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Yakovlev V, Lapato DM, Rana P, Ghosh P, Frye R, Roberson-Nay R. Neuron enriched extracellular vesicles' MicroRNA expression profiles as a marker of early life alcohol consumption. Transl Psychiatry 2024; 14:176. [PMID: 38575599 PMCID: PMC10994930 DOI: 10.1038/s41398-024-02874-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
Alcohol consumption may impact and shape brain development through perturbed biological pathways and impaired molecular functions. We investigated the relationship between alcohol consumption rates and neuron-enriched extracellular vesicles' (EVs') microRNA (miRNA) expression to better understand the impact of alcohol use on early life brain biology. Neuron-enriched EVs' miRNA expression was measured from plasma samples collected from young people using a commercially available microarray platform while alcohol consumption was measured using the Alcohol Use Disorders Identification Test. Linear regression and network analyses were used to identify significantly differentially expressed miRNAs and to characterize the implicated biological pathways, respectively. Compared to alcohol naïve controls, young people reporting high alcohol consumption exhibited significantly higher expression of three neuron-enriched EVs' miRNAs including miR-30a-5p, miR-194-5p, and miR-339-3p, although only miR-30a-5p and miR-194-5p survived multiple test correction. The miRNA-miRNA interaction network inferred by a network inference algorithm did not detect any differentially expressed miRNAs with a high cutoff on edge scores. However, when the cutoff of the algorithm was reduced, five miRNAs were identified as interacting with miR-194-5p and miR-30a-5p. These seven miRNAs were associated with 25 biological functions; miR-194-5p was the most highly connected node and was highly correlated with the other miRNAs in this cluster. Our observed association between neuron-enriched EVs' miRNAs and alcohol consumption concurs with results from experimental animal models of alcohol use and suggests that high rates of alcohol consumption during the adolescent/young adult years may impact brain functioning and development by modulating miRNA expression.
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Affiliation(s)
- Vasily Yakovlev
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA.
| | - Dana M Lapato
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Pratip Rana
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Preetam Ghosh
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Rebekah Frye
- Neuroscience Program, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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Abudahab S, Kronfol MM, Dozmorov MG, Campbell T, Jahr FM, Nguyen J, AlAzzeh O, Al Saeedy DY, Victor A, Lee S, Malay S, Lapato DM, Halquist MS, McRae M, Deshpande LS, Slattum PW, Price ET, McClay JL. Genome-wide analysis of hepatic DNA methylation reveals impact of epigenetic aging on xenobiotic metabolism and transport genes in an aged mouse model. GeroScience 2024:10.1007/s11357-024-01137-9. [PMID: 38558216 DOI: 10.1007/s11357-024-01137-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
Hepatic xenobiotic metabolism and transport decline with age, while intact xenobiotic metabolism is associated with longevity. However, few studies have examined the genome-wide impact of epigenetic aging on these processes. We used reduced representation bisulfite sequencing (RRBS) to map DNA methylation changes in liver DNA from mice ages 4 and 24 months. We identified several thousand age-associated differentially methylated sites (a-DMS), many of which overlapped genes encoding Phase I and Phase II drug metabolizing enzymes, in addition to ABC and SLC classes of transporters. Notable genes harboring a-DMS were Cyp1a2, Cyp2d9, and Abcc2 that encode orthologs of the human drug metabolizing enzymes CYP1A2 and CYP2D6, and the multidrug resistance protein 2 (MRP2) transporter. Cyp2d9 hypermethylation with age was significantly associated with reduced gene expression, while Abcc2 expression was unchanged with age. Cyp1a2 lost methylation with age while, counterintuitively, its expression also reduced with age. We hypothesized that age-related dysregulation of the hepatic transcriptional machinery caused down-regulation of genes despite age-related hypomethylation. Bioinformatic analysis of hypomethylated a-DMS in our sample found them to be highly enriched for hepatic nuclear factor 4 alpha (HNF4α) binding sites. HNF4α promotes Cyp1a2 expression and is downregulated with age, which could explain the reduction in Cyp1a2 expression. Overall, our study supports the broad impact of epigenetic aging on xenobiotic metabolism and transport. Future work should evaluate the interplay between hepatic nuclear receptor function and epigenetic aging. These results may have implications for studies of longevity and healthy aging.
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Affiliation(s)
- Sara Abudahab
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Mohamad M Kronfol
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas Campbell
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA, USA
| | - Fay M Jahr
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Jasmine Nguyen
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Ola AlAzzeh
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Dalia Y Al Saeedy
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Ashley Victor
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Sera Lee
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Shravani Malay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Matthew S Halquist
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA, USA
| | - MaryPeace McRae
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Laxmikant S Deshpande
- Department of Neurology, Virginia Commonwealth University, Richmond, VA, USA
- Department of Pharmacology and Toxicology, Virginia Commonwealth University, Richmond, VA, USA
| | - Patricia W Slattum
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
- Virginia Center On Aging, Virginia Commonwealth University, Richmond, VA, USA
| | - Elvin T Price
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA
| | - Joseph L McClay
- Department of Pharmacotherapy and Outcomes Science, School of Pharmacy, Virginia Commonwealth University, Dr. Joseph L. McClay, 6Th floor Smith Building, 410 North 12Th Street, Medical College of Virginia Campus, Richmond, VA, 23298-0533, USA.
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Kinser PA, Bodnar-Deren S, Amstadter AB, Lapato DM, Thacker LR, Johnson JA, Aubry C, Johnson A, Gault C, Hill-Thomas A, Russell S, Lanni S, Freeman A. Study protocol for the Mindful Moms Study: A randomized controlled trial evaluating a mindful movement intervention for marginalized pregnant people experiencing depression. Contemp Clin Trials 2023; 132:107302. [PMID: 37500008 PMCID: PMC10529983 DOI: 10.1016/j.cct.2023.107302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/22/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
More than 1 in 5 pregnant people in the United States experience depressive symptoms. Although treatments exist, many people remain under- or un-treated due to concerns about stigma, side effects, and costs of medications or psychotherapy, particularly those who are marginalized (defined as those who are minoritized, low-income, or with low-educational attainment). Further, the standard depression treatments do not address social connectedness, which is a potentially modifiable factor involved in depressive symptom etiology. This protocol presents the rationale, design, and status of the two-arm longitudinal parallel group randomized controlled trial - the Mindful Moms Study - which aims to evaluate the effects and mechanisms of a group-based mindful physical activity (yoga) intervention in marginalized pregnant people with depressive symptoms (n = 200) compared to a prenatal education control group. The primary aim is to evaluate effects of group assignment on depressive symptom severity, anxiety, and perceived stress over time from baseline to six weeks postpartum. Secondary aims include understanding the role of social connectedness as a moderator of the effects and to identify genome-wide DNA methylation patterns associated with depressive symptoms and perceived social connectedness at postpartum. A focus on adequate symptom management through non-pharmacologic, accessible therapies that address social connectedness during pregnancy in marginalized women is an urgent clinical and research priority. The successful completion of this study will provide important insights into social connectedness as a mechanism to decrease depressive symptoms in a largely understudied population. Trial registration: NCT04886856.
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Affiliation(s)
- Patricia A Kinser
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA; Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA.
| | - Susan Bodnar-Deren
- Department of Sociology, Virginia Commonwealth University, Richmond, VA, USA
| | - Ananda B Amstadter
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Dana M Lapato
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA; Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA
| | - Leroy R Thacker
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Jennifer A Johnson
- Department of Sociology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Christine Aubry
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
| | - Anisa Johnson
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
| | - Candice Gault
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
| | - Ariel Hill-Thomas
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
| | - Sally Russell
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
| | - Susan Lanni
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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Yakovlev V, Lapato DM, Rana P, Ghosh P, Frye R, Roberson-Nay R. Neuron Enriched Exosomal MicroRNA Expression Profiles as a Marker of Early Life Alcohol Consumption. bioRxiv 2023:2023.06.09.544235. [PMID: 37333185 PMCID: PMC10274862 DOI: 10.1101/2023.06.09.544235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background Alcohol consumption may impact and shape brain development through perturbed biological pathways and impaired molecular functions. We investigated the relationship between alcohol consumption rates and neuron-enriched exosomal microRNA (miRNA) expression to better understand the impact of alcohol use on early life brain biology. Methods Neuron-enriched exosomal miRNA expression was measured from plasma samples collected from young people using a commercially available microarray platform while alcohol consumption was measured using the Alcohol Use Disorders Identification Test. Linear regression and network analyses were used to identify significantly differentially expressed miRNAs and to characterize the implicated biological pathways, respectively. Results Compared to alcohol naïve controls, young people reporting high alcohol consumption exhibited significantly higher expression of four neuron-enriched exosomal miRNAs including miR-30a-5p, miR-194-5p, and miR-339-3p, although only miR-30a-5p and miR-194-5p survived multiple test correction. The miRNA-miRNA interaction network inferred by a network inference algorithm did not detect any differentially expressed miRNAs with a high cutoff on edge scores. However, when the cutoff of the algorithm was reduced, five miRNAs were identified as interacting with miR-194-5p and miR-30a-5p. These seven miRNAs were associated with 25 biological functions; miR-194-5p was the most highly connected node and was highly correlated with the other miRNAs in this cluster. Conclusions Our observed association between neuron-enriched exosomal miRNAs and alcohol consumption concurs with results from experimental animal models of alcohol use and suggests that high rates of alcohol consumption during the adolescent/young adult years may impact brain functioning and development by modulating miRNA expression.
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Affiliation(s)
- Vasily Yakovlev
- Department of Radiation Oncology, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Preetam Ghosh
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Rebekah Frye
- Neuroscience Program, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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Mohanraj L, Lapato DM, Toor A, Swift-Scanlan T. DNA Methylation Research in Autologous Hematopoietic Stem Cell Transplant Population. Biol Res Nurs 2023; 25:220-226. [PMID: 36242509 DOI: 10.1177/10998004221132251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Despite increased sophistication in DNA methylation (DNAm) measurement and methods, conducting studies in specific populations such as the hematopoietic stem cell transplant (HCT) population, presents unique challenges and study design considerations. In this article, we explain the motivation for investigating DNAm in the HCT population, highlighting important study design features and key findings in a longitudinal prospective pilot study of DNAm in 32 patients undergoing autologous HCT in Central Virginia, USA. We also discuss limitations and challenges to generating robust results. We observed that HCT does not prevent high-quality DNA from being extracted from whole blood for DNAm research and that longitudinal prospective studies that span pre- and 2-months post-HCT are feasible. Critically, we did not observe significant impacts of cancer diagnosis, time since transplant, age, or chromosomal sex on overall DNAm data dimensionality. These observations demonstrate that while extreme care is required to ensure generalizable, accurate, and interpretable results, researchers should not avoid HCT-DNAm research simply for fear that the transplant procedure or presence of a cancer diagnosis will prevent meaningful conclusions from being drawn. DNAm is an attractive biomarker that is understudied in patients undergoing HCT and needs to expand to improve precise prediction of HCT outcomes.
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Affiliation(s)
- Lathika Mohanraj
- Department of Adult Health and Nursing Systems, 16197VCU School of Nursing, Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, VCU School of Medicine, Richmond, VA, USA
| | - Amir Toor
- Department of Internal Medicine, VCU School of Medicine, Richmond, VA, USA
| | - Theresa Swift-Scanlan
- Endowed Professor and Director, Biobehavioral Research Lab, 16197VCU School of Nursing, Richmond, VA, USA
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Maes HHM, Lapato DM, Schmitt JE, Luciana M, Banich MT, Bjork JM, Hewitt JK, Madden PA, Heath AC, Barch DM, Thompson WK, Iacono WG, Neale MC. Genetic and Environmental Variation in Continuous Phenotypes in the ABCD Study®. Behav Genet 2023; 53:1-24. [PMID: 36357558 PMCID: PMC9823057 DOI: 10.1007/s10519-022-10123-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 10/11/2022] [Indexed: 11/12/2022]
Abstract
Twin studies yield valuable insights into the sources of variation, covariation and causation in human traits. The ABCD Study® (abcdstudy.org) was designed to take advantage of four universities known for their twin research, neuroimaging, population-based sampling, and expertise in genetic epidemiology so that representative twin studies could be performed. In this paper we use the twin data to: (i) provide initial estimates of heritability for the wide range of phenotypes assessed in the ABCD Study using a consistent direct variance estimation approach, assuring that both data and methodology are sound; and (ii) provide an online resource for researchers that can serve as a reference point for future behavior genetic studies of this publicly available dataset. Data were analyzed from 772 pairs of twins aged 9-10 years at study inception, with zygosity determined using genotypic data, recruited and assessed at four twin hub sites. The online tool provides twin correlations and both standardized and unstandardized estimates of additive genetic, and environmental variation for 14,500 continuously distributed phenotypic features, including: structural and functional neuroimaging, neurocognition, personality, psychopathology, substance use propensity, physical, and environmental trait variables. The estimates were obtained using an unconstrained variance approach, so they can be incorporated directly into meta-analyses without upwardly biasing aggregate estimates. The results indicated broad consistency with prior literature where available and provided novel estimates for phenotypes without prior twin studies or those assessed at different ages. Effects of site, self-identified race/ethnicity, age and sex were statistically controlled. Results from genetic modeling of all 53,172 continuous variables, including 38,672 functional MRI variables, will be accessible via the user-friendly open-access web interface we have established, and will be updated as new data are released from the ABCD Study. This paper provides an overview of the initial results from the twin study embedded within the ABCD Study, an introduction to the primary research domains in the ABCD study and twin methodology, and an evaluation of the initial findings with a focus on data quality and suitability for future behavior genetic studies using the ABCD dataset. The broad introductory material is provided in recognition of the multidisciplinary appeal of the ABCD Study. While this paper focuses on univariate analyses, we emphasize the opportunities for multivariate, developmental and causal analyses, as well as those evaluating heterogeneity by key moderators such as sex, demographic factors and genetic background.
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Affiliation(s)
- Hermine H. M. Maes
- grid.224260.00000 0004 0458 8737Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, PO Box 980033, Richmond, VA 23298-0033 USA ,grid.224260.00000 0004 0458 8737Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA USA ,grid.224260.00000 0004 0458 8737Massey Cancer Center, Virginia Commonwealth University, Richmond, VA USA
| | - Dana M. Lapato
- grid.224260.00000 0004 0458 8737Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, PO Box 980033, Richmond, VA 23298-0033 USA
| | - J. Eric Schmitt
- grid.25879.310000 0004 1936 8972Departments of Radiology and Psychiatry, University of Pennsylvania, Philadelphia, PA USA
| | - Monica Luciana
- grid.17635.360000000419368657Department of Psychology, University of Minnesota, Minneapolis, USA
| | - Marie T. Banich
- grid.266190.a0000000096214564Department of Psychology and Neuroscience, University of Colorado, Boulder, USA ,grid.266190.a0000000096214564Institute of Cognitive Science, University of Colorado, Boulder, USA
| | - James M. Bjork
- grid.224260.00000 0004 0458 8737Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA USA
| | - John K. Hewitt
- grid.266190.a0000000096214564Institute of Cognitive Science, University of Colorado, Boulder, USA ,grid.266190.a0000000096214564Institute for Behavioral Genetics, University of Colorado, Boulder, USA
| | - Pamela A. Madden
- grid.4367.60000 0001 2355 7002Department of Psychiatry, Washington University in St Louis, St Louis, MO USA
| | - Andrew C. Heath
- grid.4367.60000 0001 2355 7002Department of Psychiatry, Washington University in St Louis, St Louis, MO USA
| | - Deanna M. Barch
- grid.4367.60000 0001 2355 7002Department of Psychiatry, Washington University in St Louis, St Louis, MO USA
| | - Wes K. Thompson
- grid.266100.30000 0001 2107 4242Division of Biostatistics and Department of Radiology, Population Neuroscience and Genetics Lab, University of California at San Diego, La Jolla, CA USA
| | - William G. Iacono
- grid.17635.360000000419368657Department of Psychology, University of Minnesota, Minneapolis, USA
| | - Michael C. Neale
- grid.224260.00000 0004 0458 8737Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, PO Box 980033, Richmond, VA 23298-0033 USA ,grid.224260.00000 0004 0458 8737Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA USA
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Lancaster EE, Lapato DM, Peterson RE. Understanding the genetics of peripartum depression: Research challenges, strategies, and opportunities. Front Genet 2022; 13:1022188. [PMID: 36468033 PMCID: PMC9714263 DOI: 10.3389/fgene.2022.1022188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/18/2022] [Indexed: 09/12/2023] Open
Abstract
Peripartum depression (PD) is a common mood disorder associated with negative outcomes for mother and child. PD is an understudied disorder in psychiatric genetics, and progress characterizing its genetic architecture has been limited by a lack of disorder-specific research, heterogeneous and evolving phenotypic definitions, inadequate representation of global populations, low-powered studies, and insufficient data amenable to large meta-analyses. The increasing availability of large-scale, population-level efforts, like biobanks, have the potential to accelerate scientific discovery and translational research by leveraging clinical, molecular, and self-report data from hundreds of thousands of individuals. Although these efforts will not fully equip researchers to confront every challenge posed by systemic issues in data collection, such as the reliance on minimal phenotyping strategies, the field is in a position to learn from other successful psychiatric genetic investigations. This review summarizes the current state of PD genetics research and highlights research challenges, including the impact of phenotype depth, measurement, and definition on the replicability and interpretability of genomic research. Recommendations for advancing health equity and improving the collection, analysis, discussion, and reporting of measures for PD research are provided.
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Affiliation(s)
- Eva E. Lancaster
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States
| | - Dana M. Lapato
- Department of Human and Molecular Genetics, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States
| | - Roseann E. Peterson
- Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States
- Department of Psychiatry and Behavioral Health, Institute for Genomics in Health, State University of New York Downstate Health Sciences University, Brooklyn, NY, United States
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Lancaster EE, Lapato DM, Jackson-Cook C, Strauss JF, Roberson-Nay R, York TP. Maternal biological age assessed in early pregnancy is associated with gestational age at birth. Sci Rep 2021; 11:15440. [PMID: 34326348 PMCID: PMC8322056 DOI: 10.1038/s41598-021-94281-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Maternal age is an established predictor of preterm birth independent of other recognized risk factors. The use of chronological age makes the assumption that individuals age at a similar rate. Therefore, it does not capture interindividual differences that may exist due to genetic background and environmental exposures. As a result, there is a need to identify biomarkers that more closely index the rate of cellular aging. One potential candidate is biological age (BA) estimated by the DNA methylome. This study investigated whether maternal BA, estimated in either early and/or late pregnancy, predicts gestational age at birth. BA was estimated from a genome-wide DNA methylation platform using the Horvath algorithm. Linear regression methods assessed the relationship between BA and pregnancy outcomes, including gestational age at birth and prenatal perceived stress, in a primary and replication cohort. Prenatal BA estimates from early pregnancy explained variance in gestational age at birth above and beyond the influence of other recognized preterm birth risk factors. Sensitivity analyses indicated that this signal was driven primarily by self-identified African American participants. This predictive relationship was sensitive to small variations in the BA estimation algorithm. Benefits and limitations of using BA in translational research and clinical applications for preterm birth are considered.
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Affiliation(s)
- Eva E Lancaster
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, 23220, USA.
| | - Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Colleen Jackson-Cook
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23220, USA.,Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23220, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Jerome F Strauss
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23220, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, 23220, USA.,Department of Psychology, Virginia Commonwealth University, Richmond, VA, 23220, USA
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23220, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, 23220, USA
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Lapato DM, Moore AA, Findling R, Brown RC, Roberson-Nay R. An Update on Precision Medicine Advances In Neurodevelopmental Disorders. Psychiatr Ann 2021; 51:175-184. [PMID: 37609560 PMCID: PMC10443929 DOI: 10.3928/00485713-20210309-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Neurodevelopmental disorders, including autism spectrum disorder (ASD) and attention-deficit/hyper-activity disorder (ADHD), represent a group of conditions that manifest early in child development and produce impairments across multiple domains of functioning. Although a number of pharmacological and psychosocial treatments exist to improve the symptoms associated with these syndromes, treatment advances have lagged. The Precision Medicine Initiative was launched with the goal of revolutionizing medicine by progressing beyond the historical one-size-fits-all approach. In this review, we evaluate current research efforts to personalize treatments for ASD and ADHD. Most pharmacogenetic testing has focused on the cytochrome P450 enzyme family with a particular focus on CYP2D6 and CYP2C19, which are genes that produce an enzyme that acts as a key metabolizer of many prescribed medications. This article provides an update on the state of the field of pharmacogenetics and "therapy-genetics" in the context of ASD and ADHD, and it also encourages clinicians to follow US Food and Drug Administration recommendations regarding pharmacogenetic testing.
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Affiliation(s)
- Dana M. Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University
| | - Ashlee A. Moore
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University
- Department of Psychiatry Virginia Commonwealth University
| | | | - Ruth C. Brown
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University
- Department of Psychiatry Virginia Commonwealth University
| | - Roxann Roberson-Nay
- Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University
- Department of Psychiatry Virginia Commonwealth University
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10
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York TP, Latendresse SJ, Jackson-Cook C, Lapato DM, Moyer S, Wolen AR, Roberson-Nay R, Do EK, Murphy SK, Hoyo C, Fuemmeler BF, Strauss JF. Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth. Epigenetics 2020; 15:1243-1258. [PMID: 32448018 DOI: 10.1080/15592294.2020.1767277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is highly sensitive to in utero perturbations and has an established role in both embryonic development and regulation of gene expression. The foetal genetic component has been previously shown to contribute significantly to the timing of birth, yet little is known about the identity and behaviour of individual genes. The aim of this study was to test the extent genome-wide DNA methylation levels in umbilical cord blood were associated with gestational age at birth (GA). Findings were validated in an independent sample and evidence for the regulation of gene expression was evaluated for cis gene relationships in specimens with multi-omic data. Genome-wide DNA methylation, measured by the Illumina Infinium Human Methylation 450 K BeadChip, was associated with GA for 2,372 CpG probes (5% FDR) in both the Pregnancy, Race, Environment, Genes (PREG) and Newborn Epigenetic Study (NEST) cohorts. Significant probes mapped to 1,640 characterized genes and an association with nearby gene expression measures obtained by the Affymetrix HG-133A microarray was found for 11 genes. Differentially methylated positions were enriched for actively transcribed and enhancer chromatin states, were predominately located outside of CpG islands, and mapped to genes enriched for inflammation and innate immunity ontologies. In both PREG and NEST, the first principal component derived from these probes explained approximately one-half (58.1% and 47.8%, respectively) of the variation in GA. Gene pathways identified are consistent with the hypothesis of pathogen detection and response by the immune system to elicit premature labour as a consequence of unscheduled inflammation.
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Affiliation(s)
- Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA
| | - Shawn J Latendresse
- Department of Psychology and Neuroscience, Baylor University , Waco, TX, USA
| | - Colleen Jackson-Cook
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA.,Department of Pathology, Virginia Commonwealth University , Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA
| | - Sara Moyer
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA
| | - Aaron R Wolen
- Transplant Research Institute, Department of Surgery, University of Tennessee Health Science Center , Memphis, TN, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University , Richmond, VA, USA
| | - Elizabeth K Do
- Department of Health Behavior and Policy, Virginia Commonwealth University , Richmond, VA, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University , Durham, North Carolina, USA
| | - Catherine Hoyo
- Epidemiology and Environmental Epigenomics Laboratory, Center for Human Health and the Environment, North Carolina State University , Raleigh, NC, USA
| | - Bernard F Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University , Richmond, VA, USA
| | - Jerome F Strauss
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA
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11
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Lapato DM, Roberson-Nay R, Kirkpatrick RM, Webb BT, York TP, Kinser PA. DNA methylation associated with postpartum depressive symptoms overlaps findings from a genome-wide association meta-analysis of depression. Clin Epigenetics 2019; 11:169. [PMID: 31779682 PMCID: PMC6883636 DOI: 10.1186/s13148-019-0769-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/22/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Perinatal depressive symptoms have been linked to adverse maternal and infant health outcomes. The etiology associated with perinatal depressive psychopathology is poorly understood, but accumulating evidence suggests that understanding inter-individual differences in DNA methylation (DNAm) patterning may provide insight regarding the genomic regions salient to the risk liability of perinatal depressive psychopathology. RESULTS Genome-wide DNAm was measured in maternal peripheral blood using the Infinium MethylationEPIC microarray. Ninety-two participants (46% African-American) had DNAm samples that passed all quality control metrics, and all participants were within 7 months of delivery. Linear models were constructed to identify differentially methylated sites and regions, and permutation testing was utilized to assess significance. Differentially methylated regions (DMRs) were defined as genomic regions of consistent DNAm change with at least two probes within 1 kb of each other. Maternal age, current smoking status, estimated cell-type proportions, ancestry-relevant principal components, days since delivery, and chip position served as covariates to adjust for technical and biological factors. Current postpartum depressive symptoms were measured using the Edinburgh Postnatal Depression Scale. Ninety-eight DMRs were significant (false discovery rate < 5%) and overlapped 92 genes. Three of the regions overlap loci from the latest Psychiatric Genomics Consortium meta-analysis of depression. CONCLUSIONS Many of the genes identified in this analysis corroborate previous allelic, transcriptomic, and DNAm association results related to depressive phenotypes. Future work should integrate data from multi-omic platforms to understand the functional relevance of these DMRs and refine DNAm association results by limiting phenotypic heterogeneity and clarifying if DNAm differences relate to the timing of onset, severity, duration of perinatal mental health outcomes of the current pregnancy or to previous history of depressive psychopathology.
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Affiliation(s)
- Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA. .,Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA.
| | - Roxann Roberson-Nay
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA.,Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Robert M Kirkpatrick
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA.,Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Bradley T Webb
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA.,Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, USA.,Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, USA
| | - Patricia A Kinser
- School of Nursing, Virginia Commonwealth University, Richmond, VA, USA
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12
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Moore AA, Lapato DM, Brotman MA, Leibenluft E, Aggen SH, Hettema JM, York TP, Silberg JL, Roberson-Nay R. Heritability, stability, and prevalence of tonic and phasic irritability as indicators of disruptive mood dysregulation disorder. J Child Psychol Psychiatry 2019; 60:1032-1041. [PMID: 30994196 PMCID: PMC6692198 DOI: 10.1111/jcpp.13062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/12/2019] [Indexed: 12/01/2022]
Abstract
BACKGROUND Little is known about genetic and environmental influences on the components of disruptive mood dysregulation disorder (DMDD), tonic irritability (i.e., irritable mood) and phasic irritability (i.e., temper outbursts). This study examined prevalence, stability, and heritability of tonic irritability, phasic irritability, and a DMDD proxy (pDMDD) based on DSM-5 criteria. METHODS pDMDD was derived using data from clinical interviews of parents and their twins (N = 1,431 twin pairs), ages 8-17, participating in Waves 1 and 2 of the Virginia Twin Study of Adolescent Behavioral Development. Biometrical modeling was used to compare a common pathway model (CPM) and an independent pathway model (IPM), and heritability estimates were obtained for pDMDD using the symptoms of irritable mood (tonic irritability; DMDD Criterion D), intense temper outbursts (phasic irritability; DMDD Criterion A), and frequent temper outbursts (phasic irritability; DMDD Criterion C). RESULTS Lifetime prevalence of pDMDD was 7.46%. The stability of DMDD symptoms and the pDMDD phenotype across approximately one year were moderate (.30-.69). A CPM was a better fit to the data than an IPM. Phasic irritability loaded strongly onto the pDMDD latent factor (.89-.96) whereas tonic irritability did not (.28). Genetic influences accounted for approximately 59% of the variance in the latent pDMDD phenotype, with the remaining 41% of the variance due to unique environmental effects. The heritability of tonic irritability (54%) was slightly lower than that of frequent and intense temper (components of phasic irritability; 61% and 63%, respectively). CONCLUSIONS Compared to tonic irritability, phasic irritability appears to be slightly more stable and heritable, as well as a stronger indicator of the latent factor. Furthermore, environmental experiences appear to play a substantial role in the development of irritability and DMDD, and researchers should seek to elucidate these mechanisms in future work.
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Affiliation(s)
- Ashlee A. Moore
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
- Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA
| | - Dana M. Lapato
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Melissa A. Brotman
- Emotion and Development Branch, National Institutes of Mental Health, National Institutes of Health Department of Health and Human Services, Bethesda, MD
| | - Ellen Leibenluft
- Emotion and Development Branch, National Institutes of Mental Health, National Institutes of Health Department of Health and Human Services, Bethesda, MD
| | - Steven H. Aggen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - John M. Hettema
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Timothy P. York
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Judy L. Silberg
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
| | - Roxann Roberson-Nay
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
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13
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Lapato DM, Moyer S, Olivares E, Amstadter AB, Kinser PA, Latendresse SJ, Jackson-Cook C, Roberson-Nay R, Strauss JF, York TP. Prospective longitudinal study of the pregnancy DNA methylome: the US Pregnancy, Race, Environment, Genes (PREG) study. BMJ Open 2018; 8:e019721. [PMID: 29743320 PMCID: PMC5942473 DOI: 10.1136/bmjopen-2017-019721] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 01/08/2023] Open
Abstract
PURPOSE The goal of the Pregnancy, Race, Environment, Genes study was to understand how social and environmental determinants of health (SEDH), pregnancy-specific environments (PSE) and biological processes influence the timing of birth and account for the racial disparity in preterm birth. The study followed a racially diverse longitudinal cohort throughout pregnancy and included repeated measures of PSE and DNA methylation (DNAm) over the course of gestation and up to 1 year into the postpartum period. PARTICIPANTS All women were between 18 and 40 years of age with singleton pregnancies and no diagnosis of diabetes or indication of assisted reproductive technology. Both mother and father had to self-identify as either African-American (AA) or European-American (EA). Maternal peripheral blood samples along with self-report questionnaires measuring SEDH and PSE factors were collected at four pregnancy visits, and umbilical cord blood was obtained at birth. A subset of participants returned for two additional postpartum visits, during which additional questionnaires and maternal blood samples were collected. The pregnancy and postpartum extension included n=240 (AA=126; EA=114) and n=104 (AA=50; EA=54), respectively. FINDINGS TO DATE One hundred seventy-seven women (AA=89, EA=88) met full inclusion criteria out of a total of 240 who were initially enrolled. Of the 63 participants who met exclusion criteria after enrolment, 44 (69.8%) were associated with a medical reason. Mean gestational age at birth was significantly shorter for the AA participants by 5.1 days (M=272.5 (SD=10.5) days vs M=277.6 (SD=8.3)). FUTURE PLANS Future studies will focus on identifying key environmental factors that influence DNAm change across pregnancy and account for racial differences in preterm birth.
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Affiliation(s)
- Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Sara Moyer
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Ananda B Amstadter
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Patricia A Kinser
- Department of Family and Community Health Nursing, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shawn J Latendresse
- Department of Psychology and Neuroscience, Baylor University, Waco, Texas, USA
| | - Colleen Jackson-Cook
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
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