Student Projects 2010

Genetics and Population Health

• Asthma and other common genetic diseases
• Epigenetics
• Epidemiology of Endometrial Cancer
• Factors affecting quality of life in Pancreatic Cancer Patients
• Germline Genetic Mutations in Familial Cancer

Infectious Diseases

• Bacterial Pathogenesis and Vaccines
• Lifecycle gene targets during Malaria Infection
• Studies on malaria enzymes involved in gene regulation
• Effect of natural products on Scabies
• Sustainable Mosquito Control
• Scabies mite serpins
• Parasitic Worms and disease

Immunology

• Bone Marrow Transplantation
• Harvesting Cancer Stem cells for Immunotherapy
• Immune events in Malaria and Leishmaniasis
• Novel vaccine delivery and group A Streptococcus
• Dendritic cells mediated protection against Malaria
• Protein targets of protective immunity against Malaria
• Chiungunya virus infection and SerpinB2

Cancer & Cell Biology

• Cancer Genetics
• Genes that regulate Iron metabolism
• Genetic Changes in Colon and Colorectal Cancer
• Human hSSB1 and DNA replication
• Radiation Signaling and Disease
• Ataxia-telangiectasia and ATM kinase activation
• Ataxia with oculomotor apraxia in DNA damage response and RNA metabolism
• The role of SmcHD1 in genomic imprinting

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How to apply:
Contact the Laboratory Head related to the project area of interest (see below).   Application and admission details in "Becoming a Student".

Legend:
P   = PhD, MPhil project
H   = Honours project
TU = Top-Up available

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Epigenetics Laboratory
Prof Emma Whitelaw
07-3845 3600
Dr Suyinn Chong
07-3845 3596
Email Emma.Whitelaw@qimr.edu.au
Email Suyinn.Chong@qimr.edu.au

[H, P]

Epigenetics and telomeres

We are a molecular genetics lab, interested in mammalian genes where expression is regulated by epigenetic modification. Epigenetic modifications are established in early development and are associated with cell committment during differentiation. Once established these marks are relatively permanent.

Telomeres are specialised DNA-protein structures at the ends of chromosomes that protect them from fusion and degradation. In humans, telomere shortening is associated with aging and age-related diseases.

We are interested in the role of epigenetics in determining telomere length. This Hons/PhD project will involve the characterisation of telomeres in epigenetic mutants generated in our mouse mutagenesis screen.

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Endometriosis Lab
Dr Penny Webb
Phone: 3362-0281
Email: Penny.Webb@qimr.edu.au

[P,  MPhil]

Endometrial cancer - Patterns of Care, Survival and Quality of Life

Background: Endometrial cancer (cancer of the lining of the uterus) is the 6th most common cancer in Australian women with more than 1,600 new diagnoses each year in Australia. Although overall survival is good, many women will experience a recurrence and 15-20% will die from their disease within 5 years and it is not possible to reliably predict which women require more aggressive treatment or, conversely, those who will not benefit from additional treatment. Furthermore, more than 10,000 women alive in Australia today have been treated for endometrial cancer in the past 10 years but very little is known about their ongoing health and quality of life.

The Australian National Endometrial Cancer Study (ANECS) is a national population-based case-control study that includes 1400 women with endometrial cancer. Women provided detailed lifestyle information at recruitment and we are now recontacting them to a sk about their current health and quality of life and are collecting extensive clinical information from their medical records.

Project Aims:
A number of potential areas could be investigated, for example:

1. An investigation of the role of hormonal factors including pregnancy, breastfeeding and use of oral contraceptives and hormone replacement therapy and the timing of these events in determining risk of endometrial cancer
2. To describe the variability in primary and adjuvant treatment in a large cohort of Australian women diagnosed with endometrial cancer and to relate this to clinical (e.g. surgeon specialty, hospital size) and sociodemographic factors (e.g. age, obesity, rural vs urban, private vs public);
3. To evaluate the role of routine follow-up to detect early recurrence in women treated for endometrial cancer and, specifically, the utility of vaginal vault cytology in this follow-up;
4. To document 3-year recurrence-free and overall survival by tumour subtype, stage and grade and assess the value of clinical parameters in predicting prognosis;
5. To describe quality of life, psychosexual health and supportive care needs of endometrial cancer survivors;
6. To assess the impact of (i) treatment-related factors (e.g. surgeon speciality, hospital size), (ii) patient characteristics (e.g. age, obesity) and (iii) lifestye factors (e.g. diet, physical activity, smoking) on recurrence-free and overall survival and quality of life:

Some experience in statistics and data analysis is essential and a background in epidemiology and/or an interest in cancer are highly desirable.

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Cancer & Population Studies Group
Prof Adèle Green
Dr Rachael Neale
Phone: 3845-3598
Email: Rachel.Naeale@qimr.edu.au
[ P ]

Supportive care needs and factors affecting quality of life in Pancreatic Cancer Patients

Project Leader: Dr Rachel Neale

Background

Pancreatic cancer has the worst survival of any cancer, making it the 4th most common cause of cancer death in Australia. The poor prognosis is due to multiple factors, including late presentation combined with aggressive tumour biology, complex surgery and no effective systemic treatments. The combination of these factors creates a unique situation with respect to available treatment modalities, patterns of care, supportive care needs and quality of life. We propose a comprehensive study exploring supportive care needs and factors affecting quality of life in Queensland.

Approaches

This project will be embedded in the Queensland Pancreatic Cancer Study (QPCS).
Patients who participate in the baseline survey for the QPCS will be eligible for participation in the supportive care needs and quality of life study. They will be asked to complete additional questionnaires and/or interviews at 3-monthly intervals for up to one year. The results of these questionnaires will be linked to epidemiological and clinical information obtained by the QPCS.

The results of this project could be used to improve care coordination, or to implement approaches to improve supportive care, to improve quality of life of Queensland patients with pancreatic cancer.

Degree

This project would be suitable for a PhD candidate.

An additional PhD project could be undertaken in which the supportive care needs and quality of life of carers of patients with pancreatic cancer could be explored.

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Genetic Epidemiology
Prof Nick Martin
Dr Manuel Ferreira
Phone: 3845-3552
Email: Manuel.Ferreira@qimr.edu.au
[ P, H ]

Asthma and other allergic disease

Project Leader: Dr Manuel Ferreira

Project 1 Large-scale genetic approaches to identify asthma risk genes

Supervisors: Dr Manuel Ferreira, Dr David Duffy
[ P ]

Asthma currently affects 10% of the Australian population and is directly responsible for an estimated >1million work days lost, >36,000 hospital admissions, 402 deaths and $606 million health costs a year.
These figures are high by international standards and more than other common chronic diseases, such as diabetes. A complete understanding of the genetic and environmental factors for asthma is critical to design new treatments or prevention strategies that can effectively reduce the disease burden.

This project will capitalise on an excellent genetic resource currently being collected by the Australian Asthma Genetics Consortium (AAGC, http://genepi.qimr.edu.au/aagc/). By June 2010, we expect to have whole-genome genotype data available for over 2,000 asthma patients and 10,000 healthy controls. As part of this project, we will apply state-of-the art statistical genetics approaches to identify new genetic variants robustly associated with asthma risk. These approaches include whole-genome association analysis, copy-number variation analysis, gene-by-gene and gene-by-environment interaction analyses, multivariate approaches, etc.

Interested applicants should have a good understanding of basic genetic and statistical concepts, be highly motivated and have or be willing to develop computer skills with statistical software such as R.

Project 2. Multi-locus tests for genetic association studies

Supervisor: Dr Manuel Ferreira
[ P ]

For many common diseases such as asthma, hundreds or thousands of genetic variants with weak effects are now predicted to contribute to disease risk. Under this highly polygenic model, most available methods for the analysis of whole-genome data are adequately powered only when analysing data for many thousands of patients and healthy individuals.

We will develop new multi-locus statistical methods for genetic association studies that can increase our ability to identify new disease risk variants from whole-genome data. These methods will extend an approach we developed recently (see reference 28 in References) and will be applied to real-life datasets collected as part of ongoing studies in our Genetic Epidemiology unit, from psychiatric disease to asthma.

Interested applicants should have a good understanding of basic genetic and statistical concepts, be highly motivated and have or be willing to develop computer skills in different languages, such as R and C++.

Project 3. Genetic regulation of monocyte levels in humans.

Supervisors: Dr Manuel Ferreira (QIMR), Prof Ian Frazer (UQ)
[ P, H ]

Monocytes represent 10% of all white-blood cells and have important immune functions, including the removal of apoptotic cells and toxic compounds . They play a key role in healing after myocardial infarction and contribute to the development of inflammatory diseases, including atherosclerosis. It is thus important to understand the mechanisms that regulate monocyte development from their bone marrow progenitors and how these might relate to disease.

Using a genome-wide association approach, our lab has recently identified a small region on chromosome 9 that contains a gene that controls the number of monocytes that circulate in the peripheral blood (see reference 36 in References ). There is virtually no available information on this gene, which we expect to be a key player in monocyte development. We will use a number of approaches to characterise this gene, from molecular biology techniques (including DNA sequencing) to statistical genetics. We will characterise exons, assess gene expression in different tissues and determine how mutations in this gene influence monocyte development.

Interested applicants should have a background in molecular biology, with a good understanding of basic genetic and statistical concepts.

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Infectious Diseases

Bacterial Pathogenesis Laboratory
Prof Sri Sriprakash
Dr David McMillan
07-3845 3712
Bacterial Vaccines Laboratory
Email David.McMillan@qimr.edu.au
[ H, P,  TU]

Bacterial Pathogenesis and Vaccines

Bacterial Pathogenesis and Vaccine research in our labs is divided into two main areas:

A. Beta-hemolytic streptococci

Streptococcus pyogenes, commonly known as Group A Streptococcus (GAS), is a bacterial pathogen that infects the throat and skin and is able to cause a wide range of diseases in humans. These range from relatively benign pharyngitis (commonly known as 'strep throat') to more serious and potentially fatal diseases such as acute post-streptococcal glomerulonephritis (APSGN), rheumatic heart disease and invasive diseases. Group G streptococcus (GGS) is closely related to GAS, and causes a similar diseases. More than half a million people may die from streptococcal disease in any one year. Many of these deaths occur in developing countries.

In Australia, the Indigenous population suffers disproportionately from GAS related diseases. The aim of research in the Bacterial Pathogenesis Laboratory is to acquire a greater understanding of the pathogenesis of Streptococcus.

Our major research initiatives in this area are:

1. The molecular epidemiology of group A streptococcus.
2. Evolution of streptococci.
3. The role of streptococcal virulence factors in pathogenesis.
4. Novel vaccine strategies to combat GAS infection
.

B. Hospital acquired bacterial infections

Hospital acquired infections directly cause 7,000 Australian deaths per annum. Intravascular devices (i.e. catheters) are the single most important cause of hospital acquired blood stream infection. IVDs provide a site of attachment for bacteria, and also provide a portal by which bacteria can migrate from an unsterile external environment to the normally sterile environment of the blood.

Post-attachment, many microbial communities form biofilms which are characterised by the presence of encasing extracellular polymeric substances (EPS). Bacteria in biofilms exhibit different phenotypes than free-living cells, including increased resistance to antibiotics. The most common bacteria isolated from catheters is coagulase-negative staphylococci. Other major bacterial species include Pseudomonas aeruginosa, Klebsiella pneumoniae and Proteus mirabilis. Detection and identification of the bacteria found on IVDs, including arterial catheters, has relied on culture dependent techniques.

With collaborators at Griffith University, we are developing new molecular methods to study bacterial colonisation of IVDs.

Our major research initiatives in this area are:

1. Development of a better understanding of bacterial colonisation of catheters.
2. Development of novel rapid diagnostics for detecting bacteria on IVDs.

Project 1: Characterisation of an insertion element from group A streptococci

Background

Group G streptococcus (GGS) is a Gram-positive organism that infects humans. Normally considered a commensal organism or opportunistic pathogen, several studies have now demonstrated that GGS is able to cause a range of diseases similar to that of it's close relative group A streptococcus (GAS). We have recently demonstrated that DNA is transferred between GGS and GAS via a mobile genetic element (MGE) called ICESde3396. MGEs are important in microbiology as they provide a mechanism for 'supercharged' evolution.

We have now identified a second MGE in GGS called IS3396. The goal of this project is too genetically and functionally characterise this MGE. We will also determine if this element can be transferred to other bacteria.

Aims

1. to provide the full genetic sequence of IS3396.
2. to compare IS3396 to other insertion sequences present in streptococci and other bacterial species
3. to demonstrate transfer of IS3396 from GGS3396 to other bacterial species.
4. to investigate the presence of IS3396 in clinical streptococcal isolates.

Methods you will learn

PCR, Nucleotide sequencing, bioinformatic analysis, cloning, conjugation.

References:

1. Davies MR, McMillan DJ, Van Domselaar GH, Jones MK and KS Sriprakash KS. Phage 3396 from a Streptococcus dysgalactiae subsp. equisimilis pathovar may have its origins in streptococcus pyogenes. J Bacteriol. 2007 Apr;189(7):2646-52.
2. Davies MR, Tran TN, McMillan DJ, Gardiner DL, Currie BJ, Sriprakash KS. Inter-species genetic movement may blur the epidemiology of streptococcal diseases in endemic regions. Microbes Infect 2005;7(9-10):1128-38.

Project 2: Next generation group A streptococcal vaccines

Background

Group A streptococcus is a Gram-positive organism that is associated with a wide range of diseases in humans. These include pharyngitis, skin diseases and the post-infectious sequelae rheumatic fever and rheumatic heart disease. To combat streptococcal disease, researchers at QIMR have developed a promising anti-streptococcal vaccine candidate called J14.
J14 is a 29mer peptide derived from the C-repeat region of the M-protein, the major GAS virulence factor. Antibodies raised against J14 are opsonic, and protect mice from challenge with GAS.

Researchers within the Bacterial Pathogenesis Laboratory are currently optimising the J14 vaccine. In this project, two new J14 based vaccine candidates will be produced and tested. The first candidate consists of four J14 sequences linked as a single fusion protein. The second candidate consists of 4 J14 variants, also linked as a fusion protein. The latter approach has been adopted because the J14 sequence is only found in the third C-repeat region. By including the J14 variants found in other C repeat regions, we hope to create a vaccine that induces antibodies that can target multiple regions in the one protein.

Aims

1. To express and purify JJo4 (vaccine candidate 1).
2. To express and purify JJo4v (vaccine candidate 2)
3. To investigate the antigenic properties both candidates.
4. To determine whether antibodies raised against these candidates bind to the surface of GAS
5. To determine whether these vaccine candidates protect against with group A streptococcus.

Methods you will learn

PCR, cloning, DNA sequencing, protein expression and purification, immunization, ELISA, challenge, bactericidal assays, immunoflourescence microscopy, FACS.

Project 3: Multi-locus sequence typing of group G streptococcus

QIMR Co-Supervisor: Dr Michael Batzloff

Background

Group G streptococcus (GGS) is a Gram-positive organism that infects humans. Normally considered a commensal organism or opportunistic pathogen, several studies have now demonstrated that GGS is able to cause a range of diseases similar to that of it's close relative group A streptococcus. The virulence factors that enable GGS to cause these diseases are unknown. It is also unknown whether GGS strains capable of causing disease comprise a distinct evolutionary lineage from those strains incapable of causing disease.

MLST is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. MLST profiles are created by generating nucleotides sequences for seven conserved house-keeping genes, that are not subject to evolutionary pressure. MLST profiles can then be compared bioinformatically to infer evolutionary relationships. Our laboratory has collection of clinically defined GGS isolates collected from Australia, India and Fiji.

The strains were collected from individuals present with different streptococcal diseases, including invasive disease. We also have a collection of non-disease associated GGS isolates. We already have generated MLST data on the Australian and Indian isolates. In this study we will use MLST to investigate the evolutionary relationships between the Fijian GGS isolates.

Aims

Specifically we will:

1. Determine the MLST profile of selected Fijian group G streptococcal isolates
2. Determine if Fijian MLST profiles differ from MLST profiles of GGS from other countries
3. Determine if MLST profiles segregate with streptococcal disease

References

1. Davies MR, Tran TN, McMillan DJ, Gardiner DL, Currie BJ, Sriprakash KS. Inter-species genetic movement may blur the epidemiology of streptococcal diseases in endemic regions. Microbes Infect 2005;7(9-10):1128-38.
2. McGregor KF, Bilek N, Bennett A, et al. Group A streptococci from a remote community have novel multilocus genotypes but share emm types and housekeeping alleles with isolates from worldwide sources. J Infect Dis 2004;189(4):717-23.

Project 4: Identification of bacterial species forming biofilms on the surface of intravascular devices

Supervisors:
Dr David McMillan, QIMR
Prof Claire Rickard, Griffith University

Background

Many hospital acquired infections are associated with intravascular devices (IVDs), including arterial catheters. IVDs provide a site of attachment for bacteria, and also provide a portal by which bacteria can migrate from an unsterile external environment to the normally sterile environment of the blood. Detection of bacteria on intravascular devices still relies primarily on culture-dependent techniques. The common diagnostic 'roll-plate' technique fails to identify bacteria found on the inner surface of the IVDs, and also fails to identify non-culturable bacteria present on the outer surface.

We hypothesise that a molecular, culture independent examination of biofilms (including analysis of the interior surface) that form on arterial catheters will help our understanding of the variety organisms that are present in this niche environment. In particular, amplification and nucleotide sequencing of the 16S rRNA gene has the potential to provide a comprehensive inventory of bacteria present on IVDs. Such techniques have been recently employed to examine bacterial populations on urinary catheters.

Such information may lead to novel diagnostic or treatment regimes that result in improved patient outcomes and reduce cost of treatment.

Aims

1) To produce 16S rRNA libraries representing bacteria found on the inner and outer surface of catheters. 2) By interrogating these libraries, identify the bacterial species present on the surface of IVDs 2) To correlate bacterial species and bacterial load with clinical presentation

Methods you will learn

Bacterial culture, purification and bacterial DNA, polymerase chain reaction, cloning, bioinformatic analysis.

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Malaria Biology Laboratory
Dr Katharine Trenholme
Dr Don Gardiner
07-3362 0432
Email Katharine.Trenholme@qimr.edu.au

[ H,  P]

Lifecycle gene targets during Malaria Infection

General Information

There are an estimated 300-500 million clinical cases of malaria each year, resulting in between 1.5 and 2.7 million deaths annually. These are mainly caused by infection with the malaria parasite Plasmodium falciparum. The Malaria Biology Laboratory group at QIMR is involved in a number of projects that are designed to provide us with important information about Plasmodium falciparum and the way this organism functions. Many of the projects in our laboratory have both molecular and cellular components and involve determining the function of genes.

The molecular approaches often rely on transfection, a process that allows us to introduce foreign DNA into parasites so that we can determine function. We can alter genes, "knock" them out, tag them or simply permit them to be expressed in an environment where they may not have been previously expressed. We are also involved in assessing the ability of particular parasite proteins to protect the host from infection and recently we have become interested in assessing the activity of some novel anti-malarial agents as well as extending our molecular experience into the drug action and drug resistance arena.

Hons, Masters/PhD Projects are available in the following subject areas:

Committment to Gametocytogenesis in P falciparum

Gametocytogenesis is a poorly understood stage of the parasite lifecycle that is essential for transmission of the parasite from the human to the mosquito host. We are exploring this stage as a potential focus for intervention strategies. Gametocytes, the sexual stages of the malaria parasites, are essential for transmission of the malaria parasite through the mosquito vector, and represents a vulnerable stage in parasite development. This switch is sensitive to environmental stimuli suggesting the existence of a signal transduction pathway between the environment and the parasite. but little is known about the process by which the malaria parasite interacts with its environment.

Through extensive data base searching we have identified candidates for regulators or mediators of signal transduction in the human malaria parasite Plasmodium falciparum. We will examine expression, localization and function of these candidate molecules using molecular and transgenic approaches.

The project will involve techniques including tissue culture, molecular biology techniques (cloning, transfection), protein expression and purification and microscopy.

Further Reading

Dixon M, Thompson J, Gardiner DL, & Trenholme KR. Sex In Plasmodium - A sign of Commitment. Trends Parasitol. 2008 Apr;24(4):168-75

Transcriptional control of gametocytogenesis

Although the genes controlling transcription in gametocytes have not yet been properly identified in P. falciparum, a novel family of proteins which may form a component of the transcriptional machinery have recently been recognized. This family of proteins represent a lineage-specific expansion of proteins containing the AP2 integrase DNA binding domain, similar to that described in plants.

This family of transcription factors is thought to bind various regulatory elements distinct from the main promoter element, leading to differential gene expression. Using micro-array data on all the annotated P. falciparum genes, kindly supplied by our collaborator K. Le Roch, we have identified members of this family of genes significantly up-regulated when gametocytogenesis is induced.

Further Reading

Balaji S, Babu MM, Iyer LM, Aravind L. Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res. 2005 Jul 21;33(13):3994-4006.

De Silva EK, Gehrke AR, Olszew De Silva EK, Gehrke AR, Olszewski K, León I, Chahal JS, Bulyk ML, Llinás M. Specific DNA-binding by apicomplexan AP2 transcription factors. Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8393-8.

Protein trafficking within the malaria parasite

Malaria parasites extensively remodel their host's red cells, post-invasion, including the placement of numerous parasite virulence proteins upon the red cell surface. How the parasite directs these proteins to the surface of the infected red cell is poorly understood, but is an area of intense study.

Further Reading

Dixon WMA, Spielmann T, Hawthorne PL, Anderson KL, Trenholme KR, Gardiner DL. Targeting of the Ring Exported Protein 1 to the Maurer's clefts is mediated by a two phase process. Traffic. 2008 Jun 10. [Epub ahead of print]

Hanssen E, Hawthorne P, Dixon MW, Trenholme KR, McMillan P, Spielman T, Gardiner DL, Tilley L. Targeted mutagenesis of the ring exported protein-1 of Plasmodium falciparum disrupts the architecture of Maurer's cleft organelles. Mol Microbiol. 2008 Jun 18.

Spielmann T, Hawthorne PL, Dixon MWA, Hannemann M, Klotz K, Kemp DJ, Klonis N, Tilley L, Trenholme KR, and Gardiner DL. A cluster of ring stage-specific genes linked to a locus implicated in cytoadherence in Plasmodium falciparum codes for PEXEL negative and PEXEL positive proteins exported into the host cell. Mol Biol Cell. 2006 Aug;17(8):3613-24

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Clinical Tropical Medicine Laboratory
Dr Kathy Andrews
Dr James McCarthy
07-3845 3725
Email Kathy.Andrews@qimr.edu.au

[H,  P]

Studies on malaria enzymes involved in gene regulation

Malaria is responsible for over 2 million deaths annually, making it the most lethal parasite-mediated infectious disease. Most deaths are caused by P. falciparum. No vaccine is currently available for this disease and resistance to antimalarial drugs is a global problem. New anti-malarial agents that act against novel parasite targets are a high priority to combat multi-drug resistant parasites.

Enzymes involved in gene regulation and cell cycle progression have yet to be exploited as potential new antimalarial targets. Our work focuses on these pathways, in particular enzymes involved in histone modification (P. falciparum histone deacetylases (PfHDACs). Understanding the role of these enzymes on parasite gene regulation and development will allow us to more rationally target these, and interacting proteins for, development of new antimalarial therapies.

This project may involve investigating the role of PfHDACs on parasite development, identifying new inhibitors of PfHDACs, generating transgenic parasites, or studying the basic biology of PfHDACs.
For further information contact Dr Kathy Andrews
References:

1. Pasvol, G., Weatherall, D.J., Wilson, R.J., Smith, D.H. & Gilles, H.M. Fetal haemoglobin and malaria. Lancet 1, 1269-72 (1976)
2. Pasvol, G., Weatherall, D.J. & Wilson, R.J. Effects of foetal haemoglobin on susceptibility of red cells to Plasmodium falciparum. Nature 270, 171-3 (1977)
3. Shear, H.L. et al. Transgenic mice expressing human fetal globin are protected from malaria by a novel mechanism. Blood 92, 2520-6 (1998)
4. Witt, O. et al. Induction of fetal hemoglobin expression by the histone deacetylase inhibitor apicidin. Blood 101, 2001-7 (2003)
5. Andrews, K.T. et al. Anti-malarial effect of histone deacetylation inhibitors and mammalian tumour cytodifferentiating agents. Int J Parasitol 30, 761-8 (2000)
6. Glenn, M.P. et al. Antiproliferative and phenotype-transforming antitumor agents derived from cysteine. J Med Chem 47, 2984-94 (2004)

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Clinical Tropical Medicine Laboratory
Dr Kate Mounsey
07-3362 0408
Dr James McCarthy
07-3845 3725
Email Kate.Mounsey@qimr.edu.au

[H,  M  P]

Scabies

Immunopathology of an experimental infestation of Sarcoptes scabiei var. suis in dexamethasone treated pigs

Dexamethasone (DEX) is a glucocorticosteriod (GC) commonly used to simulate stress induced-immunosuppression. It is often used in animal models to promote infection and exacerbate infectious responses. We have recently established an experimental infestation of the scabies mite, Sarcoptes scabiei on pigs as a disease model and source of material for molecular-based research on human scabies. We are treating mange model pigs with dexamethasone in an attempt to maintain optimal severity of infestation and prolong infection.

There is little information regarding the effects of DEX on animal immunity, particularly in pigs. Similarly, little is understood regarding host immune responses to scabies.

As with other parasitic diseases, the protective versus pathogenic response to scabies is thought to be mediated by Th- responses, with hyper-infested patients and non-protected hosts hypothesised to display a Th-2 biased response. The delayed hypersensitivity response to scabies is proposed to occur due to proliferation of Tregs and IL10 secretion, however much work needs to be done to further elucidate host immune responses to scabies.

This project will compare and contrast immune markers of interest in mange infested pigs undergoing dexamethasone treatment compared to non-immunosuppressed pigs. In order to optimise mite infestation whilst maintaining the highest possible standards of animal health and welfare, a better understanding of the effect of DEX on the general health, innate immunity, and scabies specific immune responses in pigs is critical.

Acaricidal activity of natural product-derived compounds on scabies mites

Scabies is a skin disease caused by the ectoparasitic mite Sarcoptes scabiei. Infection causes significant morbidity, with an estimated 300 million people affected at any one time. Recent data indicates that there is increasing tolerance of scabies mites to the acaricides permethrin and ivermectin- the two most commonly used treatments for scabies. The emergence of drug resistance is a serious threat to control programs in scabies endemic regions, such as remote aboriginal communities in northern Australia. As such, alternative drugs for scabies will likely be needed in future.

Natural product compounds are potential new sources of alternative acaricides. Most natural product-based research to date has focussed on a small number of essential oil extracts, and very only very limited screening has been performed using Sarcoptes scabiei. This project will utilize a recently established experimental model of scabies to evaluate the acaricidal activity of several natural product extracts and compounds. Mites will be harvested on a regular basis and tested using in-vitro drug sensitivity bioassays against a range of natural products.

Results obtained from this preliminary screening stage may have profound implications on the development of new drugs for scabies

We welcome interested honours / masters / PhD students to discuss opportunities regarding this project.

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Mosquito Control Laboratory
Dr Peter Ryan
07-3362 0351
Email Peter.Ryan@qimr.edu.au
Email Tim Hurst,Jason Jeffery & Jonathan Darbro

[H,  P]

Mosquito Control

PhD student top up Scholarships and APA Top Up Scholarships available for 2009

The School of Integrative Biology, The University of Queensland
Laboratories of Professor Scott O'Neill and Dr Elizabeth McGraw
The Queensland Institute of Medical Research

Dr Peter Ryan and Prof Brian Kay, Mosquito Control Laboratory and the Australian Centre for International and Tropical Health and Nutrition The UQ/QIMR team is internationally recognised for its contribution to the fields of Wolbachia endosymbionts and host interaction, medical entomology including biological control of medically important vectors, and translation of research into practical public health interventions. Based on this track record, we have been funded by the NHMRC to develop new methodologies for the management of emerging vector-borne disease threats in Australia.

The project involves the infection of mosquito vectors with an endosymbiotic bacterium, Wolbachia pipientis, that is capable of reducing insect lifespan. Characterisation of the Wolbachia life-shortening affects in a range of globally important mosquito vectors (Aedes, Culex spp) and the affect of this life-shortening on arbovirus (dengue, Chikungunya, Ross River, and Barmah Forest viruses) transmission efficiency will be determined.

We will also extend our current transcription profiling methods and develop new proteomic and metabonomic based methods for determining insect age, and undertake field assessments of vector population age structure to determine pathogen transmission risk and the applicability of Wolbachia and other novel control strategies.

Current student projects may include laboratory assessments of transcriptomic, proteomic and metabonomic changes with age in mosquitoes and the development of new tools to determine vector population age structure. Techniques involved include real time RT-PCR, mass spectrometry and H1 Nuclear Magnetic Resonance in collaboration with the Institute for Molecular Bioscience, University of Queensland.

Other projects may include artificial transinfection of mosquito species, the study of Wolbachia induced pathogenesis, an examination of mosquito life history traits, characterisation of the human host seeking and biting behaviour of infected mosquitoes, arbovirus vector-competence assessments, laboratory and field based assessments of insect age grading and vector population age structure.

We are seeking students with experience in any of the following fields; molecular biology, biochemistry, evolutionary biology, genetics, entomology, microbiology, and behaviour.

The School of Integrative Biology (SIB) is a vibrant unit with a history of and an ongoing commitment to research excellence and postgraduate mentoring. Examples of SIB support for postgraduates include travel grants, writing workshops, media training, social events with visiting speakers, postgraduate retreat weekends, etc.

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Scabies Laboratory
Dr Katja Fischer
Dr Angela Mika
07-3362 0416
Email Angela.Mika@qimr.edu.au

[H,  MPhil]

Scabies mite serpins

Scabies is a disease of worldwide importance caused by burrowing of the parasitic mite Sarcoptes scabiei into the lower stratum corneum of the human epidermis. High prevalence is common in disadvantaged populations such as indigenous Aboriginal communities in the Northern Territory, immunodeficient patients and residents of nursing homes.

Scabies is often accompanied by streptococcal infections with significant sequelae (cellulitis, septicaemia, and glomerulo-nephritis), and with the highest prevalence in younger children. In recent years resistance against the standard chemotherapy treatments emerged.

The scabies laboratory group at QIMR works on a number of projects including serine proteases, cysteine proteases and serine protease inhibitors (Serpins). The overall aim of these projects is to find out how the scabies mite evades the human immune system. This may lead to new vaccine and drug development in the future.

The project work would include a broad range of methods in molecular biology, enzymology, and protein biochemistry.

Hons/Masters Projects are available in 2009 in the following subject areas:

Expression and functional analysis of serpin B9

Since pre-work experiments showed that other scabies mite Serpins are able to inhibit parts of the human immune system, we want to find out, whether Serpin B9 is able to inhibit the human complement system, the blood clotting cascade, and/or the inflammatory response.

Screening of scabies mite cDNA libraries for unknown serpins

Six scabies mite serpins were identified until now, but preliminary work indicates the presence of several more variants in the scabies genome. The identification of new serpin sequences, and their sequence analysis would be very interesting.

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Molecular Parasitology Laboratory
Prof Don McManus
07-3362 0401
Email Don.McManus@qimr.edu.au

[H,  P,  TU]

Parasitic Worms and disease

Our laboratory researches the biology and epidemiology of parasitic worms of humans and we aim to develop new interventions and diagnostic procedures that will lead to their elimination. We work on schistosomiasis and echinococcosis (hydatid disease), two major diseases caused by parasitic worms.

The schistosomiasis research has a field focus in China and we have the following projects suitable for Honours and PhD students:

• Epidemiological and human genetic studies to determine genetic factors associated with infection and disease. Do variants in the IL-5 gene contribute to risk of acute schistosomiasis, the manifestation of a hyper-allergenic response to infection with Schistosoma japonicum?
• Analysing the molecular and cellular mechanisms leading to formation of fibrotic hepatic lesions, the major contributing source of the chronic disease of schistosomiasis;
• Using a gene microarray, that contains the majority of the schistosome transcriptome, along with protein arrays, proteomics analysis and laser capture microscopy to investigate differential gene expression during different stages of the schistosome lifecycle, strain variation and the effect of drugs and vaccines on schistosome worms.
• Studies on schistosome iron metabolism, dyneins, secreted enzymes and surface molecules, including and receptors, such as the insulin receptor, to determine their potential as novel targets for drugs and vaccines.
• Assessment of vaccines in murine models and buffaloes in China.

Projects for Honours and PhD students on echinococcosis include:

• Field and epidemiological studies in China and the use of advanced immunological and microarray techniques to test whether patients with the disease have different cytokine and immunoglobulin expression profiles;
• Genetic studies to determine whether specific polymorphisms both within the major histocompatibility complex (MHC) (HLA) and non-HLA genes influence host susceptibility to infection and disease progression
.
• The development of highly sensitive and specific blood testS for diagnosis of patients infected with cystic hydatid disease and its application for detection of the disease in sheep and marsupials.
• Development of a dog vaccine against echinococcosis in collaboration with several interested commercial partners.

For examples of some of our recent work, see the following papers.

• Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium, Liu, F., Zhou, Y., Wang, Z.Q., Lu, G., Zheng, H., Brindley, P.J., McManus, D.P., Blair, D., Zhang, Q.H., Zhong, Y., Wang, S., Han, Z.G., Chen, Z. (2009). The Schistosoma japonicum genome reveals unique features of host-parasite interplay. Nature 460: 345-352
.
• McManus, D.P., Li, Y., Gray, D.J., and Ross, A.G. (2009). Conquering 'snail fever': schistosomiasis and its control in China. Expert Review of Anti-infective Therapy 7:473-485.
• Gobert, G.N., McManus, D.P., Nawaratna, S., Moertel, L., Mulvenna, J. and Jones, M.K. (2009). Tissue specific profiling of the human pathogen Schistosoma japonicum by integrated laser microdissection microscopy and microarray analysis. PLoS Neglected Tropical Diseases 3:e469.
• McManus, D.P. and Loukas A. (2008). The current status of vaccines for schistosomiasis. Clinical Microbiology Reviews 21: 225-242.
• Zhang, W. and McManus, D.P. (2008). Vaccination of dogs against Echinococcus granulosus: a means to control hydatid disease? Trends in Parasitology 24:419-424. Gray, D.J., Williams, G.M., Li, Y.S. and McManus, D.P. (2008). Transmission dynamics of Schistosoma japonicum in the lakes and marshlands of China. PLoS ONE 3:e4058.
• Da'Dara, A.A., Li, Y.S., Xiong, T., Zhou, J., Williams, G.A., McManus, D.P., Feng, Z., Yu, X.L , Gray, D.J. & Harn, D.A. (2008). DNA-based vaccine protects against zoonotic schistosomiasis in water buffalo. Vaccine 26:3617-3625.
• Moertel, L., Gobert, G. & McManus, D.P. (2008). Comparative real time PCR and enzyme analysis of selected gender-associated molecules in Schistosoma japonicum. Parasitology 135:575-583.
• Ellis, M.K., Zhen Zhen Zhao, Z.Z., Chen, H-G., Montgomery, G.W., Li, T.S. & McManus, D.P. (2007). Analysis of the 5q31-33 locus shows an association between SNP variants in the IL-5 gene and symptomatic infection with the human bloodfluke, Schistosoma japonicum. Journal of Immunology 179: 8366-8371.
• Ellis, M.K., Raso, G., Li, Y.S., Rong, Z., Chen, H. and McManus, D.P. (2007). Familial aggregation of human susceptibility to co- and multiple helminth infections in a population from the Poyang Lake region, China. International Journal for Parasitology 37:1153-1161.
• Jones, M.K., McManus, D.P., Sivadorai, P., Glanfield, A., Moertel, L., Belli, S.I., Gobert, G.N. (2007). Tracking the fate of iron in early development of human blood flukes. The International Journal of Biochemistry & Cell Biology 39:1646-1658.
• Glanfield, A., McManus, D.P., Anderson G.J. and Jones, M.K. (2007). Pumping iron: a potential target for novel therapeutics against schistosomes. Trends in Parasitology 23:583-588.
• Zhang, W.B., Zhang, Z.Z., Shi, B.X., Li, J., You, H., Tulson, G., Dang, X.S., Song, Y.C., Yimiti, T., Wang, J.C., Jones, M.K. and McManus, D.P. (2006). Vaccination of dogs against Echinococcus granulosus, the cause of cystic hydatid disease in humans. Journal of Infectious Diseases 194: 966-974.
• Liu, F., Lu, J., Hu, W., Wang, S-Y., Cui, S-J., Chi,, M., Yan, Q., Wang, X-R., Song, H-D., Xu, X-N., Wang, J-J., Zhang, X-L., Zhang, X., Wang, Z-Q., Xue, C-L., Brindley, P.J., McManus D.P., Yang, P-Y., Feng Z., Chen, Z. and Han, Z-G. (2006). New perspectives on host parasite interplay by comparative transcriptomic and proteomic analyses of the human blood fluke Schistosoma japonicum. PLOS Pathogens Apr 14;2(4).

Scholarship top-ups are available. For more information, contact Professor Don McManus.

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Immunology Division

Bone Marrow Transplantation Laboratory
Prof Geoff Hill
07-3845 3763
Dr Kelli McDonald
07-3362 0404
Email Geoff.Hill@qimr.edu.au
Email Kelli.MacDonald@qimr.edu.au

[H, P]

Bone Marrow Transplantation

Allogeneic Bone Marrow Transplantation remains the procedure of choice for the cure of a number of haematologic malignancies (e.g. leukemia and lymphoma) and severe immunodeficiencies. The procedure results in cure rates up to 75% but is limited by its serious complications, particularly graft-versus-host disease (GVHD).

This is the process whereby the newly transplanted immune system recognises the transplant recipient as "foreign" and mounts a rejection response. Recently the use of cytokines has allowed the transplantation of blood stem cells (referred to as stem cell transplantation-SCT) that has replaced BMT in clinical practise.

Our laboratory has been at the forefront of understanding how these cytokines effect GVHD.1-8 We aim to improve transplant outcome by utilising preclinical transplant models where immunological mechanisms of transplant rejection can be dissected so that rational therapeutic strategies can be developed and trialed in clinical practise.

Our laboratory has established NH&MRC program and project grant funding together with additional grants from the QLD cancer council, Leukeumia Foundation and Pharma. There are two NH&MRC fellows within the lab, multiple experienced RA's and additional post-docs that ensure a very productive environment.

We have the following exciting projects that utilize novel new reagents that are suitable for Honours and particularly PhD students.

The contribution of dendritic cell paralysis and failure of maturation to immune suppression after BMT.

BMT is characterized by marked immune suppression and subsequent opportunistic infections. We have shown that development of GVHD after transplantation prevents the maturation and function of dendritic cells, the white cell subtype that is critical for initiating immune responses.

This project will focus on the characterization of these defects, their cause and development of an effective therapeutic strategy to overcome this defect. Ultimately this will improve immune reconstitution and reduce the incidence of life threatening infections in transplant recipients.

Characterization of the requiurments for control of cytomegalovirus infections after BMT.

The archetypal infection after BMT is that caused by re-activation of the cytomegalovirus, causing infection in lung (pneumonia), bowel (enteritis), liver (hepatitis) and brain ( encephalitis). The cellular mechanisms by which CMV is controlled after BMT and the influence of GVHD on this process remains poorly understood. In association with our program collaborator (Dr Mariapia Degli-Esposti)9,10 we are generating the first models of true CMV reactivation after BMT so that these questions can finally be addressed.

Additionally, in collaboration with Assoc Prof Rajiv Khanna at QIMR we are trialing the efficacy of the first CMV vaccine in the BMT setting in an attempt to eliminate CMV as a source of disease in transplantation.

Characterization of the effect of stem cell tranplantation on Th17 differentiation after clinical BMT.

Recently, a completely new paradigm of T cell differentiation has been identified, termed Th17 because of the generation of IL-17 by CD4 T cells. Our preliminary animal data suggests these T cells have an important role in particular complications after transplantation. This study will be undertaken on a clinical cohort of transplant recipients at the RBWH transplant unit to translate these findings to the clinic and provide a rational for a subsequent therapeutic trial to manipulate this pathway in the transplant setting.

The immunological consequences of alternative stem cell mobilization strategies

. There are increasing therapeutic alternatives to the use of G-CSF (granulocyte colony stimulating factor) for stem cell mobilization. Most of these are chemokine antagonists and it is likely that the mobilization of stem cells in normal donors for use in transplantation will evolve into combinations of G-CSF and these agents.

We have described the immunological effects of G-CSF on immune function and in this project will extend these studies to these new agents. This will be critical to the translation of these agents to the clinic as it is not clear whether the immune modulation seen in current stem cell mobilization protocols is due to G-CSF or stem cell mobilization itself. These studies will provide the rationale for new protocols of stem cell mobilization in clinical transplantation.

For more information about these projects please contact Prof Geoff Hill or Dr Kelli MacDonald.

References

1. MacDonald KP, Rowe V, Clouston AD, et al. Cytokine expanded myeloid precursors function as regulatory antigen-presenting cells and promote tolerance through IL-10-producing regulatory T cells. J Immunol. 2005;174:1841-1850.
2. MacDonald KP, Rowe V, Bofinger HM, et al. The colony-stimulating factor 1 receptor is expressed on dendritic cells during differentiation and regulates their expansion. J Immunol. 2005;175:1399-1405.
3. Macdonald KP, Kuns RD, Rowe V, et al. Effector and regulatory T-cell function is differentially regulated by RelB within antigen-presenting cells during GVHD. Blood. 2007;109:5049-5057
.
4. Morris ES, MacDonald KPA, Rowe V, et al. Donor treatment with pegylated G-CSF augments the generation of IL-10 producing regulatory T cells and promotes transplant tolerance. Blood. 2004;103:3573-3581.
5. Morris ES, Macdonald KP, Rowe V, et al. NKT cell-dependent leukemia eradication following stem cell mobilization with potent G-CSF analogs. J Clin Invest. 2005;115:3093-3103.
6. Morris ES, MacDonald KP, Hill GR. Stem cell mobilization with G-CSF analogs: a rational approach to separate GVHD and GVL? Blood. 2006;107:3430-3435
.
7. Rowe V, Banovic T, Macdonald KP, et al. Host B cells produce IL-10 following TBI and attenuate acute GVHD after allogeneic bone marrow transplantation. Blood. 2006;107:2485-2492.
8. Banovic T, MacDonald KP, Morris ES, et al. TGF-beta in allogeneic stem cell transplantation: friend or foe? Blood. 2005;106:2206-2214.
9. Andrews DM, Scalzo AA, Yokoyama WM, Smyth MJ, Degli-Esposti MA. Functional interactions between dendritic cells and NK cells during viral infection. Nat Immunol. 2003;4:175-181.
10. Andrews DM, Andoniou CE, Granucci F, Ricciardi-Castagnoli P, Degli-Esposti MA. Infection of dendritic cells by murine cytomegalovirus induces functional paralysis. Nat Immunol. 2001;2:1077-1084.
11. Walker S, Fazou C, Crough T, et al. Ex vivo monitoring of human cytomegalovirus-specific CD8+ T-cell responses using QuantiFERON-CMV. Transpl Infect Dis. 2007;9:165-170.

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Dendritic Cells and Cancer Laboratory
A/Prof Alejandro Lopez
Ph: 07-3845 3794
Email Alejandro.Lopez@qimr.edu.au

[ H, P]

Harvesting Cancer Stem cells for Immunotherapy

A disruption of somatic stem cells is postulated as the origin of cancer(1). The idea that transformed stem cells initiate tumours was first confirmed in the 1990s, based on studies of acute myeloid leukaemia and has since been strengthened by findings related to brain and breast cancer.

In 2003 Clarke and colleagues provided evidence that a small population of human breast cancer cells, identified as CD44+, CD24-/low Lineage-, had the ability to form tumours when as few as 100 cells of this phenotype were transplanted into NOD/SCID mice(2). While no conclusive evidence is available, it appears that other markers and biological patterns might be more specific in identifying CSC and this is the focus of intensive research.

If transformed cells with stem cell-like properties are indeed one of the major culprits in tumour establishment and growth, conventional approaches, which target the heterogeneous body of cancer cells in a relatively non-specific fashion, will spare the tumour stem cells due to their unique properties.

We investigate the potential use of these cells in the development of immunotherapies.

Current research in our laboratories investigates various aspects of the biology and immunology of these cells:

• Phenotypic markers
• Optimal growth conditions
• Immunological footprint
• Key antigens
• Tumour inducing potential

Most of the current knowledge on CSC relates to breast cancer and our research on dendritic cells (DC) as key elements on the development of this disease(3) suggests that combining DC with BCSC would be an attractive immunotherapeutic approach. At the same time, we investigate CSC in melanoma, prostate cancer and glioblastoma.

A number of projects are available and they develop expertise in a wide array of techniques including:

• Flow cytometry including intracellular cytokine production assays
• Specialised tissue culture
• Functional immunological techniques including ELISA, ELISPOT
• T-cell cloning and evaluation
• Tumour xenograft models

1. Morrison, B. J., C. W. Schmidt, S. R. Lakhani, B. A. Reynolds, and J. A. Lopez. 2008. Breast cancer stem cells: implications for therapy of breast cancer. Breast Cancer Res 10:210.
2. Al-Hajj, M., M. S. Wicha, A. Benito-Hernandez, S. J. Morrison, and M. F. Clarke. 2003. Prospective identification of tumorigenic breast cancer cells. Proc Natl Acad Sci U S A 100:3983-3988.
3. Pinzon-Charry, A., C. Schmidt, and J. A. Lopez. 2006. Dendritic cell immunotherapy for breast cancer. Expert Opin Biol Ther 6:591-604.

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Immunology and Infection Laboratory
Dr Christian Engwerda
Ph: 07-3362 0428
Email Christian.Engwerda@qimr.edu.au

[ H, P]

Immune events in malaria and leishmaniasis

Cerebral malaria (CM) and visceral leishmaniasis (VL) are significant parasitic diseases in the developing world. We work with experimental models of CM caused by Plasmodium berghei and VL caused by Leishmania donovani. Both protozoan parasites induce strong inflammatory immune responses by their hosts that contribute to the development of tissue pathology. One of the major aims of the Immunology and Infection laboratory is to understand how these inflammatory responses are initiated, identify the immune cells that cause pathology and to devise strategies to protect the host from disease, without impeding the development of protective immunity.

We focus on two stages of infection. First, the priming of parasite-specific T cells that produce inflammatory mediators, and second, the migration of activated T cells to sites of infection and their interaction in local tissue micro-environments. Many of our studies are performed in situ with infected tissue so that we avoid changes to cell behaviour once they have been removed from local tissue micro-environments. Therefore, these studies require the use of unique reagents and specialised techniques such as immunohistochemistry, confocal microscopy, and whole-tissue imaging. Other techniques used extensively in our laboratory include real-time RT-PCR, FACS, Western blotting and various molecular and cell biology techniques.

Students in our laboratory would become familiar with all of these techniques. There is also opportunity for successful Honours students to enrol for PhD studies and continue work in the Immunology and Infection laboratory. PhD students awarded a competitive scholarship (eg. Australian Postgraduate Award) will receive a $10,000 top-up scholarship.

Developing vaccines to prevent malaria and visceral leishmaniasis

We are currently developing strategies to use killed, whole parasite vaccines to prevent malaria and visceral leishmaniasis. To date, we have had partial success in using these vaccines to generate anti-parasitic immunity. However, one part of our current approach that requires improvement is the choice of adjuvant. Therefore, this project will investigate different adjuvants and immunomodulatory strategies to improve vaccine efficacy. As part of these studies, a wide range of immunological parameters will be examined, including T cell responses and the generation of immunological memory.

This work will be the first step in developing effective vaccines that can prevent malaria and visceral leishmaniasis in humans.

References:

1. Good M.F., H. Xu, M. Wykes, and C. R. Engwerda. 2005. Development and regulation of cell-mediated immune responses to blood stages of malaria: Implications for Vaccine Research. Ann Rev Immunol 23:69
2. DeWalick, S., F. H. Amante, L. M. Randall, Y, Zhou, K. P. A. MacDonald, G. R. Hill and C. R. Engwerda. 2007. Cutting Edge: Conventional dendritic cells, but not plasmacytoid dendritic cells, mediate experimental cerebral malaria caused by Plasmodium berghei ANKA. J. Immunol. 178: 6033-6037.
3. Amante, F. H., A. C. Stanley, L. M. Randall, Y. Zhou, A. P. Waters, C. J. Janse, M. F. Good, G. R. Hill and C. R. Engwerda. 2007. A role for natural regulatory T cells in the pathogenesis of experimental cerebral malaria. Am. J. Path. 171: 548-549.
4. Randall, L. M., F. H. Amante, Y. Zhou, A. C. Stanley, A. Haque, F. Rivera, K. Pfeffer, S. Scheu, G. R. Hill, K. Tamada and C. R. Engwerda. 2008. Cutting Edge: Selective blockade of LIGHT-LTR signalling protects mice from experimental cerebral malaria caused by Plasmodium berghei ANKA. J. Immunol. 181:7458

The generation of parasite-specific T cell responses during malaria and visceral leishmaniasis

An important feature of many parasitic infections is that T cell responses are impaired. We now have research tools available that allow us to track developing parasite-specific T cell responses in vivo during either malaria of visceral leishmaniasis. This project will use these tools to examine the tissue sites where T cell responses are generated, as well as to identify the antigen presenting cells (APC) that interact with parasite-specific T cells. By identifying the different types of APC that activate T cells during infection and the tissue sites where these events occur, we will be able to determine ways to improve T cell activation. This will allow the design of better vaccines or immunomodulatory strategies to prevent and/or treat disease.

Furthermore, by identifying different APC involved in generating anti-parasitic immunity we can also devise ways to manipulate these cells to directly improve disease outcomes.

References:

1. Engwerda, C. R., M. Ato, S. Stager, C. E. Alexander, A. C. Stanley and P. M. Kaye. 2004. Distinct roles for lymphotoxin alpha and TNF in murine visceral leishmanaisis. Am J Pathol 165: 2123.
2. Stanley, A. C., and C. R. Engwerda. 2006. Balancing Immunity and Pathology in Visceral Leishmaniasis. Immunol Cell Biol 85:138
3. Stanley, A. C., Y. Zhou, F. H. Amante, L. M. Randall, A. Haque, D. G. Pellicci, M. J. Smyth, D. I. Godfrey, and C. R. Engwerda. 2008. Activation of invariant NKT cells exacerbates experimental visceral leishmaniasis. PLoS Pathogens 4: e1000028
4. Stanley, A. C., J. E. Dalton, S. H. Rossotti, K. P. MacDonald, Y. Zhou, F. Rivera, W. A. Schroder, A. Maroof, G. R. Hill, P. M. Kaye, and C. R. Engwerda. 2008. VCAM-1 and VLA-4 modulate dendritic cell IL-12p40 production in experimental visceral leishmaniasis. PLoS Pathogens 4: e1000158

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Molecular Immunology Laboratory
Dr Colleen Olive
07-3362 0431
Email Colleen.Olive@qimr.edu.au

[H,  P]

The Vaccines and Immunity group

Novel vaccine adjuvant delivery systems and group A streptococcus

Investigation of T-helper polarising capacity of Toll-like receptor-stimulated dendritic cells

The development of new approaches to vaccine therapies is fundamental and essential research, with broad-reaching applications to an array of infectious diseases. Dendritic cells (DCs) are the major target of vaccine therapies, as they are the key mediators between innate detection of antigen, and development of appropriate adaptive (T-helper) immune responses. The balance between inflammatory and anti-inflammatory cytokine production in DCs is crucial in determining the type of T-helper responses, in that IL-12 drives polarisation of CD4+ T-cells towards Th1 and mediates immunity to intracellular pathogens, whereas IL-4 is involved in skewing a Th2 response crucial for immunity against parasitic infections. We have shown that DCs stimulated by multiple TLR ligands synergistically enhanced cytokine production.
This project aims to investigate the nature of T-helper responses elicited in response to TLR-stimulated DCs.

Investigation of cell signaling pathways of Toll-like receptor-stimulated dendritic cells

The manipulation of TLR signaling pathways in DCs favouring Th1 or Th2 polarisation is a potential strategy with which to fine-tune the generation of particular immune responses elicited by peptide vaccines, depending on the nature of the specific target pathogens. The hypothesis is that the molecular dissection of the cell signaling mechanisms that underpin TLR synergy in DCs will lead to new ways to polarise DC activation to best support the desired outcome to vaccine therapies.

This project will explore TLR synergy and cell signaling in DCs, and will include investigation of the kinetics of nuclear transcription factor-kappa B (NF-kB), mitogen-activated protein kinases (MAPK), and phosphoinositide 3-kinase (PI3K) activation in response to single and dual TLR-stimulated DCs.

Role of Syk-Card9-Bcl10-Malt1 and Raf-1 signaling in Toll-like receptor activated dendritic cells

The innate immune system recognises various pathogens through different pattern recognition receptors (PRRs) such as Toll-like receptors (TLRs). The activation of these receptors initiates a series of signaling pathways which leads to the rapid activation of nuclear transcription factor-kappa B (NF-kB) and mitogen-activated protein kinases (MAPK), and production of inflammatory cytokines. Rather than function in isolation, it is becoming increasing clear that interplay between different classes of PRRs is vital for establishing effective immunity.

We are particularly interested in understanding the cross-talk between TLRs and the C-type lectin receptor Dectin-1 (another type of PRR) in DCs. This project will investigate the Syk-signaling pathway in TLR-activated DCs. The Syk pathway is important in signaling through Dectin-1 and anti-fungal immunity. Signaling through Dectin-1 also induces a second independent pathway through the kinase Raf-1.

There is evidence for Dectin-1 cross-talk with TLR2 signaling in that Dectin-1 enhances TLR2-induced cytokine responses in a Syk-independent but Raf-1 dependent manner. This project will investigate whether signaling through other TLRs can be modulated by Dectin-1 and the role of Syk and Raf-1 in this dectin-1-TLR cross-talk.

Induction of type I interferons in plasmacytoid dendritic cells stimulated by multiple Toll-like receptor agonists and the role of PI3K-mTOR signaling

The production of type I interferons (IFN- / ) in plasmacytoid DCs (pDCs) is crucial for antiviral immunity and depends on recognition of viral components by TLRs. This project will investigate the potential for TLR synergy in pDCs in enhancing antiviral responses. This project will also investigate the role of the rapamycin-sensitive phosphoinositide 3-kinase (PI(3)K)-mTOR signaling pathway, which has recently been shown to be important in the TLR-mediated induction of type I interferons in pDCs. Our recent data indicate an important role for the PI3K pathway as a positive regulator of TLR signaling in simultaneously TLR stimulated DCs however this project will specifically focus on the pDC subset of DCs.

Modulation of Toll-like receptor expression and cross-talk among Toll-like receptors and their ligands

To date 13 mammalian TLRs have been identified and together they form a major class of PRRs important in pathogen sensing. Each TLR can recognise a particular pathogen-associated molecular pattern (PAMP) for example TLR4 is responsible for the recognition of bacterial lipopolysaccharide whereas TLR3 recognises viral RNA. This project aims to investigate whether various TLR ligands can modulate the expression of different TLRs and identify positive and negative TLR regulatory networks, which could potentially identify new approaches to modulate immune responses.

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Molecular Immunology Laboratory
Dr Michelle Wykes
07-3362 0429
Email Michelle.Wykes@qimr.edu.au

[H,  P]

Understanding the role of Dendritic cells in mediating protection against malaria.

Malaria kills up to 5 million people each year, mostly children under 5. The severity of malaria can range from asymptomatic to lethal infections involving severe anemia and cerebral disease. However, the molecular and cellular factors responsible for these differences in disease severity are poorly understood. Identifying the factors that mediate virulence will contribute to developing cures for malaria.

Background

Since immunity is initiated by Dendritic cells (DC), we studied their function following infection with either a non-lethal or lethal strain of the rodent parasite, Plasmodium yoelii, to identify their contribution to disease severity.

Principal Findings

DC from non-lethal infections were fully functional and capable of secreting cytokines and stimulating T cells. In contrast, DC from lethal infections were not functional [1-3].

Conclusions/Significance

Our studies have shown for the first time that during a malaria infection DC function is essential for survival. More importantly, the functions of these DC are determined by the strain of parasite. Our studies may explain in part, why natural malaria infections may have different outcomes.

Hypothesis

Understanding the cellular and molecular basis of protection by DC against malaria will lead to novel therapies.

Approaches

We have previously shown that DC from mice with non-lethal infections can protect against lethal infections. We now have evidence that different DC populations mediate protection by different mechanisms. As such, we will use cell transfer studies to identify the mechanism.

References

1. Wykes MN, Good MF. What really happens to dendritic cells during malaria? Nat Rev Microbiol 2008
2. Wykes MN, Liu XQ, Beattie L, et al. Plasmodium Strain Determines Dendritic Cell Function Essential for Survival from Malaria. PLoS Pathog 2007;3:e96
3. Wykes MN, Liu XQ, Jiang S, Hirunpetcharat C and Good MF. Systemic tumor necrosis factor generated during lethal Plasmodium infections impairs dendritic cell function. J Immunol 2007;179:3982-7.

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Molecular Vaccinology Laboratory
Dr Denise Doolan
07-3362 0382
Email Denise.Doolan@qimr.edu.au

[H,  P]

Evaluation of natural product based adjuvants for vaccination

Natural products have greatly contributed to the therapeutic treatment of numerous human diseases, and approximately one third of the world's top-selling drugs are natural products or their derivatives. However, natural products have not been extensively evaluated for vaccine applications. There is an urgent unmet need for compounds which can enhance vaccine efficacy and which are nontoxic and suitable for clinical use, and there is a particular need for compounds which can adjuvant vaccine-induced cellular immunity.

Accordingly, this research project will investigate the imunomodulatory or therapeutic activity of a subset of natural products derived from plants or marine invertebrates, in preclinical vaccine models of malaria or cancer. The aim is to identify and characterize compounds within natural product collections that have significant vaccine adjuvant activity, as assessed by T cell and antibody responses and protection.

The identification of such compounds would have important implications for developing effective vaccines against a range of pathogens which threaten public health.

References

1. Doolan DL, Southwood S, Freilich DA, et al. 2003. Identification of Plasmodium falciparum antigens by antigenic analysis of genomic and proteomic data. Proc Natl Acad Sci USA. 100(17):9952-57.
2. Doolan DL, Aguiar JC, Weiss WR, et al. 2003. Utilization of genomic sequence information to develop malaria vaccines. J Exp Biol. 206(21):3789-3802.
3. Doolan DL and Martinez-Alier N. 2006. Immune response to pre-erythrocytic stages of malaria parasites. Curr Mol Med. Feb. 6(2):169-85.
4. Doolan DL, Mu Y, Hirst S, et al. Profiling the humoral immune response to Plasmodium falciparum infection in clinically distinct cohorts of humans using protein microarrays. Proteomics. In Press.
5. Doolan DL, Dobaño C, and Baird KJ. Acquired immunity against malaria. Clin. Micro. Rev. In Press.

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Immunovirology Laboratory
Prof Andreas Suhrbier
07-3362 0415
Email Andreas.Suhrbier@qimr.edu.au

[  P]

Arthritis caused by chikungunya virus

Chikungunya virus (CHIKV) is a mosquito borne alphavirus, related to Ross River virus, that has caused periodic outbreaks of predominantly rheumatic disease in Africa and Asia. "Chikungunya" is derived from the Makonde language (Tanzania) and means "that which bends up", referring to the joint-pain-induced posture of afflicted individuals.

Recently the largest documented outbreak of CHIKV disease occurred in the Indian Ocean islands and India during 2004-2007. Over 260,000 cases (?1/3 of the population) were reported in Reunion Island (France) with 1.39 million cases in India and a small outbreak of ?200 cases also occurring in Italy. CHIKV has been declared a high priority pathogen by the NIH (USA) and is a PC3 organism. No licensed vaccine or particularly effective drug is available for human use for any alphavirus.

We have recently developed the first adult wild type mouse model of CHIKV arthritis, which we now hope to exploit to answer some fundamental questions about the mechanisms (cytokines, chemokines, viral evasion of host responses, viral induction of cell death etc) that cause arthritis and the factors used by the mouse ultimately to cure the disease.

Understanding these processes will also have important implications for treatment of autoimmune arthritides like rheumatoid arthritis. Array technology, knockout mouse strains, and a series of immunological techniques will be applied to the problem. Ultimately the model will be used to test new prophylactic (eg vaccines) and therapeutic interventions.

The undecided Serpin

SerpinB2, also known as plasminogen activator inhibitor type-2 (PAI-2), is one of the most abundantly expressed proteins in differentiating keratinocytes (4-7% of total protein) and activated monocyte/macrophages (1-2% of total protein). It is expressed at nearly all sites of inflammation and inappropriate expression is associated with a number of diseases including pre-eclampsia, asthma, periodontal disease and cancer.

SerpinB2 is a member of the Clade B or ovalbumin-like serine protease inhibitor (ov-serpin) subgroup of the serpin superfamily, which includes proteinase inhibitor 6, 8 & 9, MENT, Bomapin and maspin. SerpinB2 is well described as an inhibitor of the extracellular urokinase plasminogen activator (uPA), with SerpinB2 able to inhibit uPA in vitro. Unfortunately, evidence that this represents the major physiological role of SerpinB2 in vivo is not compelling. SerpinB2-/- mice show no defect in the plasminogen activation system, and the double knockout PAI-1-/-/SerpinB2-/- animals show no additional defect in plasminogen activation over PAI-1-/- mice.

A bewildering array of functions for SerpinB2 have been reported; with the true physiological role of SerpinB2 entirely unclear. We have recently generated for the first time a fully backcrossed SerpinB2 knockout mouse, which we are exploiting to understand the physiological role of SerpinB2.

Recent experiments have illustrated that SerpinB2 expression in macrophages regulates the Th1 bias of antibody and T cells responses. This entirely novel observation begins to explain the clinical findings for SerpinB2 expression and has opened up an entire area for research. Using a number of molecular, biochemical and immunological techniques we hope to unravel the exact molecular mechanism whereby SerpinB2 expression leads to suppression of inflammatory cytokine release from activated macrophages.

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Cancer and Cell Biology Division

Cancer Genetics Laboratory
Dr Georgia Chenevix-Trench
07-3362 0390
Email Georgia.Trench@qimr.edu.au
[ H,  P]

Cancer Genetics

Inherited predisposition to breast and ovarian cancer is caused in part by mutations in the BRCA1 and BRCA2 genes, but only about one third of families with a strong family history of breast cancer carry mutations in these genes. We are looking for other genes which might predispose to breast or ovarian cancer, using families from the Australasian consortium of familial breast cancer, kConFab (http://www.kconfab.org), to identify high-penetrance genes, and case-control studies to identify low-penetrance genes. Furthermore, BRCA1/2 mutations show incomplete penetrance and variable expression.

In collaboration with the international Consortium for Investigators of Modifiers of BRCA1/2 (CIMBA), we are studying BRCA1/2 mutation carriers in order to identify genes that modify the expression of BRCA1/2. We also have an interest in genes involved in response to chemotherapy in ovarian cancer patients, and plan to do a genome-wide association study of this trait in cases from the Australian Ovarian Cancer Study (http://www.aocstudy.org/).

PhD student projects in the laboratory

Genes involved in intrinsic resistance to chemotherapy in patients with ovarian cancer

Ovarian cancer kills approximately 750 Australian women each year. Response to chemotherapy varies widely - a few patients will be cured, most will respond initially but eventually relapse, and about one third will progress while on treatment. The purpose of this project is to find genes that influence a woman's response to chemotherapy. This could identify patients who are now exposed to the toxic effects of chemotherapy without significant benefit and allow selection of better chemotherapy.

We will carry out a genome-wide association study in the Australian Ovarian Cancer Study to identify candidate genes, and then validate them in independent data sets. Once we have identified these genes we will carry out functional assays to understand their role in drug response.

The ATM gene as a breast cancer predisposition gene

The laboratory is making use of an excellent resource that has been collected in Australia for the study of breast cancer genetics, namely the Kathleen Cuningham Foundation Consortium for Familial Breast Cancer (kConFab - http://www.kconfab.org). kConFab is a cohort study of multiple case breast cancer families from whom extensive genetic, clinical and epidemiological data are available, as well as biological specimens. Collection is complete on more than 1200 families but mutations in BRCA1 and BRCA2 have only been identified in about 35% so a major focus of the laboratory is to look for additional breast cancer susceptibility genes.

In particular, we are investigating the ATM gene, and other known and novel genes whose products interact with ATM and BRCA1/2. In collaboration with Drs Kumkum K hanna (QIMR) and Sean Tavtigian (IARC) we have identified a class of ATM variants that appear to confer a moderate risk of breast cancer (Chenevix-Trench et al., 2002; Thompson et al., 2005; Tavtigian et al, in press). We now want to conduct mRNA and miR expression profiling of lymphoblastoid cell lines from ATM carriers to help determine which exactly variants in the gene are likely to be associated with breast cancer risk, and to uncover the pathways that lead to breast cancer.

Genomic characterization of familial breast tumours

We are currently characterizing a panel of BRCA1, BRCA2 and non-BRCA1/2 (BRCAx) tumours by mRNA and miR expression, copy number and methylation profiling. One of the main aims of this project is to look for subtypes of BRCAx tumours, and see whether they run in families, as a prelude to linkage analysis of homogeneous groups of BRCAx families. To date we have some evidence that two different types of methylation patterns occur in BRCAx tumours, which may indicate that there are two main 'BRCAx' genes, or two classes of these genes.

Next generation sequencing approaches to finding novel breast cancer susceptibility genes

About 5% breast cancers occur in women with multiple cases in their families. Among these families, about one third are caused by inherited mutation the BRCA1 and BRCA2 genes, and about 2-3% by mutations in other genes, such as ATM. We plan to use whole exome sequencing of distantly related, affected members of families with multiple cases of breast cancer at a young age, to find putative breast cancer predisposition mutations that they share in common. In addition we will sequence some familial breast tumours, and their matching germline samples, to find putative breast cancer predisposition that have been homozygously inactivated in the tumour, as predicted by the Knudson hypothesis.

Somatic mutations in basal-like breast tumour - an opportunity for individualized treatment?

Basal-like breast cancers have a poor outcome. We have found that somatic mutations in a wide variety of oncogenes are relatively common in this subtype of breast cancer and we now plan to characterise the abnormal oncogenic pathways in basal-like breast tumours and cell lines. We will use the cell lines to perform experiments with inhibitors of these oncogenes and pathways in order to determine their effect on growth and tumor formation in mice.

Low penetrance breast and ovarian cancer susceptibility genes, and modifier genes for BRCA1 and BRCA2

As members of the Breast Cancer Association Consortium (BCAC), the Consortium for Investigators of Modifiers of BRCA1/2 (CIMBA), and the Ovarian Cancer Association Consortium (OCAC) we have been very successful recently in finding validated low-risk and modifying genes, from both candidate gene approaches and genome wide association studies (GWAS). We now plan to carry out our own GWAS of serous ovarian cancer, using a DNA pooling approach and then to explore the functional significance of genes found to be associated with increased risk of cancer.

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Molecular Cancer Epidemiology Laboratory
Dr Amanda Spurdle
07-3362 0371
Email Amanda.Spurdle@qimr.edu.au

[ H,  P]

Analysis of mismatch repair gene Sequence Variants of Unclassified Clinical Significance

Supervisors: Amanda B Spurdle (QIMR), Bryony Thompson (QIMR), Melissa A Brown (UQ)

Background: Mutations in the mismatch repair (MMR) genes predispose carriers to high risk of endometrial and colorectal cancer. Routine diagnostic MMR gene screening of individuals from cancer-rich families identifies numerous nucleotide sequence changes. Rare intronic variants outside of established consensus splicing sites and nucleotide changes predicted to cause missense substitutions are difficult to classify with respect to their clinical significance, and are termed unclassified variants. Our laboratory is currently involved in the development of prediction models for classification of MMR unclassified variants, which assess if a variant is likely to be causing cancer from the segregation of the variant in families, the family history profile of the presenting individual, tumour features, and the amino acid conservation and physicochemical properties of the predicted alteration. We are also using splicing assays to assess clinical significance of variants.

Project Aims: This project would use splicing assays on LCLs and multifactorial analysis to assess the clinical significance of unclassified variants in MMR genes. Techniques employed will include segregation analysis (assessing the presence of the variant in families), collation of tumour histopathological features from records and collaborative studies, pedigree construction and evaluation for family history of cancer, and thorough literature review for existing information. RNA assays will involve RNA extraction from LCLs, cDNA synthesis, and semi-quantitative PCR to assess gross splicing abnormalities and quantitative PCR to assess allele-specific expression differences. Results will be compared to bioinformatic predictions of splicing aberrations to inform development of splicing prediction algorithms.

Outcome: Functional and multifactorial analysis of specific unclassified variants will provide evidence regarding their pathogenicity.

Analysis of BRCA1/2 Sequence Variants of Unclassified Clinical Significance

Supervisors: Amanda B Spurdle (QIMR), Melissa A Brown (UQ), Phillip Whiley (QIMR/UQ)
[This Honours/PhD project can be developed for a PhD proposal, with addition of more complex functional assays.]

Background: Mutations in the BRCA1 and BRCA2 genes are thought to be responsible for about 40% of breast cancers in multiple-case families. Routine diagnostic BRCA1 and BRCA2 gene screening of individuals from high-risk families identifies numerous nucleotide sequence changes. Rare nucleotide changes predicted to cause missense substitutions are difficult to classify with respect to their clinical significance and are termed unclassified variants (UVs). Some variants may be classified as high-risk using multifactorial likelihood analysis, which estimates odds of causality using data on co-occurrence of the UV with pathogenic mutations in the same gene, co-segregation of the UV with affected status, amino acid conservation and physicochemical properties, and tumour features. However a large proportion of UVs remained unclassified, and splicing assays can be helpful in assessing their significance.

Project Aims: This project would use splicing assays on LCLs and multifactorial analysis to assess the clinical significance of unclassified variants in BRCA1 and BRCA2.
Techniques employed will include segregation analysis (assessing the presence of the variant in families), collation of tumour histopathological features from records and collaborative studies, pedigree construction and evaluation for family history of cancer, and thorough literature review for existing information. RNA assays will involve RNA extraction from LCLs, cDNA synthesis, and semi-quantitative PCR to assess gross splicing abnormalities and quantitative PCR to assess allele-specific expression differences. Results will be compared to bioinformatic predictions of splicing aberrations to inform development of splicing prediction algorithms.

Outcome: Functional and multifactorial analysis of specific UVs will provide evidence regarding their pathogenicity.

Characterization of Genetic Defects in Population-based Endometrial Cancer Patients and Their Cancer-affected Relatives

Intended Supervisors: Amanda B Spurdle (QIMR), Joanne Young (QIMR).
[PhD or Honours Project]

Background: Endometrial cancer is the most common invasive gynaecological cancer in Australia. Family history of endometrial cancer among first-degree relatives is associated with up to 3-fold increased risk of endometrial cancer. Such familial cases are thought to be largely due to mutations in the mismatch repair (MMR) genes MSH2, MLH1, MSH6 or PMS2, causing Lynch Syndrome. PTEN genes may contribute to familial endometrial cancer as part of Cowden syndrome. The breast-ovarian cancer genes BRCA1 and BRCA2 may also predispose to endometrial cancer. We are currently conducting the Australian National Endometrial Cancer Study (ANECS), a specific aim of which is to assess risk of endometrial cancer in women according to history of cancer in extended family members, including 2nd and 3rd degree relatives.

Preliminary review of ANECS data suggests that ~40% of endometrial cases present with a family history suggestive of an underlying genetic defect: 34% of cases report features characteristic of high-risk gene defect (diagnosis less than 50y, prior cancers, or ?2 affected relatives), overlapping with 26% of cases with history suggestive of specific high-risk gene mutations. Indeed, IHC pre-screening results suggest that MMR gene defects may be 3X more common than reported before.

Importantly, endometrial cancer cases likely to carry MMR gene mutations report family history profiles that do NOT fit classical criteria for Lynch syndrome families, and 64% of these are unlikely to have been prioritized for MMR gene mutation testing in clinics. These results highlight the importance of population-based studies in assessing penetrance and cancer phenotype associated with mutations.

Project Aims (a subset of these will form part of the intended PhD):

1. To clarify the family cancer history profile associated with high-risk gene mutation status by mutation screening of known endometrial cancer genes in endometrial probands and their cancer-affected relatives.
2. To assess the role of other high-risk cancer genes, particularly "breast-cancer genes" BRCA1 and BRCA2 as candidate causative factors in endometrial cancer probands reporting a family history of endometrial and other cancers.
3. To identify tumour features associated with mutation status of high-risk endometrial cancer genes to prioritize mutation screening of cases with little or no family history, using pathology review and assessment of candidate immunohistochemical and somatic genetic tumour markers.

Outcome: Results will inform definitions of familial cancer syndromes from an endometrial cancer perspective. It will thereby improve genetic counselling for endometrial cancer patients and their families. It will also have a more general impact on the genetic counselling of other cancer patients and their families, since endometrial cancer is a feature of several multi-cancer syndromes.

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Iron Metabolism Laboratory
Prof Greg Anderson
07-3362 0187
Email Greg.Anderson@qimr.edu.au
[ H,  P]

Molecular Basis of Intestinal Nutrient Transport

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Gasteroenterology Laboratory
Dr Kevin Spring
Prof Barbara Leggett
07-3362 0170;  07-3636 3110
Email Barbara_Leggett@health.qld.gov.au;
[P ]

Genetic Changes in Colon and Colorectal Cancer

Characterisation of the genetic changes underlying the progression of a pre-cancerous colonic polyp to colon cancer will increase our understanding of this disease and improve treatment options.

We are studying both polyps and cancers in an effort to identify genetic markers for progression, prognosis and response to therapy.

Colorectal cancer continues to be one of the most common internal malignancies occurring in the Australian population. One in twenty-three of our population will develop it during their lifetimes and half of these cases will not survive beyond five years. However, colorectal cancer has a great potential for prevention as most of these malignancies develop within pre-cancerous growths called polyps which can be removed at colonoscopy.

Colorectal cancer is a somewhat heterogeneous disorder. Across the spectrum of colorectal cancer types, there is a gradient of genetic causation tempered by the effects of environment such as smoking, diet and the use of anti-inflammatory drugs.

Over the last decade our laboratory has contributed to the growing understanding that these different influences result in a number of distinct subtypes of colorectal cancer. These develop along different molecular genetic pathways and have characteristic somatic changes.

This work has important implications for improving prevention and therapy of the disease.

PhD project

Potential PhD projects will examine candidate genes for a role in the development of colorectal cancer. Such genes will be selected either by a traditional candidate gene approach, or as a result of expression or methylation profiling experiments. Putative tumour suppressor genes can be evaluted by a number of techniques to examine expression changes, altered methylation, mutation and gene deletion.

This would then be compared with important molecular events characteristic of specific colon cancer subgroups. Gene candidates can then be expressed in cell lines for functional analysis. Correlation can then be sought between the observed genetic alterations, tumour pathology and clinical outcomes based on our detailed patient records.

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Signal Transduction Laboratory
Dr Derek Richard
07-3362 3339
Email Derek.Richard@qimr.edu.au
[H]

Human hSSB1 and DNA replication

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This affords a considerable degree of protection against chemical or physical damage and preserves it's coding potential. However, there are many situations, either due to DNA damage or during programmed cellular processes such as DNA replication and transcription, when the DNA duplex is separated into two single-stranded DNA (ssDNA) strands. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB).

In eukaryotes it was believed the SSBs had been replaced by the heterotrimeric protein RPA. We have however found that the human genome encodes two distinct SSBs that have remained highly homologous even through 3 billion years of evolution.

Our data shows hSSB1 is an essential component of the homologous repair complex and is essential for the formation and survival of cancer cells but not primary cells.

There are a number of projects available within this laboratory including biomarker and drug target discovery, molecular characterization of hSSB1 and hSSB2 interacting proteins, the role of hSSB1 in nucleotide excision repair and the role of hSSB1 in DNA replication.

For further information on any of these exciting projects please refer to our latest publication "Single-stranded DNA-binding protein hSSB1 is critical for genomic stability." Nature 2008

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Radiation Biology and Oncology Laboratory
Prof Martin Lavin
07-3362 0341
Email Martin.Lavin@qimr.edu.au
[H,  P]

Radiation Signaling and Disease

The major emphasis of our research is the recognition of damage in DNA using human and animal models to investigate genome instability, cancer predisposition and neurodegeneration.
Research is also directed to isolating novel therapeutic compounds from snake venom, early detection of prostate cancer and identification of genes in development.

Much of our work focuses on the gene defective in the human genetic disorder ataxia-telangiectasia (A-T), ATM, that plays a central role in recognising double-strand breaks in DNA, and signalling of these breaks to slow the passage of cells through the cell cycle so that the DNA damage can be repaired. Failure to recognise and repair this damage in A-T patients results in increased frequency of cancer and a progressive neurodegeneration. Being able to slow or halt the progress of this neurodegeneration would be of great benefit to A-T patients.

More recently we have extended this work to include investigations on other ataxia syndromes where a defect in DNA repair is also implicated in the phenotype.

Student projects:

• Mouse models for cancer predisposition
• Mouse models for neurodegenerative human syndromes
• Use of antioxidants to protect against neurodegeneration
• Mechanism of action of aprataxin mutated in ataxia oculomotor apraxia type 1
• Characterization of senataxin mutated in ataxia oculomotor apraxia type 2
• Role of the hSMG-1 protein kinase in stress granule formation
• Identification of novel proteins in snake venom with potential therapeutic activity
• Early detection of prostate cancer
• DNA damage and aging

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Radiation Biology and Oncology Laboratory
Dr Sergei Koslov
Prof Martin Lavin
07-3362 0344
Email Sergei.Kozlov@qimr.edu.au
Email Martin.Lavin@qimr.edu.au
[H,  P]

Ataxia-telangiectasia and ATM kinase activation

A-T is a prominent example of a genetic disease which over the years stimulated fundamental research into an understanding of major cellular processes. ATM (ataxia-telangiectasia, mutated) protein mutated in the disease, is involved in multiple aspects of cellular metabolism, such as response to DNA damage, cell cycle and genetic stability.

ATM belongs to superfamily of phosphatidylinositol (PI) 3-kinase related proteins and was found to be a protein kinase which is rapidly activated in the presence of DNA double strand breaks but the mechanism of ATM kinase activation remains poorly understood.

The importance of autophosphorylation in regulation of ATM kinase activity was suggested (Kozlov et al 2003, J Biol Chem, v.278:9309), followed by identification of S1981 as a major autophosphorylation site of ATM in vivo (Bakkenist and Kastan, 2003 Nature, v.421:499).

It was speculated that ATM can "sense" unknown changes in the higher order chromatin structure caused by DNA double-strand breaks (DSB) away from the actual site of the break. Protein phosphatases PP5, PP2A and PP2C phosphatase Wip1 (Ali et al 2004 Genes Dev. v.18:249; Goodarzi et al, 2004, EMBO J. v.23:4451; Shreeram et al, 2006, Mol Cell. v.23:757) have also been implicated in the regulation of ATM kinase activity.

Regulation of ATM kinase activity by acetylation via interaction with acetyltransferases Tip60 and hMOF1 was also observed (Sun et al 2005, Proc Natl Acad Sci U S A. v.102:13182; Gupta et al 2005, Mol Cell Biol., v.25:5292). Mre11/Rad50/Nbs1 (MRN) complex was found to be necessary for the optimal activation of ATM kinase (Uziel et al 2003, EMBO J., v. 22:5612; Lee and Paull 2004, Science, v.304:93; Costanzo et al 2004 PLoS Biol; v.2:E110; Lee and Paull 2005, Science, v.308:551).

We have recently completed a study of the human ATM kinase autophosphorylation sites (Kozlov et al, 2006 EMBO J, v.25:3504). Our current work is based on a hypothesis that ATM kinase activation is a multi-step process of sensing of alterations in global chromatin and nuclear structure and involves multiple post-translational modifications.

PhD projects are available to investigate the role of ATM kinase as a "chromatin status" sensor and establish an essential role of post-translational modifications in the ATM kinase activation.

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Radiation Biology and Oncology Laboratory
Dr Olivier Becherel
Prof Martin Lavin
07-3362 0341
Email Olivier.Becherel@qimr.edu.au
Email Martin.Lavin@qimr.edu.au
[H]

Ataxia with oculomotor apraxia in DNA damage response and RNA metabolism

Ataxia oculomotor apraxia (AOA) is a common phenotype found in several degenerative disorders of the nervous system. Ataxia refers to lack of coordination and oculomotor apraxia describes the difficulty in moving the eyes. These debilitating diseases include ataxia-telangiectasia (A-T), A-T like disorder (A-TLD), both of which are characterized by a defective response to DNA damage and cancer predisposition, and ataxia oculomotor apraxia type 1 (AOA1) and type 2 (AOA2).

The gene mutated in AOA1, APTX, was identified in 2001 and encodes for aprataxin, a novel protein involved in DNA repair/DNA damage processing. In the case of AOA2, the gene mutated, SETX, was recently discovered and encodes for senataxin, a novel protein predicted to contain a seven-motif domain at its C-terminus, typical of the superfamily I of DNA/RNA helicases. Preliminary results on senataxin and recent data on aprataxin suggest a potential role of these two proteins in the repair/processing of DNA breaks and RNA metabolism.

To gain further insight and ultimately pinpoint their cellular roles during the response to DNA damage and in RNA metabolism, several studies are under way, such as:

1. Role of senataxin in DNA transcription and mRNA splicing (localisation, dynamics and splicing efficiency
2. Down-regulation of genes mutated in recessive spinocerebellar ataxias by stable small interfering RNA
3. Cloning and expression of GST-fusion proteins for protein-protein interaction studies

A panel of methods are used in the various aspects of the study and include classical molecular biology techniques (e.g: cloning, PCR), biochemistry (e.g: protein expression and purification, analysis of protein-protein interactions), cell culture, and cell biology (e.g: microscopy, immunofluorescence).

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Transgenics Laboratory
Dr Graham Kay
07-3362 0341
Email Graham.Kay@qimr.edu.au
[H,  P]

The role of SmcHD1 in genomic imprinting

Genomic imprinting is an epigenetic mechanism that marks the parental origin of the alleles of certain genes for exclusive expression of either the maternally or paternally inherited allele. This monoallelic expression of imprinted genes is controlled by imprinting centres that are differentially DNA methylated between the parental alleles during gametogenesis. The differential methylation is maintained after fertilisation and throughout development, but erased and reset in the next generation’s germline. Approximately 90 imprinted genes have been identified and these exist either within clusters of imprinted genes controlled by a single imprinting centre or as single imprinted genes isolated within regions of biallelicly expressed genes.

Many parallels have been drawn between genomic imprinting and X chromosome inactivation, both being epigenetic mechanisms that result in monoallelic gene expression. Many of the paradigms ofepigenetic gene silencing that were established through studies of X inactivation have since been found to also apply to genomic imprinting.

Recently in an ENU mutagenesis screen for epigenetic modifiers we have identified a novel gene, SmcHD1, that is necessary for the correct silencing of many genes on the inactive X chromosome. Female embryos homozygous for mutant SmcHD1 fail to silence many genes on the inactive X chromosome resulting in mid-gestation failure.

Homozygous males are relatively unaffected being viable as adults and fertile. In our ongoing studies we have observed prominent deregulated expression levels of imprinted genes in both male and female homozygous SmcHD1 mutant embryos, suggesting that SmcHD1 is also involved in maintaining expression of imprinted genes. The proposed project will pursue this observation to specifically study the role of SmcHD1 in maintaining the integrity of genomic imprinting of autosomal genes.

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How to apply: Contact the Laboratory Head related to the project area of interest (see above) in the first instance.

Application details here.