Doctor of Philosophy in Medical Genetics (PhD)
Sex differences and X chromosome inactivation in the human placenta (focused on epigenetic and gene expression profiling)
Sex differences at the genetic/epigenetic level in early development. Role of small non-coding RNAs in placental and fetal development. Epigenetic tools for improved diagnosis in the prenatal and neonatal periods.
Strong background in genetics and stats/bioinformatics preferred. Students accepted into the Medical Genetics or GSAT rotation programs are prioritized.
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Thank you @wprobins27 for being such a #GreatSupervisor. I certainly couldn't have asked for a better supervisor. Thank you for creating a conducive learning environment #SupervisorAppreciationWeek #UBC
Acute chorioamnionitis (aCA), a preterm birth (PTB) associated inflammatory condition, can have adverse effects on the health of the baby. This condition is characterized by inflammatory lesions in the fetal membranes and can also involve the chorionic plate in the placenta. Histologic examination of the placenta is the gold standard for diagnosing aCA, but is only possible after delivery; thus, this method is not suitable for prenatal diagnosis of aCA. This necessitates the development of non-invasive biomarkers to allow effective management of the disease and hence, reduce the incidence of PTB. Additionally, genetic variation in immune-system genes may contribute to the placenta’s inflammatory responses, thus influencing susceptibility to aCA. The overarching objective of this dissertation is to understand how genetic, epigenetic, and miRNA variation in the placenta is associated with the disruption of immune balance in aCA. To achieve this, I first examined the association of single nucleotide polymorphisms (SNPs) in innate immune system genes and aCA status. I observed that differences in IL6 (rs1800796) placental allele frequencies were associated with the presence of aCA. Further, I showed the IL6 SNP may regulate IL6 gene expression and DNA methylation (DNAme) in the placenta, and alter disease risk to aCA. Secondly, using the Illumina HumanMethylation850 BeadChip, I characterized epigenetic variation associated with aCA in placenta and fetal membranes. Specifically, I observed that aCA-affected placentas showed a unique DNAme profile that may reflect an increase in immune cell number as a response to inflammation and/or represent activation of the innate immune response in the placenta. Lastly, I investigated whether altered miRNA profiles were associated with aCA-affected placentas. Expression was quantified for six inflammation-related miRNAs using quantitative real-time PCR. I observed that expression of miR-518b and miR-338-3p were differentially expressed in aCA-affected placentas. I also showed that miR-518b expression in placenta was associated with IL6 (rs1800796) genotype, where carriers of the C allele exhibited decreased miR-518b expression compared to the carriers of the G allele. In summary, this research uniquely investigated genetic alterations, DNAme, and miRNA expression patterns in aCA-affected placentas, adding insights into the processes likely impacting immune function during aCA.
Preeclampsia (PE), characterized by maternal hypertension and proteinuria, is the leading cause of maternal and perinatal morbidity and mortality worldwide. PE can be subdivided into early-onset PE (EOPE), diagnosis
High-throughput methods have resulted in a large volume of studies measuring genome-wide DNA methylation (DNAm) in association with human health and disease. Understanding of DNAm patterns may be translated, for example, into predicting children at risk for illness or identifying etiological subtypes within a heterogeneous disease. Addressing biological and technical factors affecting measurement of genome-wide DNAm is essential to reduce false discovery in such studies. This dissertation develops principles for analyzing genome-wide DNAm, with the aim of improving collection and analysis of human developmental data. To this end, I present four studies employing several techniques to measure genome-wide DNAm: DNAm of L1 and Alu repetitive elements in addition to Illumina 27k and 450k DNAm microarrays. In the first of these studies, I found that tissue type, gestational age, technical platform and CpG density contribute to variable measurement of genome-wide DNAm. Subsequent studies primarily used the 450k array to measure genome-wide DNAm, a technology targeting 485,577 sites in the genome. A detailed annotation of the 450k array was created and tested, to enhance this platform’s utility. Array probes targeting sites containing SNPs (4.3%) and non-specific probes (8.6%) were identified, and I examined how these compromised probes may result in spurious discoveries. A pilot study in placental tissue identified batch effects in 450k data. A computational tool was applied to reduce the batch signal, but I demonstrated that when applied to a problematic study design, false biological signal may be introduced. The workflow for processing and analyzing genome-wide DNAm data was finally applied to profile five tissues ascertained from second trimester neural tube defect (NTD)-affect pregnancies. Despite research, medical interventions and public health changes, NTDs remain the second most common congenital abnormality in many parts of the world, and the etiology of these cases is unknown. Using the 450k array, I found 3,342 differentially methylated sites in the kidneys of spina bifida cases compared to gestational-age matched controls, but little alteration in genome-wide DNAm in other NTD tissues. This dissertation contributes methodologies and analytical tools that will help manage bias, improve reproducibility and reduce false discoveries in studies of genome-wide DNAm.
Recurrent miscarriage (RM), defined as 3 or more consecutive spontaneous losses of pregnancy before 20 weeks gestation, affects 1-2% of couples and has a complex etiology. Half of miscarriages from RM cases are caused by chromosomal abnormalities in the embryo and while there are several associated maternal factors, underlying causes and clinically relevant biomarkers have been elusive. I hypothesized that genetic and/or epigenetic factors associated with maternal meiotic non-disjunction, reproductive aging and endocrinological profile, or placental functioning will contribute to the etiology of RM. In these case-control studies, I investigated the association between RM and 1) maternal mutations in synaptonemal complex protein 3 (SYCP3), 2) maternal telomere lengths, 3) maternal polymorphisms in genes in the hypothalamus-pituitary-ovarian (HPO) axis and 4) placental DNA methylation patterns. The findings suggest that maternal mutations in SYCP3 and polymorphisms in HPO axis genes may not contribute significantly to risk for RM. No mutations in SYCP3 were identified in women with RM with at least one trisomic conception. While associations between polymorphisms within the estrogen receptor β, activin receptor 1, prolactin receptor and glucocorticoid receptor genes and RM were identified, these were not significant after correction for multiple comparisons. Aspects of chromosomal biology may be important factors in the etiology of RM. Women with RM had significantly shorter telomeres compared to controls, suggesting altered rates of biological aging. In the placental villi of RM samples, there were few differences in DNA methylation at targeted sites when compared to isolated miscarriages and elective terminations. However, gene ontology analysis showed that imprinted genes and immune response pathways were overrepresented among those sites differentially methylated between RM and elective termination placentas. The RM group additionally had an increase in the number of outlier cases at a select number of imprinted loci. Furthermore, several placental samples from both cases and controls showed aberrant DNA methylation profiles at many loci investigated, suggesting these samples may have global dysregulation of DNA methylation and/or differences in placental composition/functioning. These studies have improved our understanding of mechanisms involved in RM and will contribute to the direction of future research.
Dysregulation of placental and fetal epigenetics can affect gene expression patterns, including the parent-of-origin dependent expression in imprinted genes. While defects of imprinted genes have been implicated in some adverse pregnancy outcomes, little is currently known about the role of epigenetics in regulating normal or pathological human pregnancy and development. The objective of this thesis is to provide fundamental DNA methylation profiles of human fetal and placental development so as to offer insights into the etiology of human disease and adverse pregnancy outcomes. Taking advantage of the unbalanced parental genomic constitutions in triploidies, 45 novel imprinted genes were identified by comparing the genome-wide DNA methylation profiles between 10 diandries and 10 digynies. A comparison of DNA methylation profiles between placentas of different gestations and other somatic tissues showed tissue-specific and gestational age-specific DNA methylation changes in many imprinted genes. To gain insight into the genomic pattern of tissue-specific methylation, DNA methylation profile was evaluated in 5 somatic tissues (brain, kidney, lung, muscle and skin) from eight normal second-trimester fetuses. Tissue-specific differentially methylated regions (tDMRs) were identified in 195 loci, suggesting that tissue-specific methylation is established early in the second trimester. Importantly, only 17% of the identified fetal tDMRs were found to maintain this same tissue-specific methylation in adult tissues, implicating an extensive epigenetic reprogramming between fetus and adult. Besides intra-individual differences, there is also substantial DNA methylation variation between individuals. While many sites show a continuous pattern of DNA methylation variation between different placentas, WNT2, TUSC3 and EPHB4 were identified to have epipolymorphisms at their promoter region. The methylation status at the TUSC3 promoter showed an association with preeclampsia, suggesting a role of DNA methylation change in adverse pregnancy outcomes. A further investigation of DNA methylation profiles in 26 placentas from preeclampsia, IUGR and control subjects showed 34 loci were hypomethylated in the early-onset preeclamptic placentas, with TIMP3 having a potential of being a biomarker for the disorder. These results provided comprehensive DNA methylation profiles for both normal and abnormal fetal and placental tissues, which contribute to the biological and clinical aspects of the pathogenesis of fetal and placental disorders.
Neonates have a uniquely structured immune system characterized by immunotolerance, an unprimed adaptive immune system, and a heavy reliance on innate immune responses. Although this prevents excessive hyperinflammatory responses during gestation and postnatal microbial colonization of the neonate, it also confers vulnerability to infection. This risk is heightened in those born preterm (prior to 37 weeks gestation), as development of their immune system is interrupted by early birth.Throughout gestation, the predominant hematopoietic organ shifts in a defined temporal pattern. Each hematopoietic source produces different types of immune cells in different proportions, to accommodate the needs of the developing fetus. One of the greatest differences between these organs is the release of nucleated red blood cells (nRBCs) into circulation – ranging from the yolk sac, which exclusively releases primitive nRBCs, to the bone marrow, in which erythroid cells are enucleated before entering circulation. Although generally regarded as a consequence of high erythropoietic demand in the fetus, recent functional studies have indicated an immunosuppressive role for fetal nRBCs as well.DNA methylation (DNAm) is the addition of a methyl group to a cytosine base, a modification which does not change the underlying genetic sequence. DNAm mediates hematopoietic lineage commitment and can be a useful marker for cell composition and immune function in blood. Using the Illumina Infinium HumanMethylation450 BeadChip microarray, this thesis establishes DNAm profiles for major cord blood hematopoietic cells in both term and preterm births. In-depth examination of DNAm in term nRBCs revealed that epigenetic marks in this enigmatic cell population are likely highly regulated. Comparisons between cord blood hematopoietic cells collected from term versus preterm births allowed for the identification of both cell-specific and systemic prematurity-associated differential methylation. These findings contribute to current understanding of the molecular mechanisms behind preterm birth and highlight candidate genes for follow-up gene expression or functional analysis of preterm hematopoietic cell populations, including CDC42EP1, CLIP2, FBXO31, the oncogene WWTR1, and tumour suppressor genes STK10 and RARRES3.
Preeclampsia is a leading cause of maternal and fetal death throughout the world. It is caused by placental dysfunction and clinically characterized by hypertension and other adverse outcomes. Early-onset preeclampsia (EOPET) is a severe form of the disorder. Despite much investigation, the underlying biology of EOPET is unclear. It is known that disrupted oxygen delivery and altered cellular differentiation are characteristics of preeclampsia placentas, and that this likely has an effect on the placental molecular profile. This thesis primarily investigates DNA methylation, a key component in regulating gene expression, in placentas and cellular states related to EOPET. Investigating placental cells exposed to hypoxia, we found 147 CpG sites in cytotrophoblast whose DNA methylation was significantly altered by exposure to hypoxia for 24 hours. Many of these sites overlapped with the 223 CpG sites that were altered between normoxic cytotrophoblast and syncitiotrophoblast, however the change was in the opposite direction (hypomethylated vs. hypermethylated), implying hypoxia can molecularly prevent differentiation in trophoblast cells. Expanding on these findings to look at DNA methylation in placental tissue from preeclampsia pregnancies, we found significant differences at 282 CpG sites. Several of these differences occurred in genes that have functional relevance for the development of EOPET. Many of the candidate genes also showed differential gene expression in preeclampsia placentas. To investigate the utility of these candidate CpGs as 1st trimester EOPET biomarkers, placentas with increased susceptibility to preeclampsia (trisomy 16) were investigated across gestational ages. There were many DNA methylation differences in 3rd trimester trisomy 16 placentas that were shared with chromosomally normal 3rd trimester EOPET placentas, suggesting a common molecular profile of preeclampsia prone placentas, regardless of etiology. Comparing 1st trimester trisomy 16 against 3rd trimester trisomy 16, we found 77 CpG sites differentially methylated in both conditions, and further found 3 changes in first trimester trisomy 16 shared with 3rd trimester EOPET. Overall, these studies have identified several molecular changes in EOPET and related conditions that provide insight into the biology of the disorder while also providing novel candidates to investigate further in a clinical setting.
Each year, many pregnancies are associated with obstetrical complications such as maternal pre-eclampsia (PET) and fetal intrauterine growth restriction (IUGR). Poor placentation is thought to contribute to these complications, but specific causes are largely unknown. Mouse models suggest that epigenetic mechanisms, in particular genomic imprinting, that alter gene regulation may help regulate placental development and embryonic growth. The first goal of this thesis is to examine if epigenetic modifications (i.e. DNA methylation) and altered expression of imprinted genes in the human placenta are contributing factors to PET and IUGR. The second goal of this thesis is to identify imprinted loci that are useful in the diagnosis of placental pathologies that associated with abnormal imprinting, including triploidy, hydatidiform moles, and placental mesenchymal dysplasia. I found that DNA methylation at the imprinting control region 1 (ICR1) on chromosome 11p15.5 was significantly decreased in IUGR placentas (p