Student Projects 2009

Cancer & Cell Biology

• Membrane Trafficking
• Radiation Signaling and Disease
• Ataxia-telangiectasia and ATM kinase activation
• Cloning of Novel Snake Venom Proteins
• Ataxia with oculomotor apraxia in DNA damage response and RNA metabolism
• Cancer Genetics
• Genes that regulate Iron metabolism
• anti-Cancer Drugs from the Rainforest
• Eph Receptor Biology

Infectious Diseases

• Parasitic Helminth vaccine
• Bacterial Pathogenesis and Vaccines
• Antimalarial action of antiretroviral inhibitors
• Lifecycle gene targets during Malaria Infection
• Studies on malaria enzymes involved in gene regulation
• Effect of Dexamethasone on Scabies infection
• Sustainable Mosquito Control
• Scabies mite serpins
• Parasitic Worms and disease

Genetics and Population Health

• Skin tumour gene expression, medication use and sunscreen application
• Factors affecting quality of life in Pancreatic Cancer Patients
• Epidemiology of Endometrial Cancer
• Pigmentary characteristics and risk of cutaneous Melanoma
• Assessing the role of germline genetic mutations in Familial Cancer
• Genetic Changes in Colon and Colorectal Cancer
• Epigenetics
• Supportive Care Needs of Indigenous Cancer Patients

Immunology

• Bone Marrow Transplantation
• Quantitative Expression Profiling of EBV microRNAs
• 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

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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

Cancer and Cell Biology Division

Membrane Transport Laboratory
A/Prof Nathan Subramaniam
07-3362 0179
Dr Daniel Wallace
07-3362 0173
Email Daniel.Wallace@qimr.edu.au
Email Nathan.Subramaniam@qimr.edu.au
[ H, P ]

Membrane Trafficking

In recent years it has become very evident that a large number of human disorders can be attributed to defects in the trafficking and localisation of molecules, predominantly membrane proteins. By studying how mammalian cells regulate the synthesis, assembly, trafficking and localisation of membrane proteins implicated in these human disorders we hope to advance our understanding of these disorders with the prospect of a better therapeutic intervention.

Characterisation of the hepcidin-binding domain of ferroportin

Iron is an essential element for life and the levels of iron in the body are tightly regulated. A deficiency of iron can lead to anaemia and an excess can cause tissue damage and disease, as in hereditary haemochromatosis. One of the key events in the regulation of body iron homeostasis is the interaction between the liver-expressed iron-regulatory hormone hepcidin and the iron transporter ferroportin.

Hepcidin is secreted from the liver in response to high iron levels or inflammation. Hepcidin functions to reduce serum iron levels by binding to ferroportin on the surface of cells and targeting it for internalisation and degradation [1]. In this way hepcidin reduces the amount of iron absorbed through the intestine and released from macrophages. Mutations in both ferroportin and hepcidin lead to various types of hereditary haemochromatosis [2].

Recently the hepcidin-binding domain (HBD) of ferroportin was determined and comprises a 19 amino acid extracellular loop of the protein [3].

Hypothesis/Aims

To study the interaction of hepcidin with the ferroportin-HBD, and the effect of mutations on binding. These studies will form the basis for the development of a serum hepcidin assay.

Approaches

• Recombinant epitope-tagged forms of the HBD of ferroportin will be generated by PCR and standard molecular biology protocols. Ferroportin disease-causing mutations will be inserted into the HBD including C326Y and S338R
.
• Recombinant wild-type and mutant hepcidin will be generated. These will be generated in cell lines and involve cell culture and cell biology related experiments. The effect of wild type and mutant HBD on binding to wild type and mutant forms of hepcidin will be determined by pull down experiments and immunoprecipitation.
• These reagents will be used to develop an assay to quantitate soluble serum hepcidin in mouse models of iron overload and anaemia. Ultimately the assay will be used to analyse hepcidin levels in patient serum.

References

1. Nemeth, E., et al., Hepcidin regulates cellular iron efflux by binding to ferroportin and inducing its internalization. Science, 2004. 306(5704): p. 2090-3.
2. Wallace, D.F. and V.N. Subramaniam, Non-HFE haemochromatosis. World J Gastroenterol, 2007. 13(35): p. 4690-8.
3. De Domenico, I., et al., The hepcidin-binding site on ferroportin is evolutionarily conserved. Cell Metab, 2008. 8(2): p. 146-56.

Role of Mon1B in trafficking

Introduction and Aims

Mon1 is a member of a protein family implicated in protein trafficking. Two closely related homologues Mon1A and 1B have recently been identified. Modulation of Mon1 activity or function may affect other trafficking of other proteins including the expression of cell surface receptors. Polymorphisms in Mon1A have been shown to affect the secretion of IL10 and other proteins. This project aims to define the role of Mon1 in trafficking of these receptors and identify the effect of polymorphisms in this protein on its structure and function.

Research Methodology

The project makes use of a number of molecular biology, biochemical and cell biology techniques. These include PCR, cloning, site-directed mutagenesis, DNA preparation, proteomics, immunoblotting, cell culture, transfections, immunofluorescence, confocal microscopy.
1. Cloning of Mon1 B, epitope-tagged mammalian expression, recombinant protein and antibody generation, expression studies.
Human Mon1B will be PCR'ed either from a human cDNA library or from EST. cDNA's will be cloned into GST and mammalian expression vectors with a myc-epitope tag. Recombinant protein will be isolated and used to immunize rabbits to produce antibodies. Epitope-tagged (flag) Mon1 B will be transfected into human cell lines - liver, macrophage and enterocyte. Stably expressing cells will be selected with puromycin. Localisation and expression will be analysed by immunofluorescence confocal microscopy, immunoblotting and pulse-chase studies. Colocalisation studies will be performed with appropriate markers. Antibodies obtained will be affinity purified. The expression of endogenous Mon1B in various tissues and cell lines will be determined by real-time RT PCR, immunoblotting and confocal microscopy.

2. Identification of Mon1 interacting proteins
Antibodies against Mon1A and B generated in rabbits will be used to co-immunoprecipitate Mon1 A and B and putative interacting proteins. Proteins will be identified by mass spectrometry. The interaction of these proteins will be validated using GST pull-downs and co-immunopreciptations. cDNAs encoding novel interacting proteins will be cloned and these experiments repeated.

References

1. Wang F, Paradkar PN, Custodio AO, McVey Ward D, Fleming MD, Campagna D, Roberts KA, Boyartchuk V, Dietrich WF, Kaplan J, Andrews NC. Genetic variation in Mon1a affects protein trafficking and modifies macrophage iron loading in mice. Nat Genet. 2007 Aug;39(8):1025-32.
2. Dong S, Dong C, Liu L, Che Y, Sun M, Hu F, Li J, Li Q. Identification of a novel human sand family protein in human fibroblasts induced by herpes simplex virus 1 binding. Acta Virol. 2003;47(1):27-32.

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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 Geoff Birrell
Prof Martin Lavin
07-3362 0337
Email Geoff.Birrell@qimr.edu.au
Email Martin.Lavin@qimr.edu.au
[H,  P]

Cloning of Novel Snake Venom Proteins

Our lab has identified over 725 proteins in venoms from 20 Australian snakes (Birrell et al, Mol Cell Proteomics. 2007 (6):973-86.

We also have obtained the cDNA sequence for many of these. A Summer Vacation project exists to PCR amplify and sequence several novel genes from snake venom gland cDNA. The sequences will be aligned and compared with those from other snakes.

This will increase both our understanding of phylogenetic relationships between snakes and the potential for novel venom proteins as human therapeutics.

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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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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 train in cases from the Australian Ovarian Cancer Study (http://www.aocstudy.org/).

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 Dr Kumkum Khanna (QIMR) we have identified highly penetrant, dominant negative ATM mutations in breast cancer families (Chenevix-Trench et al., 2002; Thompson et al., 2005) and further work is underway to determine the frequency and penetrance of ATM mutations in familial breast cancer. In addition we want to conduct mRNA and miR expression profiling of tissues from ATM carriers to help determine which variants in the gene are likely to be associated with breast cancer risk, and to uncover the pathways that lead to breast cancer.

An ATM knock-in mouse model

We have made a knock in mouse for the breast cancer-associated mutation in ATM, 7271T>G. The homozygotes display features consistent with a mild form of ataxia telangiectasia. We are currently monitoring cohorts of female heterozygotes and homozygotes for the development of mammary, and other, cancers.

Genomic characterization of familial breast tumours

We are currently characterizing a panel of BRCA1, BRCA2 and BRCAx tumours by mRNA and miR expression, copy number and methylation profiling. The main aims of this project are 1) 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 and 2) to identify novel methylation targets. We predict that this work will provide novel biomarkers to test as early diagnostic markers for breast cancer.

Evaluation of the ABC breast cancer cluster

In collaboration with Drs Sunil Lakhani (UQ), Beth Newman (QUT) and Glenn Francis (PAH), we are starting to investigate the molecular features of the cluster of breast tumours that have arisen in women working at the Australian Broadcasting Corporation studio in Toowong, Brisbane.

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). Using high-throughput genotyping of single nucleotide polymorphisms, mainly in candidate genes, we have been very successful recently in finding validated low-risk and modifying genes and are now moving towards genes identified through Genome Wide Association Studies.

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

Molecular Basis of Intestinal Nutrient Transport

The major focus of our laboratory is to elucidate the mechanisms of cellular iron transport and the way in which these processes are regulated. A particular goal is to describe the pathways of intestinal iron absorption and to understand how absorption is altered in disorders of iron metabolism, such as the iron loading disease haemochromatosis.

Over the last few years the identification of several novel metal transport and regulatory molecules has revolutionised our understanding of this important class of human diseases. The project areas listed below are all designed to enhance our understanding of iron homeostasis by integrating contemporary genetic and molecular studies with biochemical and physiological approaches.

Areas in which projects are available include, but are not restricted to, the following:

• Mechanisms of intestinal iron transport in the perinatal period and the consequences of altered iron status on pregnancy outcome
• The regulation and mechanism of iron transport across the eneterocyte basolateral membrane
• Transcriptional analysis of intestinal iron transport and hepatic iron regulatory genes
• The role of the haem oxygenases in cellular iron trafficking
• Regulation of iron homeostasis in haemolytic anaemias
• The search for novel iron metabolism genes using mouse mutagenesis screens
• Natural history of the common human iron loading disorder haemochromatosis

Some examples of our recent publications include:

1. Shayeghi M, Latunde-dada GO, Oakhill JS, Takeuchi K, Laftah A, Halliday N, Khan Y, Warley A, McCann FE, Hider RC, Frazer DM, Anderson GJ, Vulpe CD, Simpson RJ and McKie AT. 2005. Identification of an intestinal heme transporter. Cell. 122: 789-801.
2. Wilkins SJ, Frazer DM, Millard KN, McLaren GD and Anderson GJ. 2006. Iron metabolism in the hemoglobin deficit mouse: Correlation of diferric transferrin with hepcidin expression. Blood. 107: 1659-1664.
3. Anderson GJ and Frazer DM. 2006. Iron metabolism meets signal transduction. Nat Genet. 38: 503-504.
4. Chen H, Huang G, Su T, Gao H, Attieh ZK, McKie AT, Anderson GJ and Vulpe CD. 2006. Decreased hephaestin activity in the intestine of copper-deficient mice causes systemic iron deficiency. J Nutr 136: 1236-1241.
5. Frazer DM, Wilkins SJ and Anderson GJ. 2007. Elevated iron absorption in the neonatal rat reflects high expression of iron transport genes in the distal alimentary tract. Am J Physiol. 293: G525-531.
6. Allen KJ, Gurrin LC, Constantine CC, Osborne NJ, Delatycki MB, Nicoll AJ, McLaren CE, Bahlo M, Fletcher AS, Nisselle AE, Forrest S, Vulpe CD, Anderson GJ, Southey MC, Giles GG, English DR, Hopper JL, Olynyk JK, Powell LW and Gertig DM. 2008. Iron-overload-related disease in HFE hereditary hemochromatosis. N Engl J Med. 358: 221-230.
7. Anderson GJ and Darshan D. 2008. Small molecule dissection of BMP signalling. Nature Chem Biol. 4:15-16.

Opportunities exist for suitably qualified students to conduct their Honours and PhD research in the Iron Metabolism Laboratory at QIMR.
For further information please contact Dr Greg Anderson on (07) 3362-0187 or at Greg.Anderson@qimr.edu.au.

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Drug Discovery Laboratory
Prof Peter Parsons
07-3362 0316
Email Peter.Parsons@qimr.edu.au
[ H,  P]

Anti-Cancer Drugs from the Rainforest

Australian Rainforest Foundation Honours Scholarship: click here

This scholarship is offered for study primarily in the Drug Discovery Group at QIMR. As part of a collaborative project, this group has identified a family of bioactive compounds that occur in related plant species of the North Queensland rainforest. The compounds are active in cell signalling pathways relevant to controlling cancer, and are likely to influence the ecology of their source plants in their natural setting, particular in providing protection against herbivores. Much remains to be learnt about all aspects.

The Scholar will focus on one or more of the following:

1. the structures of a family of bioactive compounds from the rainforest and their distribution in related species,
2. structure/bioactivity relationships in relation to their anticancer activity, or
3. the ecological implications in terms of defence.

A wide range of supervisory experience will be provided for the particular project path chosen, along with mentoring to help achieve a high quality Honours report. Training will be given in a range of techniques including HPLC, MS, cell culture, flow cytometry and gene expression.

Applicants should have a sound undergraduate record in the particular area of interest selected for study, and must be acceptable for enrolment in the relevant department of a university in Queensland.

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Leukemia Foundation Research Unit
Dr Andrew Boyd
Ph: 07-3362 0302
Dr Mark Spanavello
Ph: 07-3362 0321
Email Andrew.Boyd@qimr.edu.au
Mark.Spanavello@qimr.edu.au
[ H, P]

Eph Receptor Biology

Our research concentrates on the Eph family of receptor tyrosine kinases, a group of proteins that are highly regulated during development but are minimally expressed during adulthood. These proteins and their ligands, the ephrins, are upregulated in many neoplastic malignancies including leukaemias.

The Ephs and ephrins generally mediate cell repulsion through bidirectional signaling and are mediators of metastasis through this process. Developmentally, Ephs and ephrins are important in a number of roles that include axon guidance and boundary formation, again through their repellent signaling.

Recently we have begun investigating the role of EphA4 in spinal cord injuries. Both the EphA4 KO mouse and normal mice treated with EphA4 antagonists show remarkable recovery following injury.

We wish to explore the activation and blocking of EphA4 using an in vitro model and a number of inhibitors that we have developed in our lab.

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Infectious Diseases

Helminth Biology
Dr Alex Loukas
Ph: 07-3845 3702
Email Alex.Loukas@qimr.edu.au
[ H, P]

Vaccines against blood-feeding parasites

The Helminth Biology laboratory is interested in parasitic helminths (worms) that parasitize humans. These large parasites are long-lived and have developed incredibly sophisticated mechanisms to allow them to survive and proliferate within almost hlaf the world's population.

Much of the success of these worms can be attributed to the proteins they secrete into host tissues. These proteins are involved in migration, feeding and evasion/manipulation of the host's immune response.

Our lab explores the nature and functions of these parasite excretory/secretory (ES) proteins using various molecular and immnological techniques. We have exploited our knowledge of these parasite proteins and used them to develop vaccines that interrupt key physiological processes that are essential for parasite survival. By harnessing the potent immunomodulatory properties of helminths, we are also exploring the potential of helminth ES proteins as therapies for autoimmune disorders, particularly inflammatory bowel diseases.

Major PhD projects in the lab include:

1. Understanding the molecular biology of blood-feeding in hookworm parasites
2. Developmental molecular biology of hookworm larvae
3. Using surface tetraspanins as recombinant vaccines for schistosomiasis
4. Using intestinal proteases as anti-blood-feeding recombinant vaccines for hookworm disease
5. Hookworm ES proteins as therapies for auto-immune disorders
6. Understanding how the liver fluke, Opisthorchis viverrini, causes liver cancer in SE Asia

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

• Tran et al. (2006) Tetraspanins on the surface of Schistosoma mansoni are protective antigens against schistosomiasis. Nature Med. 12(7):835-40
• Loukas et al. (2005) Vaccination with recombinant aspartic hemoglobinase reduces parasite load and blood loss after hookworm infection in dogs PLoS Med. 2(10):e295.
• Loukas et al. (2006) Hookworm vaccines: past, present, and future Lancet Infect Dis. 6(11):733-41.
• Sripa et al. (2007) Liver fluke induces cholangiocarcinoma. PLoS Med. 4(7):e201

Scholarship top-ups are available. For more information, contact Dr Alex Loukas.

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Bacterial Pathogenesis Laboratory
Assoc Prof Sri Sriprakash
Dr David McMillan
07-3845 3712
Bacterial Vaccines Laboratory
Dr Michael Batzloff
07-3845 3703
Email David.McMillan@qimr.edu.au
[ H, P,  TU]

Bacterial Pathogenesis and Vaccines

NB: Honours scholarships available in Bacterial Pathogenesis worth up to $5000
Contact Dr David McMillan for details

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 Tina Skinner-Adams
07-3362 0419
Dr Don Gardiner
07-3362 0432
Email Tina.Skinner-Adams@qimr.edu.au
Email Don.Gardiner@qimr.edu.au

[ H,  P]

Investigating the antimalarial action of the antiretroviral protease inhibitors

Background

Malaria and HIV are two of the most devastating infectious diseases of humans, together resulting in some 5 million deaths annually. As the global epidemiology of malaria and HIV overlap in many regions of the world, malaria and HIV co-infection is also a significant problem. Although the consequences of co-infection with HIV and malaria parasites are not fully understood, available evidence suggests that these infections act synergistically and together result in worse outcomes than each disease individually.

Little is known about the consequences of drug interactions in co-infected individuals and the importance of understanding these chemotherapeutic interactions is now being recognized and considered a high priority. Our group has determined that a group of drugs known to kill HIV also inhibits the growth of malaria. We are now investigating the antimalarial action of these drugs in the hope that these studies will lead to the development of a new class of antimalarial drugs, and a better understanding of how we can exploit their actions in the field. We are also investigating the pharmacodynamic and pharmacokinetic interactions of these drugs with other antimalarial and antiretroviral agents so that we can understand the consequences of drug interactions in the clinic.

Aims

1. To investigate the antimalarial action of the antiretroviral protease inhibitors (APIs)
2. To investigate the interactions and consequences of antiretroviral and antimalarial drug combinations.

Approaches

The project is likely to involve techniques including tissue culture, molecular biology techniques (cloning, transfection), drug assays, protein expression and purification, microscopy, and in silico modelling.

Reference

Skinner-Adams TS, Gardiner DL, McCarthy J, Andrew KT. HIV and malaria coinfection: interactions and consequences of chemotherapy. Trends in Parasitology, 2008, 24(6): 264-271

If you are interested in a PhD or Hons project in any of these areas we encourage you to contact us as soon as possible for further discussions.

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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]

Effect of Dexamethasone on Scabies infection

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.

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
Dr Leon Hugo
07-3362 0355

Email Peter.Ryan@qimr.edu.au
Email Leon Hugo,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.

• 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).
• 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.
• 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.
• 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.
• 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.

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

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Genetics and Population Health

Cancer & Population Studies Group
Prof Adčle Green
Dr Jolieke van der Pols
Phone: 3845-3591
Email: Jolieke.VanDerPols@qimr.edu.au [ H ]

Gene expression in the skin and associations with medication use and sunscreen application

Background

The p53 gene is a tumour suppressor gene that is commonly mutated in skin cancer and sun-exposed skin. In previous work we have shown for the first time that expression of p53 in the skin is a marker of past UV exposure and that this may be mitigated by regular application of sunscreen (van der Pols et al. Am J Epidemiol 2006).

We now want to investigate whether expression of NFkappaB, a UV-induced transcription factor with tumour promoting effects, can also be mediated by sunscreen use. UV exposure also enhances COX-2 expression, which increases keratinocyte (skin cell) proliferation. Non-steroidal anti-inflammatory drugs (e.g. aspirin, ibuprofen) inhibit COX-2 (6), but evidence is needed whether use of such medication can modify cutaneous COX-2 expression levels in the population.

Aims

Determine whether:

1. Sunlight exposure and use of sunscreen is associated with expression of NFkappaB in the skin, and
2. Use of NSAIDs is associated with reduced expression of COX-2 in the skin.

Methods

Immunohistochemical staining for COX-2 and NFkappaB of 120 skin biopsies from participants in the Nambour skin cancer study has already been carried out. The student will interpret and score staining patterns followed by basic statistical analyses to study associations between gene expression levels and UV-exposure/sunscreen use and medication use (and related) variables.

Collaborations

Dr. Glen Boyle, Drug Discovery Group (QIMR) and Prof. Konrad Muller, pathologist at the Royal Brisbane and Women's Hospital.

Public health significance

Knowledge generated by this project will provide evidence to improve skin cancer prevention, for example through better identification of high risk individuals and identification of targets for therapeutic interventions.

Student requirements

This project is suitable for a student with variable working hours since no lab work other than microscopic reading of the slides is required and data analyses can be carried out off-site (e.g. on a laptop).
A basic understanding of data analysis is required. Our aim is publication in a peer-reviewed journal at completion of the project. Please contact Jolieke for more information.

Supervisor: Dr. Jolieke van der Pols, Cancer and Population Studies group, QIMR.

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Cancer & Population Studies Group
Prof Adčle 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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Cancer & Population Studies Group
Dr Penny Webb
Phone: 3362-0281
Email: Penny.Webb@qimr.edu.au

[MPhil,  P]

Epidemiology of endometrial cancer

Endometrial cancer (cancer of the uterus or womb) is the 6th most common cancer in Australian women. More than 1500 women were diagnosed with endometrial cancer in 2001 and the numbers are increasing each year.

Background

There are two main types of endometrial cancer: "type I" cancers are related to oestrogen and most often occur in women who are overweight; "type 2" cancers are much less common but have a poor prognosis and little is known about what causes them.

The Australian National Endometrial Cancer Study (ANECS) is a national population-based case-control study that includes almost 1500 women with endometrial cancer and a group of cancer-free control women. Women provided detailed information about their reproductive and medical history, diet, smoking and alcohol consumption, physical activity and hormone use. They also provided blood samples for genetic and biochemical studies.

Project Aims

A number of potential projects are available, for example:

1. An investigation of the role of metabolic factors including body size, weight change, physical activity and medical conditions such as diabetes in determining risk of endometrial cancer
2. 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
3. An investigation of the role of dietary factors and/or dietary patterns in determing endometral cancer risk.

There is also an opportunity to combine any of the above with genetic and/or biochemical analyses.

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

Outcomes

Better understanding of what causes endometrial cancer and identification of women at high risk will help us to prevent endometrial cancer from occurring in future.

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Cancer & Population Studies Group
Dr Catherine Olsen
Phone: 3362-0265
Email: Catherine.Olsen@qimr.edu.au

[H,  MPhil]

Pigmentary characteristics and risk of cutaneous melanoma

Cancers of the skin are the most commonly occurring malignancies in fair-skinned populations, associated with substantial costs for their diagnosis and treatment.

Background

The world's highest rates for skin cancer are seen in Queensland (1), where over 100,000 histologically-confirmed skin cancers (BCC, SCC, melanomas and others) are excised each year in a population of only 4 million. The costs of diagnosing and treating non-melanoma skin cancer account for 12% of Australia's annual expenditure for cancer, more than is spent treating any other cancer in our population.

The search for high risk groups and preventive measures has therefore become particularly important.

The aim of a major project funded by Xstrata is to identify the relative importance of all clinically recognisable risk factors that identify those at increased risk of melanoma, and to thereby predict an individual's risk of melanoma.

Pigmentary characteristics, including lighter skin colour, red or blond hair colour, blue eye colour, and propensity to sunburn individually confer risk of melanoma (2). Many studies have attempted to evaluate the relative importance of various phenotypic factors in risk prediction for melanoma, however, to date, there has been no concise review prioritizing these phenotypic variables in their order of importance.

Aims

The aim of the project would be to evaluate and summarize recent data regarding major phenotypic factors (skin colour/type, eye colour, hair colour) that are important in predicting increased risk for melanoma.

Approaches

The approach will entail conducting systematic reviews and meta-analyses of the epidemiological evidence relating to pigmentary risk factors including skin colour/type, hair colour, and eye colour.

Data will be collected through detailed protocol-specific literature searches and quantitatively synthesized using meta-analysis techniques to derive pooled relative risk estimates.

This project will contribute to the larger scale study aimed at developing a risk prediction tool for melanoma for use in a clinical setting.

References

1. MacLennan, R., Green, A. C., McLeod, G. R., and Martin, N. G. Increasing incidence of cutaneous melanoma in Queensland, Australia. J Natl Cancer Inst 1992;84:1427-32.
2. Tucker, M. A., and Goldstein, A. M. Melanoma etiology: where are we? Oncogene 2003;22:3042-52.

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

[ H,  P]

Assessing the role of germline genetic mutations in Familial Cancer

BRCA1/2 Sequence Variants of Unclassified Clinical Significance

Intended Supervisors: Amanda B Spurdle (QIMR), Melissa A Brown (UQ).

Mutations in the BRCA1 and BRCA2 genes are thought to be responsible for about 40% of breast cancers in multiple-case families.

Background

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 in addition we have evidence to suggest that some variants which are classified as having little clinical significance may nevertheless have partially compromised function.

Project Aims

This project would aim to use a battery of established functional assays (some domain-specific) to provide proof of compromised function for variants classified as high risk using multifactorial modelling, and to assess the possibility of partially compromised function (level of function, number of assays compromised) associated with variants considered to be of little clinical significance.

In addition, the project plan is to develop generic assays of BRCA1 and BRCA2 function to assess risk of variants irrespective of their location within the protein, to further improve the assessment of clinical significance of UVs, namely assays for epithelial cell transformation - reflecting overall tumour suppressor activity of BRCA1 or BRCA2.

Outcome

Functional analysis of specific UVs will provide evidence regarding their pathogenicity. Development of generic assays will allow for comparison of functional relevance of variants in domains across the gene.

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

Intended Supervisors: Amanda B Spurdle (QIMR), Joanne Young (QIMR).

Endometrial cancer is the most common invasive gynaecological cancer in Australia.

Background

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)

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.

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.

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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Gasteroenterology Laboratory
Dr Vicki Whitehall
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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Epigenetics Laboratory
Dr Emma Whitelaw
07-3845 3600
Email Emma.Whitelaw@qimr.edu.au

[H, P]

Epigenetics

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.

Our ENU mutagenesis screen, the first of its kind in the world, has been very fruitful so far, revealing new aspects of the biology of development - (Blewiitt et al (2005) PNAS 102:7629-34 and Chong et al (2007) Nature Genetics, 39:614-22.

We are now about to initiate a major expansion of this screen and it is likely that new members of the laboratory will become involved in some way in this study.

To determine the molecular mechanisms involved in establishing epigenetic states in mammals we have used random mutagenesis in mice to find novel modifiers of epigenetic gene regulation. Mutant mouse lines will be phenotyped by breeding experiments and molecular techniques, eg Northern blots and bisulphite sequencing. Mapping by PCR-based amplification of microsatellite markers will be used to link the mutation to a small chromosome interval, and ultimately gene sequencing will be performed to identify the underlying point mutation.

We are also keen to study the nature of epigenetic differences between monozygotic (genetically identical twins). We believe that these changes could explain the phenotypic differences seen within twin pairs. We are currently establishing genome wide approaches to this problem. These studies will not involve mouse work and may suit some students more than others.

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Indigenous Health Research Program
Dr Gail Garvey
Phone: 3845-3746
Dr Vanessa Beesley
Phone: 3362-0270
Dr Patricia Valery
Phone: 3362-0224
Email: Gail.Garvey@qimr.edu.au Email: Vanessa.Beesley@qimr.edu.au
Email: Patricia.Valery@qimr.edu.au

[MPhil,  P]

The Supportive Care Needs of Indigenous Cancer Patients in Queensland

Background

Australian Indigenous people experience more aggressive cancers and a higher cancer mortality rate than their non-Indigenous counterparts. This poor prognosis and the unique barriers Indigenous patients face to access quality cancer treatment and care is likely to mean that Indigenous cancer patients are faced with specific and high levels of unmet supportive care needs.

Approaches

We propose to conduct a comprehensive study which will:

1. validate a need assessment instrument for Indigenous cancer patients;
2. assess the supportive care needs of Queensland Indigenous cancer patients over time and;
3. explore the role of health workers in meeting these needs.

There are many aspects to this project that a student could take ownership of. For example, the qualitative pilot work interviewing patients about the validity of the needs assessment instrument, the psychometric analysis of the instrument, the baseline assessment of unmet support needs in the Indigenous population, the assessment of change in needs over time or the exploration of how effective health workers are at meeting these needs.

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

Degree

Masters or PhD students will be considered. Due to the varying arms of this project we could potentially support more than one Masters/PhD candidate.

Indigenous students are encouraged to apply.

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Immunology Division

Bone Marrow Transplantation Laboratory
Dr 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 Dr 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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Clinical Immunohaematology Laboratory
Dr Jamie Nourse
07-3845 3134
Dr Maher Gandhi
07-3845 3792
Email Jamie.Nourse@qimr.edu.au
Email Maher.Gandhi@qimr.edu.au
[H ]

Quantitative Expression Profiling of EBV microRNAs:

during the initial phases of in vitro EBV infection of Naive B-cells as a model of EBV transformation in lymphoma.

Epstein-Barr virus (EBV) is a ubiquitous herpesvirus that establishes a lifelong persistent infection of B cells in more than 90% of the adult population. EBV mostly infects in a latent manner where only a small number of viral genes are expressed and the host cell is not killed. However, EBV is able to transform B-cells in vitro and is associated with a variety of disorders including mononucleosis, Burkitt and Hodgkin lymphoma and, in immunosupressed patients, lymphoproliferative disorders.

EBV associated lymphoma types reflect the state of the cell at time of transformation, including the differentiation stage of cell, as well as the EBV latency gene expression program of the infecting virus. EBV expression programs drive naive B-cell differentiation with latency III (growth) activating the B-cell, latency II (default), differentiating the activated B-cell into a memory B-cell, latency 0 (latency) allowing lifetime persistence of the virus, and finally latency I (EBNA1) allowing the viral DNA to divide.

Recently EBV has been shown to express microRNAs (miRNAs), small non-coding RNAs (21-24bp) that can post-transcriptionally down regulate the expression of mRNAs bearing complementary target sequences. EBV miRNAs exhibit no notable similarity with known host cell miRNAs and their role in the pathogenesis of EBV remains unclear.

This study investigates the hypothesis that EBV miRNAs regulate B-cell differentiation and transformation. This will be achieved through the use of real time RT-PCR to quantify the expression profile of EBV miRNAs during infection of naive B-cells in vitro, modelling the initial stages of EBV infection and differentiation, as well as on a range of patient lymphoma samples. This will be performed in coordination with profiling of EBV latency genes to correlate miRNA expression with latency profile and transformation stage.

The outcomes of this work aim to establish if EBV miRNA expression programs are involved in the transformation of B-cells in vitro, whether EBV miRNA expression is associated with EBV latency programs, and finally to determine if EBV miRNA expression profile is associated with lymphoma type.

1. Pfeffer et al (2004). Identification of virus-encoded microRNAs. Science 304: 734-6.
2. Cai et al (2006). Epstein-Barr virus microRNAs are evolutionarily conserved and differentially expressed. PLoS Pathog 2(3): e23.
3. Thorley-Lawson and Gross (2004). Persistence of the Epstein-Barr Virus and the Origins of Associated Lymphomas N Engl J Med;350:1328-37.

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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, laser micro-dissection and whole-tissue imaging.

Students in our laboratory would become familiar with all of these techniques. There will also be opportunities for successful Honours students to enrol for PhD studies and continue work in the Immunology and Infection laboratory.

Project 1  Defining early immune events following Plasmodium berghei infection

The activation of parasite-specific T cell responses is a key event in the pathogenesis of cerebral malaria (CM) in mice caused by Plasmodium berghei. Dendritic cells (DCs) play an important role in the activation of T cells by presenting parasite antigens, providing co-stimulatory signals and producing pro- and anti-inflammatory cytokines that influence the phenotype of activated T cells. We will isolate splenic DC's from mice at various times after infection with P. berghei to determine the co-stimulatory molecules and cytokines being expressed by these cells.

Initially, we will study the important co-stimulatory molecules CD80, CD86 and CD40, as well as the pro-inflammatory cytokine IL-12 and anti-inflammatory cytokine IL-10. Blocking antibodies raised against these molecules will be administered to mice prior to infection and the effects of DC function and T cell activation will be analysed, as well as effects on the development of CM. This work will be the first step in identifying the key molecules that activate T cells involved in the development of pathology during CM. Once identified, strategies to modulate their expression can be devised with the aim of preventing the development of cerebral malaria in humans.

Techniques used in this project will include cell biology, molecular biology, histology, microscopy and analysis of blood parasite levels. Resources are available to continue this work as a PhD project.

Reference: Good M. F., H. Xu, M. Wykes and C. R. Engwerda. 2005. Ann Rev Immunol 23:69.

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

[H,  P]

Novel vaccine adjuvant delivery systems and group A streptococcus

Infection with group A streptococcus (GAS) is responsible for causing rheumatic fever (RF) and rheumatic heart disease (RHD), which can account for more than 350,000 deaths each year. The development of a vaccine represents the best primary prevention solution to combat these diseases.

Background

My research over the last seven years has focused on the development of a synthetic multiepitope mucosal GAS prophylactic vaccine based on the Lipid-Core Peptide (LCP) system. I have published 20 research papers and six review articles on this area.

My research has progressed to the design of dual antigen (M protein and SfbI)-containing vaccines designed to provide superior protective immunity, when compared to single antigen vaccines, against GAS and which can be delivered nasally. Research is focused on the development of a novel mucosal GAS vaccine.

Projects are available for Honours and PhD scholars in 2009.

Hypothesis

Our hypothesis is that LCP-GAS vaccines activate dendritic cells (DC), which are potent antigen-presenting cells, possibly through interaction with Toll-like receptors (TLR).

Approaches

• A substantial component of the research will involve animal handling, in addition to laboratory procedures for the assessment of the induction of protective immune responses.
• To define the cells involved in generating protective mucosal immune responses after intranasal delivery of LCP-based vaccine candidates, cellular responses will be determined in NALT. FACS staining of NALT cells will be used for the expression of T-cell markers CD3, CD4 and CD8, and T-cell subsets, and B-cell antigen using commercially available antibodies.
• Enumeration of antigen-specific antibody-secreting cells will be determined by ELISPOT following cell isolation. Recall of lymphocyte cellular responses will be determined to vaccine candidate antigens by a standard T-cell proliferation assay. Cell supernatants will be analysed for cytokine production using commercial ELISA kits.
• Splenocytes and NALT cells will be prepared from immunised mice and used to assess the expression of activation markers on spleen and NALT DC by FACS analysis to determine the expression of MHC Class II, and activation markers CD40, CD80 and CD86 on live gated CD11c+ cells. To assess activation of DC in vitro, immature DC will be generated from bone-marrow cell precursors, isolated from the femurs of naďve mice, by culture with GM-CSF for 6 days prior to stimulation (24 hrs) with LCP-based GAS vaccines or appropriate controls. FACS analysis will be used to assess CD marker expression as above. Cell supernatants will be analysed for IL-6, IL-10, IL-12p40/p70, and TNF- production using ELISA kits.
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