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Updated: Sep 15, 2025

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Whole genome DNA methylation patterns in tissue and cfDNA associated with fibrosis reflect the complex signature of

Jongseong Ahn1, Soyeon Kim2,3, Jae Yoon Jeong4

  • 1IMBdx, Seoul, Republic of Korea.

Plos One
|July 17, 2025
PubMed

Insights

This study reveals how DNA methylation patterns in liver tissue and cell-free DNA are linked to metabolic dysfunction-associated steatotic liver disease (MASLD) fibrosis, considering sex differences. Whole-genome methylation sequencing identified distinct pathways associated with fibrosis in males and females.

Area of Science:

  • Genomics
  • Epigenetics
  • Hepatology

Background:

  • Metabolic dysfunction-associated steatotic liver disease (MASLD) can progress to severe liver conditions, involving inflammation and fibrosis.
  • DNA methylation (DNAm) is increasingly linked to MASLD, but its association with fibrosis, especially considering sex differences, requires further investigation.
  • Existing studies often focus on specific CpG sites or liver tissue, limiting comprehensive analysis.

Purpose of the Study:

  • To investigate the association between DNA methylation and MASLD-related fibrosis using whole-genome methylation sequencing (WGMS).
  • To explore sex-specific differences in DNA methylation patterns related to MASLD fibrosis.
  • To analyze DNA methylation in both liver tissue and cell-free DNA (cfDNA).

Main Methods:

  • Whole-genome methylation sequencing (WGMS) was performed on liver tissue and cfDNA from MASLD patients.
  • Data were filtered and grouped by sex to identify DNA methylation sites associated with fibrosis.
  • Pathway analysis was conducted on identified CpG bins, and hepatic tissue deconvolution was used to assess immune cell presence.

Main Results:

  • WGMS identified overlapping and distinct DNA methylation pathways associated with MASLD and fibrosis across tissue and cfDNA, varying between sexes and genomic regions.
  • Hepatic tissue deconvolution confirmed the presence of immune cells and an increase in liver-derived cfDNA associated with fibrosis.
  • Sex-specific differences in DNA methylation patterns related to fibrosis were observed.

Conclusions:

  • WGMS is a powerful platform for comprehensively analyzing MASLD alterations and their association with fibrosis.
  • DNA methylation patterns in both liver tissue and cfDNA provide insights into MASLD fibrosis, with notable sex-specific variations.
  • The study highlights the potential of cfDNA methylation as a non-invasive biomarker for MASLD fibrosis.

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