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Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma
Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-se...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5514065/ https://www.ncbi.nlm.nih.gov/pubmed/28717182 http://dx.doi.org/10.1038/s41598-017-05537-0 |
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author | Bjørklund, Sunniva Stordal Panda, Anshuman Kumar, Surendra Seiler, Michael Robinson, Doug Gheeya, Jinesh Yao, Ming Alnæs, Grethe I. Grenaker Toppmeyer, Deborah Riis, Margit Naume, Bjørn Børresen-Dale, Anne-Lise Kristensen, Vessela N. Ganesan, Shridar Bhanot, Gyan |
author_facet | Bjørklund, Sunniva Stordal Panda, Anshuman Kumar, Surendra Seiler, Michael Robinson, Doug Gheeya, Jinesh Yao, Ming Alnæs, Grethe I. Grenaker Toppmeyer, Deborah Riis, Margit Naume, Bjørn Børresen-Dale, Anne-Lise Kristensen, Vessela N. Ganesan, Shridar Bhanot, Gyan |
author_sort | Bjørklund, Sunniva Stordal |
collection | PubMed |
description | Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort. Alternative exon usage was widespread, and although common events were shared among three subtypes, ER+ HER2−, ER− HER2−, and HER2+, many events on the exon level were subtype specific. Additional RNA-seq analysis was carried out in an independent cohort of 43 ER+ HER2− and ER− HER2− primary breast tumors, confirming many of the exon events identified in the TCGA cohort. Alternative splicing and transcriptional events detected in five genes, MYO6, EPB41L1, TPD52, IQCG, and ACOX2 were validated by qRT-PCR in a third cohort of 40 ER+ HER2− and ER− HER2− patients, showing that these events were truly subtype specific. |
format | Online Article Text |
id | pubmed-5514065 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-55140652017-07-19 Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma Bjørklund, Sunniva Stordal Panda, Anshuman Kumar, Surendra Seiler, Michael Robinson, Doug Gheeya, Jinesh Yao, Ming Alnæs, Grethe I. Grenaker Toppmeyer, Deborah Riis, Margit Naume, Bjørn Børresen-Dale, Anne-Lise Kristensen, Vessela N. Ganesan, Shridar Bhanot, Gyan Sci Rep Article Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort. Alternative exon usage was widespread, and although common events were shared among three subtypes, ER+ HER2−, ER− HER2−, and HER2+, many events on the exon level were subtype specific. Additional RNA-seq analysis was carried out in an independent cohort of 43 ER+ HER2− and ER− HER2− primary breast tumors, confirming many of the exon events identified in the TCGA cohort. Alternative splicing and transcriptional events detected in five genes, MYO6, EPB41L1, TPD52, IQCG, and ACOX2 were validated by qRT-PCR in a third cohort of 40 ER+ HER2− and ER− HER2− patients, showing that these events were truly subtype specific. Nature Publishing Group UK 2017-07-17 /pmc/articles/PMC5514065/ /pubmed/28717182 http://dx.doi.org/10.1038/s41598-017-05537-0 Text en © The Author(s) 2017 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Bjørklund, Sunniva Stordal Panda, Anshuman Kumar, Surendra Seiler, Michael Robinson, Doug Gheeya, Jinesh Yao, Ming Alnæs, Grethe I. Grenaker Toppmeyer, Deborah Riis, Margit Naume, Bjørn Børresen-Dale, Anne-Lise Kristensen, Vessela N. Ganesan, Shridar Bhanot, Gyan Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma |
title | Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma |
title_full | Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma |
title_fullStr | Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma |
title_full_unstemmed | Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma |
title_short | Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma |
title_sort | widespread alternative exon usage in clinically distinct subtypes of invasive ductal carcinoma |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5514065/ https://www.ncbi.nlm.nih.gov/pubmed/28717182 http://dx.doi.org/10.1038/s41598-017-05537-0 |
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