Michael Kobor


Research Interests

Chromatin Biology
molecular biology
Social Epigenetics

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Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.

Associations of DNA methylation with individual differences in Parkinson's disease susceptibility (2023)

Parkinson’s disease (PD) is a common neurodegenerative disorder with increasing worldwide prevalence. Although a number of genes and environmental factors influencing PD susceptibility have been identified, the mechanisms underpinning their joint contributions to disease pathogenesis are not fully understood. DNA methylation (DNAm) is an epigenetic mark that is sensitive to genetics and environment and can influence gene transcription. Due to these properties, DNAm has been proposed as a contributor to PD etiology and also as a potential early-stage biomarker. However, the complex interindividual etiology of PD and the inability to its study progression in human brain tissue present challenges in researching the role of DNAm in PD pathogenesis. In this dissertation, I investigated the associations of DNAm with genetic and environmental factors influencing PD susceptibility and with early-stage PD in human populations. Using a human dopaminergic neuron cell line, I found that overexpressing the wild type or A30P mutant form of the SNCA gene induced thousands of site-specific DNAm changes. These DNAm changes were associated with altered DNA hydroxymethylation (DNAhm) and transcription of glutamate signaling genes. Additionally, I investigated the impacts of overexpressing wild type SNCA in mice housed in a standard or enriched environment paradigm by profiling hippocampal DNAm and DNAhm, and integrating these results with previously generated RNA-seq and ChIP-seq (H3K4me1, H3K4me3, H3K27ac). SNCA overexpression was associated with similar DNAhm and H3K27ac alterations when mice were housed in a standard or enriched environment, and with environment-dependent changes to H3K4 and DNA methylation. In particular, environment prevented some SNCA-induced changes to H3K4me1, a select few of which correlated with gene expression. Finally, I investigated the contributions of sex, genetic background, and pesticide exposure to blood DNAm signatures of early-stage PD in a sample of 218 agricultural workers and their spouses. Differentially methylated regions associated with early-stage PD differed by sex and were influenced by genetic background to a greater degree than pesticide exposure. Altogether, I have enhanced our understanding of the impacts of PD-associated genotypes and environments on the brain and blood epigenome, and laid a foundation for further studies of the role of the epigenome in PD etiology.

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Associations of DNA methylation with adversity throughout the life course (2021)

Interpersonal and societal adversity experienced throughout life, such as abuse or low socio-economic status (SES), have been associated with negative health outcomes. Many of these diseases share the common thread of inflammation, inspiring the hypothesis that chronic stress resulting from adverse experiences over activates the hypothalamic-pituitary- adrenal (HPA) axis resulting in dysregulation of the immune system. DNA methylation (DNAm), a methyl group covalently bound to cytosine bases for the purposes of this thesis, is one of many epigenetic mechanisms involved in responding to environmental signals in the genomic context. As such, this modification may be particularly pertinent to understanding how adverse experiences can become embedded in a way that results in lifelong health disparities.The overarching aim of this dissertation is to understand how various measures of adversity throughout the life-course could associate with DNAm differences between individuals. Initially, I compared whole blood DNAm patterns amongst elderly individuals with different years of education, household assets and self-reported measures of economic standing in childhood and older adulthood, in addition to a composite socioeconomic (SES) measure. I found there were significantly more DNAm associations with older adulthood relative to retrospective childhood SES measures, and the subjective SES measures displayed a dampened signal relative to objective ones. Next, I investigated the relationship between the inflammatory biomarker serum IL-6, lifetime SES measures and purified monocyte DNAm patterns amongst adults. Here, I found the relationship between some CpGs and IL-6 was partially explained by SES. Additionally, differences in SES-associated DNAm sites were seen predominantly amongst individuals who experienced low early life and high adulthood SES. Finally, I investigated how childhood abuse associated with DNAm in spermatozoa of adult men. Though this was a small pilot study, I found a subset of differentially methylated regions associated with childhood abuse. These associations were stable over a two-month period and survived adjusting for current life adversity measures. Overall, these findings provide evidence that the tissue, timing, and measure of adversity experienced are important considerations for social epigenetic studies and can yield unique DNAm patterns in a context-specific way.

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Diverse functions of Rtt107 in the Saccharomyces cerevisiae DNA damage response (2021)

Cells are routinely confronted with DNA damage and depend on genome maintenance factors to prevent cell death, as well as mutations and genomic rearrangements. The DNA damage response includes DNA repair and cell cycle checkpoints, which arrest sensitive processes such as DNA replication while damage is repaired. Rtt107 is an evolutionarily conserved Saccharomyces cerevisiae protein that is required for resistance to agents that cause replicative stress and DNA damage. Rtt107 has been best characterized as a scaffold that acts in response to DNA damage, localizing to phosphorylated H2A and binding to diverse protein partners, including Slx4. However, other functions of Rtt107 remain unclear. Mutants lacking Rtt107 exhibit prolonged checkpoint activation after replicative stress, and the “checkpoint dampening” model proposes that Rtt107-Slx4 reduces checkpoint activity by limiting formation of a Rad9-Dpb11 complex that promotes checkpoint activity. In this dissertation, I identified higher levels of DNA damage in cells lacking Rtt107 during replicative stress. This presented an alternative cause of checkpoint activity, and I showed that the Rad9-Dpb11 complex was not primarily responsible for prolonged checkpoint activity in this context. Based on these findings, I proposed a revised model of Rtt107 function during replicative stress, in which Rtt107 primarily reduced checkpoint activity by limiting DNA damage levels. I next explored Rtt107’s less well-understood function in limiting spontaneous genome instability, and found that this was partially distinct from its function in the context of treatment with replicative stress. Specifically, Rtt107 bound to the DNA repair protein Rad55 to limit spontaneous loss of heterozygosity, and spontaneous crossover events. I next focused on the regulation of Rtt107, specifically the phosphorylation of Rtt107’s SQ/TQ cluster domain (SCD) by the Mec1 kinase after treatment with DNA damaging agents. To address inconsistencies between prior reports on the importance of Rtt107 phosphorylation, I reviewed prior work on this subject and demonstrated that phosphorylation of Rtt107’s SCD was dispensable for growth during chronic treatment with DNA damaging agents. Collectively, my dissertation reveals how Rtt107 acts with various partners and in different contexts to confer resistance to agents that cause replicative stress and DNA damage, and to prevent spontaneous genome instability.

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DNA methylation microarray data reduction for co-methylation analysis (2020)

DNA Methylation (DNAm) is an epigenetic modification that is present across the human genome, primarily in the context of CpG di-nucleotides. In human population studies, high throughput bead chip microarray assays are the prevalent way to simultaneously measure the methylation state of many thousands of genomic CpG sites. Proximal genomic CpGs have correlated methylation state within a single cell and often function as a single biological unit. The prevailing common methylation state of such multiple CpGs within a common biological unit has been the subject of intense study, due to its immediate relevance for gene expression regulation and ultimately for health and disease. I designed and implemented a method for a biologically motivated DNAm array data reduction, which constructs co-methylated regions (CMRs), while incorporating information about the genomic CpG background from the reference human genome annotation. The method relies on the correlations of CpG methylation across individuals for proximal CpG probes. The method aims for enhanced statistical performance in terms of statistical power and specificity, including for downstream applications. For example, Epigenome Wide Association Studies (EWAS), an important such application, often places the focus on group “hits” with multiple adjacent CpGs that are significant, because their gnomic proximity makes it more likely that the detected correlations are not spurious. The CMRs capture such groups and I showed that the CMRs constructed in whole blood public data have high statistical specificity in the context of EWAS for chronological age and biological sex. When the composite CMR methylation measures were used to perform EWAS for age and sex, they had high sensitivity and specificity, including uncovering additional associated CpGs not detected by conventional EWAS. The utility of the data reduction method was further discussed within the broader context of applying machine learning algorithms for high dimensional DNAm array data analysis.

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Contributions of intrinsic and environmental factors to early life DNA methylation (2019)

Many early experiences and exposures are known to cause health disparities later in life, suggesting that they are somehow ‘biologically embedded’. The mechanisms underlying ‘biological embedding’ are currently not well understood. However, emerging evidence has implicated a potential contribution from epigenetic modifications, such as DNA methylation (DNAm), which has been shown to associate with early life experiences of low socioeconomic status. Additional related experiences have also been connected with DNAm, including parental stress, childhood maltreatment or deprivation, and maternal mental health problems during the perinatal period. The relationship between early life experience and epigenetics is complicated by internal psychological and physiological factors, as well as genetic variation, which can account for 20% to 80% of inter-individual epigenetic differences. As well, stress reactivity and temperament are predictive of how a child may interact with his or her environment and can affect how such exposures are internalized. Thus, the main objectives of my dissertation were to elucidate the relationships between childhood environment, DNAm, genetic variation, and behaviour, to understand how these systems influence one another. Using matched DNAm profiles from blood and buccal tissue from a cross-sectional cohort of Canadian children, I uncovered tissue-specific and -shared DNAm signatures in order to glean the utility of accessible tissues in epigenetic association studies. In a longitudinal cohort, I tested the hypothesis that indicators of children’s early internal, biological and behavioural responses to stressful challenges are linked to stable patterns of DNAm later in life; I found relationships between biobehavioural response propensities in early life and patterns of DNAm in DLX5 and IGF2 genes at ages 15 and 18. Finally, I examined the epigenetic correlates of familial socioeconomic status in matched childhood peripheral blood and dried neonatal blood spot samples, allowing me to assess the DNAm pattern over time. Together these findings build upon our current understanding of the role of DNAm in biological embedding and more broadly, the field of social epigenetics.

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DNA methylation variation across the human life course (2018)

Aging is a multifaceted process occurring in all living organisms, and it involves the breakdown of biological robustness. Although much research has revealed fascinating features of cellular mechanisms related to aging and lifespan, we have yet to understand the underpinnings driving this inevitable progression. Epigenetics is one area of aging research that has developed significant interest as certain modifications, such as DNA methylation, have been proposed to mediate the relationship between the environment and gene expression as well as have age-associated patterns. Interestingly, predictors of age based on DNA methylation of
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Tissue-specific investigations of DNA methylation variation in human neurobiological diseases (2018)

Epigenomic variation represents an emerging focus in human health research, particularly in regards to neurobiological disease susceptibility and pathogenesis. DNA methylation (DNAm), which involves the covalent attachment of a methyl group to a cytosine primarily at CpG dinucleotides, has been widely assessed in the context of epigenome-wide association studies (EWASs), with DNAm associations identified across a broad range of disease states, environmental exposures and genetic backgrounds. However, DNAm profiling in neurobiological diseases is challenged by the fact that DNAm variation is highly tissue-specific and target brain tissues may be difficult or impossible to collect from postmortem samples, in living individuals undergoing treatment interventions or in pediatric populations. As such, the use of cell-culture models or accessible peripheral tissues such as blood or buccal swabs represent alternative approaches used in human neurobiological DNAm studies to identify potential biomarkers of disease or treatment response. The overarching aim of my dissertation was to apply and evaluate various tissue-specific approaches to investigate DNAm variation across different neurobiological diseases. To this end, I performed four separate studies to assess disease-associated DNAm from a) post-mortem brain samples, b) primary brain-derived cell culture models and c) accessible peripheral tissues. Specifically, I examined DNAm patterns related to Huntington’s disease pathogenesis and tissue-specific Huntingtin gene expression in postmortem human cortex samples. I subsequently compared DNAm profiles from glioblastoma multiforme tumours and matched primary cell cultures enriched for brain-tumour initiating cell populations, identifying a homeobox-enriched signature of differential DNAm between the paired samples. Beyond brain-specific DNAm patterns, I also explored the use of a disease-relevant blood cell type, CD³⁺ T-lymphocytes, to detect DNAm alterations associated with alcohol dependence in patients undergoing a clinical intervention. Finally, I assessed DNAm variability and the influence of genetic variation on DNAm in peripheral blood and buccal epithelial cells from two pediatric cohorts, highlighting a number of potential considerations and practical implications for the appropriate design and interpretation of early-life EWAS analyses in these tissues. Overall, these findings provide evidence to implicate DNAm variation in neurological function and pathology as well as present potential opportunities for the identification of novel biomarkers in accessible tissues.

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Epigenetic signatures of prenatal alcohol exposure (2017)

Prenatal alcohol exposure (PAE) can alter the development, function, and regulation of neurobiological and physiological systems, causing lasting cognitive alterations, behavioral deficits, immune dysfunction, and increased vulnerability to mental health problems. In humans, the spectrum of these deficits is known as fetal alcohol spectrum disorder (FASD). Although the molecular underpinnings are not fully elucidated, epigenetic mechanisms are a prime candidate for the programming of physiological systems by PAE, as they may bridge environmental stimuli and neurodevelopmental outcomes. DNA methylation is also emerging as a potential biomarker of early-life events, which may aid in earlier FASD diagnoses. Thus, my overarching aim was to identify epigenetic mechanisms that may contribute to the deficits associated with FASD and act as biosignatures of PAE. Specifically, I used genome-wide approaches to assess underlying gene expression programs and epigenomic profiles in a rat model of PAE and clinical cohorts of individuals with FASD. In the rat model, I identified alterations to gene expression programs in the brain of adult PAE females under steady-state and immune challenge conditions. Building on these long-term alterations to transcriptomic programs, I identified altered DNA methylation patterns persisting from birth to weaning in the hypothalamus PAE animals, suggestive of early reprogramming of neurobiological systems. In parallel, I found concordant alterations to DNA methylation profiles in the hypothalamus and white blood cells of PAE animals, which may reflect systemic effects and potential biomarkers of PAE. To complement the animal model, I also investigated DNA methylation patterns in two clinical cohorts of FASD, where I identified an epigenetic signature of FASD in buccal epithelial cells. As these results raised the possibility of an epigenetic biomarker, I investigated the relevance of DNA methylation as a diagnostic method for PAE, and successfully generated a predictive algorithm that could classify individuals with FASD versus controls. Overall, these findings provide evidence for the biological embedding of PAE’s effects through changes in gene expression and DNA methylation, while setting the stage for the development of novel biomarkers. Ultimately, these may aid in the development of targeted interventions and early screening tools to mitigate the deficits associated with FASD.

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Coordinated Activities of Chromatin Modifying Complexes in DNA Regulation in Saccharomyces cerevisiae (2015)

No abstract available.

Diverse mechanisms of transcription regulation by RNA polymerase II in saccharomyces ceresisiae (2015)

No abstract available.

Functional characterization of Rtt107 in the DNA damage response in Saccharomyces cerevisiae (2014)

No abstract available.

Deciphering the function of chromatin modifiers in genome regulation and maintenance in saccharomyces cerevisiae (2012)

No abstract available.

Mechanism of Deposition and Functional Characterization of the Histone Variant H2A.Z in Saccharomyces cerevisiae (2012)

No abstract available.

Genome-wide analysis of chromatin modification patterns and their functional associations with major cellular processes in Saccharomyces cerevisiae (2010)

No abstract available.

Master's Student Supervision

Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.

Dispersed measures of cord blood DNA methylation do not reflect third trimester bisphenol exposure (2023)

Bisphenols are ubiquitously used plasticizers that pose a risk to human health due to their endocrine-disrupting properties, and prenatal exposure to bisphenols may lead to adverse birth and pregnancy outcomes. The epigenetic modification, DNA methylation (DNAm), has been studied as a possible molecular vestige of prenatal bisphenol exposure due to its sensitivity to prenatal chemical exposures and links to long-term health outcomes. Recent studies have identified that loci-specific differential DNAm may associate with prenatal bisphenol exposure; however, no studies to date have explored associations between prenatal bisphenol exposure and composite DNAm-based biomarkers, such as gestational epigenetic age acceleration (GEAA), which refers to the deviation between a DNAm-based prediction of gestational age (GA) and clinically measured GA, that has been proposed to reflect potential developmental impacts. To address this research gap, we conducted sex-stratified robust linear regression analyses between GEAA, and global DNAm proxied through LINE1 and Alu element DNAm, measured from cord blood and prenatal daily intake levels of bisphenol A (BPA), bisphenol F (BPF), and bisphenol S (BPS) in the longitudinal Barwon Infant Study (BIS) birth cohort (n = 603). No associations between estimated prenatal daily intake levels of BPA, BPS, BPF, nor their weighted sum, measured in third trimester maternal urine, and cord blood GEAA or global DNAm, were detected across sexes. Our results indicate that prenatal bisphenol exposures in the third trimester may not have a discernible impact on two biomarkers derived from dispersed cord blood DNAm — GEAA as a biomarker of fetal development, and repetitive element DNAm as a biomarker of global DNAm, at birth. This study provides clarification on molecular biomarkers that may reflect prenatal bisphenol exposure, and the study characteristics, such as the health of the study cohort and consideration of sex in study design, that may influence the study findings.

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Epigenetic signatures of developmental psychopathology : time-varying associations of general psychopathology across childhood and adolescence with late adolescent DNA methylation (2023)

Psychopathology is known to fluctuate throughout childhood and adolescence, in association with a variety of intrinsic (e.g., genetic) and extrinsic (e.g., environmental) factors. DNA methylation (DNAm) is a commonly studied epigenetic modification that can reflect the interplay between genetics and environments. DNAm is a stable, reversible mark added onto DNA that can regulate gene expression and may serve as a biomarker of psychopathology. Many studies have identified links between DNAm and childhood and adolescent psychopathology, but most have been limited by assessing narrow timeframes. The present study harnessed a wealth of longitudinal data from a community-based cohort of children in Wisconsin (n=170) to examine the General Psychopathology Factor (GPF) – a broad construct capturing shared variance between psychiatric symptoms – across childhood and adolescence, in relation to DNAm from buccal epithelial cells collected at age 18. To determine which GPF timepoint (of 7 timepoints across age 9-18) or GPF trajectory (of 5 derived trajectory measures) provided the best explanation of age 18 DNAm patterns, a two-phase comparative statistical approach was employed, consisting of screening measures for high-dimensional data and the Structured Life-Course Modelling Approach (SLCMA). The SLCMA identified which GPF measure explained the most DNAm variation at 298,415 methylation sites (CpGs). At 12,910 CpGs, the selected GPF measure explained more DNAm variation than expected by chance (R² > 3.7%). After multiple test correction, 486 medium-confidence (Padjusted
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A broader role for the RNAPII phosphatase, FCP1, in transcription regulation (2021)

Transcription is the process by which DNA is copied into RNA in the cell. In eukaryotes, protein coding genes are transcribed by the enzyme RNA Polymerase II (RNAPII). RNAPII has a unique and highly conserved repeating heptad sequence at the C-terminus of its largest subunit, Rpb1, known as the C-terminal domain (CTD). The CTD is differentially phosphorylated throughout the transcriptional cycle, a property that is important for the dynamic recruitment of transcription-associated factors. The phosphorylation status of the CTD is maintained by several CTD-modifying enzymes. Two such CTD-modifying enzymes are the phosphatase, Fcp1, and the kinase, Cdk8. This thesis focuses on exploring the genetic interaction between FCP1 and CDK8. It expands the growing body of work that implicates Cdk8 as a stress response regulator, and identifies a role for Fcp1 in the stress response. Given that Fcp1 is essential, I probed the genes and pathways most sensitive to the truncation of fcp1, and uncovered an unexpected role for FCP1 and CDK8 in the regulation of Skn7 and the expression of Skn7-dependent oxidative stress response genes. Loss of CDK8 was able to overcome the transcriptional and posttranscriptional alterations caused by truncating fcp1 by increasing Skn7 stability, protein levels, and normalizing the expression of target genes. I also explored a role for FCP1 in Rpb1 biology. Truncation of fcp1 caused higher levels of Rpb1 protein that still associated with chromatin, despite not associating with Rpb3, another RNAPII subunit. It also resulted in higher levels of a lower molecular weight form of Rpb1. Additionally, this thesis expands the connection between FCP1 and CDK8 to include RPN4, a transcriptional activator of proteasome and stress response genes. Rpn4 has previously been shown to mediate the suppression of some CTD truncation phenotypes by loss of CDK8. Here, I found that the combined loss of RPN4 and CDK8 was able to normalize the increased levels of Rpb1 caused by the truncation of fcp1. Collectively, this thesis has expanded on our understanding of Fcp1 function in the cell and its role in transcription regulation.

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Genome-wide Analysis of DNA Methylation Variance in Healthy Human Subjects (2015)

DNA methylation is a type of epigenetic modification that modulates gene expression by acting as an intermediate between genes and environment; this in turn could trigger phenotypic changes with widespread implications in both disease and population models. Unlike DNA sequence, which is relatively stable and finite, DNA methylation presents itself differently in different tissues, and it is described as the sum of interactions affecting attachment of methyl groups to DNA mostly as a result of development and aging, with minor influences from stochastic variability, and environmental factors. Most studies involving DNA methylation focus on finding epigenetic changes related to pathogenicity or disease, as a result, there are certain foundational questions that remain unanswered. In order to translate the current knowledge into reliable insights, it is important to answer these questions, then standardize research methods and establish reference epigenomes. Here we begin to address this challenge through two avenues: epigenomic characterization and environmental interaction. To characterize the epigenome, we monitored the peripheral blood mononuclear cell DNA methylation levels from healthy subjects over a circadian day, a month, and under prolonged sample storage. We also investigated tissue specific variability in DNA methylation by comparing matched peripheral blood mononuclear and buccal epithelial cell samples from healthy subjects. Lastly, we analyzed the impact of diesel exhaust on the DNA methylation. We discovered that while overall DNA methylation was stable within a circadian day, certain loci demonstrated significant changes over the course of a month. Prolonged sample storage, on the other hand, had an even larger effect on DNA methylation. When we compared differences across tissues, we found that although both tissues showed extensive probe-wise variability, the specific regions and magnitude of that variability differed strongly between tissues. Lastly, in light of environmental influences, we observed that DNA methylation was sensitive to even short-term exposure to diesel exhaust, and we identified associated CpG sites across the functional genome, as well as in Alu and LINE1 repetitive elements, with most of these exposure sensitive sites demonstrating loss of DNA methylation.

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Prenatal alcohol exposure programs steady-state gene expression and the gene expression response to inflammation in the adult rat brain (2013)

Prenatal alcohol exposure results in alterations in numerous physiological systems, including neuroendocrine and neuroimmune systems. The purpose of this study was to determine whether prenatal ethanol exposure results in long-term alteration of neural gene expression, particularly in genes related to neuroendocrine and neuroimmune function. Utilizing a well-established animal model of prenatal ethanol exposure, ethanol was administered to pregnant Sprague-Dawley dams throughout gestation in a liquid diet fed ad libitum (36% calories derived from ethanol). Maltose-dextrin was isocalorically substituted for ethanol in a liquid control diet for a pair-fed group, and a control group received a pelleted control diet ad libitum. In young adulthood, an adjuvant-induced arthritis paradigm was utilized, where female offspring were injected with either saline or complete Freund’s adjuvant, to induce an inflammatory response and elucidate dysregulated neuroimmune pathways. Gene expression was analyzed in the prefrontal cortex and hippocampus at both the peak and resolution of arthritis using whole genome gene expression microarrays. Within saline-injected animals, prenatal alcohol exposure alone resulted in significant changes in gene expression in both the prefrontal cortex and hippocampus. Included were multiple genes related to, cell death, transcriptional regulation, neuronal signaling and neurodevelopment. Among the genes involved in neurodevelopment, Acs13 has also been shown to be variably methylated in humans according to in utero exposure to environmental factors. Prenatal alcohol exposure also altered the gene expression response to adjuvant-induced arthritis. Many genes showed a significantly different pattern of expression in ethanol-exposed animals compared to both pair-fed and control, in both prefrontal cortex and hippocampus. These genes were either differentially up- or downregulated in ethanol-exposed compared to control animals or failed to show the adjuvant-induced change in regulation shown by controls. As well, several of these genes were mediators of the response to immune or stress challenge, such as Lcn2 and Bhlhe40. Genes found to be differentially expressed in this study are potential mediators contributing to the long-term alterations in neuroendocrine and neuroimmune function observed in prenatal alcohol exposure.

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