Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and Are Targetable by BET Bromodomain Inhibition

Abstract

Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT and PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, resulting in high expression levels of the oncogene required for tumor growth. Although kinase inhibition is an effective therapy for many patients with GIST, disease progression from kinase-resistant mutations is common and no other effective classes of systemic therapy exist. In this study, we identify regulatory regions of the KIT enhancer essential for KIT gene expression and GIST cell viability. Given the dependence of GIST upon enhancer-driven expression of RTKs, we hypothesized that the enhancer domains could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell-cycle arrest, apoptosis, and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to superior cytotoxic effects in vitro and in vivo, with BBI preventing tumor growth in TKIresistant xenografts. Resistance to select BBI in GIST was attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST. Significance: Expression and activity of mutant KIT is essential for driving the majority of GIST neoplasms, which can be therapeutically targeted using BET bromodomain inhibitors.

Perturbing Enhancer Activity in Cancer Therapy

“…The same pattern of activation of distinct BET-dependent super enhancers was also reported in chronic lymphocytic leukemia [82]. Enhancers driving the transcription of receptor tyrosine kinases that play a fundamental role in gastrointestinal stromal tumor have also shown dependence on BET family members [83].…”

Perturbing Enhancer Activity in Cancer Therapy

“…The same pattern of activation of distinct BET-dependent super enhancers was also reported in chronic lymphocytic leukemia [89]. Enhancers driving the transcription of receptor tyrosine kinases that play a fundamental role in gastrointestinal stromal tumors have also shown dependence on BET family members [90].…”

KIT and platelet-derived growth factor receptor α wild-type gastrointestinal stromal tumor associated with neurofibromatosis type 1: Two case reports

“…The pathogenesis of NF-1-associated GISTs has not been established. Several studies have confirmed that NF-1-associated GISTs are different from sporadic GISTs with respect to clinicopathologic characteristics, and KIT and PDGFRA gene mutations[1,5]. Moreover, the age and location of onset differ.…”

“…The data revealed that none of the six tumors from the two patients had a KIT exon 9, 11, 13, or 17, PDGFRA exon 12 or 18, or BRAFV600E mutation, which typically occurs in sporadic GISTs. It is reported most of the GISTs associated with NF-1 are well differentiated histologically, small in size, exhibit low proliferative activity, are often benign, and have a good prognosis[1,4]. Surgical resection of GIST is still the preferred method.…”

“…Gastrointestinal stromal tumors (GISTs) are mesenchymal neoplasms characterized by activating mutations in the related receptor tyrosine kinases [ KIT and platelet-derived growth factor receptor α ( PDGFRA )][1,2].…”