Methylation of the Glucocorticoid Receptor (NR3C1) in Placenta Is Associated with Infant Cry Acoustics

The Emerging Role of Epigenetics in Metabolism and Endocrinology

Each cell in a multicellular organism has its own phenotype despite sharing the same genome. Epigenetics is a somatic, heritable pattern of gene expression or cellular phenotype mediated by structural changes in chromatin that occur without altering the DNA sequence. Epigenetic modification is an important factor in determining the level and timing of gene expression in response to endogenous and exogenous stimuli. There is also growing evidence concerning the interaction between epigenetics and metabolism. Accordingly, several enzymes that consume vital metabolites as substrates or cofactors are used during the catalysis of epigenetic modification. Therefore, altered metabolism might lead to diseases and pathogenesis, including endocrine disorders and cancer. In addition, it has been demonstrated that epigenetic modification influences the endocrine system and immune response-related pathways. In this regard, epigenetic modification may impact the levels of hormones that are important in regulating growth, development, reproduction, energy balance, and metabolism. Altering the function of the endocrine system has negative health consequences. Furthermore, endocrine disruptors (EDC) have a significant impact on the endocrine system, causing the abnormal functioning of hormones and their receptors, resulting in various diseases and disorders. Overall, this review focuses on the impact of epigenetics on the endocrine system and its interaction with metabolism.

Newborn Cry Acoustics in the Assessment of Neonatal Opioid Withdrawal Syndrome Using Machine Learning

IMPORTANCE

The assessment of opioid withdrawal in the neonate, or neonatal opioid withdrawal syndrome (NOWS), is problematic because current assessment methods are based on subjective observer ratings. Crying is a distinctive component of NOWS assessment tools and can be measured objectively using acoustic analysis.

OBJECTIVE

To evaluate the feasibility of using newborn cry acoustics (acoustics referring to the physical properties of sound) as an objective biobehavioral marker of NOWS.

DESIGN, SETTING, AND PARTICIPANTS

This prospective controlled cohort study assessed whether acoustic analysis of neonate cries could predict which infants would receive pharmacological treatment for NOWS. A total of 177 full-term neonates exposed and not exposed to opioids were recruited from Women & Infants Hospital of Rhode Island between August 8, 2016, and March 18, 2020. Cry recordings were processed for 118 neonates, and 65 neonates were included in the final analyses. Neonates exposed to opioids were monitored for signs of NOWS using the Finnegan Neonatal Abstinence Scoring Tool administered every 3 hours as part of a 5-day observation period during which audio was recorded continuously to capture crying. Crying of healthy neonates was recorded before hospital discharge during routine handling (eg, diaper changes).

EXPOSURES

The primary exposure was prenatal opioid exposure as determined by maternal receipt of medication-assisted treatment with methadone or buprenorphine.

MAIN OUTCOMES AND MEASURES

Neonates were stratified by prenatal opioid exposure and receipt of pharmacological treatment for NOWS before discharge from the hospital. In total, 775 hours of audio were collected and trimmed into 2.5 hours of usable cries, then acoustically analyzed (using 2 separate acoustic analyzers). Cross-validated supervised machine learning methods (combining the Boruta algorithm and a random forest classifier) were used to identify relevant acoustic parameters and predict pharmacological treatment for NOWS.

RESULTS

Final analyses included 65 neonates (mean [SD] gestational age at birth, 36.6 [1.1] weeks; 36 [55.4%] female; 50 [76.9%] White) with usable cry recordings. Of those, 19 neonates received pharmacological treatment for NOWS, 7 neonates were exposed to opioids but did not receive pharmacological treatment for NOWS, and 39 healthy neonates were not exposed to opioids. The mean of the predictions of random forest classifiers predicted receipt of pharmacological treatment for NOWS with high diagnostic accuracy (area under the curve, 0.90 [95% CI, 0.83-0.98]; accuracy, 0.85 [95% CI, 0.74-0.92]; sensitivity, 0.89 [95% CI, 0.67-0.99]; specificity, 0.83 [95% CI, 0.69-0.92]).

CONCLUSIONS AND RELEVANCE

In this study, newborn acoustic cry analysis had potential as an objective measure of opioid withdrawal. These findings suggest that acoustic cry analysis using machine learning could improve the assessment, diagnosis, and management of NOWS and facilitate standardized care for these infants.

Differential Placental DNA Methylation of NR3C1 in Extremely Preterm Infants With Poorer Neurological Functioning

BACKGROUND

Understanding underlying mechanisms of neurodevelopmental impairment following preterm birth may enhance opportunities for targeted interventions. We aimed to assess whether placental DNA methylation of selected genes affected early neurological functioning in preterm infants.

METHODS

We included 43 infants, with gestational age <30 weeks and/or birth weight <1,000 g and placental samples at birth. We selected genes based on their associations with several prenatal conditions that may be related to poor neurodevelopmental outcomes. We determined DNA methylation using pyrosequencing, and neurological functioning at 3 months post-term using Prechtl's General Movement Assessment, including the Motor Optimality Score-Revised (MOS-R).

RESULTS

Twenty-four infants had atypical MOS-R, 19 infants had near-optimal MOS-R. We identified differences in average methylation of NR3C1 (encoding for the glucocorticoid receptor) [3.3% (95%-CI: 2.4%-3.9%) for near-optimal vs. 2.3% (95%-CI: 1.7%-3.0%), p = 0.008 for atypical], and at three of the five individual CpG-sites. For EPO, SLC6A3, TLR4, VEGFA, LEP and HSD11B2 we found no differences between the groups.

CONCLUSION

Hypomethylation of NR3C1 in placental tissue is associated with poorer neurological functioning at 3 months post-term in extremely preterm infants. Alleviating stress during pregnancy and its impact on preterm infants and their neurodevelopmental outcomes should be further investigated.

The clinical significance of the glucocorticoid receptors: Genetics and epigenetics

The impacts of glucocorticoids (GCs) are mainly mediated by a nuclear receptor (GR) existing in almost every tissue. The GR regulates a wide range of physiological functions, including inflammation, cell metabolism, and differentiation playing a major role in cellular responses to GCs and stress. Therefore, the dysregulation or disruption of GR can cause deficiencies in the adaptation to stress and the preservation of homeostasis. The number of GR polymorphisms associated with different diseases has been mounting per year. Tackling these clinical complications obliges a comprehensive understanding of the molecular network action of GCs at the level of the GR structure and its signaling pathways. Beyond genetic variation in the GR gene, epigenetic changes can enhance our understanding of causal factors involved in the development of diseases and identifying biomarkers. In this review, we highlight the relationships of GC receptor gene polymorphisms and epigenetics with different diseases.

Biobehavioral organization shapes the immune epigenome in infant rhesus Macaques (Macaca mulatta)

How individuals respond to and cope with stress is linked with their health and well-being. It is presumed that early stress responsiveness helps shape the health of the developing organism, but the relationship between stress responsiveness and early immune function during development is not well-known. We hypothesized that stress responsiveness may shape epigenetic regulation of immune genes in infancy. We investigated whether aspects of behavioral responsiveness and hypothalamic-pituitary adrenal stress-response were associated with epigenome-wide immune cell DNA methylation patterns in 154 infant rhesus monkeys (3-4 months old). Infants' behavioral and physiological responses were collected during a standardized biobehavioral assessment, which included temporary relocation and separation from their mother and social group. Genome-wide DNA methylation was quantified using restricted representation bisulfite sequencing (RRBS) from blood DNA collected 2-hours post-separation. Epigenome-wide analyses were conducted using simple regression, multiple regression controlling for immune cell counts, and permutation regression, all corrected for false discovery rate. Across the variables analyzed, there were 20,368 unique sites (in 9,040 genes) at which methylation was significantly associated with at least one behavioral responsiveness or cortisol measure across the three analyses. There were significant associations in 442 genes in the Immune System Process ontology category, and 94 genes in the Inflammation mediated by chemokine and cytokine signaling gene pathway. Out of 35 candidate genes that were selected for further investigation, there were 13 genes with at least one site at which methylation was significantly associated with behavioral responsiveness or cortisol, including two intron sites in the glucocorticoid receptor gene, at which methylation was negatively correlated with emotional behavior the day following the social separation (Day 2 Emotionality; β = -0.39, q < 0.001) and cortisol response following a relocation stressor (Sample 1; β = -0.33, q < 0.001). We conclude that biobehavioral stress responsiveness may correlate with the developing epigenome, and that DNA methylation of immune cells may be a mechanism by which patterns of stress response affect health and immune functioning.

Epigenome-wide analysis identifies genes and pathways linked to acoustic cry variation in preterm infants

BACKGROUND

Preterm birth places infants at higher risk of adverse long-term behavioral and cognitive outcomes. Combining biobehavioral measures and molecular biomarkers may improve tools to predict the risk of long-term developmental delays.

METHODS

The Neonatal Neurobehavior and Outcomes in Very Preterm Infants study was conducted at nine neonatal intensive care units between April 2014 and June 2016. Cries were recorded and buccal swabs collected during the neurobehavioral exam. Cry episodes were extracted and analyzed using a computer system and the data were summarized using factor analysis. Genomic DNA was extracted from buccal swabs, quantified using the Qubit Fluorometer, and aliquoted into standardized concentrations. DNA methylation was measured with the Illumina MethylationEPIC BeadArray, and an epigenome-wide association study was performed using cry factors (n = 335).

RESULTS

Eighteen CpGs were associated with the cry factors at genome-wide significance (α = 7.08E - 09). Two CpG sites, one intergenic and one linked to gene TCF3 (important for B and T lymphocyte development), were associated with acoustic measures of cry energy. Increased methylation of TCF3 was associated with a lower energy-related cry factor. We also found that pitch (F₀) and hyperpitch (F₀ > 1 kHz) were associated with DNA methylation variability at 16 CpG sites.

CONCLUSIONS

Acoustic cry characteristics are related to variation in DNA methylation in preterm infants.

IMPACT

Preterm birth is a major public health problem and its long-term impact on health is not well understood. Cry acoustics, related to prematurity, has been linked to a variety of medical conditions. Biobehavioral measures and molecular biomarkers can improve prediction tools for long-term developmental risks of preterm birth. Variation in epigenetic modulation in preterm infants provides a potential link between preterm birth and unfavorable developmental outcomes.

Combined neurodevelopmental exposure to deltamethrin and corticosterone is associated with Nr3c1 hypermethylation in the midbrain of male mice

Attention-Deficit Hyperactivity Disorder (ADHD) is one of the most common neurodevelopmental disorders and manifests inattention, hyperactivity, and impulsivity symptoms in childhood that can last throughout life. Genetic and environmental studies implicate the dopamine system in ADHD pathogenesis. Work from our group and that of others indicates that deltamethrin insecticide and stress exposure during neurodevelopment leads to alterations in dopamine function, and we hypothesized that exposure to both of these factors together would lead to synergistic effects on DNA methylation of key genes within the midbrain, a highly dopaminergic region, that could contribute to these findings. Through targeted next-generation sequencing of a panel of cortisol and dopamine pathway genes, we observed hypermethylation of the glucocorticoid receptor gene, Nr3c1, in the midbrain of C57/BL6N males in response to dual deltamethrin and corticosterone exposures during development. This is the first description of DNA methylation studies of Nr3c1 and key dopaminergic genes within the midbrain in response to a pyrethroid insecticide, corticosterone, and these two exposures together. Our results provide possible connections between environmental exposures that impact the dopamine system and the hypothalamic-pituitary-adrenal axis via changes in DNA methylation and provides new information about the presence of epigenetic effects in adulthood after exposure during neurodevelopment.

The placenta-brain-axis

All mammalian species depend on the placenta, a transient organ, for exchange of gases, nutrients, and waste between the mother and conceptus. Besides serving as a conduit for such exchanges, the placenta produces hormones and other factors that influence maternal physiology and fetal development. To meet all of these adaptations, the placenta has evolved to become the most structurally diverse organ within all mammalian taxa. However, commonalities exist as to how placental responses promote survival against in utero threats and can alter the trajectory of fetal development, in particular the brain. Increasing evidence suggests that reactions of the  placenta to various in utero stressors may lead to long-standing health outcomes, otherwise considered developmental origin of health and disease effects. Besides transferring nutrients and gases, the placenta produces neurotransmitters, including serotonin, dopamine, norepinephrine/epinephrine, that may circulate and influence brain development. Neurobehavioral disorders, such as autism spectrum disorders, likely trace their origins back to placental disturbances. This intimate relationship between the placenta and brain has led to coinage of the term, the placenta-brain-axis. This axis will be the focus herein, including how conceptus sex might influence it, and technologies employed to parse out the effects of placental-specific transcript expression changes on later neurobehavioral disorders. Ultimately, the placenta might provide a historical record of in utero threats the fetus confronted and a roadmap to understand how placenta responses to such encounters impacts the placental-brain-axis. Improved early diagnostic and preventative approaches may thereby be designed to mitigate such placental disruptions.

Prenatal stress and models explaining risk for psychopathology revisited: Generic vulnerability and divergent pathways

The present review revisits three hypothesized models that potentially could explain how prenatal maternal stress influences fetal development, birth outcomes, and subsequent developmental psychopathology. These models were mostly based on animal models, and new evidence for these models from human studies is evaluated. Furthermore, divergent trajectories from prenatal exposure to adversities to offspring affected outcomes are reviewed, including the comparison of studies on prenatal maternal stress with research on maternal substance use and maternal malnutrition during pregnancy. Finally, new directions in research on the mechanism underlying prenatal stress effects on human offspring is summarized. While it is concluded that there is abundant evidence for the negative associations between prenatal maternal stress and offspring behavioral, brain, and psychopathological outcomes in humans, there is no consistent evidence for specific mechanisms or specific outcomes in relation to stress exposure in utero. Rather, principles of multifinality and equifinality best describe the consequences for the offspring, suggesting a generic vulnerability and different pathways from prenatal adversities to developmental psychopathology, which complicates the search for underlying mechanisms. New and promising directions for research are provided to get a better understanding of how prenatal stress gets under the skin to affect fetal development.

Epigenetic mechanisms in the placenta related to infant neurodevelopment

As the 'third brain' the placenta links the developing fetal brain and the maternal brain enabling study of epigenetic process in placental genes that affect infant neurodevelopment. We described the characteristics and findings of the 17 studies on epigenetic processes in placental genes and human infant neurobehavior. Studies showed consistent findings in the same cohort of term healthy infants across epigenetic processes (DNA methylation, genome wide, gene and miRNA expression) genomic region (single and multiple genes, imprinted genes and miRNAs) using candidate gene and genome wide approaches and across biobehavioral systems (neurobehavior, cry acoustics and neuroendocrine). Despite limitations, studies support future work on molecular processes in placental genes related to neurodevelopmental trajectories including implications for intervention.