Bioinformatic approaches to the analysis of alternative splicing variants in cancer biology

Author(s):  
Lue Ping Zhao ◽  
Jessica Andriesen ◽  
Wenhong Fan
Cancers ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 18
Author(s):  
Jose J. G. Marin ◽  
Maria Reviejo ◽  
Meraris Soto ◽  
Elisa Lozano ◽  
Maitane Asensio ◽  
...  

The two most frequent primary cancers affecting the liver, whose incidence is growing worldwide, are hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), which are among the five most lethal solid tumors with meager 5-year survival rates. The common difficulty in most cases to reach an early diagnosis, the aggressive invasiveness of both tumors, and the lack of favorable response to pharmacotherapy, either classical chemotherapy or modern targeted therapy, account for the poor outcome of these patients. Alternative splicing (AS) during pre-mRNA maturation results in changes that might affect proteins involved in different aspects of cancer biology, such as cell cycle dysregulation, cytoskeleton disorganization, migration, and adhesion, which favors carcinogenesis, tumor promotion, and progression, allowing cancer cells to escape from pharmacological treatments. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the available information regarding the impact of AS on liver carcinogenesis and the development of malignant characteristics of HCC and iCCA, whose understanding is required to develop novel therapeutical approaches aimed at manipulating the phenotype of cancer cells.


Lung Cancer ◽  
2009 ◽  
Vol 64 (3) ◽  
pp. 271-276 ◽  
Author(s):  
Francesca Malentacchi ◽  
Lisa Simi ◽  
Caterina Nannelli ◽  
Matteo Andreani ◽  
Alberto Janni ◽  
...  

Cancers ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 666 ◽  
Author(s):  
Andrew T. Ludlow ◽  
Aaron L. Slusher ◽  
Mohammed E. Sayed

The reactivation of telomerase in cancer cells remains incompletely understood. The catalytic component of telomerase, hTERT, is thought to be the limiting component in cancer cells for the formation of active enzymes. hTERT gene expression is regulated at several levels including chromatin, DNA methylation, transcription factors, and RNA processing events. Of these regulatory events, RNA processing has received little attention until recently. RNA processing and alternative splicing regulation have been explored to understand how hTERT is regulated in cancer cells. The cis- and trans-acting factors that regulate the alternative splicing choice of hTERT in the reverse transcriptase domain have been investigated. Further, it was discovered that the splicing factors that promote the production of full-length hTERT were also involved in cancer cell growth and survival. The goals are to review telomerase regulation via alternative splicing and the function of hTERT splicing variants and to point out how bioinformatics approaches are leading the way in elucidating the networks that regulate hTERT splicing choice and ultimately cancer growth.


2020 ◽  
Vol 21 (19) ◽  
pp. 6984
Author(s):  
Hye-Yeon Seok ◽  
Jimin Ha ◽  
Sun-Young Lee ◽  
Hyoungjoon Bae ◽  
Yong-Hwan Moon

AtERF73/HRE1 is an AP2/ERF transcription factor in Arabidopsis and has two distinct alternative splicing variants, HRE1α and HRE1β. In this study, we examined the differences between the molecular functions of HRE1α and HRE1β. We found that HRE1α and HRE1β are both involved in hypoxia response and root development and have transactivation activity. Two conserved motifs in the C-terminal region of HRE1α and HRE1β, EELL and LWSY-like, contributed to their transactivation activity, specifically the four E residues in the EELL motif and the MGLWS amino acid sequence at the end of the LWSY-like motif. The N-terminal region of HRE1β also showed transactivation activity, mediated by the VDDG motif, whereas that of HRE1α did not. The transactivation activity of HRE1β was stronger than that of HRE1α in Arabidopsis protoplasts. Both transcription factors transactivated downstream genes via the GCC box. RNA-sequencing analysis further supported that both HRE1α and HRE1β might regulate gene expression associated with the hypoxia stress response, although they may transactivate different subsets of genes in downstream pathways. Our results, together with previous studies, suggested that HRE1α and HRE1β differentially transactivate downstream genes in hypoxia response and root development in Arabidopsis.


Author(s):  
Isabel Lastres-Becker ◽  
David Nonis ◽  
Joachim Nowock ◽  
Georg Auburger

2004 ◽  
Vol 21 (1) ◽  
pp. 65-71 ◽  
Author(s):  
Yuichi ISHIKAWA ◽  
Masaki ENDO ◽  
Kiyomi ABE ◽  
Keishi OSAKABE ◽  
Nobuyoshi NAKAJIMA ◽  
...  

2020 ◽  
Vol 293 ◽  
pp. 113466 ◽  
Author(s):  
Alex Romero ◽  
Matías Vega ◽  
Natacha Santibáñez ◽  
Johana Spies ◽  
Tatiana Pérez ◽  
...  

Sign in / Sign up

Export Citation Format

Share Document