Offered by The University of Melbourne Department of Paediatrics and The Murdoch Childrens Research Institute
To find out more about our course and our projects, please come to our Information Night:
Wednesday, 3rd September 2008 5.30pm
10th Floor Seminar Room
Murdoch Childrens Research Institute
Royal Children's Hospital
Refreshments provided.
Please note that the project list will be updated regularly with new projects and opportunities.
- Using children's genes in research
- The ethics of surgically assigning sex to children
- Research, young people and the internet
- Establishing whether the gene polymorphism responsible for Crohns disease in the mouse has a role in promoting human inflammatory bowel disease.
- Genes which prevent cancer development: how gastrokine 2 (GKN2) acts as a tumour suppressor gene.
- The role of IL-11 in promoting the gastric cancer phenotype.
- Tumour associated macrophages and gastric cancer
- Characterisation of a novel gene and mouse model of ciliary dyskinesia
- Determining of the molecular basis of childhood dystonia
- Investigations into chromosome instability and human disease predisposition
- Novel mechanisms of chromosome and genome regulation and disease aetiology
- Gene regulation studies of the Friedreich ataxia locus
- Epigenetic factors in Friedreich ataxia
- Folate supplementation, neurodevelopment and epigenetics
- Epigenetics of mammalian germ and stem cell development
- Identification of genes involved in disorders of sexual development
- Identification and classification of elements regulating genes involved in gonadal differentiation
- Cardiac molecular signaling mechanisms during the progression of heart failure
- Dissecting Survival And Apoptosis Pathways In Myeloid Cells
- The role of saturated and unsaturated fatty acids in the development of childhood obesity, and subsequent risk of Type 2 diabetes.
- Growth Factor CheckPoints in Neuroblastoma Cells Tumorigenesis: Cellular and Molecular Mechanisms
- Major or minor birth defects? Hospitalisations as a measure of morbidity.
- Helping broken bones heal
- The mechanisms of airway remodelling in asthma
- Experiences of a genetic counselling intervention to facilitate communication within families
- Identifying the molecular mechanisms underlying a common craniofacial disorder, Pierre Robin Sequence
- Examination of Pneumococcal Immune Responses
- Neuropathogenic mechanisms of mitochondrial dysfunction
- Dissecting the role of IGF Binding Proteins in adipogenesis and insulin resistance.
- Characterization of rare or novel rotavirus strains causing acute diarrhoea in Australian children.
- Understanding the role of infectious agents in children with early onset Crohn’s disease
- Characterisation and treatment of mice with mitochondrial cardiomyopathy
- FUNKY MICE AS A MODEL FOR MITOCHONDRIAL DISORDERS
- Stop codon readthrough in a mouse model of MMA
- Stem cell transplantation for the treatment of MMA
- Pharmacological upregulation of MUT for the treatment of MMA
- Hearing loss: why?
- Gene expression in ear hair cells
- RNA interference therapy: Applications in ß-thalassaemia
- Genetic and Epigenetic Regulation of the Structure and Function of Human Chromosomes
- Epigenetic factors that regulate the chromatin at the telomeres in pluripotent embryonic stem cells.
- Stem cells and gene therapy: Targeted integration of functional genomic loci
- Discovering novel genes that cause childhood mitochondrial disorders.
- Investigating the role of altered methylation in schizophrenia
- Epigenetics and the interaction between folate and vitamin D metabolism at the fetomaternal interface
- Is there an association between altered epigenetic profile in first trimester placenta with adverse pregnancy outcome?
- The role of Epigenetics in Paediatric Leukaemia development and outcome.
- mRNA surveillance in human disease: How cells detect and degrade deleterious mutant mRNA (nonsense-mediated mRNA decay)
- How do type I collagen mutations cause brittle bone disease?
- How do cancer cells move in tissues?
- Control of neural crest stem cells migration in 3D tissue: clues to understand Hirschsprung’s Disease
- Experimental arthritis in genetically-modified mice
- Arthritis studies: Identifying the mechanism of ADAMTS-5 action in ADAMTS-5 null, ADAMTS-5-deficient and ADAMTS-5-resistant mice
- Characterisation of the functional role of PArkin Co-Regulated Gene (PACRG)
- Understanding the immunological properties of cord blood derived-multilineage stem cells
- Understanding the haemostatic system in neonates and children
- Mapping neural control of human intestine: cholinergic innervation
- How does neural innervation of the intestine change with age?
- TICTOC trial: use of trancutaneous stimulation to speed up the bowel in children with chronic constipation.
- Developing a pig model to study intestinal motility and effects of electrical stimulation.
- Neural and motility defects following surgical removal of the bowel.
- Memory outcomes following fetal exposure to anti-epileptic medications
- Mothers’ perception of long-term effects of drugs taken during pregnancy
- Neuropsychological profiles of children with B12 deficiency
1. Using children's genes in research
| Dr Merle Spriggs Ethics Laboratory and Community Genetics T 90905237 E merle.spriggs@mcri.edu.au |
A/Professor Lynn Gillam Ethics Laboratory and Community Genetics T 0417 536 785 E l.gillam@unimelb.edu.au |
Increasingly, genetic testing of children is becoming part of pediatric research. While a considerable amount of attention has been paid to the ethics of predictive testing in children for adult onset conditions there is little written about the ethical conduct of pediatric genetic research, especially that involving complex behavioural traits.
Questions that arise include:
• Is it ethically acceptable to enroll children and young people in gene-based prevention trials for traits such as obesity, addiction and ADHD?
• When is it ethically defensible for a parent to consent to their child taking part in such research?
Ethical issues include competence, proxy consent, autonomy and developing autonomy, best interests, discrimination, stigma, privacy, genetic determinism and the right not to know.
This project could be literature based, interview based or based on a questionnaire. The precise topic is negotiable and the methods are negotiable.
2. The ethics of surgically assigning sex to children
| Dr Merle Spriggs Ethics Laboratory and Community Genetics T 9090 5237 E merle.spriggs@mcri.edu.au |
A/Professor Lynn Gillam Ethics Laboratory and Community Genetics T 0417 536 785 E l.gillam@unimelb.edu.au |
Intersex conditions are variously referred to as ‘developmental anomalies of the external genitalia’, ‘atypical sexual differentiation’, and ‘ambiguous genitalia’. Controversy surrounding the surgical management of intersex conditions in newborns is an important ethical issue because it:
• Raises questions about the authority of parents and others to make irrevocable decisions for young children
• Tests the idea that surgery is only justified when it is for disease or malfunction
• Raises questions about what constitutes disease or malfunction
• Poses questions about what we should base treatment decisions on when there is little guidance in terms of evidence of outcomes
• Illustrates the shift from physician-centred medicine and paternalism to patient-centred medicine
• Highlights the need for evidence in the form of systematic outcome studies
This project could be literature based, interview based or based on a questionnaire. The precise topic is negotiable and the methods are negotiable.
3. Research, young people and the internet
| Dr Merle Spriggs Ethics Laboratory and Community Genetics T 9090 5237 E merle.spriggs@mcri.edu.au |
A/Professor Lynn Gillam Ethics Laboratory and Community Genetics T 0417 536 785 E l.gillam@unimelb.edu.au |
Internet communities and personal webspaces are a rich source of qualitative data for health and social researchers. It is a particularly fertile source for those whose research areas involve children and young people. Although there is some guidance for conducting research online, there are no detailed or universally accepted ethics guidelines for research of homepages, blogs or webspaces such as MySpace. Questions that arises are – “If MySpace is a public webspace, can research be done without consent?” “If it is thought that consent should be obtained, how should it be obtained in this context?” Most teenagers use the internet without parental supervision and generally, researchers can use information that is in the public domain without obtaining consent. On the internet however, what is public and what is private is not so clear. Added to this, are the difficult issues around consent in research involving children and young people. In the context of research, children and young people are considered to be a vulnerable population requiring special protection such as consent from a parent or guardian. The immature judgment of some young people may also mean that a distinction between private and public is not meaningful. This project will investigate and analyse the ethical issues, especially consent issues in research involving internet spaces in which children or young people participate. The precise topic and the methods used can be negotiated with the supervisors
| Dr Louise Judd Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 99366501 E lmj@unimelb.edu.au |
Professor Andrew Giraud Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 83416446 E andrew.giraud@mcri.edu.au |
The human inflammatory bowel diseases, Crohns disease and ulcerative colitis, are debilitating gut conditions which are becoming more prevalent in children, and increase the chance of development of colorectal cancer in adulthood. In order to better understand the genetic contribution to disease development, we are currently developing a new mouse model of Crohns disease by screening mice derived from an ENU mutagenesis screen at the Australian Phenomics Institute in Canberra. The Crohns disease mouse has a single point mutation, and mapping studies which will pin-point the gene responsible are almost complete. The aim of this project will be to characterize the gene mutation, develop a genotyping assay to detect it and to work out how a polymorphism in the affected gene causes inflammation-associated pathology. A further aim of this project is to determine if the affected mouse gene is also mutated in humans. In collaboration with A/Prof Ian van Driel (BIO21).
5. Genes which prevent cancer development: how gastrokine 2 (GKN2) acts as a tumour suppressor gene.
| Dr Trevelyan Menheniott Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 99366502 E treve.menheniott@mcri.edu.au |
Professor Andrew Giraud Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 83416446 E andrew.giraud@mcri.edu.au |
Gastric cancer is the second biggest cause of cancer mortality in the world. It is caused mainly by chronic infection by the bacterium H. pylori, and is promoted by chronic inflammation in childhood in susceptible individuals. We have established that the protein GKN2 is highly expressed by the mouse and human gastric mucosa, and that its expression is strongly suppressed in cancer development. Moreover, H. pylori infection, which promotes gastric ulceration, inflammation and cancer, produces a dramatic fall in GKN2 expression.We have also shown that this suppression can be reversed by using new experimental drugs. This project will use the GKN2 knockout mouse, cell lines transfected with GKN2 or mutant versions of the protein, GKN2 DNA probes and antibodies, and drugs that increase GKN2 expression, to evaluate how this protein can be manipulated to reverse tumour growth.
6. The role of IL-11 in promoting the gastric cancer phenotype.
| Dr Louise Judd Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 99366501 E lmj@unimelb.edu.au |
Dr Trevelyan Menheniott Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 99366502 E treve.menheniott@mcri.edu.au |
We have recently established that IL-11 is the most important cytokine driving gastric tumour development in our mouse model of gastric cancer, and importantly that increased expression is associated with human gastric adenocarcinoma development. This project will establish the gene targets for IL-11 in the stomach, which gastric cells synthesise IL-11, and how H. pylori infection induces IL-11 activation to promote stomach pathology.
7. Tumour associated macrophages and gastric cancer
| Dr Louise Judd Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 99366501 E lmj@unimelb.edu.au |
Professor Andrew Giraud Gastrointestinal Research in Inflammation and Pathology (GRIP) Infection, Immunity and Environment T 83416446 E andrew.giraud@mcri.edu.au |
We know that tumour associated macrophages play a key role in promoting tumour growth in a number of different cancers, however very little is known of these cells in the development and progression of gastric cancer. Out lab is uniquely placed to study gastric cancer with a well characterized mouse model, the FF model that develops cancer dependent on the activation of the oncogenic transcription factor STAT3. In this model the presence of macrophages in the stomach is crucial for cancer development. Recently we have developed systems in the FF model to specifically reduce activation of STAT3 in macrophages. The aims of this project are twofold, the first is to analyse the phenotype of these macrophages in vitro to determine how crucial STAT signaling is to cell function and the second will examine the gastric tumour outcome in the FF mice that lack the ability to signal through STAT3 in macrophages.
8. Characterisation of a novel gene and mouse model of ciliary dyskinesia
| Dr Paul Lockhart Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 61-3-8341 6322 E paul.lockhart@mcri.edu.au |
A/Professor Martin Delatycki Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 61-3-8341 6284 E martin.delatycki@ghsv.org.au |
Cilia are evolutionarily conserved microtubule-based hair-like organelles that project from nearly all mammalian cell types. Although they perform remarkably diverse functions they share a similar basic structure, consisting of a basal body, axoneme and ciliary membrane. Defects in cilial function have classically being associated with human phenotypes such as neural tube and patterning defects, male infertility and sinusitis. However, recent studies have broadened the range of associated syndromes and phenotypes to include obesity, diabetes and hypertension. There is limited understanding of the genes and proteins involved in the formation and function of cilia, but recent studies have taken advantage of mice models to study the pathogenesis of ciliary dysfunction in vivo. We have identified a novel mouse model characterised by male infertility and hydrocephalus (enlarged ventricles within the brain). We have identified the defective gene and have preliminary data suggesting it is a key protein required for the functioning of motile cilia. This project will utilise a range of molecular and cellular techniques to characterise the phenotype of the mouse and determine the molecular function of the gene involved.
9. Determining of the molecular basis of childhood dystonia
| Dr Paul Lockhart Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 83416322 E paul.lockhart@mcri.edu.au |
Dr Kirstee Martin Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 83416286 E kirstee.martin@mcri.edu.au |
Dystonia is a common movement disorder which is characterised by involuntary sustained muscle contractions and abnormal movement. The condition affects approximately 1 in 5000 people, but remains poorly understood with limited treatment options.
Mutation of the TorsinA gene causes dominant early-onset general torsion dystonia, the most common heritable form of the disease. TorsinA is highly expressed in a subset of neurons within the brain, particularly the basal ganglia and associated motor circuits. Although the normal function of TorsinA is currently unknown we have preliminary data suggesting the protein functions as a chaperone and transports substrates within the neuron. We have performed a 2-hybrid screen and identified several proteins that interact with TorsinA. The aim of this project is to further characterise these interacting proteins and investigate their contribution to the disease phenotype. The project will involve a range of molecular and cellular techniques, initially utilising cellular models. In addition, we have established colonies of transgenic mice with specific defects in the TorsinA gene. These mice will allow us to identify the molecular pathways disrupted during disease and provide the means to develop and test novel therapeutic treatments.
10. Investigations into chromosome instability and human disease predisposition
| Dr Paul Kalitsis Chromosome and Chromatin Research Laboratory and Community Genetics T 83416300 E paul.kalitsis@mcri.edu.au |
Professor KH Andy Choo Chromosome and Chromatin Research Laboratory and Community Genetics T 83416306 E andy.choo@mcri.edu.au |
Approximately 10 quadrillion cell divisions occur in the lifetime of a human. Each divisional event requires the accurate distribution of the newly-replicated chromosomes to the daughter cells. Any faults occurring during this process can cause an imbalance in chromosome number and lead to clinical conditions such as Down syndrome, pregnancy loss, infertility, and cancer. Our laboratory investigates the cellular and molecular mechanisms that are responsible for such chromosome imbalances. One project involves the use of a fluorescent protein chromosome instability mutant screening assay in mouse embryonic stem cells to identify genes and environmental agents that contribute to chromosome missegregation events. Another project uses affinity purification and mass spec/proteomic techniques to identify novel chromatin protein components using known essential chromosome proteins as affinity baits. We anticipate finding many new genes/proteins whose functions will be further studied using techniques such as RNAi gene knockdown and gene knockout in cells and mice. These studies are expected to contribute important new insight into key mechanisms regulating chromosome stability and their potential role in causing the plethora of known chromosome-related human diseases.
11. Novel mechanisms of chromosome and genome regulation and disease aetiology
| Dr Damien Hudson Chromosome and Chromatin Research Laboratory and Community Genetics T 83416300 E damien.hudson@mcri.edu.au |
Professor KH Andy Choo Chromosome and Chromatin Research Laboratory and Community Genetics T 83416306 E andy.choo@mcri.edu.au |
In order for our genetic material to be faithfully segregated into two daughter cells, the chromosomes must compact nearly 10,000 fold. Prior to this event chromosomes are an amorphous mass of DNA, but upon compaction they form visible X-shaped structures known as mitotic chromosomes.
A key component in this process is a multi subunit complex termed condensin. The aims of this project are to understand how condensin directs chromosome condensation and to find which components condensin interacts using gene knockout technology, and integrated proteomics and biochemistry. Furthermore we aim to look at the non-mitotic roles of condensin where a growing body of evidence suggests condensin has key roles in gene regulation and DNA repair. Critically malfunction of condensin is associated with human disease including cancer and immune deficiency. We expect to find novel interactors contributing to chromosome structure and to understand the mechanism of action of condensin and how it might contribute to disease.
12. Gene regulation studies of the Friedreich ataxia locus
| Dr Joseph Sarsero Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 8341-6285 E joe.sarsero@mcri.edu.au |
A/Professor Martin Delatycki Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 8341-6284 E martin.delatycki@ghsv.org.au |
Friedreich ataxia (FRDA) is an autosomal recessive disorder characterised by neurodegeneration and cardiomyopathy. The presence of a GAA trinucleotide repeat expansion in the first intron of the FXN gene results in an insufficiency of the mitochondrial protein, frataxin. An understanding of FXN gene regulatory mechanisms may enable upregulation of FXN expression as a form of therapy for FRDA. Our laboratory has been undertaking the identification of long-range cis-acting regulatory elements controlling human FXN gene expression by: i) the targeted deletion of conserved non-coding sequences in an FXN-EGFP genomic reporter construct, and ii) the generation of nested deletions of DNA sequences upstream of the FXN gene fused to a reporter gene. This project will build on our current findings and further delineate regions involved in FXN gene regulation. The project will involve a range of molecular and cellular techniques.
13. Epigenetic factors in Friedreich ataxia
| Dr Joseph Sarsero Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 8341-6285 E joe.sarsero@mcri.edu.au |
A/Professor Martin Delatycki Genetic Health Research (Bruce Lefroy Centre) Laboratory and Community Genetics T 8341-6284 E martin.delatycki@ghsv.org.au |
Friedreich ataxia (FRDA) is an autosomal recessive disorder characterised by neurodegeneration and cardiomyopathy. The presence of a GAA trinucleotide repeat expansion in the first intron of the FXN gene results in an insufficiency of the mitochondrial protein, frataxin. Evidence suggests that the mutation may induce epigenetic changes and heterochromatin formation, thereby impeding gene transcription. This project will examine the correlation between the age of onset and severity of disease symptoms with the size of the GAA expansions, transcript levels, the amount of residual frataxin produced, and DNA methylation patterns. The project will involve a range of molecular and cellular techniques including PCR, real-time RT-PCR, western blot, lateral flow (dipstick) immunoassays and bisulfite sequencing. These studies are expected to contribute new insights into the mechanisms involved in mediating gene silencing in FRDA.
14. Folate supplementation, neurodevelopment and epigenetics
| Dr Richard Saffery T 8341 6341 E richard.saffery@mcri.edu.au |
Dr David Godler T 8341 6307 E david.godler@mcri.edu.au |
DNA methylation has been implicated in chromatin condensation, regulation of global transcriptional activity and nuclear organization. Folate is a principal methyl donor in the majority of biochemical reactions, and is an indirect substrate for S-adenosyl-L-methionine (SAM). Although folate deficiency can cause genome-wide DNA hypomethylation through depletion of SAM; limited folate intake has been also shown to induce silencing of many tumour suppressor genes, attributed to regional hypermethylation. To date the molecular relationship between these two paradoxical phenomena is unknown, however it indicates presence of a finely tuned regulatory mechanism of site-specific epigenetic changes affected by folic acid supplementation – a mechanism that is evident from our preliminary findings. Furthermore, there is ample evidence to suggest that these disturbances result in aberrant gene expression associated with abnormal neurodevelopment. This project aims to study the epigenetic bases behind the neurodevelopmental defects associated with folate over or under supplementation in a mouse model, with a longer-term view to extend the study to humans.
15. Epigenetics of mammalian germ and stem cell development
| Dr Jeffrey Mann Stem Cell Epigenetics Laboratory and Community Genetics T 9936 6516 E jeff.mann@mcri.edu.au |
2nd supervisor's name is missing |
The health of reproductive stem cells can be measured by genetic integrity, that is, are there mutations in the DNA code which can lead to congenital abnormalities? Also, their health can be measured by epigenetic integrity, epigenetics being the overlying system of regulatory controls of genes or DNA sequence. Germ cells are unique in undergoing a large scale rebuilding of their epigenetic architecture, in preparation for their own unique developmental programme, and for the developmental programme of the fertilised egg. In doing so, mistakes can be made (epimutations), and these can be as severe in consequence as genetic mutations. The aim of our research is to find out more about how and why reproductive stem cells undergo this large scale rebuilding of epigenetic systems. Also, how mistakes are made in this process, and how these may affect the development of germ cells and embryos. Please contact Jeff Mann for further information on specific projects.
16. Identification of genes involved in disorders of sexual development
| Professor Andrew Sinclair Molecular Development Early Development and Disease T 83416424 E andrew.sinclair@mcri.edu.au |
Dr Stefan White Molecular Development Early Development and Disease T 83416426 E stefan.white@mcri.edu.au |
Intersex disorders, ranging in severity from genital abnormalities to complete sex reversal, are surprisingly common and as such represent a major paediatric concern. The cause of these problems is most often the failure of the complex network of genes that regulate development of testes or ovaries. Our research seeks to understand the molecular basis of testis and ovary development and how mutations in key genes can lead to abnormalities. Mutations in known genes explain 20% of intersex cases but we have no explanation for the remaining 80%. DNA samples from >50 sex-reversed patients with gonadal dysgenesis (XX males and XY females) have been collected, and we are currently applying a range of powerful methodologies to look for mutations in these patients. These techniques include screening for deletions and duplications using high-density microarrays and multiplex ligation-dependent probe amplification, and identifying sequence changes using high-throughput deep sequencing and DNA denaturation analysis.
| Professor Andrew Sinclair Molecular Development Early Development and Disease T 83416424 E andrew.sinclair@mcri.edu.au |
Dr Stefan White Molecular Development Early Development and Disease T 83416426 E stefan.white@mcri.edu.au |
| Dr Thomas Ohnesorg T 83416426 E |
Intersex disorders, ranging in severity from genital abnormalities to complete sex reversal, are surprisingly common and as such represent a major paediatric concern. The cause of these problems is most often the failure of the complex network of genes that regulate development of testes or ovaries. However, we understand relatively little of this regulatory network. Our research seeks to understand the molecular basis of testis and ovary development and how key genes are regulated. We are currently studying regulatory elements controlling a range of genes involved in gonadal differentiation. Methods that are being applied include DNaseI hypersensitivity analysis, Chromatin Immunoprecipitation and reporter assays. Other methods involved include cell culture, (quantitative) PCR and expression analysis.
18. Cardiac molecular signaling mechanisms during the progression of heart failure
| Dr Salvatore Pepe Heart Research Critical Care and Neurosciences T 93454114 E salvatore.pepe@mcri.edu.au |
A/Professor Joe Smolich Heart Research Critical Care and Neurosciences T 93454571 E joe.smolich@mcri.edu.au |
| Professor Dan Penny T 93455922 E |
Congenital and acquired myocardial disorders, despite diverse etiology, commonly involve a reduced capacity to manage oxygen and nitrogen free radical metabolism. Chronic augmented oxidative stress, particularly in fetal and neonatal development, not only leads to post-translational structural modification of proteins, but also impacts gene transcription, ultimately with consequences to structural, metabolic and functional remodeling during adaptive and maladaptive heart failure. These pathological changes remain to be well defined in the developing heart at molecular and cellular level in order for potential therapeutic targets to be identified. Students ideally should have a background in at least one of the following: biochemistry, immunology, genetics or pharmacology. Studies will explore novel molecular signaling pathways (intracellular/mitochondrial/nuclear) using unique in vitro and ex vivo models and a range of immunohistochemical, biochemical, molecular, genetic and cell biology methods.
19. Dissecting Survival And Apoptosis Pathways In Myeloid Cells
| A/Professor Paul Ekert Cancer Early Development and Disease T 93455008 E paul.ekert@rch.org.au |
Dr Anissa Jabbour Cancer Early Development and Disease T 93455835 E anissa.jabbour@mcri.edu.au |
Growth and survival of haemopoietic cells is regulated by growth factors such as Interleukin-3 (IL-3). When IL-3 is removed, dependent cells kill themselves by a mechanism that can be regulated by the Bcl-2 family of apoptosis regulators. The genes that regulate this process are likely to be important in the development of leukaemia since leukemic cells acquire the ability to survive and proliferate independently of growth factors. We have identified members of the Bcl-2 family that are required for apoptosis to occur in the absence of IL-3 and also genes that couple growth factor signalling to the survival of haemopoietic cells. Some of these genes do, as predicted, have important roles in myeloid leukaemia. The projects in the laboratory seek to determine how growth factors promote cell survival, and how the genes we have identified are regulated by growth factor signalling. The projects will provide students with opportunities to master a wide range of cell biological and molecular biological techniques, including PCR, cloning, tissue culture, flow cytometry, confocal microscopy, Western blotting and co-immunoprecipitation. In addition, students will learn about gene expression techniques and gene discovery, as they address the importance of various genes in the biology of tumours such as leukaemia.
| Dr Matthew Sabin Hormone Research Early Development and Disease T 93456986 E matthew.sabin@mcri.edu.au |
Dr Vincenzo Russo Hormone Research Early Development and Disease T 93457931 E vince.russo@mcri.edu.au |
| Professor George Werther T 93455951 E |
Childhood obesity is increasing in prevalence and is associated with insulin resistance and Type 2 diabetes in susceptible individuals. At the MCRI, we have recently developed a major cross-theme research group (http://www.mcri.edu.au/projects/m-powr/default.asp) to investigate the questions of: which children are most at risk of developing obesity, and which are then most likely to develop co-morbidities?
Insulin resistance is known to be an important factor in the predisposition to future disease in obese individuals. The effect of different dietary factors on the development of insulin resistance in childhood is, however, extremely difficult to investigate in large populations of children, due to so many other confounding factors. We have therefore developed a unique juvenile pig model with which to assess dietary influences on adiposity/insulin resistance.
The first of these studies has recently been completed with pigs fed (from weaning) different dietary fats and sugar. All tissue samples and bloods have been obtained and samples are cryopreserved and ready for analysis. There will therefore be no delay in obtaining ethics/obtaining samples for this project.
Specifically, we hypothesise that juvenile pigs fed saturated fats will become centrally obese and insulin resistant, whilst pigs fed unsaturated fats will become generally obese and not insulin resistant. The role of increased sugar in the diet in these processes is unknown. Adipose tissue biopsies will be examined for the relative mRNA concentrations of Fatty Acid Synthase and Stearoyl CoA Desaturase (major enzymes controlling lipogenesis) and muscle samples will be analysed for factors important in insulin signalling. These data will demonstrate, along with the body composition data and measures of insulin sensitivity (already measured using DEXA and hyperinsulinaemic euglycaemic clamps respectively), how diets in early life impact upon future risk of obesity and Type 2 diabetes.
The successful applicant will be involved in the whole process from decision-making (e.g. choice of analyses), to undertaking laboratory work and assisting in the writing of publications & data presentation.
| Dr Vincenzo Russo Hormone Research Early Development and Disease T 93457931 E vince.russo@mcri.edu.au |
Professor George Werther Hormone Research Early Development and Disease T 93455951 E george.werther@rch.org.au |
Neuroblastoma is a common and devastating childhood cancer, highly invasive and resistant to treatment. Cells derived from these tumours are undifferentiated aggressive and disseminating. By modulating the growth factor environment of these cells we have discovered a number of critical genes involved in arrested differentiation, proliferation and motility of neuroblasts. The products of these genes control key cell cycle checkpoints, intracellular signaling and the activation of modulators of the extracellular matrix. We aim to dissect further these cellular and molecular mechanisms, particularly those related to the cell cycle and growth factor / cytokine signaling and reorganization of the extracellular matrix.
The methodological approach includes: cell cycle analysis by FACS; RNA extraction & molecular hybridisation (real time PCR and gene-array): functional gene analysis with validated siRNA: nuclear extracts and gel shift assay (EMSA); cell extracts, receptor activation and signaling pathway analysis (immunoblotting, phospho- protein, pathway inhibitors, etc): signaling-protein interactions using wild type and mutated signaling molecules. This project is designed for Ph.D. candidates (3 years), however part of these studies are suitable to be developed as Hons projects (1 year).
22. Major or minor birth defects? Hospitalisations as a measure of morbidity.
| A/Professor Jane Halliday Public Health Genetics Laboratory and Community Genetics T 83416260 E jane.halliday@mcri.edu.au |
Ms Evelyne Muggli Public Health Genetics Laboratory and Community Genetics T 83416291 E evi.muggli@mcri.edu.au |
The project will utilise an administrative dataset to identify cases with one of two selected birth defects and follow their hospitalisation patterns over time. This will give us the opportunity to monitor the impact of these conditions over the course of the children’s lives. The results of this study will provide us with important information to inform health policy, better plan for services and direct future research on the clinical management of these children.
Two examples of birth defects to be studied:
• Hypospadias are among the most common birth defects of the male genitalia, involving an abnormally placed urinary opening. While hypospadias is generally considered a ‘mild’ birth defect, there are degrees of severity and the impact of this condition on the course of a child’s life is not well documented. The prevalence of hypospadias in male babies is 40 per10,000.
• Tetralogy of Fallot (TOF) is a congenital heart defect, involving three to four anatomical abnormalities. TOF is the most common cause of the cyanotic ‘blue baby’ syndrome. Total surgical repair is possible, but surgical success and long-term outcome vary and lifetime follow-up is necessary. TOF occurs in approximately 3-6 births per 10,000.
| A/Professor Amanda Fosang Arthritis and Rheumatology Musculoskeletal Disorders T 83416466 E amanda.fosang@mcri.edu.au |
Dr Kumara Kaluarachchi Arthritis and Rheumatology Musculoskeletal Disorders T 83416431 E kumara.kaluarachchi@mcri.edu.au |
| Dr Stephanie Gauci T 83416431 E |
The cost of skeletal fractures to society is monumental and any improvement in the rate or extent of fracture healing will produce an enormous socioeconomic benefit. When bones fracture, blood from the bone and surrounding tissue forms a clot, which is invaded by fibroblasts and cartilage progenitor cells. The next phase of repair is the formation of a soft cartilage callus that stabilises the fractured bone. Gradually this soft callus is mineralised and the cartilage template is resorbed and replaced by woven bone, and finally by mature lamellar bone. This project will focus on the cartilage callus. Very little is known about how the callus is resorbed and replaced, yet without this process the bone cannot heal. We have developed a mutant mouse strain with a genetic defect in cartilage remodelling. The mice are unique in the world and are ideally suited to the study of callus formation and bone repair. The project will use an in vivo fracture model to identify mechanisms critically important for bone healing. The study aims to identify molecules and/or pathways that can be developed as therapies for improving the rate and quality of bone healing in fractures.
24. The mechanisms of airway remodelling in asthma
| Dr Simon Royce Allergy and Immune Disorders Infection, Immunity and Environment T 93456882 E simon.royce@mcri.edu.au |
A/Professor Mimi Tang Allergy and Immune Disorders Infection, Immunity and Environment T 93455911 E mimi.tang@rch.org.au |
Airway remodelling refers to the structural changes that occur in the airways of asthmatics. During the pathogenesis of this disease airway remodelling results in thickening of the airway wall, and the consequent reduction in luminal diameter results in worsened lung function and susceptibility to death in the event of an asthma attack. However, the sequence and aetiology of interrelated remodelling changes are not well elucidated. This project will investigate the mechanisms by which airway remodelling occurs and the specific contributions of inflammatory markers, cytokines and matrix proteins and their regulators to this process. Much of this work will be done in vitro using lung fibroblasts and epithelial cells, with tissue also available from biopsies and animal models of asthma. Real time PCR, ELISA and morphological techniques will be used.
25. Experiences of a genetic counselling intervention to facilitate communication within families
| A/Professor Sylvia Metcalfe Genetics Education and Health Research Laboratory and Community Genetics T 83416309 E sylvia.metcalfe@mcri.edu.au |
Dr Jan Hodgson Genetics Education and Health Research Laboratory and Community Genetics T 83416308 E jan.hodgson@mcri.edu.au |
| A/Professor Clara Gaff T 83416241 E |
We are conducting an NHMRC funded project of a randomised controlled trial of a genetic counselling intervention to facilitate communication to at risk family members after diagnosis and genetic testing of an inherited condition.
Utilising a qualitative approach the project will aim to explore the experiences of the trial participants and health professionals carrying out the intervention.The findings will form part of the process evaluation for the study.
| Dr Peter Farlie Craniofacial Research Musculoskeletal Disorders T 8341 6409 E peter.farlie@mcri.edu.au |
Christopher Gordon Craniofacial Research Musculoskeletal Disorders T 8341 6418 E christopher.gordon@mcri.edu.au |
Pierre Robin Sequence (PRS) is a common craniofacial disorder consisting of small lower jaw, posteriorly placed tongue and cleft secondary palate. These defects lead to serious feeding and respiratory difficulties in infants. The underlying cause is thought to involve inadequate growth of the facial skeleton during embryonic stages. In several PRS patients, we have identified chromosomal translocations and microdeletions far upstream of SOX9, a gene encoding a transcription factor with known roles in the development of the craniofacial skeleton. We have hypothesised that in PRS patients, these chromosomal lesions remove DNA regulatory elements that normally act over a large genomic distance to drive SOX9 expression in craniofacial tissues. This Honours project will address the following questions: Where exactly do the regulatory elements exist in the genomic sequence upstream of SOX9? In which embryonic tissues do the elements drive SOX9 expression? Which signalling pathways and transcription factors converge on these elements to co-ordinate SOX9 expression? The project will involve cross-species genomic sequence analysis and construction and electroporation of GFP reporter plasmids into chicken embryos to enable tissue-specific expression to be visualised. This project has the potential to uncover the molecular mechanisms of a human disease, and will provide a solid grounding in developmental biology techniques.
27. Examination of Pneumococcal Immune Responses
| Dr Paul Licciardi Allergy and Immune Disorders Infection, Immunity and Environment T 93455554 E paul.licciardi@mcri.edu.au |
Anne Balloch Allergy and Immune Disorders Infection, Immunity and Environment T 93456419 E anne.balloch@mcri.edu.au |
| A/Professor Mimi Tang T 93455911 E |
Pneumococcal disease is a significant global health problem with approximately one million child deaths each year. Infection with the bacterium Streptococcus pneumoniae (pneumococcus) can lead to invasive pneumococcal diseases (IPD) such as pneumonia, meningitis and bacteraemia. Polysaccharides on the capsule of the organism (of which there are 91 different serotypes) are the predominant virulence factor and are included in pneumococcal vaccines to elicit specific antibody-based protection. The Pneumococcal Laboratory at MCRI is currently undertaking a large-scale clinical trial in Fiji (FiPP Study; NHMRC and NIH funded) based on alternative pneumococcal vaccination strategies. Recent studies in the laboratory have identified specific antibodies that cross-react with several different pneumococcal serotypes. New-generation immunoassays measuring the specific antibody response are essential for accurate interpretation of clinical outcomes following vaccination. This project will further examine the role of cross-reactivity on pneumococcal immunity and the correlation with functional antibody capacity. Experimental techniques used in this project include indirect and competition ELISA as well as functional antibody avidity measurement and/or in vitro opsonophagocytic assays.
28. Neuropathogenic mechanisms of mitochondrial dysfunction
| Dr Denise Kirby Mitochondrial & Metabolic Research Laboratory and Community Genetics T 83416234 E denise.kirby@mcri.edu.au |
A/Professor David Thorburn Mitochondrial & Metabolic Research Laboratory and Community Genetics T 83416235 E david.thorburn@mcri.edu.au |
Mitochondrial dysfunction causes a range of early-onset neurological conditions and contributes to neurodegenerative conditions such as Parkinson Disease. The mechanisms of neuronal damage are unknown, and study of these at a cellular level may lead to improved treatment and greater understanding of the role of both nuclear- and mitochondrial-DNA mutations in both rare and common conditions. This project will focus on the most common respiratory chain defect, complex I deficiency, by characterising two cell culture models of complex I deficiency:
1. Olfactory stem cell cultures derived from nasal epithelial biopsies from patients with mtDNA mutations affecting complex I activity or with Parkinson disease, which can be differentiated into neurons and glia.
2. Neural cell cultures from two mouse models with complex I deficiency due to mutations in two different nuclear complex I subunits.
We will study the effects of mutations on mitochondrial membrane potential, reactive oxygen species, ATP production and cellular calcium dynamics. Such studies could highlight potential therapeutic approaches and allow us to monitor the effects of therapy.
29. Dissecting the role of IGF Binding Proteins in adipogenesis and insulin resistance.
| Dr Vincenzo Russo Hormone Research Early Development and Disease T 93457931 E vince.russo@mcri.edu.au |
Dr Matthew Sabin Hormone Research Early Development and Disease T 93456986 E matthew.sabin@mcri.edu.au |
| Professor George Werther T 93455951 E |
Excessive pre-adipocyte proliferation, and subsequent differentiation into mature adipocytes, is a key step in the development of obesity. The Insulin-like Growth Factor (IGF) system plays a crucial role in these processes, with the IGFs being potent promoters of adipocyte differentiation. The biological actions of IGFs are modulated by a family of IGF-binding proteins (IGFBPs), with IGFBP-2 being the most abundant IGFBP secreted by differentiating pre-adipocytes. Overexpression of IGFBP-2 in transgenic mice is associated with reduced susceptibility to obesity and improved insulin sensitivity, thus suggesting a potential role for IGFBP-2 in the inhibition of adipogenesis. Conversely, mice overexpressing a mutant form of IGFBP-2, uniquely developed by this laboratory, have increased fat deposition. The nature of the IGFBP-2 mutation suggests that this regulation of adipogenesis is IGF independent – ie it is due to a unique action of IGFBP2. The precise mechanism, however, remains unclear and is the focus for this novel project.
In order to investigate this, we propose to use a murine pre-adipocyte cell line (3T3-L1) in which to examine how pre-adipocyte differentiation is altered in the presence of either normal IGFBP-2 or a set of uniquely developed IGFBP-2 mutants.
The methodological approaches include: pre-adipocyte cell culture and subsequent differentiation; cell lysis and extraction; cell cycle analysis by FACS; RNA extraction & molecular hybridisation (real time PCR and gene-array); functional gene analysis with validated siRNA where possible; receptor expression and phosphorylation status as a means of assessing insulin and adipogenic signaling pathways (immunoblotting, phospho- protein, use of pathway inhibitors).
| Dr Carl Kirkwood Enteric Viruses Infection, Immunity and Environment T 83416439 E carl.kirkwood@mcri.edu.au |
Professor Ruth Bishop Enteric Viruses Infection, Immunity and Environment T 93455062 E r.bishop@mcri.edu.au |
Rotavirus is the major cause of acute gastroenteritis in children in developed and developing countries, including over 500,000 deaths annually. In Australia over 10,000 children are admitted to hospital each year. This disease burden has led to the development of 2 rotavirus vaccines. These vaccines were introduced into the routine immunisation schedule in Australia for all newborn infants on 1st July 2007. It is likely that this introduction will increase the pressure on circulating wild-type rotavirus strains in the community, altering the forces and balances that drive rotavirus evolution. There is concern that previously rare strains, novel strains or antigenic variants produced by genetic shift or drift will emerge and decrease vaccine efficacy.
The National Rotavirus Reference Centre undertakes surveillance and serotype characterisation of rotavirus strains causing severe gastroenteritis in young children throughout Australia. Occasionally rare or novel types are identified in children. This research project will involve the genetic and antigenic characterisation of novel rotavirus strains, using a range of molecular biology techniques such as RT-PCR, sequence analysis and northern hybridisation.
31. Understanding the role of infectious agents in children with early onset Crohn’s disease
| Dr Carl Kirkwood Enteric Viruses Infection, Immunity and Environment T 83416439 E carl.kirkwood@mcri.edu.au |
Dr Josef Wagner Enteric Viruses Infection, Immunity and Environment T 83416450 E josef.wagner@mcri.edu.au |
Crohn’s disease is a major cause of morbidity throughout the world. It is an incurable condition associated with chronic inflammation of the gastrointestinal tract of genetically susceptible individuals. Crohn’s disease usually begins in early adulthood and is treated with potent immunosuppressive medications, but often requires surgery. We have conducted preliminary studies designed to identify an infectious agent in gut biopsy tissue obtained from children with suspected Crohn’s disease. Using microarray and subtractive hybridisation techniques we have identified a candidate viral agent that we propose could initiate the gut damage and ongoing immune activation. This project will continue to utilise molecular techniques to genetically characterise the viral agent in children with Crohn’s disease and develop specific PCR detection assays to determine the prevalence of the virus in clinical specimens collected from children at disease onset.
32. Characterisation and treatment of mice with mitochondrial cardiomyopathy
| A/Professor David Thorburn Mitochondrial & Metabolic Research Laboratory and Community Genetics T 8341 6235 E david.thorburn@mcri.edu.au |
Dr Bi-Xia Ke Mitochondrial & Metabolic Research Laboratory and Community Genetics T 8341 6287 E bi-xia.ke@mcri.edu.au |
Disorders of mitochondrial energy generation cause a wide range of diseases. Severe mitochondrial defects affect ~1/5000 individuals, often causing childhood neurodegenerative diseases. Complex I deficiency is the most common mitochondrial enzyme defect in humans. Currently, no effective treatment for mitochondrial disease is available. Animal models will be useful for the study of novel treatments. We recently generated one of the first mouse models of complex I deficiency by knockdown of the NDUFS6 gene. This project will characterise the phenotype of mice using a range of echocardiographical, histological, metabolic, physiological, molecular and immunochemical approaches. In addition, therapeutic trials will be carried out on this mouse model using approaches such as (1) nutritional intervention with a high fat diet to allow partial bypass of Complex I and (2) stimulating mitochondrial biogenesis using agents such as bezafibrate to upregulate transcription of respiratory chain genes. Our expectation is that this project will lead to a better understanding of pathogenic mechanisms of complex I deficiency and improvement of treatment strategies.
33. FUNKY MICE AS A MODEL FOR MITOCHONDRIAL DISORDERS
| A/Professor David Thorburn Mitochondrial & Metabolic Research Laboratory and Community Genetics T 83416235 E david.thorburn@mcri.edu.au |
Dr Jasper Komen Mitochondrial & Metabolic Research Laboratory and Community Genetics T 83416287 E jasper.komen@mcri.edu.au |
The oxidative phosphorylation (OXPHOS) system in mitochondria consists of five protein complexes (I-V) and is responsible for the generation of energy for the cell in the form of ATP production. Pathogenic mutations in genes encoding OXPHOS proteins result in a variety of neurodegenerative disorders collectively called mitochondrial disorders. The mitochondrial disorders are among the most common type of inherited diseases. Furthermore, OXPHOS dysfunction is believed to play an important role in more common diseases, such as Parkinson disease and diabetes. Recently we have obtained a mouse model (NDUFS4-/- , a.k.a. Funky mice) for Complex I deficiency, the most common type of mitochondrial disorder. Funky mice develop neurodegenerative symptoms similar to those seen in affected children. In this project we will attempt to further characterize the Funky mice via biochemical, histological, immunochemical and molecular biological analyses of blood and tissues (i.e., SDS-PAGE, immunohistochemistry, RT-PCR). Physiological studies will also be performed in order to characterise surrogate endpoints for monitoring disease progression and effects of treatments (high fat diet or stimulation of mitochondrial biogenesis) to ameliorate the symptoms of the Funky mice.
34. Stop codon readthrough in a mouse model of MMA
| Dr Heidi Peters Clinical Services GHSV / VCGS (Clinical / Diagnostic) T 83416257 E heidi.peters@mcri.edu.au |
Dr Nicole Buck Cell & Gene Therapy Laboratory and Community Genetics T 83416236 E nicole.buck@mcri.edu.au |
A large number of diseases including Methylmalonic aciduria (MMA), cystic fibrosis, b-thalassemia and Duchenne muscular dystrophy are caused by premature stop mutations. One way to treat these diseases is to reduce the efficiency of translation termination at stop codons and produce some full length protein. Drugs such as gentamicin can influence the fidelity of the stop codon recognition process and enhance the extent of read-through.
We have developed a mouse colony of MMA mice with a stop codon mutation. This project involves characterising the model and treatment of the mice with gentamicin and potentially PTC124 (a new drug currently being trialled). The work will involve the acquisition of a broad range of molecular and cellular biological techniques including tissue culture, flow cytomtery, liver enzymology and measurement of metabolite levels by mass-spectrometry.
35. Stem cell transplantation for the treatment of MMA
| Dr Heidi Peters Clinical Services GHSV / VCGS (Clinical / Diagnostic) T 83416257 E heidi.peters@mcri.edu.au |
Dr Nicole Buck Cell & Gene Therapy Laboratory and Community Genetics T 83416236 E nicole.buck@mcri.edu.au |
Methylmalonic aciduria is an autosomal recessive inborn error of organic acid metabolism, affecting approximately 1/140,000 children. The condition results from a functional defect in the enzyme methylmalonyl CoA mutase.
This project aims to investigate the degree to which a transplanted immature liver cell line can reduce disease and biochemical phenotypes observed in a mouse model with an intermediate phenotype for the human disorder MMA.
We have established colonies of transgenic mice which will be transplanted and then characterised biochemically and phenotypically. Tissues will be examined for the presence and level of EGFP expression using fluorescent microscopy, RT-PCR of mRNA, western blot and flow cytometry. The activity of the transplanted cells will also be confirmed by specific liver enzyme assays and measurement of metabolite levels by mass-spectrometry.
This project will lead on to extending the work to examine methods of increasing the level of production of MMA enzyme from the cell line. This would involve the use of both viral gene therapy techniques and non viral methods prior to transplantation.
36. Pharmacological upregulation of MUT for the treatment of MMA
| Dr Heidi Peters Clinical Services GHSV / VCGS (Clinical / Diagnostic) T 83416257 E heidi.peters@mcri.edu.au |
Dr Nicole Buck Cell & Gene Therapy Laboratory and Community Genetics T 83416236 E nicole.buck@mcri.edu.au |
Methylmalonic aciduria (MMA) is an autosomal recessive inborn error of the propionate metabolic pathway. One form of this disease is caused by mutations in methylmalonyl-CoA mutase gene (MUT) resulting in reduced levels of enzyme activity. The pharmacological up-regulation of residual mutase activity is one approach to advance treatment strategies for these patients.
The aim of the project is to create a cellular assay system to identify potential compounds which increase the amount of methylmalonyl-CoA mutase activity. The work will then be translated into a mouse model. These mice will allow us develop and test novel therapeutic treatments for MMA. The work will involve the acquisition of a broad range of molecular and cellular biological techniques including tissue culture, flow cytomtery and enzymology.
| A/Professor Henrik Dahl Genetic Hearing Research Early Development and Disease T 83416253 E henrik.dahl@mcri.edu.au |
Dr Shehnaaz Manji Genetic Hearing Research Early Development and Disease T 83416254 E shehnaaz.manji@mcri.edu.au |
| Kerry Miller T 83416254 E |
Dr Louise Williams T 83416254 E |
Ten percent of the Australian population has a significant hearing loss. The major objective of our research is to identify and understand the causes of deafness in children and adults so that deafness can be prevented or new therapies developed. We have identified several mouse strains with inherited hearing loss. These mice are a new, unique and valuable resource for studying the contribution of genetic and environmental factors to hearing loss. We are identifying and characterising new “deafness” genes in these mouse strains. These genes will be identified through database mining and DNA sequencing. We will then study the function and expression of these novel “deafness” genes to expand our understanding of how the ear develops and functions. Expression of “deafness” genes will be analysed by in-situ and immunohistochemical techniques using isolated mouse inner ears, as well as by biochemical methods in tissue cultures. These investigations will be complemented by analysis of human DNAs and provide much needed insights into hearing loss in humans.
This project provides an opportunity to work with and develop skills in a wide variety of techniques, encompassing the biology of hearing loss at both the DNA and protein levels.
38. Gene expression in ear hair cells
| A/Professor Henrik Dahl Genetic Hearing Research Early Development and Disease T 83416253 E henrik.dahl@mcri.edu.au |
Dr Shehnaaz Manji Genetic Hearing Research Early Development and Disease T 83416254 E shehnaaz.manji@mcri.edu.au |
A goal of our laboratory is to develop cell-based therapies for hearing loss using progenitor or terminally differentiated hair cells generated in vitro. Hearing loss affects more than six hundred million people worldwide. The financial, social and personal costs of deafness to affected people, their families and the society are significant. Management options include learning sign language or fitting hearing aids or cochlear implants. However, none of these options are fully satisfactory. The availability of stem cells has given us the opportunity to develop novel therapies based on replacing or regenerating cells in the inner ear. For such cell-based therapies to work we need to understand the differentiation pathways that the inner ear hair cells and their supporting cells follow during the development of the auditory system. We are able to isolate inner ear hair cells from mice with green fluorescent hair cells at different developmental stages by fluorescence-activated cell-sorting (FACS). RNA will be isolated from these cells and analysed on microarrays. This project will focus on analysing the microarray data and studying selected developmentally regulated genes using techniques
commonly used to study gene expression.
39. RNA interference therapy: Applications in ß-thalassaemia
| Dr Jim Vadolas Cell & Gene Therapy Laboratory and Community Genetics T 8341 6232 E jim.vadolas@mcri.edu.au |
Dr Heidi Peters Cell & Gene Therapy Laboratory and Community Genetics T 8341 6233 E heidi.peters@mcri.edu.au |
Severe ß-thalassaemia (ß-thalassaemia major) is an inherited haemoglobinopathy arising from mutated ß-globin genes, resulting in reduced ß-globin chain synthesis. Much of the pathology of this disease is due to excess a-globin chains forming toxic insoluble precipitates in erythroid cells resulting in cell death, ineffective erythropoiesis and severe anaemia. Decreased a-globin chain synthesis leads to milder symptoms, exemplified by individuals who co-inherit a- and ß-thalassaemia. Therefore, a possible therapeutic strategy in the treatment of ß-thalassemia could include targeted reduction of a-globin chains to mimic co-inheritance of a/ß-thalassemia. RNA interference (RNAi) is an innovative new strategy for modulating gene expression and this pathway can potentially be exploited to mediate reductions in a-globin. Our group has identified key regions in the a-globin mRNA sequence which can be targeted with high efficiency using short-interfering RNA (siRNA) to mediate significant reductions in a-globin expression. We have also successfully demonstrated that RNAi-mediated reduction of a-globin results in phenotypic improvements in ß-thalassaemic cells. This project aims to develop strategies for targeted delivery of siRNA into erythroid progenitor cells. Initial studies will be conducted in vitro and will involve culture of both cell lines and primary cells. Analytical techniques such as electroporation, cellular transfections, reverse transcription, Real-Time PCR, Western Blotting and flow cytometry will also be utilised. Further studies may also be conducted in vivo using our unique humanised ß-thalassaemia mouse models.
40. Genetic and Epigenetic Regulation of the Structure and Function of Human Chromosomes
| Professor KH Andy Choo Chromosome and Chromatin Research Laboratory and Community Genetics T 83416306 E andy.choo@mcri.edu.au |
Dr Lee Wong Chromosome and Chromatin Research Laboratory and Community Genetics T 83416240 E lee.wong@mcri.edu.au |
This project aims to study the role of genetic and epigenetic factors in regulating the structural and functional integrity of chromosomes and chromatin. We will use normal centromeres, neocentromeres (a new class of centromere devoid of alpha-satellite repetitive DNA first discovered by us), and human artificial chromosomes to investigate how different chromatin-modifying proteins (including constitutive centromere proteins, histone variants, boundary element insulator and DNA repair checkpoint proteins) and non-coding RNA components (including centromeric alpha-satellite and retrotransposon transcripts) are organised at the centromere regions. The organisation will be defined at the linear chromatin level using molecular biology analysis, and at the 3-D level using electron microscopy. The knowledge gained will be fundamental to our understanding of how genetic and epigenetic factors regulate centromere hierarchical assembly and its function in the maintenance of mitotic activity.
| Dr Lee Wong Chromosome and Chromatin Research Laboratory and Community Genetics T 83416240 E lee.wong@mcri.edu.au |
Professor KH Andy Choo Chromosome and Chromatin Research Laboratory and Community Genetics T 83416306 E andy.choo@mcri.edu.au |
There is currently a huge interest in understanding how embryonic stem (ES) cell pluripotency is controlled, and what (epigenetic) changes occur at the chromatin level during differentiation. However, until the present study, no one has investigated the chromatin status of the telomere in pluripotent and differentiating ES cells. In our study, we have found that the telomere chromatin of the pluripotent ES cells is unique compared to that of the differentiating ES cells. Specifically we show enrichment of histone variant H3.3 at the telomeric chromatin in mouse ES cells. The study involving RNAi-depletion of H3.3 that results in impairment of the telomere structure also confirms that H3.3 is essential for the maintenance of telomeric integrity in these cells. This project involves the investigation of the roles of H3.3 and its interacting partner as a ‘reprogramming cue’ for the maintenance of prolonged telomere-self renewal in pluripotent ES cells, and in other adult stem cells.
42. Stem cells and gene therapy: Targeted integration of functional genomic loci
| Dr Jim Vadolas Cell & Gene Therapy Laboratory and Community Genetics T 8341 6232 E jim.vadolas@mcri.edu |
Dr Heidi Peters Cell & Gene Therapy Laboratory and Community Genetics T 8341 6233 E heidi.peters@mcri.edu.au |
One of the major obstacles to successful gene therapy is the random integration of the therapeutic transgene, which is associated with insertional mutagenesis and oncogenesis. Using specific elements derived from adeno-associated virus (AAV) our research group has developed a novel strategy to enhance the delivery, and site-specific integration of large DNA molecules into the human genome. We have recently shown that we can enhance the delivery, and facilitate the site-specific integration of the entire human ß-globin locus. This project will investigate the site-specific integration of functional genomic loci into stem cells. Reporter gene expression and fluorescence in situ hybridisation will be used to monitor targeted integration and tissue-specific expression. In vitro differentiation will be used to assess the capacity of modified stem cells to differentiate along multiple lineages. We propose that this non-viral gene therapy strategy may be used in conjunction with patient-derived stem cells to facilitate persistent and stable transgene expression while avoiding the risks associated with random integration.
43. Discovering novel genes that cause childhood mitochondrial disorders.
| A/Professor David Thorburn Mitochondrial & Metabolic Research Laboratory and Community Genetics T 8341 6235 E david.thorburn@mcri.edu.au |
Dr Alison Compton Mitochondrial & Metabolic Research Laboratory and Community Genetics T 8341 6234 E alison.compton@mcri.edu.au |
Mitochondria are the powerhouses of the cell, generating cellular energy through the oxidative phosphorylation (OXPHOS) system. Pathogenic mutations in genes required for correct assembly of the OXPHOS protein complexes (I-V) result in a variety of neurodegenerative disorders collectively known as mitochondrial disorders. Over 90 (nuclear and mitochondrial) genes are known causes of mitochondrial disease, however there are still many more novel disease genes awaiting discovery. We recently identified four novel (nuclear) disease genes in which mutations cause severe childhood-onset OXPHOS complex I deficiency, the most common mitochondrial enzyme defect in humans. These are NDUFS6 (Kirby et al., 2004 J Clin Invest 114: 837-45), NDUFAF1 (Dunning et al., 2007 EMBO J 26: 3227-37), C8ORF38 (Pagliarini et al., 2008 Cell 134:112–123) and C20ORF7 (manuscript under review). Recently, our collaborators at the Broad Institute, Harvard have compiled a compendium of 1098 ‘mitochondrial’ genes called Mitocarta, including 19 novel genes proposed to be involved in OXPHOS complex I biogenesis (Pagliarini et al., 2008 Cell 134:112–123). We are currently performing high throughput sequencing of 88 ‘mitochondrial’ genes in 110 of our patients with defined complex I defects. This project will follow up on sequence variants identified in that study to identify novel OXPHOS disease genes and determine their normal function and disease pathogenesis using a combination of cell biology, molecular biology and biochemical approaches.
44. Investigating the role of altered methylation in schizophrenia
| Dr Richard Saffery Developmental Epigenetics Early Development and Disease T 83416341 E richard.saffery@mcri.edu.au |
Dr Jeff Craig Developmental Epigenetics Early Development and Disease T 83416346 E jeff.craig@mcri.edu.au |
Despite the relatively high prevalence (approaching 1%) and devastating social and financial impact, there is presently no “objective” biological test to screen for Schizophrenia risk. The identification of SZ biomarkers is a crucial step towards improving current diagnosis, developing new presymptomatic treatments, identifying high-risk individuals and disease subgroups, and assessing the efficacy of preventative interventions at a rate that is not currently possible. In addition, the identification of brain-specific biomarkers of SZ has the potential to reveal valuable insights into the development of this disorder.
We have data demonstrating that, SZ cases have lower serum folate level than controls with altered epigenetic modification of specific genes in the prefrontal cortex compared to disease free brains.
We now aim to further characterise specific epigenetic biomarkers of SZ in post-mortem brain samples, to identify peripheral epigenetic biomarkers of SZ in blood; and to characterise the downstream functional consequences of this altered methylation profile.
| Dr Richard Saffery Developmental Epigenetics Early Development and Disease T 83416341 E richard.saffery@mcri.edu.au |
Dr Jeff Craig Developmental Epigenetics Early Development and Disease T 83416346 E jeff.craig@mcri.edu.au |
| Dr Adam Balic T 93454116 E |
The fetomaternal interface (placenta: decidua) represents a major site of accumulation of active vitamin D. However the exact role of this remains to be elucidated but may involve immune modulation, regulation of cell division, and/or maximal transfer of VitD to the developing fetus.
Recent data have demonstrated a role of epigenetic modification generally (and DNA methylation specifically) in the regulation of genes involved vitamin D metabolic enzymes that control vitamin D bioavailability and action. As one-carbon donors derived from maternal dietary folate are critical for the establishment of DNA methylation, we believe that sub-optimal circulating levels of vitamin D and folate may act cooperatively to alter vitamin D bioavailability in the developing pregnancy.
| Dr Richard Saffery Developmental Epigenetics Early Development and Disease T 83416341 E richard.saffery@mcri.edu.au |
A/Professor Jane Halliday Public Health Genetics Laboratory and Community Genetics T 83416260 E jane.halliday@mcri.edu.au |
| Dr Jeff Craig T 83416346 E |
The developing pregnancy is faced with substantial challenges, including a complete dependence on the placental ‘buffer’ for nutritional requirements, protection from adverse circulating maternal factors (such as cortisol), and isolation from the maternal immune system. Placental insufficiency has been linked to adverse outcomes of pregnancy loss, Intrauterine Growth Restriction (IUGR), premature delivery, and/or pre eclampsia. We have generated novel data for the specific epigenetic (DNA methylation-induced) silencing of several different metabolic pathway genes as part of human placentation. Given the demonstrated interplay between various environmental/dietary factors and altered epigenetic profile, we believe that disruption of this methylation in early development may play an important role in the aetiology of such conditions.
This project will examine DNA methylation profile of CVS and amniotic fluid samples taken as part of routine prenatal diagnostic procedures. Using routinely collected perinatal data on all births, it will be possible to determine if there is an association of aberrant epigenetic profile with adverse pregnancy outcome. This will then be matched with linked birth outcome data, to examine the association of aberrant epigenetic profile and adverse pregnancy outcome.
47. The role of Epigenetics in Paediatric Leukaemia development and outcome.
| Dr Jeff Craig Developmental Epigenetics Early Development and Disease T 83416346 E jeff.craig@mcri.edu.au |
Dr Nicholas Wong Developmental Epigenetics Early Development and Disease T 83416205 E nick.wong@mcri.edu.au |
| Dr Richard Saffery T 83416341 E |
Leukaemia is the most common form of cancer in children, accounting for over 30% of newly diagnosed cases. Most cases involved specific genomic rearrangements (translocations). However, these are neither sufficient nor absolutely necessary for disease development. Despite the fact that ~80% of cases are successfully treated by chemotherapy, the underlying causes of childhood leukaemia remain unclear and cannot be explained by genetic or environmental factors alone. Epigenetics is an emerging field examining the modulation of gene expression in the absence of underlying genetic change. We believe disruption of epigenetic profile could play a major role in the aetiology of paediatric leukaemia in conjunction chromosome translocations. This project will catalogue epigenetic changes at gene promoters from archived matched leukaemia and remission bone marrow samples in an attempt to identify changes in associated with development or outcome of specific leukaemia subtypes.
| Professor John Bateman Skeletal Biology and Disease Musculoskeletal Disorders T (03) 8341 6422 E john.bateman@mcri.edu.au |
Dr Jacqueline Tan Skeletal Biology and Disease Musculoskeletal Disorders T (03) 9345 6601 E jaqueline.tan@mcri.edu.au |
Cells have several critical quality control processes to reduce the impact of mutations on cell function. We are studying nonsense-mediated decay (NMD), a mRNA quality mechanism that degrades mRNA containing premature stop codons. Since mutations that introduce premature stop codons account for one-third of inherited disorders, NMD is of immense importance in many diseas