Researchers use a combination of third generation long-read RNA sequencing technology and short-read RNAseq to characterize the splicing landscape of prostate cancer

Researchers from the Icahn School of Medicine characterize the transcriptional splicing landscape of a prostate cancer cell line treated with a previously identified synergistic drug combination. They use a combination of third generation long-read RNA sequencing technology and short-read RNAseq to create a high-fidelity map of expressed isoforms and fusions to quantify splicing events triggered by treatment. The researchers find strong evidence for drug-induced, coherent splicing changes which disrupt the function of oncogenic proteins, and detect novel transcripts arising from previously unreported fusion events.

A schematic of study design

rna-seq Three biological replicates of short read RNAseq were generated for untreated (DMSO) and treated (TM) and used for subsequent analysis; long read sequencing were performed for untreated and treated samples. Both technologies were combined for isoform quantification and identification of fusion events.

Chen X, Houten S, Allette K, Sebra RP, Stolovitzky G, Losic B. (2018) Characterization of drug-induced splicing complexity in prostate cancer cell line using long read technology. Pac Symp Biocomput 23:8-19. [article]

Leave a Reply

Your email address will not be published. Required fields are marked *

*

Time limit is exhausted. Please reload CAPTCHA.