June 6, 2022
Looking Beyond Coding DNA
What role does the untranslated portion of the genome play in cancer progression? It turns out that altered splicing in some noncoding regions of mRNA transcripts promotes oncogene expression in tumor cells.
To better understand and quantify this phenomenon, scientists at King Abdullah University of Science and Technology (KAUST) developed a new interactive web portal using RNA-seq-based splicing data from the Cancer Genome Atlas and corresponding tissues from the Genotype-Tissue Expression. The researchers identified and quantified 7,917 splice sites in the 3’ untranslated regions (3’UTRs) in RNA-seq data from samples across 10 cancer types from the Cancer Genome Atlas.
An RNA-Seq-Based Tool for Investigating Splicing in 3’UTRs
The tool is called “SpUR” (Splicing in Untranslated Regions), and includes over 1,000 different splicing events that are found in cancers for the nearly 8,000 samples and their corresponding normal tissues. Since the tool is freely available, it is a valuable resource for independent research teams to investigate the roles of individual splicing events commonly found in cancer.
Blocking Aberrant Splicing May be a New Therapeutic Strategy
The creation of this database followed from the observation by lead researchers Gao, Zhang and Salhi that tumor aggression-related genes seemed to have higher incidences of altered downstream splicing, and that higher numbers of these splice variants correlates with poorer survival outcomes. In fact, blocking the splicing process in 3’UTRs of liver cancer cells helped suppress tumor growth in vitro. Their work, by Chan et. al., was published in Nature Cell Biology last month.
Outsourcing Bioinformatics Analysis
Though the SpUR tool is freely available, and illustrates the power of scRNA-seq for research, the initial process of interpreting single cell RNA-seq data is a challenging computational and bioinformatic task. Outsourcing your bioinformatic analysis to experts like our team at Bridge Informatics helps eliminate common challenges with these projects. If you’re interested, book a free discovery call with us today to discuss your project needs, or download our services overview.
Jane Cook, Journalist & Content Writer, Bridge Informatics
Jane is a Content Writer at Bridge Informatics, a professional services firm that helps biotech customers implement advanced techniques in management and analysis of genomic data. Bridge Informatics focuses on data mining, machine learning, and various bioinformatic techniques to discover biomarkers and companion diagnostics. If you’re interested in reaching out, please email daniel.dacey@old.bridgeinformatics.com or dan.ryder@old.bridgeinformatics.com.
Sources:
https://www.nature.com/articles/s41556-022-00913-z
