Transcriptome-wide identification and study of cancer-specific splicing events across multiple tumors

Oncotarget
Yihsuan S TsaiZefeng Wang

Abstract

Dysregulation of alternative splicing (AS) is one of the molecular hallmarks of cancer, with splicing alteration of numerous genes in cancer patients. However, studying splicing mis-regulation in cancer is complicated by the large noise generated from tissue-specific splicing. To obtain a global picture of cancer-specific splicing, we analyzed transcriptome sequencing data from 1149 patients in The Cancer Genome Atlas project, producing a core set of AS events significantly altered across multiple cancer types. These cancer-specific AS events are highly conserved, are more likely to maintain protein reading frame, and mainly function in cell cycle, cell adhesion/migration, and insulin signaling pathways. Furthermore, these events can serve as new molecular biomarkers to distinguish cancer from normal tissues, to separate cancer subtypes, and to predict patient survival. We also found that most genes whose expression is closely associated with cancer-specific splicing are key regulators of the cell cycle. This study uncovers a common set of cancer-specific AS events altered across multiple cancers, providing mechanistic insight into how splicing is mis-regulated in cancers.

References

Feb 2, 2002·Nature·Laura J van 't VeerStephen H Friend
Jun 12, 2002·Molecular Biology of the Cell·Michael L WhitfieldDavid Botstein
Jul 13, 2002·Science·William G FairbrotherChristopher B Burge
Dec 18, 2002·Critical Reviews in Clinical Laboratory Sciences·David NaorYoram Faitelson
Dec 20, 2002·The New England Journal of Medicine·Marc J van de VijverRené Bernards
Jan 15, 2003·BMC Bioinformatics·Gary D Bader, Christopher W V Hogue
Nov 3, 2004·Cancer Research·Julian P Venables
Jun 16, 2005·Nature Reviews. Molecular Cell Biology·Arianne J MatlinChristopher W J Smith
Feb 21, 2007·Nature Structural & Molecular Biology·Rotem KarniAdrian R Krainer
Feb 27, 2007·Oncogene·J M Adams, S Cory
Nov 4, 2008·Nature·Eric T WangChristopher B Burge
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 11, 2009·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Joel S ParkerPhilip S Bernard
Oct 6, 2009·Nature Methods·Yang WangZefeng Wang
Aug 31, 2010·Nucleic Acids Research·Kai WangJinze Liu
Nov 9, 2010·Nature Methods·Yarden KatzChristopher B Burge
Dec 15, 2010·Molecular Oncology·Aleix Prat, Charles M Perou
Sep 15, 2011·The EMBO Journal·Clare V LefaveLuca Cartegni
Sep 18, 2012·Nature Structural & Molecular Biology·Yang WangZefeng Wang
Oct 18, 2012·Nature Reviews. Molecular Cell Biology·Stephanie Kervestin, Allan Jacobson
Dec 18, 2012·Nature Structural & Molecular Biology·Yang WangZefeng Wang
Feb 7, 2013·Nature Reviews. Molecular Cell Biology·Alberto R KornblihttManuel J Muñoz
Apr 23, 2013·Scientific Reports·Jeyanthy EswaranRakesh Kumar
Aug 29, 2013·International Journal of Cell Biology·Claudio Sette
Sep 28, 2013·Nature Genetics·UNKNOWN Cancer Genome Atlas Research NetworkJoshua M Stuart
Oct 23, 2013·Cancer Discovery·Jian Zhang, James L Manley
Jan 24, 2014·Nature Reviews. Molecular Cell Biology·A Gregory Matera, Zefeng Wang
Mar 25, 2014·Seminars in Cell & Developmental Biology·Giuseppe BiamontiClaudia Ghigna
Apr 12, 2014·PLoS Genetics·Feng-Yang ZongJingyi Hui

❮ Previous
Next ❯

Citations

Oct 3, 2018·Nucleic Acids Research·Nuno Saraiva-Agostinho, Nuno L Barbosa-Morais
Oct 12, 2018·Carcinogenesis·Shuangshuang MaoJie He
Sep 4, 2019·Journal of Cellular Biochemistry·Jiali WangLihua Liu
Sep 18, 2017·Journal of Integrative Bioinformatics·Vladimir N BabenkoYuriy L Orlov
Aug 1, 2015·World Journal of Gastroenterology : WJG·Takahiro KishikawaKazuhiko Koike
Aug 1, 2019·Scientific Reports·Alexander Bernd KnierimTorsten Schöneberg
Apr 19, 2020·Nature Reviews. Clinical Oncology·Sophie C BonnalJuan Valcárcel
Nov 18, 2015·Current Opinion in Oncology·Cherine Abou FaycalBeatrice Eymin
May 12, 2017·Scientific Reports·Je-Keun RheeTae-Min Kim
Jun 14, 2017·Human Genetics·Fabiana Marcelino MelisoLuiz O Penalva
Jun 10, 2016·Nature Communications·Shihao ShenYi Xing
Nov 16, 2019·BMC Medical Genomics·Yaomin LiYawei Liu
Feb 14, 2019·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Timothy J RobinsonSteven R Patierno
Mar 3, 2021·Communications Biology·Romain DarrigrandSébastien Apcher

❮ Previous
Next ❯

Methods Mentioned

BETA
RNA-seq
PCA

Software Mentioned

DAVID
MISO
CLUSTALW
MapSplice
RSEM
MCODE
PAM50

Related Concepts

Related Feeds

Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.

Cancer -Omics

A variety of different high-throughput technologies can be used to identify the complete catalog of changes that characterize the molecular profile of cohorts of tumor samples. Discover the latest insights gained from cancer 'omics' in this feed.

Adhesion Molecules in Health and Disease

Cell adhesion molecules are a subset of cell adhesion proteins located on the cell surface involved in binding with other cells or with the extracellular matrix in the process called cell adhesion. In essence, cell adhesion molecules help cells stick to each other and to their surroundings. Cell adhesion is a crucial component in maintaining tissue structure and function. Discover the latest research on adhesion molecule and their role in health and disease here.

© 2022 Meta ULC. All rights reserved