Development of a cfDNA 5mC/5hmC-based Biomarker Panel to Predict Targeted Therapy Efficacy in mCRC

Purpose

The EpiDRIVE study aims to identify cfDNA-based epigenetic determinants of response in metastatic colorectal cancer (mCRC) patients treated with EGFR- or VEGF-targeted therapy. By integrating 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) profiling, this study seeks to develop a predictive biomarker panel capable of differentiating responders from non-responders to targeted therapy.

Condition

  • CRC (Colorectal Cancer)

Eligibility

Eligible Ages
Over 18 Years
Eligible Sex
All
Accepts Healthy Volunteers
No

Inclusion Criteria

  • Histologically confirmed metastatic colorectal adenocarcinoma (mCRC). - Received EGFR-targeted therapy (cetuximab/panitumumab) or VEGF-targeted therapy (bevacizumab). - Availability of pre-treatment plasma sample for cfDNA analysis. - Documented radiologic response evaluation (RECIST 1.1). - RAS/BRAF mutation status known.

Exclusion Criteria

  • Inadequate cfDNA quality or low cfDNA yield. - Non-adenocarcinoma histology. - Concurrent or prior other active malignancy. - Active inflammatory or autoimmune disease affecting cfDNA methylation profiles.

Study Design

Phase
Study Type
Observational
Observational Model
Case-Control
Time Perspective
Retrospective

Arm Groups

ArmDescriptionAssigned Intervention
Discovery Cohort - Long PFS Group (Responder) Patients with metastatic colorectal cancer (mCRC) who received EGFR- or VEGF-targeted therapy and achieved a progression-free survival (PFS) ≥ 12 months, classified as clinical responders. Pre-treatment plasma cfDNA samples were analyzed by genome-wide 5mC/5hmC sequencing to identify epigenetic determinants associated with durable treatment response.
  • Diagnostic Test: cfDNA 5mC/5hmC Sequencing (EpiDRIVE Discovery Phase)
    High-throughput genome-wide sequencing of cfDNA methylation (5mC) and hydroxymethylation (5hmC) profiles from pre-treatment plasma samples in the discovery cohort to identify epigenetic determinants of targeted-therapy response (PFS ≥ 12 months vs < 12 months).
Discovery Cohort - Short PFS Group (Non-Responder) Patients with mCRC who received EGFR- or VEGF-targeted therapy and showed progression-free survival (PFS) < 12 months, classified as non-responders. Pre-treatment cfDNA samples were analyzed using genome-wide 5mC/5hmC sequencing and compared with long-PFS responders to identify differential methylation and hydroxymethylation patterns associated with resistance.
  • Diagnostic Test: cfDNA 5mC/5hmC Sequencing (EpiDRIVE Discovery Phase)
    High-throughput genome-wide sequencing of cfDNA methylation (5mC) and hydroxymethylation (5hmC) profiles from pre-treatment plasma samples in the discovery cohort to identify epigenetic determinants of targeted-therapy response (PFS ≥ 12 months vs < 12 months).
Training Cohort - Long PFS Group (Responder) Independent mCRC cohort with PFS ≥ 12 months following EGFR- or VEGF-targeted therapy. Candidate cfDNA 5mC/5hmC markers identified in the discovery phase were validated using targeted sequencing (EpiDRIVE assay) to construct the predictive epigenetic biomarker panel.
  • Diagnostic Test: EpiDRIVE Assay (Targeted Sequencing / qPCR Validation)
    Targeted sequencing or qPCR-based validation of cfDNA 5mC/5hmC markers identified from the discovery phase to develop and validate a predictive biomarker model discriminating patients with long vs short progression-free survival after EGFR-/VEGF-targeted therapy.
Training Cohort - Short PFS Group (Non-Responder) Independent mCRC patients with PFS < 12 months after targeted therapy. Targeted sequencing using the EpiDRIVE assay was conducted to refine and optimize the predictive model by comparing short- vs long-PFS cases.
  • Diagnostic Test: EpiDRIVE Assay (Targeted Sequencing / qPCR Validation)
    Targeted sequencing or qPCR-based validation of cfDNA 5mC/5hmC markers identified from the discovery phase to develop and validate a predictive biomarker model discriminating patients with long vs short progression-free survival after EGFR-/VEGF-targeted therapy.
Validation Cohort - Long PFS Group (Responder) Separate validation cohort of mCRC patients achieving PFS ≥ 12 months under EGFR- or VEGF-targeted therapy. qPCR-based EpiDRIVE assay was used to confirm predictive accuracy of the cfDNA 5mC/5hmC biomarker panel in identifying durable responders.
  • Diagnostic Test: EpiDRIVE Assay (Targeted Sequencing / qPCR Validation)
    Targeted sequencing or qPCR-based validation of cfDNA 5mC/5hmC markers identified from the discovery phase to develop and validate a predictive biomarker model discriminating patients with long vs short progression-free survival after EGFR-/VEGF-targeted therapy.
Validation Cohort - Short PFS Group (Non-Responder) Independent validation cohort of mCRC patients with PFS < 12 months after targeted therapy. cfDNA was analyzed using the qPCR-based EpiDRIVE assay to assess model specificity and distinguish non-responders from long-term responders.
  • Diagnostic Test: EpiDRIVE Assay (Targeted Sequencing / qPCR Validation)
    Targeted sequencing or qPCR-based validation of cfDNA 5mC/5hmC markers identified from the discovery phase to develop and validate a predictive biomarker model discriminating patients with long vs short progression-free survival after EGFR-/VEGF-targeted therapy.

Recruiting Locations

City of Hope Medical Center
Duarte, California 91016
Contact:
Ajay Goel, PhD
626-218-3452
ajgoel@coh.org

More Details

Status
Recruiting
Sponsor
City of Hope Medical Center

Study Contact

Ajay Goel, PhD
626-359-8111
ajgoel@coh.org

Detailed Description

Metastatic colorectal cancer (mCRC) remains one of the leading causes of cancer-related death. Although targeted agents such as anti-EGFR (cetuximab, panitumumab) and anti-VEGF (bevacizumab) therapies have improved survival, treatment response varies widely even among molecularly defined subgroups. Traditional biomarkers, including RAS/BRAF mutation and tumor sidedness, fail to accurately predict therapeutic efficacy. Recent studies highlight the potential of cell-free DNA (cfDNA) methylation (5mC) and hydroxymethylation (5hmC) as sensitive, non-invasive indicators of tumor biology and treatment dynamics. The EpiDRIVE study integrates cfDNA 5mC/5hmC sequencing and targeted validation to discover and verify epigenetic determinants of therapeutic response. Discovery phase: Whole-genome 5mC/5hmC profiling to identify differentially modified regions between responders and non-responders. Training phase: Targeted sequencing to establish a predictive cfDNA epigenetic panel (EpiDRIVE panel). Validation phase: qPCR-based validation of selected markers in an independent cohort to confirm predictive accuracy. This study aims to provide a non-invasive biomarker framework to predict and monitor efficacy of EGFR- and VEGF-targeted therapies in mCRC, ultimately guiding personalized treatment selection.