TKI Treatment Sequencing in Advanced Gastrointestinal Stromal Tumors

Prior to the early 2000s, patients with advanced gastrointestinal stromal tumors (GIST) had very poor prognoses owing to a lack of effective therapies. The development of tyrosine kinase inhibitors at the turn of the century significantly improved the overall survival for patients with GIST. The resounding success of imatinib in the first clinical trial of a tyrosine kinase inhibitor to treat GIST led to its approval for first-line therapy for advanced GIST; this study was open to all comers and not restricted to any GIST subtype(s). The trials that led to the approvals of second-, third-, and fourth-line therapy for advanced GIST were also open to all patients with advanced/metastatic GIST. Only in retrospect do we realize the role that the molecular subtypes played in the results observed in these studies. In this review, we discuss the studies that led to the US Food and Drug Administration approval of imatinib (first line), sunitinib (second line), regorafenib (third line), and ripretinib (fourth line) for advanced KIT-mutant GIST. In addition, we review how information about GIST molecular subtypes has been used to accelerate the approval of other targeted therapies for non-KIT mutant GIST, leading to the approval of five additional drugs indicated for the treatment of specific GIST molecular subtypes. We also discuss how our understanding of the molecular subtypes will play a role in the next generation of therapeutic approaches for treating advanced GIST.

Abstract 660: Predicting imatinib responses in exon 18 PDGFRA-mutant GIST

Gastrointestinal stromal tumor (GIST) is the most common GI sarcoma and frequently harbor oncogenic mutations in KIT or platelet derived growth factor receptor alpha (PDGFRA) receptor tyrosine kinases. While type II tyrosine kinase inhibitors (TKIs) revolutionized the treatment of KIT-mutant GIST, they are thought to be ineffective for many PDGFRA-mutant GIST cases. Over 80% of PDGFRA mutations in GIST occur in exon 18 and patients with the most common mutation, D842V, are resistant to imatinib and other type II TKIs, leading to poor outcomes. However, beyond D842V, numerous other PDGFRA exon 18 mutations have been observed. From curated data of a large cohort of PDGFRA-mutant GISTs, we have identified nearly 50 unique PDGFRA exon 18 mutations, including both point mutations and complex indels. Although it is largely unknown how these mutations respond to imatinib, currently most, if not all, PDGFRA exon 18 mutations are assumed to be imatinib resistant. Using cell models, we tested some of the most commonly observed mutations in this cohort. Contrary to dogma, we observed that some exon 18 mutations tested were imatinib sensitive. We also observed that imatinib sensitivity seemed to be dependent on the properties of the residue in the 842-codon position, which encodes a key auto-inhibitory residue. We then hypothesized that imatinib sensitivity of every known or future reported PDGFRA exon 18 mutation might be predicted based on the 842 residue. To test the predictive potential of the 842 residue, we created mutagenic libraries that included every amino acid substitution at the 842 position. We expressed each mutation in Ba/F3 cells and assessed imatinib sensitivity via immunoblotting for phosphorylated-PDGFRA. Overall, 40% of tested mutations were sensitive to imatinib, further debunking the belief that all PDGFRA exon 18 mutations are imatinib resistant. In agreement with our hypothesis, we found that any hydrophobic residue at the 842 position conferred imatinib resistance (IC50 > 100nM), and all other amino acids tested to date were imatinib sensitive (IC50 < 100nM). Based on these data alone, over 55% of the 50 unique mutations identified from our PDGFRA-mutant GIST patient cohort would be predicted to be imatinib sensitive, demonstrating the importance of understanding the biochemical properties of various exon 18 mutations to predict treatment outcomes. Our predictive model would help identify patients with PDGFRA exon 18 mutations that could benefit from using front-line imatinib as an alternative to avapritinib, which has been recently approved for first-line treatment for all PDGFRA exon 18 mutant GIST. Imatinib, which has been used clinically for over 20 years, has a superior safety and tolerability profile compared to avapritinib. This paradigm shifting approach has the potential to transform patient care and outcomes by optimizing the sequencing of TKIs for PDGFRA-mutant GIST patients.

Citation Format: Homma M. Khosroyani, Lillian R. Klug, Johanna Falkenhorst, Sebastian Bauer, Michael C. Heinrich. Predicting imatinib responses in exon 18 PDGFRA-mutant GIST [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 660.

Cancer-associated fibroblast secretion of PDGFC promotes gastrointestinal stromal tumor growth and metastasis

Targeted therapies for gastrointestinal stromal tumor (GIST) are modestly effective, but GIST cannot be cured with single agent tyrosine kinase inhibitors. In this study, we sought to identify new therapeutic targets in GIST by investigating the tumor microenvironment. Here, we identified a paracrine signaling network by which cancer-associated fibroblasts (CAFs) drive GIST growth and metastasis. Specifically, CAFs isolated from human tumors were found to produce high levels of platelet-derived growth factor C (PDGFC), which activated PDGFC-PDGFRA signal transduction in GIST cells that regulated the expression of SLUG, an epithelial-mesenchymal transition (EMT) transcription factor and downstream target of PDGFRA signaling. Together, this paracrine induce signal transduction cascade promoted tumor growth and metastasis in vivo. Moreover, in metastatic GIST patients, SLUG expression positively correlated with tumor size and mitotic index. Given that CAF paracrine signaling modulated GIST biology, we directly targeted CAFs with a dual PI3K/mTOR inhibitor, which synergized with imatinib to increase tumor cell killing and in vivo disease response. Taken together, we identified a previously unappreciated cellular target for GIST therapy in order to improve disease control and cure rates.

Resistance to Avapritinib in PDGFRA-Driven GIST Is Caused by Secondary Mutations in the PDGFRA Kinase Domain

Gastrointestinal stromal tumors (GIST) harboring activating mutations of PDGFRA respond to imatinib, with the notable exception of the most common mutation, D842V. Avapritinib is a novel, potent KIT/PDGFRA inhibitor with substantial clinical activity in patients with the D842V genotype. To date, only a minority of PDGFRA-mutant patients treated with avapritinib have developed secondary resistance. Tumor and plasma biopsies in 6 of 7 patients with PDGFRA primary mutations who progressed on avapritinib or imatinib had secondary resistance mutations within PDGFRA exons 13, 14, and 15 that interfere with avapritinib binding. Secondary PDGFRA mutations causing V658A, N659K, Y676C, and G680R substitutions were found in 2 or more patients each, representing recurrent mechanisms of PDGFRA GIST drug resistance. Notably, most PDGFRA-mutant GISTs refractory to avapritinib remain dependent on the PDGFRA oncogenic signal. Inhibitors that target PDGFRA protein stability or inhibition of PDGFRA-dependent signaling pathways may overcome avapritinib resistance. SIGNIFICANCE: Here, we provide the first description of avapritinib resistance mechanisms in PDGFRA-mutant GIST.This article is highlighted in the In This Issue feature, p. 1.

Abstract 3005: Comprehensive profile of platelet derived growth factor receptor alpha (PDGFRA) mutations in gastrointestinal stromal tumors

Gastrointestinal stromal tumors (GIST) most commonly harbor oncogenic mutations in KIT tyrosine kinase, which can be targeted by the tyrosine kinase inhibitor, imatinib. However, a subset of GIST, approximately 10% of cases, instead contain mutations in a related kinase, PDGFRA. Historically, advanced PDGFRA-mutant GIST patients have had poor prognosis, primarily because the majority of these tumors are driven by the activating mutation PDGFRA D842V, which is strongly resistant to imatinib and other kinase inhibitors approved for GIST. This amino acid, D842, is within the activation loop of PDGFRA, which contains conserved motifs that change conformation depending on an active or inactive state of the kinase domain. The PDGFRA D842V mutation leads to the loss of polar interactions in the activation loop, which then stabilize the active confirmation of the kinase. Imatinib, a type II kinase inhibitor, binds only to inactive conformation of KIT and PDGFRA. This makes imatinib and other type II kinase inhibitors incapable of binding to the PDGFRA D842V-mutant receptor. The lack of effective treatments for this mutation in particular led to the development of novel kinase inhibitors to target PDGFRA, such as avapritinib (BLU-285), a type I kinase inhibitor which is capable of binding the active conformation and has been shown to potently inhibit PDGFRA D842V in vitro and in the clinic. However, our understanding of the biochemical effect of avapritinib and other PDGFRA inhibitors against all known primary and secondary PDGFRA mutations is still unknown. We have collected clinical data from over 200 PDGFRA-mutant GIST patients, the largest database of its kind to date. We found that over half of all these GIST bear D842V mutations, but nearly 50 unique mutations make up the mutations seen in the remaining GIST cases. Using in vitro models, we profiled the sensitivity of avapritinib and other novel inhibitors such as crenolanib, ripretinib (DCC-2618), and AZD3229 against many of the observed PDGFRA mutations. We also used three-dimensional modeling in silico to demonstrate the consequences of PDGFRA activating mutations on kinase function and drug binding. We also modeled and characterized novel secondary mutations in PDGFRA seen in drug resistant tumors. From our results, we have curated a comprehensive data set that can be used to inform clinicians about possible treatment options for PDGFRA-mutant GIST, and also provide implications for treatments of other PDGFRA-mutant cancers.

Citation Format: Homma Khosroyani, Lillian R. Klug, Ajia Town, Jonas Lategahn, Johanna Falkenhorst, Susanne Grunewald, Thomas Mühlenberg, Christiane Ehrt, Eve Wardelmann, Wolfgang Hartmann, Hans-Ulrich Schildhaus, Sascha Jung, Paul Czodrowski, Abbas Agaimy, Piotr Rutkowski, Daniel Rauh, Sebastian Bauer, Michael C. Heinrich. Comprehensive profile of platelet derived growth factor receptor alpha (PDGFRA) mutations in gastrointestinal stromal tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3005.

LMTK3 is essential for oncogenic KIT expression in KIT-mutant GIST and melanoma

Certain cancers, including gastrointestinal stromal tumor (GIST) and subsets of melanoma, are caused by somatic KIT mutations that result in KIT receptor tyrosine kinase constitutive activity, which drives proliferation. The treatment of KIT-mutant GIST has been revolutionized with the advent of KIT-directed cancer therapies. KIT tyrosine kinase inhibitors (TKI) are superior to conventional chemotherapy in their ability to control advanced KIT-mutant disease. However, these therapies have a limited duration of activity due to drug-resistant secondary KIT mutations that arise (or that are selected for) during KIT TKI treatment. To overcome the problem of KIT TKI resistance, we sought to identify novel therapeutic targets in KIT-mutant GIST and melanoma cells using a human tyrosine kinome siRNA screen. From this screen, we identified lemur tyrosine kinase 3 (LMTK3) and herein describe its role as a novel KIT regulator in KIT-mutant GIST and melanoma cells. We find that LMTK3 regulated the translation rate of KIT, such that loss of LMTK3 reduced total KIT, and thus KIT downstream signaling in cancer cells. Silencing of LMTK3 decreased cell viability and increased cell death in KIT-dependent, but not KIT-independent GIST and melanoma cell lines. Notably, LMTK3 silencing reduced viability of all KIT-mutant cell lines tested, even those with drug-resistant KIT secondary mutations. Furthermore, targeting of LMTK3 with siRNA delayed KIT-dependent GIST growth in a xenograft model. Our data suggest the potential of LMTK3 as a target for treatment of patients with KIT-mutant cancer, particularly after failure of KIT TKIs.

Biochemical, Molecular, and Clinical Characterization of Succinate Dehydrogenase Subunit A Variants of Unknown Significance

Purpose: Patients who inherit a pathogenic loss-of-function genetic variant involving one of the four succinate dehydrogenase (SDH) subunit genes have up to an 86% chance of developing one or more cancers by the age of 50. If tumors are identified and removed early in these high-risk patients, they have a higher potential for cure. Unfortunately, many alterations identified in these genes are variants of unknown significance (VUS), confounding the identification of high-risk patients. If we could identify misclassified SDH VUS as benign or pathogenic SDH mutations, we could better select patients for cancer screening procedures and remove tumors at earlier stages.Experimental Design: In this study, we combine data from clinical observations, a functional yeast model, and a computational model to determine the pathogenicity of 22 SDHA VUS. We gathered SDHA VUS from two primary sources: The OHSU Knight Diagnostics Laboratory and the literature. We used a yeast model to identify the functional effect of a VUS on mitochondrial function with a variety of biochemical assays. The computational model was used to visualize variants' effect on protein structure.Results: We were able to draw conclusions on functional effects of variants using our three-prong approach to understanding VUS. We determined that 16 (73%) of the alterations are actually pathogenic, causing loss of SDH function, and six (27%) have no effect upon SDH function.Conclusions: We thus report the reclassification of the majority of the VUS tested as pathogenic, and highlight the need for more thorough functional assessment of inherited SDH variants. Clin Cancer Res; 23(21); 6733-43. ©2017 AACR.

Using molecular diagnostic testing to personalize the treatment of patients with gastrointestinal stromal tumors

INTRODUCTION

The diagnosis and treatment of gastrointestinal stromal tumor (GIST) has emerged as a paradigm for modern cancer treatment ('precision medicine'), as it highlights the importance of matching molecular defects with specific therapies. Over the past two decades, the molecular classification and diagnostic work up of GIST has been radically transformed, accompanied by the development of molecular therapies for specific subgroups of GIST. This review summarizes the developments in the field of molecular diagnosis of GIST, particularly as they relate to optimizing medical therapy. Areas covered: Based on an extensive literature search of the molecular and clinical aspects of GIST, the authors review the most important developments in this field with an emphasis on the differential diagnosis of GIST including mutation testing, therapeutic implications of each molecular subtype, and emerging technologies relevant to the field. Expert commentary: The use of molecular diagnostics to classify GIST has been shown to be successful in optimizing patient treatment, but these methods remain under-utilized. In order to facilitate efficient and comprehensive molecular testing, the authors have developed a decision tree to aid clinicians.

Abstract 191: LMTK3 is a novel regulator of oncogenic KIT in KIT-mutant cancers

Multiple cancers, such as gastrointestinal stromal tumors (GIST) and melanoma, have been shown to be caused by somatic activating mutations in the receptor tyrosine kinase KIT. The major cause of death in patients with advanced KIT-mutant cancers is due to KIT tyrosine kinase inhibitor-resistant metastatic disease. Resistance develops almost exclusively because of secondary mutations within KIT, highlighting the importance of KIT in the proliferation and survival of these tumors. Therefore, strategies that affect KIT protein expression and maturation may be therapeutic. In order to identify regulators of KIT that may represent novel targets, we performed an siRNA screen in multiple KIT-mutant cancer cell lines. From these screens we identified lemur tyrosine kinase 3 (LMTK3) as a novel KIT regulator and potential target in KIT-mutant cancers. LMTK3 has been implicated as an important protein in multiple cancers, including leukemia, breast, and colon cancer. However, the oncogenic function of LMTK3 is not entirely clear. Despite its name, lemur tyrosine kinase 3 is, in fact, a serine/ threonine kinase. Beyond its enzymatic kinase function, LMTK3 has also been shown to have important scaffolding functions. LMTK3 has not been previously known to interact with KIT, but does regulate the stability of other receptors. We have found that LMTK3 silencing reduced the viability of all KIT-mutant GIST and melanoma cells tested to date, including those with ATP binding pocket and activation loop resistance mutations. Importantly, LMTK3 silencing decreased the viability of KIT-mutant cells specifically, as silencing of LMTK3 in cells lacking KIT mutations did not affect their viability. Further, we found the decrease in cell viability was due to induction of apoptosis, as seen by cleavage of PARP within 96 hours of LMTK3 silencing. Because these cells depend so heavily on KIT and loss of KIT signaling results in cell death, we hypothesized that LMTK3 silencing may be affecting this pathway. Indeed, with LMTK3 silencing there was a significant decrease in phosphorylated KIT (Y719), which was accompanied by decreased phospho-AKT (S473). We also observed a robust decrease in total KIT protein levels. However, there was no decrease in KIT transcript levels, suggesting that LMTK3 plays a role in regulating KIT at the protein level. While other KIT protein regulators, such as HSP90, have been suggested as therapeutic targets for GIST, the ubiquitous functions of these targets makes these treatments sub-optimal, often causing toxicity. Silencing of LMTK3, on the other hand, specifically kills KIT-mutant cancer cells. Furthermore, as a kinase, inhibition of LMTK3 by a small molecule may be possible, and we are in the process of identifying LMTK3 inhibitors. LMTK3 is a positive regulator of oncogenic KIT in GIST and melanoma and represents a novel, tractable target in KIT-mutant cancers.

Citation Format: Lillian R. Klug, Jeffery W. Tyner, Michael C. Heinrich. LMTK3 is a novel regulator of oncogenic KIT in KIT-mutant cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 191.

Combination therapy for KIT-mutant mast cells: targeting constitutive NFAT and KIT activity

Resistant KIT mutations have hindered the development of KIT kinase inhibitors for treatment of patients with systemic mastocytosis. The goal of this research was to characterize the synergistic effects of a novel combination therapy involving inhibition of KIT and calcineurin phosphatase, a nuclear factor of activated T cells (NFAT) regulator, using a panel of KIT-mutant mast cell lines. The effects of monotherapy or combination therapy on the cellular viability/survival of KIT-mutant mast cells were evaluated. In addition, NFAT-dependent transcriptional activity was monitored in a representative cell line to evaluate the mechanisms responsible for the efficacy of combination therapy. Finally, shRNA was used to stably knockdown calcineurin expression to confirm the role of calcineurin in the observed synergy. The combination of a KIT inhibitor and a calcineurin phosphatase inhibitor (CNPI) synergized to reduce cell viability and induce apoptosis in six distinct KIT-mutant mast cell lines. Both KIT inhibitors and CNPIs were found to decrease NFAT-dependent transcriptional activity. NFAT-specific inhibitors induced similar synergistic apoptosis induction as CNPIs when combined with a KIT inhibitor. Notably, NFAT was constitutively active in each KIT-mutant cell line tested. Knockdown of calcineurin subunit PPP3R1 sensitized cells to KIT inhibition and increased NFAT phosphorylation and cytoplasmic localization. Constitutive activation of NFAT appears to represent a novel and targetable characteristic of KIT-mutant mast cell disease. Our studies suggest that combining KIT inhibition with NFAT inhibition might represent a new treatment strategy for mast cell disease.

STRAD pseudokinases regulate axogenesis and LKB1 stability

Background

Neuronal polarization is an essential step of morphogenesis and connectivity in the developing brain. The serine/threonine kinase LKB1 is a key regulator of cell polarity, metabolism, tumorigenesis, and is required for axon formation. It is allosterically regulated by two related and evolutionarily conserved pseudokinases, STe20-Related ADapters (STRADs) α and β. The roles of STRADα and STRADβ in the developing nervous system are not fully defined, nor is it known whether they serve distinct functions.

Results

We find that STRADα is highly spliced and appears to be the primal STRAD paralog. We report that each STRAD is sufficient for axogenesis and promoting cell survival in the developing cortex. We also reveal a reciprocal protein-stabilizing relationship in vivo between LKB1 and STRADα, whereby STRADα specifically maintains LKB1 protein levels via cytoplasmic compartmentalization.

Conclusions

We demonstrate a novel role for STRADβ in axogenesis and also show for the first time in vivo that STRADα, but not STRADβ, is responsible for LKB1 protein stability.