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Characterizing isoform switching events in esophageal adenocarcinoma
Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment-naïv...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society of Gene & Cell Therapy
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9437810/ https://www.ncbi.nlm.nih.gov/pubmed/36090744 http://dx.doi.org/10.1016/j.omtn.2022.08.018 |
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author | Zhang, Yun Weh, Katherine M. Howard, Connor L. Riethoven, Jean-Jack Clarke, Jennifer L. Lagisetty, Kiran H. Lin, Jules Reddy, Rishindra M. Chang, Andrew C. Beer, David G. Kresty, Laura A. |
author_facet | Zhang, Yun Weh, Katherine M. Howard, Connor L. Riethoven, Jean-Jack Clarke, Jennifer L. Lagisetty, Kiran H. Lin, Jules Reddy, Rishindra M. Chang, Andrew C. Beer, David G. Kresty, Laura A. |
author_sort | Zhang, Yun |
collection | PubMed |
description | Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment-naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification based on TP53 status increased the number of significant isoform switches to 135, suggesting switching events affect cellular functions based on TP53 mutation and tissue histopathology. Analysis of isoforms agnostic, exclusive, and shared with mutant TP53 revealed unique signatures including demethylation, lipid and retinoic acid metabolism, and glucuronidation, respectively. Nearly half of isoform switching events were identified without significant gene-level expression changes. Importantly, two TP53-interacting isoforms, RNF128 and WRAP53, were significantly linked to patient survival. Thus, analysis of isoform switching events may provide new insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC. |
format | Online Article Text |
id | pubmed-9437810 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Society of Gene & Cell Therapy |
record_format | MEDLINE/PubMed |
spelling | pubmed-94378102022-09-10 Characterizing isoform switching events in esophageal adenocarcinoma Zhang, Yun Weh, Katherine M. Howard, Connor L. Riethoven, Jean-Jack Clarke, Jennifer L. Lagisetty, Kiran H. Lin, Jules Reddy, Rishindra M. Chang, Andrew C. Beer, David G. Kresty, Laura A. Mol Ther Nucleic Acids Original Article Isoform switching events with predicted functional consequences are common in many cancers, but characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was used to detect levels of RNA transcripts and identify specific isoforms in treatment-naïve esophageal tissues ranging from premalignant Barrett’s esophagus (BE), BE with low- or high-grade dysplasia (BE.LGD, BE.HGD), and EAC. Samples were stratified by histopathology and TP53 mutation status, identifying significant isoform switching events with predicted functional consequences. Comparing BE.LGD with BE.HGD, a histopathology linked to cancer progression, isoform switching events were identified in 75 genes including KRAS, RNF128, and WRAP53. Stratification based on TP53 status increased the number of significant isoform switches to 135, suggesting switching events affect cellular functions based on TP53 mutation and tissue histopathology. Analysis of isoforms agnostic, exclusive, and shared with mutant TP53 revealed unique signatures including demethylation, lipid and retinoic acid metabolism, and glucuronidation, respectively. Nearly half of isoform switching events were identified without significant gene-level expression changes. Importantly, two TP53-interacting isoforms, RNF128 and WRAP53, were significantly linked to patient survival. Thus, analysis of isoform switching events may provide new insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC. American Society of Gene & Cell Therapy 2022-08-17 /pmc/articles/PMC9437810/ /pubmed/36090744 http://dx.doi.org/10.1016/j.omtn.2022.08.018 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Original Article Zhang, Yun Weh, Katherine M. Howard, Connor L. Riethoven, Jean-Jack Clarke, Jennifer L. Lagisetty, Kiran H. Lin, Jules Reddy, Rishindra M. Chang, Andrew C. Beer, David G. Kresty, Laura A. Characterizing isoform switching events in esophageal adenocarcinoma |
title | Characterizing isoform switching events in esophageal adenocarcinoma |
title_full | Characterizing isoform switching events in esophageal adenocarcinoma |
title_fullStr | Characterizing isoform switching events in esophageal adenocarcinoma |
title_full_unstemmed | Characterizing isoform switching events in esophageal adenocarcinoma |
title_short | Characterizing isoform switching events in esophageal adenocarcinoma |
title_sort | characterizing isoform switching events in esophageal adenocarcinoma |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9437810/ https://www.ncbi.nlm.nih.gov/pubmed/36090744 http://dx.doi.org/10.1016/j.omtn.2022.08.018 |
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