Regulation of KIT gene expression in gastrointestinal stromal tumor
Gastrointestinal stromal tumor (GIST) is a sarcoma frequently driven by activating mutations in oncogenic KIT. While tyrosine kinase inhibitors benefit most GIST patients, resistance mutations invariably develop in KIT that produce treatment resistance; no other therapeutic strategies are available. Even in advanced disease, GIST remains absolutely dependent upon oncogenic KIT signaling, and alternative means of disrupting KIT are urgently needed. Little is understood about mechanisms governing KIT gene expression. We previously implicated the transcription factor HAND1 in driving KIT expression and clinical outcomes in GIST. We have generated critical new data isolating GSK3 as the primary governor of KIT transcription, which controls native KIT expression through activating HAND1. HAND1, in turn, regulates the canonical BAF (cBAF) chromatin remodeling complex, which is a central mechanism required to coordinate transcription. GSK3 itself is negatively regulated by KIT signaling, establishing a novel feedback loop whereby the level of KIT expression is controlled through GSK3. Our overall hypothesis is that GSK3 regulates KIT gene expression through the activation of HAND1, which interacts with the cBAF complex to establish GIST’s recurrent chromatin state.
In Aim 1, we elucidate GSK3’s role in activating KIT gene expression, exploiting proteomic data and functional mutations to detail downstream HAND1 regulation (1A). Through a mechanistic understanding of GSK3 function, we will establish precise mechanisms of KIT locus control (1B). Leveraging GIST xenograft models, we will demonstrate effects of dual GSK3 and KIT inhibition as a therapeutic strategy (1C). We next explore the consequences of HAND1’s interaction with cBAF in Aim 2. Using a genetically encoded degradation tag, we will determine the effects of acute HAND1 loss on cBAF function (2A). Genetic and pharmacologic disruption of the cBAF complex will establish its unique and essential function in GIST (2B). Finally, the therapeutic opportunity from disrupting the HAND1-BAF interaction will be established in GIST xenograft models (2C). Aim 3 will define the feedback loop whereby KIT signaling controls KIT gene expression by negatively regulating GSK3. This feedback loop will be interrogated using KIT and GSK3 inhibitors and functional GSK3 mutations (3A). The signaling intermediates downstream of KIT responsible for GSK3 inhibition will be established using pharmacologic and genetic approaches (3B). Finally, we will determine how different KIT mutations augment GSK3, and how this feedback loop represents a novel mechanism of resistance to tyrosine kinase inhibitors (3C).
Armed with robust GIST models and clinical samples, rigorous scientific methodology, critical preliminary data, and a hypothesis driven approach, our proposal will define the regulatory mechanisms governing KIT gene expression essential to GIST biology and nominate novel therapeutic strategies in GIST.