Researchers found widespread DNA-methylation differences associated with preterm birth in maternal peripheral blood and neonatal cord blood, with far more reported regions in cord blood than in peripheral blood. It was a case-control comparison, so the findings show an association rather than a cause.
Across the two blood compartments, the researchers identified 1,151 differentially methylated regions and 25,336 individual differentially methylated loci. The totals included 290 regions and 4,976 loci in peripheral blood, compared with 861 regions and 20,360 loci in cord blood. The regional analysis required at least three CpG sites per region.
A paired look at mothers and newborns
The analysis compared matched maternal peripheral blood and neonatal cord blood from 15 preterm and 7 full-term deliveries involving mother-infant pairs. It was a hospital-based case-control investigation at the Women’s Wellness and Research Center in Qatar, conducted from September 2022 to December 2024.
The team used long-read nanopore sequencing to detect methylation at CpG sites. Forty-four samples were sequenced on individual R10.4 flowcells. The statistical analysis adjusted for sample type, gestational age, maternal age and infant sex when testing individual methylation sites.
For regional signals, the analysis used a p-value threshold below 0.01, a false-discovery-rate cutoff of 0.01 and at least three CpG sites per region. Individual sites were retained when the false-discovery rate was below 0.01 and the methylation difference exceeded 0.1 between the groups.
Most of the strongest signals were increases
In maternal peripheral blood, 124 exonic regions were highlighted. They included 109 hypermethylated genes and 15 hypomethylated genes. MED28, PSMB11 and WNT7B were among the leading hypermethylated genes, while EXTL3 and MMP9 were among the leading hypomethylated genes.
Cord blood showed 409 exonic regions, including 365 hypermethylated and 44 hypomethylated genes. LOC401478, ISG20, LMTK3, TCAF2 and COL4A2 were among the leading hypermethylated genes. The study reported no hypomethylated exonic regions meeting the same highlighted significance threshold.
Among the most statistically striking individual sites, 19 were found in maternal peripheral blood and 15 in cord blood using the study’s genome-wide threshold. Sixteen of the maternal signals were hypermethylated and three hypomethylated; in cord blood, 13 were hypermethylated and two were hypomethylated.
Different tissues, overlapping biology
Separate enrichment analyses linked maternal-blood genes with neurodevelopment, cell-junction organization, ion transport, Wnt and calcium signaling, cAMP signaling, and neuroactive ligand-receptor pathways. Cord-blood genes were linked with axonogenesis, synapse assembly, vascular development, MAPK and Rap1 signaling, oxytocin signaling, calcium signaling, and neuroactive ligand-receptor pathways.
The comparison found 120 shared loci, alongside 20,240 cord-specific loci and 4,770 peripheral-specific loci. Of the shared loci, 91 were consistently hypermethylated across both tissues, 28 were consistently hypomethylated and one showed opposite directions.
DPPA3 and ABCA1 were examples of shared hypermethylated signals, while GKN1 was a shared hypomethylated signal. The researchers also identified 14 regions altered in both tissues, and these shared regions were enriched in developmental and morphogenetic processes, including skeletal system morphogenesis, dorsal and ventral pattern formation, and cellular responses to fibroblast growth factor.
What the findings leave open
Because this was a case-control comparison, the methylation patterns are associations rather than evidence of a causal mechanism. The study also did not show whether the highlighted genes changed their activity. RNA sequencing was not performed, so direct correlations between methylation and gene expression were not assessed.
The comparison involved only 15 preterm and 7 full-term deliveries, and the shared signals were not independently validated. The reported findings therefore remain unvalidated associations. Direct testing of gene expression and independent replication would be needed to determine whether the patterns are consistent and biologically meaningful.
The human study received institutional review-board approval, and participants provided written informed consent. The authors report no financial support for the research or publication and no commercial or financial relationships that could constitute a potential conflict of interest. The study states that its datasets are available in a GitHub repository.
Paper data and sources
Original title: Epigenetic profiling of preterm birth: a dual-tissue methylation patterns using long-read sequencing
Authors: Linga B, Ibrahim F, Razzaq A et al.
Journal/Repository: Frontiers in epigenetics and epigenomics
Status: Peer-reviewed
First online: 2026-10-07
DOI: Not available
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