Splicing Modulation as a Potential Treatment for Vemurafenib-Resistant Melanoma

Tumors resistant to vemurafenib express a specific BRAF isoform. NCI investigators have discovered splicing modulators that antagonize the BRAF isoform and inhibit growth of drug-resistant tumors.

Over half of melanomas contain mutations in the serine/threonine kinase BRAF. The most common mutation, BRAF(V600E), leads to excessive activation of the MAPK proliferation pathway. Vemurafenib is a potent kinase inhibitor with remarkable clinical activity in BRAF(V600E)-positive melanoma tumors. Patients initially respond to treatment with vemurafenib, but inevitably develop resistance. One known resistance mechanism is aberrant splicing of the BRAF RNA. To understand the molecule mechanism of BRAF mis-splicing, Tom Misteli, Ph.D., and Maayan Salton, Ph.D., of CCR’s Laboratory of Receptor Biology and Gene Expression, and NCI colleagues set out on a molecular investigation to identify the mechanism behind generation of the vemurafenib-resistant BRAF isoforms. Their results led to insight into the molecular mechanism of BRAF splicing in vemurafenib resistance and point to splicing inhibitors as a novel therapeutic strategy to overcome vemurafenib resistance.

The researchers started out by examining the C3 cell line which was generated by chronically exposing patient-derived BRAF(V600E)-mutated cells to vemurafenib. They found that in addition to full-length BRAF C3 cells also make BRAF3-9, an isoform that lacks exons 4-8. Sequencing revealed a C-to-G mutation in C3 cells located in a major regulatory region of splicing in intron 8 and this mutation was sufficient to promote the production of BRAF3-9. Further investigation of the mechanism pointed to the spliceosome component SF3B1 as a critical regulator of BRAF splicing. This was an important observation since small molecule modulators of SF3B1 exist, pointing to the possibility of their use to combat vemurafenib-resistance by inhibiting aberrant BRAF splicing. Indeed, treatment of C3 cells with splicing modulator decreased BRAF3-9 levels, decreased MAPK signaling and proliferation.

To test whether splicing modulation is a viable therapeutic strategy for vemurafenib-resistant tumors in vivo, the NCI scientists used a xenograft model and found that splicing modulators prevented vemurafenib-resistant tumor growth, and halted the growth of already formed vemurafenib-resistant tumors. These results strongly support further exploration of RNA splicing modulators, possibly in combination with MAPK inhibitors, as therapeutic agents in drug-resistant melanoma.

Summary Posted: Fri, 05/01/2015


Salton M, Kasprzak WK, Voss T, Shapiro BA, Poulikakos PI, and Misteli T. Inhibition of vemurafenib-resistant melanoma by interference with pre-mRNA splicing. Nature Communications. May 14, 2015. PubMed Link