The actionable transcriptome: a framework for incorporating RNA sequencing into precision oncology

Comprehensive, multiplexed RNA sequencing (RNA-seq) is increasingly being incorporated into molecular tumour-profiling assays owing to overall cost-effectiveness related to enhanced detection of clinically actionable biomarkers. RNA-seq assays are now quite robust, with turnaround times of a few weeks and reasonable costs that support integration into routine clinical workflows. In this Perspective, we propose a framework for incorporating RNA levels and other RNA-seq data into precision oncology that considers RNA levels of oncogenes, tumour suppressors and diverse therapeutic targets, as well as multigene diagnostic, prognostic and predictive signatures; chimeric gene fusion transcripts; splice variants; RNA-based variant and/or mutation calling; and oncoviral gene expression; among other factors. Additionally, we provide a list of genes representing the current actionable transcriptome focused on the predictive utility of RNA-level overexpression of oncogenes and underexpression of tumour-suppressor genes. This list also includes cell-surface targets, given that RNA profiling has demonstrated that many tumour types have clinically relevant expression levels of such targets. The RNA expression levels of certain genes might also be associated with biological features such as homologous recombination deficiency and DNA mismatch repair defects. Taken together, comprehensive RNA profiling can help to identify additional actionable alterations beyond those detected via DNA sequencing and overcome the challenges faced by conventional low-plex assays (such as immunohistochemistry and in situ hybridization), thereby enhancing therapeutic opportunities for personalized cancer care.