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Profiling of prognostic alternative splicing in melanoma

Fu‑Chao Ma, Rong‑Quan He, Peng Lin, Jin‑Cai Zhong, Jie Ma, Hong Yang, Xiao‑Hua Hu, Gang Chen
2019 Oncology Letters  
Alternative splicing can lead to the coding of proteins that act as promoters of cancer, which is associated with the progression of cancer.  ...  However, to the best of our knowledge, no systematic survival analysis of alternative splicing in melanoma has previously been reported.  ...  Alternative splicing can lead to the coding of several types of proteins.  ... 
doi:10.3892/ol.2019.10453 pmid:31423168 pmcid:PMC6607279 fatcat:7hgrxoaznjhkpd7ixye7wsv5ei

The Sequence Ontology: a tool for the unification of genome annotations

Karen Eilbeck, Suzanna E Lewis, Christopher J Mungall, Mark Yandell, Lincoln Stein, Richard Durbin, Michael Ashburner
2005 Genome Biology  
Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a  ...  Exons as alternative parts of transcripts EM-operators can also be used to classify the exons of alternatively spliced genes.  ...  This is particularly so with regard to modes of alternative splicing, as each of the EM operations suggests a distinct category by means of which two alternatively spliced transcripts can be related to  ... 
doi:10.1186/gb-2005-6-5-r44 pmid:15892872 pmcid:PMC1175956 fatcat:5ys5nkm235hphfqtl3nqlcwxg4

Colorectal Cancer with EML4-ALK Fusion Gene Response to Alectinib: A Case Report and Review of the Literature

Sheng-Yen Hsiao, Hong-Lin He, Teng-Song Weng, Cheng-Yao Lin, Chien-Ming Chao, Wen-Tsung Huang, Chao-Jung Tsao
2021 Case Reports in Oncology  
However, advanced CRC with ALK gene alteration responds to ALK inhibitor. It is reasonable to check ALK gene alteration in clinical practice for CRC.  ...  Anaplastic lymphoma kinase (ALK) gene alternation is one of potential target for biomarker-guided therapy for CRC.  ...  Acknowledgments We would like to thank Foundation Medicine for providing data of comprehensive genetic profiling.  ... 
doi:10.1159/000511069 pmid:33776709 pmcid:PMC7983623 fatcat:ydwh73kpjranzd56t7g56dfhzy

Downstream intronic splicing enhancers

Julian P. Venables
2007 FEBS Letters  
Alternative splicing leads to multiple proteins from individual genes and the most common deviation from the norm is precise exon omission.  ...  Mutations that cause this can be found deep in introns, especially downstream of the cassette exon.  ...  Alternative transcripts can result from splicing these alternative terminal exons to common internal exons.  ... 
doi:10.1016/j.febslet.2007.08.012 pmid:17716673 fatcat:f3q2gimy4na7ditwiufsmz7hce

Genome-wide identification of alternative splicing associated with histone deacetylase inhibitor in cutaneous T-cell lymphomas

Shirong Yu, Jingzhan Zhang, Yuan Ding, Xiaojing Kang, Xiongming Pu
2022 Frontiers in Genetics  
Human histone deacetylase inhibitors (HDACi) targeted therapy has become a promising treatment strategy in recent years, but some patients can develop resistance to the drug, leading to treatment failure  ...  Student's t-tests were performed to evaluate the significance of changes in ratios for AS events, and regulated alternative splicing events (RASEs) were defined as events with p values less than 0.05.  ...  Acknowledgments We are grateful to all of the participants and their family for cooperation. We also thank Chao Cheng from Ablife Inc. For his kind help in the performance of the bioinformatics.  ... 
doi:10.3389/fgene.2022.937623 pmid:36147491 pmcid:PMC9485882 fatcat:grh7m7jrqbgkteuekhfap5ruw4

Aberrant alternative splicing in breast cancer

2019 Journal of Molecular Cell Biology  
Strikingly, alternative splicing is closely associated with breast cancer development. Here, we seek to provide a general review of the relationship between alternative splicing and breast cancer.  ...  Based on the statistical data, breast cancer is one of the top leading causes of cancer-related deaths in women worldwide.  ...  For example, ASOs can dramatically switch SMN2 splicing patterns, leading to nearly complete inclusion of exon 7 and thus significantly increasing functional SMN protein (Hua et al., 2010) .  ... 
doi:10.1093/jmcb/mjz033 pmid:31065692 pmcid:PMC6884705 fatcat:ikx4fvx27raghjgm5ycparw3cu

CD47 target: from theory to reality

John Wu
2014 Biomedical Research and Therapy  
This high expression help tumor cells to escape from the immune system. To date, the CD47 receptor becomes the interesting target in cancer treatment.  ...  From these results, some clinical trials were suggested to test the safety and efficacy of anti-CD47 therapy.  ...  CD47 consists of an extracellular IgV domain, a five times transmembranespanning domain, and a short alternatively spliced cytoplasmic tail.  ... 
doi:10.7603/s40730-014-0007-4 fatcat:rjt2eh6hmveedg4ewaymc3nhpm

Function of alternative splicing

Olga Kelemen, Paolo Convertini, Zhaiyi Zhang, Yuan Wen, Manli Shen, Marina Falaleeva, Stefan Stamm
2013 Gene  
The overall function of alternative splicing is to increase the diversity of mRNAs expressed from the genome.  ...  Due to its widespread usage and molecular versatility, alternative splicing emerges as a central element in gene regulation that interferes with almost every biological function analyzed.  ...  A change in alternative splicing can lead to human diseases, as summarized in section 3.1.4.  ... 
doi:10.1016/j.gene.2012.07.083 pmid:22909801 pmcid:PMC5632952 fatcat:4t6cozxi2vffnnkhm6difvwhnu

Regulatory roles and mechanisms of alternative RNA splicing in adipogenesis and human metabolic health

Yunqi Chao, Yonghui Jiang, Mianling Zhong, Kaiyan Wei, Chenxi Hu, Yifang Qin, Yiming Zuo, Lili Yang, Zheng Shen, Chaochun Zou
2021 Cell & Bioscience  
Therefore, significant attempts have been finally made to overview novel detailed discussion on the prospects of splicing machinery with obesity and metabolic disorders to supply featured potential management  ...  Here, we integrate the available findings on specific splicing events and distinct functions of different splicing regulators as examples to highlight the directive biological contribution of AS mechanism  ...  About 95% of human multi-exon genes can undergo splicing process [3] ; nevertheless, a large majority of alternatively spliced variants may not be translated into proteins, so very few annotated alternative  ... 
doi:10.1186/s13578-021-00581-w pmid:33795017 fatcat:52u6raeepjetre5tcj5yp65qpy

Krüppel-Like Factor 6 Splice Variant 1: An Oncogenic Transcription Factor Involved in the Progression of Multiple Malignant Tumors

Kang Hu, Qing-Kang Zheng, Rui-Jie Ma, Chao Ma, Zhi-Gang Sun, Nan Zhang
2021 Frontiers in Cell and Developmental Biology  
Krüppel-like factor 6 splice variant 1 (KLF6-SV1), being one of the alternative KLF6 splicing isoforms, participates in tumor occurrence and development and has the potential to become a new target for  ...  Recently, it has been considered to play a role in combatting cancer.  ...  All the authors contributed to manuscript revision, read and approved the submitted version.  ... 
doi:10.3389/fcell.2021.661731 pmid:33816511 pmcid:PMC8017371 fatcat:gnmvouipv5guxocesaivr6dc2q

Alternative splicing factor ASF/SF2 is down regulated in inflamed muscle

Z Xiong
2006 Journal of Clinical Pathology  
treatments can be facilitated by the ongoing study of alternative splicing of autoantigen transcripts.  ...  Aim: To examine the novel hypothesis that the expression of an essential alternative splicing factor, alternative splicing factor 2 (ASF/SF2), is modulated in muscle inflammation.  ...  Funding was also provided by the Myositis Association of America, the Kostas Family Foundation and TT Chao Scholar Award (X-FY).  ... 
doi:10.1136/jcp.2005.032961 pmid:16574722 pmcid:PMC1860460 fatcat:ks3nhaiqs5axteizaut567ouxa

Alternative splicing of mRNA in colorectal cancer: new strategies for tumor diagnosis and treatment

Yanyan Chen, Mengxi Huang, Xiaolong Liu, Yadi Huang, Chao Liu, Jialong Zhu, Gongbo Fu, Zengjie Lei, Xiaoyuan Chu
2021 Cell Death and Disease  
This process leads to several mature transcript variants with diverse physiological functions.  ...  AbstractAlternative splicing (AS) is an important event that contributes to posttranscriptional gene regulation.  ...  It initiates a cascade of events that eventually lead to programmed cell death.  ... 
doi:10.1038/s41419-021-04031-w pmid:34330892 pmcid:PMC8324868 fatcat:yrpmarxnkrgh7jmi545fcsojiu

Function, clinical application, and strategies of Pre-mRNA splicing in cancer

Cuixia Di, Syafrizayanti, Qianjing Zhang, Yuhong Chen, Yupei Wang, Xuetian Zhang, Yang Liu, Chao Sun, Hong Zhang, Jörg D Hoheisel
2018 Cell Death and Differentiation  
Pre-mRNA splicing is a fundamental process that plays a considerable role in generating protein diversity. Pre-mRNA splicing is also the key to the pathology of numerous diseases, especially cancers.  ...  Furthermore, this review discusses emerging strategies how to modulate pathologic aberrant splicing isoforms, which are attractive, novel therapeutic agents in cancer.  ...  In addition to protein diversity, AS can also lead to reduced translation of mRNAs through introduction of a premature stop codon leading to sequestration and degradation of transcripts in the nucleus;  ... 
doi:10.1038/s41418-018-0231-3 pmid:30464224 pmcid:PMC6748147 fatcat:yh2ralegevfchh4irxryqmuf3e

Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant

Jeroen J. Smits, Suzanne E. de Bruijn, Cornelis P. Lanting, Jaap Oostrik, Luke O'Gorman, Tuomo Mantere, M. F. van Dooren, S. G. Kant, H. H. W. de Gier, E. H. Hoefsloot, M. P. van der Schroeff, L. J. C. Rotteveel (+31 others)
2021 Human Genetics  
Short-read whole-genome sequencing of the six M1 cases without this haplotype and the two M0/CEVA cases only revealed previously overlooked or misinterpreted splice-altering SLC26A4 variants in two cases  ...  We found this haplotype and a delimited V1-CEVA haplotype to be significantly enriched in our M1 patient cohort (10/16 cases). The CEVA haplotype was also present in two M0 cases (2/12).  ...  Indeed, an in vitro splice assay confirmed that the alternative splice acceptor site is used, which leads to the partial deletion of exon 5 and a truncated protein [p.  ... 
doi:10.1007/s00439-021-02336-6 pmid:34410491 pmcid:PMC9035008 fatcat:23v7fwia65gfxflbe4h7l2rl5q

TrkB Truncated Isoform Receptors as Transducers and Determinants of BDNF Functions

Lino Tessarollo, Sudhirkumar Yanpallewar
2022 Frontiers in Neuroscience  
Brain-derived neurotrophic factor (BDNF) belongs to the neurotrophin family of secreted growth factors and binds with high affinity to the TrkB tyrosine kinase receptors.  ...  The TrkB gene, in addition to the full-length receptor, encodes a number of isoforms, including some lacking the catalytic tyrosine kinase domain.  ...  ACKNOWLEDGMENTS This review is dedicated to Dionisio Martin-Zanca (1952, a great mentor and scientist.  ... 
doi:10.3389/fnins.2022.847572 pmid:35321093 pmcid:PMC8934854 fatcat:mekxelf4yfhljo3ruxp3ti5eju
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