Association of Combination of Conformation-Specific KIT Inhibitors With Clinical Benefit in Patients With Refractory Gastrointestinal Stromal Tumors: A Phase 1b/2a Nonrandomized Clinical Trial

Abstract

Importance: Many cancer subtypes, including KIT-mutant gastrointestinal stromal tumors (GISTs), are driven by activating mutations in tyrosine kinases and may initially respond to kinase inhibitors but frequently relapse owing to outgrowth of heterogeneous subclones with resistance mutations. KIT inhibitors commonly used to treat GIST (eg, imatinib and sunitinib) are inactive-state (type II) inhibitors.

Objective: To assess whether combining a type II KIT inhibitor with a conformation-complementary, active-state (type I) KIT inhibitor is associated with broad mutation coverage and global disease control.

Design, setting, and participants: A highly selective type I inhibitor of KIT, PLX9486, was tested in a 2-part phase 1b/2a trial. Part 1 (dose escalation) evaluated PLX9486 monotherapy in patients with solid tumors. Part 2e (extension) evaluated PLX9486-sunitinib combination in patients with GIST. Patients were enrolled from March 2015 through February 2019; data analysis was performed from May 2020 through July 2020.

Interventions: Participants received 250, 350, 500, and 1000 mg of PLX9486 alone (part 1) or 500 and 1000 mg of PLX9486 together with 25 or 37.5 mg of sunitinib (part 2e) continuously in 28-day dosing cycles until disease progression, treatment discontinuation, or withdrawal.

Main outcomes and measures: Pharmacokinetics, safety, and tumor responses were assessed. Clinical efficacy end points (progression-free survival and clinical benefit rate) were supplemented with longitudinal monitoring of KIT mutations in circulating tumor DNA.

Results: A total of 39 PLX9486-naive patients (median age, 57 years [range, 39-79 years]; 22 men [56.4%]; 35 [89.7%] with refractory GIST) were enrolled in the dose escalation and extension parts. The recommended phase 2 dose of PLX9486 was 1000 mg daily. At this dose, PLX9486 could be safely combined with 25 or 37.5 mg daily of sunitinib continuously. Patients with GIST who received PLX9486 at a dose of 500 mg or less, at the recommended phase 2 dose, and with sunitinib had median (95% CI) progression-free survivals of 1.74 (1.54-1.84), 5.75 (0.99-11.0), and 12.1 (1.34-NA) months and clinical benefit rates (95% CI) of 14% (0%-58%), 50% (21%-79%), and 80% (52%-96%), respectively.

Conclusions and relevance: In this phase 1b/2a nonrandomized clinical trial, type I and type II KIT inhibitors PLX9486 and sunitinib were safely coadministered at the recommended dose of both single agents in patients with refractory GIST. Results suggest that cotargeting 2 complementary conformational states of the same kinase was associated with clinical benefit with an acceptable safety profile.

Trial registration: ClinicalTrials.gov Identifier: NCT02401815.

Conflict of interest statement

Conflict of Interest Disclosures: Dr Trent reported serving as a consultant Deciphera, Blueprint Medicines, C4 Therapeutics, Epizyme, Daiichi Dankyo, Cogent Biosciences, and Bayer. Dr Wagner reported receiving grants from Plexxikon during the conduct of the study; and receiving grants from Aadi Bioscience, Daiichi Sankyo, Deciphera, Eli Lilly, Five Prime, and Karyopharm and receiving personal fees from Daiichi Sankyo, Deciphera, Eli Lilly, Five Prime, Loxo, MundiPharma, NanoCarrier, Novartis, Boston Clinical Research Institute, IQVIA, and OncLive outside the submitted work. Dr Shields reported receiving research support from Plexxikon during the conduct of the study. Dr Chugh reported receiving grants from Plexxikon during the conduct of the study; and receiving grants from AADi, Novartis, Medivation, Advenchen, Epizyme, Springworks, and GlaxoSmithKline; receiving personal fees and nonfinancial support from Janssen; receiving personal fees from Immune Design, Ipsen; receiving nonfinancial support and grants from Mundipharma and Qilu Puget Sound outside the submitted work. Dr Tap reported receiving personal fees from Plexxikon during the conduct of the study; personal consulting fees from Daiichi Sankyo, Eli Lilly, EMD Serono, Eisai, Mundipharma, C4 Therapeutics, Blueprint, GlaxoSmithKline, Agios, Deciphera, and NanoCarrier outside the submitted work; in addition, Dr Tap had a patent for Companion Diagnostic for CDK4 inhibitors—14/854,329 pending, MSK/SKI Identification and development of biomarkers for CDK4 inhibition in cancer, and a patent for Enigma and CDH18 as companion Diagnostics for CDK4 inhibition—SKI2016-021-03 pending, MSK/SKI Identification and development of biomarkers for CDK4 inhibition in cancer; and serving on a scientific advisory board for Certis Oncology Solutions, Stock Ownership; serving as cofounder for Atropos Therapeutics, Stock Ownership; and serving on a scientific advisory board for Innova Therapeutics. Dr Patnaik reported receiving institutional research funding from Plexxikon during the conduct of the study. Dr Tinoco reported receiving personal fees from Deciphera and personal fees from Intellisphere outside the submitted work. Dr Michelson reported serving as a consultant for Cogent Biosciences and being a former employee of Plexxikon during the conduct of the study. No other disclosures were reported.

Figures

Figure 1.. Type I Inhibitor PLX9486 Binds to Mutant KITD816V With High Atomic Efficiency

The aspartate to valine substitution in KITD816V promotes hydrophobic packing between V816 and Y646, locking the activation look (A-loop) in an extended, aspartate-phenylalanine-glycine–-in conformation conducive to adenosine triphosphate and substrate binding.

Figure 2.. Trial Profile

The study enrolled 39 PLX9486-naive patients and reenrolled 3 patients from previous cohorts in part 2e. Reasons for study discontinuation are provided for each cohort. Disease progression includes both progressive disease per Response Evaluation Criteria in Solid Tumors, version 1.1, and clinical progression.

Figure 3.. Clinical Responses and Duration

A, Waterfall plot of best percent changes for sums of target lesion diameters for 34 evaluable PLX9486-naive patients with gastrointestinal stromal tumor (GIST) grouped by treatment (PLX9486 ≤ 500 mg, PLX9486 1000 mg, or PLX9486 plus sunitinib). B, Changes in sums of target lesion diameters over the course of treatment. C, Progression-free survival (PFS) by treatment. CR indicates complete response; NE, not evaluable; PD, progressive disease; PR, partial response; SD, stable disease.