1664MO - Tumor-naïve methylomes and fragmentomes during pembrolizumab (P) in metastatic cancer patients

Background

Decrease in circulating tumour DNA (ctDNA) by cycle 3 (C3) of P predicts favorable response. However, matched tissue sequencing is often needed to measure ctDNA mutation concentration (MC). ctDNA demonstrates cancer-specific methylation (CSM) and higher short fragment fraction (SFF). We report the first joint analysis of tumour-naïve cell-free methylomes and fragmentomes in a P-treated cohort.

Methods

In INSPIRE (NCT02644369), we measured CSM and SFF from tumour-naïve cell-free methylated DNA immunoprecipitation & sequencing (cfMeDIP-seq) at baseline (B) and C3 during P immunotherapy. SFF was defined as fraction of fragments shorter than mononucleosome median (146 bp). We independently trained a pan-cancer methylation signature on PanCanAtlas 450K arrays, then further filtered out leukocyte-methylated regions, yielding 298 CpGs. Methylation probabilities were inferred from coverage in 300 bp bins. CSM was the sum of probabilities across the 298 CpG signature. MC was measured with bespoke 16-mutation ctDNA panels (Signatera), guided by tissue exomes. Cox model adjusted hazard ratios (aHR) and p-values were corrected for cohort.

Results

51 patients were included, median follow-up: 18.2 months. Cohorts included head & neck n=12, breast n=10, ovary n=10, melanoma n=8, and others n=11. CSM was strongly correlated with MC (r=0.85, p<0.001). SFF was moderately correlated with CSM and MC (both r>0.55, p<0.001). Table shows associations of B-to-C3 ΔMC, ΔSFF, and ΔCSM with overall survival (OS) and progression-free survival (PFS). Decrease in any ctDNA metric was correlated with longer OS and PFS, with ΔMC and ΔCSM being statistically significant. To combine ΔCSM and ΔSFF, we devised a joint prognostic score, which yielded superior association with OS and PFS. Table: 1664MO

Conclusions

CSM is an accurate tumour-naïve metric of ctDNA, using bespoke ctDNA as a gold standard. ΔCSM predicts OS and PFS comparably to ΔMC. Combining ΔCSM and ΔSFF from the same assay yields superior OS and PFS prediction.

Clinical trial identification

NCT02644369.

Editorial acknowledgement

Legal entity responsible for the study

University Health Network.

Funding

Major funding support for the project was made possible by the Princess Margaret Cancer Foundation, Ontario Institute for Cancer Research and Terry Fox Research Institute. Merck did not provide direct funding for the study but contributed the study drug in kind.

Disclosure

A. Abdul Razak: Financial Interests, Personal, Advisory Role: Adaptimmune, Bayer, GlaxoSmithKline, Medison, Inhibrx; Financial Interests, Personal, Expert Testimony: Medison; Financial Interests, Institutional, Funding: Deciphera, Karyopharm Therapeutics, Pfizer, Roche/Genentech, Bristol Myers Squibb, MedImmune, Amgen, GlaxoSmithKline, Blueprint Medicines, Merck, AbbVie, Adaptimmune, Iterion Therapeutics, Neoleukin Therapeutics, Daiichi Sankyo, Symphonogen, Rain Therapeutics. A. Spreafico: Financial Interests, Personal, Other, Honoraria: Bristol Myers Squibb, Janssen Oncology; Financial Interests, Institutional, Advisory Role: Bristol Myers Squibb, Merck, Novartis, Oncorus, Medison & Immunocore; Financial Interests, Institutional, Funding: Alkermes, Array BioPharma, AstraZeneca/MedImmune, Bayer, Bristol Myers Squibb, GlaxoSmithKline, Janssen Oncology, Merck, Northern Biologics, Novartis, Replimune, Roche, Surface Oncology, Symphogen, Amgen, Treadwell Therapeutics; Financial Interests, Institutional, Other, Travel Expenses: Bayer, Bristol Myers Squibb, Idera, Janssen Oncology, Merck, Roche. P.L. Bedard: Financial Interests, Institutional, Invited Speaker: AstraZeneca, Bicara, BMS, Amgen, Novartis, Genentech/Roche, Sanofi, Merck, Pfizer, Zymeworks, Nektar Therapeutics, Lilly, Seagen; Financial Interests, Institutional, Research Grant: Pfizer; Financial Interests, Institutional, Funding: Servier; Non-Financial Interests, Invited Speaker, Executive Board Member: Breast International Group; Non-Financial Interests, Leadership Role, Chair: AACR Project GENIE; Non-Financial Interests, Leadership Role, Past Chair IND Committee Member, Breast Site Steering Committee: Canadian Clinical Trials Group; Non-Financial Interests, Advisory Role: Seagen, Lilly, Amgen, Merck, BMS, Pfizer, Gilead. A.R. Hansen: Financial Interests, Institutional, Advisory Role: AstraZeneca, Bristol Myers Squibb, Eisai, GlaxoSmithKline, Merck, Novartis; Financial Interests, Institutional, Research Grant: Astellas Pharma, AstraZeneca/MedImmune, BioNTech, Boehringer Ingelheim, Bristol Myers Squibb, GlaxoSmithKline, Janssen, Karyopharm Therapeutics, Merck, Neoleukin Therapeutics, Pfizer/EMD Serono, Roche/Genentech. S. Lheureux: Financial Interests, Personal, Advisory Role: AstraZeneca, Merck, GlaxoSmithKline, Eisai, Novocure, Shattuck Labs, Novartis; Financial Interests, Personal, Other, Honoraria: AstraZeneca, Eisai, Merck, GlaxoSmithKline; Financial Interests, Institutional, Funding: Tesaro, AstraZeneca, Roche/Genentech, Regeneron, Merck, GlaxoSmithKline, Repare Therapeutics. D. Torti: Financial Interests, Personal, Full or part-time Employment: Ezra AI; Financial Interests, Personal, Stocks/Shares: Ezra AI. T.J. Pugh: Financial Interests, Personal, Advisory Role: Chrysalis Biomedical Advisors, Axiom Healthcare Strategies; Financial Interests, Personal and Institutional, Proprietary Information: Hybrid-Capture Sequencing for Determining Immune Cell Clonality; Financial Interests, Personal, Other, Honoraria: Merck; Financial Interests, Institutional, Funding: Roche. L.L. Siu: Financial Interests, Personal, Advisory Board: Merck, Pfizer, AstraZeneca, Morphosys, Roche, GeneSeeq, Loxo, Oncorus, Symphogen, Seattle Genetics, Voronoi, Treadwell Therapeutics, Arvinas, Tessa, Navire, Relay Therapeutics, Rubius, Janpix; Financial Interests, Personal, Other, Spouse is co-founder: Treadwell Therapeutics; Financial Interests, Personal, Stocks/Shares, Spouse has stock ownership: Agios; Financial Interests, Institutional, Invited Speaker: Novartis, Bristol Myers Squibb, Pfizer, Boehringer Ingelheim, GlaxoSmithKline, Roche/Genentech, AstraZeneca, Merck, Astellas, Bayer, Amgen, Symphogen, Intensity Therapeutics, Mirati, Shattucks, Avid. All other authors have declared no conflicts of interest.