Investigating IGF2BP1 as a novel Therapeutic Target for Ewing Sarcoma

Project Summary Ewing sarcoma (ES) is the second most prevalent bone cancer among children. Aggressive in nature, ES is driven by a fusion transcription factor of which EWS/FLI1 accounts for ~85% of cases. Drugging EWS/FLI1 is difficult, as it is highly disordered. New ES therapies that modulate novel therapeutic targets are urgently needed.

Recently, the Stegmaier Lab collaboratively used CRISPR-Cas9 to develop a Pediatric Cancer Dependency Map, which is integrated into the Broad Institute’s larger Cancer Dependency Map (DepMap). More than 18,000 genes were knocked out in >100 pediatric cell lines and the abundance of each guide RNA was monitored after

21 days. Data has been standardized across all cell lines so gene dependencies (i.e., genes that cancer lineages depend on for growth) can be found. Mining this data, I identified IGF2BP1 as a potential ES dependency. IGF2BP1 is an oncofetal RNA binding protein (RBP) that protects mRNA transcripts from degradation. My

preliminary data confirms ES cells have decreased proliferation in the context of IGF2BP1 knockout (KO). In Aim 1, I will use CRISPR-Cas9 to KO IGF2BP1 in a panel of ES cell lines and PDX models to validate IGF2BP1 as a novel ES dependency. Since targeted degradation offers superior temporal control to genetic KO, I will also

use the dTAG system to determine how induced degradation of IGF2BP1 impacts ES biology. Next, in Aim 2, I will determine the molecular mechanism underlying the IGF2BP1 dependency. EWS/FLI1 and Lin28B, another oncofetal RBP, are the top two gene dependencies positively correlated with IGF2BP1 in DepMap. Therefore, I

will determine how IGF2BP1 KO affects these proteins and their mRNA. I will also use an unbiased, integrated omics approach to identify other mRNAs that interact with IGF2BP1 in ES. Finally, in Aim 3, I will biochemically characterize the IGF2BP1 dependency, determining which domains are necessary to support ES cell growth

and how IGF2BP1 recognizes ES relevant substrates. Together, this project will validate IGF2BP1 as a novel therapeutic target in ES and uncover new mechanisms of ES maintenance, and the IGF2BP1-substrate interactions characterized could be leveraged to identify novel IGF2BP1 inhibitors. I will gain skills in CRISPR-Cas9 genome editing, functional genomics, as well as in vivo experimentation, and I

will become a pediatric solid tumor expert upon completion of my fellowship training plan. Dana-Farber (DFCI) is a globally renowned cancer institute and the perfect place for my training because DFCI and its affiliates have many experimental and academic resources like the Broad Institute’s computational bootcamp. My postdoctoral

training, along with my chemical biology expertise from graduate school, will put me in a perfect position to start my independent research career focused on developing new chemical tools to study pediatric cancers.