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Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome
Women with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS) have up to 85% lifetime risk of female breast cancer (BC). We previously showed that PHTS-derived BCs are distinct from sporadic BCs both at the clinical and genomic levels. In this study, we examined somatic copy number variati...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10322985/ https://www.ncbi.nlm.nih.gov/pubmed/37407629 http://dx.doi.org/10.1038/s41525-023-00361-0 |
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author | Brewer, Takae Yehia, Lamis Bazeley, Peter Eng, Charis |
author_facet | Brewer, Takae Yehia, Lamis Bazeley, Peter Eng, Charis |
author_sort | Brewer, Takae |
collection | PubMed |
description | Women with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS) have up to 85% lifetime risk of female breast cancer (BC). We previously showed that PHTS-derived BCs are distinct from sporadic BCs both at the clinical and genomic levels. In this study, we examined somatic copy number variations (CNV) and transcriptome data to further characterize the somatic landscape of PHTS-derived BCs. We analyzed exome sequencing data from 44 BCs from women with PHTS for CNV. The control group comprised of 558 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. Here, we found that PHTS-derived BCs have several distinct CNV peaks compared to TCGA. Furthermore, RNA sequencing data revealed that PHTS-derived BCs have a distinct immunologic cell type signature, which points toward cancer immune evasion. Transcriptomic data also revealed PHTS-derived BCs with pathogenic germline PTEN variants appear to have vitamin E degradation as a key pathway associated with tumorigenesis. In conclusion, our study revealed distinct CNV x transcript features in PHTS-derived BCs, which further facilitate understanding of BC biology arising in the setting of germline PTEN mutations. |
format | Online Article Text |
id | pubmed-10322985 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-103229852023-07-07 Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome Brewer, Takae Yehia, Lamis Bazeley, Peter Eng, Charis NPJ Genom Med Article Women with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS) have up to 85% lifetime risk of female breast cancer (BC). We previously showed that PHTS-derived BCs are distinct from sporadic BCs both at the clinical and genomic levels. In this study, we examined somatic copy number variations (CNV) and transcriptome data to further characterize the somatic landscape of PHTS-derived BCs. We analyzed exome sequencing data from 44 BCs from women with PHTS for CNV. The control group comprised of 558 women with sporadic BCs from The Cancer Genome Atlas (TCGA) dataset. Here, we found that PHTS-derived BCs have several distinct CNV peaks compared to TCGA. Furthermore, RNA sequencing data revealed that PHTS-derived BCs have a distinct immunologic cell type signature, which points toward cancer immune evasion. Transcriptomic data also revealed PHTS-derived BCs with pathogenic germline PTEN variants appear to have vitamin E degradation as a key pathway associated with tumorigenesis. In conclusion, our study revealed distinct CNV x transcript features in PHTS-derived BCs, which further facilitate understanding of BC biology arising in the setting of germline PTEN mutations. Nature Publishing Group UK 2023-07-05 /pmc/articles/PMC10322985/ /pubmed/37407629 http://dx.doi.org/10.1038/s41525-023-00361-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Brewer, Takae Yehia, Lamis Bazeley, Peter Eng, Charis Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome |
title | Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome |
title_full | Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome |
title_fullStr | Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome |
title_full_unstemmed | Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome |
title_short | Integrating somatic CNV and gene expression in breast cancers from women with PTEN hamartoma tumor syndrome |
title_sort | integrating somatic cnv and gene expression in breast cancers from women with pten hamartoma tumor syndrome |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10322985/ https://www.ncbi.nlm.nih.gov/pubmed/37407629 http://dx.doi.org/10.1038/s41525-023-00361-0 |
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