Deciphering the Molecular Mechanism of Alternative Splicing Changes in Cancer
- Yang, Taegyun
- Advisor(s): Xing, Yi;
- Graeber, Thomas
Abstract
Alternative splicing (AS) is an elaborately regulated molecular process incorporating different exons, expanding the proteome diversity from a single gene. AS is involved in virtually all biological processes and diseases, in which the AS process is often dysregulated. Dysregulated AS in cancer is so prevalent that it is now considered a hallmark of cancer. This dysregulation introduces a novel modality to target cancer through splicing modulation. Recent developments in RNA-Sequencing technologies have enabled transcriptome-wide quantification of AS changes in biological processes and diseases, requiring the development of computational methods for deciphering the molecular regulatory mechanisms for the observed AS changes in biological processes, diseases, and treatments.AS process is regulated by multitudes of RNA binding proteins (RBPs), each playing unique roles in the splicing processes, where molecular changes in RBPs causes AS changes in biological processes. Thus, the mechanism of AS changes can be attributed to molecular changes in RBPs, but determining the causal RBPs, based on the observed AS changes, has been challenging due to the complexity of AS regulation. We present Splicing Profile Analysis using RBP KD/KO Signatures (SPARKS), a computational framework to infer causal RBPs by quantifying the similarity in AS between the study of interest and the perturbation of RBPs from a large-scale RBP perturbation database. We verified that splicing factor perturbation leads to unique AS changes, which SPARKS leverages to identify causal RBPs. We demonstrated the efficacy of SPARKS in identifying the causal RBPs in RBP perturbation experiments and biological processes with known regulatory mechanisms in AS. We applied SPARKS to the AS changes in AML patients with the recurrent somatic mutation in U2AF1 and uncovered that the mutant U2AF1 and PTBP1 are involved in the AS changes. We also discovered the candidate RBPs responsible for pan-cancer AS changes upon PRMT5 inhibition therapy, EFTUD2, PCBP2, and PRPF8. Integrating the molecular changes on the candidate RBPs, we generated a potential model for the mechanism of action for PRMT5 inhibition in splicing. In summary, this work illustrates a computational analysis framework to decipher the molecular mechanisms of alternative splicing regulation in biology, disease, and therapy.