Pregnancy Leaves Lasting Epigenetic Footprints in Women’s Blood, Study Finds

For decades, epidemiologists have noticed a strange pattern in women’s health: having children seems to protect against some diseases while raising the risk of others. Childbearing lowers a woman’s chances of developing hormone receptor positive breast, ovarian, and endometrial cancers, yet even uncomplicated pregnancies are associated with elevated risks of Alzheimer’s disease, stroke, and myocardial infarction compared with women who have never given birth. What has remained stubbornly unclear is the biological mechanism behind these divergent outcomes. A new study published in Epigenetics Communications offers a tantalizing clue, suggesting that pregnancy and childbirth leave measurable, long-lasting marks on DNA methylation in a woman’s blood, changes that persist for months or even years after delivery and that touch genes linked to cancers, neurodegenerative disease, and more.

DNA methylation is one of the body’s most important epigenetic regulatory systems. It involves the addition or removal of methyl groups at cytosine-phosphate-guanine (CpG) sites along the DNA strand, frequently in promoter regions, and these chemical tags act like volume knobs for gene expression, dialing genes up or down without altering the underlying genetic code. Methylation patterns shift dramatically during periods of physiological upheaval, and pregnancy is no exception. Previous research has documented methylation changes in maternal blood across gestation, including gains of methylation in genes involved in morphogenesis and losses in genes promoting maternal-infant bonding. Other studies have tied methylation shifts to complications such as gestational diabetes and preeclampsia. But a critical question lingered: do these pregnancy-induced changes simply wash away after delivery, or do they endure as a kind of molecular memory?

The research team, led by Su Chen and Miranda Johs of the University of Nebraska Medical Center alongside collaborators at the University of Memphis, University of Southampton, University of Michigan, Michigan State University, and the David Hide Asthma and Allergy Research Centre, was designed to answer exactly that question, and to fix two persistent gaps in the literature. First, most prior studies of parous women, those who have given birth, lacked nulliparous controls, women who have never given birth, making it impossible to isolate the effect of childbearing itself. Second, only a single small pilot study had ever examined whether methylation changes persist beyond the immediate postpartum period. The new work addressed both problems by comparing methylation profiles of parous and nulliparous women at two timepoints in young adulthood, ages 18 and 26, which correspond to pre-pregnancy and at least six months postpartum for the mothers in the sample.

The discovery cohort came from the Isle of Wight (IOW) birth cohort, a three-generation study established in the United Kingdom between 1989 and 1990 to prospectively follow the natural history of asthma and allergy. Of 750 female participants, 144 had DNA methylation measured at both ages 18 and 26, and 89 of those women had childbearing history validated through medical records. Twenty-eight had given birth at least six months before the age-26 measurement, while 61 had not. The researchers screened 389,355 CpG sites, the overlap between the Illumina HumanMethylation450 and MethylationEPIC platforms, using a training-testing screening method called ttScreening, which repeatedly splits samples into training and test sets to filter out uninformative sites. Linear regression analyses followed, adjusting for six blood cell type proportions, residual methylation at age 18, body mass index change, smoking categories, and socioeconomic status.

The result was striking: 184 CpG sites were significantly differentially methylated between parous and nulliparous women after correction for multiple testing. To guard against a cohort-specific fluke, the team pursued replication in an entirely independent population, the ELEMENT cohort from Mexico City, a multi-generation birth cohort of Hispanic women followed for nearly three decades. In the ELEMENT subsample of 54 women, 105 of the 184 CpGs showed regression coefficients pointing in the same direction as the Isle of Wight findings, and 13 of those were statistically significant. Seven of the replicated sites showed lower methylation in parous women and six showed higher methylation, a pattern consistent across both cohorts despite their differences in ethnicity, geography, and age structure. The 13 replicated CpGs mapped to 16 unique genes.

Among those genes, one stands out with particular force: TM2D3, a gene previously implicated in late-onset Alzheimer’s disease through exome-wide association analysis. In the Isle of Wight data, methylation at cg01537571, a site within a CpG island near the transcription start site of TM2D3, was significantly lower in parous women in both cohorts, and methylation at this site correlated positively with gene expression. When the team examined RNA sequencing data from blood samples at age 26, TM2D3 was the only gene among the 16 that showed significantly lower expression in parous compared with nulliparous women. This convergence is provocative given that increased parity has independently been identified as a risk factor for Alzheimer’s disease, hinting that the methylation change at TM2D3 could be one thread connecting reproductive history to neurodegenerative vulnerability.

Another gene of interest is SEMA3A, which encodes semaphorin 3A, a guidance cue signaling molecule that directs developing neurons during embryogenesis and continues to regulate neuroplasticity in adulthood. SEMA3A showed decreased methylation in parous women and appeared in the study’s gene-disease network linked to neoplasms, mental disorders, and reproductive conditions. The gene plays paradoxical roles in cancer: it promotes tumor progression in hepatocellular carcinoma by enhancing proliferation, migration, and invasion, yet acts as a tumor suppressor in head, neck, and breast cancers, where it boosts antitumoral M1 macrophage proliferation and recruits CD8-positive T cells and natural killer cells to repress tumor growth. The authors speculate that lower methylation near the SEMA3A transcription start site in parous women could conceivably relate to their reduced breast cancer risk, though they caution that whether blood methylation mirrors changes in breast tissue remains unknown.

Beyond these two headline genes, the disease association analysis using the DisGeNET database painted a broader picture. Ten of the 16 genes, including SEMA3A, AKAP13, SLC15A2, DOK2, ADAMTS17, ADARB2, NUP37, PLD5, TPK1, and SLC15A3, were most notably linked with neoplasms, mental disorders, and nervous system diseases such as Parkinson’s disease, schizophrenia, and autism, along with substance use disorders. The breadth surprised even the researchers, who had anticipated connections to reproductive cancers but had not expected substance abuse disorders to surface. Gene expression data confirmed that methylation at cg19086905 (ADAMTS17) and cg13375690 (PDE7A) was negatively associated with expression of those genes, providing functional support for at least some of the methylation signals. Notably, several of the identified genes are expressed in the brain, including TM2D3, SLC15A2, PLD5, ADARB2, and PARPBP, while MAP1LC3C, NUP37, and ADAMTS17 are expressed in breast tissue, tissue-specific patterns that may matter enormously for translating blood-based findings into disease mechanisms.

The study’s design carries genuine strengths. Comparing parous women at pre- and post-pregnancy timepoints against matched nulliparous controls in both discovery and replication cohorts is rare, and the six-month minimum postpartum window avoided the transient methylation fluctuations that may have confounded earlier work sampling just two to four days after delivery. Replication across a 98 percent White UK cohort and an all-Hispanic Mexican cohort supports both internal validity and generalizability. Yet the authors are candid about limitations: the parous groups were small, with 28 women in the Isle of Wight and roughly 20 in the ELEMENT analysis; nulliparous status relied on medical records; the duration required for postpartum methylation to stabilize is unknown; and blood serves only as a proxy for changes in other tissues, with roughly half of the identified genes not routinely expressed in whole blood. Factors that change during pregnancy, such as smoking or income, could not be assessed in nulliparous women at comparable times.

Even with those caveats, the implications are considerable. If the methylation changes observed in blood leukocyte DNA reflect parallel epigenetic remodeling in tissues such as the breast or brain, they could furnish a plausible mechanism for how childbearing reshapes a woman’s disease risk across her lifetime, offering a molecular bridge between reproductive history and outcomes ranging from cancer to Alzheimer’s disease. The researchers emphasize that further studies are needed, particularly cohorts with follow-up into later life, to determine whether these parous-related methylation signatures actually predict health outcomes rather than merely accompanying them. For now, the study adds a compelling piece to a growing body of evidence, from brain imaging traces of childbirth to parity-linked dementia risk, that motherhood writes itself into the body in ways science is only beginning to read, one methyl group at a time.

Subject of Research: Persistent effects of childbearing on blood DNA methylation in women

Article Title: Assessing the effect of childbearing on blood DNA methylation through comparison of parous and nulliparous females

Article References: Chen, S., Johs, M., Karmaus, W., Holloway, J. W., Kheirkhah Rahimabad, P., Goodrich, J. M., Peterson, K. E., Dolinoy, D. C., Arshad, S. H., & Ewart, S. (2024). Assessing the effect of childbearing on blood DNA methylation through comparison of parous and nulliparous females. Epigenetics Communications, 4(1), Article 2. https://doi.org/10.1186/s43682-024-00025-9

Image Credits: AI Generated

DOI: 10.1186/s43682-024-00025-9

Keywords: DNA methylation, pregnancy, childbearing, epigenetics, parous, nulliparous, CpG sites, TM2D3, SEMA3A, Alzheimer's disease, breast cancer, Isle of Wight cohort