Genomics of Early Growth and Cardio-Metabolic Health

Genome-wide association studies (GWAS) have identified maternal and fetal genetic variants associated with birth weight in European ancestry populations. However, the genetic architecture of longitudinal fetal growth may not overlap with that of birth weight. Birth weight does not represent the trajectory of fetal growth throughout pregnancy. Two fetuses with different sizes at a given gestational age may arrive at the same size at birth although undergoing different growth rates. Fetal growth rate has clinical values such as improved prediction of small for gestational age, placental insufficiency, and fetal death that cannot be obtained from a one-time fetal size measure. We previously found that the contribution of genetics to fetal growth relative to environmental factors varies throughout pregnancy, with a peak observed at end of second trimester and early third trimester. The trajectory of fetal growth varies with the genome-wide average levels of maternal genetic ancestry. Genetic regions with higher levels of African and Amerindigenous ancestry have been associated with fetal growth measures, pointing to molecular pathways involved in fetal growth regulation and ancestry-related differences. We are investigating genome-wide maternal loci to identify genetic variants associated with longitudinal trajectory of fetal weight throughout pregnancy by combining datasets of pregnancy cohorts (NICHD Fetal Growth Studies and nuMoM2b) across groups of pregnant women with African, East Asian, European, and Hispanic ancestry. Fetal weight was calculated from fetal biometry measured by ultrasound at 2 to 5 gestational time points, and birth weight was measured at delivery. Using a meta-regression approach that accommodates ancestry-related allelic-effect heterogeneity, we identified novel genetic variants associated with change in fetal weight trajectory. For most of the identified loci, allelic-effect heterogeneity was significantly correlated with ancestry. Functional annotations and integration with regulatory genomics and phenotypic databases are under way.

Polygenic effects on fetal growth of maternal genetic variants associated with cardio-metabolic diseases can differ based on genetic ancestry. We investigated whether genetic ancestry contributes to the influence of maternal type 2 diabetes genetic risk score on fetal growth, and whether maternal obesity interacts with genetic ancestry in influencing birth weight, placental weight, and risk of large-for-gestational-age at birth. Genetic ancestry was quantified using two alternative approaches: (1) genetic ancestry distance, which quantifies the similarity of an individual’s genome to a given population genome reference; and (2) genetic ancestry proportion, which quantifies the genome-wide average for an ancestry group. We found that the association of maternal type 2 diabetes genetic risk score with fetal weight varied based on a women’s genetic ancestry distance from African, European, Amerindigenous, and East Asian reference genomes. Incorporating genetic ancestry distance revealed that diabetes polygenetic risk influenced fetal growth beginning at early second trimester of pregnancy, which is earlier than previous reported. We also observed that genetic ancestry modified the association between maternal obesity and birth outcomes.

Maternal cardio-metabolic status during pregnancy influences the success of pregnancy as well as long-term child and maternal health outcomes. Placental molecular features can be altered by maternal cardio-metabolic dysregulations. Therefore, epigenetic mechanisms in the placenta may be a potential link between maternal cardio-metabolic status, fetal growth, and offsprings' future risk of cardio-metabolic diseases. Accelerated aging of the placenta can reduce its functional capacity and is implicated in adverse pregnancy outcomes, including fetal growth restriction, preeclampsia, and preterm birth. Using the concept of “epigenetic clocks,” placental epigenetic age acceleration can be determined as the difference between the epigenetic and gestational age of the placenta and indicates the biological age of the placenta relative to its chronological gestational age. We previously found that accelerated placental epigenetic aging is associated with fetal growth in a sex-dependent manner. Maternal obesity, gestational weight gain, and dyslipidemia are associated with placental epigenetic age acceleration. These studies highlight that the placental “clock” can be a new avenue to study the molecular etiologies of fetal growth abnormalities, and as a biomarker for tracking prenatal environmental and genetic predisposition. We also previously found that the methylation and transcriptome of the placenta are also associated with maternal cardio-metabolic status, psychosocial factors, plasma levels of chemical exposures, and fetal growth outcomes. Funded by the NICHD Office of the Director’s Strategic Planning Award, we are investigating the link between longitudinally measured maternal plasma markers of glycemia, oxidative stress, and inflammation measured at four gestational time points during pregnancy and placental age acceleration at delivery.

One of the contributors to maternal metabolic health during pregnancy is psychosocial health and social support, an important resilience factor with positive effects on health and well-being as well as on pregnancy and fetal outcomes. The placental epigenome may provide clues to molecular processes relevant to maternal psychosocial health and social support during pregnancy, and how this may influence offspring health outcomes. We conducted studies to investigate: (1) whether maternal depression at each pregnancy trimester is associated with accelerated aging of the placenta; and (2) to identify placental DNA methylation loci associated with social support. We found increased placental age acceleration among women with depressive symptoms during their second trimester and those with sustained depression during first and second trimester compared with women without depressive symptoms. The association between depression and placental age acceleration was stronger in male fetus pregnancies. We also identified placental methylation loci associated with maternal social support, including fetal sex-specific associations. The functions of the genes near the differentially methylated loci overlap with pathways related to immune response relevant to fetal growth, energy metabolism, and neurodevelopment.

Genetic modulation of placental function can vary by context-specific factors such as fetal sex, which have profound implications in placental function and pregnancy outcomes. Investigation of sex differences during early development can unlock the early-life origins of physiologic trait levels and disease risk shaped by sex. Our previous work showed that sex differences exist in the relations between placental epigenetic aging and fetal growth. Placental gene expression linked with increased odds of small-for-gestational age neonates involves pathways that differ between male and female fetuses. Maternal cardio-metabolic and psychosocial influences on the placental epigenome also vary by fetal sex.

Accommodating fetal sex in placental genomic studies is useful to refine complex processes involved in fetal growth, adaptive response to environmental exposures, and for developing tailored interventions. Multi-omic molecular features of the placenta can provide a remarkable opportunity to investigate the biological embedding of sex-biased genetic influences. Our previous study showed that an overwhelmingly significant proportion of fetal genetic variants known to be associated with birth weight also regulate placental gene expression and methylation in their vicinity. The identified target genes are broadly enriched for hormonal, immune response and cardio-metabolic pathways. These other gene-regulatory effects on placenta can vary by fetal sex, and can potentially impact pregnancy outcomes. We are investigating fetal sex–dependent epigenetic and transcriptomic regulation in human placenta in well characterized, ancestrally diverse cohorts, and their link with human neonatal traits and adult diseases. We found extensive sex differences in placental methylation levels and in fetal genetic regulation of placental methylation, whereas relatively limited sex bias was observed for placental gene expression and its genetic regulation. Sex-biased genetic loci in placenta colocalized with known genetic loci associated with birth weight and adult chronic diseases, including breast cancer, asthma, and autoimmune conditions. We also found enrichment of sex-biased loci for human imprinted genes, a parent-of-origin–dependent gene-expression regulation critical for placental and fetal development. Overall, the genomic insights from our study highlight that the placenta is actively involved in setting the developmental foundation of health outcomes shaped by fetal sex, and offer knowledge potentially valuable for early diagnosis of diseases, and for developing biomarkers and novel therapeutics.

Placental epigenome, transcriptome, and its epigenetic age acceleration are under substantial genetic control. The implicated genes and genetic mechanisms that link placental age acceleration and fetal growth are yet to be identified. Moreover, African ancestry populations remain under-represented in perinatal genomics research, including fetal growth. To address these research gaps, we initiated a new study as part of the Study of Pregnancy and Neonatal Health (SPAN) study to establish a prospective pregnancy cohort, over-sampled for African American pregnant women in the gGAP (genomics in growth and placenta) aim. gGAP will integrate multi-omics approaches (genome-wide genotypes, placental methylation, placental gene expression) to identify and functionally characterize genetic mechanisms that underpin placental epigenetic aging, longitudinal fetal growth, and the links between the two in a multi-ancestral cohort oversampled by African Americans. The goals of gGAP in SPAN are to: (1) investigate the fetal genome’s contribution in the genetic architecture of fetal growth for which data are lacking; (2) interrogate the effect on fetal growth of gene-environment interactions in the context of maternal psychosocial, obstetric, and cardio-metabolic factors; (3) refine causal loci by leveraging genomic variation of multi-ancestral populations and build a perinatal multi-omics resource in an under-represented population; and (4) integrate genomics with placental imaging, histopathology, and proteomics for an in-depth mechanistic investigation of fetal growth and other pregnancy outcomes.

SPAN data collection is ongoing at four clinical sites across the United States. At baseline (less than 20 gestational weeks), pregnant women complete a detailed assessment using questionnaire items and physical examination, and provide blood, saliva, and urine samples. During third trimester, fetal biometry ultrasound examination and blood collection are undertaken. At delivery, cord blood and placental biopsy tissue are collected, gross examination and photographic image of the placenta are taken, and neonatal anthropometry, body composition, and neuro-behavioral measures are obtained. Detailed chart abstraction is completed including first- and second-trimester fetal biometry obtained by clinical ultrasound.

A key motivation for our research program is to understand the mechanistic basis of the relationship between early life growth and later life cardio-metabolic health. Genetic factors with overlapping effects on birthweight and cardio-metabolic diseases in later life may partly explain early origins of later-life health, complementing other mechanisms such as in utero programming. Longitudinal cohorts with repeatedly measured anthropometry measures are crucial to understanding shared as well as age-specific genetic mechanisms involved in growth and metabolic phenotypes. Also, the genetic factors that influence early childhood growth- and obesity-related phenotypes are not well understood, particularly in African Americans with a disproportionately high burden of childhood obesity and its health consequences.

To address these research gaps, we initiated a new genetic study embedded in the collaborative perinatal project (CPP). The CPP is a prospective pregnancy cohort that enrolled more than 48,000 pregnant women (46% White, 46% African American, 7% Puerto Rican, 1% others) at 12 medical centers in the United States in 1959–1965. Women were followed during pregnancy. Children were monitored at seven consecutive times that cover important developmental milestones from birth through early school ages (birth, 4, 8, and 12 months and 3, 4, and 7 years). Through a pilot study, we optimized approaches to achieve high quality and reproducible genotyping of DNA from CPP stored biospecimens. Currently, genotyping is ongoing at a large scale with the following aims, to : (1) establish a genomic database for children in the CPP cohort (n= 10,800; 5,400 African American and 5,400 European American); (2) identify genetic influences on early growth anthropometry and obesity-related phenotypes at seven longitudinal time points from birth through school age, using multi-ancestral and admixture mapping approaches; and (3) identify molecular pathways in the link between fetal and early childhood growth and developmental phenotypes.

The study will facilitate insights into early origins of adult diseases and interventions by determining genetic effects that are transient and those that are sustained across ages. The CPP cohort enrolled participants prior to lifestyle changes that led to the obesity epidemic. This lack of major obesogenic environment is advantageous to identify genes whose effect on obesity is largely genetic. The potential interaction between genetic factors discovered via the CPP and recent environmental modifiers will be evaluated in other recent cohorts.