2201P - Malignant pleural mesothelioma (MPM)-specific DNA methylation patterns in patients using liquid biopsies

Background

Circulating tumor (ct)DNA profiling in MPM has been limited by the molecular heterogeneity of MPM without identification of recurrent mesothelioma-specific mutations, prohibiting development of mutational-based custom panels. Cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) on plasma cell-free DNA (cfDNA) that distinguishes MPM plasma samples from healthy non-cancer controls (NCC) based on epigenetic changes by analyzing differential methylation regions (DMR) could overcome this limitation.

Methods

Pre-treatment cell-free methylomes of 39 MPM patients and 16 healthy non-cancer controls (NCC) were examined through cfMeDIP-seq. cfMeDIP-seq libraries were sequenced at a depth of 70 million reads, paired-end, on the NovaSeq 6000. For all analyses, chromosomes 1-22 were binned into 300-bp windows (total of 9.6e6 genome-wide windows); reads from cfMeDIP-seq were tallied per bin.

Results

39 patients with MPM (77% epithelioid, 15% biphasic, 8% sarcomatoid) and 16 NCC (10 asbetos exposed) were analzyed. Patients with MPM had a median age of 70 years; 94% were male; 80% reported prior asbestos exposure. Differential methylation analysis identified 626 windows (log2 fold-change > 1, p-adjusted < 0.05) hypermethylated in MPM and 568 windows hypermethylated in NCC. The MPM methylome was enriched for CpG islands (5.8% of significant DMRs) and shores (8.8%), whereas in NCC predominantly open-sea regions (92.1%) were hypermethylated and only in 0.17% of CpG-islands. MPM was also enriched for promoter regions (3.2%) compared to NCC (0.0%). KEGG-pathway analysis corresponding to significant DMRs in MPM samples identified several important pathways including microRNAs in cancer, focal adhesion, and proteoglycans in cancer. There were also several promotors significantly hypermethylated in MPM that are also implicated in other cancers such as RPS27, USP39, ZUP1, ADAP1, NCAPG2, BRSK2, TMEM216, and KLHL11.

Conclusions

ctDNA global methylome profiling is a promising tool to identify novel biological pathways and targets in MPM. There is potential for future use of cfMeDIP-Seq in MPM screening, minimal residual disease, and therapeutic monitoring.

Clinical trial identification

Editorial acknowledgement

Legal entity responsible for the study

The authors.

Funding

Vontobel-Stiftung (research grant for this work); Dr. Hans Altschüler Stiftung (research grant for this work); Swiss Cancer Research Foundation (fellowship grant).

Disclosure

S. Schmid: Financial Interests, Institutional, Advisory Board: AstraZeneca, MSD, BMS, Merck; Financial Interests, Institutional, Funding: Janssen, BMS, AstraZeneca; Financial Interests, Personal, Other, Congress travel support: Takeda, MSD, Amgen; Financial Interests, Institutional, Speaker, Consultant, Advisor: MSD. B. Lok: Financial Interests, Institutional, Funding: Pfizer, AstraZeneca; Non-Financial Interests, Institutional, Other: AstraZeneca; Financial Interests, Personal, Other: AstraZeneca. S. Bratman: Financial Interests, Personal, Other, Financial payments, employment, equity/stock, licencing: Adela; Financial Interests, Institutional, Other, Equity/stocl, licensing: Adela; Financial Interests, Personal, Royalties: Roche. M. Frueh: Financial Interests, Institutional, Advisory Board: BMS, AstraZeneca, MSD, Takeda, Roche, Lilly, Boehringer Ingelheim, Novartis, Amgen; Financial Interests, Institutional, Funding: BMS. G. Liu: Financial Interests, Personal, Advisory Board: AstraZeneca, Takeda, Novartis, Lilly, Pfizer, Merck, EMD Serono, Jazz, BMS; Financial Interests, Institutional, Funding: Boehringer Ingelheim, Takeda, AstraZeneca, EMD Serono. All other authors have declared no conflicts of interest.