The development of targeted small molecule drugs has revolutionized the treatment of many cancers by selectively targeting key driver oncogenes. However, the durability of molecularly targeted agents is limited by the development of resistance, often via protein-altering secondary mutations. In this project, we propose a novel therapeutic paradigm that side-steps protein mutation-driven resistance by targeting oncogenes at the messenger RNA (mRNA) level through a process referred to as alternative mRNA processing. With improvements in DNA sequencing technology, studies now indicate that 94% of all protein coding genes are alternatively spliced. Functional consequences of splicing have been shown across a wide array of biological processes, including cancer. Despite the emerging importance of alternative processing in cancer, direct therapeutic approaches that exploit this phenomenon remain sparse. At the end of 2016, the Food and Drug Administration approved the first splicing-based therapy in children with muscular degenerative conditions, laying the groundwork for splicing-based therapy to be potentially used in cancer.
Dr. Robinson is a practicing radiation oncologist and clinician-scientist who previously developed a suite of novel bioinformatics tools (SplicerAV and SplicerEX) that predicted that the key oncogene called the Epidermal Growth Factor Receptor (EGFR) can be manipulated via alternative splicing to produce variants that lack critical signaling domains and ultimately act as decoy receptors that inhibit EGFR signaling. In this approach, we describe what we refer to as “Splice-Ablation Kinase Inhibition,” or “SAKI.” SAKI manipulates alternative mRNA splicing by targeting specific pre-mRNA sequences to splice out exons located in key oncogene domains to (1) attack oncogenes at the mRNA level, (2) directly inhibit expression of functional oncogenes, and (3) replace it with dominant negative variants that act to further antagonize oncogene signaling. Splicing-targeted therapy represents an entirely new category of antineoplastic agents and is a paradigm shift from current small molecules and antibodies, which target oncogenes at the protein level. A splicing-based antineoplastic therapy has many potential advantages, including the ability to (1) bypass entire exons harboring driver and resistance mutation hotspots within activating kinase or other signaling domains; (2) target oncogenes with currently undruggable protein structures; (3) drive expression of dominant negative decoy proteins, which may further inhibit oncogene-binding partners; (4) create soluble decoys for membrane-bound oncogenes that are capable of paracrine inhibition in bystander or stromal cells; and (5) preferentially inhibit pathologically over-expressed (OE) genes for which splicing regulation is less robust. Although potentially applicable to virtually any oncogene, in this project we use SAKI to target the Epidermal Growth Factor Receptor (EGFR) in non-small cell lung cancer (NSCLC).
We chose this as an ideal model to study SAKI for several reasons: (1) EGFR is the most commonly mutated NSCLC driver kinase in patients; (2) EGFR is only temporarily inhibited by Tyrosine Kinase Inhibitors (TKIs), which provide only 1-2 years additional survival before EGFR-resistant mutations develop; (3) these mutations are well characterized; (4) EGFR-targeted therapy is the Principal Investigator mentor’s expertise (Dr. Haura), with a training environment that provides cutting-edge reagents and multiple EGFR NSCLC cell models with TKI-sensitive and TKI-resistant counterparts. Combined with the co-mentor’s (Dr. Chalfant) expertise in mRNA splicing mechanism and RNA biology, this project represents an innovative area of research and provides rich career development and training in EGFR signaling, TKI-resistance, and mRNA splicing regulation, with long-term potential to provide novel, clinically translatable agents that may be beneficial across numerous, currently resistant treatment settings. |