Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.

Content Provider	Europe PMC
Author	Ebrahimie, Esmaeil Rahimirad, Samira Tahsili, Mohammadreza Mohammadi-Dehcheshmeh, Manijeh
Copyright Year	2021
Abstract	Alternative ribonucleic acid (RNA) splicing can lead to the assembly of different protein isoforms with distinctive functions. The outcome of alternative splicing (AS) can result in a complete loss of function or the acquisition of new functions. There is a gap in knowledge of abnormal RNA splice variants promoting cancer stem cells (CSCs), and their prospective contribution in cancer progression. AS directly regulates the self-renewal features of stem cells (SCs) and stem-like cancer cells. Notably, octamer-binding transcription factor 4A spliced variant of octamer-binding transcription factor 4 contributes to maintaining stemness properties in both SCs and CSCs. The epithelial to mesenchymal transition pathway regulates the AS events in CSCs to maintain stemness. The alternative spliced variants of CSCs markers, including cluster of differentiation 44, aldehyde dehydrogenase, and doublecortin-like kinase, α6β1 integrin, have pivotal roles in increasing self-renewal properties and maintaining the pluripotency of CSCs. Various splicing analysis tools are considered in this study. LeafCutter software can be considered as the best tool for differential splicing analysis and identification of the type of splicing events. Additionally, LeafCutter can be used for efficient mapping splicing quantitative trait loci. Altogether, the accumulating evidence re-enforces the fact that gene and protein expression need to be investigated in parallel with alternative splice variants.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8567453&blobtype=pdf
Journal	World Journal of Stem Cells [World J Stem Cells]
Volume Number	13
DOI	10.4252/wjsc.v13.i10.1394
PubMed Central reference number	PMC8567453
Issue Number	10
PubMed reference number	34786151
e-ISSN	19480210
Language	English
Publisher	Baishideng Publishing Group Inc
Publisher Date	2021-10-01
Access Restriction	Open
Rights License	This article is an open-access article that was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution NonCommercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/Licenses/by-nc/4.0/ ©The Author(s) 2021. Published by Baishideng Publishing Group Inc. All rights reserved.
Subject Keyword	Alternative splicing Stem cell Cancer stem cell Transcriptome Expression analysis
Content Type	Text
Resource Type	Article
Subject	Cell Biology Genetics Molecular Biology Genetics (clinical) Histology