# DNA methylation associated with the serum alanine aminotransferase concentration: evidence from Chinese monozygotic twins

## TL;DR

This study finds that DNA methylation at specific sites is linked to blood ALT levels in Chinese twins, suggesting epigenetic factors influence liver function.

## Contribution

The study identifies novel CpG sites and genes, such as FLT4 and RELB, associated with ALT levels through epigenetic mechanisms in a Chinese population.

## Key findings

- 85 CpGs were found to be genome-wide significant, located in 16 genes including FLT4 and RELB.
- Causal inference showed that 61 CpGs in 14 genes influence ALT levels.
- Validation in a community sample confirmed hypomethylation and hypermethylation in CpGs linked to abnormal ALT.

## Abstract

To identify nongenetic factors influences on DNA methylation (DNAm) variations associated with blood Alanine Aminotransferase (ALT) concentration, this study conducted an epigenome-wide association study (EWAS) on Chinese monozygotic twins.

A total of 61 pairs of Chinese monozygotic twins involved in this study. Whole blood samples were analyzed for DNAm profiling using the Reduced Representation Bisulfite Sequencing (RRBS) technique. We examined the relationship between DNAm levels at each CpG site and serum ALT using a linear mixed-effects model. Enrichment analysis and causal inference analysis was conducted, and differentially methylated regions (DMRs) were further identified. Candidate CpGs were validated in a community sample. Genome-wide significance were calculated by Bonferroni correction (p < 2.14 × 10–7).

We identified 85 CpGs reaching genome-wide significance (p < 2.14 × 10–7), located in 16 genes including FLT4, ADARB2, MRPS31P2, and RELB. Causal inference suggested that DNAm at 61 out of 85 significant CpGs within 14 genes influenced ALT level. 52 DMRs and 1765 pathways such as low voltage-gated calcium channel activity and focal adhesion were identified having influences on ALT levels. Further validation using community population found four CpGs mapped to FLT4 and three to RELB showing hypomethylation and hypermethylation in cases with abnormal ALT (ALT > 40 U/L), respectively.

This study identified several differentially methylated CpG sites associated with serum ALT in the Chinese population, particularly within FLT4 and RELB. These findings provide new insights into the epigenetic modifications underlying liver function.

The online version contains supplementary material available at 10.1186/s13148-025-01869-1.