Background Metastatic gastrointestinal stromal tumors (GIST) are lethal tumors of the GI tract characterized by gain of function mutations in KIT or PDGFRα. Transient first-line control is achieved through the inhibition of tyrosine kinase signaling using the KIT inhibitor imatinib, though most patients progress after 2–3 years. Progression through successive lines of therapy results in a molecularly heterogeneous disease with diverse subtypes, driven by distinct collections of exon-specific KIT mutations which directly inform therapy decisions. To address the unmet need of comprehensive understanding of GIST, we used tumor-informed whole exome liquid biopsy to identify and track the evolution of multiple concurrent heterogeneous resistance mechanisms in individual patients receiving tyrosine kinase inhibitors (TKIs).

Methods Baseline matched tumor, normal and longitudinal plasma samples were obtained from 15 metastatic, heavily pretreated GIST patients. Following baseline sample collection, all patients received systemic TKI therapy, and were monitored until disease progression. Paired tumor and normal samples were profiled using the ImmunoID NeXT Platform®, an augmented exome/transcriptome platform and analysis pipeline which generates comprehensive tumor and immune information. Exome-scale cfDNA profiling of matched plasma samples was performed using the NeXT Liquid BiopsyTM platform to detect somatic variants.

Results Baseline solid tumor WES confirmed primary sensitizing KIT mutations in all 15 (100%) patients, and secondary KIT mutations in 7/15 patients (47%). Serial plasma whole exome sequencing identified evolution and expansion of clones harboring newly formed, druggable, exon-specific KIT mutations which evolved prior to identification of tumor progression using standard imaging techniques. In addition to these variants, we detected node-specific enrichment of PI3K-AKT and MAPK pathway mutations in plasma of patients with shorter overall survival (OS), which may contribute to the observed immune evasion. Accompanying these changes, we also detected significant association between gene copy-number profiles and duration of OS (P = 0.0097). Investigation of immune signatures using univariate cox modeling revealed a significant association between TCRβ diversity and reduced OS (HR = 2.55, log rank P = 0.04).

Conclusions Comprehensive genomic profiling (WES and RNA-Seq) of paired tumor tissue and WES of serially collected ctDNA identified evolving druggable KIT mutations and other molecular alterations which preceded clinical disease progression. These findings suggest liquid biopsy-based monitoring of late-stage GIST malignancies may be useful for early identification of treatment resistance, providing treatment guidance prior to traditional approaches.

Ethics Approval Ethics approval was granted by the MD Anderson Human Research Protection Program, and all participants gave informed consent prior to participation.