Open AccessAlternate Splicing in Head and Neck Cancer: An Update
Author(s) -
Amrita Nandan,
Vishwas Sharma,
Himanshu Narayan Singh,
Amit Chandra,
Rupal Tripathi,
S. Dhirendra,
Ravi Mehrotra
Publication year - 2018
Publication title -
journal of global oncology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.002
H-Index - 17
ISSN - 2378-9506
DOI - 10.1200/jgo.18.19600
Subject(s) - computational biology , rna splicing , rna seq , intron , rna , exon , gene , alternative splicing , bioinformatics , gene expression , transcriptome , genetics , biology
Background: Alternate splicing (AS) is a regulatory process during gene expression that allows a single gene to code multiple proteins. Sequencing of RNA (RNA-Seq) is a high throughput technology, which has been used in various studies to identify AS mechanisms in head and neck cancer (HNC). Until date, there is no available review that could update us with the major outcomes from these studies. Aim: To perform a comprehensive literature search for AS studies on HNC via RNA-Seq. Methods: A systematic literature search was performed following PRISMA guidelines to give a complete picture of AS in HNC identified through RNA-Seq. In addition, comprehensive search was also performed to identify the bioinformatics softwares that analyses RNA-Seq data for finding AS in cancer. Results: Six studies were found that used RNA-Seq data for identifying AS events in HNC. Five softwares were used by these studies to identify AS events, of which Suppa and AltAnalyze can also categorize all four AS events to subtypes, i.e., cassette exon skipping (ES), intron retention (IR), mutually exclusive exon (MXE), and alternative 5′ and 3′ splice site (ASS). Additionally, SplAdder, ASprofile, JuncBASE, and MATS softwares have been used to identify and categorize AS events in cancers other than HNC. Conclusion: Alternate splicing in HNC is a complex regulatory process of gene expression. It can be studied through RNA-Seq using various bioinformatics softwares. SplAdder, ASprofile, JuncBASE, and MATS have been used to identify and characterize other cancers, but not implemented in HNC, and hence could be used for studying AS in HNC.