cancer research at peter mac research at the forefront of discovery

Cancer Research at
Peter MacCallum
Cancer Centre
2012 Projects
For more information contact:
Dr Caroline Owen
T: +61 3 9656 1930
E: caroline.owen@petermac.org
Peter Mac is Australia’s only public hospital solely dedicated to cancer
and home to the largest cancer research group in Australia.

CANCER RESEARCH AT PETER MAC
RESEARCH AT THE FOREFRONT OF DISCOVERY
RESEARCH OVERVIEW
For 60 years, Peter Mac has been providing high quality treatment and multidisciplinary care for cancer
patients and their families. It houses Australia’s largest and most progressive cancer research group, one of
only a handful of sites outside the United States where scientists and clinicians work side-by-side.
Peter Mac’s unique integration of science and clinical care enables the development and application of
innovative new methods of cancer diagnosis, treatment and education. This has enabled Peter Mac to build an
international reputation for its clinical and research work.
As Australia’s foremost cancer centre Peter Mac’s mission is to provide quality treatment and support to
patients and their families, and broadly influence cancer care in the community through multidisciplinary
patient care services, research and education.
Cancer is a complex set of diseases, and modern cancer research institutes like the Peter Mac therefore
conduct research that covers a diversity of topics that range from laboratory-based studies into the
fundamental mechanisms of cell growth, translational studies that seek more accurate cancer diagnosis,
clinical trials with novel treatments, and research aimed to improve supportive care.
The proximity and strong collaborative links of clinicians and scientists provides unique opportunities for medical
advances to be moved from the ‘bench to the bedside' and for clinically orientated questions to guide our
research agenda. As such, our research programs are having a profound impact on the understanding of
cancer biology and are leading to more effective and individualised patient care.
WHY PETER MAC?
Collaborative interaction with national and international peers is a lynchpin of any vibrant program. Peter Mac
is continually seeking to work with the best worldwide and the world’s best are increasingly seeking out Peter
Mac researchers to interact with.
Why work or study at Peter Mac? In speaking to current and past researchers and students, it is immediately
evident that the two factors most strongly influencing their decision to join and stay at Peter Mac are firstly, the
opportunity to be mentored by a strong and collegiate group of senior researchers and secondly, the superb
research infrastructure that enables them to perform virtually any type of experiment they require at affordable
cost. This is a strong vindication of our strategy of identifying, seeding and supporting the growth of an
enabling environment, both in terms of talented senior personnel and first-class research infrastructure.
RESEARCH STRUCTURE
CANCER RESEARCH DIVISION
The Cancer Research Division at Peter Mac is home to over 420 laboratory-based scientists and support staff,
including approximately 80 higher degree (mainly PhD) and Honours students. Supported by nine core
technology platforms, our 26 research laboratories are organized into six programs of laboratory-based
programs and translational research:
• Cancer Cell Biology • Growth Control & Differentiation
• Cancer Genetics & Genomics • Cancer Therapeutics
• Cancer Immunology Research • Tumour Angiogenesis
Research is supported by our core facilities and platform technologies. These core infrastructure groups are
the backbone of the division and ensure that the researchers are outfitted with the equipment and expertise
needed to facilitate their research. An important role of the Core Groups is to also identify, import, and develop
new technologies.
CLINICAL RESEARCH
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Peter Mac is proud of its long history of involvement in clinical research. The structure of clinical services at
Peter Mac fosters an environment in which clinicians from various specialties can work together with allied
health and supportive care staff on clinical research projects with a disease-specific focus. Research in the
clinical services are structured into the following areas:
Breast Assoc. Prof. Boon Chua boon.chua@petermac.org
Gastrointestinal: Dr Michael Michael michael.michael@petermac.org
Gynae-oncology: Dr Kailash Narayan kailash.narayan@petermac.org
Haematology: Assoc Prof John Seymour john.seymour@petermac.org
Head and Neck: Assoc Prof June Corry june.corry@petermac.org
Lung: Assoc Prof David Ball david.ball@petermac.org
Melanoma and Skin Assoc. Prof David Speakman david.speakman@petermac.org
Neuro-oncology Dr Damian Tange damian.tange@petermac.org
Paediatric, Adolescent, Young Adult and Late Effects: Dr Greg Wheeler greg.wheeler@petermac.org
Sarcoma: Prof Peter Choong peter.choong@petermac.org
Uro-oncology Dr Farshad Foroudi farshad.foroudi@petermac.org
PLATFORM TECHNOLOGIES
Peter Mac has platform technologies that underpin an enabling environment and allow Peter Mac researchers
to be internationally competitive in an increasingly technology-driven environment. Peter Mac’s core
technologies and expertise are also made available to external researchers on a collaborative or cost-recovery
basis, thereby increasing research output in the wider bioscience community. Key technologies at Peter Mac
include:
Biostatistics at Peter Mac is the leading biostatistical centre focusing on cancer clinical trials in Australia.
The centre provides statistical expertise for national cancer trials groups including the Trans Tasman
Radiation Oncology Group (TROG) and the Australasian Leukaemia and Lymphoma Study Group (ALLG).
Clinical research nurse core. Peter Mac currently has a team of research nurses to support a sophisticated
clinical and translational research program. These nurses provide necessary skills to coordinate phase I firstin-man
clinical trials involving complex procedures such as tumor biopsies for evaluation of molecular targets,
serial PET scans and complex pharmacokinetic sampling.
Flow Cytometry and Cell Sorting. We offer multi-parameter (five colour) flow cytometric analysis for
identifying rare populations of cells within complex mixtures such as human bone marrow, and two fully
supported fluorescent activated cell sorting (FACS) instruments for isolating cells such as blood progenitor
cells under sterile conditions.
Genomics, Microarray Technology and Predictive Medicine. Peter Mac has been the leading site in
Australia in the application of gene microarray technology for predicting outcomes of human cancer or an
individual’s likely response to a given therapy.
Microscopy Imaging and Research Core Facility is a world-class facility encompassing all aspects of
microscopy such as immunofluorescence, laser capture, confocal and transmission electron microscopy.
Molecular Pathology is a central platform to successful translational research by providing robust diagnostic
molecular analyses of tumours. Molecular Pathology at Peter Mac provides diagnostic testing for familial
breast and colorectal cancer, and is a national reference centre for testing for specific mutations in cancer
samples.
Molecular Imaging. The centre for molecular imaging is a world leader in the clinical use of PET scanning in
cancer. The facility includes three chemists, contains a cyclotron, two small animal PET scanners for
translational research and automated production facilities for a number of novel tracers. These tracers provide
the capacity to image diverse biological processes including hypoxia, lipid synthesis, cell proliferation and
amino acid transport.
Tissue/Tumour Bank. Peter Mac has been a leader in the development of sophisticated biospecimen and
clinically annotated cancer samples collection. We are the host institute for the Australian Biospecimen Bank
(ABN-Oncology), a federally funded project to enable national cancer sample collection and facilitated access
to tissue resources.
Transgenic and SPF Facility. We currently breed and maintain approximately 20,000 mice, representing
over 130 different strains of transgenic and gene-targeted mice that are immune-deficient or cancer. Peter
Mac’s Animal Ethics Committee (AEC) has an important role in overseeing the ethical conduct of any work
involving the use of animals for scientific purposes, conforming to the NHMRC Australian Code of Practice for
the Care and Use of Animals for Scientific Purposes.
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RESEARCH EDUCATION PROGRAM
Peter Mac brings together Education and Research in a dynamic and life changing way. We strive to develop
a world-class educational experience for students at a leading Australian cancer research institution.
The majority of students completing projects at Peter Mac are enrolled through the University of Melbourne
and other Victorian universities. However, we welcome inquiries from students from all Universities throughout
Australia and overseas. We boast a diverse student population from all over the world.
Our postgraduate PhD and Honours contribute significantly to the success of Peter Mac, and our Cancer
Research Division is home to over 80 honours and post-graduate students. The attraction of high-quality
students to undertake Doctor of Philosophy (PhD), Doctor of Medical Science (DMedSci), medical doctorates,
and Honours programs in our laboratories continues as a priority. Our comprehensive student program
includes mentor programs, dedicated student scientific review committees, onsite workshops and seminars, an
annual retreat, and opportunities to contribute to our community and outreach programs.
The following pages highlight some of the projects available for future students in 2012.
If you are interested in a particular project, use the contact details to follow up with the listed supervisors to
learn more about the project.
For more information about research opportunities in the Cancer Research Division contact:
Dr Caroline Owen, Education & Communication Coordinator (Research)
Peter MacCallum Cancer Centre, St. Andrew’s Place, East Melbourne, Victoria, Australia 3002
Tel: +61 3 9656 1930 Email: caroline.owen@petermac.org
or visit:
http://www.petermac.org/research/EducationCareers
PROJECT DESCRIPTIONS BY PROGRAM
CANCER GENETICS PROGRAM page 4
Cancer Genetics & Genomics page 4
Sarcoma Genomics & Genetics page 5
Surgical Oncology page 6
VBCRC Genetics page 7
Molecular Pathology page 8
CANCER IMMUNOLOGY PROGRAM page 9
Cancer Cell Death page 9
Cellular Immunity page 9
Immune Signalling page 10
Immunotherapy page 11
Haematology Immunology Translational
Research Laboratory (HITRL) page 12
CANCER THERAPEUTICS PROGRAM page 13
Gene Regulation page 13
Melanoma Research page 14
Victorian Centre for Functional
Genomics page 14
Molecular Imaging & Translational Medicine
Program page 14
CANCER CELL BIOLOGY PROGRAM page 15
Cell Cycle & Development page 15
Cell Cycle and Cancer Genetics page 16
Cell Growth & Proliferation page 17
Epithelial Stem Cell Biology page 18
Metastasis Research page 18
Molecular Radiation Biology page 19
Tumour Suppression page 20
Tumour Microenvironment page 21
TUMOUR ANGIOGENESIS PROGRAM page 23
ONCOGENIC SIGNALLING & GROWTH
CONTROL PROGRAM page 24
CLINICAL RESEARCH page 31
FURTHER INFORMATION page 31
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CANCER GENOMICS PROGRAM
www.petermac.org/Research/CancerGenomicsProgram
The Cancer Genomics program seeks to use sophisticated high throughput genomic technologies to improve our
understanding of the biology of cancer and to progress the clinical management of cancer patients through the
development of individualized approaches to treatment. Research in the program focuses primarily on breast, upper
gastrointestinal and ovarian cancers and sarcoma, and involves some of the largest familial and population-based cancer
cohorts in the world. These studies address questions of general importance to solid cancers, including inherited
susceptibility to cancer and genome-wide changes in gene expression, as well as more specific questions such as
prediction of response to therapy and the use of gene expression profiling for accurate cancer diagnosis.
CANCER GENETICS & GENOMICS
MOLECULAR ANALYSIS OF PLATINUM
RESISTANCE IN OVARIAN CANCER
Supervisors: Prof. David Bowtell, Dr Dariush
Etemadmoghadam and Dr Prue Cowin
Ovarian cancer is the 5th most common cancer in
women, and most lethal gynaecologic malignancy.
Despite aggressive surgery and platinum-based
chemotherapy, the majority of women experience
recurrence and ~70% will succumb to the disease.
Resistance to chemotherapy, or platinum resistance, is
the major barrier to long-term remissions, however the
underlying molecular mechanisms are poorly
understood. We are part of the Australian Ovarian
Cancer Study (AOCS), one of the largest ovarian cancer
cohort studies in the world. We are also one of the two
Australian projects funded through a $27 million NHMRC
grant to participate in the International Cancer Genomics
Consortium (ICGC).
We recently performed a combined gene expression and
DNA copy number change (CNC) analysis of serous
ovarian cancer in a well-defined cohort of women who
failed primary therapy. We identified 19q12 amplification
as the most dominant amplicon associated with primary
treatment failure. The 19q12 amplification is a high-level
focal amplification that consistently targets a cluster of
only several genes; including the cell cycle gene
CCNE1; and URI, recently been associated with
activation of the mTOR/S6K pathway and control of
apoptosis. It is not yet clear how these genes or other
cooperating mutations may contribute to primary
chemotherapy resistance.
Molecular and functional exploration into mechanisms of
platinum-resistance in ovarian cancer will form the basis
of the project. The student will learn key molecular
biological techniques and will be exposed to large-scale
human genetic studies that are making use of the
emerging technologies, including microarrays and next
generation sequencing. This honours project will provide
the student with the opportunity to contribute insights
into one of the most clinically significant questions in
ovarian cancer, platinum resistance.
For more information about this project contact:
Prof. David Bowtell, Tel: +61 3 9656 1356, E-mail:
david.bowtell@petermac.org
MOLECULAR ANALYSIS OF OVARIAN CLEAR CELL
CARCINOMAS
Supervisors: Prof. David Bowtell, Dr Dariush
Etemadmoghadam, Dr Prue Cowin
Ovarian clear cell adenocarcinoma (OCCA) is a clinically
significant subtype of ovarian cancer, accounting for
~10% of invasive ovarian cancers. OCCA have a poor
response rate to standard therapy (only 11-15%),
indicating the need for novel therapies. The occurrence
of OCCA is associated with co-existent endometriosis
and may arise from endometriotic cysts, however very
little is known of OCCA biology. To understand its
molecular drivers, our laboratory recently performed the
most extensive molecular analysis of OCCA to date. We
found very consistent data associated with de-regulated
cytokine signalling. A central observation was the
induction of hypoxia response genes including
IL6/pSTAT3/HIF as measured by microarray,
biochemical studies in OCCA cell lines and
immunohistochemical staining of human tumour
samples. IL6 has tumour-promoting actions on both
malignant and stromal cells in a range of experimental
cancer models, is a downstream effector of oncogenic
ras, and has been implicated in several human cancers.
This project will investigate the functional significance of
IL6 activation in ovarian cancer cell lines. Expression of
HIF2a/EPAS1 is the most highly correlated gene with IL6
in OCCA tumour samples. Interestingly, the hypoxic
response in renal clear cell carcinoma cells is dependent
on HIF2a. This observation suggests a role for HIF2a in
OCCA. Through molecular and functional techniques,
the student will explore a model where strong upregulation
of IL6 expression leads to increased HIF
expression, promoting a proangiogenic response and
facilitation adaption of cancer cells to hypoxia. This
project will provide the the opportunity to contribute
insights into one of the most clinically significant
questions in ovarian cancer, platinum resistance.
For more information about this project contact:
Professor David Bowtell, Tel: +61 3 9656 1356, E-mail:
david.bowtell@petermac.org
UNDERSTANDING DRIVERS OF A NOVEL
MOLECULAR SUBTYPE OF HIGH-GRADE SEROUS
OVARIAN CANCER
Supervisors: Prof David Bowtell, Dr Dariush
Etemadmoghadam, Dr Prue Cowin
Ovarian cancer is the 5-6th most common cause of
cancer death in women in Western countries, with ~800
deaths per year in Australia, with high-grade serous
ovarian cancers accounting for the majority of deaths
(>60%). Recently, molecular subtyping of ovarian cancer
has revealed four molecular categories of HG-SOC.
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Each molecular subtype, designated C1, C2, C4 and C5
by Tothill et al, presents with a distinct expression
pattern and differing clinical outcomes. We are part of
the Australian Ovarian Cancer Study (AOCS), one of the
largest ovarian cancer cohort studies in the world. We
are also one of the two Australian projects funded
through a $27 million NHMRC grant to participate in the
International Cancer Genomics Consortium (ICGC).
We have recently shown that the C5 subtype is
associated with amplification and over-expression of
MYCN, over-expression of LIN28B, repression of Let-7
family members, and over-expression of HMGA2. This
work for the first time defines an oncogenic pathway
specific to a molecular subtype of serous ovarian
cancers, and opens a new door to patient tailored
molecular therapies.
This project involves further definition of this oncogenic
pathway through specific over-expression and
knockdown of MYCN in ovarian cancer cell lines in vitro.
The student will learn key molecular biological and tissue
culture techniques. The Bowtell lab has a very strong
reputation in cancer genetics and genomics, and in
fundamental studies in cancer cell biology.
For more information about this project contact:
Prof. David Bowtell, Tel: +61 3 9656 1356, E-mail:
david.bowtell@petermac.org
VALIDATION OF CANDIDATE GENES INVOLVED IN
THE PROGRESSION OF GASTRIC CANCER
Supervisors: Assoc Prof Alex Boussioutas, Dr. Rita
Busuttil
Gastric cancer (GC) is the fourth most common cancer
globally and in many western countries is usually only
diagnosed at advanced stage giving patients a 5-year
survival rate of less than 20%. GC has distinct
premalignant stages that have significant propensity to
progress. The premalignant cascade consists of easily
identifiable histological stages from chronic atrophic
gastritis (ChG), intestinal metaplasia (IM) and dysplasia.
The progression through these stages, particularly IM,
takes years, offering a large window of opportunity to
intervene. Not all patients with IM will progress and
selection of patients for high-risk surveillance would
reduce the burden of unnecessary screening, patient
anxiety and improve outcomes due to early detection of
disease.
Relatively little is known about the key genetic events
leading to IM. Our laboratory is currently in the process
of completing the first comprehensive analysis of IM in
the world and seeks to identify candidate genes involved
in the progression of IM to GC that can be used to
reliably predict the progression to GC in humans by
using a genomics based approach. Identification of such
genes offers an opportunity to study the molecular
mechanisms involved and pinpoint targets for prevention
and therapy. The aim of this project is validate these
candidate genes using an independent data set and then
characterizing these genes using functional assays and
animal models.
The project will use broad range techniques including
bioinformatics, cell culture, animal models and molecular
biology.
For more information about this project contact:
Assoc. Prof. Alex Boussioutas, Tel: +61 3 9656 1287, Email:
alex.boussioutas@petermac.org
Dr. Rita Busuttil, Tel: +61 3 9656 1287, E-mail:
rita.busuttil@petermac.org
ROLE OF THE TUMOUR MICROENVIRONMENT IN
GASTRIC CANCER
Supervisors: Assoc. Prof. Alex Boussioutas, Dr. Rita
Busuttil
Gastric cancer (GC) is the fourth most common cancer
globally and 7th in incidence in Australia. It has a poor
survival rate which can be attributed to the advanced
stage at diagnosis in most patients. The molecular and
cellular mechanisms underlying the development of GC
are not well described.
Traditionally cancer research involved studying the
cancer cell itself. More recently, there has been growing
interest in studying the normal cells and molecules which
surround the cancer cell. This tumour microenvironment
consists of a variety of stromal cell types including cells
such as fibroblasts. It is believed that the dynamic
communication between tumour cells and the
surrounding cell types may play a major role in cancer
initiation, progression and establishment of metastatic
disease. The aim of this project is to investigate tumourstromal
interactions in gastric cancer utilizing established
and primary cell lines. Once the molecular pathways by
which a tumour cell progresses has been elucidated it is
possible that these processes could be exploited in the
development of novel therapeutics.
This project will use a broad range of techniques such as
live cell microscopy, cell culture techniques and siRNA
to interrogate the function of gene products that
influence tumour-stroma communication.
Our previous genomic experiments has provided us with
a number of exciting candidate genes that may be
involved in this interaction. This is novel research that
may have a major benefit to our understanding of cancer
and improve patient outcomes.
For more information about this project contact:
Assoc. Prof. Alex Boussioutas, Tel: +61 3 9656 1287, Email:
alex.boussioutas@petermac.org
Dr. Rita Busuttil, Tel: +61 3 9656 1287, E-mail:
rita.busuttil@petermac.org
SARCOMA GENOMICS & GENETICS
ROLE OF IMMUNOMODULATORS IN THE
DEVELOPMENT & PROGRESSION OF
OSTEOSARCOMA IN VIVO.
Supervisors: Assoc. Prof. David Thomas, Dr. Maya
Kansara
The Sarcoma Genetics and Genomics laboratory studies
tumours of soft tissue and bone. Osteosarcoma is the
most common cancer of bone. These tumours are highly
metastatic and often metastasise to lung via the
hematogenous route. Treatment involves aggressive
surgery with intensive adjuvant chemotherapy. Although
these measures have improved prognosis, a third of
those diagnosed will die from this disease.
Understanding how osteosarcoma arises and persists
will enable the development of targeted therapies. The
skeleton and the immune system share a number of
cytokines and transcription factors and therefore may
mutually influence each other; the study of these cells
and their interactions has been termed
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osteoimmunology. In this project we will investigate the
interaction between the immune system and bone
cancer in an in vivo mouse model of osteosarcoma. The
project will use broad range techniques including mouse
models of cancer, histology, cell culture, flow cytometry,
and molecular profiling.
For more information about this project contact:
Assoc. Prof. David Thomas. Tel +61 3 9656 1238 Email
david.thomas@petermac.org
Dr. Maya Kansara Tel +61 3 9656 1618 Email
maya.kansara@petermac.org
SURGICAL ONCOLOGY
HOW DO PIK3CA MUTATIONS CAUSE CANCER?
Supervisor: Assoc. Prof. Wayne Phillips
The phosphoinositide 3-kinase (PI3K)/Akt signalling
pathway controls a range of fundamental cellular
processes which, when de-regulated, are considered
hallmarks of cancer. While it is now well established that
somatic mutations in PIK3CA, the gene coding for the
p110α catalytic subunit of PI3K, are one of the most
common, and thus potentially one of the most important,
genetic abnormalities in many human tumours.
However, it remains unclear how these mutations drive
tumourigenesis.
We have recently generated a novel mutant mouse with
which to study the role of PIK3CA mutation in vivo and in
vitro. This mouse has been designed with a Cre
recombinase (Cre)-inducible knock-in of the most
common tumour-associated PI3K mutation,
PIK3CAH1047R. Our strategy of making the knock-in
inducible with Cre allows us to target the expression of
the mutant to specific tissues using mice expressing Cre
under the control of appropriate tissue-specific
promoters. We can also knock-in the mutation into cells
growing in culture allowing us to examine the effects of
PIK3CAH1047R mutation in vitro under defined
conditions.
Two potential projects are being offered.
(1) PIK3CAH1047R in oesophageal cancer.
Oesophageal epithelial cells will be isolated from
our PIK3CAH1047R mouse and use our novel 3D in
vivo culture systems to examine the effect of
PIK3CAH1047R expression in the growth and
differentiation of the oesophageal epithelium and
the development of cancer.
(2) PIK3CAH1047R in breast cancer. Mammary
epithelial cells will be isolated from our
PIK3CAH1047R mouse and use these to examine
the signaling pathways by which PIK3CAH1047R
induces tumourigenesis and regulates the growth
and differentiation of mammary epithelial cells.
For more information about this project contact:
Assoc. Prof. Wayne Phillips, Tel: +61 3 9656 1842;
Email: wayne.phillips@petermac.org
UNDERSTANDING BARRETT’S OESOPHAGUS AND
OESOPHAGEAL ADENOCARCINOMA.
Supervisors: Dr. Nicholas Clemons and Assoc. Prof.
Wayne Phillips
Over the past thirty years there has been a dramatic
increase in the incidence and prevalence of
oesophageal adenocarcinoma, a cancer with particularly
high mortality. The reason for the increase is not clear
but is thought to reflect an increase in the occurrence of
its recognised precursor lesion, Barrett’s oesophagus.
Barrett’s oesophagus is a metaplastic abnormality in
which the normal stratified squamous epithelium of the
oesophagus is replaced by an intestinal-type columnar
epithelium. The risk of adenocarcinoma in patients with
Barrett’s oesophagus is approximately 30-125-fold
greater than that in the general population. The origin of
Barrett’s oesophagus is a matter of conjecture. There is
compelling etiological evidence that gastro-oesophageal
reflux disease is a major contributing factor but the
actual molecular and cellular mechanism(s) underlying
the phenotypic change are not clear. Furthermore, it is
unclear what the key molecular drivers of progression
from Barrett’s to cancer are, which has contributed to the
clinical problem of indentifying those patients with
Barrett’s oesophagus that are most at risk of progression
to cancer.
Our group has developed novel in vivo and in vitro
models that allow the 3-D reconstitution of the
oesophageal epithelium from mouse or human tissue
and cell lines. Projects are available for Honours or PhD
students to use these models to investigate the
molecular and cellular mechanisms underlying the
development of Barrett’s oesophagus and/or the
progression of Barrett’s oesophagus to adenocarcinoma.
Possible projects include:
• Determining the signalling pathways involved in the
transition of the normal squamous oesophageal
epithelium to Barrett’s intestinal-like epithelium.
Possible pathways/genes to study include: Sonic
Hedgehog signalling pathway, SOX9, GATA and
HNF transcription factors and microRNAs miR203
and miR205
• Investigating the effect of the stromal
microenvironment in Barrett’s carcinogenesis
• Investigating Aurora A kinase inhibition in
combination with chemotherapy as a novel treatment
for oesophageal adenocarcinoma
• Elucidating a role for miniSox9, a novel splice variant
of Sox9, in Barrett’s carcinogenesis
Understanding the biology underlying this condition will
ultimately help us to design effective strategies for the
management and treatment of Barrett’s oesophagus and
to predict, and/or prevent, progression to oesophageal
adenocarcinoma.
References:
1. • Phillips WA, et al. J Gastenterol Hepatol 2011 26(4): 639-48
2. • Wang DH, et al. Gastroenterology 2010 138(5): 1820-22.
For more information about this project contact:
Dr Nicholas Clemons, Tel: +61 3 9656 1849; Email:
nicholas.clemons@petermac.org
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VBCRC CANCER GENETICS
The Cancer Genetics laboratory uses an integrative
genomics approach to investigate genes involved in
breast and ovarian cancer, whereby data from several
genome-wide platforms are combined to more rapidly
define critical cancer-causing genes.
GENOMIC ANALYSIS OF EARLY BREAST
NEOPLASMS
Supervisor: Assoc. Prof. Ian Campbell,
We have previously undertaken genomic analysis of
DCIS, the immediate precursor to invasive breast
carcinoma, and found that in many cases this tumour
already contains a plethora of genomic events highly
similar to IDC. In order to identify the earliest genomic
events in the development of breast cancer, this project
will analyse less advanced breast neoplasms such as
atypical ductal hyperplasia (ADH). These early lesions
have not been previously analysed at high resolution
and are likely to contain few, but highly relevant,
genomic events.
Techniques used in the project will include cutting edge
technologies such as whole-exome next generation
sequencing as well as microdissection of tumour
material, DNA/RNA extraction, and expression
microarrays. There will be a strong bioinformatics
component and potentially functional assays of
candidate genes in cell culture.
For more information about this project contact:
Assoc. Prof. Ian Campbell,
Email: ian.campbell@petermac.org
IDENTIFICATION OF HIGHLY PENETRANT GENES IN
FAMILIAL BREAST AND OTHER CANCERS USING
NEXT-GENERATION SEQUENCING
Supervisor: Assoc. Prof. Ian Campbell, Dr Ella
Thompson, Dr Alison Trainer
The ability to identify disease-causing mutations in highrisk
cancer families has broad implications for those
affected in terms of risk assessment and management
as well as treatment. A major initiative over the last year
has been the application of next generation sequencing
(NGS) to identify cancer predisposition genes. We are
performing whole exome sequence analysis of germline
DNA from multiple affected relatives from over 75 high
risk non-BRCA1/non-BRCA2 breast cancer families with
the aim of identifying segregating, rare, non-synonymous
variants that are likely to include novel predisposing
mutations. In addition, we also aim to analyse families
with other cancer types including male breast cancer,
colorectal cancer and papillary thyroid cancer to identify
the predisposing genes.
This project will perform and analyse NGS data to
identify candidate gene variants identified and validate
these variants in the family in which the variant was
found including segregation analysis. After validation,
the gene will be further analysed for mutations in other
families and individuals with the same cancer type. For
breast cancer this latter validation may be undertaken
using a boutique exon capture and NGS of 200
additional breast cancer families. Techniques used will
include DNA sequencing (NGS and Sanger), PCR, high
resolution melting and potentially assays of gene
transcription or function.
For more information about this project contact:
Assoc. Prof. Ian Campbell,
Email: ian.campbell@petermac.org
MUCINOUS OVARIAN CARCINOMA IS A DISTINCT
OVARIAN SUBTYPE REQUIRING ALTERNATIVE
CHEMOTHERAPEUTIC REGIMES
Supervisors: Assoc. Prof. Ian Campbell, Dr. Kylie
Gorringe
Mucinous ovarian carcinoma (MOC) differs in
appearance and behavior from the other common
epithelial ovarian cancer subtypes. MOC is frequently
confused with metastases from organs such as the
appendix, but it is not known if this resemblance
extends to similarities in genetic alterations. Advanced
MOC does not respond well to conventional ovarian
cancer chemotherapies, indicating a need for more
subtype-specific therapies. We hypothesis that genomic
aberrations in MOC will be similar to those in mucinous
cancers from other organs. Consequently, MOC may be
better treated with chemotherapeutics that show
success with other mucinous tumours.
This project will obtain genomic data from primary MOC
and compare this with data from metastases to the
ovary from extra-ovarian sites (initially presenting as
ovarian), appendiceal tumours, diffuse gastric tumours,
mucinous colorectal tumours and pancreatic tumours.
Techniques used will include copy number and
expression arrays and next-generation sequencing. Cell
lines representative of MOC will be used to compare
treatments with typical ovarian chemotherapies such as
cisplatin with therapies more commonly used in other
cancer types such as colorectal cancers.
For more information about this project contact:
Assoc. Prof. Ian Campbell, Email:
ian.campbell@petermac.org
Dr. Kylie Gorringe, Email: kylie.gorringe@petermac.org
FUNCTIONAL AND GENETIC CHARACTERISATION
OF OVARIAN ONCOGENES
Supervisors: Assoc. Prof. Ian Campbell, Dr. Kylie
Gorringe
Ovarian cancer is a disease characterised by complex
genomic rearrangements including high-level copy
number amplifications but the majority of the genes in
these regions that drive ovarian cancer remain
unidentified. Cataloguing these target genes will provide
useful insights into disease etiology and may provide an
opportunity to develop novel diagnostic and therapeutic
interventions. We have recently undertaken a highthroughput
siRNA knockdown screen of 300 candidate
genes located in recurrent regions of high-level gene
amplification and have identified a number of promising
candidate oncogenes. This project will select a subset of
these genes for further characterisation, including
validation of the effect of knockdown, screening tumours
for mutations using custom exon capture and NGS,
stable shRNA gene knockdown in cell culture for various
in vitro and in vivo assays, the effects of small molecule
inhibitors and immunohistochemistry.
For more information about this project contact:
Assoc. Prof. Ian Campbell, Email:
ian.campbell@petermac.org
Dr. Kylie Gorringe, Email: kylie.gorringe@petermac.org
7

MOLECULAR PATHOLOGY
IT’S IN THE BLOOD: THE EFFECT OF
CONSTITUTIONAL METHYLATION ON DISEASE
PREDISPOSITION.
Supervisors: Assoc. Prof. Alexander Dobrovic, Dr.
Michael McManus
Constitutional methylation refers to the presence of the
aberrant methylation of a given gene through multiple
tissues of the body. In most cases, it arises from the
combination of the presence of a predisposing genetic
variant in cis and a predisposing genetic background of
modifiers in trans. The methylation seems to arise
stochastically often giving rise to mosaic patterns.
Constitutional methylation of familial cancer genes has
been recently described as a new mechanism of cancer
predisposition [1]. It predisposes to a similar spectrum
of cancers as germline mutations in the same gene in
those cases where the constitutional methylation is
acting as the driver of tumorigenesis. Moreover, it may
drive a similar cluster of pathological features within
each of those tumours. This may in turn allow the
deduction of whether methylation in a particular gene is
acting as a driver or a passenger. In the case of
BRCA1, we have recently shown that detectable
methylation of the BRCA1 gene in the peripheral blood
is strongly associated with the same characteristic
cancer pathology as BRCA1 germline mutation [2].
The role of individual alleles of sequence variants in
determining methylation has become an area of active
research. We have shown that constitutional
methylation in the peripheral blood of the MGMT gene
is highly dependent on the presence of the T allele of
the rs16906252 promoter SNP [3]. Trans effects are
also likely to be important in determining methylation as
the T allele does not always result in detectable
methylation and overall levels of mosaicism are quite
variable.
The project seeks to examine the hypothesis that a
significant proportion of early onset cancer can be
explained by constitutional methylation. We also
propose that constitutional methylation may also
underlie the development of other diseases of middle
and old age. Details of the project will be worked out
with the student at the time of commencement.
References
1. Dobrovic A, Kristensen LS. Int J Biochem Cell Biol. 41: pp.
34-39, 2009.
2. Wong EM et al.. Cancer Prev Res. 4:23-33. 2011.
3. Candiloro IL, Dobrovic A. Cancer Prev Res, 2: pp. 862-7,
2009
For more information about this project contact:
Assoc. Prof. Alexander Dobrovic, Tel: +61 3 9656 1807,
Email: alexander.dobrovic@petermac.org
IDENTIFICATION OF BIOMARKERS IN PATIENTS
WITH DUCTAL CARCINOMA IN SITU.
The advent of mammographic breast cancer screening
has resulted in a significant increase in the number of
breast cancers such that DCIS accounts for ~ 20-25% of
all breast cancers. The identification of appropriate
treatment options is particularly urgent for DCIS where
therapy is primarily aimed at reducing the risk of
recurrence and progression to invasive carcinoma.
Treating with radiotherapy and hormonal therapy
reduces the risk of recurrence (both for DCIS and
invasive disease) by ~50% but for most patients this
would involve substantial over treatment and use of
valuable resources. With the increasing costs of cancer
therapeutics and targeted drugs, it will become essential
to accurately identify patients that will benefit from
particular treatment regimens. Although conventional
pathological measures and some candidate biomarkers
have been reported to be useful in predicting relapse
their sensitivity and specificity are low. Thus it is critical
that detailed evidence on the biology and the selection of
treatment are gathered to support patients with DCIS.
We propose to study a well-characterized cohort of
cases of human DCIS to identify biomarkers that can be
used to determine whether a patient is likely to recur or
progress to invasive carcinoma. We propose to extract
DNA and miRNAs and examine for methylation and
miRNA differences using methodologies that are up and
running within the laboratory. Candidates will be
confirmed on an independent validation cohort.
Candidates will be exposed to state of the art molecular
pathological methods, human pathology and interact with
diagnostic and research sections of the Institute. The
goal is to develop assays that can be used in the
diagnostic laboratory for patient care.
For more information about this project contact:
Prof. Stephen Fox, Tel: +61 3 9656 1515 Email:
stephen.fox@petermac.org
Assoc. Prof. Alexander Dobrovic, Tel: +61 3 9656 1807,
Email: alexander.dobrovic@petermac.org
IDENTIFYING THE ROLE OF LYMPHATIC VESSEL
REMODELLING IN HUMAN CANCER
Supervisors: Prof. Stephen Fox, Assoc. Prof. Marc
Achen, Assoc. Prof.. Steven Stacker
Angiogenesis, the generation of blood vessels from the
existing blood supply, is essential for tumour growth and
metastases. Indeed cancers cannot grow beyond 2 mm
in diameter without establishing a blood supply. Recent
progress in the molecular characterisation of blood
vessels has led to the development of a new class of
anti-cancer drugs targeting “angiogenesis”. As an
extension of these studies our Program of research is
developing ways to explore the role of lymphatic vessels
and the process of lymphangiogenesis in tumor growth
and metastasis. In collaboration with the Victorian
Centre for Functional Genomics we have undertaken a
genome-wide siRNA screen to uncover molecules that
are functionally important for the migration of human
lymphatic endothelial cells and their capacity to remodel
and form new vessels. We have identified a group of
genes which represents about 0.25% of the human
genome which is critically important for lymphatic
endothelial cell function in primary human cells.
Our research program seeks to determine the role of
these genes in the growth and progression of human
cancer using a systematic analysis of human tumor
samples. This would include patient tissue sets which
contain lymphatic vessels within primary tumors of
different organs, sentinel lymph nodes and patient tissue
before and after specific treatment regimes including
chemotherapy, immunotherapy and radiotherapy. The
project will incorporate techniques of modern molecular
and cellular biology with molecular pathology and
bioinformatics. The pattern and level of expression of
such factors in human cancers and their regulation gives
the project is a unique translational opportunity
combining expertise from a basic research discovery
program to a fully functional molecular pathology
8

esearch unit. The expected outcomes of the project are
the development of diagnostic tools for human disease
involving the lymphatic network.
For more information about this project contact:
Prof. Stephen Fox, Tel: +61 3 9656-5263;
stephen.fox@petermac.org;
Assoc. Prof. Marc Achen, Tel: +61 3 9656-
5264marc.achen@petermac.org;;
Assoc. Prof. Steven Stacker, Tel: +61 3 9656-5263
steven.stacker@petermac.org
See also Angiogenesis Program, page 22
CANCER IMMUNOLOGY RESEARCH PROGRAM
www.petermac.org/Research/CancerImmunologyProgram
The Cancer Immunology Program is identifying ways in which the immune system can be harnessed to prevent and
control cancer. We are interested in the very early stages of how immune cells can pick up and respond to the presence
of cancer cells. We have demonstrated that specific toxins made by “killer T cells” can prevent the onset of certain
cancers (immune surveillance), and are developing genetic technologies to modify and expand the activity of these cells
to treat established malignancies. In addition, we are defining the molecular means by which new classes of anti-cancer
drugs kill cancer cells, so that rational choices can be made on the most appropriate cancer chemotherapy for a patient.
CANCER CELL DEATH
REGULATION AND FUNCTION OF PERFORIN, A
KEY EFFECTOR MOLECULE OF CYTOTOXIC
LYMPHOCYTES
Supervisors: Dr. Ilia Voskoboinik, Prof. Joe Trapani
Perforin is a pore-forming toxin expressed in cytotoxic
lymphocytes, a subtype of immune cells, which
recognise and destroy virus-infected or cancerous cells.
Functional perforin is essential for the killing activity of
cytotoxic lymphocytes and, more generally, for
maintaining immune homoeostasis. We have
demonstrated that the loss of PRF function due to
detrimental bi-allelic mutations in the perforin gene leads
to a catastrophic immunoregulatory disorder, Familial
Haemophagocytic Lymphohistiocytosis (FHL) [1]. At the
same time, partial perforin deficiency appeared to be a
strong predisposition factor for haematological
malignancies in early adolescence [2].
Our biochemical studies have revealed the structural
basis for perforin membrane binding [3] and
oligomerisation [4], which were further supported by the
structural studies of perforin monomer and the entire
pore [5]. We have also identified a unique intracellular
transport mechanism that protects cytotoxic lymphocytes
as they shuttle the toxic perforin protein through the
secretory pathway to the cell surface [6].
While these studies have led to some of the major
advances in the field, they also raised new important
questions, which we are now in position to address.
A prospective student will be a part of a successful
multidisciplinary research team of immunologists,
biochemists, cell biologists, geneticists and clinical
scientists.
We offer the following projects:
• Structure-function analysis of perforin,
• Genetic regulation of perforin in cancer patients,
• Molecular basis of granule exocytosis in cytotoxic
lymphocytes.
References
1. Voskoboinik et al. (2004) J. Exp. Med., 200, 811-16.
2. Chia et al. (2009) Proc. Natl. Acad. Sci. USA, 106, 9809-14.
3. Voskoboinik et al. (2004) J. Biol. Chem., 280, 8426-34.
4. Baran et al. (2009) Immunity, 30, 684-95.
5. Law et al. (2010) Nature, 468, 447-51.
6. Brennan et al. (2011) Immunity, 34, 879-92.
For more information about these projects contact:
Dr. Ilia Voskoboinik, Tel: +61 3 9656 1657, Email:
ilia.voskoboinik@petermac.org
Prof. Joe Trapani, Tel: +61 3 9656 1326, Email:
joe.trapani@petermac.org
CELLULAR IMMUNITY
RECOGNITION OF H2-M3 BY LY49 AND
SUBSEQUENT REGULATION OF NK CELL
RESPONSES.
Natural Killer (NK) cells clearly contribute to immune
responses to cancer and viruses. Unlike adaptive
immune lymphocytes such as B and T cells, the receptor
repertoire of NK cells is independent of rearrangement
and requires another form of regulation to mediate
specificity. Each NK cell expresses a range of
stimulatory or inhibitory receptors, which allows them to
target cells with increased or decreased ligand
expression. The regulation of NK cell responses is
balanced by interactions that transmit signals mediating
activation or inhibition. Under normal conditions NK cells
are repressed through the recognition of MHC class I by
inhibitory Ly49 molecules. Among this family, Ly49A is
enigmatic in that it is expressed in mice where the MHC
is not recognised. We have described a novel pathway
of NK cell regulation through Ly49A recognition of the
non-classical MHC class I molecule H2-M3. Our results
demonstrate that the absence of H2-M3 prevents
licensing in C57BL/6J mice, which results in NK cell
hypo responsiveness and manifests as increases in
tumour burden. In contrast, blockade of H2-M3 in mice
with a recognised Ly49A ligand results in increased NK
cell activation and a reduction in tumour burden.
We are seeking an honours student to pursue a role for
other Ly49 molecules in the recognition of H2-M3. This
project will entail cloning and expression of plasmids,
animal handling, tissue culture of primary cells and cell
lines as well as Flow Cytometry.
For more information about this project contact:
Dr Daniel Andrews, Tel: +61 3 9656 1752, E-mail:
Daniel.andrews@petermac.org
9

GRANZYMES AS MEDIATORS OF CYTOKINE
RELEASE.
Supervisors : Dr. Dan Andrews, Dr. Nikola Baschuk and
Prof. Mark Smyth
Lymphocyte perforin and serine protease granzymes are
well-recognized extrinsic mediators of apoptosis. We
have demonstrated that cytotoxic lymphocyte granule
components profoundly augment the myeloid cell
inflammatory cytokine cascade in response to TLR4
ligation. A lack of granzyme M (GrzM) results in reduced
serum IL-1a, IL-1b, TNF, and IFN-g levels and
significantly reduced susceptibility to lethal
endotoxicosis. These altered responses were also
observed in granzyme A-deficient but not granzyme Bdeficient
mice. A role for APC–NK cell cross-talk in the
inflammatory cascade was highlighted, as GrzM was
exclusively expressed by NK cells and resistance to LPS
was also observed on a RAG-1/GrzM-double deficient
background. Collectively, the data suggest that NK cell
GrzM augments the inflammatory cascade downstream
of LPS-TLR4 signaling, which ultimately results in lethal
endotoxicosis.
We are seeking an honours student to pursue the
mechanisms by which granzyme M induces cytokine
release. This project will entail biochemical
experimentation (Western Blot), cloning and expression
of plasmids, animal handling, tissue culture of primary
cells and cell lines as well as Flow Cytometry.
For more information about this project contact:
Dr Daniel Andrews, Tel: +61 3 9656 1752, E-mail:
Daniel.andrews@petermac.org
Dr Nikola Baschuk, Tel: +61 3 9656 1752, E-mail:
nikola.bsdchuk@petermac.org
THE IDENTITY, ROLE AND FUNCTION OF IMMUNE
CELLS AT SITES OF METASTASIS IN BREAST
CANCER.
Supervisors: Dr. Andreas Moeller & Prof. Mark Smyth
Immune cells are key mediators of anti-tumour and protumour
functions at both the primary and metastatic
sites of breast cancer. While the role of monocyte
derived cells at the primary site of breast cancer is
slowly being understood, there is very little known about
the role and composition of immune cells at metastatic
sites. We have generated a unique breast cancer
model, utilizing fluorescently marked immune and
tumours cells, to assess the immune cell infiltrate at
metastatic sites in breast cancer. We found that immune
cell infiltration into metastatic sites is directed and
orchestrated by the primary tumours, and results in a
permissive environment at secondary sites for
metastatic outgrowth.
In this project, bone marrow chimeras and orthotopic
breast cancer mouse models will be used to determine
the composition and function of the immune cell infiltrate
at the metastatic site. Using FACS and
Immunohistology, the immune cell lineages will be
investigated in great detail. Isolated immune cells, which
are induced by tumours to populate the metastatic site,
will be assessed for their cytokine production.
Furthermore, the frequency of metastasis will be
assessed in experiments where the immune cell
lineages which populate the metastatic site have been
ablated. These experiments will provide an insight into
the metastatic progression of breast cancer and will be
the first of their kind. Ultimately the goal is to understand
the identity, role and function of immune cells at the
metastatic site and explore the potential to use this
information to reduce metastatic tumour burden in
breast cancer patients. Students will have access to
unique reagents and mice, and will acquire skills in
mouse tumour model experimentation, immune cell
isolation, multi-colour flow cytometry, IHC, and other
basic cellular immunology techniques.
For more information about this project contact:
Dr. Andreas Moeller, Tel: +61 3 9656 1287, E-mail:
andreas.moeller@petermac.org
Prof. Mark Smyth,Tel: +61 3 9656 3728, E-mail:
mark.smyth@petermac.org
ESCAPE BY BREAST CANCER CELLS
Supervisors: Dr Belinda Parker, Dr Daniel Andrews
Over 80% of patients who die from their breast cancer
succumb due to the development of metastatic disease.
The mechanisms of breast cancer spread to bone are
largely unknown. Our recent studies using a unique
model of breast cancer have revealed that cancer cells
growing in bone suppress an immune defence pathway
called the Type I interferon pathway, and that restoration
of this pathway blocks cancer spread.
Our studies provide evidence that breast cancer cells
have the ability to modulate the immune response to
avoid being recognised and eliminated. This allows
breast tumour cells to survive in bone and grow into
lethal tumours that are currently untreatable. We are
looking to extend these studies. This project aims to
identify the immune responses that are activated in
response to this pathway and if restoration of such
responses is critical in blocking the spread of breast
cancer to bone.
Through both national and international collaborations,
we have access to rare models of breast cancer and the
tools required to study the role of Type I IFNs at an
internationally competitive level. A broad range of
techniques will be utilised for this PhD project, including
histological analysis, flow cytometry, confocal and light
microscopy, real time PCR, molecular cloning, cell
culture, animal models of breast cancer, in vitro and in
vivo metastasis assays.
For more information about this project contact:
Dr Belinda Parker, Tel: +61 3 9656 1285, Email:
belinda.parker@petermac.org
Dr Daniel Andrews, Tel: +61 3 9656 1752, Email:
daniel.andrews@petermac.org
IMMUNE SIGNALLING
THE ROLE OF SIGNALING & POLARITY PROTEINS IN
ASYMMETRIC CELL DIVISION OF T LYMPHOCYTES
Supervisors: Dr Jane Oliaro and Dr Sarah Russell
Our laboratory studies the role of signaling and polarity
proteins in T lymphocyte biology. Polarity - or the
compartmentalisation of proteins within a cell - is critical
for T lymphocyte functions such as migration,
immunological synapse formation and cytotoxic activity
during an immune response. More recently, we
demonstrated that asymmetric cell division of T
lymphocytes in response to antigen presentation may be
used to generate effector and memory T lymphocytes
(Chang et al. Science, 2007) - a process regulated by
polarity proteins in other cell types. This observation
10

provides a potential mechanism for generating the
diversity of T lymphocytes required for an effective
immune response, and suggests that a conserved
mechanism based on asymmetric cell division also
exists in immune cells.
This project will investigate the role of polarity proteins
and the cell surface receptor, CD46, in the regulation of
asymmetric cell division of T lymphocytes. CD46 is a
receptor for a number of pathogens, including measles
virus, and signaling through CD46 can affect T
lymphocyte polarity, function and fate in human T and
NK cells (Oliaro et al. PNAS, 2006). CD46 has
previously been shown to interact with members of the
polarity network, and pathogens that bind to CD46 may
utilise this to alter T lymphocyte responses. The project
will focus on how polarity proteins control asymmetric
cell division, whether signaling through CD46 affects this
process, and what the consequences are for T
lymphocyte fate and function.
The project will involve some animal experimentation,
immunological techniques such as tissue culture and
flow cytometry, and both fixed and live imaging of cells
using our state of the art microscopy facilities.
For more information about this project contact:
Dr. Jane Oliaro, Tel: +61 3 9656 1657, Email:
jane.oliaro@petermac.org
THE ROLE OF POLARITY PROTEINS AND
ASYMMETRIC CELL DIVISION IN LYMPHOCYTE
FATE DECISIONS AND CANCER
Supervisor: Dr Sarah Russell
Cellular diversity during development is often generated
through the segregation of cell fate determinants into
one daughter cell upon cell division, a process termed
asymmetric cell division (ACD). ACD is classically
considered to occur in the cells of solid tissues, and is
controlled by a group of proteins including the Scribble
and Par3 complex, many of which have been identified
as tumour suppressor genes in Drosophila. Recent
studies from a number of groups have led to a working
model by which these genes exert tumour suppressive
effects by coordinating ACD of epithelial cells. By
orchestrating cell fates such as self renewal potential,
control of ACD can play important roles in the initiation
and prognosis of epithelial cancers.
Our laboratory has recently obtained exciting new data
to indicate that a similar process controls the fate
decisions of lymphocytes. We have now developed a
number of mouse models with which to test the role of
polarity and asymmetric cell division in hematopoiesis,
immunity and leukemogenesis, and have generated
exciting preliminary data to indicate the involvement of
polarity in these processes. PhD projects are available to
use these mouse models to investigate the effects of
deletion of individual polarity proteins on the
development of hematopoietic cells, to determine
whether the polarity proteins influence the development
or progression of leukaemia, and to establish how
phenotypes in these mice relate to lymphocyte polarity.
The project involves a wide range of techniques,
including animal experimentation, multi-parameter flow
cytometry and state-of-the-art microscopy.
For more information about this project contact:
Dr. Sarah Russell, Tel: +61 3 9656 3727, Email:
sarah.russell@petermac.org
DEVELOPMENT OF A MICROFLUIDIC BIOREACTOR
USING NOVEL DYNAMIC VALVING FOR CELL
MANIPULATION
Supervisor: Dr Sarah Russell
The elucidation of biological signalling pathways for
diverse processes such as cancer and immunity has
recently been revolutionized by access to highthroughput
functional genomic screens. Such screens
have created a currently unmet need for microfluidics
devices that will enable very high throughput
(parallelism) and fast analysis time. The aim of this
project is to fabricate microfluidic devices with which to
control and monitor the response of cells to genomic and
pharmacological intervention. Novel mechanisms for
trapping and releasing cells based on dynamic valving
using pneumatically operated valves will be developed.
A range of microfabrication techniques will be used to
design, fabricate and integrate the microstructures and
valves, including femtosecond pulse laser etching, CO2
laser cutting, hot embossing and soft lithography. The
student will primarily work at the Centre for Micro-
Photonics, but will also interact with biologists at Peter
Mac to assess the applicability of the microfabricated
devices.
For more information about this project contact:
Dr. Sarah Russell, Tel: +61 3 9656 3727, Email:
sarah.russell@petermac.org
IMMUNOTHERAPY
USING CAANCER TO FIGHT CANCER
Supervisors: Assoc Prof Michael Kershaw, Dr Phil Darcy
Research has shown that cancer can develop resistance
to chemotherapy and radiotherapy, and its pervasive
nature can make a mockery of our best attempts at
surgical removal. Cancer can also evade our most
powerful immune therapies through a number of
mechanisms that include stealth and potent suppression
of immunity.
Given the resilience and versatility of cancer, in this
project we wish to test the concept that the best way to
fight cancer might be with another cancer. We propose
to produce a kind of leukaemia that we can manipulate
to possess many cancer-fighting abilities, while retaining
absolute control over its growth and malignant
properties. Leukocytes endowed with the abilities to
localize to tumours, execute cytotoxicity and overcome
immune inhibition, while retaining the cancer-associated
attributes of persistence and resistance to death, might
beat cancer cells at their own game.
Currently, T cells can be genetically modified to
recognize and respond to cancer cells in a limited way,
and adoptive transfer of these T cells can inhibit small
tumours in mice. Larger widespread disease is refractory
to this form of immunotherapy. Factors that contribute to
the failure of adoptive immunotherapy include a poor
ability of T cells to localize to tumours, together with
inhibition of T cell activity at the tumour site and a failure
to persist in large numbers. Genes exist that can be
used to remedy these problems, but our ability to get
enough genes into mouse primary T cells to satisfy all
these requirements is limited by the low ability of mouse
T cells to grow in vitro. Therefore, immortalizing mouse T
cells would give us the opportunity to insert many genes
and test their ability to defeat cancer.
11

Immortalization will be achieved using oncogenes in a
tetracycline-inducible genetic vector system. This project
will use molecular biology and a range of immunological
assays to determine the anti-tumour activity of genemodified
immune cells in mouse models of cancer.
For more information about this project contact:
Assoc. Prof. Michael Kershaw, Tel: +61 3 9656 1177;
Email: michael.kershaw@petermac.org
PROVIDING ‘HELP’ FOR EFFECTIVE CANCER
IMMUNOTHERAPY
Supervisors Dr. Phillip Darcy, Assoc Prof Michael Kershaw
Adoptive immunotherapy involving transfer of tumourspecific
T cells into patients has shown remarkable antitumour
effects and has led to remission of disease in a
proportion of patients with metastatic melanoma. To
broaden this approach against other malignancies,
genetic modification of T cells with single-chain (scFv)
chimeric receptors that specifically target tumour
associated antigen has emerged as a promising
approach1,2. To date, evidence in patients and in
immunocompromised mouse models have shown a
correlation between effective anti-tumour responses and
increased transfer of CD4+ T cell helper cells. However,
the question of whether increased transfer of genemodified
CD4+ T cells may cause associated pathology
has not been properly assessed. The proposed study
will employ novel tools involving transgenic mice which
express target antigen on both normal tissue and
tumour cells. These models more closely reflect the
patient setting. Studies will be undertaken to genetically
modify enriched CD8+ and CD4+ T cell populations with
anti-tumour scFv receptors and evaluate both the antitumour
efficacy and potential pathology to normal tissue
following adoptive transfer of CD8+ and CD4+ T cells at
varying ratios. This project’s results will have direct
implications for enhancing this type of therapy for
cancer patients.
The project will involve a number of molecular and
biochemical methods including flow cytometry, ELISA,
cytokine and proliferation assays. The student will also
become competent in tissue culture (retroviral
transduction of T cells and tumour cells) and handling of
mice. We are looking for a highly motivated student
who is interested in developing effective treatments for
cancer.
For more information about this project contact:
Dr. Phillip Darcy, Tel: +61 3 9656 1177; Email:
phil.darcy@petermac.org
Assoc. Prof. Michael Kershaw, Tel: +61 3 9656 1177;
Email: michael.kershaw@petermac.org
References
1. Morgan RA, et al. Science 2006;314:126-9.
2. Kershaw MH, et al. Nat Rev Immunol 2005;5:928-40.
HAEMATOLOGY IMMUNOLOGY
TRANSLATIONAL RESEARCH
ESTABLISHING A HUMANIZED MOUSE MODEL OF
CANCER
Supervisors: Dr Andy Hsu, Paul Neeson
Research into the causes and treatment of cancer
ideally requires pre-clinical animal models that closely
recapitulate human disease. Our laboratory specializes
in blood cancers with a focus on multiple myeloma (MM)
and chronic lymphocytic leukemia (CLL), which are
malignancies of the bone marrow.
There are no accurate models of human MM and CLL in
mice as most models use mouse cancer cells. For the
few models that use human MM or CLL cells, these are
transplanted into immune-deficient mice that lack an
immune system to prevent graft rejection. However this
is not ideal as these models do not have an active
immune system. Recently, a world wide groundbreaking
study described a ‘humanized’ mouse model whereby
human stem cells are engrafted into immune-deficient
mice to establish a functional human immune system.
Our lab aims to take this further by establishing
humanized mouse models using stem cells from MM or
CLL patients. Once these mice are adults, we aim to
transplant in MM or CLL cells (from the same patients
where the stem cells were derived), thus creating a
world’s first patient-derived humanized mouse model.
These models harboring both a functional human
immune system and cancer will become exceptionally
powerful tools to study cancer biology and therapy. The
aims of this exciting Honours project are two-fold: 1) to
optimize the humanized mouse model, and 2) to
establish the first humanized MM and/or CLL model.
Traggiai et al. Development of a human adaptive immune
system in cord blood-cell transplanted mice. Science, 304:104
(2004).
For more information about these project contact:
Dr. Andy Hsu, Tel: +61 3 9656 3657, Email:
andy.hsu@petermac.org,
Dr. Paul Neeson, Tel: +61 3 9656 3657, Email:
paul.neeson@petermac.org
12

CANCER THERAPEUTICS RESEARCH PROGRAM
www.petermac.org/Research/CancerTherapeuticsProgram
The Cancer Therapeutics program, together with the Molecular Imaging and Translational Medicine Program, integrates
various basic research activities, platform technologies, and pre-clinical model systems available within the Peter Mac to
discover, develop, characterise and refine novel cancer therapeutics for clinical use. Basic research within the program is
focused on increased understanding of the biological basis of disease patterns and treatment outcomes observed in the
clinic, preclinical testing of novel therapeutics, development of imaging methods and biomarker assays to follow treatment
efficacy and investigation of cellular pathways involved in response to anticancer therapies.
GENE REGULATION
NEW THERAPIES FOR JAK2-DRIVEN
MALIGNANCIES
Supervisors: Dr Michaela Waibel, Dr Vanessa Solomon,
Prof Ricky Johnstone
Activating mutations in the JAK2 tyrosine kinase have
been associated with hematological malignancies
including acute leukaemias and myeloproliferative
neoplasms such as polycythemia vera and essential
thrombocythemia. Several clinical trials are currently
underway to test the efficacy of specific inhibitors of
JAK2 in the treatment of these diseases; thus far they
have shown only moderate success, and there remains
a need for improved therapies for JAK2-driven diseases.
We have been working to define the molecular pathways
that are activated by constitutively active JAK2 mutants,
and to use this knowledge to rationally design new
molecularly targetted therapies to treat JAK2-driven
malignancies. This project will determine the role of the
PI3 Kinase/AKT pathway in JAK2-driven leukaemias and
its interactions with other signalling pathways. We will
build on our experience with murine models of JAK2driven
acute lymphocytic leukaemia and molecularly
targetted agents, using in vitro, in vivo and ex vivo
analyses to determine the efficacy of inhibitors of the PI3
Kinase/AKT pathway in treating disease. A PhD project
extend this work into other JAK2-driven diseases
including xenografted human samples.
For more information about these projects contact:
Assoc. Prof. Ricky Johnstone, Tel: +61 3 9656 3727;
Email: ricky.johnstone@petermac.org
DEVELOPMENT OF GENETICALLY ENGINEERED
MOUSE MODELS OF AML TO STUDY
TUMOURIGENESIS AND RESPONSE TO NOVEL
THERAPEUTICS.
Supervisor: Prof. Ricky Johnstone
The genetic heterogeneity of cancer influences the
trajectory of tumour progression and may underlie
clinical variation in therapy response. To model such
heterogeneity, we aim to produce genetically and
pathologically accurate mouse models of common forms
of human acute myeloid leukaemia (AML) expressing
oncogenic fusion proteins involving the mixed lineage
leukaemia gene (MLL). MLL is fused with one of over
60 distinct partner genes through chromosomal
translocations in various human acute leukaemias,
resulting in the formation of multiple MLL fusion proteins
(MLL-FPs). MLL-FPs are capable of leukemic
transformation and dysregulation of multiple genes,
often through the aberrant recruitment of epigenetic
modifying enzymes such as histone deacetylases and
methyltransferases. Using retoviral gene transduction of
hemopoietic stem cells to express diverse MLL-FPs we
will produce mice that develop AML driven by different
ongogenic fusion proteins. These mice will be utilized to
study disease onset and progression and determine the
oncogenic potential of different MLL-FPs. Moreover,
these mouse models will be used to test the efficacy of
epigenetic modifying agents such as histone dacetylase
inhibitors and histone methyltransferase inhibitors as
well as conventional chemotherapeutic drugs.
These studies will assess the importance of genetic
information in guiding the treatment of human AML and
determine if genetically engineered mouse models of
human cancer can accurately predict therapy response
in patients.
For more information about this project contact:
Assoc. Prof. Ricky Johnstone, Tel: +61 3 9656 3727;
Email: ricky.johnstone@petermac.org
DEVELOPING NEW THERAPEUTIC STRATEGIES TO
TREAT MULTIPLE MYELOMA.
Supervisor: Prof. Ricky Johnstone
Multiple myeloma (MM) is an incurable disease and
there is clearly an unmet medical need for new
therapeutic options. The primary aims of this project are
to utilize a novel mouse model of MM to assess the
therapeutic effects of combining novel tumour cellselective
apoptosis-inducing small molecules and
biological agents. We will additionally dissect the
molecular and biological events that underpin the single
agent and combination therapy effects. The agents
under investigation are the histone deacetylase inhibitor
(HDACi) vorinostat, the proteosome inhibitor bortezomib
and activators of the TRAIL death receptor pathway. As
single agents, these are either currently in use for the
treatment of MM or are in clinical development. We and
others have recently demonstrated that a combination of
vorinostat and the agonistic anti-TRAIL receptor
monoclonal antibody (mAb) MD5-1, or bortezomib and
MD5-1 can cure mice bearing cancers that are resistant
to either agent used as a monotherapy. Moreover, a
combination of bortezomib and HDACi has been shown
to synergistically kill a variety of tumour cell lines.
We hypothesise that novel anti-cancer agents such as
vorinostat, bortezomib and activators of the TRAIL
pathway used alone or more likely in combination will
provide therapeutic benefit for patients with MM. In
addition, we propose that a detailed understanding of
the molecular mechanisms of action of novel anti-cancer
agents will lead to the development of rational
combination strategies that will provide significantly
greater therapeutic benefit than single agent therapy.
For more information about these projects contact:
Assoc. Prof. Ricky Johnstone, Tel: +61 3 9656 3727;
Email: ricky.johnstone@petermac.org
13

MELANOMA RESEARCH
Melanoma is a common cancer and a source of
significant morbidity and mortality in our community,
particularly among 20-40 year-olds where it is the most
common cause of cancer death. As a result, melanoma
causes the second/third most years of lost productive life
of all cancers in males/females. Disturbingly, the
incidence of melanoma is increasing in Australia and
deaths attributable to the disease are projected to
increase accordingly. Compounding the increasing
disease and economic burden imposed by melanoma in
our community is the lack of effective therapies for
patients with advanced disease.
Our research program seeks to address the problem of
melanoma using two approaches. First, through
improving understanding of normal melanocyte
development, we aim to identify mechanisms of
melanomagenesis and thereby develop strategies for
improved disease prevention. Second, through use of a
highly efficient model of human melanoma progression
that replicates closely the biology of this disease in
patients, we aim to identify mechanisms of melanoma
propagation and metastasis. Our close links with the
clinical research activities of the Peter Mac Melanoma
Unit enable rapid clinical translation of our lab
discoveries in order to help patients.
CHARACTERIZATION OF NORMAL MELANOCYTE
DEVELOPMENT
Supervisors: Dr. Mark Shackleton, Assoc. Prof. Grant
McArthur
This project will adapt classical stem cell biology
techniques developed in other solid organ systems
(Nature 439:84) to the study of normal melanocyte
development. Using sophisticated mouse models,
melanocytes at different stages of development will be
conditionally tagged, isolated and functionally
characterized. The oncogenic effects of various genetic
and environmental stimuli on melanocyte lineage
subpopulations will then be studied, and strategies
explored to prevent oncogenesis in different contexts.
Complementary studies of human melanocyte
development will also be performed. The techniques
used will include working with mouse models, cell
culture, flow cytometry and cell sorting, microarraybased
gene expression studies, and quantitative PCR.
For more information about this project contact:
Dr. Mark Shackleton, Tel: +61 3 9656 5235; Email:
mark.shackleton@petermac.org
IDENTIFICATION OF DETERMINANTS OF
MELANOMA PROGRESSION
Supervisors: Dr. Mark Shackleton and Assoc. Prof.
Grant McArthur
This project will use a novel human melanoma
tumourigenesis assay (Nature 456:593) to study how
melanomas progress once they have formed. This assay
offers a unique opportunity to study human cancer
biology, genetics and epigenetics at the clonal level. By
comparing the malignant and molecular properties of
sister clonal tumours, this approach enables direct
correlation of tumour phenotype and
genotype/epigenotype in a way that is likely to reveal
those molecular aberrations that are functionally relevant
to malignant progression and potentially target-able by
modern therapeutic approaches. Multiple projects within
this framework are planned, involving a wide range of
techniques: working with fresh human tumour
specimens and analyzing clinical data, mouse handing
and surgery, immunostaining and flow cytometry, and
molecular studies such as SNP genotyping, DNA
methylation analysis, NextGen sequencing and
functional genomics.
For more information about this project contact:
Dr. Mark Shackleton, Tel: +61 3 9656 5235; Email:
mark.shackleton@petermac.org
THE ROLE OF POLARITY REGULATORS IN
MELANOMA
Supervisors: Dr Patrick Humbert, Dr Mark Shackleton
See Cell Cycle & Cancer Genetics in Cell Biology
Program page 16
VICTORIAN CENTRE FOR
FUNCTIONAL GENOMICS
USING FUNCTIONAL GENOMICS APPROACHES TO
IDENTIFY GENES THAT REGULATE BREAST
CARCINOMA INVASION AND METASTASIS
Supervisors: Dr. Kaylene Simpson, Assoc. Prof. Robin
Anderson
The Functional Genomics Facility at the Peter Mac
provides the infrastructure, resources and expertise to
perform genome-scale RNA interference screens. We
offer both shRNA and siRNA strategies to knockdown
gene expression to researchers Australia-wide. Such
access places us in the unique and exciting position of
enabling and discussing cutting edge gene discovery
projects from diverse scientific backgrounds on a daily
basis. The Facility also has a research interest in the
mechanisms regulating breast carcinoma invasion and
metastasis and this project would be directly involved
with Assoc Prof Robin Anderson's metastasis laboratory.
We are interested in speaking with people who share an
interest in fundamental gene discovery, particularly in
relation to breast cancer. We have well established cellbased
and animal tumour models in which genes
promoting invasion and metastasis can be tested
functionally and their mechanism of action explored.
Projects related to identifying novel gene targets that
may regulate the cytoskeletal changes associated with
acquisition of cell motility, invasion and ultimately
metastasis are on offer.
For more information about this project contact:
Dr Kaylene Simpson. Tel: +61 3 9656 1790; Email:
kaylene.simpson@petremac.org
MOLECULAR IMAGING &
TRANSLATIONAL MEDICINE PROGRAM
The Centre for Molecular Imaging coordinates
translational research in human subjects, building on our
expertise in both clinical and pre-clinical cancer imaging
using PET.
The major focus of our program is the development of
novel radiopharmaceutical tracers for PET and in using
metabolic imaging to facilitate drug development. Major
initiatives underpinning these roles include being a core
partner in a cooperative research consortium (CRC) for
Biomedical Imaging Development and being a preferred
14

clinical imaging site for national and international drug
development trials. The latter role has generated
substantial industry support for phase I/II trials of new
drugs that utilise advanced imaging techniques to
monitor therapeutic response. Radionuclide therapy,
including novel radioligands and combination treatment
with radiosensitising chemotherapy, is an important
aspect of the clinical program.
18 F -FPHCys AS A RELIABLE IMAGING BIOMARKER
TO MONITOR EARLY EFFICACY OF PI3K/mTOR
TARGETED CANCER THERAPIES BY POSITRON
EMISSION TOMOGRAPHY (PET)
Supervisors: Dr. Delphine Denoyer, Dr. Carleen
Cullinane, Prof. Rod Hicks
Abnormal cell signalling contributes to the progression of
many cancers. The development of anticancer drugs
that specifically targets the PI3K/mTOR signalling has
dramatically improved the way cancer patients are
treated. However, PI3K/mTOR targeted therapy is not
always successful, even when the tumours harbour the
malfunctioning proteins. Consequently, non-responding
patients are often treated unnecessarily when they
would otherwise respond to alternative therapies.
Currently, multiple biopsies are the only way drug
efficacy can be determined at the molecular level. This is
often impractical for some patients due to the
inaccessibility of the tumour. Positron Emission
Tomography (PET) allows serial non-invasive imaging of
the tumour and has the potential to identify early
molecular changes induced by treatment. However,
there are currently no reliable imaging biomarkers
available to monitor PI3K/mTOR targeting treatment by
PET. Recently, we identified a new amino acid analogue
of methionine, 18F-FPHCys, with excellent potential for
imaging solid tumours. Tumours are 18F-FPHCys-avid
due to their high expression of LAT1 amino acid
transporter compared to normal tissues. We have
observed that blocking PI3K/mTOR pathway significantly
decreased tumour cell accumulation of 18F-FPHCys
indicating a strong relationship between PI3K/mTOR
signalling and LAT1-dependent 18F-FPHCys uptake.
The overall objective of this research project is to
investigate the potential of 18F-FPHCys-PET as a
reliable imaging tool for the detection of early molecular
responses to PI3K/mTOR treatment in cancer. This
project is suitable for Honours students and will make
use of various techniques including cell culture, protein
and molecular techniques (protein immunoblotting,
immunohistochemistry, real time quantitative PCR, use
of siRNA technology) as well as in vivo PET imaging.
For more information about this project contact:
Dr. Delphine Denoyer, Tel: +61 3 9656 1274, Email:
Delphine.Denoyer@petermac.org
Dr. Carleen Cullinane, Tel: +61 3 9656 1275, Email:
carleen.cullinane@petermac.org
Prof. Rod Hicks, Tel: +61 3 9656 1854, Email:
Rod.Hicks@petermac.org
CAMBRIDGE INSTITUTE FOR MEDICAL
RESEARCH – PETER MACCALLUM
CANCER CENTRE COLLABORATION
CHROMATIN MODIFYING ENZYMES IN THE
HAEMATOLOGICAL MALIGNANCIES
Supervisors: Dr. Mark Dawson (Cambridge), Prof Ricky
Johnstone, Assoc. Prof. Grant McArthur
Location: Cambridge Institute For Medical Research,
University of Cambridge, UK and Peter MacCallum
Cancer Centre, University of Melbourne, Australia
A PhD student position is available at the Cambridge
Institute For Medical Research under the supervision of
Dr. Mark Dawson. The position is available for 3 years
and the successful candidate will spend the initial phase
of their PhD at Cambridge, UK and will complete their
PhD in Melbourne, Australia.
The aim of our research is to define the molecular
mechanisms by which chromatin-modifying enzymes
contribute to the development and/or maintenance of
haematological malignancies. We have a particular
interest in understanding how the dysregulation of these
enzymes contributes to the process of self-renewal in
leukaemia stem cells. Chromatin is a combination of
DNA and proteins called histones. The chemical
modification of both histones and DNA by highly
conserved enzymes plays a critical role in the regulation
of all DNA based processes such as transcription, DNA
repair and replication. Consequently, when these
enzymes are mutated the results are often devastating
and lead to the induction and/or maintenance of various
cancers including leukaemia. Understanding the
molecular mechanisms by which these enzymes
contribute to cancer will provide a unique opportunity to
specifically target these enzymes with novel epigenetic
therapies.
The research will initially be conducted at the University
of Cambridge, one of the world’s most prestigious
academic institutions with a renowned reputation for
excellence in scientific research and achievement. This
unique position will afford the successful candidate the
opportunity to be involved with research groups that
have pioneered the fields of cancer stem cells and
chromatin biology.
Recent publications relating to this subject area:
Dawson MA et al., Nature 2011;
Dawson MA et al., Nature 2009;
Griffiths DS et al., Nature Cell Biology 2011;
Dawson MA et al., Molecular Cell 2010
Huntly BJ el al., Cancer Cell 2004.
For more information about this project contact:
Assoc. Prof. Ricky Johnstone, Tel: +61 3 9656 3727;
Email: ricky.johnstone@petermac.org
Dr Mark Dawson, Email: mafd2@cam.ac.uk
15

CELL BIOLOGY RESEARCH PROGRAM
www.petermac.org/Research/CancerCellBiologyProgram
Diverse areas of cellular and molecular biology important in cancer are being explored within this program. We are looking
at regulation of the cell cycle, the signalling pathways within tumour cells and host cells adjacent to tumours that drive
tumour growth and metastasis and the importance of the aberrant regulation of apoptosis in tumour cells. Since
radiotherapy is a major treatment modality for cancer, we are investigating how radiation kills cells and ways to improve the
application of this therapy to patients.
CELL CYCLE & DEVELOPMENT
HOW CELL POLARITY REGULATORS AFFECT
SIGNALLING PATHWAYS
Supervisor: Dr Linda Parsons, Assoc. Prof. Helena
Richardson, Dr Patrick Humbert
The cell cycle and development lab uses sophisticated
genetic and cell biological analysis of the animal model
system, the vinegar fly Drosophila, to address
fundamental questions in cancer biology. The cell cycle
and development lab consists of a dynamic group of
people, with researchers at all stages of their career. Dr
Linda Parsons is a senior postdoctoral researcher with
extensive experience in working with Drosophila and
supervising students. The project will suit those who
enjoy working on genetically tractable model organisms
and are interested in a holistic understanding of cancer.
The project will encompass a wide range of cell biology
(microscopy), biochemistry, genetics and molecular
biology techniques.
This project focuses on how signaling pathways are
affected by the cell polarity (shape) regulators, Lgl,
aPKC or Crb, in mediating their effects on cell
proliferation, survival and tumourigenesis. The project
will involve genetic, biochemical and cell biological
approaches to determine which signaling pathways are
altered and their functional importance upon depletion of
Lgl or activation of aPKC or Crb in Drosophila. The
research will also be extended to analyze the role of the
mammalian homologs of these genes in the regulation of
signaling pathways in mammalian cells in collaboration
with Dr Patrick Humbert.
For more information about this project contact:
Assoc. Prof. Helena Richardson, Tel: +61 3 9656 1466,
Email: helena.richardson@petermac.org
COOPERATIVE TUMOURIGENESIS: ANAYSIS OF
NOVEL TUMOUR SUPPRESSORS IN RAS
ONCOGENE DRIVEN EPITHELIAL TUMOURS
Supervisor: Assoc. Prof. Helena Richardson, Dr Patrick
Humbert
The cell cycle and development lab uses sophisticated
genetic and cell biological analysis of the animal model
system, the vinegar fly Drosophila, to address
fundamental questions in cancer biology. The cell cycle
and development lab consists of a dynamic group of
people, with researchers at all stages of their
career. The project will suit those who enjoy working on
genetically tractable model organisms and are interested
in a holistic understanding of cancer. The project will
encompass a wide range of cell biology (microscopy),
biochemistry, genetics and molecular biology
techniques.
We have carried out a genetic screen in flies for novel
tumour suppressors that cooperate with the Ras
oncogene to promote invasive overgrowth of neural-
epithelial tissue. This project will use sophisticated
Drosophila genetics, and molecular, cell biology and
biochemical approaches to determine how one of these
novel tumour suppressors affects the hallmarks of
cancer in vivo in Drosophila. The project will extend into
the analysis of the mammalian homolog of this gene in
tumourigenesis in mammalian epithelial cells, in
collaboration with Dr Patrick Humbert.
For more information about this project contact:
Assoc. Prof. Helena Richardson, Tel: +61 3 9656 1466,
Email: helena.richardson@petermac.org
ANALYSIS OF DROSOPHILA MODELS OF BRAIN
CANCER
Supervisor: Dr Kirsten Allan, Assoc. Prof. Helena
Richardson
The cell cycle and development lab uses sophisticated
genetic and cell biological analysis of the animal model
system, the vinegar fly Drosophila, to address
fundamental questions in cancer biology. The cell cycle
and development lab consists of a dynamic group of
people, with researchers at all stages of their career. Dr
Kirsten Allan is a postdoctoral researcher with extensive
experience in Drosophila. The projects will suit those
who enjoy working on genetically tractable model
organisms and are interested in a holistic understanding
of cancer. The project will encompass a wide range of
cell biology (microscopy), biochemistry, genetics and
molecular biology techniques.
We are using sophisticated genetic and cell biological
approaches to model human brain cancers in
Drosophila. In particular we are interested in
understanding the importance of regulators of cellular
architecture, including the actin cytoskeleton, in the
tumourigenic properties of these cancers. The project
will involve the use of transgenic RNAi lines and small
molecule inhibitors to knockdown these regulators to
assess their importance in brain tumour models.
For more information about this project contact:
Assoc. Prof. Helena Richardson, Tel: +61 3 9656 1466,
Email: helena.richardson@petermac.org
CELL CYCLE & CANCER GENETICS
FUNCTIONAL CHARACTERIZATION OF THE
SCRIBBLE POLARITY NETWORK IN PROSTATE
CANCER METASTASIS
Supervisors: Dr Patrick Humbert and Dr Helen Pearson
Cell polarity refers to the asymmetry of cells within a
tissue and is a fundamental property of all mammalian
cells. Loss of cell polarity (the orientation of cells within a
tissue) is one of the hallmarks of epithelial cancer, and is
correlated with more aggressive and invasive cancers.
16

However how loss of cell polarity occurs and how it
contributes at the molecular level to tumour formation
remains poorly understood.
Metastatic spread of tumours is the major cause of
cancer related morbidity in patients. We have recently
shown that the tumour suppressive functions of the cell
polarity gene Scribble are highly conserved in
mammalian epithelial tissues. Indeed, Our analysis of
mice genetically engineered to mutate Scribble in
prostate tissue have indicated that Scribble disruption
can promote loss of cell polarity, hyperplasia and in
combination with oncogene activation prostate cancer in
the mouse. Disruption of Scribble also correlates with
poor outcome in prostate cancer patients. Whether
disruption of human Scribble can contribute to tumour
metastasis however is not known.
This project aims to examine using in vitro and in vivo
transplantation models the role Scribble and associated
proteins may play in prostate cancer metastasis. A
better understanding of this pathway and how loss of
tissue architecture can occur and impact on cancer
progression will lead to the discovery of novel prognostic
factors, novel chemotherapeutic targets and
fundamental insights in to epithelial tumour biology and
cancer progression.
For more information about this project contact:
Dr. Patrick Humbert, Tel: +61 3 9656 3526, Email:
patrick.humbert@petermac.org
STRUCTURAL AND BIOCHEMICAL
CHARACTERIZATION OF POLARITY COMPLEXES
IN CANCER
Supervisors: Dr Patrick Humbert and Dr Nathan Godde
Every cell in our body has an intrinsic orientation (or
polarity) that is controlled by a universal set of genes
known as polarity genes. Loss of this orientation is a
defining early feature in cancers, and has been linked to
cancer spread or metastasis. Our team has previously
identified the gene Scribble as a new human polarity
gene that controls cell orientation and tumour growth.
Scribble works in concert with the two other proteins
called Discs Large (Dlg) and Lethal giant larvae (Lgl) to
define the polarity of a cell. Using mouse models and
samples from tumour patients we have shown that
Scribble acts as a suppressor of tumours. In particular,
we have shown that lowering levels of Scribble in normal
cells increases the risk of cancer by disorganizing the
tissue and by increasing the speed at which cells grow
within the tissue.
We now need to establish how Scribble and its partners
contribute to tumour formation and metastasis and
clarify their molecular mechanism of action, to enable
targeting of these proteins for therapeutic purposes. This
projects aims to gain deeper insight into the nature of
the physical interactions that allow Scribble and its
partners to perform its function using combination of
biochemical, yeast-two-hybrid, proteomics and functional
assays. Structural and biochemical information will be
validated for their functional relevance in our well
established mouse and cellular models, and therefore
rapidly translated into biological information directly
relevant to human cancer patients and their outcome.
We believe that studies investigating the mechanism of
how this complex is formed may lead to the discovery of
new prognosis factors and new chemotherapeutic
targets, as well as a better understanding of cancer
biology and cancer progression.
For more information about this project contact:
Dr. Patrick Humbert, Tel: +61 3 9656 3526, Email:
patrick.humbert@petermac.org
THE ROLE OF POLARITY REGULATORS IN
MELANOMA
Supervisors: Dr Patrick Humbert, Dr Mark Shackleton
Cell polarity refers to the asymmetry of cells within a
tissue and is a fundamental property of all mammalian
cells. Loss of cell polarity (the orientation of cells within a
tissue) is one of the hallmarks of solid tumours, and is
correlated with more aggressive and invasive cancers.
This project aims to understand how cell polarity
regulators can control Melanoma progression. In order
to do this, you will characterize novel conditional mouse
models engineered to allow specific loss of function of
polarity regulators in melanocytes. In addition, mice
genetically sensitized to melanoma will be utilized to test
the role of polarity regulators in the initiation and
progression of melanoma. These studies will utilize a
combination of in vitro and in vivo analysis and will
provide essential information as to how genes that
regulate tissue architecture can impact on melanoma.
These studies may therefore lead to the discovery of
novel prognostic factors, novel chemotherapeutic targets
and fundamental insights in to melanocyte biology and
melanoma progression.
For more information about this project contact:
Dr. Patrick Humbert, Tel: +61 3 9656 3526, Email:
patrick.humbert@petermac.org
Dr. Mark Shackleton, Tel: +61 3 9656 5235; Email:
mark.shackleton@petermac.org
CELL GROWTH & PROLIFERATION
THE HIPPO PATHWAY, REGENERATION AND
CANCER
Supervisor: Dr. Kieran Harvey
In the cell growth and proliferation laboratory we are
interested in how tissue growth is controlled during
development and regeneration. We are also interested
in how deregulation of signalling pathways that control
tissue growth contributes to the genesis of human
cancer. We utilise the model organism, drosophila
melanogaster (vinegar fly), and mammalian cell culture
to discover and investigate genes involved in tissue
growth and cancer. Our approach is to identify genes
involved in cancerous-like growth in flies and then use
human and mouse models to determine whether the
human counterparts of these fly cancer genes have a
role in human cancer. Approximately 70% of human
disease genes are conserved in flies, making it an
excellent model for these studies.
One newly identified signaling pathway that our
laboratory helped to discover and actively studies is the
salvador-warts-hippo (hippo) pathway, which controls
organ size during development (reviewed in references
3 and 9, below). This pathway controls organ size by
restricting cells from growing and dividing excessively,
properties central to the formation of cancer. The hippo
pathway is conserved in humans and several studies
from our laboratory and others have implicated this
pathway in the genesis of human cancer (eg. 2). By
studying various aspects of this pathway we aim to
understand how organ size is correctly specified during
17

development, and how deregulation of this pathway
contributes to human cancer. Broad research aims:
• to understand how the hippo pathway controls the size
of developing, and regenerating, organs.
• to understand how hippo pathway deregulation
contributes to the genesis of human cancers.
We currently have several projects based around these
aims which we would like to discuss with students.
For more information about these projects contact:
Dr Kieran Harvey, Tel: +61 3 9656 1291, Email:
kieran.harvey@petermac.org
References from our laboratory relevant to the project:
1. F. Grusche et al. (2011). Dev Biol. 3550, 255-266.
2. X. Zhang et al. (2011). Oncogene. 30, 2810-2822.
3 F. Grusche et al. (2010). Curr Biol. 20, r574-582.
4. C. Milton et al. (2010). Development. 137, 735-43.
5. X. Zhang et al. (2009). Cancer Res. 69, 6033-6041.
6. K.F. Harvey et al. (2008). J Cell Biol. 25, 691-696.
7. F.C. Bennett and K.F. Harvey (2006). Curr Biol. 16, 2101-
2110.
8. K.F. Harvey et al. (2003). Cell 114, 457-467.
9. N. Tapon et al. (2002). Cell 110, 467-478.
EPITHELIAL STEM CELL BIOLOGY
EPIDERMAL STEM CELLS AND THEIR
MICROENVIRONMENT: INVESTIGATION OF THE
MOLECULAR REGULATORS OF NORMAL SKIN
REPLACEMENT, WOUND HEALING AND CANCER IN
HUMAN SKIN
Supervisors: Dr. Pritinder Kaur, and Dr. Holger Schlüter,
Human skin epidermis is a constantly renewing tissue,
where the combined action of relatively quiescent
keratinocyte stem cells and their committed progeny
undergo tightly regulated proliferation to replace normal
skin tissue. A hallmark of stem cells is the capacity to
regenerate the tissue of origin for a prolonged period of
time and to constantly self-renew. Our lab recently
demonstrated in long-term tissue reconstitution assays
that the greatest capability of tissue reconstitution
resides within the candidate keratinocyte stem cells.
However, it is also clear that stem cell properties such
as self-renewal and tissue replacement can be
enhanced by cellular and molecular regulators found in
the microenvironment, although this remains poorly
characterized. A dermal cell type i.e. pericytes, isolated
using specific antibodies and flow cytometry can
enhance the proliferative capacity of human keratinocyte
stem cells and their committed progeny independent of
angiogenesis. In epithelial cancers, pericyte involvement
can predict cancer progression and disease-free survival
in patients despite treatment with current cancer
therapies.
Two projects are available for PhD students with the
following aims:
1. Investigate the role of specific candidate molecules
synthesised and secreted by pericytes identified in
our laboratory, that will improve the growth of skin
cells.
2. Investigate the role of the same molecules secreted
by pericytes that promote tumour growth in models of
skin, ovarian and breast cancer.
Both projects use techniques routinely employed in our
laboratory such as tissue culture of primary cells, cell
sorting using a fluorescence-activated cell sorter,
standard molecular and cell biological methods like
cloning or SDS-PAGE, as well as microscopy (light and
electron) and mouse models of tissue regeneration,
cancer and wound healing.
The results of these studies will have the following
impact on human skin biology:
1. Increase understanding of how stem cells and their
environment manage to routinely replace skin cells
2. Understand how stem cells escape from regulatory
mechanisms that prevent cancer development
3. Understand the role of stem cells and their
environment in promoting wound healing
4. Improve current methods for expanding skin cells for
transplantion onto patients with large skin deficits
e.g. burns patients.
5. Improve diagnosis of patients with aggressive
epithelial cancers e.g. ovarian & breast
For more information about this project contact:
Dr. Pritinder Kaur, Tel: +61 3 9656 3714; Email:
pritinder.kaur@petermac.org
Dr. Holger Schlüter, Tel: +61 3 9656 3713; Email:
holger.schlueter@petermac.org
METASTASIS RESEARCH
REGULATION OF BREAST CANCER METASTASIS
BY microRNA GENES
Supervisor: Dr. Cameron Johnstone, Assoc. Prof. Robin
Anderson
The project will explore the role of microRNA genes in
breast cancer metastasis using both in vitro and in vivo
approaches. MicroRNA genes currently under
examination in the laboratory include those with potential
roles in potentiating (miR-21), or inhibiting (miR-146,
miR-15/16, and mir-200 families) metastasis. In vitro
techniques to be used include proliferation, adhesion,
migration, invasion, and apoptosis/anoikis assays. The
laboratory utilises both the '4T1' syngeneic mouse model
of breast cancer progression as well as human breast
cancer cell line xenografts in immunocompromised mice
to study metastasis in vivo. These approaches are
underpinned by real-time bioluminescent (luciferase)
and biofluorescence (tdTomato) imaging.
For more information about this project contact:
Dr. Cameron Johnstone, Tel: +61 3 9656 1771, Email:
cameron.johnstone@petermac.org
THE ROLE OF MYOEPITHELIAL PROTEINS IN
BLOCKING BREAST CANCER INVASION
Supervisors: Dr Belinda Parker, Dr Andreas Moeller
Breast cancer begins in the epithelial cells, a single layer
of cells that surround the lumen of breast ducts. Ductal
carcinoma in situ (DCIS) is considered a benign form of
breast cancer, where tumour cells have started to divide
but have not spread beyond the confines of the ducts
nor have they recruited new blood vessels. Invasion
beyond the ducts and through the breast tissue (invasive
ductal carcinoma; IDC) is associated with an increased
risk of metastasis. For progression to invasive
carcinoma, tumour cells need to pass the
myoepithelium, a layer of cells surrounding the ducts,
and invade the surrounding protein matrix. There is
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increasing evidence that the myoepithelium functions to
suppress progression from DCIS to IDC, both by
providing a physical barrier and by expressing specific
proteins that are inhibitory to tumour cell invasion.
Our studies indicate that the cysteine cathepsin
proteases have important roles in tumour cell invasion
and that inhibitors of these proteases, including the
physiological inhibitor stefin A, prevent cancer
progression by blocking invasion. In breast tissue stefin
A is abundant in the myoepithelial layer surrounding
normal ducts, possibly inhibiting degradation of the
matrix surrounding the ductal system and preventing
invasive carcinoma. The objectives of this project are to
test the contribution of stefin A to myoepithelial cellinduced
suppression of invasion and determine if the
expression of this inhibitor in benign cancers can predict
risk of cancer recurrence in patients.
This project will utilize in vitro and in vivo models of
tumourigenesis to test if stefin A in the myoepithelial
cells is critical for suppressing the progression of DCIS
to IDC. A broad range of techniques will be used
including 3D tissue culture, confocal and light
microscopy, molecular cloning, shRNA interference,
immunohistochemistry and immunofluoresence and in
vitro invasion assays
For more information about this project contact:
Dr Belinda Parker, Tel: +61 3 9656 1285, Email:
belinda.parker@petermac.org
Dr Andreas Moeller, Tel: +61 3 9656 1287, E-mail:
andreas.moeller@petermac.org
MECHANISMS AND THERAPY OF BREAST CANCER
METASTASIS TO BRAIN
Supervisor: Dr. Normand Pouliot
Breast cancer affects 1 in 10 women in Australia and is
fatal once it has spread to and compromised the function
of distant organs such as the brain. However, the
molecular mechanisms regulating metastasis to brain
remain largely unknown, due in part to the lack of
clinically relevant animal models in which to study
disease progression. Moreover, despite improved
detection methods and the introduction of novel targeted
therapies against systemic disease extending the life of
patients, the lack of effectiveness of these treatments
against brain metastasis has led to an increase in the
incidence of advanced breast cancer patients
developing aggressive brain metastases.
We have now developed and characterised a unique
and clinically relevant mouse model of spontaneous
breast cancer metastasis to brain. The model is ideally
suited to identify and investigate the function of brain
metastasis genes in vivo and to test novel therapies
against this devastating disease. Thus, the overall
objective of this research project will be to characterise
the function of selected genes in metastasis to brain and
to test the efficacy of various inhibitors alone or in
combination with radiation against brain-metastatic
breast tumour cells both in vitro and in vivo. The project
is suitable for both Honours and PhD students and will
make use of a variety of techniques ranging from basic
cell culture and in vitro functional assays (proliferation,
migration, invasion, survival) to molecular techniques
and in vivo therapies in animals.
For more information about this project contact:
Dr. Normand Pouliot, Tel: +61 3 9656 1285; Email:
normand.pouliot@petermac.org
TARGETING TUMOUR-STROMA INTERACTIONS TO
TREAT BREAST CANCER METASTASIS TO BONE.
Supervisor: Dr. Normand Pouliot
Our laboratory focuses on the identification and
characterisation of genes involved in the spread
(metastasis) of breast tumours to specific organs. By far,
the most commonly affected organ in advanced breast
cancer patients is bone, leading to severe and
debilitating skeletal complications. While recent work
has led to the development of more effective therapies
against bone metastases, a particular subtype of
aggressive breast tumours called triple negative (TN)
remains largely resistant to treatment. Therefore,
targeting factors present in the bone environment that
support the growth of TN tumours rather than directly
targeting tumour cells has been proposed as an
alternative/complementary to prevent or delay the
development of TN bone metastases in advanced breast
cancer patients. To test this, the project will make use of
a unique mouse model of TN breast cancer that
aggressively metastasises to bone to investigate the
effectiveness of therapies targeting various stromal
factors thought to contribute to bone metastasis
including the extracellular matrix protein laminin-511 and
two soluble factors secreted by bone cells, transforming
growth factor-β and Gas6. The project is suitable for
both Honours and PhD students and will make use of a
variety of techniques ranging from basic cell culture, in
vitro functional assays (proliferation, migration, invasion,
fluorescence imaging, survival), immunohistochemistry,
molecular techniques and the use of inhibitors for in vivo
therapy in animals.
For more information about this project contact:
Dr. Normand Pouliot, Tel: +61 3 9656 1285; Email:
normand.pouliot@petermac.org
INVESTIGATING THE MECHANISMS OF IMMUNE
ESCAPE BY BREAST CANCER CELLS
Supervisors: Dr Belinda Parker, Dr Daniel Andrews
See Cellular Immunity Laboratory in the Cancer
Immunology Program.
MOLECULAR RADIATION BIOLOGY
PROTECTION OF RADIATION-INDUCED DAMAGE
BY METHYLPROAMINE AND ANALOGUES
Supervisors: Dr. Pavel Lobachevsky, Dr Alesia
Ivashkevich & Assoc. Prof. Roger Martin
Normal tissue damage associated with radiotherapy has
motivated Peter Mac’s development of a new class of
DNA-binding radioprotecting drugs that could be applied
topically to normal tissues at risk. Methylproamine, the
lead compound, reduces radiation induced cell kill at low
concentrations, apparently by reducing radiation-induced
DNA damage. Our program of lead optimization,
collaborating with Assoc Prof Jonathan White (University
of Melbourne, School of Chemistry), has identified new,
improved analogues, and proof-of-principle of topical
radioprotection has been established in mouse oral
mucosa.
Our research has raised more fundamental questions
which are potential research projects. Many of these
questions concern the mechanism of radioprotection,
and in this context, our collection of methylproamine
analogues with a range of radioprotective efficacies are
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an important resource. The mechanistic
questions/issues include:
• Protection of radiation-induced DNA damage by
methylproamine. There is evidence in support of the
hypothesis that radioprotection is due to repair of
initial radiation-induced DNA damage. Subsiduary
questions concern the spectrum of chemical lesions
involved, and the extent to which each of these is
“repaired’ or suppressed by DNA-bound
radioprotector. This project will involve studies of
DNA damage and protection in both purified DNA
using the plasmid model and DNA in cultured cells.
• Investigations of combinations of radioprotectors.
Our recent studies indicate that combinations of
radioprotectors can provide a greater extent of
radioprotection thatn single agents. This project will
explore this potential, first in cell culture systems,
and then in mouse models.
For more information about this project contact:
Assoc. Prof. Roger Martin, Tel: +61 3 9656 1290; Email:
roger.martin@petermac.org
Dr. Pavel Lobachevsky, Tel: +61 3 9656 1357; Email:
pavel.lobachevsky@petermac.org
THE POTENTIAL OF DNA LIGANDS LABELLED
WITH AUGER-EMITTERS FOR
ENDORADIOTHERAPY AND IMAGING OF
TUMOURS.
Supervisors: Dr. Pavel Lobachevsky, Assoc. Prof. Roger
Martin
Auger-emitters are a special class of radioisotopes
characterized by highly focused radiochemical damage.
The general requirement to position an Auger-emitter
very close to DNA to fully exploit the cytotoxic potential
of Auger emission is well-established, but a more recent
development is the integration of this requirement into a
general tumour targeting strategy. The focus of this
strategy is a conjugate of the radioactive DNA ligand
linked to a tumour targeting protein specific for an
appropriate cell surface receptor. The combination of
both positron and Auger electron emission in the decay
scheme of 124 I presents very special opportunities. The
positron-emission feature of 124 I enables this “sink” effect
to be exploited in the context of PET imaging generally,
as well as in conjunction with Auger therapy. Adoption
of the general strategy for imaging-only applications
requires re-design of the DNA ligands so that the iodine
atom is positioned away from the DNA helix so as to
minimise DNA damage (as distinct from maximising
DNA damage for combined therapy/PET imaging
objective).
Potential are in two distinct arenas:
• Design and evaluation of new labelled DNA ligands.
In collaboration with Assoc Prof Jonathan White
(University of Melbourne, School of Chemistry), new
iodinated DNA ligands are being designed and
synthesised. These ligands have the iodine atom
positioned at varying distances from the axis of the
DNA helix. The overall aim of the program is to
establish the relationship between distance of the
iodine atom from DNA and the extent of DNA
breakage, particularly DNA double-strand breaks
(DNAdsbs). This project will focus on a new ligand
designed to exhibit minimal DNA damage.
• Exploration of various new targeting protein/receptor
systems for tumour imaging/therapy. In collaboration
with the CRC for BioImaging Development, headed
by Professor Rod Hicks, the current emphasis is on
the somatostatin receptor system and octreotide
derivatives as targeting peptides. Somatostatin
receptors are overexpressed in a range of tumours.
This project aims to conjugate the DNA ligand
labelled with an Auger electron emitting isotope to
octreotide and investigate biological properties of the
conjugate such as affinity to somastotatin receptors,
intracellular distribution, radiotoxicity, biodistribution
in an animal model.
For more information about this project contact:
Assoc. Prof. Roger Martin, Tel: +61 3 9656 1357; Email:
roger.martin@petermac.org
Dr. Pavel Lobachevsky, Tel: +61 3 9656 1357; Email:
pavel.lobachevsky@petermac.org
EVALUATION OF RADIOSENSITIVITY OF
RADIOTHERAPY PATIENTS.
Supervisors: Dr. Pavel Lobachevsky, Dr Alesia
Ivashkevitch, Assoc. Prof. Roger Martin
In the context of the radioprotector program described
above, a relatively new assay of radiation-induced DNA
damage has been established in the lab. The assay is
based on a very early event in the response of cells to
radiation-induced DNA damage, namely
phosphorylation of histone H2AX to form γ-H2AX.
Fluorescent foci are detectable in cells by
immunofluorescence using labelled γ-H2AX-antibodies,
within minutes after irradiation. Preliminary studies have
established a radiation dose-response for isolated
human lymphocytes irradiated ex vivo, and this will be
evaluated as the basis for an assay of radiosensitivity of
radiotherapy patients. The assay is facilitated by
software developed by Dr Lobachevsky for automatic
counting of γ-H2AX foci. If the assay is validated, it has
obvious application for design of individualised
radiotherapy.
This project involves collaborators at Peter Mac (Prof.
Stephen Fox and Assoc. Prof.Trevor Leung) and NIH in
USA (Drs William Bonner and Olga Sedelnikova).
For more information about this project contact:
Assoc. Prof. Roger Martin, Tel: +61 3 9656 1357; Email:
roger.martin@petermac.org
Dr. Pavel Lobachevsky, Tel: +61 3 9656 1357; Email:
pavel.lobachevsky@petermac.org
DEVELOPMENT OF A NOVEL SCREENING TEST TO
ASSESS INDIVIDUAL RADIOSENSITIVITY OF
RADIOTHERAPY PATIENTS
Supervisor: Dr. Olga Martin
A few percent of patients experience abnormally severe
side-effects of radiotherapy, due to innate (genetically
determined) radiosensitivity (RS). If such patients could
be identified, this would enable radiation oncologists to
prescribe customized radiotherapy schedules, with
increased prospects of cure.
The importance of this clinical problem has prompted
numerous attempts to develop effective assays by using
blood and other normal tissues from radiotherapy
patients. However until recently, these have been
unsuccessful, largely due to limitations of methodology,
such as sensitivity, reproducibility, reliability and a long
time delay (2-3 weeks) to obtain the results. Also,
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previous assays required that the cells were
“transformed” so they could proliferate indefinitely, and
this procedure itself changes their RS.
An important feature of this project is the rapid “readout”
of the γ-H2AX assay, which enables use of
untransformed primary cells. The assay is based on a
very early event in the response of cells to radiationinduced
DNA damage, namely phosphorylation of
histone H2AX to form γ-H2AX. Fluorescent foci are
detectable in cells by immunofluorescence using
labelled anti-γ-H2AX antibodies, within minutes after
irradiation. We are using primary lymphocytes and
plucked hair follicles, which are subsequently irradiated
and then assayed. In the context of validation, there is
the access to a retrospective collection of ex-RT patients
at PeterMac, who experienced abnormally severe sideeffects,
together with matched controls. The database of
ex-RT patients was assembled by Dr Trevor Leong, a
radiation oncologist. The first stage of the project
involves testing the ex-RT patients, and comparison of
the assay results with the extent of clinically reported
radiation-induced side effects.
This project involves collaborators at Peter Mac (Prof.
Stephen Fox and Assoc. Prof.Trevor Leung)
For more information about this project contact:
Dr Olga Martin (Department of Radiation Oncology), Tel:
+61 3 9656 1357; Email: olga.martin@petermac.org
TUMOUR SUPPRESSION
The major goal of our research is to restore tumour
suppression to trigger selective elimination of cancer
cells. To achieve that we need to identify the key
regulatory nodes in tumour suppression.
Ultimately, we aim to apply and translate the knowledge
we are deriving from our basic research to the cancer
clinic. The work in our lab focuses on two key tumour
suppressors, p53 and PML (promyelocytic leukemia
protein). P53 is considered to be the most important
agent of the body for fighting cancer. It plays a key role
in the cellular response to stress conditions, such as
damage to DNA. Upon activation, p53 acts to eliminate
cells of cancerous potential by halting their growth. In
70% of all human cancers, it loses its anticancer
properties through direct mutations. The mutant forms of
p53 acts to promote cancer and metastasis. Likewise,
PML is commonly targeted during cancer development
and its loss contributes to aggressive and invasive
cancers. To better treat cancer we need to understand
how these key tumour suppressors are controlled in
normal and cancer cells. Our lab discovered how the
protein stability of p53 (Haupt et al., 1997 Nature) and
PML (Luoria-Hayon et al., 2009, CDD) is regulated. We
are using this information in order to manipulate the
expression and function of these tumour suppressors in
order to trigger selective killing of cancer cells. We are
seeking Honours and PhD students to undertake
projects on this area of research. Three examples are
outlined below, but other projects are available.
EXPLORING THE REGULATION OF MUTANT p53
Supervisors: Assoc Prof. Ygal Haupt, Dr. Sue Haupt
The p53 tumour suppressor is tightly controlled by an
extensive network of positive and negative regulators.
Work from our lab and others revealed that the tumour
suppressor PML is a key positive regulator of p53.
Since mutant p53 is the most common genetic event in
human cancer we have investigated how it is regulated
in cancer cells. Surprisingly, we found that PML also
activates the function of mutant forms of p53.
Specifically, we showed that PML is essential for the
oncogenic activities of mutant p53, suggesting that
tumour suppression by PML depends on the status of
p53 (Haupt et al., 2009 Cancer Res). These findings
demonstrated that PML regulates both mutant and wild
type p53. This imposes a potential risk to cancer
patients that express mutant p53.
The aim of the first project is to explore the interplay
between mutant p53 and key regulators of wild type
p53. The project will involve work with cancer cell lines
and testing our findings in transgenic mouse models. In
addition the project will expose students to a variety of
molecular, cellular and biochemical techniques.
The aim of the second project is to use the results
derived from a whole genome shRNA screen for novel
regulators of mutant p53 stability. This project will
involve validation of the best hits from the screen and
characterization of their role in the regulation of mutant
p53. The project will involve ubiquitination assays, cell
culture and mouse models.
REGULATION OF THE ONCOGENIC PML-RARa IN
ACUTE PROMYELOCYTIC LUEKEMIA (APL).
Supervisor: Assoc. Prof. Ygal Haupt
We have recently discovered that the E6AP E3 ligase
regulates the tumour suppressor PML (Luoria-Hayon et
al., 2009 CDD). When PML is translocated to the
retinoic acid receptor (RARa) a fusion protein PML-
RARa is generated which inhibits myeloid
differentiation. This fusion protein is the prototype of
APL and it exists in the majority of patients. Treatments
of APL patients with all trans retinoic acid (ATRA) or
arsenic trioxide promotes the degradation of the fusion
protein, and results in terminal differentiation of APL
cells and is responsible for the high rate of successful
cure of these patients. However, the mechanisms by
which these drugs promote the degradation of the
fusion protein are poorly understood. The aim of this
project is to explore the role of E6AP in the regulation of
the PML-RARa and to define the role of E6AP in the
response of APL cells to these drugs. This will be
achieved by measuring the status of PML-RARa in APL
cells expressing or lacking E6AP. The project will
involve a variety of molecular, cellular and biochemical
techniques.
THE INVOLVEMENT OF THE UBIQUITIN
PROTEASOME SYSTEM IN CANCER
DEVELOPMENT.
Supervisor: Assoc. Prof. Ygal Haupt, Dr. Kamil
Wolyniec, Dr. Sue Haupt
We have recently discovered that E6AP is the major
regulator of PML stability by acting as its E3 ubiquitin
ligase (Luoria-Hayon et al., 2009 CDD). PML is
frequently downregulated or lost in many different
cancer types however the mechanism is unknown. We
hypothesize that this PML loss is due to upregulation of
E6AP. Our recent results strongly support this
hypothesis in prostate cancer and in B lymphoma. The
aim of this project is to explore the type of cancers in
which the E6AP/PML tumour suppression pathway is
deregulated, and to test whether restoration of PML by
interference with E6AP is an effective mechanism to
inhibit cancer cell growth. This would provide a
rationale for novel anti-cancer treatment. The project
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will involve measuring the status of E6AP and PML in
human cancer samples. Further, the hypothesis will be
tested in cancer cell lines and in relevant mouse
models for cancer.
For more information about these projects contact:
Assoc. Prof. Ygal Haupt Tel: +61 3 9656 5871
E-Mail: ygal.haupt@petermac.org
MANIPULATING METAL IONS AS A NOVEL
APPROACH TO CANCER TREATMENT
Elevated copper in both malignant tissue and serum is
emerging as a hallmark of cancer, having been
established in a range of cancer types including breast,
ovarian, cervical, lung, stomach, prostate and leukemia.
We are developing a therapeutic approach aimed at
exploiting elevated copper in cancer cells, which
involves the use of copper specific ionophores. An
ionophore by definition transports specific metal(s) into
cells often allowing them to become bioavailable. We
have recently discovered that prostate cancer cells have
a remarkable elevation in intracellular copper and are
consequently sensitive to copper-ionophore treatment.
We have demonstrated that the copper-ionophore
clioquinol can selectively target and destroy cancerous
prostate cells without harming normal prostate cells (see
http://www.ncbi.nlm.nih.gov/pubmed/21426304). As
copper is critically involved in multiple facets of cancer
development and progression and that copper
accumulation is emerging as a hallmark of cancer, an
exciting opportunity exists to develop a therapeutic
strategy that might be applicable to a variety of cancer
types.
Our project brings together the fields of cancer research
and copper biology, to interrogate and develop coppertargeted
treatments for prostate cancer. Specifically, we
aim to (1) determine at what stage in prostate cancer
development intracellular copper accumulates, (2) when
during prostate cancer development cells become
sensitive to copper-ionophore treatment, (3) how
prostate cancer development affects cellular copper
homeostasis and (4) to evaluate the therapeutic efficacy
of copper-ionophores in the treatment of human prostate
cancer using preclinical mouse models. We are looking
for motivated and enthusiastic students (both Honours
and PhD) to help achieve some of these aims. Students
will carry out research in a broad field of disciplines
ranging from, molecular biology, biochemistry, cell
biology, animal models and metallomics.
For more information about this project contact:
Dr. Michael Cater, Tel +61 3 9656 5889, Email:
michael.cater@petermac.org or
Assoc. Prof. Ygal Haupt, Tel +61 3 9656 5871, Email:
ygal.haupt@petermac.org.
TUMOUR MICROENVIRONMENT
INVESTIGATING THE TUMOUR/STROMA
MICROENVIRONMENT IN BREAST CANCER
Supervisors: Dr. Andreas Moeller
Breast cancer is the most common cancer in women,
with approximately one in ten women developing this
disease during their lifetime. The metastatic spread of
the tumour to distant organs is the most common cause
of morbidity in breast cancer patients, and treatment
options for metastatic disease are limited. Our research
focuses on understanding the progression of breast
cancers, especially the interaction of tumour cells with
surrounding cells that make up the tumour
microenvironment. These cells include infiltrating
immune and mesenchymal cell lineages, that play a role
in hypoxia and neo-angiogenesis (development of new
blood vessels) and the process of metastasis to distant
organs. We are developing new approaches to translate
this knowledge into novel treatment options for breast
cancer patients. To achieve these aims, we have
generated novel knockout and transgenic breast cancer
mouse models, which we are using in conjunction with
state-of-the-art techniques including imaging, FACS,
microarray, and drug development.
This project will investigate the interaction of tumour
cells with their surrounding stroma, and how this
interaction enables the tumour to grow and eventually
metastasise. Understanding the relationship of tumour
cells with the surrounding stroma in the tumour
microenvironment is crucial in order to therapeutically
target tumour progression. Apart from tumour cells, the
tumour microenvironment is comprised of several
different cells types, including endothelial cells (involved
in new blood vessel formation), fibroblasts (involved in
wound healing and fibrotic responses) and immune cells
(involved in immune surveillance). Using isolated cell
lines and co-culture experiments, cytokine and growth
factor secretion will be assessed by the student and
observations verified by qPCR, ELISA and IHC on both
individual cell lines and tumour samples. This approach
will shed light on the communication between tumour
cells and their surrounding, non-tumour cell lineages.
For more information about this project contact:
Dr. Andreas Moeller, Tel: +61 3 9656 1287, E-mail:
andreas.moeller@petermac.org
THE IDENTITY, ROLE & FUNCTION OF IMMUNE
CELLS AT SITES OF METASTASIS IN BREAST
CANCER.
Supervisors: Dr. Andreas Moeller & Prof. Mark Smyth
See Cellular Immunity in Cancer Immunology
Program
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TUMOUR ANGIOGENESIS PROGRAM
www.petermac.org/Research/TumourAngiogenesisProgram
A tumour establishes a blood supply by secreting proteins that attract the growth of blood vessels (angiogenesis) from
surrounding tissue. This allows the tumour to grow more rapidly and to spread to distant sites in the body via the blood
vasculature. This spread of tumour cells is known as metastasis and is the most lethal aspect of cancer. We and others
have shown that tumours also attract the growth of lymphatic vessels (lymphangiogenesis) which facilitates metastatic
spread via the lymphatics.
We seek to identify and characterize the signalling pathways which control tumour angiogenesis and lymphangiogenesis,
with a view to targeting them in the clinic to restrict the growth and spread of cancer. These pathways include those
triggered by the vascular endothelial growth factors (VEGFs) and VEGF receptors on blood vessels and lymphatics. This
approach to cancer therapeutics has previously given rise to therapeutic agents, including a neutralizing antibody targeting
VEGF-A, known as Avastin (or bevacizumab).
Another focus of the laboratory is an alternative molecular signaling pathway involving the Wnt ligands and the Ryk receptor
that is thought to be important in cancer biology. This intriguing pathway is essential for embryonic development and may
play a role in the proliferation of cancer cells and tumour metastasis. A deeper understanding of this pathway will facilitate
attempts to inhibit Wnt/Ryk signaling in the setting of cancer. Our studies of signaling for tumour growth and metastasis
involve technologies relating to molecular biology, cell biology, protein chemistry, developmental biology and genetic models
of disease.
DEFINING SIGNALLING PATHWAYS THAT
CONTROL THE RESPONSE OF ENDOTHELIUM TO
CANCER THERAPY
Supervisor: Assoc. Prof. Steven Stacker
The formation and alteration of blood and lymphatic
vessels are important for the growth and spread of
spread of cancer. Targeting the process of angiogenesis
by blocking the action of vascular growth factors with
agents such as Avastin has already shown promise for
cancer therapy. To understand the response of
endothelial cells to cancer therapy, including biologicals,
radiotherapy and chemotherapy we are establishing
screening systems using human endothelial cells of
blood vascular and lymphatic origin. These screens will
involve the selection of endothelial cells in various anticancer
therapeutic regimes, followed by rescue using a
library of shRNA. Such screens would give insight into
the signalling pathways required for escape from general
anti-cancer therapeutics and current anti-angiogenesis
approaches.
This project will investigate a specific endothelial subset
in combination with a suitable anti-cancer treatment
protocol, and rescue using a library of shRNA from the
Victorian Centre for Functional Genomics. The student
will identify and characterise specific genes involved in
the rescue and these would be further characterised
using in vitro and in vivo assays of angiogenesis and/or
lymphangiogenesis that are established in the
laboratory. This information wo;; form the basis for
developing an understanding of the complex signalling
networks present in endothelial cells and how these may
be targeted in cancer.
During this project the student will develop skills
including tissue culture of primary cells, in vitro cell and
molecular biology assays, use of si and shRNA to
enable gene knockdown and bioinformatics analysis.
The project is designed to isolate key molecules that
control the endothelium of blood and lymphatic vessels
in the context of anti-cancer therapy.
For more information about this project contact:
Assoc. Prof. Steven Stacker, Tel: +61 3 9656 5263,
Email: steven.stacker@petermac.org
ANALYSIS OF MOLECULES REGULATING THE
GROWTH OF BLOOD VESSELS AND LYMPHATICS
IN CANCER
The growth of blood vessels (angiogenesis) and
lymphatic vessels (lymphangiogenesis) is central to the
growth and spread of cancer. In the Tumour
Angiogenesis Program, Peter MacCallum Cancer
Centre, we have identified protein growth factors, cell
surface receptors and signalling pathways that control
these important processes, including members of the
vascular endothelial growth factor (VEGF) family. The
project will explore the regulation of these molecules in
cancer and normal development, with a focus on in vivo
studies using mouse genetic models of disease
developed in our Program. Our Program is a leader in
such in vivo models of angiogenesis and
lymphangiogenesis, and we have established novel
models of growth factor activation and function important
for this project. The project will have a view to
therapeutics designed to restrict tumour angiogenesis
and lymphangiogenesis, and thereby inhibit the spread
of cancer. It will have elements of translational
research, and will involve the latest techniques of cell
biology, molecular biology, microscopy, molecular
pathology, genetics, bioinformatics and biotechnology.
References::
Achen et al., Cancer Cell 7:121-127, 2005
Francois et al., Nature 456:643-648, 2008
Harris et al., FASEB J. 25:2615-2625, 2011
McColl et al., FASEB J. 21:1088-1098, 2007
McColl et al., J. Exp. Med. 198:863-868, 2003
For more information about this project contact:
Assoc. Prof. Marc Achen; Tel: 61-3-9656-5264; Email:
Marc.achen@petermac.org
TARGETING GROWTH FACTOR ACTIVATION IN
ANIMAL MODELS OF CANCER
Supervisor: Assoc. Prof. Marc Achen
Angiogenesis, growth of lymphatic vessels
(lymphangiogenesis), immune suppression and
recruitment of tumour stroma are important features of
cancer biology that are in part driven by protein growth
factors. Many of these growth factors are secreted from
tumour cells in inactive forms which require activation by
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proteases. For example, we have shown that proteolytic
activation of members of the vascular endothelial growth
factor (VEGF) family of proteins is an important step in
promoting tumour angiogenesis and lymphangiogenesis
in cancer which in turn facilitates tumour growth and
spread. We have shown that the proteases involved are
members of the proprotein convertase (PC) family of
enzymes which also activate a range of other growth
factors with roles in cancer biology. These findings
suggest that targeting members of the PC family may be
useful for restricting the growth and spread of cancer.
This project will explore the effect of targeting individual
members of the PC family on tumour growth and spread
in animal models. PCs in tumour cells or tumour stroma
will be targeted by siRNAs, small molecule inhibitors or
other technologies and effects on primary tumour growth
and metastatic spread will be monitored.
During this project the student will develop skills in cell
biology, tissue culture and animal models of disease. It
is envisaged that the student will ascertain if targeting
certain families of proteases which activate growth
factors in cancer is a beneficial strategy for restricting
the growth and spread of cancer.
For more information about this project contact:
Assoc. Prof. Marc Achen; Tel: 61-3-9656-5264; Email:
Marc.achen@petermac.org
ONCOLGENIC SIGNALLING AND GROWTH CONTROL AND PROGRAM
www.petermac.org/Research/OncogenicSignallingGrowthControlProgram
The Oncogenic Signalling and Growth Control Program consists of three groups (Pearson, Hannan and McArthur) with
extensive and complementary expertise in areas ranging from proteomics and protein chemistry, through signal
transduction and cell biology to the regulation of gene transcription and protein translation. A major focus of our work is in
understanding the mechanisms of regulation of ribosome biogenesis, and protein translation, and how these processes
impact on differentiation and are corrupted in tumour cells. A number of current projects employ state-of-the-art
biochemistry, molecular and cell biology to characterize the basis of the regulation of these fundamental processes.
REGULATION OF CHROMATIN REMODELING OF
THE rRNA GENES IN MOUSE EMBRYONIC STEM
CELLS
Supervisors: Assoc. Prof. Ross Hannan, Dr Nadine Hein
In somatic mammalian cells over 50% of the ~200 copies
of the rRNA genes are silenced though CpG methylation.
Given that rRNA gene transcription is limiting for growth
silencing of half the rRNA gene capacity seems counter
intuitive. Interestingly there is an increasing body of
evidence to suggest that rDNA silencing is critical not
only for suppressing unwanted recombination within the
rDNA repeat and general nucleolar organization but also
for controlling, to some extent, general heterochromatin
of the nucleus. For example in budding yeast the NAD+dependent
histone deacetylase Sir2 (Silent information
regulator 2) is required to repress recombination in the
rDNA locus and promote yeast longevity. Similarly,
Drosophila mutants that are defective in the histone H3
Lys 9 (H3K9) methyltransferase Su(var)3-9 and other
factors involved in heterochromatin formation exhibit
increased nucleolar fragmentation and the generation of
extrachromosomal rDNA circles. In addition to
suppression of recombination, it appears that the
perinucleolar heterochromatin might serve as a distinct
nuclear space with a primary function in maintaining
repressive chromatin states. For example the inactive X
chromosome (Xi) must continuously visit the
perinucleolar compartment during S phase to maintain its
epigenetic status. Similarly it has been well documented
that a fraction of human centromeres cluster around
nucleoli in vivo. Thus the reason for the silencing of over
50% of the rRNA genes repeats in mammalian cells is
not clear. In our view it seems unlikely it is to simply to
limit rRNA synthesis rates and growth. This is because
experimental reactivation of silent rRNA genes following
deletion of the methyltransferese DMNT1 severely
disrupts nucleolar structure and function and has been
associated with no change or even decreased rRNA
gene transcription (T. Moss pers commun).
(i) This project will use mouse embryonic stems (ES)
cells to explore the biological function of rRNA gene
silencing. Unlike somatic cells mouse ES cells are highly
tolerant to large scale CpG demethylation and thus
provide a mechanism to explore its consequences on
rDNA transcription and nucleolar/nucleoplasmic structure
and function. The effects of methylation independent
manipulation of the proportion of active rRNA genes, rchromatin
remodeling, cell morphology and rDNA
stability will be examined in ES cells through
manipulating levels of the Pol I transcription factor UBF.
This will be compared to the effects of altering
methylation dependent silencing though manipulation of
DNMT1 levels.
(ii) The Pol I-specific transcription initiation factor Rrn3
and the cytoarchitectural Pol I transcription factor UBF
are thought to play a critical role in integrating growth
factor, nutrient and stress signals with rDNA
transcription. In somatic cells deletion of UBF and Rrn3
is lethal. Surprisingly while UBF null mice die before
implantation, Rrn3 null mice survive until E9.5. These
data suggest that at very early stage in development
rDNA transcription may be independent of Rrn3 activity.
This project would test this hypothesis using inducible
knockout of Rrn3.
For more information about this project contact:
Assoc. Prof. Ross Hannan, Tel: +61 3 9656 1747, Email:
Ross.Hannan@petermac.org
Dr Nadine Hein, Tel: +61 3 9656 1806, Email:
nadine.hein@petermac.org
HIJACKING GROWTH FACTOR RECEPTOR
SIGNALING IN CANCER
Supervisors: Dr. Amee George and Assoc. Prof. Ross
Hannan
Aberrant receptor tyrosine kinase (RTK) signalling leads
to the activation of a plethora of downstream signalling
pathways (such as the MAPK and PI3K pathways)
involved in growth, proliferation, migration, invasion and
angiogenesis, all of which are important factors in the
development and progression of cancer. One
mechanism proposed to contribute to the dysregulation
of this signalling is a phenomenon called G proteincoupled
receptor (GPCR) RTK transactivation, where
GPCR signalling mechanisms ‘hijack’ well-known cellular
24

signalling machinery to drive various cellular outcomes
distal of the RTK. In particular, our lab has an interest in
the transactivation of the epidermal growth factor
receptor (EGFR) by signalling through the well-known
renin-angiotensin system type I receptor (AT1R), a
GPCR. This is known to occur in selected cell types, and
while the exact mechanism remains unclear, current
theories suggest Gq/11-dependent metalloproteases,
such as members of the ADAM family of proteins (e.g.
ADAM 10, 12 and 17) are activated after stimulation of
the receptor with angiotensin II (AngII), causing the
shedding of EGF ligands, which activate the EGFR and
promote cellular growth. We have developed a stable
cellular model of AngII-mediated EGFR transactivation,
and work is currently underway to perform a high-content
genome-wide functional genomics screen (using RNAi
technologies) through the Victorian Centre for Functional
Genomics (VCFG) to determine the molecular
mechanisms underlying EGFR transactivation.
To investigate this mechanism in cancer in more detail,
we will screen a number of human cancer cell lines for
expression of the AT1R using qRT-PCR, and following
on from this, test their propensity to transactivate RTKs
(such as EGFR) by stimulating the cells with AngII and
look at activation of signalling molecules by Western
blotting analysis. We will also introduce the receptor into
cancer cells using retroviral delivery, use FACS to enrich
the population of cells containing the ectopically
expressed receptor, and subsequently determine
whether overexpression of the AT1R increases the
likelihood of cells to transactivate RTKs. We will clone
the constitutively active mutant AT1R (N111G) receptor
into a retroviral vector and stably introduce this receptor
into untransformed, partially transformed or fully
transformed human cell lines to determine the effect of
the activated receptor on cellular growth and
proliferation, migration and invasion in an array of
different assays.
For more information about these projects contact:
Assoc. Prof. Ross Hannan, Tel: +61 3 9656 1747, Email:
ross.hannan@petermac.org
Dr. Amee George, Tel: +61 3 9656 3758, Email:
amee.george@petermac.org
A COMPLETELY NEW STRATEGY FOR THE
TREATMENT OF CANCER BASED ON DISRUPTION
OF RNA POLYMERASE I
Supervisors: Assoc. Prof. Ross Hannan, Dr Gretchen
Poortinga, Dr Nadine Hein, Dr Megan Bywater
Increased transcription of ribosomal RNA (rRNA) genes
(rDNA) by Pol I is a common feature of human cancer
but it’s contribution to the malignant phenotype until now
has remained unclear. To explore this we have
collaborated with Cylene Pharmaceuticals to develop
and test the world’s first small molecule inhibitors of Pol I
as therapeutics for cancer. We have shown that one
such inhibitor, CX-5461, induces a period of complete
disease remission in mice transplanted with Em-Myc
lymphomas (a model which recapitulates many of the
features of human Burkitt’s lymphoma), while
maintaining a normal B-cell population. Tumour specific
cell death in response to CX-5461 was rapid, occurring
well before ribosome levels decreased, due to p53dependent
induction of apoptosis as a consequence of
activation of a recently described nucleolar surveillance
pathway . We also observed similar responses in mouse
models of acute myeloid leukaemia (eg., AML1/ETO9a;
MLL/ENL). Encouraged by this data, we carried out a
preliminary survey of which types of human cancers best
respond to Pol I inhibition. Our data demonstrated that
CX-5461 significantly increased the anti-proliferative
capacity in human haematological tumour cell lines
compared to solid tumours dependent on the mutational
status of p53. Thus we hypothesise that haematological
malignancies have a unique nucleolar biology that render
them especially susceptible to activation of p53 and
apoptotic cell death following perturbations of ribosome
biogenesis. Thus we propose that CX-5461 and other
strategies that target Pol I transcription represent a novel
class of drugs to treat a broad range of human cancers
of haematological origin.
There are multiple projects available suitable for Hons
and PhD projects that will extend the intriguing data
outlined above to address the following specific aims; (i)
to determine whether the efficacy of CX-5461 in
transgenic models of lymphoma and leukaemia are
recapitulated in human hematological cancers and to
determine which subtypes of haematological cancers
best respond; (ii) to identify the molecular mechanism(s)
by which inhibition of Pol I transcription by CX-5461
selectively kills malignant B cells; (iii) to determine how
the therapeutic efficacy of CX-5461 compares to existing
therapeutic approaches and whether it has efficacy in
malignancies that have failed conventional therapy; (iv)
to determine the mechanisms underlying relapse to
inhibition of Pol I transcription; (v) to identify predictive
biomarkers of efficacy of CX-5461 in human
haematological cancers; (vi) to determine whether rDNA
class switching of rRNA genes underlies the sensitivity of
haematological malignancies to inhibition of Pol I and
whether class switching can serve as a predicative
marker for sensitivity to CX-5461. Methodologies: These
studies will employ a broad range research techniques
including but not limited to transgenic animal models of
malignancy xenograft studies; molecular biology;
chromatin biology; next gen sequencing; biochemistry;
protein chemistry; extensive cell culture approaches;
cellular signaling studies; immunofluroescence and in
situ hybridisation.
For more information about this project contact:
Assoc. Prof. Ross Hannan, Tel: +61 3 9656 1747, Email:
Ross.Hannan@petermac.org
r-CHROMATIN REMODELING DURNG MALIGNANT
TRANSFORMATION
Supervisors: Dr Elaine Sanij, Dr Gretchen Poortinga
The major focus of our work is in understanding the
mechanisms of regulation of ribosome biogenesis, and
protein translation and to determine how these
processes impact on differentiation and are corrupted in
tumour cells. This is a critical area of cancer research as
increasing evidence suggests that deregulation of mRNA
translation either at the level of ribosome biogenesis or
function is at least permissive, and may be directly
contributory to the etiology and progression of cancer.
However the molecular processes that regulate ribosome
biogenesis and translation are complex and their
relationship to cancer pathology is only just beginning to
be understood. Fundamental questions that our research
is attempting to address include: (1) does aberrant
regulation of components of the ribosome biogenesis
machinery directly contribute to the transformed
phenotype and is this due to the deregulation of total or
specific mRNA translation?; (2) which components of the
ribosome biogenesis machinery are deregulated in
cancer cells and what are the molecular mechanism(s)
25

esponsible for their deregulation?; and (3) do any of the
identified factors represent suitable targets for cancer
therapy? Our long-term goal is to develop novel
therapeutic approaches that target fundamental aspects
of cancer growth control and to translate these to the
clinic.
A typical human cell contains ~200 copies of the rRNA
genes arranged in tandemly repeated arrays located in
nucleolar organizing regions (NORs). Remarkably,
despite rRNA gene transcription being limiting for growth,
over 50% of the rRNA genes are believed to be
transcriptionally silent at any one time. The epigenetic
mechanisms controlling the activity status of individual
ribosomal genes and the reasons why a majority are
silenced in higher eukaryotes remain unresolved
questions. The prevailing model is that the relative
amounts of active and inactive ribosomal genes are
stably maintained and are not regulated in higher
eukaryotic cells. Contrary to this we have found that the
pool of active ribosomal genes is not static as previously
thought but decreases during terminal differentiation of
granulocytes, most likely due to decreased expression of
a Pol I transcription factor UBF. Moreover our
preliminary studies with a model of B-cell lymphoma
demonstrated that when a B-cell progresses towards
malignancy there is a dramatic reactivation of previously
pseudo-silent ribosomal genes that correlates with
increased UBF expression and UBF loading on the rRNA
genes. This project will examine the hypothesis that
alterations in the UBF expression and number of active
rRNA genes is an important first step in the overactivation
of ribosome biogenesis that is associated with
cell transformation. The study will focus on the Em-Myc
model of lymphoma and use genetic and epigenetic
approaches to modulate UBF levels in these malignant
cells to examine the consequences of manipulating
active rDNA for the development of lymphoma. Further
we will examine in detail the chromatin of the rDNA
repeats during transition from premalignacy to
malignancy in order to determine the epigenetic marks
and mechanisms responsible for the conversion of
pseudosilenced rDNA to active rDNA.
For more information about this project contact:
Dr Elaine Sanij, Tel: +61 3 9656 3758, Email:
elaine.sanij@petermac.org
Dr Gretchen Poortinga, Tel: +61 3 9656 1279, Email:
gretchen.poortinga@petermac.org
ROLE OF AP-1 TRANSCRIPTION FACTORS DURING
CANCER PROGRESSION
Supervisors: Dr Amardeep Dhillon, Assoc. Prof. Ross
Hannan
The spread of tumours by invasion and metastasis leads
to the destruction of vital body functions is the major
cause of mortality in many types of cancers. These
complex processes require tumour cells to modify gene
expression in order to adapt to new environments and
overcome physiological barriers maintaining tissue
homeostasis. The orchestration of these events is
mediated by transcription factors embedded within
specific oncogene or tumour suppressor networks
operating in the cell.
Activator Protein-1 (AP-1) transcription factors consist of
specific, context-dependent protein complexes formed
predominantly by members of the Fos (c-Fos, FosB, Fra-
1, Fra-1), Jun (c-Jun, JunB, JunD), ATF and MAF
families. They regulate gene expression in response to
numerous physiological (e.g. growth factors, cytokines)
and pathological (e.g. oncogenes, stresses) stimuli. They
also represent a key point of convergence for many
common cancer-associated signaling networks.
This project aims to identify direct targets and gene
expression programs regulated by AP-1 in metastatic
colorectal cancers. The work will involve a combination
of genomic analyses, bioinformatics, cell biological
approaches and analysis of patient tissue specimens.
This research is expected to provide new insights into
how the expression of genes required for the spread of
CRC is orchestrated, uncover gene expression
signatures predictive of CRC progression, and identify
new therapeutic targets to impede the progression of
aggressive forms of the disease.
For more information about this project contact:
Dr. Amardeep Dhillon, Tel: +61 3 9656 1279, Email:
Amardeep.Dhillon@petermac.org
Assoc. Prof. Ross Hannan, Tel: +61 3 9656 1747, Email:
Ross.Hannan@petermac.org
REGULATION OF TRANSCRIPTION BY AP-1
COMPLEXES IN CANCER CELLS
Supervisors: Dr Amardeep Dhillon, Assoc. Prof. Ross
Hannan
The progression of cancers involves dynamic changes in
gene expression, which is orchestrated by transcription
factors embedded within specific oncogene or tumour
suppressor networks. Neutralising the activities of these
transcription factors may therefore represent an
attractive strategy to impede cancer progression. Our
long-term goal is to develop this concept and test its
clinical potential.
The Activator Protein-1 (AP-1) transcription factor
complex is a downstream target of many common
cancer-associated signaling networks. It consists of a
context-specific dimeric core formed predominantly by
members of the Fos (c-Fos, FosB, Fra-1, Fra-1), Jun (c-
Jun, JunB, JunD), ATF and MAF families. These dimers
bind to DNA and regulate gene expression in response
to numerous physiological (e.g. growth factors,
cytokines) and pathological (e.g. oncogenes, stresses)
stimuli.
We have recently used proteomics to examine the nature
of AP-1 complexes required for the expression of key
genes involved in tumour progression. This project aims
to unravel the mechanism by which the AP-1 complexes
regulate transcription of these genes. The work will
involve functional characterisation of candidate AP-1associated
chromatin remodeling factors and
components of the RNA polymerase II complex that we
have recently identified. In addition, we will develop new
proteomic approaches to characterise native
transcription factor complexes, which we will use to
determine the molecular composition of different AP-1
dimeric complexes in tumour cells.
For more information about this project contact:
Dr. Amardeep Dhillon, Tel: +61 3 9656 1279, Email:
Amardeep.Dhillon@petermac.org
Assoc. Prof. Ross Hannan, Tel: +61 3 9656 1747, Email:
Ross.Hannan@petermac.org
26

GENOME WIDE LOSS RNA INTERFERENCE
SCREENS TO IDENTIFY GENES MODULATE rDNA
TRANSCRIPTION AND CELL SIZE
Supervisors: Assoc. Prof. Ross Hannan, Assoc., Prof.
Rick Pearson, Dr Kate Hannan.
The problem was most succinctly put in a recent review
“Size is a fundamental attribute impacting cellular design,
fitness, and function. Size homeostasis requires a
doubling of cell mass with each division. In yeast,
division is delayed until a critical size has been achieved.
In metazoans, cell cycles can be actively coupled to
growth, but in certain cell types extracellular signals may
independently induce growth and division. Despite a long
history of study, the fascinating mechanisms that control
cell size have resisted molecular genetic insight.”
We plan to use RNAi to functionally screen the entire
human genome to identify genes that couple growth to
proliferation and which rDNA transcription and regulate
cell size. We have recently established the Victorian
Centre for Functional Genomics (VCFG), a facility
accessible to all Australian medical researchers that
uses two complimentary approaches to perform
functional genome wide loss of function screens. Firstly it
utilizes high-throughput short hairpin microRNAi (shRNAmir)
libraries delivered by pools of lentivirus for largescale
functional genomic screens. This technology is the
first of its kind in Australia and offers the unique
opportunity to perform genome-wide loss of function
screens. However the system does have limitations that
constrain the scope of screens that can be performed.
As such, we also use Dharmacon siRNA libraries
allowing knockdown of a single gene in a single well of a
tissue culture plate serve as complementary platforms to
that already available within the VCFG. Such a
complementary system incorporating robotics and
integrated high content, fluorescence-based image
analysis to allow high throughput screening is warranted
if we are to develop a truly world class facility that
provides Australian researchers with unparalleled access
to cutting edge whole genome knockdown technologies.
We plan to use the Dharmacon RNAi library to
functionally screen the entire human genome to identify
genes that couple growth to proliferation and which
regulate rDNA transcription and cell size. Two types of
screens will be employed:
(i) Screens for regulators of Pol I transcription based
on a 45S reporter; This screen is based on the
observation that despite a relatively good understanding
of a few core components of the Pol I transcription
apparatus, for the large part the signalling pathways and
downstream protein complexes that regulate mammalian
rDNA transcription are poorly defined. To identify
regulators of rDNA transcription, stable cell lines coexpressing
the Cherry red expression vector (pmCherry-
1, Clontech) and Pol1shRNAi-Red knockdown construct
will be selected by FACS for clones that exhibit half
maximal red florescence (HEK-PolI-shRNAI-Red Med )
compared to control cells expressing the cherry red
vector alone. Such clones when screened with the
shRNA mir library will allow for the identification of
repressors (increased red fluorescence) or activators
(reduced red fluorescence) of Pol I transcription.
(ii) Screens that re-couple growth to proliferation:
This screen is based on the following observations;
some growth factors / genes are able to drive increased
proliferation, that is to say they drive growth which leads
to cells that cycle faster at the same size as the parental
cells. Another set of growth factors / genes drive
increased growth which doesn’t lead to increased
proliferation but rather larger cells that divide either at the
same rate or a slower rate than the parental cells. Why
for this later group the increased growth doesn’t lead to
increased proliferation is not clear but it suggests that
additional signals are needed. We have found that overexpression
of AKT increases cell growth in the
immortalised human fibroblasts (BJ cells) without driving
proliferation, resulting in a large cell phenotype. In
contrast, overexpression of AKT in transformed BJs
leads to increased proliferation at a normal size. We
hypothesise that in tumour cells, additional mutations are
required to convert increased PI3K/AKTdependentsignalling
into a proliferative advantage. To
address this hypothesis we will use a genome-wide
screen using shRNA mirs and monitor cell size to identify
genes required to recouple the AKT large size phenotype
to a proliferative advantage.
(iii) Screens to identify signals that couple Pol I
transcription to the cell cycle and senescence. We
are currently collaborating with Cylene Pharmaceuticals
to test a range of novel small molecule Pol I inhibitors
with the ultimate aim of using these drugs as clinical
interventions to regress cancer. We have demonstrated
that CX-5461 (SL-1 inhibitor) induces cell cycle arrest at
G1 and G2 and potentially senescence in BJ fibroblasts.
In this study we will use the Dharmacon siRNA libraries
to functionally screen the human genome for genes that
confer resistance to CX-5461 induced cell cycle arrest
and senescence. These studies will provide important
insights into the signaling pathways that emanated form
the nucleolus upon inactivation of Pol I transcription.
They will also identify genes that confer resistance to
CX-5461 which will be clinically relevant if Pol I inhibitors
are to be used for therapeutic intervention in cancer.
For more information about this project contact:
Dr Kate Hannan, Tel: +61 3 9656 1279, Email:
kate.hannan@petermac.org
USING STRUCTURAL BIOLOGY APPROACHES TO
UNDERSTAND THE MOLECULAR MECHANISMS OF
NEW GENERATION RNA POLYMERASE I
INHIBITORS TO TREAT CANCER.
Supervisors: Assoc. Prof. Ross Hannan, Dr Bill
McKinstry
Transcription of the ribosomal RNA (rRNA) genes
(rDNA) by the dedicated RNA Polymerase I (Pol I) gives
rise to the 18S and 28S rRNAs, which along with the 5S
rRNA form the nucleic acid backbone of ribosomes. The
abundance and activity of ribosomes dictates the protein
synthetic capacity of a cell and thus ribosome biogenesis
constitutes a fundamental rate-limiting step for growth
and proliferation. Perhaps not surprisingly dysregulation
of ribosome biogenesis is a consistent feature of human
cancer. However, its contribution to the malignant
phenotype until now has remained unclear. To directly
test whether rRNA synthesis might represent a novel
target for cancer therapy we have collaborated with
Cylene Pharmaceuticals to develop and assess the
world¹s first small molecule inhibitors of rDNA
transcription by Pol I. One such inhibitor CX-5461
(Drygin et al Cancer Res 2010) , is orally available and
inhibits Pol I-driven transcription in the low nanomolar
range by preventing the association of the Pol I-specific
transcription initiation selectivity factor SL-1 with the
rDNA promoter, exhibiting greater than 200-fold
selectivity relative to the inhibition of Pol II-driven
transcription.
27

In order to better understand the mechanism of action of
CX-5461 and to generate 2nd generation inhibitors of Pol
I transcription, we propose to determine the crystal
structure of SL-1 alone and in complex with CX-5461.
To do this we will use high throughput cloning
approaches to produce multiple expression constructs of
SL-1 and combine this with parallel expression and
purification studies to maximise the likelihood of
obtaining soluble SL-1 protein for crystallisation trials.
Crystallisation trials will be performed at CSIRO’s
Collaborative Crystallisation Centre, which provides
state-of-the-art macromolecular crystallisation facilities
using high throughput robotics and nano-drop technology
to screen 100’s of different crystallisation conditions
using minimal amounts of protein. X-ray diffraction
studies on the crystals will be undertaken at the
Australian synchrotron, and diffraction data processed by
standard crystallographic programs. The structure of
CX-5461 bound to SL-1 will provide us the blueprint to
develop 2 nd generation inhibitors of Pol1 transcription
using libraries of drug fragments and surface plasmon
resonance, crystallography and NMR technologies.
This will be a collaborative project between Ross
Hannan at the Peter Mac, and Bill McKinstry at the
CSIRO Materials Science and Engineering, Parkville
Melbourne.
For more information about this project contact:
Assoc. Prof. Ross Hannan , Tel: +61 3 9656 1747,
Email: Ross.Hannan@petermac.org
Dr. Bill McKinstry, Tel: +61 3 9662 7283, Email:
bill.mckinstry@csiro.au
EPIGENETIC REGULATION OF POL I
TRANSCRIPTION BY UBF.
Supervisors: Assoc. Prof. Ross Hannan, and Dr. Elaine
Sanij
The RNA Polymerase-1 specific nucleolar transcription
factor UBF belongs to the sequence non-specific class of
HMG1-box proteins. Through DNA binding of its HMG
boxes, UBF is thought to induce a nucleosome -like
structure termed the “enhancesome” which is thought to
be essential for the assembly of the preinitiation complex
(PIC) at the promoters of ribosomal genes (rDNA). The
important role ascribed to UBF in regulation of rDNA
transcription is reflected by observations that key
growth/proliferation regulatory pathways PI3K/mTOR/S6,
Ras/Raf/ERK, c-MYC and cell cycle control, converge on
this factor. We and others have shown that UBF DNA
binding in vivo is not restricted to the promoter but is also
found on multiple sites across the entire transcribed
rDNA repeat suggesting roles for UBF in addition to, or
other than, PIC formation. One interpretation of this data
is that UBF binding to high affinity sites across the active
chromatin structure of rDNA, ie UBF modulates rchromatin.
We have begun studies to examine this
possibility.
We have used RNAi to deplete UBF in proliferating cells
and have examined the consequence on rDNA
transcription, the structure of the nucleoli, and the site of
rDNA transcription. Transient transfection of NIH3T3
cells with siRNA against UBF reduced endogenous
levels of UBF by over 90%. Chromatin
immunoprecipitation (ChIP) revealed that depletion of
UBF resulted in a significant decrease of UBF bound
across the rDNA repeat and changes in the relative
levels of acetylated histone associated with the rDNA.
Quantitative AgNOR staining using transmission electron
microscopy demonstrated a >50% decrease in silver
staining of the fibrillar centres (FC) of the nucleolus.
Thus, our data suggest that depletion of UBF leads to a
decrease in the number of transcriptionally competent
ribosomal genes. This conclusion was supported from
the results of psoralen cross-linking experiments.
Paradoxically the 70% reduction in transcribed genes
leads to only a 20% decrease in rDNA transcription
suggesting that transcription on the remaining active
genes is increased. There is a precedent for this in
yeast. Interestingly knockdown of UBF using an inducible
microRNA approach induced a G1-S cell cycle block
before changes in rRNA levels or translation were
observed supporting recent studies suggesting that
rDNA transcription is a check point for G1-S progression.
Results from microarray experiments examining the
effect of acute UBF depletion on the cellular
transcriptome suggest that UBF has roles outside Pol I
transcription.
(i) Epigenetic Mechanism of UBF action: To define
the effect of decreased UBF expression on the rchromatin
status and Pol I transcription. A particularly
important question to come from our studies is whether
active rDNA repeats are nucleosomal or not. Data from
yeast suggest they are not. Mammalian studies are
unclear. Our data suggest they are nucleosomal, or at
least associated with histones, perhaps in a lexisomal
state. Experiments in collaboration with Sui Huang
(Northwestern Medical School, USA) and Lawrence
Rothblum (Oklahoma Medical School, USA) will explore
this question further using a version of UBF targeted via
a lac repressor fusion protein to a heterochromatic,
amplified chromosome region containing lac operator
repeats. We have also developed a UBF rescue assay
whereby we can rescue UBF RNAi mediated knockdown
with RNAi resistant versions of UBF. This will allow us to
undertake a detailed structure function analysis of UBF
to differentiate the domains in this factor required for
gene activation and chromatin remodeling etc. Another
interesting related project underway is to examine the
Pol I independent roles of UBF by microarray and ChIP-
Sequencing. An additional long-term experiment will be
crystallize UBF1 and UBF2 on the rDNA to obtain
structural data to explain their differing abilities to
regulate chromatin.
Cell culture studies combined with inducible viral
mediated UBF RNAi and over expression, structure
function analysis, epigenetic modifications at the rDNA
locus both biochemically (ChIP, ChIP-chop, C3 assays,
methylation), and cell biologically (confocal IF, FISH,
Fibre-FISH etc).
(ii) Epigenetic regulation of Pol I transcription during
differentiation and development: To determine
whether changes in UBF expression are a
physiologically relevant mechanism by which Pol I
transcription is regulated in mammalian cells and
whether the decreased expression of UBF is a
prerequisite for loss of rDNA transcription during
differentiation and quiescence. Specifically, we have
demonstrated that UBF expression drops dramatically
during differentiation of skeletal muscle, cardiac muscle,
and more recently in granulocytes which correlates with
decreased rDNA transcription. We will examine if the
loss of UBF during differentiation also leads to a
decreased number of active genes and altered rchromatin.
We will determine whether enforced
expression of UBF can delay or block the down
regulation of rDNA transcription and differentiation. We
will examine whether enforced expression of UBF in
28

differentiated cells (either cardiomycytes or differentiated
granulocytes) can lead to alterations in r-chromatin and
the number of transcriptionally competent genes. We
have developed conditional KO of UBF with our
collaborator Tom Moss (Quebec, Canada) and we are
making inducible transgenic RNAi approaches. This will
allow us to look at the consequences of manipulating
UBF levels and number of active genes during
development, in genetic mouse models of cancer and in
embryonic stem cells (the later being of considerable
interest as there is considerable anecdotal evidence that
Pol I transcription is wired differently in stem cells).
For more information about this project contact:
Assoc. Prof. Ross Hannan, Tel: +61 3 9656 1747, Email:
Ross.Hannan@petermac.org
Dr Elaine Sanij, Tel: +61 3 9656 3758, Email:
elaine.sanij@petermac.org
THE UPSTREAM BINDING FACTOR UBF
REGULATES GENOME STABILITY
Supervisors: Assoc. Prof. Ross Hannan, Dr. Elaine Sanij
RNA Polymerase I (Pol I) transcribes the 200 copies of
ribosomal DNA (rDNA) to produce the 45S precursor of
the 18S, 5.8S and 28S ribosomal RNAs (rRNAs), which
together with the 5S rRNA form the RNA backbone of
the ribosome. Initiation of rDNA transcription requires the
binding of the Selectivity Factor (SL1) and the Upstream
Binding Factor (UBF), which together form the
preinitiation complex at the rDNA promoter, facilitating
the recruitment of Pol I.
In addition to transcription initiation, UBF plays an
equally important role in regulating promoter escape,
transcription elongation and maintenance of the open
chromatin structure required for transcription.
Interestingly, depletion of UBF does not affect the rate of
rDNA transcription – a 70-80% reduction in UBF equates
to a modest 15% reduction in rRNA synthesis (Sanij, et
al. 2008). Despite the relatively unchanged
transcriptional ouput, cells eventually enter cell cycle
arrest and exhibit chromosomal aberrations, nucleolar
disorganization and senescence, suggesting that UBF
has additional non-nucleolar functions within the cell that,
when perturbed, lead to defects in cell cycle progression.
Chromatin Immunoprecipitation (ChIP) sequencing was
performed to identify novel UBF target genes and the
results
 demonstrated
 UBF
 enrichment
 at
 2212
 genomic
regions within 10kb of known Polymerase II (Pol II)
transcription start sites (TSS). To determine if UBF might
directly regulate transcription of the identified genes, we
performed expression array analysis in control and UBF
depleted cells. Gene ontology analysis was performed to
identify the molecular functions of genes whose
expression significantly changed following UBF
knockdown and were also bound by UBF within 200 bp
of their TSS. The analysis demonstrated significant
overrepresentation of genes belonging nucleosome
organization and DNA packaging, chromatin assembly
and regulation of transcription, chromatin condensation
and G2-M cell cycle progression, and DNA repair. In
addition, we have detected increased relocalisation of
UBF from the nucleoli into the nucleoplasm following
inhibition of Pol I activity, which correlates with increased
UBF enrichment at a subset of these Pol II genes. We
therefore hypothesize that UBF plays a global role in the
regulation of chromatin through positive transcriptional
regulation of histones, histone assembly factors and
DNA repair genes. This project will address the following
specific aims:
1: to define the molecular mechanism by which UBF
modulates Pol II target gene expression and determine
how UBF is selectively recruited to specific Pol II
transcribed loci.
2: to explore the biological relevance of UBF's role in Pol
II gene transcription by addressing the hypothesis that
UBF is a dual Pol I and Pol II transcription factor which
functions to allow cells to sense changes in Pol I
transcription and to adapt appropriately through inducing
global modifications in chromatin.
For more information about this project contact:
Assoc. Prof. Ross Hannan, Tel: +61 3 9656 1747, Email:
Ross.Hannan@petermac.org
Dr Elaine Sanij, Tel: +61 3 9656 3758, Email:
elaine.sanij@petermac.org
COOPERATION BETWEEN PI3K/AKT/mTOR AND
MYC REGULATES RIBOSOME BIOGENEIS AND
GROWTH DURING CANCER
Supervisors: Assoc Prof. Rick Pearson, Dr Kate Hannan,
Assoc Prof. Ross Hannan
The molecular mechanism(s) that activate Pol I
transcription are still a matter for debate. Both direct
activation of Pol I transcription by growth factor
dependent kinases (eg., ERK, PI3K and JNK)
interaction with oncogenes and tumor suppressors (eg.,
p53, Rb, Myc), and regulation by cell cycle kinases
(CDK2/4/6) have been implicated in the process .
Moreover, both initiation and elongation steps have been
proposed to be rate limiting.
We have shown that cells blocked in the cell cycle
through over expression of p27 fail to down regulated
rDNA transcription demonstrating, at least in this model
system, that growth factor dependent signaling is
dispensable for high rates of Pol I transcription. This is in
direct odds with the prevailing models for Pol I activation.
One possibility is that direct growth factor activation of
Pol I transcription factors is necessary to stimulate rDNA
transcription in Go cells but as cell progress past start or
during the ongoing cell cycle dependent kinases may
play the prominent role in regulating rDNA transcription.
Moreover we found that acute, 3 hr removal of serum
from exponentially growing NIH3T3 cells inhibited 45S
synthesis by 70% without changing Pol I loading
suggesting elongation and/or processing had been
preferentially inhibited. Sustained removal of serum for
greater than 24hrs, was required to also reduce Pol I
loading and thus initiation. Serum stimulation of serum
starved cells, led to a slow recovery of rDNA
transcription which did not reach maximal levels until 6-
12hrs following stimulation, which correlated
quantitatively and temporally with increased Pol I
loading. Consistent with this, over expression of
recombinant Rrn3 was able to increase Pol I loading and
45S synthesis above serum stimulated levels for up to
3hrs following serum restimulation but not at later time
points. Together these data suggest that as cells move
out of G0 arrest into G1, initiation is limiting for 45S
synthesis. However elongation and or processing quickly
become rate limiting at later stages. These data
demonstrate in exponentially growing cells Pol I
elongation and or rRNA processing are major targets for
growth factor signalling to ribosome biogenesis.
With the advent of inducible RNAi approaches to rapidly
silence the above kinases, the availability of specific
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inhibitors for cyclin-dependent growth factor kinases, and
MEFS null for many of the above genes, it is now
possible to take a holistic approach to elucidate the
mechanism of activation and maintenance of Pol I
transcription in mammalian cells. We will use a
combination of the above approaches to define the
factors that control Pol I transcription elongation and
rRNA processing in response to growth factor
manipulation. As part of this project we will create novel
molecular beacons to measure by Pol I transcription in
individual cells by florescence microscopy, which will
allow for the first time to follow rDNA transcription during
the ongoing cell cycle and how it responds to inhibitors of
various signaling pathways.
For more information about this project contact:
Dr Kate Hannan, Tel: +61 3 9656 1279, Email:
kate.hannan@petermac.org
Assoc. Prof. Rick Pearson, Tel: +61 3 9656 1247, Email:
Rick.Pearson@petermac.org
MECHANISMS OF RESISTANCE TO THE B-RAF
INHIBITOR DRUG VEMURAFENIB
Supervisors: Dr Petranel Ferrao and A/Pr Grant
McArthur
Vemurafenib (previously known as PLX4032) is a
specific inhibitor of the mutant B-Raf V600E protein recently
approved by the FDA (USA) for the treatment of
metastatic melanoma. Dramatic responses to
Vemurafenib were observed in patients with metastatic
melanoma expressing B-Raf V600E during the clinical trials
conducted at Peter Mac and other centres around the
world. However, some patients acquire resistance to the
drug. The main mechanism of resistance has been
reported to be via re-activation of the MAPK signalling
pathway either upstream or downstream of Raf 1 .
We have assessed the ability of various proteins
commonly expressed and/or mutated in melanoma, to
confer resistance to Vemurafenib in B-Raf V600E
melanoma cells. This project will investigate the factors
determining the ability of various genes to confer
resistance in melanoma, assessing expression of the
identified proteins able to confer resistance in clinical
samples from melanoma patients showing resistance.
The efficacy of selected combinational therapies with
Vemurafenib to overcome resistance mediated by
specific oncoproteins, will also be assessed. The results
will determine the potential benefit of combination
therapies in the treatment of metastatic melanoma, in an
attempt to avert or overcome drug resistance.
1 Nazarian et al Nature 2010 doi:10.1038/nature09626;
Johannessen et al Nature 2010 doi:10.1038/nature09627;
Wagle et al JCO 2011 DOI: 10.1200/JCO.2010.33.2312
For more information about this project contact:
Dr Petranel Ferrao. Tel: 03 9656 1806. Email:
petranel.ferrao@petermac.org
THERAPEUTIC TARGETING OF THE PI3K PATHWAY
IN ENDOMETRIAL AND OVARIAN CANCER.
The oncogenic PI3K/mTOR pathway is commonly
deregulated in human cancers and novel therapies
targeting this pathway is an exciting focus of many
clinical trials. We are interested in using genetically
engineered mouse models to understand how PI3K
pathway mutations contribute to tumourigenesis; and
then utilizing such tumour models in pre-clinical
evaluation of novel therapeutics.
Endometrial and ovarian cancer commonly exhibit
mutations in multiple PI3K pathway genes, including the
oncogene PIK3CA and tumour suppressor PTEN,
making these tumour types potentially susceptible to
PI3K pathway inhibitors. As such, endometrial cancer
patients are currently being treated in human clinical
trials using mTOR inhibitors. Our lab is currently in
various stages of development of both endometrial and
ovarian cancer mouse models via tissue specific genetic
manipulation of these PI3K pathway components.
This project will 1) explore the role of PI3K pathway
mutations in the development of disease in one of these
gynecological cancer models and/or 2) evaluate the in
vivo consequences of PI3K pathway inhibition using
novel targeted therapeutics in tumour-bearing mice.
These in vivo experiments may be complemented with
in vitro cell culture analysis of drug efficacy in human
cancer cell lines – analyzing drug responses such as
perturbation of pathway signaling, cell cycle, cell death
or senescence.
The project will use analysis of mouse models of cancer
and the preclinical evaluation of targeted therapies, and
ex vivo analysis of mutant tissues and/or tumours,
immunohistochemistry, western blotting and microscopy;
and in vitro cell culture and drug response analysis.
For more information about this project contact:
Dr Kathryn Kinross. Tel: 03 9656 1806. Email:
kathryn.kinross@petermac.org
CHK INHIBITOR THERAPEUTICS IN THE
TREATMENT OF VARIOUS MALIGNANCIES
Supervisors: Dr Petranel Ferrao and A/Pr Grant
McArthur
Several specific inhibitors of the cell cycle checkpoint
kinase CHK1 are currently in clinical trials. These drugs
were originally developed for use in combination with
DNA damaging agents such as conventional
chemotherapeutic agents or irradiation. Our recent
studies have demonstrated that CHK inhibitors are
effective as single agent therapeutics in MYC-driven
lymphoma 1 . We are currently validating specific
predictors of sensitivity to CHK inhibitor drugs in various
other malignancies. Recent studies suggest that CHK1 is
a potential target for therapy in Acute Myeloid Leukaemia
(AML) and paediatric neuroblastoma.
There are two separate projects:
1. To assess the efficacy of several CHK1 inhibitor
drugs in leukaemia, using in vitro drug response assays
on human AML cell lines and in vivo therapy experiments
in spontaneous mouse models of leukaemia.
2. To assess the efficacy of specific CHK1 inhibitor
drugs in vitro on Myc driven human and murine
neuroblastoma cell lines, and in a MYC-driven murine
model of neuroblastoma in vivo.
The results of these projects will determine the potential
benefit of CHK inhibitors in the treatment of two
malignancies that have poor prognosis following
conventional therapies currently used.
1 Ferrao et al Oncogene 2011 adv online pub
doi:10.1038/onc.2011.358
For more information about this project contact:
Dr Petranel Ferrao, Tel: +61 3 9656 1806, Email:
petranel.ferrao@petermac.org
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CLINICAL RESEARCH
Clinical research at Peter Mac is structured to reflect the multidisciplinary teams that work together to care for
our patients. Clinicians from various specialties work together with allied health and supportive care staff on
clinical research projects with a disease-specific focus. In addition to the tumour stream clinical groups
outlined earlier in this document, research in the clinical services are structured into the areas outlined below.
SURGICAL ONCOLOGY CLINICAL RESEARCH
For clinically focused Surgical Oncology research opportunities, contact Executive Director of Cancer Surgery:
Assoc. Prof. Alexander (Sandy) Heriot. Email Alexander.heriot@petermac.org
RADIATION ONCOLOGY RESEARCH
For clinically focused Radiation Oncology research opportunities, contact Executive Director of Radiation Oncology:
Prof. Gillian Duchesne. Email gillian.duchesne@petermac.org
SUPPORTIVE CARE RESEARCH
For clinically focused Supportive Care research opportunities, contact:
Assoc. Prof. Penny Schofield. Email penelope.schofield@petermac.org
HAEMATOLOGY RESEARCH
For clinically focused Haematology research opportunities, contact:
Prof. John Seymour. Email john.seymour@petermac.org
MEDICAL ONCOLOGY RESEARCH
For clinically focused Medical Oncology research opportunities, contact:
Assoc. Prof. Danny Rischin. Email danny.rischin@petermac.org
NURSING AND RESEARCH
For clinically focused Medical Oncology research opportunities, contact:
Assoc. Prof. Danny Rischin. Email danny.rischin@petermac.org
FAMILIAL CANCER CENTRE
For clinically focused familial cancer research opportunities, contact:
Dr Gillian Mitchell. Email gillian.mitchell@petermac.org
CONTACT AND FURTHER INFORMATION
VISIT US ON THE WEB FOR MORE INFORMATION ABOUT:
Our research, our people, annual reports, the laboratories and research facilities, our history, publications,
where we are and maps of how to find Peter Mac.
http://www.petermac.org/research
PETER MACCALLUM CANCER CENTRE
RESEARCH DIVISION
Smorgan Family Building
St Andrews Place, East Melbourne
VIC 3002
Postal Address:
Locked Bag 1 A’Beckett Street, VIC 8006
Phone: +61 3 9656 1238
Fax: +61 3 9656 1411
EDUCATION AND COMMUNICATIONS
COORDINATOR
Dr Caroline Owen
Email: caroline.owen@petermac.org
Phone: +61 3 9656 1930
http://www.petermac.org/research/EducationCareers
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