CtDNA analysis of NTRK fusion and mechanisms of acquired resistance to TRK inhibitors.

Abstract

3062 Background: The regulatory approval of TRK tyrosine kinase inhibitors (TKIs) represented a landmark in tissue-agnostic drug development. Adult and pediatric patients harboring NTRK fusions derive meaningful clinical benefits from the first-generation TRK TKIs larotrectinib and entrectinib. However, characterizing NTRK fusions and resistance mechanisms to TRK TKIs by circulating tumor DNA (ctDNA) remains to be studied. Methods: Patients with NTRK-fusion-positive tumors who received TRK TKIs and had ctDNA analyzed using next-generation sequencing (NGS) were retrospectively identified. Samples were collected at multiple time points, including pre-TRK TKI, on-treatment, and post-progression. Mechanisms of resistance to TRK TKIs were examined when post-progression ctDNA samples were available. Results: Twenty-seven patients, with a median age of 57 years (range 28-81) and 11 different cancer types were identified. Twenty-two patients (81%; 22/27) had at least one ctDNA-positive sample (tumor burden greater than 0). A total of 67 ctDNA samples were analyzed by MSKCC ACCESS ctDNA pipeline, of which 10 samples (15%; 10/67) were collected before any TRK TKI. Forty-two samples (63%; 42/67) had positive ctDNA and NTRK fusion was detected in 16 ctDNA samples (24%; 16/67), including 9 (56%) NTRK1 fusions and 7 (44%) NTRK3 fusions. Among the pre-TRK TKI samples (n=10), 2 samples (20%, 2/10) had NTRK fusions detected. A total of 8 patients had post-progression samples with a resistance mechanism identified, of which 5 patients received larotrectinib and 3 entrectinib. The ctDNA samples revealed 7 patients (88%; 7/8) with on-target resistance and 1 patient (12%; 1/8) with off-target resistance. Among on-target mutations identified, the most common involved the solvent front residue (86%, n=6/7: n=2 NTRK3 G623R, n=2 NTRK1 G595R, n=1 NTRK3 G623E, n=1 NTRK3 623L) followed by the xDFG motif (14%, n=1/7: n=1 NTRK1 G667C). Regarding off-target alterations, one patient developed a BRAF V600E mutation. Conclusions: The use of plasma ctDNA can improve the identification of NTRK fusions through non-invasive techniques and potentially identify subsequent resistance mechanisms after the administration of the TRK TKIs.