P2.03-36 DNA Methylation: A More Sensitive Marker for Treatment Monitoring?

Abstract

Detection of genomic aberrations in cell-free DNA (cfDNA), requiring ultra-deep sequencing due to the low allelic frequencies (AF) of mutation, has been utilized to monitor treatment response. However, 20%-30% of patients yield no mutation from plasma genotyping despite deep sequencing depth, thus necessitating alternative monitoring method. The role of aberrant DNA methylation in the process of tumorigenesis both at individual genes and a genome-wide scale has been well elucidated. We investigated the potential of DNA methylation as a biomarker for treatment monitoring. We investigated the performance of mutation and DNA methylation as biomarkers to evaluate response to osimertinib using a DNA methylation panel consisting of 100,000 CpG sites and a targeted panel for mutation detection consisting of 168 lung cancer related genes with an average sequencing depth of 1,000x and 10,000x, respectively. Longitudinal plasma samples from 6 patients undergoing osimertinib were collected prior to treatment and at regular interval until disease progression, ranged from 6 to 9 times. Methylation level of a given sample was reflected by the percentage of significantly methylated blocks, which were significantly hypermethylated blocks comparing to healthy individuals. All patients had EGFR sensitizing mutation and T790M at baseline. Four patients had additional concurrent mutations, including TP53, RB1, OR6F1 and BRCA2. At PD, all patients had detectable mutations except for one and 3 developed EFGR C797S. Four patients had at least two times of no detectable mutation during treatment. Among them, P05 and P06 had 5 and 6 times of no detectable mutation, respectively. In contrast, all patients had significantly methylated blocks detected at every point. In general, the trend of changes in mutation AF corresponds to the changes in the percentage of significantly methylated blocks in all patients except for one, who only had mutations detected at baseline and had consistently detectable DNA methylation at every point. Collectively, DNA methylation reached nadir at best response and gradually increased thereafter. An elevation of mutation AF or the emergence of new mutation(s) (molecular PD) was observed in 4 patients prior to PD assessed by imaging. In all patients, an elevation of DNA methylation was observed prior to PD assessed by imaging; among them, 3 had changes in DNA methylation prior to molecular PD, suggesting DNA methylation may be a more sensitive biomarker. Collectively, our study demonstrates DNA methylation, continuously increasing from the nadir (best response), can be utilized as a biomarker for treatment monitoring.