Genome-wide gene expression analysis in black South African women who develop gestational diabetes mellitus

A thesis submitted to the Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy December 2017.Gestational diabetes mellitus (GDM) is characterized by high blood glucose levels that first develop during pregnancy. GDM has been linked with many adverse short and long term health outcomes for the developing foetus as well as for the mother. The Developmental Origins of Health and Disease (DOHaD) concept suggests that in the presence of adverse stimuli, the foetus will adapt, through epigenetic mechanisms, to ensure its immediate survival. For this reason, epigenetic modifications are emerging as mediators linking early environmental exposures during pregnancy with programmed changes in gene expression that alter offspring growth and development. The objective of this research study was to explore the role of altered gene expression and methylation in the development of GDM and determine whether these alterations are inherited by the exposed foetus. Transcriptome sequencing was performed on mRNA extracted from blood samples collected from six women with GDM and from six controls; as well as from exposed (N=6) and unexposed placenta (N=6). Genes that displayed significant (p2 and <-2) between cases and controls were identified from the blood (N=60) and placenta (N=56) datasets. Gene ontology and enrichment was performed using DAVID and PANTHER with the aim to narrow down the candidate gene lists. The ten most likely candidate genes for differential gene expression from the blood dataset were G6PD, DCXR, TKT, ALDOA, PGLS, KCNQ1, C14orf80, KCNQ1, SLC25A22 and GSK3A. Gene enrichment revealed that five of these significantly under-expressed genes (G6PD, DCXR, TKT, ALDOA and PGLS) encode enzymes in the pentose phosphate pathway (PPP). In the placental dataset the top ten candidate genes were CXCR1, CXCR2, G6PD, TKT, IGFBP-1, IGFBP-2, IGFBP-6, GGT3P, MMP12 and GLT1D1. The direction and fold change of differential expression of all twenty genes were validated using TaqMan qPCR probes. Of these twenty genes, the five most promising biological candidates (G6PD, TKT, IGFBP-1, IGFBP-2 and IGFBP-6) were identified and the level of promoter region methylation was assessed using EpiTech Methyl II PCR Assays. The level of methylation in the promoter region of G6PD in both blood and placenta tissue was found to be significantly higher (p=1.90 x 10-5 and p=1.2 x 10-11 respectively) in the case groups, correlating with decreased mRNA expression levels. There was a significant negative correlation between G6PD mRNA expression in the blood and placenta with the level of maternal glucose at fasting (p=0.006 and p=0.001, respectively), 1-hr (p=0.016 and p=0.007, respectively) and 2-hr post OG (p=0.045 in placenta). We observed a significant positive correlation between G6PD promoter region methylation in both blood and placental tissues with maternal glucose levels at fasting (p=0.023 and p=0.001, respectively) and at 1-hr post OG (p=0.001 and p=0.004, respectively). IGFBP-1 was found to be significantly under-expressed in exposed placental tissue and hypermethylated (p=1.1 x 10-6) at the promoter region when compared to unexposed samples. There was a significant negative correlation between the expression of IGFBP-1 mRNA in the blood and placenta with foetal birth weight (p=0.005 and p=0.017, respectively). Our results suggest that high glucose levels, an important characteristic of GDM, result in the disturbance of the pentose phosphate pathway, a pathway linked closely to glycolysis, and the IGF-axis, which is important in foetal growth and development. In GDM there is suppression of G6PD mRNA expression in both the blood and placental tissue which influences the pentose phosphate pathway. We hypothesize that this is mediated through an epigenetic mechanism since it is correlated with increased methylation of the G6PD promoter region. Down regulation of G6PD would suppress the PPP and reduce the levels of NADPH production, which may in turn lead to an increase in oxidative stress and an adverse outcome in the mother and foetus. With regard to the IGF-axis, our results demonstrated that IGFBP-1 and IGFBP-2 mRNA expression in the placenta may be inhibited due to the presence of high glucose and insulin levels and this decrease in mRNA expression is likely implicated in the abnormal foetal growth which is often associated with GDM. This study has provided novel insights into gene expression and DNA methylation changes in the blood of women with GDM and the placenta of their female offspring that involve genes in the PPP and the IGF-axis.LG201

A Genome-Wide association Study of Obstructive Heart Defects among Participants in the National Birth Defects Prevention Study

Obstructive heart defects (OHDs) share common structural lesions in arteries and cardiac valves, accounting for ~25% of all congenital heart defects. OHDs are highly heritable, resulting from interplay among maternal exposures, genetic susceptibilities, and epigenetic phenomena. A genome-wide association study was conducted in National Birth Defects Prevention Study participants (

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications

This work was supported by a restricted research grant of Bayer AG