Michelle L. Wright

The EPIIC hypothesis: Intrapartum effects on the neonatal epigenome and consequent health outcomes

There are many published studies about the epigenetic effects of the prenatal and infant periods on health outcomes. However, there is very little knowledge regarding the effects of the intrapartum period (labor and birth) on health and epigenetic remodeling. Although the intrapartum period is relatively short compared to the complete perinatal period, there is emerging evidence that this time frame may be a critical formative phase for the human genome. Given the debates from the National Institutes of Health and World Health Organization regarding routine childbirth procedures, it is essential to establish the state of the science concerning normal intrapartum epigenetic physiology. EPIIC (Epigenetic Impact of Childbirth) is an international, interdisciplinary research collaboration with expertise in the fields of genetics, physiology, developmental biology, epidemiology, medicine, midwifery, and nursing. We hypothesize that events during the intrapartum period - specifically the use of synthetic oxytocin, antibiotics, and cesarean section - affect the epigenetic remodeling processes and subsequent health of the mother and offspring. The rationale for this hypothesis is based on recent evidence and current best practice.

DNA methylation as a biomarker for preeclampsia.

Background: Preeclampsia contributes significantly to pregnancy-associated morbidity and mortality as well as future risk of cardiovascular disease in mother and offspring, and preeclampsia in offspring. The lack of reliable methods for early detection limits the opportunities for prevention, diagnosis, and timely treatment. Purpose: The purpose of this study was to explore distinct DNA methylation patterns associated with preeclampsia in both maternal cells and fetal-derived tissue that represent potential biomarkers to predict future preeclampsia and inheritance in children. Method: A convenience sample of nulliparous women (N = 55) in the first trimester of pregnancy was recruited for this prospective study. Genome-wide DNA methylation was quantified in first-trimester maternal peripheral white blood cells and placental chorionic tissue from normotensive women and those with preeclampsia (n = 6/group). Results: Late-onset preeclampsia developed in 12.7% of women. Significant differences in DNA methylation were identified in 207 individual linked cytosine and guanine (CpG) sites in maternal white blood cells collected in the first trimester (132 sites with gain and 75 sites with loss of methylation), which were common to approximately 75% of the differentially methylated CpG sites identified in chorionic tissue of fetal origin. Conclusion: This study is the first to identify maternal epigenetic targets and common targets in fetal-derived tissue that represent putative biomarkers for early detection and heritable risk of preeclampsia. Findings may pave the way for diagnosis of preeclampsia prior to its clinical presentation and acute damaging effects, and the potential for prevention of the detrimental long-term sequelae.

First trimester vitamin D status and placental epigenomics in preeclampsia among Northern Plains primiparas.

AIMS As maternal vitamin D status has been associated with preeclampsia, the purpose of this study was to determine variations in DNA methylation patterns and associated protein expression in placental genes regulating vitamin D metabolism. MAIN METHODS A convenience sample of 48 pregnant nulliparous women, including 11 later diagnosed with preeclampsia, were recruited in this prospective study. Using a case-control design in two groups of women, we administered a food frequency questionnaire to determine vitamin D dietary intake. Laboratory measures included serum vitamin D levels (25[OH]D), DNA methylation patterns and protein expression in placental genes regulating vitamin D metabolism (1α-hydroxylase, CYP27B1; vitamin D receptor, VDR; retinoid X receptor, RXR) from placental tissue collected at delivery among those diagnosed with preeclampsia and those who remained normotensive throughout pregnancy. KEY FINDINGS There were no significant differences in vitamin D dietary intake or mean serum 25[OH]D levels, although the proportion of women with deficient 25[OH]D levels was higher in the preeclampsia group (46%) than the normotensive group (20%). Placenta samples from women with preeclampsia also had increased DNA methylation of CYP27B1, VDR and RXR genes with lower protein expression levels limited to RXR. SIGNIFICANCE Hypermethylation of key placental genes involved in vitamin D metabolism suggests uncoupling of processes that may interfere with placentation and availability of vitamin D at the maternal-fetal interface.

Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients

Metabolic syndrome is a cluster of three or more metabolic disorders including insulin resistance, obesity, and hyperlipidemia. Obesity has become the epidemic of the twenty-first century with more than 1.6 billion overweight adults. Due to the strong connection between obesity and type 2 diabetes, obesity has received wide attention with subsequent coining of the term “diabesity.” Recent studies have identified unique contributions of the immensely diverse gut microbiota in the pathogenesis of obesity and diabetes. Several mechanisms have been proposed including altered glucose and fatty acid metabolism, hepatic fatty acid storage, and modulation of glucagon-like peptide (GLP)-1. Importantly, the relationship between unhealthy diet and a modified gut microbiota composition observed in diabetic or obese subjects has been recognized. Similarly, the role of diet rich in polyphenols and plant polysaccharides in modulating gut bacteria and its impact on diabetes and obesity have been the subject of investigation by several research groups. Gut microbiota are also responsible for the extensive metabolism of polyphenols thus modulating their biological activities. The aim of this review is to shed light on the composition of gut microbes, their health importance and how they can contribute to diseases as well as their modulation by polyphenols and polysaccharides to control obesity and diabetes. In addition, the role of microbiota in improving the oral bioavailability of polyphenols and hence in shaping their antidiabetic and antiobesity activities will be discussed.

Establishing an analytic pipeline for genome-wide DNA methylation.

The need for research investigating DNA methylation (DNAm) in clinical studies has increased, leading to the evolution of new analytic methods to improve accuracy and reproducibility of the interpretation of results from these studies. The purpose of this article is to provide clinical researchers with a summary of the major data processing steps routinely applied in clinical studies investigating genome-wide DNAm using the Illumina HumanMethylation 450K BeadChip. In most studies, the primary goal of employing DNAm analysis is to identify differential methylation at CpG sites among phenotypic groups. Experimental design considerations are crucial at the onset to minimize bias from factors related to sample processing and avoid confounding experimental variables with non-biological batch effects. Although there are currently no de facto standard methods for analyzing these data, we review the major steps in processing DNAm data recommended by several research studies. We describe several variations available for clinical researchers to process, analyze, and interpret DNAm data. These insights are applicable to most types of genome-wide DNAm array platforms and will be applicable for the next generation of DNAm array technologies (e.g., the 850K array). Selection of the DNAm analytic pipeline followed by investigators should be guided by the research question and supported by recently published methods.

Changes in vaginal community state types reflect major shifts in the microbiome

ABSTRACT Background: Recent studies of various human microbiome habitats have revealed thousands of bacterial species and the existence of large variation in communities of microorganisms in the same habitats across individual human subjects. Previous efforts to summarize this diversity, notably in the human gut and vagina, have categorized microbiome profiles by clustering them into community state types (CSTs). The functional relevance of specific CSTs has not been established. Objective: We investigate whether CSTs can be used to assess dynamics in the microbiome. Design: We conduct a re-analysis of five sequencing-based microbiome surveys derived from vaginal samples with repeated measures. Results: We observe that detection of a CST transition is largely insensitive to choices in methods for normalization or clustering. We find that healthy subjects persist in a CST for two to three weeks or more on average, while those with evidence of dysbiosis tend to change more often. Changes in CST can be gradual or occur over less than one day. Upcoming CST changes and switches to high-risk CSTs can be predicted with high accuracy in certain scenarios. Finally, we observe that presence of Gardnerella vaginalis is a strong predictor of an upcoming CST change. Conclusion: Overall, our results show that the CST concept is useful for studying microbiome dynamics.

The Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) Study Design and Methods for Complex DNA Analysis

The Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure (InterGEN) study aims to delineate the independent and interaction effects of genomic (genetic and epigenetic) and psychological–environmental (maternally perceived racial discrimination, mental health, and parenting behavior) factors on blood pressure (BP) among African American mother–child dyads over time. The purpose of this article is to describe the two-step genetic and epigenetic approach that will be executed to explore Gene × Environment interactions on BP using a longitudinal cohort design. Procedure for the single collection of DNA at Time 1 includes the use of the Oragene 500-format saliva sample collection tube, which provides enough DNA for both the Illumina Multi-Ethnic Genotyping and 850K EPIC methylation analyses. BP readings, height, weight, percentage of body fat, and percentage of body water will be measured on all participants every 6 months for 2 years for a total of 4 time points. Genomic data analyses to be completed include multivariate modeling, assessment of population admixture and structure, and extended analyses including Bonferroni correction, false discovery rate methods, Monte Carlo approach, EIGENSTRAT methods, and so on, to determine relationships among both main and interaction effects of genetic, epigenetic, and psychological environmental factors on BP.

Genome Sequencing Technologies and Nursing: What Are the Roles of Nurses and Nurse Scientists?

Background Advances in DNA sequencing technology have resulted in an abundance of personalized data with challenging clinical utility and meaning for clinicians. This wealth of data has potential to dramatically impact the quality of healthcare. Nurses are at the focal point in educating patients regarding relevant healthcare needs; therefore, an understanding of sequencing technology and utilizing these data are critical. Aim The objective of this study was to explicate the role of nurses and nurse scientists as integral members of healthcare teams in improving understanding of DNA sequencing data and translational genomics for patients. Approach A history of the nurse role in newborn screening is used as an exemplar. Discussion This study serves as an exemplar on how genome sequencing has been utilized in nursing science and incorporates linkages of other omics approaches used by nurses that are included in this special issue. This special issue showcased nurse scientists conducting multi-omic research from various methods, including targeted candidate genes, pharmacogenomics, proteomics, epigenomics, and the microbiome. From this vantage point, we provide an overview of the roles of nurse scientists in genome sequencing research and provide recommendations for the best utilization of nurses and nurse scientists related to genome sequencing.

Lead toxicity and genetics in Flint, MI

It has been well established that lead poisoning, as defined by the CDC as blood lead levels (BLLs) at or above 5 μg/dl, can lead to long-term neurotoxic effects in children and requires immediate treatment.1,2 As such, the CDC has long recommended clinicians’ assess to all patients for lead exposure and test BLLs for all at-risk patients.1 Furthermore, it is increasingly recognised that there is no safe level of lead for children due to the irreversible lifelong detrimental effects of lead exposure.2,3 Since the disaster of lead contaminated drinking water in Flint, MI has been uncovered, action has been taken to test children for lead poisoning. However, when children are tested and results show that lead levels are below the 5 μg/dl criteria no further follow-up is conducted with these children, as they are deemed ‘healthy’. This practice is problematic, given that other studies have shown that blood lead levels, even at rates lower than the poison range can be detrimental to a childs health.3–5 The estimated population of Flint is ~99,002, with about 27% of the residents categorised as children under the age of 18 years.6 Therefore, more than ~26,730 children, of whom 60% are African Americans (N = 16,038), have been exposed to environmental lead in the drinking water. A key factor, which almost certainly affects the range of susceptibility to lead poisoning, is a childs genetic makeup. Current models for the neurotoxic effects of lead implicate the enzyme arylsulfatase A (ASA) as a particularly significant target of lead in the central nervous system (CNS).7 Reduced levels of cellular ASA by lead has been suggested to augment the other detrimental affects of the metal, resulting in the death or impaired function of oligodendroglia progenitor cells (OPCs) and lead to CNS dysfunction. Certain single-nucleotide polymorphisms (SNPs) of the gene for ASA (ARSA) cause greatly reduced levels of the enzyme with no obvious phenotype. One of these (Asn350Ser), first characterised in 1989,8 when homozygous, causes up to a 60% reduction in the intracellular levels of the enzyme.9 The homozygous presentation results in metachromatic leukodystrophy, leading to loss of developmental milestones in children and death at a young age. Low ASA activity in individuals with a heterozygous presentation can be identified via signs and symptoms, and it is suggested that these symptoms may be amplified when the individual is exposed to even low levels of environmental lead.4 Some symptoms of this heterozygous pseudodeficiency and environmental lead exposure may include: learning disabilities; behaviour problems’ high blood pressure; tremors; seizure disorder; low sperm count and so on. This SNP is of particular relevance to the current situation in Flint, MI because a study conducted by one of us (J.Y.T.) and colleagues in 20024 of 107 African-American children in Detroit showed that this population had a gene frequency of ~0.45 for the Asn350Ser SNP, heterozygosity at this position often referred to as a pseudodeficiency. This frequency is much higher than what is seen in people of European ancestry (CEU = 0.14) and higher frequency of this allele has been consistently reported in populations of African ancestry (ASW = 0.36).10 These findings suggest that the Flint, MI population suffering lead exposure requires a more effective approach than simply measuring lead levels and setting a cutoff at 5 μg/dl. The question of the appropriate response to the interaction of genetics and lead toxicity was recently commented on by Poretz7 who stated ‘Identification of susceptible children for targeted concern and treatment would help alleviate the impact of the toxicant on the at-risk population.’ We agree strongly with this premise. Genotyping, followed by targeted intervention in Flint, of children who are at higher risk for lead poisoning should be carried out immediately, particularly for those who test below the poison mark. The current cutoff for clinical intervention at 5 μg/dl is inadequate and incorrect, especially for children who are carriers or homozygous for the Asn350Ser SNP. On the basis of these works, it is strongly suggested that children in Flint be genetically tested for ASA pseudodeficiency (heterozygotes) and risk assessed for neurological deficits due to long-term environmental lead exposure. Currently, this testing is not being conducted, which means people with ASA carrier status may experience detrimental effects at a lower exposure threshold, will not receive much-needed treatment that would help mitigate long-term health problems. Not treating people, particularly children, who may be at risk of both ASA pseudodeficiency with concurrent lead exposure could lead to long-term health problems including neurological impairment, neuropsychiatric disorders, increases in blood pressure and more. On the basis of this hypothesis, there is no time to waste testing and caring for lead-exposed people, particularly children, as this is an urgent matter that further exemplifies the need for immediate action. Because such a large population in Flint has been affected by environmental lead exposure, this would be the prime sample for examining the mechanistic biochemical pathways involved in expression of symptoms and for changes in clinical care protocols among an effected sample not controlled by laboratory conditions. Flint offers a unique environmental factor where all of the residents have been exposed to environmental lead in the drinking water, which is why all children should be tested. We believe that all children should be tested for all possible genotypes of the ASA pseudodeficiency. If these children are shown to be carriers, then the families should be afforded the same opportunities for treatment that children with high level of lead exposure receive (e.g., nutritional interventions to decrease absorption, physical therapy, behavioural therapy, educational assistance and so on). If these children are not tested and treated, this is a gross missed opportunity for nurses and other health providers to utilise precision medicine techniques to its’ full potential to help improve the health of people in need. Ignoring symptoms, their underlying causes, and deeming patients as healthy with no requirement for follow-up goes against the premise of ‘symptom science’ detailed by the National Institutes of Health/National Institute of Nursing Research/ and we as health providers can and will do better. Now is the time to use symptom science in combination with genomics to improve lives and healthcare of an otherwise underserved population in the United States. Families can be easily tested with non-invasive measures such as saliva samples. The risk (cost)-benefit ratio of genotyping consenting individuals in Flint lies in favour of such testing. Such genetic testing may well lead to improvement of the physical, physiological and/or mental health of those exposed to the lead contaminated drinking water. This is an initial suggestion that requires high priority in terms of immediate and long-term follow-up of people exposed long-term to the environmental toxin lead. Information gathered by using a precision approach in Flint can be used in other metropolitan areas and the approach can be applied to investigate variation in symptoms when large-scale toxic exposures occur. Flint is not the first community to experience lead toxicity from the water supply, in the early 2000s a similar exposure occurred in Washington DC in a predominately African-American quadrant of the city. As cities continue to age, infrastructure deteriorates and debt burdens increase, there remains potential for similar catastrophic events to occur. The type of precision genetic-testing approach proposed here can be utilised not only in Flint but also in other at-risk communities in the United States and Globally.

A perspective for sequencing familial hypercholesterolaemia in African Americans

African Americans suffer disproportionately from poor cardiovascular health outcomes despite similar proportions of African Americans and Americans of European ancestry experiencing elevated cholesterol levels. Some of the variation in cardiovascular outcomes is due to confounding effects of other risk factors, such as hypertension and genetic influence. However, genetic variants found to contribute to variation in serum cholesterol levels in populations of European ancestry are less likely to replicate in populations of African ancestry. To date, there has been limited follow-up on variant discrepancies or on identifying variants that exist in populations of African ancestry. African and African-American populations have the highest levels of genetic heterogeneity, which is a factor that must be considered when evaluating genetic variants in the burgeoning era of personalised medicine. Many of the large published studies identifying genetic variants associated with disease risk have evaluated populations of mostly European ancestry and estimated risk in other populations based on these findings. The purpose of this paper is to provide a perspective, using familial hypercholesterolaemia as an exemplar, that studies evaluating genetic variation focused within minority populations are necessary to identify factors that contribute to disparities in health outcomes and realise the full utility of personalised medicine.