Circulating cell-free DNA methylation profiles as noninvasive multiple sclerosis biomarkers: A proof-of-concept study

Area of Science:

• Epigenetics
• Neuroimmunology
• Biomarker Discovery

Background:

• Multiple sclerosis (MS) lacks non-invasive biomarkers for comprehensive disease assessment.
• Current methods struggle to simultaneously classify subtypes, evaluate disability, and predict progression.

Purpose of the Study:

• To investigate the clinical utility of plasma cell-free DNA (cfDNA) methylation profiling.
• To assess cfDNA methylation for distinguishing MS from controls, identifying subtypes, and predicting disability.
• To evaluate cfDNA methylation as a single, non-invasive diagnostic and prognostic assay.

Main Methods:

• Low-coverage whole-genome bisulfite sequencing (WGBS) of 75 plasma cfDNA samples.
• Identification and analysis of differentially methylated CpGs and regions (DMRs).
• Comparison of cfDNA methylation performance against neurofilament light chain (NfL) and GFAP.

Main Results:

• Thousands of DMRs significantly distinguished MS patients from controls and stratified MS subtypes and disability levels.
• DMRs were enriched in immune and neural regulatory elements, with motifs linked to neuronal function and T-cell differentiation.
• cfDNA methylation outperformed NfL and GFAP in distinguishing MS subtypes and severity (AUCs 0.67-0.82).
• Prognostic regions identified by cfDNA methylation predicted future disability with high accuracy (AUC=0.81).

Conclusions:

• Circulating cfDNA methylation profiles show significant potential as non-invasive biomarkers for MS.
• This approach may enable concurrent diagnosis, subtype classification, and prognosis in MS.
• Further validation with higher-depth sequencing and independent cohorts is warranted.