Mechanisms of RNA dysregulation in cancer. Trends in Pharmacological Sciences, 2021.

Tumor antigens arising from RNA dysregulation may represent an extensive but largely unexplored repertoire of novel cancer immunotherapy targets. Multiple mechanisms of RNA dysregulation, e.g. dysregulated RNA splicing, RNA modifications, transposable element expression, and chimeric fusion transcripts, have been demonstrated as sources of immunotherapy targets.

Multiomic and big data strategies to discover RNA dysregulation-derived immunotherapy targets. Trends in Pharmacological Sciences, 2021.

Recently, our lab developed IRIS (Isoform peptides from RNA splicing for Immunotherapy target Screening), a computational platform leveraging large-scale short-read RNA-seq data of cancer and normal transcriptomes to discover splicing-derived tumor antigens for TCR and CAR-T therapies. 

IRIS employs rMATS-turbo, our lab’s ultra-fast and widely used tool for alternative splicing analysis, to large-scale short-read RNA-seq data to identity high-confidence antigens. Currently, we are investigating ways to integrate long-read data and proteomics data into the IRIS pipeline to better characterize antigens.