Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers
Abstract Background Alterations in genes encoding chromatin regulatory proteins are prevalent in cancers and may confer oncogenic properties and molecular changes linked to therapy resistance. However, the impact of copy number alterations (CNAs) of the SWItch/Sucrose NonFermentable (SWI/SNF) comple...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | Hereditas |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s41065-021-00203-y |
| _version_ | 1818730801889542144 |
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| author | Zhiwei Xing Buhuan Ma Weiting Sun Yimin Sun Caixia Liu |
| author_facet | Zhiwei Xing Buhuan Ma Weiting Sun Yimin Sun Caixia Liu |
| author_sort | Zhiwei Xing |
| collection | DOAJ |
| description | Abstract Background Alterations in genes encoding chromatin regulatory proteins are prevalent in cancers and may confer oncogenic properties and molecular changes linked to therapy resistance. However, the impact of copy number alterations (CNAs) of the SWItch/Sucrose NonFermentable (SWI/SNF) complex on the oncogenic and immunologic properties has not been systematically explored across human cancer types. Methods We comprehensively analyzed the genomic, transcriptomic and clinical data of The Cancer Genome Atlas (TCGA) dataset across 33 solid cancers. Results CNAs of the SWI/SNF components were identified in more than 25% of all queried cancers, and tumors harboring SWI/SNF CNAs demonstrated a worse overall survival (OS) than others in several cancer types. Mechanistically, the SCNA events in the SWI/SNF complex are correlated with dysregulated genomic features and oncogenic pathways, including the cell cycle, DNA damage and repair. Notably, the SWI/SNF CNAs were associated with homologous recombination deficiency (HRD) and improved clinical outcomes of platinum-treated ovarian cancer. Furthermore, we observed distinct immune infiltrating patterns and immunophenotypes associated with SWI/SNF CNAs in different cancer types. Conclusion The CNA events of the SWI/SNF components are a key process linked to oncogenesis, immune infiltration and therapeutic responsiveness across human cancers. |
| first_indexed | 2024-12-17T23:07:34Z |
| format | Article |
| id | doaj.art-36a6093cefbb48e88933c8795b3c92ed |
| institution | Directory Open Access Journal |
| issn | 1601-5223 |
| language | English |
| last_indexed | 2024-12-17T23:07:34Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | Hereditas |
| spelling | doaj.art-36a6093cefbb48e88933c8795b3c92ed2022-12-21T21:29:12ZengBMCHereditas1601-52232021-10-01158111310.1186/s41065-021-00203-yComprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancersZhiwei Xing0Buhuan Ma1Weiting Sun2Yimin Sun3Caixia Liu4The Affiliated Hospital of Inner Mongolia Medical UniversityInner Mongolia Medical UniversityInner Mongolia Medical UniversityNational Engineering Research Center for Beijing Biochip TechnologyThe Affiliated Hospital of Inner Mongolia Medical UniversityAbstract Background Alterations in genes encoding chromatin regulatory proteins are prevalent in cancers and may confer oncogenic properties and molecular changes linked to therapy resistance. However, the impact of copy number alterations (CNAs) of the SWItch/Sucrose NonFermentable (SWI/SNF) complex on the oncogenic and immunologic properties has not been systematically explored across human cancer types. Methods We comprehensively analyzed the genomic, transcriptomic and clinical data of The Cancer Genome Atlas (TCGA) dataset across 33 solid cancers. Results CNAs of the SWI/SNF components were identified in more than 25% of all queried cancers, and tumors harboring SWI/SNF CNAs demonstrated a worse overall survival (OS) than others in several cancer types. Mechanistically, the SCNA events in the SWI/SNF complex are correlated with dysregulated genomic features and oncogenic pathways, including the cell cycle, DNA damage and repair. Notably, the SWI/SNF CNAs were associated with homologous recombination deficiency (HRD) and improved clinical outcomes of platinum-treated ovarian cancer. Furthermore, we observed distinct immune infiltrating patterns and immunophenotypes associated with SWI/SNF CNAs in different cancer types. Conclusion The CNA events of the SWI/SNF components are a key process linked to oncogenesis, immune infiltration and therapeutic responsiveness across human cancers.https://doi.org/10.1186/s41065-021-00203-ySWI/SNF complexCopy number alterationImmune cell infiltrationGenome instability |
| spellingShingle | Zhiwei Xing Buhuan Ma Weiting Sun Yimin Sun Caixia Liu Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers Hereditas SWI/SNF complex Copy number alteration Immune cell infiltration Genome instability |
| title | Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers |
| title_full | Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers |
| title_fullStr | Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers |
| title_full_unstemmed | Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers |
| title_short | Comprehensive characterization and clinical relevance of the SWI/SNF copy number aberrations across human cancers |
| title_sort | comprehensive characterization and clinical relevance of the swi snf copy number aberrations across human cancers |
| topic | SWI/SNF complex Copy number alteration Immune cell infiltration Genome instability |
| url | https://doi.org/10.1186/s41065-021-00203-y |
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