Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment
Recent advances in single-cell technologies, particularly single-cell RNA-sequencing (scRNA-seq), have permitted high throughput transcriptional profiling of a wide variety of biological systems. As scRNA-seq supports inference of cell-cell communication, this technology has and continues to anchor...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-04-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.885267/full |
| _version_ | 1818263586358689792 |
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| author | Kate Bridges Kathryn Miller-Jensen Kathryn Miller-Jensen Kathryn Miller-Jensen |
| author_facet | Kate Bridges Kathryn Miller-Jensen Kathryn Miller-Jensen Kathryn Miller-Jensen |
| author_sort | Kate Bridges |
| collection | DOAJ |
| description | Recent advances in single-cell technologies, particularly single-cell RNA-sequencing (scRNA-seq), have permitted high throughput transcriptional profiling of a wide variety of biological systems. As scRNA-seq supports inference of cell-cell communication, this technology has and continues to anchor groundbreaking studies into the efficacy and mechanism of novel immunotherapies for cancer treatment. In this review, we will highlight methods developed to infer inter- and intracellular signaling from scRNA-seq and discuss how they have contributed to studies of immunotherapeutic intervention in the tumor microenvironment (TME). However, a central challenge remains in validating the hypothesized cell-cell interactions. Therefore, this review will also cover strategies for integration of these scRNA-seq-derived interaction networks with existing experimental and computational approaches. Integration of these networks with imaging, protein secretion measurements, and network analysis and mathematical modeling tools addresses challenges that remain with scRNA-seq to enhance studies of immunosuppressive and immunotherapy-altered signaling in the TME. |
| first_indexed | 2024-12-12T19:21:22Z |
| format | Article |
| id | doaj.art-097a58840a6c463298ba0d25ad077094 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-12T19:21:22Z |
| publishDate | 2022-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-097a58840a6c463298ba0d25ad0770942022-12-22T00:14:36ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-04-011310.3389/fimmu.2022.885267885267Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor MicroenvironmentKate Bridges0Kathryn Miller-Jensen1Kathryn Miller-Jensen2Kathryn Miller-Jensen3Department of Biomedical Engineering, Yale University, New Haven, CT, United StatesDepartment of Biomedical Engineering, Yale University, New Haven, CT, United StatesDepartment of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, United StatesSystems Biology Institute, Yale University, New Haven, CT, United StatesRecent advances in single-cell technologies, particularly single-cell RNA-sequencing (scRNA-seq), have permitted high throughput transcriptional profiling of a wide variety of biological systems. As scRNA-seq supports inference of cell-cell communication, this technology has and continues to anchor groundbreaking studies into the efficacy and mechanism of novel immunotherapies for cancer treatment. In this review, we will highlight methods developed to infer inter- and intracellular signaling from scRNA-seq and discuss how they have contributed to studies of immunotherapeutic intervention in the tumor microenvironment (TME). However, a central challenge remains in validating the hypothesized cell-cell interactions. Therefore, this review will also cover strategies for integration of these scRNA-seq-derived interaction networks with existing experimental and computational approaches. Integration of these networks with imaging, protein secretion measurements, and network analysis and mathematical modeling tools addresses challenges that remain with scRNA-seq to enhance studies of immunosuppressive and immunotherapy-altered signaling in the TME.https://www.frontiersin.org/articles/10.3389/fimmu.2022.885267/fullsingle-cell RNA-sequencing (scRNA-seq)cell-cell communication networktumor microenvironmentimmunotherapyspatial profilingsingle-cell secretomics |
| spellingShingle | Kate Bridges Kathryn Miller-Jensen Kathryn Miller-Jensen Kathryn Miller-Jensen Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment Frontiers in Immunology single-cell RNA-sequencing (scRNA-seq) cell-cell communication network tumor microenvironment immunotherapy spatial profiling single-cell secretomics |
| title | Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment |
| title_full | Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment |
| title_fullStr | Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment |
| title_full_unstemmed | Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment |
| title_short | Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment |
| title_sort | mapping and validation of scrna seq derived cell cell communication networks in the tumor microenvironment |
| topic | single-cell RNA-sequencing (scRNA-seq) cell-cell communication network tumor microenvironment immunotherapy spatial profiling single-cell secretomics |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.885267/full |
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