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Genomic Medicine Research

We are very dedicated to our research. Below is a list of the projects we are currently researching.

Epigenetics Research

Imprinted gene programming and reprogramming in somatic tissues

Faulty programming of DNA methylation at imprinted loci, often in the germ line, is a prominent cause of human disease.

Epigenetic research led by the Walsh Laboratory is using mouse embryonic stem cells (ESC) as a model system to investigate whether imprints can be reprogrammed in somatic tissues.

A range of curated imprints are examined in these ESC lacking the methyltransferases DNMT1 or 3A/B, as well as rescued cells with the enzymes restored, using a range of wet-lab techniques. Potential reprogramming ability of imprints could suggest exciting avenues for possible therapeutic intervention.

Analysis of methylation patterns in methylation-defective systems

Methylation of DNA sequences at promoters, CpG islands and other elements plays a vital role in regulating gene activity. In human, loss of methylation is known to play a causative role in imprinting disorders such as Prader-Willi Syndrome (PWS) and Beckwith Weidemann Syndrome (BWS) and in inappropriate germline gene expression in cancers. As such, identifying the genes that experience differential methylation when under the influence of pharmacological demethylating treatments such as Aza, may provide valuable additional insights and/or novel biomarkers for these syndromes.

As part of a Medical Research Council (MRC) funded study the Genomic Medicine Group as part of an EWAS led approach, are using the Illumina 450k BeadChip array to assess genome wide methylation levels of in-house generated cell lines with stable knock downs of the maintenance methyltransferase DNMT1 in immortalised human adult cell lines.

A range of bioinformatics tools and software packages are used to mine the data including R and its methylation specific package-RnBeads and Galaxy. The Walsh Laboratory's use of the novel generated 450k data can correlate unique methylation signatures with pharmacological treatments and inform groups of genes sensitive to demethylation events such as the imprinted genes. The Genomic Medicine Research Group is now investigating a number of new target loci for examination in imprinted disorders and metabolic disease based on the extensive mining of this epigenome wide methylation data.

This research is supported by funding form the Medical Research Council (MRC) and the Department for Employment & Learning (DEL). For more information on this research topic published by Prof Colum Walsh:

http://dev.biologists.org/content/141/6/1313

EpiFASSTT

EpiFASSTT or Epigenetic effects on children's psychosocial development in a randomised trial of folic acid supplementation in second and third trimester, is a biopsychosocial approach investigating the effects of maternal folate status during the second and third trimester of pregnancy on cognitive, social and emotional development of the offspring.

We explore how this correlates with epigenetic changes in the genome at birth and whether these changes persist throughout the lifetime. This will reveal the extent to which environmental stressors can affect a person's future health and generate new knowledge in an area of current public health importance.

For more information about this multidisciplinary research project: http://bristol.ac.uk/integrative-epidemiology/epigenetics-social-science-network/research-projects/epifasstt/

For an exclusive interview on the Epigenetic effects of folic acid supplementation in pregnancy with Prof. Colum Walsh, a short video is available online for members; https://www.epigenomicsnet.com/users/5610-stella-bennett/videos/7104-video2

Prostate Cancer

The role of microRNAs in Disease

A key focus of research in the McKenna laboratory is on the role of microRNAs (miRNAs) in disease. miRNAs are small, non-coding RNA molecules that regulate gene expression by interacting with messenger RNAs (mRNAs). In various diseases, several miRNAs are abnormally expressed, raising the possibility that miRNAs will be useful for diagnosis, prognosis, and potential therapeutic intervention. Our main disease focus is prostate cancer and the functionality and novel targets of selected miRNAs are being studied to discover how they may contribute to the development and progression of cancer.  In collaboration with the Walsh lab, we are also investigating how epigenetic regulation leads to the abnormal expression of several miRNAs which drives cancer progression.

miRNAs are also stably preserved in serum, so we are particularly interested in developing miRNA serum profiling as a valuable clinical tool for monitoring disease. In collaboration with colleagues in NICHE at UU, we are measuring circulating serum levels of miRNAs as a biomarker for hypertension, a risk factor for Cardiovascular Diseases (CVD). CVDs are the leading cause of morbidity and mortality in the world and there is a clear clinical need for a novel diagnostic markers and new therapeutic interventions for CVD.

Our miRNA research projects are all aligned with the Personalised Medicine and Stratified Medicine strategic initiatives at UU.

This research is supported by funding from Department for Employment & Learning, Western Health and Social Care Trust, Innovation Office at UU and Northern Ireland Chest Heart and Stroke Association https://nichs.org.uk/. Our team members collaborate externally with a number of colleagues in academia, industry and clinical institutions.

Hypoxia in the development of Prostate Cancer

We are interested in exploring how hypoxia-related mechanisms of prostate cancer progression may explain why androgen deprivation therapy in patients often fails within 2 years. We are currently investigating how combining novel drugs with existing therapies can improve tumour growth control, and prevent subsequent relapse, by impacting upon molecular pathways in the tumour cells. In particular, we are interested in targeting cancer stem cells, which are likely to contribute to malignant progression, by using hypoxia-activated prodrugs (HAPs) and AKT inhibitors. This work involves a number of in vitro and in vivo approaches, including a reliable xenograft mouse model of tumour hypoxia, which allows us to monitor longitudinal genetic and physiological changes during treatment.

This research is supported by funding from Department for Employment & Learning and Prostate Cancer UK http://prostatecanceruk.org/ . Our team members collaborate externally with a number of colleagues in academia and industry, including collaborators in Almac Drug Discovery https://www.almacgroup.com/discovery/ and Oncotherics Ltd www.oncotherics.com/

Vision Research

Evidence Based Clinical Research

The Genomic Medicine Research Group work in close collaboration with Cathedral Eye Clinic assessing cataract and refractive surgery visual outcomes for 1000s of surgeries performed within the ophthalmic community to inform best practice.

Through extensive quality of vision, patient satisfaction, and personality trait surveys combined with thorough assessment of visual function with modern hi-tech equipment, we are able to inform practice to optimise visual outcomes post surgery for many refractive surgeries. The group also have an interest in dry eye research and continue to assess ocular surface parameters and patient satisfaction to better understand post surgical healing mechanisms.

Keratoconus is a disorder of the eye; changes within the cornea cause it to become thinner and more conical in shape (picture A). Corneal collagen cross-linking is now a realtively common procedure to treat keratoconus; it uses a vitamin B2 solution and ultra violet light to strengthen the collagen fibers in the eye by creating more cross-linking between them (picture B).

Research by the Genomic Medicine Research Group has shown the presence of 8-OHdG (a marker of oxidative oxidative nuclear DNA damage) within p63 positive basal limbal cells in the cornea (picture C). We have also shown that the ultra-violet light used to treat keratoconus causes an increase in oxidative nuclear DNA damage (picture D).

For more information on keratoconus: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3317091/pdf/JOP2012-526058.pdf

And for more information on the effects of the cross-linking treatment for keratoconus: http://bjo.bmj.com/content/98/2/270.long

Mutation Identification for Stratification of Eye Disease

Application of next generation sequencing technologies to genetic eye disease enhances diagnostic acumen, while identifying new targets for therapy. Sequencing the first human genome cost about $1 billion dollars and took over 13 years to complete. Today, the costs for whole genome sequencing have fallen to below £3000 and the whole process takes a matter of days. Concentrating on the 0.1% of the human genome that codes for proteins and functional RNAs, a technique known as whole exome sequencing, the cost falls to below £700. Advances in bioinformatics speed the analysis of the large amounts of data that are generated. For the first time it is now feasible and cost-efficient to search for the underlying genetic cause of disease, not by a step-by-step candidate gene approach, but by looking at all known causative genes and beyond simultaneously. Thus, whole genome and whole exome sequencing are increasingly being used, beyond the research laboratory, in a clinical setting to aid in the diagnosis of rare congenital disorders and solve diagnostic dilemmas.

Genomic Medicine Research Group members Atkinson, Moore, Moore, Nesbit and Maurizi are particularly interested in patients presenting with various corneal problems and application of whole exome sequencing holds some promise for discovering causative mutations and developing new treatments. As the future of medicine moves toward a more predictive and preventative strategy of approaching disease this research would facilitate screening for causative mutations and allow very personalised medicine approaches, such as gene silencing of mutant targets, to prevent disease onset and therefore stop blinding eye conditions develop.

Personalised Medicine for Blinding Eye Disease

The Genomic Medicine Research Group at Ulster focus on identifying the mutations which cause ocular surface disorders and in doing so they facilitate improved diagnosis and treatment in the ageing or diseased eye. This work has resulted in discovery of a number of highly disruptive mutations and subsequently development of preclinical models allowing assessment of gene therapy in a mutation or allele specific approach, paving the way for cutting edge therapeutics to be applied to the eye. The ultimate goal is to move forward how eye diseases are treated in the clinical setting with the ability to quickly detect the disease causing mutation, screen all family members, predict who will develop the disease and in a preventative measure treat prior to any damage to the delicate ocular surface occurs, thus retaining sight.

The group have focused on siRNA silencing of the mutant allele and are also developing some novel knock out replacement strategies. It is anticipated that a patient could be given eye drop formulations containing a very precise siRNA designed specifically for the mutation they carry and when applied to the front of the eye this siRNA will enter the cells and act almost like an eraser deleting all the mistaken, mutation encoded messengers which cause the disease symptoms to appear. This approach brings together stratified medicine and personalised treatment in what is now termed Precision Medicine. Group members involved in this area include: Moore, Moore, Nesbit, Allen, Atkinson,and Maurizi. This work is funded by two Fight for Sight UK Project grants and generous donations from the Cathedral Eye Research Foundation Belfast.

The Ageing and Cataractous Eye

Investigations into the role of the calcium-sensing receptor (CaSR) in the regulation of ionic homeostasis in the lens and functional analysis in the ageing and cataractous eye have the potential to prevent disease onset. The protective mechanisms that prevent damage to the proteins of the lens, important for transparency, become compromised as we age. Cataractous lenses have elevated concentrations of internal Ca2+ and this has been suggested to be a causal factor in cataract formation. However, the initial steps leading to loss of Ca2+ regulation remain to be established. A plausible candidate, the CaSR, is expressed in the lens epithelium, and is thus ideally positioned to detect and respond to changes in Ca2+concentration. Study of the changes in CaSRexpression and function in both human lenses and in a mutant CaSR mouse model, which develops cataracts, may help illuminate the mechanisms of derangement of lens homeostasis. Drugs that modulate CaSRfunction may therefore have therapeutic potential in the prevention of cataract formation and progression

The team working on this area includes: Lead Dr Andrew Nesbit; Professor Johnny Moore; Professor Tara Moore; Dr Sarah Atkinson; Miss Elenora Maurizi