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KIT ATP-Binding Pocket/Activation Loop Mutations in GI Stromal Tumor: Emerging Mechanisms of Kinase Inhibitor Escape
Thomas Mühlenberg1,2, Johanna Falkenhorst1,2, Tom Schulz3,4
1Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Duisburg-Essen, Medical School, Essen, Germany.
Purpose:
Imatinib resistance in GI stromal tumors (GISTs) is primarily caused by secondary KIT mutations, and clonal heterogeneity of these secondary mutations represents a major treatment obstacle. KIT inhibitors used after imatinib have clinical activity, albeit with limited benefit. Ripretinib is a potent inhibitor of secondary KIT mutations in the activation loop (AL). However, clinical benefit in fourth line remains limited and the molecular mechanisms of ripretinib resistance are largely unknown.
Patients And Methods:
Progressing lesions of 25 patients with GISTs refractory to ripretinib were sequenced for KIT resistance mutations. Resistant genotypes were validated and characterized using novel cell line models and in silico modeling.
Results:
GISTs progressing on ripretinib were enriched for secondary mutations in the ATP-binding pocket (AP), which frequently occur in cis with preexisting AL mutations, resulting in highly resistant AP/AL genotypes. AP/AL mutations were rarely observed in a cohort of progressing GIST samples from the preripretinib era but represented 50% of secondary KIT mutations in patients with tumors resistant to ripretinib. In GIST cell lines harboring secondary KIT AL mutations, the sole genomic escape mechanisms during ripretinib drug selection were AP/AL mutations. Ripretinib and sunitinib synergize against mixed clones with secondary AP or AL mutants but do not suppress clones with AP/AL genotypes.
Conclusion:
Our findings underscore that KIT remains the central oncogenic driver even in late lines of GIST therapy. KIT-inhibitor combinations may suppress resistance because of secondary KIT mutations. However, the emergence of KIT AP/AL mutations after ripretinib treatment calls for new strategies in the development of next-generation KIT inhibitors.
Insights
Resistance to ripretinib in gastrointestinal stromal tumors (GISTs) is driven by new KIT mutations in the ATP-binding pocket (AP) that occur with existing activation loop (AL) mutations. These AP/AL genotypes limit treatment options for advanced GIST.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Imatinib resistance in gastrointestinal stromal tumors (GISTs) is primarily driven by secondary KIT mutations, posing a significant challenge in treatment.
- While KIT inhibitors show some activity, their benefit in later lines of therapy, like fourth-line treatment with ripretinib, remains limited, and resistance mechanisms are not fully understood.
Purpose of the Study:
- To investigate the molecular mechanisms of resistance to ripretinib in patients with GISTs.
- To identify novel KIT mutations associated with ripretinib refractoriness.
Main Methods:
- Genomic sequencing of KIT resistance mutations in GIST lesions from 25 patients refractory to ripretinib.
- Validation and characterization of resistant genotypes using cell line and in silico models.
Main Results:
- GISTs progressing on ripretinib showed enrichment of secondary KIT mutations in the ATP-binding pocket (AP), often co-occurring with pre-existing activation loop (AL) mutations, forming highly resistant AP/AL genotypes.
- These AP/AL mutations were rare in the pre-ripretinib era but constituted 50% of secondary KIT mutations in ripretinib-resistant GISTs.
- In vitro models confirmed that AP/AL mutations were the primary escape mechanism from ripretinib, and while combinations like ripretinib and sunitinib suppressed some resistant clones, they were ineffective against AP/AL genotypes.
Conclusions:
- KIT remains a critical oncogenic driver in advanced GIST, even with multiple lines of therapy.
- The emergence of KIT AP/AL mutations after ripretinib treatment highlights the need for novel therapeutic strategies and next-generation KIT inhibitors.
- Combination therapies may help suppress resistance from secondary KIT mutations, but new approaches are required to overcome AP/AL mediated resistance.
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