A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires
Tumor-infiltrating B cells can play an important role in anti-tumor responses but their presence is not well understood. In this study, we extracted the B cell receptor repertoires from 9522 tumor and adjacent non-tumor samples across 28 tumor types in the Cancer Genome Atlas project and performed d...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Immunology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2021.790119/full |
| _version_ | 1818974759772225536 |
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| author | Katharine Yu Katharine Yu Akshay Ravoor Núria Malats Silvia Pineda Marina Sirota Marina Sirota |
| author_facet | Katharine Yu Katharine Yu Akshay Ravoor Núria Malats Silvia Pineda Marina Sirota Marina Sirota |
| author_sort | Katharine Yu |
| collection | DOAJ |
| description | Tumor-infiltrating B cells can play an important role in anti-tumor responses but their presence is not well understood. In this study, we extracted the B cell receptor repertoires from 9522 tumor and adjacent non-tumor samples across 28 tumor types in the Cancer Genome Atlas project and performed diversity and network analysis. We identified differences in diversity and network statistics across tumor types and subtypes and observed a trend towards increased clonality in primary tumors compared to adjacent non-tumor tissues. We also found significant associations between the repertoire features and mutation load, tumor stage, and age. Our V-gene usage analysis identified similar V-gene usage patterns in colorectal and endometrial cancers. Lastly, we evaluated the prognostic value of the repertoire features and identified significant associations with survival in seven tumor types. This study warrants further research into better understanding the role of tumor-infiltrating B cells across a wide range of tumor types. |
| first_indexed | 2024-12-20T15:45:10Z |
| format | Article |
| id | doaj.art-ad24209c07c24914bf08c34e0ab7abca |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-12-20T15:45:10Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-ad24209c07c24914bf08c34e0ab7abca2022-12-21T19:35:01ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-01-011210.3389/fimmu.2021.790119790119A Pan-Cancer Analysis of Tumor-Infiltrating B Cell RepertoiresKatharine Yu0Katharine Yu1Akshay Ravoor2Núria Malats3Silvia Pineda4Marina Sirota5Marina Sirota6Bakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United StatesDepartment of Pediatrics, University of California, San Francisco (UCSF), San Francisco, CA, United StatesBakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United StatesGenetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, SpainGenetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), and Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, SpainBakar Computational Health Sciences Institute, University of California, San Francisco (UCSF), San Francisco, CA, United StatesDepartment of Pediatrics, University of California, San Francisco (UCSF), San Francisco, CA, United StatesTumor-infiltrating B cells can play an important role in anti-tumor responses but their presence is not well understood. In this study, we extracted the B cell receptor repertoires from 9522 tumor and adjacent non-tumor samples across 28 tumor types in the Cancer Genome Atlas project and performed diversity and network analysis. We identified differences in diversity and network statistics across tumor types and subtypes and observed a trend towards increased clonality in primary tumors compared to adjacent non-tumor tissues. We also found significant associations between the repertoire features and mutation load, tumor stage, and age. Our V-gene usage analysis identified similar V-gene usage patterns in colorectal and endometrial cancers. Lastly, we evaluated the prognostic value of the repertoire features and identified significant associations with survival in seven tumor types. This study warrants further research into better understanding the role of tumor-infiltrating B cells across a wide range of tumor types.https://www.frontiersin.org/articles/10.3389/fimmu.2021.790119/fullB cell repertoireimmune repertoiretumor microenvironmenttumor infiltrationTCGA |
| spellingShingle | Katharine Yu Katharine Yu Akshay Ravoor Núria Malats Silvia Pineda Marina Sirota Marina Sirota A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires Frontiers in Immunology B cell repertoire immune repertoire tumor microenvironment tumor infiltration TCGA |
| title | A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires |
| title_full | A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires |
| title_fullStr | A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires |
| title_full_unstemmed | A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires |
| title_short | A Pan-Cancer Analysis of Tumor-Infiltrating B Cell Repertoires |
| title_sort | pan cancer analysis of tumor infiltrating b cell repertoires |
| topic | B cell repertoire immune repertoire tumor microenvironment tumor infiltration TCGA |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2021.790119/full |
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