DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma
Stomach Adenocarcinoma (STAD) is a leading cause of death worldwide. Somatic Copy Number Alterations (SCNAs), which result in Homologous recombination (HR) deficiency in double-strand break repair, are associated with the progression of STAD. However, the landscape of frequent breakpoints of SCNAs (...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1231415/full |
| _version_ | 1797665284152098816 |
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| author | Yilin Shi Huangxuan Shen |
| author_facet | Yilin Shi Huangxuan Shen |
| author_sort | Yilin Shi |
| collection | DOAJ |
| description | Stomach Adenocarcinoma (STAD) is a leading cause of death worldwide. Somatic Copy Number Alterations (SCNAs), which result in Homologous recombination (HR) deficiency in double-strand break repair, are associated with the progression of STAD. However, the landscape of frequent breakpoints of SCNAs (hotspots) and their functional impacts remain poorly understood. In this study, we aimed to explore the frequency and impact of these hotspots in 332 STAD patients and 1,043 cancer cells using data from the Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE). We studied the rates of DSB (Double-Strand Breaks) loci in STAD patients by employing the Non-Homogeneous Poisson Distribution (λ), based on which we identified 145 DSB-hotspots with genes affected. We further verified DNA cytosine deamination as a critical process underlying the burden of DSB in STAD. Finally, we illustrated the clinical impact of the significant biological processes. Our findings highlighted the relationship between DNA cytosine deamination and SCNA in cancer was associated with recurrent Somatic Copy Number Alterations in STAD. |
| first_indexed | 2024-03-11T19:42:43Z |
| format | Article |
| id | doaj.art-a8beed9c58cf4ee09bf0577befddf06a |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-11T19:42:43Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-a8beed9c58cf4ee09bf0577befddf06a2023-10-06T07:46:34ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-10-011410.3389/fgene.2023.12314151231415DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinomaYilin Shi0Huangxuan Shen1The College of Letters & Science, University of Wisconsin–Madison, Madison, WI, United StatesState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, ChinaStomach Adenocarcinoma (STAD) is a leading cause of death worldwide. Somatic Copy Number Alterations (SCNAs), which result in Homologous recombination (HR) deficiency in double-strand break repair, are associated with the progression of STAD. However, the landscape of frequent breakpoints of SCNAs (hotspots) and their functional impacts remain poorly understood. In this study, we aimed to explore the frequency and impact of these hotspots in 332 STAD patients and 1,043 cancer cells using data from the Cancer Genome Atlas (TCGA) and Cancer Cell Line Encyclopedia (CCLE). We studied the rates of DSB (Double-Strand Breaks) loci in STAD patients by employing the Non-Homogeneous Poisson Distribution (λ), based on which we identified 145 DSB-hotspots with genes affected. We further verified DNA cytosine deamination as a critical process underlying the burden of DSB in STAD. Finally, we illustrated the clinical impact of the significant biological processes. Our findings highlighted the relationship between DNA cytosine deamination and SCNA in cancer was associated with recurrent Somatic Copy Number Alterations in STAD.https://www.frontiersin.org/articles/10.3389/fgene.2023.1231415/fullstomach adenocarcinomaDNA cytosine deaminationhotspotsSomatic Copy Number AlterationsCCLE databaseTCGA database |
| spellingShingle | Yilin Shi Huangxuan Shen DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma Frontiers in Genetics stomach adenocarcinoma DNA cytosine deamination hotspots Somatic Copy Number Alterations CCLE database TCGA database |
| title | DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma |
| title_full | DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma |
| title_fullStr | DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma |
| title_full_unstemmed | DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma |
| title_short | DNA cytosine deamination is associated with recurrent Somatic Copy Number Alterations in stomach adenocarcinoma |
| title_sort | dna cytosine deamination is associated with recurrent somatic copy number alterations in stomach adenocarcinoma |
| topic | stomach adenocarcinoma DNA cytosine deamination hotspots Somatic Copy Number Alterations CCLE database TCGA database |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1231415/full |
| work_keys_str_mv | AT yilinshi dnacytosinedeaminationisassociatedwithrecurrentsomaticcopynumberalterationsinstomachadenocarcinoma AT huangxuanshen dnacytosinedeaminationisassociatedwithrecurrentsomaticcopynumberalterationsinstomachadenocarcinoma |