Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma

Abstract 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...

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Autores principales:	Sunniva Stordal Bjørklund, Anshuman Panda, Surendra Kumar, Michael Seiler, Doug Robinson, Jinesh Gheeya, Ming Yao, Grethe I. Grenaker Alnæs, Deborah Toppmeyer, Margit Riis, Bjørn Naume, Anne-Lise Børresen-Dale, Vessela N. Kristensen, Shridar Ganesan, Gyan Bhanot
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/04aae0fbd2df49be972341931d0609b5
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spelling	oai:doaj.org-article:04aae0fbd2df49be972341931d0609b52021-12-02T12:32:45ZWidespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma10.1038/s41598-017-05537-02045-2322https://doaj.org/article/04aae0fbd2df49be972341931d0609b52017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05537-0https://doaj.org/toc/2045-2322Abstract 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.Sunniva Stordal BjørklundAnshuman PandaSurendra KumarMichael SeilerDoug RobinsonJinesh GheeyaMing YaoGrethe I. Grenaker AlnæsDeborah ToppmeyerMargit RiisBjørn NaumeAnne-Lise Børresen-DaleVessela N. KristensenShridar GanesanGyan BhanotNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-15 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sunniva Stordal Bjørklund Anshuman Panda Surendra Kumar Michael Seiler Doug Robinson Jinesh Gheeya Ming Yao Grethe I. Grenaker Alnæs Deborah Toppmeyer Margit Riis Bjørn Naume Anne-Lise Børresen-Dale Vessela N. Kristensen Shridar Ganesan Gyan Bhanot Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma
description	Abstract 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	article
author	Sunniva Stordal Bjørklund Anshuman Panda Surendra Kumar Michael Seiler Doug Robinson Jinesh Gheeya Ming Yao Grethe I. Grenaker Alnæs Deborah Toppmeyer Margit Riis Bjørn Naume Anne-Lise Børresen-Dale Vessela N. Kristensen Shridar Ganesan Gyan Bhanot
author_facet	Sunniva Stordal Bjørklund Anshuman Panda Surendra Kumar Michael Seiler Doug Robinson Jinesh Gheeya Ming Yao Grethe I. Grenaker Alnæs Deborah Toppmeyer Margit Riis Bjørn Naume Anne-Lise Børresen-Dale Vessela N. Kristensen Shridar Ganesan Gyan Bhanot
author_sort	Sunniva Stordal Bjørklund
title	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_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_sort	widespread alternative exon usage in clinically distinct subtypes of invasive ductal carcinoma
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/04aae0fbd2df49be972341931d0609b5
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Widespread alternative exon usage in clinically distinct subtypes of Invasive Ductal Carcinoma

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