Chromatin accessibility regulates tyrosine kinase inhibitor resistance in Gastrointestinal Stromal Tumors

Gastrointestinal stromal tumor (GIST), the most common sarcoma, results from oncogenic mutations that usually occur in the KIT genes. Though anti-KIT tyrosine kinase inhibitors (TKIs) can be initially effective, half of patients with metastatic GIST develop drug-resistance within 20 months of starting first line (IM-imatinib) therapy, and the efficacy of later line therapies (SU-sunitinib, REG-regorafenib, RIP-ripretinib) are all <10%. This is thought to be primarily due to the accumulation of secondary resistance mutations in KIT, but treatment refractory disease often occurs even in the absence of these or other mutations. This suggests that additional mechanisms, such as changes in expression or regulation of genes or pathways, may be leading to TKI resistance. It is well established that expression of genes which regulate tumor progression is governed by transcription factor (TF) binding to gene regulatory elements, including promoters and enhancers – the accessibility of which is controlled by chromatin remodeling. Our Preliminary Data demonstrate that in vitro TKI treatment (IM, SU, RIP) of KIT-mutant GIST leads to overexpression of SOX2, a master transcriptional regulator that is known to modulate chromatin accessibility, and has been implicated in the maintenance of cancer stem cells. In turn, we find that SOX2 overexpression is sufficient to increase IM-resistance independent of secondary KIT mutations, and is strongly associated with increased open chromatin in the enhancer region of ETV1, a necessary lineage-specific survival factor for GIST tumorigenesis. Furthermore, this ETV1-associated open chromatin has AP-1 TF complex (i.e., JUN, JUNB, FOS, and FOSB) binding sites that may regulate ETV1 expression. Finally, we observe increased expression of the AP-1 complex in IM-treated human GIST. Given these observations, we hypothesize that SOX2 cooperates with AP-1 to modulate chromatin accessibility of GIST transcriptional networks, leading to increased TKI resistance in GIST. We propose to characterize treatment naïve and TKI-treated (IM, SU, RIP) KIT-mutant GIST using molecular and bioinformatic methods, including single nucleus transposase-accessible chromatin sequencing (snATAC-seq), chromatin immunoprecipitation-sequencing (ChIP-seq), and RNA-sequencing (RNA-seq). Using these techniques, we will define how SOX2- and AP-1-associated chromatin remodeling contributes to ETV1 regulation and increased TKI resistance in human GIST. This work will shed light for the first time on the transcriptional regulation of ETV1 in GIST, as well as provide a new mechanistic understanding of how genome accessibility is associated with TKI resistance, thus driving discovery of novel therapeutic targets for KIT-mutant GIST.