DNA methylation signatures as biomarkers of socioeconomic position

DNA methylation signatures of prenatal socioeconomic position associated with 36-month language outcomes

BACKGROUND

Socioeconomic position (SEP), which reflects one's position in society and access to resources, is strongly tied to neurodevelopment and is associated with epigenetic changes.

AIM

This study examined whether DNA methylation signatures of prenatal SEP, measured in birth samples, are associated with child neurodevelopmental outcomes at 36 months of age.

METHODS

Prenatal SEP DNA methylation scores were derived using 97 placenta and 127 cord blood biospecimens in the Early Autism Risk Longitudinal Investigation cohort. Participants completed the Mullen Scales of Early Learning (MSEL) and Vineland Adaptive Behavior Scales (VABS) at 36 months of age. Generalized regression analyses, adjusting for maternal age and race, were performed to test the association between SEP methylation score, for each birth biospecimen type, and MSEL and VABS scores.

RESULTS

Significant associations were observed between placenta SEP methylation score and MSEL Expressive Language outcomes (beta = -2.7, p = 0.046, 95 % CI [- 5.43, -0.05]) and Receptive Language outcomes (beta = -2.5, p = 0.037, 95 % CI [-4.82, -0.16]). In cord blood, methylation-SEP scores were significantly associated with Receptive Language outcomes (beta = -2.0, p = 0.037, 95 % CI [-3.85, -0.12]). No significant associations were observed with VABS scores.

CONCLUSION

Our results confirm associations between prenatal SEP and early childhood language development using a novel empiric DNA methylation measure of exposure.

Effects of improved on-farm crop storage on DNA methylation of mothers and their infants: evidence from a randomized controlled trial in Kenya

BACKGROUND

Stress during pregnancy can lead to adverse maternal and infant health outcomes through epigenetic changes in the hypothalamic-pituitary-adrenal axis. Among farmers in low-income countries, one important stressor is food insecurity, which can be reduced using hermetic storage bags. This study aimed to determine, for the first time, whether a hermetic storage bag intervention during pregnancy positively affects maternal and infant DNA methylation of the hypothalamic-pituitary-adrenal axis-related genes FKBP5 and NR3C1. We further analyzed whether anthropometrics, stress, and mental health were associated with DNA methylation.

METHODS

This study was part of a larger matched-pair randomized controlled trial focusing on the impact of improved on-farm storage on food security, poverty, and net income of smallholder farming households. A total of N = 149 mothers were recruited by telephone and invited to attend a study appointment at health facilities in Kakamega County, Western Kenya, with their infants in April or May 2021. During the appointment, anthropometric measurements were taken, questionnaires on stress and mental health were administered, and saliva samples were collected. Logistic and multiple linear regression were used to examine the effect of the intervention and related measures on DNA methylation.

RESULTS

Mothers in the intervention group showed higher mean NR3C1 methylation levels than those in the control group, corrected for multiple testing. Maternal postpartum body mass index was positively associated with infant NR3C1 CpG3 DNA methylation. The more stressful life events a mother had experienced in the previous 12 months (including during pregnancy), the lower her FKBP5 CpG3 methylation levels.

CONCLUSIONS

Food insecurity and stressful life events during pregnancy seem to exert significant effects on maternal DNA methylation. While these stressors did not appear to impact infant DNA methylation in the present study, maternal postpartum body mass index was significantly related to infant methylation. These findings suggest that while infants may be protected from excessive maternal glucocorticoids by placental barrier activity, maternal metabolic status is still reflected in their epigenetic make-up. Trial registration This study was part of a larger matched-pair randomized controlled trial on the impact of improved on-farm crop storage on welfare, nutrition, and human health. Registration can be found in the American Economic Association (AEA) RCT Registry, RCT ID: AEARCTR-0005845.

Development and Validation of a Novel Placental DNA Methylation Biomarker of Maternal Smoking during Pregnancy in the ECHO Program

BACKGROUND

Maternal cigarette smoking during pregnancy (MSDP) is associated with numerous adverse health outcomes in infants and children with potential lifelong consequences. Negative effects of MSDP on placental DNA methylation (DNAm), placental structure, and function are well established.

OBJECTIVE

Our aim was to develop biomarkers of MSDP using DNAm measured in placentas (N = 96 ), collected as part of the Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function double-blind, placebo-controlled randomized clinical trial conducted between 2012 and 2016. We also aimed to develop a digital polymerase chain reaction (PCR) assay for the top ranking cytosine-guanine dinucleotide (CpG) so that large numbers of samples can be screened for exposure at low cost.

METHODS

We compared the ability of four machine learning methods [logistic least absolute shrinkage and selection operator (LASSO) regression, logistic elastic net regression, random forest, and gradient boosting machine] to classify MSDP based on placental DNAm signatures. We developed separate models using the complete EPIC array dataset and on the subset of probes also found on the 450K array so that models exist for both platforms. For comparison, we developed a model using CpGs previously associated with MSDP in placenta. For each final model, we used model coefficients and normalized beta values to calculate placental smoking index (PSI) scores for each sample. Final models were validated in two external datasets: the Extremely Low Gestational Age Newborn observational study, N = 426 ; and the Rhode Island Children's Health Study, N = 237 .

RESULTS

Logistic LASSO regression demonstrated the highest performance in cross-validation testing with the lowest number of input CpGs. Accuracy was greatest in external datasets when using models developed for the same platform. PSI scores in smokers only (n = 72 ) were moderately correlated with maternal plasma cotinine levels. One CpG (cg27402634), with the largest coefficient in two models, was measured accurately by digital PCR compared with measurement by EPIC array (R 2 = 0.98 ).

DISCUSSION

To our knowledge, we have developed the first placental DNAm-based biomarkers of MSDP with broad utility to studies of prenatal disease origins. https://doi.org/10.1289/EHP13838.

Maternal outcomes related to Genetic and epigenetic Variation in the oxytocin system: A scoping review

Purpose

In this scoping review, we synthesize the literature on oxytocin and oxytocin receptor genetic and epigenetic variation in relationship to breastfeeding, maternal caregiving behavior, and maternal mental health.

Methods

A literature search was conducted in early 2022, and updated in 2023, utilizing the PRISMA scoping review reporting method, using the following MeSH headings and key terms: oxytocin, oxytocin receptor, genetics, epigenetics, methylation, pregnancy, postnatal, breastfeeding, lactation, mother-infant relations and perinatal outcomes. The search was conducted using PubMed, EMBASE, CINAHL, Google Scholar, SCOPUS, and the Cochrane Library. Inclusion criteria included: human literature which was peer reviewed and found in primary sources, printed in the English language. In addition, the study must have reported genetic/epigenetic data in either the oxytocin or oxytocin receptor gene (maternal or infant up to 12 months after birth) in relation to a breastfeeding, maternal caregiving behavior or a maternal mental health outcome. There was no date limitation. Four authors reviewed studies for eligibility. Data was extracted using a structured data extraction form.

Results

A total of 23 studies met inclusion criteria for this review (breastfeeding n = 4, maternal caregiving behavior n = 7, and maternal mental health n = 16). Seventeen papers reported on oxytocin or oxytocin receptor genotype and nine reported epigenetic associations (namely DNA methylation). These totals are greater than 23, as studies reported on multiple outcomes. One paper assessed the interaction between genotype and methylation. While a number of genotype variations were reported, the single nucleotide polymorphism rs53576 on the oxytocin receptor gene was the most studied. Overall, variation in this polymorphism was related to postnatal depression symptoms. Among numerous epigenetic markers, site -934 was the most studied methylation site, and methylation status was associated with maternal depression and maternal caregiving behavior outcomes. Results suggest that early life experiences impact adult maternal caregiving behaviors and mental health outcomes, and vary based on genetic vulnerability. Breastfeeding outcomes were minimally studied.

Conclusion

This scoping review found that genetic and epigenetic variation at the oxytocin and oxytocin receptor genes were associated with maternal caregiving behavior and mental health, likely through complex gene and environment interactions. The findings suggest that maternal early life experiences and stress impact later caregiving behaviors and mental health in the postnatal period. The findings highlight potential pathways by which environment, experiences, and genes interact to impact maternal caregiving behavior and maternal mental health.

A Multi-Omics Overview of Colorectal Cancer to Address Mechanisms of Disease, Metastasis, Patient Disparities and Outcomes

Human colorectal cancer (CRC) is one of the most common malignancies in men and women across the globe, albeit CRC incidence and mortality shows a substantial racial and ethnic disparity, with the highest burden in African American patients. Even with effective screening tools such as colonoscopy and diagnostic detection assays, CRC remains a substantial health burden. In addition, primary tumors located in the proximal (right) or distal (left) sides of the colorectum have been shown to be unique tumor types that require unique treatment schema. Distal metastases in the liver and other organ systems are the major causes of mortality in CRC patients. Characterizing genomic, epigenomic, transcriptomic and proteomic (multi-omics) alterations has led to a better understanding of primary tumor biology, resulting in targeted therapeutic advancements. In this regard, molecular-based CRC subgroups have been developed that show correlations with patient outcomes. Molecular characterization of CRC metastases has highlighted similarities and differences between metastases and primary tumors; however, our understanding as to how to improve patient outcomes based on metastasis biology is lagging and remains a major obstacle to improving CRC patient outcomes. In this review, we will summarize the multi-omics features of primary CRC tumors and their metastases across racial and ethnic groups, the differences in proximal and distal tumor biology, molecular-based CRC subgroups, treatment strategies and challenges for improving patient outcomes.