Xiaoyan Li Yushi Wu Jing Zhang Zhiyue Gu Chenyu Zhang Jinhua Leng Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironment Cancer Cell International Integration Single-cell RNA sequencing Spatially resolved transcriptomics Tumor microenvironment |
| title | Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironment |
| title_full | Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironment |
| title_fullStr | Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironment |
| title_full_unstemmed | Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironment |
| title_short | Technique integration of single-cell RNA sequencing with spatially resolved transcriptomics in the tumor microenvironment |
| title_sort | technique integration of single cell rna sequencing with spatially resolved transcriptomics in the tumor microenvironment |
| topic | Integration Single-cell RNA sequencing Spatially resolved transcriptomics Tumor microenvironment |
| url | https://doi.org/10.1186/s12935-022-02580-4 |
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