Tracking the Evolution of Resistance to ALK Tyrosine Kinase Inhibitors Through Longitudinal Analysis of Circulating Tumor DNA

Abstract

Purpose ALK rearrangements predict for sensitivity to ALK tyrosine kinase inhibitors (TKIs). However, responses to ALK TKIs are generally short-lived. Serial molecular analysis is an informative strategy for identifying genetic mediators of resistance. Although multiple studies support the clinical benefits of repeat tissue sampling, the clinical utility of longitudinal circulating tumor DNA analysis has not been established in ALK-positive lung cancer. Methods Using a 566-gene hybrid-capture next-generation sequencing (NGS) assay, we performed longitudinal analysis of plasma specimens from 22 ALK-positive patients with acquired resistance to ALK TKIs to track the evolution of resistance during treatment. To determine tissue-plasma concordance, we compared plasma findings to results of repeat biopsies. Results At progression, we detected an ALK fusion in plasma from 19 (86%) of 22 patients, and identified ALK resistance mutations in plasma specimens from 11 (50%) patients. There was 100% agreement between tissue- and plasma-detected ALK fusions. Among 16 cases where contemporaneous plasma and tissue specimens were available, we observed 100% concordance between ALK mutation calls. ALK mutations emerged and disappeared during treatment with sequential ALK TKIs, suggesting that plasma mutation profiles were dependent on the specific TKI administered. ALK G1202R, the most frequent plasma mutation detected after progression on a second-generation TKI, was consistently suppressed during treatment with lorlatinib. Conclusions Plasma genotyping by NGS is an effective method for detecting ALK fusions and ALK mutations in patients progressing on ALK TKIs. The correlation between plasma ALK mutations and response to distinct ALK TKIs highlights the potential for plasma analysis to guide selection of ALK-directed therapies.

Longitudinal monitoring of somatic genetic alterations in circulating cell‐free DNA during treatment with epidermal growth factor receptor–tyrosine kinase inhibitors

“…NGS, the results for which are usually expressed as allele frequency, has the potential to become widely adopted for liquid biopsy analysis because it is able to simultaneously identify various genetic alterations including those responsible for resistance to targeted therapy. [24][25][26][27][28][29][30][31] Our findings suggest that the monitoring of allele frequency for EGFRactivating mutations in cfDNA by NGS may also be useful for the prediction of EGFR-TKI treatment efficacy.…”

“…Such a pattern was also evident for the allele frequency of EGFR ‐activating mutations (the ratio of the number of activating mutations to the total number of EGFR alleles) as determined by ddPCR (data not shown). NGS, the results for which are usually expressed as allele frequency, has the potential to become widely adopted for liquid biopsy analysis because it is able to simultaneously identify various genetic alterations including those responsible for resistance to targeted therapy . Our findings suggest that the monitoring of allele frequency for EGFR ‐activating mutations in cfDNA by NGS may also be useful for the prediction of EGFR‐TKI treatment efficacy.…”

Clinical Utility of Cell-Free DNA for the Detection of ALK Fusions and Genomic Mechanisms of ALK Inhibitor Resistance in Non–Small Cell Lung Cancer

“…This result is similar to other studies reporting between 44 and 56% of patients with kinase domain mutations. 10,27,37,38 Notably, seven of the 16 (43.8%) patients with resistance mutations in ALK demonstrated more than one mutation. This contrasts with a recently published series of ALK positive patients who underwent tissue-based NGS after progression on second generation ALKi in which 6/48 (12%) patient specimens contained compound mutations.…”

“…Small studies, such as a recent report that identified two cfDNA ALK fusions in a cohort of 102 patients show that the detection of these alterations is feasible, albeit more technically challenging than somatic mutation detection, while a longitudinal evaluation of 22 patients was able to detect ALK fusions in 86% at progression. 18,23,25–27 Additionally, although numerous tumor-tissue based studies have demonstrated mechanisms of resistance to ALKi, the use of cfDNA for the evaluation of drug resistance mechanisms in ALK -positive NSCLC has not been published.…”

Clinical features and outcomes ofALKrearranged non‐small cell lung cancer with primary resistance to crizotinib

“…In future research, we will explore the underlying mechanism for this result. Because NGS technology has displayed impressive capability for identifying the underlying molecular profile of cancers, its clinical application as a molecular screening test might favorably alter the clinical outcomes of ALK ‐positive NSCLC patients …”