A genome‐wide study of gastric intramucosal neoplasia based on somatic copy number alterations, gene mutations, and mRNA expression patterns
Article Swipe
Yoshihiko Koike
,
Mitsumasa Osakabe
,
Ryo Sugimoto
,
Noriyuku Uesugi
,
Takayuki Matsumoto
,
Hiromu Suzuki
,
Naoki Yanagawa
,
Tamotsu Sugai
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/2056-4538.12368
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1002/2056-4538.12368
We performed comprehensive analyses of somatic copy number alterations (SCNAs) and gene expression profiles of gastric intramucosal neoplasia (IMN) using array‐based methods in 97 intestinal‐type IMNs, including 39 low‐grade dysplasias (LGDs), 37 high‐grade dysplasias (HGDs), and 26 intramucosal carcinomas (IMCs) with stromal invasion of the lamina propria to identify the molecular mechanism of IMN. In addition, we examined gene mutations using gene panel analyses. We used cluster analyses for exclusion of arbitrariness to identify SCNA patterns and expression profiles. IMNs were classified into two distinct subgroups (subgroups 1 and 2) based on SCNA patterns. Subgroup 1 showed a genomic stable pattern due to the low frequency of SCNAs, whereas subgroup 2 exhibited a chromosomal instability pattern due to the high frequencies of SCNAs and TP53 mutations. Interestingly, although the frequencies of LGD and HGD were significantly higher in subgroup 1 than in subgroup 2, IMC was commonly found in both types. Although the expression profiles of specific mRNAs could be used to categorise subgroups 1 and 2, no clinicopathological findings correlated with either subgroup. We examined signalling pathways specific to subgroups 1 and 2 to identify the association of each subgroup with signalling pathways based on gene ontology tree visualisation: subgroups 1 and 2 were associated with haem metabolism and chromosomal instability, respectively. These findings reveal a comprehensive genomic landscape that highlights the molecular complexity of IMNs and provide a road map to facilitate our understanding of gastric IMNs.
Related Topics
Concepts
Biology
Gene
Somatic cell
Genetics
Gene expression
Copy-number variation
Copy number analysis
Cancer
Germline mutation
Cancer research
Genome
Mutation
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1002/2056-4538.12368
- https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/2056-4538.12368
- OA Status
- gold
- References
- 39
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4392592410
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4392592410Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1002/2056-4538.12368Digital Object Identifier
- Title
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A genome‐wide study of gastric intramucosal neoplasia based on somatic copy number alterations, gene mutations, and
mRNA expression patternsWork title - Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2024Year of publication
- Publication date
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2024-03-01Full publication date if available
- Authors
-
Yoshihiko Koike, Mitsumasa Osakabe, Ryo Sugimoto, Noriyuku Uesugi, Takayuki Matsumoto, Hiromu Suzuki, Naoki Yanagawa, Tamotsu SugaiList of authors in order
- Landing page
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https://doi.org/10.1002/2056-4538.12368Publisher landing page
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/2056-4538.12368Direct link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
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https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/2056-4538.12368Direct OA link when available
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Biology, Gene, Somatic cell, Genetics, Gene expression, Copy-number variation, Copy number analysis, Cancer, Germline mutation, Cancer research, Genome, MutationTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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39Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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