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PreprintCited by 5RNA Research and SplicingCancer-related molecular mechanisms researchCancer Genomics and Diagnostics

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Subtype-specific alternative splicing events in breast cancer identified by large-scale data analysis

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Deguchi, Yui, Kikutake, Chie, Suyama, Mikita·2024·Scientific Reports
DOI 10.21203/rs.3.rs-4172771/v1PMC PMC11187070

Preprint — published as 10.1038/s41598-024-65035-y · Paper page

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Abstract

Genome analysis in cancer has focused mainly on elucidating the function and regulatory mechanisms of genes that exhibit differential expression or mutation in cancer samples compared to normal samples. Recently, transcriptome analysis revealed that abnormal splicing events in cancer samples could contribute to cancer pathogenesis. Moreover, splicing variants in cancer reportedly generate diverse cancer antigens. Although abnormal splicing events are expected to be potential targets in cancer immunotherapy, the exploration of such targets and their biological significance in cancer have not been fully understood. In this study, to explore subtype-specific alternative splicing events, we conducted a comprehensive analysis of splicing events for each breast cancer subtype using large-scale splicing data derived from The Cancer Genome Atlas and found subtype-specific alternative splicing patterns. Analyses indicated that genes that produce subtype-specific alternative splicing events are potential novel targets for immunotherapy against breast cancer. The subtype-specific alternative splicing events identified in this study, which were not identified by mutation or differential expression analysis, bring new significance to previously overlooked splicing events.

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Metadata

Authors
Deguchi, Y., Kikutake, C., & Suyama, M.
Affiliations
Kyushu University (JP)
Corresponding author
Suyama, Mikita
ORCID
Venue
Scientific Reports
Publisher
Research Square Platform LLC
Published
2024-04-10
Volume
14
Issue
1
Pages
14158-14158
ISSN
2045-2322 (ISSN-L)
DOI
10.21203/rs.3.rs-4172771/v1
PMC
PMC11187070
OpenAlex
W4399805464
Cited by
5
References
1
Citations by year
2026: 2 · 2025: 3
FWCI
0.68
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • Research Square (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • Japan Agency for Medical Research and Development (JP19gm1310001, CREST)
  • Japan Society for the Promotion of Science (95482, CREST, 20K15780)
  • Core Research for Evolutional Science and Technology (JP19gm1310001)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
Keywords
breast cancer, alternative splicing, tumor subtypes, splice variants, cancer immunotherapy, immunotherapy targets, gene expression profiling, TCGA, splicing events
MeSH terms
Data Analysis, Breast Neoplasms, Female, Humans, Mutation, Gene Expression Regulation, Neoplastic, Alternative Splicing, Gene Expression Profiling

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