Developing novel ALK targeting therapies through the expansion of targeted protein degradation

/ABSTRACT: This proposal aims to address a critical challenge in treating anaplastic lymphoma kinase (ALK)-driven neuroblastoma (NB) and other cancers: namely the development of resistance to targeted therapies, particularly tyrosine kinase inhibitors (TKIs). ALK is a receptor-tyrosine kinase that plays a crucial role in the development of the central and peripheral nervous systems, and its dysregulation, through mutations, fusions, and overexpression, has been implicated in several cancers, most notably NB. Despite the success of TKIs in treating ALK-driven cancers, resistance mutations in ALK often emerge, leading to disease relapse and limited long-term efficacy. One promising alternative approach to bypass resistance is targeted protein degradation through PROteolysis TArgeting Chimeras (PROTACs), small molecules that harness the ubiquitin-proteasome system to degrade specific target proteins. However, the current landscape of protein degradation therapies is limited to the near-exclusive use of two E3 ubiquitin ligases – CRBN and VHL – for PROTAC development. These ligases, while effective for certain targets, may not be optimal for all targets, and the emergence of resistance to these degrader-based therapies highlights an overlap in limitations between TKIs and PROTACs that necessitates recruitment of more diverse and effective degraders. Additionally, while at least a third of the proteome transits the endoplasmic reticulum (ER) through its membrane or lumen, almost all current degraders target cytosolic proteins leaving a large swathe of the proteome unexplored. Given ALK mutant proteins in NB often mislocalize to the ER, where they become constitutively activated and contribute to oncogenic signaling, the ER presents an untapped resource for therapeutic development through targeted protein degradation. This project intends to leverage ER-associated degradation (ERAD), a posttranslational quality control system within the ER that aids in protein homeostasis by degrading misfolded and immature proteins, to target mutant ALK. The ERAD system, which consists of membrane-embedded E3 ligases and their associated cofactors, provides a unique platform and specificity to target a previously under-explored pool of disease- related proteins, including ALK mutants. The research strategy will focus on several key innovations: (1) identifying selective protein degraders that can efficiently target ALK mutants and overcome resistance mutations, (2) expanding the therapeutic landscape of targeted protein degradation through ORFeome-based screening approaches in search novel target-degrader pairs, (3) developing genetic proof-of-principle tools to rapidly test and validate these novel degradation strategies, and (4) leveraging the specificity of organellar- based degradation to selectively degrade disease-relevant proteins localized to the ER. Ultimately, this research seeks to develop a more diverse set of tools for targeted degradation therapies, offering promising new strategies for overcoming drug resistance in ALK-driven NB and improving clinical outcomes in cancer treatment as a whole. Project Number: 1F32CA306242-01 | Fiscal Year: 2025 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Sean Johnson | Institution: UNIVERSITY OF CALIFORNIA BERKELEY, BERKELEY, CA | Award Amount: $78,040 | Activity Code: F32 | Study Section: Special Emphasis Panel[ZRG1 F04A-E (20)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11244663