Longitudinal Assessment of EGFR and MET Transcriptional Activity Using Cell-Free Chromatin Immunoprecipitation in Two Patients with EGFR-Mutated Non-Small Cell Lung Cancer

Background/Objectives: MET amplification represents the most common bypass resistance mechanism to EGFR tyrosine kinase inhibitor (TKI) treatment in EGFR-mutated non-small cell lung cancer (NSCLC). Combination therapy with the EGFR-TKI, osimertinib, and the MET-TKI, crizotinib, has demonstrated clinical efficacy in overcoming this resistance. However, assessing MET transcriptional activity during treatment remains challenging. Methods: Cell-free chromatin immunoprecipitation (cfChIP) targeting H3 lysine 36 trimethylation (H3K36me3) was employed to investigate the transcriptional activity of the EGFR and MET genes in serial liquid biopsies obtained from two patients with EGFR-mutated NSCLC. Droplet digital PCR (ddPCR) was used to quantify circulating tumor DNA (ctDNA) and cfChIP enrichment levels. Results: In PT1, H3K36me3 mEGFR and MET cfChIP enrichment increased during disease progression, with MET enrichment increasing further following the initiation of crizotinib/osimertinib combination therapy, during which the patient experienced a partial response. In PT2, MET amplification was detected in a liquid biopsy, but MET cfChIP enrichment remained low throughout the treatment course, and the patient did not respond to crizotinib. Conclusions: This two-patient feasibility study illustrates the potential of cfChIP-ddPCR for the longitudinal assessment of EGFR and MET transcriptional activity in liquid biopsies. These observations warrant further investigation of cfChIP as an approach for monitoring transcriptional activity during osimertinib/crizotinib treatment.