MPhil in Translational Research
Research projects
Following are a range of projects specially targeted to students enrolled in the MPhil in
Translational research Program with the following features;
o All these projects will produce publishable outcomes within 12-months
o All reagents/models etc are in place
o Project have a strong translational focus
Further research project options are available in many labs at The University of Queensland
Diamantina Institute (UQDI) (http://www.di.uq.edu.au/), University of Queensland School of
Medicine (UQ-SoM) (https://www.som.uq.edu.au/), Queensland University of Technology
Institute of Health and Biomedical Innovation (IHBI) (https://www.ihbi.qut.edu.au/) and
Mater Research (MR-UQ) (http://www.mmri.mater.org.au/) based at TRI. For further
information on alternative projects please refer to the specific websites of each of these
organisations.
For further information on the MPhil program please go to http://www.di.uq.edu.au/mphil-translational-research
PROTEOMIC
ANALYSIS
OF
BIOMARKERS
PROGRESSION IN ANKYLOSING SPONDYLITIS.
OF
RADIOGRAPHIC
There is substantial variation in rate of progression of ankylosis between patients with
ankylosing spondylitis. It is known that a significant component of this is due to
environmental factors including cigarette smoking, occupation, and continuous antiinflammatory use, as well as genetic factors including gender and other as yet largely
unidentified heritable factors. There is a great need to better identify individuals who are at
higher risk of progression, particularly given the increasing data suggesting that TNFinhibitor use over time reduces the rate of ankylosis in AS. The development of validated
quantitative measures of radiographic severity in AS (particularly the modified Stoke
Ankylosing Spondylitis Severity Score, mSASSS) has greatly facilitated the search for
predictive biomarkers.
A number of biomarkers have been studied in AS with none of these studies identifying a
single biomarker which is of clinical utility for AS. We will employ state-of-the-art
proteomic analysis using mass spectrometry at the University of Queensland Diamantina
Institute (UQDI) facility headed by Dr Michelle Hill.
1. To identify novel candidate biomarkers for severity and progression of ankylosis in
AS.
2. To test the utility of those biomarkers alone and in combination, and in comparison
with previously reported biomarkers, in identifying cases with mild or severe
radiographic change in AS, or rapid or slow progression of AS.
Contact:
Professor Matthew A. Brown - matt.brown@uq.edu.au
Director, UQDI
GLUCOSE HANDLING BY THE RENAL PROXIMAL TUBULES IN DIABETES
More than 1 million Australians are diagnosed with diabetes and the majority of deaths are
attributed to associated kidney or cardiovascular diseases. Complications are generally
considered to arise from chronic hyperglycaemia and therefore the primary goal in managing
diabetes is to lower blood glucose concentrations. Sodium-dependent glucose transporter-2
(SGLT2) inhibitors are a novel class of anti-hyperglycemic agent indicated for use in type 2
diabetic patients without kidney disease. They are currently under investigation as an add-on
to insulin for type 1 diabetes. Their mechanism of action is to block glucose reabsorption by
the kidney proximal tubules. The potential for these agents to stop the progression of kidney
disease in diabetes is also being tested, with initial data suggesting a reduction in the degree
of albuminuria. However, long-term data on whether SGLT2 inhibitors can prevent
complications are yet to emerge.
Under normal glucose conditions, SGLT2 is considered to account for the majority of
glucose reabsorption by the early proximal tubule. However, we have evidence for the
presence an insulin-sensitive glucose trasporter, GLUT4, which is upregulated in the
proximal tubule under diabetic conditions. The role of GLUT4 in kidney tubules is
completely unknown. It has also become apparent that the SGLT2 may be responsive to
insulin. Demonstrating that glucose reabsorption by the kidneys is altered in response to
insulin may refine the way the kidneys are targeted to control blood glucose. This study aims
to characterise how the kidneys handle glucose in diabetes, particularly the role of GLUT4
and how insulin might regulate glucose reabsorption (via SGLTs and/or GLUTs).
Aims:
i) To examine the functional role of GLUT4 in the early proximal tubule using specific
GLUT4 knock-out mice, ii) To determine the degree of glucose reabsorption by the kidneys
that is insulin sensitive using in vivo renal clearance experiments and elucidating the
contribution by SGLTs and GLUTs using specific inhibitors.
Contact:
Prof Josephine Forbes - josephine.forbes@mater.uq.edu.au
Glycation and Diabetes, Mater Research Institute-UQ, Translational Research Institute
GENETIC SUSCEPTIBILITY TO NEPHROPATHY IN DIABETES
More than 1 million Australians are diagnosed with diabetes and the majority of
deaths are attributed to associated kidney or cardiovascular diseases. However, not all
diabetic individuals will develop nephropathy, suggesting a genetic susceptibility. To date, a
number of approaches have been utilised to identify candidate genes. As with most chronic
complex diseases, this work is ongoing, since case and control groups are often dependent
upon specific disease definitions, which may not accurately encompass the underlying causal
traits. For example, the characterisation of early diabetic renal disease is problematic since it
has become clear that one of the most commonly utilised markers, albuminuria, can actually
regress spontaneously, or is not present at all in some diabetic individuals that develop end
stage renal disease (Perkins et al., 2003).
The collaborative consortium “Gene Mine” is a unique resource consisting of
hundreds of inbred mouse strains derived from eight of the most genetically diverse mouse
strains by a strict breeding program (2012). It may be considered as a vast family tree of
hundreds of “cousins” descended from eight great-grandparents, where each cousin is a
genetically homogeneous, defined inbred mouse strain. These cousin strains show enormous
variability in all traits tested, including disease susceptibility. In this project we will test a
representative sample of 40 strains before and after the induction of diabetes, by examining
GFR or renal ATP content, known determinants of renal damage. We will use these to
identify regions which account for variation in these traits.
Aims:
i) To examine GFR and ATP content of the kidney cortex in the gene mine, ii) To determine
the regions of the chromosome which account for variation in GFR and ATP content from the
gene mine.
Contact:
Prof Josephine Forbes - josephine.forbes@mater.uq.edu.au
Glycation and Diabetes, Mater Research Institute-UQ, Translational Research Institute
GENETICS AND BIOLOGY OF TRIPLE NEGATIVE MYELOPROLIFERATIVE
NEOPLASMS (MPN)
MPNs are a common group of ‘benign’ haematological malignancies characterised by the
aberrant proliferation of mature blood cells. The three most common varieties are
polycythemia vera (PV), essential thrombocythemia (ET) and idiopathic myelofibrosis
(IMF). Most cases of PV and about 50% of ET and IMF are due to a gain of function
mutation in the JAK2 kinase (V617F) which leads to growth factor-independent blood cell
proliferation. JAK2 inhibitors are finding a place in the treatment of the more severe forms of
MPN or those with a worse prognosis. A recently described mutation in calreticulin (CALR)
accounts for approximately 25% of JAK2-negative ET and IMF, while gain of function
mutations in the thrombopoietin receptor, MPL, account for another 5-10% of cases. There
remains a cohort of ET and IMF cases (15-20%) which are triple negative, and these patients
have a poor prognosis with faster progression to end stage IMF and AML. The genetic
lesions responsible for these cases are likely to shed light on the biology and genetics of
normal blood cell proliferation provide new targets for novel therapies to treat MPN. We
have undertaken extensive next generation targeted re-sequencing to find new mutations in
triple negative MPN and discovered many interesting ones. This MPhil project has two
components. The first will undertake clinical-genetic correlation studies using the MPN01
national registry which Professor Perkins manages in Brisbane. The second component will
investigate how two new mutations in the LNK kinase lead to MPNs using engineered cell
lines and protein interaction studies. The candidate will learn molecular and cellular biology
techniques and be part of a large translation laboratory at the TRI. There will also be an
opportunity to be involved in companion molecular studies for international trials in MPN
undertaken by Professor Perkins.
Supervisors: Professor Andrew Perkins and Dr Michael Tallack
Contact: Professor Andrew Perkins - andrew.perkins@mater.uq.edu.au
INVESTIGATION OF THE MECHANISM BY WHICH IKAROS MUTATIONS
CAUSE PH-LIKE ACUTE LYMPHOBLASTIC LEUKAEMIA (ALL)
Pre-B cell ALL is one of the most common malignancies of childhood. There are a broad
range of molecular lesions (translocations, copy number variations and SNPs) associated with
pre-B ALL. One of the most common of these occurs within the Ikaros transcription factor.
Ikaros can act as a transcriptional activator or repressor depending on context, and it plays an
important role in long range interactions between enhancers and promoters via DNA looping.
Ikaros mutant pre-B ALL cells have an expression signature similar to Philadelphia-positive
ALL and a similarly carry a poor prognosis. It remains unclear how loss of function of Ikaros
leads to ALL. We require new knowledge about the normal direct targets of Ikaros and how
these regulate B cell differentiation. We hypothesise loss or gain of expression of some of
these target genes is responsible for the aggressive disease. We hypothesis many of the Ikaros
bound sites in nuclei will be in distant enhancers and that disruption of DNA-looping is an
important way by which Ikaros mutations cause malignant transformation. Heterozygous loss
of function mutations in Ikaros lead to T-ALL in mice, but pre-B cell ALL also occurs if
there is addition activation of Abl kinase. We have generated a mouse model (Plstc) of
Ikaros-dependent ALL using ENU mutagenesis. Heterozygous mice develop T-ALL at 8-12
weeks of age. These mice harbour a point mutation in the DNA-binding domain of Ikaros but
the C-terminal protein interaction zinc finger domain is intact. This is reminiscent of the
human mutations which cause pre-B ALL. This MPhil project will address the direct targets
if Ikaros in pre-B cells by ChIP-seq. We will sort Pre-B cells from young mice by FACS and
perform ChIP-seq in wild type mice and also in Ikaros-Plstc mice to determine whether
binding to sites in the genome via interaction with other Ikaros family members can take
place. We will also perform RNA-seq on wild type and pre-malignant B cells which harbour
the Ikaros mutation to determine how Ikaros binding events disrupt the transcriptome. If time
permits and the first aim is successful, novel DNA-looping assays (capture-C) may be
possible. This project will provide experience in the molecular biology and bioinformatics of
next generation sequencing techniques which are becoming commonplace in translational
genetics. The Perkins laboratory a national leader in all of these NGS assays.
Supervisors: Professor Andrew Perkins and Dr Michael Tallack in collaboration with
Professor Stephen Smale (UCLA) and Professor Christopher Goodnow (Garvan
Institute)
Contact: Professor Andrew Perkins - andrew.perkins@mater.uq.edu.au
TESTING A NEW DRUG TARGET FOR EXPANSION OF HEMATOPOIETIC
STEM CELLS (HSCS) IN VITRO AND IN VIVO
Using a forward genetic screen in mice we have discovered a genetic pathway which is
involved in generation of HSCs during development. The pathway has been partly uncovered
by others using high throughput drugs screens in zebrafish and some of the pathway have
been validated in mice. We have discovered a new component of the pathway which
normally provides a break on HSC generation. This gene is targetable by drugs which are
already in the clinic for other purposes.
The project will test whether commercially available drugs can expand human HSCs from
CD34+ cord blood samples in vitro, and whether they can expand eGFP-marked HSCs from
zebrafish or mice. We will also test whether administration of these drugs via i.p. or i.v.
injection can expand murine bone marrow HSCs in vivo. We undertake RNA-seq on sorted
HSCs to determine the transcription targets which correct with HSC expansion. This should
provide insights into the downstream effectors of this novel pathway. The project will
introduce the MPhil candidate to a broad range of techniques including multi-parameter
FACS, next generation sequencing and animal models commonly used internationally to
study blood cell development (mouse and zebrafish).
Supervisors: Professor Andrew Perkins, A/Prof Ingrid Winkler and Dr Mathieu
Francois (IMB, UQ)
Contact: Professor Andrew Perkins - andrew.perkins@mater.uq.edu.au
THE ROLE OF THE IMMUNE SYSTEM AND EFFECTIVENESS OF
COMBINATION IMMUNE-BASED THERAPIES IN CANCER
Dr Mattarollo has a strong interest in tumour immunology, and particularly immunotherapy
for cancer. The outcomes of his studies have led to development of pre-clinical and clinical
trials conducted in Brisbane and Japan, investigating combination
chemotherapy/immunotherapy in cancer patients. Dr Mattarollo joined the research group led
by Professor Ian Frazer at The University of Queensland Diamantina Institute in 2007 to
undertake postdoctoral research, investigating immune regulation in animal models of
cervical cancer.
Mattarollo furthered his training in the field of cancer immunotherapy by secondment to the
laboratory of Professor Mark Smyth at the Peter MacCallum Cancer Centre in Melbourne
(2010-2012). There, he and his group developed a novel therapeutic cancer vaccine for B cell
lymphomas, and through collaboration with international colleagues in France, made
significant inroads into understanding how the immune system is required for effective
chemotherapy treatment outcomes in cancer patients. Returning to UQDI in May 2012,
Mattarollo’s vision and goal is to develop the field of at the Translational Research Institute
and UQ, and promote cross-disciplinary, multi-centre collaboration in Australia for
translational research.
Mattarollo’s group focus on developing and assessing combination immune-based therapies
in mouse models of human cancer and investigating how tumours escape control by the
immune system. Their objective is to improve treatment quality and outcomes for patients
with advanced cancers through translation-directed immunological research.
He has two project suitable for the MPhil in Translational Research;
-
NKT cell and Toll-like receptor-driven therapeutic vaccination against blood
cancers.
-
Immunosuppressive myeloid cell populations induced by B cell lymphomas.
Contact: Dr Steve Mattarollo – s.mattarollo@uq.edu.au
DEVELOPING A MULTIVARIATE
OESOPHAGEAL ADENOCARCINOMA
DIAGNOSTIC
BLOOD
TEST
FOR
Oesophageal adenocarcinoma is generally diagnosed at a late stage, leading to poor patient
outcome. Currently gastro-oesophageal endoscopy with biopsy is used to diagnose
oesophageal adenocarcinoma. This method is invasive and expensive. To improve the
diagnosis of oesophageal adenocarcinoma, our group undertook discovery and validation of
serum protein biomarkers using mass spectrometry-based proteomics. The goal of this project
is to translate a panel of biomarkers into clinical assay. The techniques may include
immunoassay development and evaluation, statistical modelling for the multivariate
diagnostic.
Pre-requisite: basic or advanced statistics preferred, lab experience will be advantageous but
not essential.
Contact: Dr Michelle Hill – m.hill2@uq.edu.au
ALTERATIONS IN REGULATORY T CELL PHENOTYPE IN TYPE 1 DIABETES
Analysis of regulatory T cell subsets within the peripheral blood of individuals with type 1
diabetes, at-risk first-degree relatives and healthy controls. A panel of phenotypic defects has
been observed in pre-clinical mouse models of type 1 diabetes, primarily driven by defects in
the interleukin 2 pathway. This project will examine whether these defects are also observed
in human type 1 diabetes, in which defects in interleukin 2 signalling are also a key
contributor to disease.
Analysis of clinical blood samples by flow cytometry to develop assays to assess regulatory T
cell function. These assays will be applied in the future to monitor regulatory T cell function
in clinical trials of therapeutic agents in type 1 diabetes.
Supervisors: Dr. Emma Hamilton-Williams, Professor Ranjeny Thomas.
Contact – Dr Emma Hamilton-Williams – e.hamilonwilliams@uq.edu.au
DEFECTS IN T CELL DEVELOPMENT LEADING TO TYPE 1 DIABETES
Project Description: Common genetic variants modify the immune response, predisposing to
a loss of T cell tolerance to self-proteins and the development of autoimmune diseases such
as type 1 diabetes. One key pathway implicated in type 1 diabetes development is the
interleukin-2 (IL-2) signalling pathway. We have exciting preliminary data that defects in IL2 genes modify early T cell development in the thymus when central tolerance is imposed.
This project will follow up on this data and investigate the mechanism through which this
occurs. A mouse model of type 1 diabetes will be utilised and events in early thymic selection
will be investigated included expression of IL-2 responsive genes (RT-PCR), measurement of
TCR signalling strength (calcium flux assay) and selection of islet-specific T cells (tetramer
staining to detect antigen-specific cells).
Outcomes: Development of an in-depth understanding of how gene variants that predispose
to autoimmunity result in a breakdown in central tolerance. Learn and master a range of
immunological techniques for assessment of T cell function.
Supervisor: Dr Emma Hamilton-Williams
Contact – Dr Emma Hamilton-Williams – e.hamilonwilliams@uq.edu.au
ROLE OF GUT MICROBIOTA IN DEVELOPMENT OF SPONDYLOARTHRITIS,
ILEITIS AND PSORIASIS IN SKG MICE
Aim
Analysis of presence and function of microbes in germ free mice reconstituted with limited
microbiota and their relationship to disease induction in susceptible and non-susceptible
mouse strains.
Expected outcomes and deliverables:
o Quantification of microbes by PCR and genotyping techniques.
o Analysis of bacterial expressed genes by sequencing and bioinformatics
techniques.
o Analysis of mouse mucosal immune system by flow cytometry, microarray
and histology.
o Clinical and histological assessment of psoriasis, Crohn’s like ileitis, arthritis
and spondylitis.
o Function of bacteria implicated in disease and regulation: culture with mouse
immune cells
Supervisory team:



Professor Ranjeny Thomas - Ranjeny.thomas@uq.edu.au
Professor Mark Morrison - m.morrison1@uq.edu.au
Professor Phil Hugenholtz
REPURPOSING DRUGS FOR TYPE 1 DIABETES
Aims
Testing approximately 15 drugs discovered in a bioinformatic screen for efficacy in
prevention and arrest of established diabetes in a mouse model of type 1 diabetes.
Developing a clinical protocol for phase 2a trials of drugs emerging from the mouse model,
in patients with recent-onset type 1 diabetes.
Expected outcomes and deliverables:
o Analysis of diabetes incidence and therapy in the non-obese mouse model of type 1
diabetes
o Preliminary studies of mechanism of action of key candidates
o Development of clinical protocol and organisation of a translational program in
recent-onset type 1 diabetes patients at a national level.
Supervisory team:
Professor Ranjeny Thomas - Ranjeny.thomas@uq.edu.au
Dr Emma Hamilton-Williams - e.hamiltonwilliams@uq.edu.au
Dr Mark Harris - mark.harris@mater.org.au
ORAL DELIVERY OF ANTI-INFLAMMATORY CYTOKINES TO THE GUT TO
TREAT INFLAMMATORY BOWEL DISEASE.
Background: Inflammatory bowel disease (IBD) is a chronic inflammatory condition
affecting the gastrointestinal tract of children and adults due to an inappropriate immune
response to resident gut bacteria. Medical treatment has progressed significantly through a
better understanding of the mechanism of disease, resulting in a better quality of life for many
patients, but there remains a need for more effective and targeted therapy. IL-22 has emerged
as an important cytokine produced by macrophages and type-3 innate lymphoid cells during
colonic inflammation. In mice, overexpression of IL-22 in the colon reduces the level of
inflammation. Oral delivery of peptides is challenging due to the numerous proteases and
harsh environment of the gut but nano-particles have emerged as a novel mode of delivery
that may allow delivery of anti-inflammatory cytokines to sites of gut inflammation. This
project focuses on developing orally available IL-22 and testing its efficacy in a murine
model of colitis.
Project description: Using a stable cell line expressing an IL-22 reporter recombinant IL-22
bound to a variety of nano-particles will be tested for receptor activity. Particles with optimal
stimulation properties will be further tested in epithelial cell lines and activation of
endogenous IL-22 examined using quantitative RT-PCR. Optimal IL-22 coated nanoparticles will then be used in a chemically induced murine colitis model as well as a
spontaneous colitis model to examine the effect on gut inflammation. In addition to assessing
histologic inflammation, RT-PCR will be utilized to interrogate pro- and anti-inflammatory
pathways as well as oxidative stress pathways.
Suitable for: Students with knowledge of molecular biology and basic immunology.
Contact;
Dr Jakob Begun - Jakob.begun@mater.uq.edu.au
Senior Research Fellow, Inflammatory Bowel Diseases