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. 2025 Oct 28:10:100442.
doi: 10.1016/j.jlb.2025.100442. eCollection 2025 Dec.

Chemotherapy response monitoring with DNA methylation-based ctDNA tumor fraction: Evidence from a real-world cohort of patients with advanced common solid malignancies

Christian D Rolfo  1 , Moh'd M Khushman  2 , Alessandro Russo  3   4 , Roberto Borea  1 , Bernard Herrman  5 , Jing Wang  5 , Jiemin Liao  5 , Carin R Espenschied  5 , Sean Gordon  5 , Katie Quinn  5 , Kimberly C Banks  5 , Arielle J Medford  6   7
Affiliations

Chemotherapy response monitoring with DNA methylation-based ctDNA tumor fraction: Evidence from a real-world cohort of patients with advanced common solid malignancies

Christian D Rolfo et al. J Liq Biopsy. .

Abstract

Background/objectives: Chemotherapy remains standard for many cancers, but challenges remain in evaluating clinical response to therapy. Epigenomic circulating tumor DNA (ctDNA) quantification is an emerging molecular approach to tumor response assessment. Here, we examine a tissue-free, methylation-based assay to demonstrate how changes in circulating tumor fraction (TF) associate with outcomes in a real-world advanced, pan-cancer cohort treated with chemotherapy.

Methods: This retrospective study evaluated patients with advanced solid tumors treated with chemotherapy and serial ctDNA testing, both pre- and post-therapy initiation. Serial samples were analyzed with an analytically validated next-generation sequencing (NGS) methylation-based ctDNA assay. The primary outcome measured was real-world time to next treatment (rwTTNT) as a surrogate for progression free survival. Secondary outcomes included real-world overall survival (rwOS) and lead time from TF increase to rwTTNT event.

Results: Among 278 eligible patients, decreasing TF was associated with improved rwTTNT (aHR 0.55 [95 % CI 0.39, 0.79] p = 0.001). Patients achieving a ≥98 % decrease at any timepoint had superior outcomes (rwTTNT aHR 0.40 [95 % CI 0.28, 0.56] p < 0.005; rwOS aHR 0.54 [95 % CI 0.38, 0.79] p < 0.005). Patients with continuous TF decrease had longer rwTTNT than those with initial decrease followed by increase (aHR 0.05 [CI 0.004-0.575] p = 0.016). Increasing TF was detected in 64 patients with a median lead time to rwTTNT of 2.27 months.

Conclusions: On-treatment changes in methylation-based TF in chemotherapy-treated patients are associated with long-term outcomes. CtDNA monitoring offers an opportunity to rapidly evaluate therapy efficacy, potentially improving clinical decision-making regarding benefit vs toxicity and long-term patient outcomes.

Keywords: Chemotherapy; Methylation; Molecular response; Monitoring; Overall survival; Tumor fraction; ctDNA.

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Conflict of interest statement

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:10.13039/100032545CDR reports personal fees for advisory board membership from Novocure; institutional fees for advisory board membership from 10.13039/100004325AstraZeneca, Imagene, MedStar, Amgem, Boeringer-Ingelheim, Hoffmann-La 10.13039/100004337Roche Ltd, 10.13039/100020707Janssen Pharmaceutical, NeoGenomics, 10.13039/100004319Pfizer, Inc. and Regeneron; Research collaboration non remunerated: Guardant, Foundation One; institutional fees as an invited speaker from COR2ED, HPM education IDEOlogy 10.13039/100004334Merck and 10.13039/100004337Roche, OneCell Dx; non-renumerated leadership roles as a scientific board member for the 10.13039/501100001685European School of Oncology (10.13039/501100001685ESO), Past Chair on the educational committee for the International Association for Study of Lung Cancer (10.13039/100005923IASLC), President for the International Society of Liquid Biopsy (ISLB) and Educational Chair for the Oncology Latin American Association (OLA); a renumerated role as Editor in Chief for Critical Reviews in Oncology Hematology (CROH); a non-renumerated role as 10.13039/501100007075ESMO Faculty Group/Speciality and Faculty Coordinator for metastatic non-small cell lung cancer for 10.13039/501100007075European Society for Medical Oncology (10.13039/501100007075ESMO); non-renumerated roles as: Scientific Board Member at 10.13039/501100001685ESO (10.13039/501100001685European School of Oncology), External advisor Board member of Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica (10.13039/501100007321GENYO), External Advisor of the School of Public Health, 10.13039/501100006393University of Granada, Spain, Scientific Committee of the Fondazione Siciliana di Oncologia, and non-renumerated analysis of liquid biopsies in a lung cancer trial for Guardant 10.13039/100018696Health. AR has received advisory board or speaker bureau honoraria from AstraZeneca, MSD, Novartis, Pfizer, BMS, Takeda, Amgen, Regeneron, Daiichi Sankyo, Merck, and Johnson & Johnson; compensated activity for editorial projects from AstraZeneca, MSD, BMS, Novartis, Roche, and Regeneron. RB reports travel grant from 10.13039/100004312Lilly. AJM has served as an advisor/consultant for AstraZeneca, Edgewood Oncology, Guardant Health, Illumina, Myriad Genetics, Natera, Novartis, SAGA Diagnostics, Reversing Early Recurrence, and Science for America, outside the submitted work. AJM's research is supported by a 10.13039/100000002National Institutes of Health K12 grant (K12CA087723). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Figures

Fig. 1
Fig. 1
A–D: Forest plots and KM curve for various tumor fraction changes from baseline to best molecular response between 21 and 140 days after start of chemotherapy. (A) rwTTNT. (B) rwOS. (C) Kaplan-Meier analysis of rwTTNT by TF decrease across the full dataset (overlapping threshold bins). (D) Cox proportional hazards model with TF change treated as a continuous variable; rwTTNT and rwOS. The “below LOQ” group refers to patients whose TF was not detected or detected but below the limit of quantification at both baseline and best molecular response timepoints.
Fig. 2
Fig. 2
A–B: Kaplan-Meier analysis and forest plot of CPH comparing with a best % TF change of ≥98 % decrease to those with <98 % decrease or increase in TF 21–140 days after start of chemotherapy. (A) Patients with ≥98 % TF decrease, had significantly longer median rwTTNT compared to those with <98 % decrease or TF increase with an adjusted HR 0.4 [95 % CI 0.28, 0.56] p < 0.005). (B) Patients with ≥98 % TF decrease had significantly improved rwOS compared to those with <98 % decrease or TF increase with an adjusted HR 0.56 [95 % CI 0.39, 0.81] p = 0.002).
Fig. 3
Fig. 3
Sub-Analysis of 54 patients with 2+ on-treatment time points. Patients with decreasing TF across all timepoints had longer median rwTTNT than patients with an initial decrease followed by an increase in TF (adjusted HR = 0.36 [CI 0.14–0.92] p = 0.033). Patients with decreasing TF across all timepoints also had longer median rwTTNT than patients with an initial increase in TF (adjusted HR = 0.02 [CI 0.001–0.31] p = 0.006).
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