Landscape of acquired resistance alterations in gastrointestinal malignancies after genomically targeted therapy

Targeted therapies directed at specific genomic alterations have transformed the management of gastrointestinal (GI) cancers; however, acquired resistance remains inevitable. Circulating tumor DNA (ctDNA) analysis via liquid biopsy provides a non-invasive approach to characterize genomic mechanisms of resistance. We therefore evaluated patterns of acquired genomic resistance in patients with GI cancers treated with targeted therapies.

Patients with GI cancers treated with standard of care or investigational therapies targeting EGFR, HER2, FGFR, MET, KRAS, BRAF for at least 60 days who underwent both baseline comprehensive genomic profiling and post-progression ctDNA sequencing were retrospectively evaluated.

Of 106 patients meeting inclusion criteria, 45 had biliary tract cancer (BTC), 42 colorectal cancer (CRC), and 19 other GI malignancies. At least one putative resistance-associated alteration was detected in ctDNA in 53% of cases. Resistance patterns were heterogeneous with 47% showing no detectable alterations and 33% harboring ≥2 resistance alterations. Among 164 total alterations, the majority were single nucleotide variants (82%), followed by amplifications (17%). Overall, 48% were classified as 'bypass' alterations-activating alternative oncogenic pathways, most commonly MAPK signaling-while 52% were 'on-target' alterations involving secondary changes within the drug target. RAS alterations represented a key mechanism of bypass resistance, accounting for 28% of all resistance alterations. Interestingly, in CRC, bypass alterations predominated (69%), whereas in BTCs, on-target alterations were more frequent (61%).

Liquid biopsies frequently identify acquired resistance following targeted therapy across GI cancers, often revealing multiple concurrent alterations. Patterns of resistance varied by tumor type, with both on-target and bypass mechanisms observed. These findings highlight common themes of resistance and support the growing clinical role of ctDNA analysis in defining resistance and guiding management in GI malignancies.