Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies

Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances...

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Autores principales:	Tülay Karakulak, Holger Moch, Christian von Mering, Abdullah Kahraman
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	alternative splicing isoform switching pan-cancer analysis bioinformatics tools and databases differential transcript usage Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/b81a7f5d0cbe4d7aadd5452cb9527017
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spelling	oai:doaj.org-article:b81a7f5d0cbe4d7aadd5452cb95270172021-11-30T13:38:58ZProbing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies2296-889X10.3389/fmolb.2021.726902https://doaj.org/article/b81a7f5d0cbe4d7aadd5452cb95270172021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmolb.2021.726902/fullhttps://doaj.org/toc/2296-889XAlternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances in sequencing technologies and analysis methods led to new insights into the extent and functional impact of disturbed alternative splicing events. In this review, we give a brief overview of the molecular mechanisms driving alternative splicing, highlight the function of alternative splicing in healthy tissues and describe how alternative splicing is disrupted in cancer. We summarize current available computational tools for analyzing differential transcript usage, isoform switching events, and the pathogenic impact of cancer-specific splicing events. Finally, the strategies of three recent pan-cancer studies on isoform switching events are compared. Their methodological similarities and discrepancies are highlighted and lessons learned from the comparison are listed. We hope that our assessment will lead to new and more robust methods for cancer-specific transcript detection and help to produce more accurate functional impact predictions of isoform switching events.Tülay KarakulakTülay KarakulakTülay KarakulakHolger MochHolger MochChristian von MeringChristian von MeringAbdullah KahramanAbdullah KahramanFrontiers Media S.A.articlealternative splicingisoform switchingpan-cancer analysisbioinformatics tools and databasesdifferential transcript usageBiology (General)QH301-705.5ENFrontiers in Molecular Biosciences, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	alternative splicing isoform switching pan-cancer analysis bioinformatics tools and databases differential transcript usage Biology (General) QH301-705.5
spellingShingle	alternative splicing isoform switching pan-cancer analysis bioinformatics tools and databases differential transcript usage Biology (General) QH301-705.5 Tülay Karakulak Tülay Karakulak Tülay Karakulak Holger Moch Holger Moch Christian von Mering Christian von Mering Abdullah Kahraman Abdullah Kahraman Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies
description	Alternative splicing is an essential regulatory mechanism for gene expression in mammalian cells contributing to protein, cellular, and species diversity. In cancer, alternative splicing is frequently disturbed, leading to changes in the expression of alternatively spliced protein isoforms. Advances in sequencing technologies and analysis methods led to new insights into the extent and functional impact of disturbed alternative splicing events. In this review, we give a brief overview of the molecular mechanisms driving alternative splicing, highlight the function of alternative splicing in healthy tissues and describe how alternative splicing is disrupted in cancer. We summarize current available computational tools for analyzing differential transcript usage, isoform switching events, and the pathogenic impact of cancer-specific splicing events. Finally, the strategies of three recent pan-cancer studies on isoform switching events are compared. Their methodological similarities and discrepancies are highlighted and lessons learned from the comparison are listed. We hope that our assessment will lead to new and more robust methods for cancer-specific transcript detection and help to produce more accurate functional impact predictions of isoform switching events.
format	article
author	Tülay Karakulak Tülay Karakulak Tülay Karakulak Holger Moch Holger Moch Christian von Mering Christian von Mering Abdullah Kahraman Abdullah Kahraman
author_facet	Tülay Karakulak Tülay Karakulak Tülay Karakulak Holger Moch Holger Moch Christian von Mering Christian von Mering Abdullah Kahraman Abdullah Kahraman
author_sort	Tülay Karakulak
title	Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies
title_short	Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies
title_full	Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies
title_fullStr	Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies
title_full_unstemmed	Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies
title_sort	probing isoform switching events in various cancer types: lessons from pan-cancer studies
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/b81a7f5d0cbe4d7aadd5452cb9527017
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Probing Isoform Switching Events in Various Cancer Types: Lessons From Pan-Cancer Studies

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