Systematic characterization of cancer transcriptome at transcript resolution

Transcribed RNAs undergo various regulation and modification to become functional transcripts. Notably, cancer transcriptome has not been fully characterized at transcript resolution. Researchers at the Shanghai Jiao Tong University School of Medicine carried out a reference-based transcript assembly across >1000 cancer cell lines. They identified 498,255 transcripts, approximately half of which are unannotated. Unannotated transcripts are closely associated with cancer-related hallmarks and show clinical significance. The researchers built a high-confidence RNA binding protein (RBP)-transcript regulatory network, wherein most RBPs tend to regulate transcripts involved in cell proliferation. They identified numerous transcripts that are highly associated with anti-cancer drug sensitivity. Furthermore, they established RBP-transcript-drug axes, wherein PTBP1 is experimentally validated to affect the sensitivity to decitabine by regulating KIAA1522-a6 transcript. Finally, the researchers  established a user-friendly data portal to serve as a valuable resource for understanding cancer transcriptome diversity and its potential clinical utility at transcript level. This study substantially extends cancer RNA repository and will facilitate anti-cancer drug discovery.

Diagram of the TAiC data portal

Fig. 6

a Overall design of the TAiC data portal. b The full resource of TAiC is available to search, browse, visualize, and download. TAiC offers access to the transcriptional atlas of transcripts, coding potential of unannotated and non-coding transcripts, RBP-transcript regulation, transcript-drug and clinical associations.

Availability – the Transcript Atlas in Cancer (TAiC) is available at: http://www.shenglilabs.com/TAiC/

Hu W, Wu Y, Shi Q, Wu J, Kong D, Wu X, He X, Liu T, Li S. (2022) Systematic characterization of cancer transcriptome at transcript resolution. Nat Commun 13(1):6803. [article]

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