Identification of therapeutic strategies to restore cell cycle control in GIST
Gastrointestinal (GI) stromal tumor (GIST) is the most common mesenchymal neoplasm of the GI tract and ~85% of cases are initiated by mutations in the KIT or PDGFRA genes that cause constitutive tyrosine kinase (TK) activity. Despite groundbreaking discoveries, managing patients with unresectable high-risk or metastatic (i.e., advanced) GIST remains a challenge. Most GIST patients have dramatic and durable responses to target-ed therapy with tyrosine kinase inhibitors (TKI) such as imatinib, but the majority of patients eventually develop resistant disease caused by the emergence of numerous subclonal TK mutations. Patients with advanced unresectable disease have a 10-year overall survival of only 23%. The lack of effective therapies for patients with TKI-resistant GIST emphasizes the critical need to identify additional therapeutic targets, particularly those de-fined by biologic vulnerabilities that are conserved across the metastatic burden of an individual patient. This proposal will test the overall hypothesis that CDK2 and RB1 are critical mediators of cell cycle dysregulation in GIST and is expected to identify the molecular mechanisms of cell cycle dysregulation that will enable the development of effective therapies for patients with aggressive GIST. We will use a combination of CRISPR/Cas9-mediated functional screens, RNA sequencing, phosphoproteomic analysis, drug testing, and genome-wide chemical mutagenesis. These studies are facilitated by a range of GIST cell lines, xenografts, and patient samples available in our program. This work builds upon our group’s recent discovery that combined inhibition of CDK2 and CDK4/6 synergistically inhibits proliferation in RB1-intact GIST and aims to deter-mine the molecular function of CDK2 in GIST (Aim 1), identify vulnerabilities that are caused by RB1 loss (Aim 2), and define mechanisms of resistance to CDK2 and CDK4/6 inhibition in GIST (Aim 3). The proposed re-search is expected to generate important insights into the mechanisms of oncogenic cell cycle dysregulation in GIST with translational potential for other CDK-dependent cancer types with canonical cell cycle dysregulation and may therefore have an impact beyond the GIST/sarcoma field. This new and substantively different departure from the status quo is expected to overcome TKI resistance in GIST, finally resulting in an efficacious ap-proach to restore cell cycle control in patients with advanced GIST. This is significant because the results will foster the development of more effective targeted therapies for cancer patients, specifically therapeutic approaches aimed at overcoming CDK inhibitor resistance. At the same time, this work is expected to provide key insights into mechanisms of resistance to CDK inhibitors and identify predictive biomarkers that improve the selection of patients most likely to benefit from therapy.