High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis
Abstract Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted i...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-12-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-43458-x |
| _version_ | 1827399413630238720 |
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| author | Amanda Janesick Robert Shelansky Andrew D. Gottscho Florian Wagner Stephen R. Williams Morgane Rouault Ghezal Beliakoff Carolyn A. Morrison Michelli F. Oliveira Jordan T. Sicherman Andrew Kohlway Jawad Abousoud Tingsheng Yu Drennon Seayar H. Mohabbat 10x Development Teams Sarah E. B. Taylor |
| author_facet | Amanda Janesick Robert Shelansky Andrew D. Gottscho Florian Wagner Stephen R. Williams Morgane Rouault Ghezal Beliakoff Carolyn A. Morrison Michelli F. Oliveira Jordan T. Sicherman Andrew Kohlway Jawad Abousoud Tingsheng Yu Drennon Seayar H. Mohabbat 10x Development Teams Sarah E. B. Taylor |
| author_sort | Amanda Janesick |
| collection | DOAJ |
| description | Abstract Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. This integrative approach allowed us to explore molecular differences that exist between distinct tumor regions and to identify biomarkers involved in the progression towards invasive carcinoma. Further, we study cell neighborhoods and identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. Here, we demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity; however, it is the integration of these technologies that leads to deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics. |
| first_indexed | 2024-03-08T19:45:38Z |
| format | Article |
| id | doaj.art-a2f0ceca53f64be098977c113f28d842 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-08T19:45:38Z |
| publishDate | 2023-12-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-a2f0ceca53f64be098977c113f28d8422023-12-24T12:23:33ZengNature PortfolioNature Communications2041-17232023-12-0114111510.1038/s41467-023-43458-xHigh resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysisAmanda Janesick0Robert Shelansky1Andrew D. Gottscho2Florian Wagner3Stephen R. Williams4Morgane Rouault5Ghezal Beliakoff6Carolyn A. Morrison7Michelli F. Oliveira8Jordan T. Sicherman9Andrew Kohlway10Jawad Abousoud11Tingsheng Yu Drennon12Seayar H. Mohabbat1310x Development TeamsSarah E. B. Taylor1410x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.10x Genomics Inc.Abstract Single-cell and spatial technologies that profile gene expression across a whole tissue are revolutionizing the resolution of molecular states in clinical samples. Current commercially available technologies provide whole transcriptome single-cell, whole transcriptome spatial, or targeted in situ gene expression analysis. Here, we combine these technologies to explore tissue heterogeneity in large, FFPE human breast cancer sections. This integrative approach allowed us to explore molecular differences that exist between distinct tumor regions and to identify biomarkers involved in the progression towards invasive carcinoma. Further, we study cell neighborhoods and identify rare boundary cells that sit at the critical myoepithelial border confining the spread of malignant cells. Here, we demonstrate that each technology alone provides information about molecular signatures relevant to understanding cancer heterogeneity; however, it is the integration of these technologies that leads to deeper insights, ushering in discoveries that will progress oncology research and the development of diagnostics and therapeutics.https://doi.org/10.1038/s41467-023-43458-x |
| spellingShingle | Amanda Janesick Robert Shelansky Andrew D. Gottscho Florian Wagner Stephen R. Williams Morgane Rouault Ghezal Beliakoff Carolyn A. Morrison Michelli F. Oliveira Jordan T. Sicherman Andrew Kohlway Jawad Abousoud Tingsheng Yu Drennon Seayar H. Mohabbat 10x Development Teams Sarah E. B. Taylor High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis Nature Communications |
| title | High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis |
| title_full | High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis |
| title_fullStr | High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis |
| title_full_unstemmed | High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis |
| title_short | High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis |
| title_sort | high resolution mapping of the tumor microenvironment using integrated single cell spatial and in situ analysis |
| url | https://doi.org/10.1038/s41467-023-43458-x |
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