Associations Between Perinatal Exposures and Neonatal DNA Methylation Open Access

Schroeder, James (2011)

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Several perinatal exposures have been linked with adverse health outcomes later in life.
Fetal exposure to maternal depression, symptoms and treatment are associated with low
birth weight, fetal cardiac defects, and impaired cognitive and emotional development.
Likewise, gestational age, often in the form of preterm delivery, is associated with an
increased rate of neonatal mortality and development of cerebral palsy, cognitive and
behavioral issues. In this study, we examined whether there was an association between
these perinatal exposures and differential methylation in >27,000 CpG loci in umbilical
cord blood DNA of neonates born to mothers participating in a prospectively-
characterized psychiatric cohort. Contrary to previous reports, we found no associations
between neonatal DNA methylation and any psychiatric diagnosis or depressive symptom
measures taken during pregnancy. However, maternal exposure to any antidepressant
during pregnancy was associated with differential methylation at TNFRSF21 and
CHRNA2, though these findings were not associated with individual antidepressant
classes. Gestational age was associated with differential methylation at 41 CpG loci in
39 genes, including genes previously implicated in labor and delivery (e.g., AVP, CRHBP
and ESR1) or that may influence the risk for adverse health outcomes later in life (e.g.
DUOX2, TMEM176A and CASP8). Twenty-six of these loci in 25 genes were then
successfully replicated in an independent, non-psychiatric cohort. These combined
findings will play an important role both in characterizing the epigenetic dynamics
contributing to labor and delivery and in assessing potential impacts of these perinatal
exposures on later-life health conditions.

Associations Between Perinatal Exposures and Neonatal DNA Methylation

M.A., Texas A&M University, 2005
Advisors: Joseph Cubells, M.D., Ph.D.
Alicia Smith, Ph.D.
A dissertation submitted to the Faculty of the
James T. Laney School of Graduate Studies of Emory University
in partial fulfillment of the requirements for the degree of
Doctor of Philosophy
Graduate Division of Biological and Biomedical Sciences
Genetics and Molecular Biology

Table of Contents

Table of Contents

Chapter 1: General Introduction 1

Epigenetics and DNA Methylation 2

Epigenetic Mechanisms During Fetal Development 4

Early-Life Impacts on Phenotypes in Later Life 6

Exposure to Maternal Mental Illness and Neonatal Health 7

Neonatal Risks of Antidepressant Exposure 8

Gestational Age and Health Outcomes 9

Animal Studies 10

Human Studies 13

Epigenetic Patterns Vary by Cell Type 14

Study Objective 15

References 20

Chapter 2: Technical Methodologies 26

Genome-wide Studies of Sequence Variation and DNA Methylation 27

Laboratory Approaches to Genomic-scale Analysis of DNA Methylation 28

Overview of the Infinium Protocol 30

Sample Preparation 31

Array Processing 31

Chip and Experiment Effects 33

HumanMethylation27 Probe Issues 35

Statistical Analysis 38

References 46

Chapter 3: DNA Methylation of Neonates Born to Women Receiving 49
Psychiatric Care

Introduction 50

Methods 51

Results 54

Discussion 56

References 62

Chapter 4: Neonatal DNA Methylation Patterns Associate with 65
Gestational Age

Introduction 66

Methods 67

Results 71

Discussion 72

References 83

Chapter 5: Summary and Conclusions 86

Figures and Tables

Chapter 1: General Introduction

Figure 1-1: Representative Model of Epigenetic Modifications 18
of Histone and DNA

Figure 1-2: Conversion of Cytosine to 5-Methyl Cytosine 19

Chapter 2: Technical Methodologies

Table 2-1: Prevalence of SNPs Under the HumanMethylation27 Probes 39
or at the Single Base Extension Nucleotide

Table 2-2: Prevalence of Flanking CpG Dinucleotides Under the 40
HumanMethylation27 Probes or at the Single Base
Extension Nucleotide

Figure 2-1: Model Depicting the HumanMethylation27 BeadChip 41
Extension Reaction

Figure 2-2: Bisulfite Conversion of Cytosine to Uracil 42

Figure 2-3: Chip Effects Shown by Average Sample Intensity 43
By BeadChip

Figure 2-4: Representative HumanMethylation27 Probe with 44
Mismatched Nucleotides

Figure 2-5: Scatterplots of Methylated vs. Unmethylated Signals 45

Chapter 3: DNA Methylation of Neonates Born to Women Receiving
Psychiatric Care

Table 3-1: Demographic and Clinical Characteristics of 59
the WMHP Subjects

Figure 3-1: Methylation of Significant CpG Sites 61

Chapter 4: Neonatal DNA Methylation Patterns Associate with Gestational Age

Table 4-1: Demographic and Clinical Characteristics of the Discovery 76
and Replication Cohorts

Table 4-2: CpG Sites Reaching Experiment-wide Significance in the 77
Discovery Cohort Compared to the Replication Cohort Results

Table 4-3: Co-occuring Gene Ontology Results for the 41 79
Experiment-wide Significant Genes in the Discovery Cohort

Figure 4-1: Scatterplots of Representative CpG Sites Associated with GA 80
with Regression Lines

Figure 4-2: Heat Map of Beta Values from Subjects with the Lowest 81
and Highest Gestational Ages from the Discovery Cohort

Figure 4-3: Samples in the Discovery Cohort that Used LMP to 82
Determine GA do not Significantly Differ From Those
Based on Obstetrician Report

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