garvan phd_projects_2013

Postgraduate Studies at the Garvan 01Why Choose the Garvan 01Garvan PhD Open Day 21st of August 2012 01

Cancer Research Program 02Colon Cancer Genetics & Biology Group 02Ovarian Cancer Group 03Tyrosine Kinase Signalling Networks in Human Cancers 04Mitotic Control Group 05Pancreatic Carcinogenesis Group 05Epigenetic Laboratory Cancer Program 06Cancer Bioinformatics Group 10

Immunology Research Program 11B Cell Biology Laboratory 11Diabetes & Transcription Factors Group 12

Diabetes & Obesity Research Program 13Bioenergetics in Disease 13Regulation of Body Composition & Glucose Homeostasis

by the Adaptor Protein Grb10 14Beta Cell Replacement Therapy 14Cooper Group - Neurodegeneration,

Cell & Molecular Biology, Genetics 15

Neuroscience Research Program 16Eating Disorders Group 16Inter-organ Signalling: A new level of regulatory control 19Bird and Swine Flu, Parkinson's Disease, Chronic Pain 21Neurodegenerative Disorders Research 23

Hearing Research Unit 24

Osteoporosis & Bone Biology Research Program 25Genetics and Epidemiology Group 26

Garvan Bioinformatics 29

How to Apply 30

Prof John Mattick Executive Director

01POSTGRADUATE STUDIES AT THE GARVAN

In partnership with the University of New South Wales, Garvan Institute provides a learning andteaching environment of excellence for PhD students who are looking forward to being part of thenext generation of great medical researchers.

As one of the world's leading medical research institutes with programs in cancer, diabetes and obesity,immunology, neuroscience and osteoporosis, Garvan is playing a leadership role in translating theamazing developments in modern biomedical research into real improvements in health care andquality of life. The joint initiative with St Vincent's Hospital in establishing The Kinghorn Cancer Centrewill enable Garvan's research discoveries to make a real difference in the prevention and treatment ofthis devastating disorder. This however is only the beginning - the future for Garvan will be to ensurethat this paradigm is expanded to all of our research areas.

A focus on the promise of genomic medicine and new technologies such as next generationsequencing, and a complementary depth of expertise in cell biology, proteomics, systems biology,bioinformatics, epigenetics and translational research together make Garvan one of the most excitingplaces to be doing medical research right now and in the future.

As well as ensuring the development of scientific knowledge and skills for the future, postgraduatescholars undertaking their PhD at Garvan are valued as important contributors to the life of theInstitute as a whole.

We look forward to you joining us.

Why Choose the Garvan_ We offer a competitive salary top-up on

eligible scholarships_ The Garvan boasts state-of-the-art research

facilities which incorporate a range of cutting-edge equipment and expertise

_ Students at Garvan (SAG), the studentrepresentative group within the GarvanInstitute provides both academic support andsocial activities in our off-campusenvironment

If you would like to find out more about thefantastic opportunities that doing your PhD atGarvan Institute can provide, please [email protected] or visitwww.garvan.org.au/education

Garvan PhD Open Day 21st of August 2012 The PhD Open Day will take place on Tuesday21st of August from 2.00 pm to 6.00 pm.

It will provide the opportunity to meetprospective supervisors, current PhD studentsand view our state-of-the art facilities. Pleaseregister your attendance athttp://bit.ly/PhDopenday.

Outside of this period, you may contact specificresearchers directly or visitwww.garvan.org.au/education for furtherinformation.

Prof Rob SutherlandCancer Research Program Leader

CANCER RESEARCH PROGRAM02

Colon Cancer Genetics and Biology GroupHow can an arthritis drug cause colon cancer in themouse? Dissecting the origins of carcinogenesis.

Project 1We have made the unexpected discovery that anarthritis drug sulindac that is also used to preventcolon cancer in people with high-risk genes, canactually cause cancer in the mouse. Sulindac hasopposite effects in different parts of the mousecolon - either preventing or causing cancer. Wehave shown that sulindac triggers a molecularpathway in the mouse that may be informative forunderstanding how colon cancer develops in humans.

Project 2We have discovered the importance of the MCC('Mutated in Colorectal Cancer') gene silencing inthe development - and potentially treatment - ofcolon cancer. We have identified new biologicalfunctions for this gene, including a role in the DNAdamage response. We now want to pursue thesefunctions further in a model that is relevant for thedisease in humans, our newly engineered MCCknockout mouse, which allows us to determine thefactors that are important in initiating andpromoting cancer.

These two major findings have provided manydifferent avenues for further research. The projectscan be tailored to suit the expertise and interests ofthe PhD candidate - ranging from cell culturemodels to sulindac and the knockout mouse.

Supervisor: A/Prof Maija Kohonen-CorishColon Cancer Genetics and Biology GroupE: [email protected]: 02 9295 8336

References1. Kohonen-Corish MR, Sigglekow ND, et al 2007. Promoter

methylation of the mutated in colorectal cancer gene is a frequentearly event in colorectal cancer. Oncogene 26:4435-41.

2. Mladenova D, Daniel J, Dahlstrom J, Bean E, Gupta R, Pickford, R,Currey N, Musgrove EA, Kohonen-Corish M. 2011. The NSAIDSulindac is chemopreventive in the mouse distal colon butcarcinogenic in the proximal colon. Gut 60:350-360

4. Pangon L, Sigglekow ND, Larance M, Al-Sohaily S, Mladenova D,Selinger C, Musgrove EA, Kohonen-Corish MRJ. 2010. 'Mutated incolorectal cancer' (MCC) is a novel target of the UV-induced DNAdamage response. Genes & Cancer 1:917-926

The Cancer Research Program at the Garvan Institute is the largest program at the Garvan and one of themost highly regarded cancer research teams in Australia and internationally. With complementary skills incancer genomics, cancer epigenomics, cancer molecular and cellular biology, cancer biomarker andtherapeutic target identification & validation and translational research, the program is focussed onunderstanding the causes of and developing new diagnostic, prognostic treatment and prevention strategiesfor the most commonly diagnosed and most lethal cancers including breast, prostate, pancreatic, colorectal,lung, and ovarian. Program Head Prof Sutherland, AO, FAA is a leader in molecular oncology and thepathophysiology of breast and prostate cancers, with over 350 primary publications in top rankingmultidisciplinary and specialist journals. Among the many successful PhD graduates are Directors of majorresearch institutes and academic departments, professorial heads of independent research groups andclinical units, and recipients of prestigious NHMRC and ARC Fellowships.

03CANCER RESEARCH PROGRAM

Ovarian Cancer GroupOvarian cancer is the most lethal gynaecologicalcancer. Every year in Australia, approximately 1200women are diagnosed with ovarian cancer and 800women die from the disease. The poor prognosis forwomen with ovarian cancer is mainly due to aninability to detect the disease at an early stage,before the cancer has spread. Indeed, over 75% ofovarian cancers are diagnosed at an advancedstage, when the 5-year survival rate is 20%. Inaddition, this poor prognosis is due in part to thedevelopment of chemotherapy resistance in womenfollowing surgery and several rounds of treatment. The Ovarian Cancer Research Group at the GarvanInstitute focuses on 3 main projects:

_ Characterisation of novel therapeutic targets inthe ovarian tumour microenvironment;

_ Development of a blood-based test for DNAmethylation as an indication of high-grade serousovarian cancer in high-risk women

_ Evaluation of biomarkers of response tochemotherapy in treated women diagnosed withovarian cancer

Available projects include:

Project 1Evaluation of TLE as a biomarker for response totaxane-based chemotherapy in ovarian cancer.

The standard ovarian cancer treatment includessurgery followed by platinum/taxane combinationchemotherapy. While a majority of patients initiallyrespond to this regimen, 75% of treated womeneventually relapse. Thus it is imperative that weidentify biomarkers that can predict women whoare likely to respond to treatment, therebysignificantly improving patient management. Wehave demonstrated that transducin-like enhancer ofsplit 3 (TLE3) expression is associated withprogression-free survival in taxane-treated ovariancancer patients. In our study, TLE3 expression wasassociated with a favourable outcome only inpatients who had received a taxane as part of theirtreatment regimen. These findings warrant anindependent evaluation of TLE3 as a potentialtherapeutic response marker for taxane-basedchemotherapy in ovarian cancer. Studies are alsonecessary to determine whether and by whatmechanisms TLE3 may serve as a functionally-based biomarker in determining response.

Project 2Effect of cMET pathway and its inhibitor INC280in ovarian cancer.

cMet, a receptor tyrosine Kinase, and its ligandHGF are both mis-regulated in ovarian cancer, withhigher expression being linked to poorer prognosis.Both HGF and cMET have been shown to enhancecell migration, adhesion and proliferation in cancercells. Inhibitors of receptor tyrosine kinases(including cMET) have been shown to be effectiveagainst ovarian cancer, thereby making itimperative to examine new therapeutic agentssuch as INC280. We hypothesize that targetingcMET activation is likely a useful therapeutic toolin ovarian cancer. We propose to examine theeffect of HGF, cMET and the cMET inhibitorINC280 on ovarian cancer growth and metastasisin ovarian cancer cell lines and in vivo models.

Supervisor: Dr Goli SamimiOvarian Cancer GroupE: [email protected]: 02 9295 8362

References1. Samimi, G., B. Z. Ring, et al. (2012). "TLE3 Expression Is

Associated with Sensitivity to Taxane Treatment in OvarianCarcinoma." Cancer Epidemiol Biomarkers Prev 21(2): 273-279.

2. Montavon, C., B. S. Gloss, et al. (2012). "Prognostic anddiagnostic significance of DNA methylation patterns in high gradeserous ovarian cancer." Gynecol Oncol 124(3): 582-588.

3. Gloss, B. S. and G. Samimi (2012). "Epigenetic biomarkers inepithelial ovarian cancer." Cancer Lett.

4. Ghosh, S., L. Albitar, et al. (2010). "Up-regulation of stromalversican expression in advanced stage serous ovarian cancer."Gynecol Oncol 119(1): 114-120.

5. Mok, S. C., T. Bonome, et al. (2009). "A gene signature predictivefor outcome in advanced ovarian cancer identifies a survivalfactor: microfibril-associated glycoprotein 2." Cancer Cell 16(6):521-532.


Tyrosine Kinase Signalling Networks inHuman CancersTyrosine kinases function in key signalling pathwaysregulating fundamental cellular processes such asproliferation, survival, metabolism and motility.Importantly, aberrant signalling by these proteinsunderpins many human cancers, and tyrosinekinases represent major targets for drugdevelopment. Research in my group is aimed atcharacterising tyrosine Kinase signalling mechanismsand networks in cancer cells, in order to developnew or improved therapies.

Recent developments in mass spectrometry-basedproteomics, coupled with affinity-based enrichmentstrategies, now allow 'global' characterisation ofparticular types of intracellular signalling event, suchas tyrosine phosphorylation. In other words, we canidentify and quantitate all of the signalling eventshappening in a cell at any given point in time. Inaddition, they enable the majority of kinasesexpressed by the cell (the 'kinome') to be co-ordinately characterised, in terms of both expressionand activation. Consequently, such approachesallow us to obtain global 'snapshots' of signalling inparticular types of cancer cell, and importantly,compare cell types, such as normal and cancer cells,or drug-sensitive and -resistant cells. My group hasestablished these technology platforms and iscurrently using them to address key questions incancer cell signalling research, such as:characterisation of the signalling networks thatdistinguish different breast cancer subgroups;whether pancreatic cancer can be subclassifiedbased on tyrosine phosphorylation patterns; andwhether changes in cellular signalling networks canidentify markers and mediators of therapeuticresponsiveness, such as to docetaxel in prostatecancer. In order to functionally interrogate the largenumbers of kinases and signalling proteins identifiedby these approaches, we are also implementingsiRNA screens that characterise the roles ofidentified candidates in regulation of cellproliferation and migration.

Examples of PhD projects available within the SignalTransduction Group are:

Project 1 characterisation of how the cellular 'kinome' isregulated by the proto-oncogene Src in basalbreast cancer cells.

We have recently identified that a particularlyaggressive form of breast cancer, termed basalbreast cancer, exhibits a prominent Src-regulatedsignalling network. This project will utilise cutting-edge chemical proteomics to characterise theimpact of Src activation on the entire kinome inbasal breast cancer cells.

Project 2 Identification of 'sensitizers' to Src inhibitors inbasal breast cancer.

Despite the presence of a prominent Src signallingnetwork in basal breast cancer cells, Src Kinaseinhibitors exert only modest effects on these cells interms of attenuation of proliferation and survival.This project will undertake a siRNA-based functionalscreen of the human 'druggable' genome in order toidentify genes whose knockdown sensitizes basalbreast cancer cells to Src Kinase inhibitors, therebyidentifying candidate combination therapies for thisdisease subtype.

Project 3 Identification of kinases and signalling proteins thatmediate prostate cancer metastasis.

It is possible to grow primary human prostatecancers as tumours in mice (xenografts). We haveaccess to xenografts that differ in their ability tospread (metastasize). Quantitative MS-basedproteomics will be used to screen these xenograftsin order to identify signalling proteins that mediatecancer metastasis.

Supervisor: Professor Roger Daly Signal Transduction Group E: [email protected]: 02 9295 8333


Mitotic Control GroupThe Mitotic Control Group sits within the Cell Cyclegroup (Prof. Liz Musgrove) of the Garvan's CancerResearch Program. It is a new exciting team that isfocused on targeting novel mitotic checkpointpathways to selectively target cancer cells. Recently,we demonstrated that correct mitotic progressionwas dependent on maintaining a tightly regulatedbalance between the activities of the phosphatasePP2A, and Kinase CDK1 [1,2]. Further, we identifiedthe novel mitotic Kinase Greatwall as the masterregulator of this balance [3,4]. These resultsdramatically altered our understanding of mitosisand opened up several new and exciting researchpathways. The primary aim of the lab is to furtherexplore and characterise these pathways, to identifynew chemotherapeutic targets and improve thesensitivity and selectivity of existing cancer drugs.

Project 1Mapping the Human Mitotic Exit Pathway.

During mitotic exit certain CDK1 substrates need toremain phosphorylated while others must bedephosphorylated to ensure the highly orderedevents of mitotic exit occur in the correct sequence.However, currently very little is known about howthis order of dephosphorylation is achieved inmammalian cells. This project aims to identify theorder of substrate dephosphorylation and thephosphatase responsible. The project will utilisequantitative live and fixed microscopy, advancedbiochemistry and Mass Spectrometry techniques.The outcomes will dramatically advance our under-standing of this fundamental stage of cell division, andmay identify novel targets for future chemotherapies.

Project 2Preventing Mitotic Exit to Kill Cancer.

Many classical and new-line chemotherapeuticstarget mitosis as a means of selectively killingcancer cells. Unfortunately, many cancer cells areresistant to these drugs. Furthermore, it is verydifficult to currently predict which cancers will besensitive or resistant. This project aims to identify acommon signature of proteins that promote andinhibit mitosis and determine if these can be used topredict response, and if subsequent targeting ofthese proteins improves current chemotherapies.This project will utilise multiple cancer cell linemodels, immunohistochemistry, and advanced live-cell imaging. The outcomes will hopefully provide acritical predictive tool and help further ourunderstanding of why cancer cells are sensitive orresistant to mitotic poisons.

References1. Burgess A et al. (2010), Proc Natl Acad Sci USA 107: 12564-12569.2. Lorca T, et al. (2010) J Cell Sci 123: 2281-2291.3. Gharbi-Ayachi A,et al. (2010) Science 330: 1673-1677.4. Vigneron S, et al. (2009) EMBO J 28: 2786-2793.

Supervisor: Dr Andrew BurgessMitotic Control GroupE: [email protected]: 02 9295 8327

Pancreatic Carcinogenesis GroupPancreatic Cancer is the fourth leading cause ofcancer death in our society. Almost 90% of thepatients succumb within a year of diagnosis,unless detection is done at very early stage.Evidence also supports a long period in whichpreneoplastic lesions are present.

The Pancreatic Carcinogenesis team is focused onidentifying key drivers and biomarkers ofpancreatic cancer through studying the earliestchanges in exocrine cell differentiation andproliferation using pancreas specific models (invitro and in vivo).

The Pancreatic Carcinogenesis group sits withinthe Pancreas Cancer Group (Prof. A. Biankin)which co-leads the Australian Pancreatic CancerGenome Initiative (APGI), a member of theInternational Cancer Genome Consortium(www.icgc.org). The APGI aims to fullycharacterise the genomic, epigenomic andtranscriptomic aberrations in tumor samples ofpancreatic cancer patients using the latest nextgeneration sequencing technologies. As such, theAPGI provides a unique resource to investigatemolecular mechanisms involved in pancreaticcarcinogenesis, to eventually reveal new targetsfor the development of novel detection methods,chemoprevention and chemotherapeutic strategies.

Specific projects available include:

Project 1Investigating the expression and the role ofcandidate gene aberrations identified by APGI inmodels of early pancreatic cancer; geneticallymodified mouse models have been introduced andneed to be further investigated. In addition,genetic manipulation is used in vivo and in vitro todefine the functional consequences and molecularmechanisms of these novel gene aberrations inmodel systems of early pancreatic cancer.

Project 2Investigating ENU-induced mutagenesis mousemodels, including forward screens to identify newgenes that can impact on exocrine pancreas celldifferentiation and proliferation and reversescreens where the effects of a known mutation ina gene of our interest (as identified by APGI) arefurther investigated for a contribution topancreatic carcinogenesis.

Supervisor: Dr. Ilse Rooman Pancreatic Carcinogenesis GroupE: [email protected] T: 02 9295 8372


Epigenetic Laboratory Cancer Program

Project 1Modelling epigenomic change during early breastcarcinogenesis using in vitro and in vivo modelsystems.

Epigenetic deregulation is an early and crucial eventin carcinogenesis so at diagnosis, tumours alreadycontain many genetic and epigenetic aberrations.Therefore, identifying the early epigenetic changesin cancer is challenging, as it is difficult to separatethe drivers of carcinogenesis from epigenetic lesionsthat are secondary passengers of carcinogenesis. Toidentify early epigenetic lesions in malignancy, ourlaboratory is exploiting a Human MammaryEpithelial Cell (HMEC) culture system as an in vitro

model of early breast carcinogenesis. In culture,HMECs undergo an initial phase of normal growthbefore entering a growth plateau. However, unlikeother normal cells, HMECs are able to overcomethis replicative barrier and enter into a secondexponential growth phase. Cells from this secondphase exhibit a much more aggressive phenotypeand these post-selection cells are considered toshare features with pre-malignant basal breastcancer cells. Recently, we have extend this in vitro

model to an in vivo mouse model system that cangenerate abnormal breast lesions that mimic humanductal carcinoma in situ (DCIS). In this PhD project,

we intend to utilise the in vitro and in vivo HMEC

systems to deliver a detailed and integrated

epigenomic map of very early breast cancer. We

will use these maps to identify potential early

biomarkers for breast cancer detection, and to

derive new understanding of the biology and

sequential epigenetic events that occur in early

breast carcinogenesis.

HypothesisEpigenetic dysregulation is an early and crucialevent in breast carcinogenesis and epigeneticaberrations occurring early during pre-malignancyshape the fate of the cancer epigenome andsubsequent cancer phenotype.

Overall AimTo integrate chromatin modification marks, DNAmethylation and RNA expression across the genomein order to investigate the relationship betweenchanges in the epigenomic landscape and thebiology of early breast cancer.

Aim 1: Epigenome ProfilingTo utilise our in vitro and in vivo HMEC modelsystems of early breast cancer to further developand generate epigenome maps of early breast cancer.

Aim 2: IntegrationTo integrate epigenomic and transcriptional maps ofpre- and post-selection cells in the in vitro and invivo HMEC systems to identify epigeneticmodifications and biological (regulatory) pathwayswhich underpin the sequential transition from pre-and post-selection state in vitro to DCIS-like in vivo.

Aim 3: PredictionTo utilise our newly acquired understanding ofepigenetic remodelling in the HMEC system and itsrole in driving early tumourigenesis from Aims 1 and2 for prediction of early methylation changes asbiomarkers of breast cancer.

PhD ProjectWe seek a motivated PhD candidate to be activelyinvolved in generation and analysis of epigeneticmaps. The project can be tailored to the interestsand/or strengths of the candidate. For moreBioinformatically oriented candidates there is anexcellent opportunity to be involved in developingof new techniques for processing and integration ofnext generation sequencing data.

References 1. Hinshelwood, R.et al Clark, S. J., Cancer Res 2007, 67, (24),

11517-27.2. Hinshelwood, R. et al Clark, S. J., Hum Mol Genet 2009, 18, (16),

3098-109.

Supervisor: Prof Susan Clark Co Supervisor: Dr Elena ZotenkoE: [email protected]: 02 9295 8315


Project 2Epigenetic mechanism: how does aberrantacetylation of the histone variant H2A.Z drivegene activation in cancer?

Epigenetic gene regulation is important in normalcell growth and differentiation and is commonlyderegulated in many diseases, including cancer.Epigenetic processes include DNA methylation,post-translational histone modification, exchange ofhistone variants and alterations in nucleosomepositioning. Our laboratory is interested in the roleof histone variants in deregulation of genetranscription in cancer cells, as the mechanismsassociated with exchange and post-translationalmodification of histone variants are still unclear.H2A.Z is an evolutionarily conserved H2A histonevariant. We recently reported for the first time thatthe acetylation of H2A.Z (acH2A.Z) is associatedwith gene deregulation in prostate cancer; activatedoncogenes gain acH2A.Z and down-regulatedtumour suppressor genes lose acH2A.Z at thetranscription start site (TSS). This exciting discoveryprovides an entirely new dimension to the “histonecode”. We hypothesize that acetylation of H2A.Z is

an important chromatin modification that drives

active transcription in normal cells but aberrant

H2A.Z acetylation leads to transcriptional

deregulation in cancer. There are however manyunresolved and key questions concerning themechanism of how H2A.Z acetylation promotesgene activation. The PhD project will address thefollowing questions, (1) Is H2A.Z acetylation acause or consequence of gene activation? 2) Whatis the mammalian enzyme(s) responsible for H2A.Zacetylation? 3) Does H2A.Z acetylation alternucleosome positioning?

Overall Aim To understand how acetylation of H2A.Z regulatesgene activation in cancer.

Aim 1: Determine how acetylation of H2A.Zchanges gene transcription.

To identify if acetylation of H2A.Z directly promotesor is a consequence of gene activation using LNCaPprostate cancer cells treated with androgens as amodel system of cancer gene activation. UsingChIP-seq we will study the genome-widealterations in H2A.Z/acH2A.Z occupancy and geneexpression upon androgen treatment. We willaddress whether transcriptional changes occur afterover- or under-expressing H2A.Z and/or acH2A.Zto determine the temporal and sequential molecularevents that drive gene transcriptional activation.This aim will address the still unresolved

mechanistic role of acH2A.Z in promoting

regulation of gene expression.

Aim 2: Identify the molecular machinery involvedin acetylation of H2A.Z.

We will perform mass spectrometry assays toidentify the complexes bound to acH2A.Z beforeand after androgen treatment. This approach willallow us to identify the factors involved in H2A.Zacetylation. We will then perform knock downexperiments to down-regulate these factors andassay the changes in gene expression and H2A.Zacetylation. These studies will identify the

complexes responsible for promoting acetylation

of H2A.Z.

Aim 3: Determine if acetylation of H2A.Z altersnucleosome occupancy.

Changes in genome-wide nucleosome occupancyby acH2A.Z will be analysed by an innovativeapproach where we will combine two state of theart techniques: gNOMe-seq assay2 [AI: ProfJones] and ChIP-seq. This technique will allow usto directly interrogate the nucleosomes containingacH2A.Z to detect changes in nucleosomelocalisation upon androgen treatment. This approach

will address how acH2A.Z affects the chromatin

structure by altering promoter nucleosome

positioning to activate gene transcription.

Significance and outcome: The project will addressfor the first time the mechanism that promotesacetylation of H2A.Z and its role in geneactivation. The outcome will directly determine ifH2A.Z acetylation is a key epigenetic regulator ofgene transcription in cancer, and will identify themolecular targets that control acH2A.Z activity.

Supervisor: Prof Susan ClarkCo Supervisor: Dr Fatima Valdes-MoraE: [email protected]: 02 9295 8315

References Valdes-Mora, F., et al Clark, S.J. Genome Res. 22, 307-321 (2012).


Project 3Establishing the importance of enhancer epigeneticreprogramming and atypical long-rangeinteractions in cancer cells.

Cancer is extraordinarily complex and the result ofwidespread genetic and epigenetic reprogramming.The phenomenon of epigenetic reprogramming(atypical silencing and activation achieved throughaltered patterns of DNA methylation, histonecomposition, histone modifications and nucleosomepositions) at gene promoters is a hallmark of cancercells, as we previously described. However, ourexisting knowledge is compartmentalised and doesnot yet adequately extend beyond promotersdespite increasing evidence that suggests that thetranscriptional profile of a cell is equally determinedby the activity of distal regulatory elements (eg.enhancers and insulators). Exciting data from ourmost recent work has challenged the views of thefield; that is, enhancers with an unexpectedly“active” epigenetic signature can regulatetranscriptionally repressed promoters. We foundthat the purpose of such enhancers was to ensurethe correct tissue-specific gene expressionpatterns, whilst retaining epigenetic flexibility thatallows normal cells to be amenable toreprogramming. Moreover, we show that cells are

rendered resistant to reprogramming when

enhancers are epigenetically silenced.

In this new PhD study, we emphasise the necessaryand dynamic functions of enhancers; raising thepossibility that epigenetic reprogramming of distalregulatory elements could contribute to cancerestablishment and progression. We hypothesize thatepigenetic reprogramming alters the three-dimensional structure of the chromatin:DNAcomplex. Imminent interest in distal regulatoryelements and their interactions ensures that thetiming of this project is highly significant.

Aim 1: To evaluate the scope of enhancerepigenetic reprogramming in cancer cells.

We will investigate the extent to which enhancerepigenetic reprogramming occurs genome-wide inprostate cancer compared to normal prostateepithelial cells. At completion, we will understand

how epigenetic reprogramming pertains to distal

regulatory elements in cancer.

Aim 2: To map epigenetic modifier-mediatedenhancer/promoter interactions.

The structure of the genome is three-dimensionaland complex interactions ensure that the correctgene expression patterns are established andmaintained. Using an innovative technology(Chromatin Interactions by Paired End TagSequencing; ChIA-PET) we will delineate howenhancers and promoters interact throughepigenetic modifiers, RAD21 (cohesin, facilitateslooping) and CTCF (blocks interactions), in normaland cancer cells. We will produce long-range

interaction maps for normal and prostate cancer

cells and address how DNA looping networks may

be disrupted.

Aim 3: To define functional roles of epigeneticmodifiers in enhancer/promoter interactions.

We propose that in cancer cells, atypicalenhancer/promoter interactions are directed byaberrant DNA methylation or binding of key DNAmodifying proteins. RAD21, CTCF and DNAmethyltransferases are all disrupted in cancer.Therefore, we will manipulate their expression incancer cells to investigate mechanisms of long-range interactions (ChIA-PET) and the structuralorganisation of chromatin (gNOMe-seq). At

completion, we will understand how RAD21, CTCF

and DNMTs contribute to atypical long-range

interactions characteristic of cancer cells.

Supervisor: Prof Susan ClarkCo Supervisor: Dr Phillippa TaberlayE: [email protected]: 02 9295 8315

References 1. Coolen, M.W. et al Clark SJ. Nature cell biology 12, 235-46

(2010).2. Taberlay, P.C. et al. Cell 147, 1283-94 (2011).


Project 4 Role of epigenetic modifiers MBD2 and TET proteinsin DNA methylation & demethylation in cancer.

Cancer development is characterised by frequenthypermethylation of CpG island gene promoters(including tumour suppressor genes), in parallel withhypomethylation of gene promoters (includingoncogenes) and repeat DNA sequences. While thevast majority of CpG islands remain unmethylated innormal cells, some CpG islands and other promoters(especially tissue-specific ones) are maintained in amethylated state. Critical, yet unanswered questionsin cancer biology remain regarding the balance ofhyper- and hypo-methylation in normal and cancercells and the potential role that CpG bindingproteins play in controlling the DNA methylationlandscape. We previously developed an in vitro

prostate cancer cell model system, where weshowed that the methyl binding domain proteinMBD2 plays a critical role in aberrant de novo DNAmethylation and that gene silencing precedesepigenetic remodelling. We now have significantnew data showing that loss of MBD2 promotesDNA demethylation. The mechanisms leading toDNA demethylation are still hotly debated, butrecently a new family of TET proteins thatenzymatically convert 5-methylcytosines (5mC) to5-hydroxymethylcytosines (5hmC) has beencharacterised. Hydroxy-methylation of cytosineresidues may be a critical facilitator of DNAdemethylation, and regulation of DNA methylationfidelity. Of particular interest, is that both MBD2and TET proteins share similar DNA binding domainsand preferentially bind CpG sites in CpG islands.

HypothesisIn a normal cell there is a dynamic balance betweenMBD2-mediated de novo methylation and TET-mediated demethylation at CpG islands to ensurethat the methylation state of CpG islands arefaithfully maintained. We propose that in cancer, thisbalance is disrupted, due to the potential differentialbinding of these factors or factor-associatedcomplexes, promoting alterations in DNAmethylation, epigenetic instability and changes ingene expression.

Overall AimTo understand the role of MBD2 and TET2&3CpG binding proteins in promoting 1) DNAmethylation and transcriptional repression, or 2)DNA demethylation and gene activation in cancer.

Aim 1: To investigate the role and scope of MBD2in promoting DNA methylation and/or its loss inpromoting demethylation and transcriptionalderegulation in cancer.

Aim 2: To investigate the role and scope ofTET2&3 in promoting 5hmC and potential DNAdemethylation and its aberrant function intranscriptional deregulation in cancer.

Aim 3: To identify potential binding partners ofMBD2 and TET2&3 and the associated complexeswhich determine differential specificity.

Outcome and significanceThe findings from this project will have a majorimpact on understanding the key steps involved inboth de novo DNA methylation and demethylationin cancer and will demonstrate sets of genes thatare coordinately deregulated in cancer. These newunderstandings may provide routes to use MBD2and/or TET proteins as pharmalogical targets incancer treatment.

Supervisor: Prof Susan ClarkCo Supervisor: Dr Clare StirzakerE: [email protected]: 02 9295 8315

References 1. Song, J. Z.; Stirzaker, C.; et al Clark, S. J., Oncogene 2002, 21, (7),

1048-612. Stirzaker, C et al Clark, S. J., Cancer Res 2004, 64, (11), 3871-7


Project 5Integrated methods for the analysis of genomicand epigenomic data.

EpigeneticsGenetics is the study of the DNA sequence and howit effects gene expression and function. Epigeneticsis the study of how gene expression is controlledindependently of the DNA sequence throughchemical modifications such as DNA methylation,chromatin modifications and expression of ncRNAs.This area of biological research is rapidly growing.Extremely large quantities of data are beinggenerated daily, presenting new computing andanalysis challenges that require strong analyticalskills. Additionally, over the course of the last fewyears it has become increasingly apparent that nosingle (epi)genomic experiment will provide answersto all biological and clinical questions. One of themajor challenges facing biologists and computationalscientists is to integrate the knowledge fromvarious genomic and epigenomic experimentalapproaches in order to gain insight into the biologicalmechanisms that underlie complex diseases.

(Epi)Genomic Data IntegrationOur research concerns the development and use ofnovel statistical and bioinformatics methods in orderto gain a better understanding of the factorsinvolved in disease. Projects would involvedeveloping new methods for the initial processingand analysis of epigenomic data: (i) miR and otherncRNA levels, (ii) ChIP-seq data for histone marks,(iii) RNA-seq and (iv) methylation levels. Further, weare interested in investigating new statistical andbioinformatics approaches to analyse the datagenerated at each stage of a genomic or epigenomicexperiment and the integration of several layers ofregulatory data with clinical information.

Supervisor: Dr Nicola ArmstrongE: [email protected]: 02 9295 8319

Cancer Bioinformatics Group

Project 1Integrate multiple dimensional -omics datagenerated by cancer genome sequencing projects.

The advances in sequencing technology have nowmade it feasible to perform massive scaleexhaustive, high throughput sequencing of nucleicacid. Several coordinated national and internationalefforts including The Cancer Genome Atlas (TCGA)and the International Cancer Genome Consortium(ICGC), have been initiated to generatecomprehensive catalogues of genomic,transcriptomic and epigenomic changes in multipledifferent tumour types. In collaboration withPancreatic Cancer group (Prof. Andrew Biankin) andSignal Transduction group (Prof. Roger Daly) withinGarvan, and Prof. Sean Grimmond's group atUniversity of Queensland's Institute for MolecularBioscience, we have the chance to integrate thepre-processed data at multiple molecular level for~400 individual pancreatic cancers (ongoing)including somatic mutations, copy numberabberations, methylation sites, mRNA expression,protein expression and phosphorylation. Although apreliminary version of an in-house integratingplatform (InterOmics) has been developed toautomate the analysis and facilitate hypothesesgeneration, we need to improve the platform byincluding multiple significant important newfunctions on data annotation, data query, datamining and user interface. This platform will be alsouseful to quickly integrate and analyze the publiclyavailable data from other ICGC and TCGA projects.

Project 2 Protein-protein interaction network analysis.

We have previously developed a Protein InteractionNetwork Analysis (PINA) platform, which is acomprehensive web resource, including a databaseof unified protein-protein interaction data integratedfrom six manually curated public databases, and aset of built-in tools for network construction,filtering, analysis and visualisation. Recently weimproved the PINA with its utility for studies ofprotein interactions at a network level, by includingmultiple collections of interaction modules identifiedby different clustering approaches from the wholenetwork of protein interactions ('interactome') forsix model organisms. There are still many interestingproblems left including: 1) Utilising protein-proteininteraction network and pathway model to help theintegration analysis mentioned in the project 1; 2)Assessing the confidence of protein-proteininteractions saved in the PINA database; 3) Includebuilt-in network alignment tools.

Selected recent publications1. Cowley, M.J., Pinese, M., Kassahn, K.S., Waddell, N., Pearson, J.V.,

Grimmond, S.M., Biankin, A.V., Hautaniemi, S. and Wu, J. (2012) PINAv2.0: mining interactome modules. Nucleic Acids Res, 40, D862-865.

2. Wu, J.*, Vallenius, T., Ovaska, K., Westermarck, J., Makela, T.P. andHautaniemi, S. (2009) Integrated network analysis platform forprotein-protein interactions, Nature Methods, 6, 75-77.

Supervisor: Dr Jianmin WuCancer Bioinformatics GroupE: [email protected]: 02 9295 8326

A/Prof Robert Brink Immunology Research ProgramLeader

11IMMUNOLOGY RESEARCH PROGRAM

Poject 2The generation of long-term immunity from thegerminal centre reaction.

Poject 3Controlling the onset of autoimmune disease inthe germinal centre reaction.

Poject 4The generation, localisation and survival ofnormal and malignant plasma cells.

Supervisor: A/Prof Robert BrinkB Cell Biology laboratoryE: [email protected]: 02 9295 8454

Dynamic in vivo two-photon imaging of mucosal immune responses to commensal andpathogenic bacteria.

The gastrointestinal mucosa is constantly exposedto commensal and pathogenic bacteria. Theimmune response to these bacteria are critical totheir containment in the gut and the prevention ofsystemic disease. One aspect of this protection isprovided by IgA antibodies which are by madeplasma cells and translocated across the epithelialcell layer into the lumen of the gut. This projectwill examine the dynamics of the mucosal IgAantibody response by transgenic B cells expressinga knock-in BCR directed against a model antigen.It will involve the use of intravital two-photonmicroscopy and optical highlighting supported bymultiparameter fluorescence activated cell sorting(FACS) and genetic analysis to probe thespatiotemporal regulation of this response.

Supervisor: Dr Tri Phan and A/Prof Robert BrinkE: [email protected]: 02 9295 8414

The work of the research team at the Garvan Immunology Program is divided between studying how aimmune system functions in a balanced way during health and how this can goes wrong in diseases suchas type I diabetes, asthma and immunodeficiency. Program Head Assoc. Prof Robert Brink and the GroupLeaders in the Immunology team regularly published in many high profile journals including Nature, Cell,

Nature Immunology, Immunity and J. Exp. Med.

Many successful PhD students trained in the Immunology Program have published at least one highly citedfirst author paper in either Immunity or J. Exp. Med.; a number have also been awarded New Investigatorof the Year honours at the annual conference of the Australasian Society of Immunology as well as theGarvan thesis prize. Since completing their PhDs, many Garvan Immunology Program alumni havesuccessfully obtained NHMRC Fellowhips for further postdoc study both in Australia and overseas at suchprestigious institutes as Harvard Medical School, Genentech, Max-Planck Institute in Berlin, StanfordUniversity, Rockefeller University (New York) and Yale University.

B Cell Biology LaboratoryOf all the cells in the body, B lymphocytes (B cells)undergo the most dramatic alterations to theirgenetic material as they develop and participate inimmune responses. The combined effects of twoindependent sets of DNA rearrangements andsomatic hypermutation of B cell immunoglobulingenes creates the diversity and specificity ofantibodies required to eliminate infectiouspathogens such as viruses and bacteria from thebody. At the same time, B cells must be preventedfrom producing antibodies against the body itself(self-tolerance).

In the B Cell Biology laboratory, we employsophisticated in vivo experimental models incombination with state-of-the-art molecular andcellular analytical approaches to investigate how Bcells produce antibodies against foreign threats butnormally avoid producing pathogenic autoantibodies.As well as defining the mechanisms by which B cellsprotect us from infectious diseases, we place aparticular focus on the role of B cells in initiatingdiseases such allergy (eg asthma), auto-immunediseases (eg lupus, arthritis) and lymphoma. Ourlaboratory publishes regularly in leading internationaljournals (Immunity, J. Exp. Med., Nature

Immunology) and collaborates with a number ofhigh profile Australian and international laboratories.

A number of projects are available for high qualityPhD candidates in 2013:

Poject 1Dynamic in vivo two-photon imaging of mucosal immune responses to commensal andpathogenic bacteria.

IMMUNOLOGY RESEARCH PROGRAM12

The role of subcapsular sinus (SCS) macrophagesin LN melanoma metastases.

The primary function of the lymph node (LN) is tofilter the lymph to trap and degrade any pathogensand cancer cells that may have infiltrated the hostorganism. Afferent lymph enters the SCS whichforms an anatomical and functional barrier to thefree diffusion of lymph borne particles. This barrieris formed by lymphatic endothelial cells and tissue-resident macrophages that express the sialic acid-binding C-type lectin CD169 (sialoadhesin). Lymphthen reaches the medullary sinuses which is alsolined by lymphatic endothelial cells and CD169+macrophages where the bulk of lymph-bornesoluble and particulate antigen is trapped andcatabolised. Cancer cells must therefore cross thislymph-tissue interface in order to invade theunderlying parenchyma. While interest has focussedon the molecular steps involved in oncogenesis andtissue invasion, there has been surprisingly littleresearch on the steps involved in the establishmentof metastatic cancer cells once they reach the LN.The project will therefore use genetic andpharmacological approaches to determine the roleof CD169+ SCS macrophages in LN metastases inan in vivo mouse model. These studies will involveintravital two-photon microscopy and directintralymphatic injection of cancer cells to monitortheir interactions with CD169+ SCS macrophagesin real-time. They will provide a molecular basis forunderstanding the earliest steps in LN metastasesand drive the development of novel therapeuticstrategies to prevent LN metastases not only inmelanoma but other cancers.

Supervisor: Dr Tri PhanE: [email protected]: 02 9295 8414

Diabetes & Transcription Factors Group

Project 1A novel therapy for liver disease?

Liver disease is the 5th most common cause ofdeath in Australia and the UK. In the UK, death fromcirrhosis has increased by >65% for men and >35%for women over the last 50 years, highlighting thelack of effective therapies. Acute liver failure (ALF)is a devastating condition with high mortality rates.It often occurs in young, previously healthyindividuals, including children. ALF has a mortalityrate of ~33-50% with intensive support includingliver transplantation. The commonest cause inAustralia is paracetamol overdose. Other causesinclude alcohol, drug reactions, surgery and sepsis.

With the exception of N-acetyl cysteine, there areno proven therapies. Many treatments includingcorticosteroids, heparin, insulin, glucagon, blood orplasma exchange and prostaglandins have beentrialled without success. A therapy that diminisheshepatocyte death or enhances replacement throughregeneration is highly desirable. This project willwork on a novel therapeutic target which ourpreliminary data demonstrates is important forhepatocyte survival, and liver outcomes.

Project 2Calcium flux and beta-cell function in diabetes.

Diabetes is increasingly common in Australia andworldwide, and it is associated with increased risksof heart disease, stroke, blindness, end stage kidneyfailure and amputations. Increased blood sugarlevels arise when the pancreatic beta-cells are nolonger able to compensate for the prevailing degreeof insulin resistance by increasing insulin secretion.Our lab works with a variety of factors whichinfluence beta-cell function, using a variety ofmouse models, and human pancreatic islets. Thisproject will examine the role of a specific factor inbeta-cell function and diabetes.

Project 3Brown fat and obesity therapy.

Over half of the Australian population is nowoverweight or obese. Current treatments forobesity are minimally effective, work onlytemporarily or have serious side effects. Brown fatis an important type of fat which consumes caloriesto produce heat, and is associated with decreasedweight in people and in animals. We have identifieda drug which increases brown fat, and preventsobesity in mice. This project will examine themechanisms behind this exciting effect.

Experience with any or all of tissueimmunohistochemistry, animal models, liver diseases or diabetes will be an advantage. Thesuccessful applicant must be willing to work withanimals and be able to work well within a fun,collaborative lab team.

Supervisor: A/Prof Jenny GuntonDiabetes and Transcription Factors GroupE: [email protected] T: 02 9295 8433

Prof David James Diabetes and Obesity ResearchProgram Leader

13DIABETES & OBESITY PROGRAM

Bioenergetics in DiseaseThe broad aim of our projects is to understand thefactors that regulate cellular energy balance undernormal conditions and in disease states. Excess bodyfat (obesity) is associated the development of anumber of major diseases (e.g. type 2 diabetes andheart disease) and we are investigating howdifferent tissues and genes contribute to the waythe body balances food intake and energyexpenditure to maintain a healthy body weight. Weare also exploring what goes wrong with cellularenergy metabolism in cancer.

Project 1Post-translational regulation of mitochondrialfunction.

Mitochondria are the major site for fuel oxidation incells and strategies that stimulate mitochondria toburn more calories may prove beneficial forpreventing obesity and insulin resistance. Recently ithas emerged that post-translational modification ofproteins in mitochondria can have major effects onthe rate of mitochondrial fuel oxidation. This projectwill use both genetic and pharmacologicalapproaches to alter post-translational modifications(e.g. acetylation) in mitochondria and examine theeffect on lipid accumulation and insulin action.

Project 2Dietary fatty acids and energy balance.

There is a clear relationship between excess intakeof dietary fat (particularly animal-based fats such aslard) and the development of obesity and insulinresistance. However there are also several classes ofdietary fatty acids that appear to have beneficialhealth effects, including medium chain fatty acidsand omega-3 fatty acids (which are rich in fish oil).This project investigates the molecular pathways thatthese dietary fatty acids switch on to prevent thedevelopment of obesity and insulin resistance.

Project 3Energy metabolism in cancer.

It has been known for some time that cancer cellsreprogram their metabolism to use fuel (fat,protein and glucose) in a different way to normalcells. This adaptation is thought to allow cancercells to make the molecular building blocks(proteins, DNA, lipids) they need to grow anddivide rapidly. It is also thought to allow cancercells to avoid the normal 'surveillance' mechanismsthat would get rid of malfunctioning cells. In thisproject we are using animal and cell models toinvestigate how cellular energy metabolism isimpacted by certain oncogenes and tumoursuppressors and by variations in specific growthfactor signalling pathways.

Recent publications 1. Wright LE, Brandon AE, Hoy AJ, Forsberg G-B, Lelliott CJ, Reznick

J, Löfgren L, Oscarsson J, Strömstedt M, Cooney GJ & Turner N.(2011). Amelioration of lipid-induced insulin resistance in ratskeletal muscle by overexpression of Pgc-1_ involves reductionsin long-chain acyl-CoA levels and oxidative stress. Diabetologia

54:1417-1426.2. Hoehn KL, Turner N (co-first author), Swarbrick MM, Wilks D,

Preston E, Phua Y, Joshi H, Furler SM, Larance M, Hegarty BD,Leslie SJ, Pickford R, Hoy AJ, Kraegen EW, James DE & Cooney GJ.(2010). Acute or chronic upregulation of mitochondrial fatty acidoxidation has no net effect on whole body energy expenditure oradiposity. Cell Metab 11: 70-76.

3. Turner N, Hariharan K, TidAng J, Frangioudakis G, Beale SM, WrightLE, Zeng XY, Leslie SJ, Li J, Kraegen EW, Cooney GJ & Ye J.(2009). Enhancement of muscle mitochondrial oxidative capacityand alterations in insulin action are lipid species-dependent:Potent tissue-specific effects of medium chain fatty acids.Diabetes 58:2547-2554.

4. Turner N & Heilbronn LK. (2008). Is mitochondrial dysfunction acause of insulin resistance? Trends Endocrinol Metab 19: 324-330.

5. Turner N, Bruce CR, Beale SM, Hoehn KL, So T, Rolph MS, CooneyGJ. Excess lipid availability increases mitochondrial fatty acidoxidative capacity in muscle: evidence against a role for reducedfatty acid oxidation in lipid-induced insulin resistance in rodents.Diabetes. 2007 56(8):2085-92.

Supervisor: Dr Nigel Turner and A/Prof Greg CooneyE: [email protected]: 02 9295 8224

Obesity is a major risk factor for many other diseases including diabetes, cardiovascular disease, Parkinson'sdisease and cancer. This indicates that these diseases are mechanistically linked. Our program takes a verybroad approach involving basic and clinical research to tackle the complexity of metabolic disease. This bydefinition requires interdisciplinary research so that we can integrate various layers of information thatdepict the behaviour of mammals as they respond to changes in their environment. We have expertise inislet, fat cell, liver and muscle biology. We use a combination of molecular, cellular, biochemical andphysiological approaches to dissect the metabolic wiring in these different organs with the ultimate goal ofpinpointing major regulatory features that both cause disease and/or may be manipulated therapeutically.

Most of our students publish first author papers in top level journals and end up doing postdoctoralfellowships in some of the best labs throughout the world. Many have gone on to successfully establish theirown labs around the world.

DIABETES & OBESITY PROGRAM14

Regulation of Body Composition &Glucose Homeostasis by the AdaptorProtein Grb10An important risk factor for Type 2 diabetes is thedevelopment of insulin resistance. Many factorscontribute to insulin resistance including thedecrease in muscle mass associated with reducedphysical activity and ageing. Consequently,understanding how the signalling pathways involvedin insulin action and maintenance of muscle massare regulated is of major significance. We are focusingon two adapter-type signalling proteins, Grb10 andGrb14, which bind directly to the insulin receptor.

We have recently demonstrated that Grb10 geneknock-out mice exhibit increased insulin signalling inskeletal muscle and adipose tissue. Furthermore,Grb10-/- mice also display increased skeletal musclemass and reduced adipose tissue content.

Since these mice have 'global' Grb10 ablation (ieGrb10 is absent from all tissues) it is unclearwhether Grb10 has roles in both muscle andadipose tissue, or whether the effect in one tissue isan indirect consequence of its role in the other. Inaddition, if Grb10 is to be targeted therapeutically,it is important to determine whether the beneficialeffects of ablating Grb10 require the absence ofGrb10 during development, or whether they can beachieved via more 'acute' ablation of this adaptor inadult mice.

To address these issues we will utilise a conditionalGrb10 allele (Grb10fl/fl) to determine how Grb10ablation in a tissue-specific and developmentalstage-specific manner affects phenotype.Grb10fl/fl mice will be crossed with miceexpressing Cre recombinase, or tamoxifen-regulatedCre, in muscle or adipose. This will enable us to'knock-out' Grb10 expression in muscle and adiposethroughout development and adulthood, oralternatively from a particular developmental stage(by timed addition of tamoxifen, which induces thegene deletion). The resulting strains will becharacterised for their muscle, fat and metabolicphenotypes, as well as for effects on signalling byinsulin and other hormones/growth factors. This willdetermine whether the effects on bodycomposition in Grb10-/- mice reflect autonomousroles for Grb10 in muscle and/or adipose, andwhether an increase in relative lean mass andimprovement in glucose homeostasis can beachieved by Grb10 ablation during adulthood.

Supervisor: Prof Roger Daly (Cancer ResearchProgram) and A/Prof Greg Cooney (Diabetes andObesity Research Program)E: [email protected]: 02 9295 8209

Beta Cell Replacement TherapyThe common forms of diabetes are characterised bythe destruction (type 1) or an insufficiency (type2) of insulin secreting pancreatic beta cells. We aretaking an interdisciplinary approach to devise novelstrategies for beta cell replacement therapy. Ourprimary experimental system is the zebrafishembryo, a model that is at the intersection ofgenetic and pharmacological research.

Project 1Cellular reprogramming of acinar cells.

We are applying insights from developmentalbiology to use the abundant pancreatic acinar celltype as a source of progenitors for beta cellregeneration. We have established an in vivo modelto induce acinar cell reprogramming and track thefate of the cells as they transition to insulinproducing beta cells. This project will focus onincreasing the efficiency and specificity of cellularreprogramming. We are particularly interested indeveloping a protocol that is responsive to themetabolic dysfunction associated with diabetes.

Project 2In vivo drug screening.

Traditional drug screens have targeted singlemolecules or cell types. While the targets are oftenwell justified, it is difficult to predict how the hitswill behave in vivo, which has contributed to thepoor success rate for new drugs in recent years. Wehave developed a number of transgenic models thatallow us to monitor metabolic parameters in intactembryos (glycemia, beta cell mass, etc.) to helpidentify the next generation of antidiabetic drugs.Projects in this area would include assaydevelopment and screening as well as mechanisticanalysis of hits that we have previously discovered.

Selected Publications 1. Hesselson D, Anderson RM, Stainier DYR. (2011) Suppression of

Ptf1a induces acinar-to-endocrine conversion. Current Biology 21,712-717.

2. Anderson RM, Bosch JA, Goll MG, Hesselson D, Dong PDS, Shin D,Chi NC, Shin CH, Schlegel A, Halpern M, Stainier DYR. (2009) Lossof Dnmt1 catalytic activity reveals multiple roles for DNAmethylation during pancreas development and regeneration.Developmental Biology 334(1), 213-223.

3. Hesselson D, Anderson RM, Beinat M, Stainier DYR. (2009) Distinctpopulations of quiescent and proliferative pancreatic _-cells identifiedby HOTcre mediated labeling. PNAS 106(35), 14896-14901.

Supervisor: Dr Daniel HesselsonE: [email protected]: 02 9295 8258

15DIABETES & OBESITY PROGRAM

Cooper Group - Neurodegeneration,Cell & Molecular Biology, GeneticsParkinsons Disease (PD) is a chronic and progressivedegenerative neurological disorder that currentlyafflicts >6 million people worldwide and is predictedto rapidly increase by 50% in the next 20 years asour population ages. Although predominantlyconsidered a movement disorder, people with PDalso experience significant non-motor symptomsincluding sleep disturbances, olfactory dysfunction,autonomic dysfunction and changes in cognition.Much earlier diagnosis and new treatments arecritically needed as (i) presently patients havealready lost ~40% of the suspectible neurons attime of diagnosis (ii) there is no cure and currenttherapies are only partially effective at treatingsome of the symptoms, while progression andspread of the disease continues. The lack ofknowledge of the underlying mechanismsresponsible for causing PD and its progression is themajor impediment to therapeutic advances. Toachieve earlier diagnoses and development oftreatments and drugs, our research centres ondiscovering the cascade of events causing the lossof neurons in Parkinsons Disease.

Our research projects utilise a wide range ofapproaches including genome-wide screening, NextGeneration sequencing, bioinformatics, cell andmolecular biology techniques, fluorescencemicroscopy, qRT-PCR, lipodomics, proteomics,metabolomics, siRNA knockdown, gene knockouts,FACS analysis, cell culture, primary neurons, transgenicmice models and human PD patient brain samples.

Identifying the underlying molecular mechanism(s)of Parkinson's Disease. Whole genome functionalscreening approaches in relevant PD models haveidentified defects in major cellular signalingpathways. These will be validated using a broadarray of genetic, cell and molecular approaches toboth confirm their association with PD and identifythe underlying molecular mechanism(s) prior totesting in human brain samples.

Preventing Parkinson's disease inter-neuronalprogression/spread. Synuclein is a centralcomponent in PD. In its toxic misfolded form,Synuclein can transfer from within a degeneratingneuron into neighbouring healthy neurons andtrigger their degeneration.

Discover the role of mitochondrial dysfunction inParkinson's disease. Mitochondrial dysfunction haslong been observed in Parkinson's disease and weare investigating how mitochondrial dysfunctioncontributes to neurodegeneration.

Identification of brain specific transcripts and non-coding RNA contributing to Parkinson's disease.Tremendous advances in NextGen sequencingallow the interrogation of whole genome RNAtranscripts from PD affected regions of the brain.

Identify the role of PARK9, autophagy & lysosomaldysfunction in Parkinson's disease. Dysfunction incellular proteostasis is a core contributor to PDand the impairment of these components are arapidly emerging field in Parkinson's Diseaseresearch.

Selected recent publications 1. Gitler et al. “Alpha-synuclein is part of a diverse and highly

conserved interaction network that includes PARK9 andmanganese toxicity.” Nat Genet. 41:308-15 (2009). ImpactFactor = 25

2. Cooper et al “Alpha-synuclein blocks ER-Golgi traffic and Rab1rescues neuron loss in Parkinson's models.” Science. 313:324-8.2006. Impact Factor = 31

Supervisor: A/Prof Antony Cooper E: [email protected] T: 02 9295 8238

Prof Herbert HerzogNeuroscience Research ProgramLeader

NEUROSCIENCE PROGRAM16

The Garvan Neuroscience program is an active, collaborative research community that investigates how thebrain functions. Research undertaken by the Program looks at the brain at many different levels, from genesand molecules to synapses, neurons, brain regions and behaviour. A wide range of models from flies, mouseto humans and state-of-the-art molecular and biochemical techniques are employed to address both basicand medically relevant problems in neuroscience. The Program's goal is to understand how the brain worksand to improve understanding, diagnosis, and ultimately develop novel therapies for neurological disorders.We are particularly interested in conditions like Parkinson's Disease, Alzheimer's Disease and generalconditions of dementia in which the natural ability of the brain to regenerate itself (via neuro-stem cells) iscompromised. Furthermore, we investigate the role of the nervous system in pain perception as well as howthe brain communicates with other organs and tissues in the body, for example to control bone formation;and in the regulation of energy balance (intake and expenditure), which affects fertility, mood, weight gain,physical fitness and how this can lead to obesity.

The majority of the PhD students trained in the Neuroscience Research Program are supported by AustralianPostgraduate Awards or NHMRC scholarships, and have received numerous presentation awards and travelfellowships to national and international meetings. Research produced by our students is published in high-ranking journals such as PNAS , J.Biol.Chem, J.Clin.Invest., JBMR , Nat. Med, PlosONE , Cell Metabolism, J.

Neurosci , Cell and Nature. We are currently looking for candidates in areas such as: Neuropeptide signalling,Neurodegenerative diseases, Neuronal control of bone density, Regulation of appetite, Neural endocrinology,Pain perception, Sleep disorders and Behavioural genetics.

Eating Disorders Group

ProjectNovel Neuropeptide Regulators of EnergyHomeostasis.

The worldwide prevalence of obesity is increasing atalarming rate, and is a major risk factor for type 2diabetes and other diseases. Although the benefitsof losing excess weight are undisputed, therecurrently exists no effective non-surgical treatmentfor obesity. Body weight and body composition suchas fat tissue mass are regulated by an interactivecomplex of energy homeostatic system. Thus tomeet the urgent and desperate need for thedevelopment of novel pharmacological tools fortreating obesity, researchers need not only to knowthe identity and functions of individual moleculesand pathways involved in the regulation of energyhomeostasis, but also to understand how thesemolecules and pathways interact. Among these,neuropeptide Y (NPY), - one of the most widelyexpressed molecule in the brain, is a known playercritically involved in the regulation of body weightad adiposity via its control on every aspects ofenergy homeostasis, such as appetite, energyexpenditure, physical activity and fuel partitioning 1.Recently, our unpublished studies show thatneuropeptide FF and NPFF receptor 2 (NPFF2R) arethe novel players in the energy homeostaticcomplex. Interestingly, our preliminary resultssuggest that NPFF system may exert its control on

energy homeostasis via interacting with NPYpathway. Therefore, this project is to 1) furtherinvestigate the mechanism by which NPFF systemregulates energy homeostasis; and 2) to investigatehow the NPFF and NPY systems interact in theseregulations. To achieve this, we will examine aspectsof energy homeostasis and factors in controllingthem in multiple mouse models where either orboth NPFF and NPY system have been geneticallyaltered. Such mouse models include mice with NPFFoverexpression by delivering the NPFF-containingadeno-associated viral vector to the adult mousebrain, germline NPFF2R knockout mice, and micewith adult-onset specific deletion of NPFF2R fromNPY neurons. By Utilising cutting edgeinternationally competitive technology and uniquegermline and conditional knockout and transgenicmouse models, this project will make highly originaland high-impact contributions to the understandingof the role of NPFF system in energy homeostasisand its interactions with the NPY pathway, and willdemonstrate whether targeting NPFF2R couldprovide the basis of novel anti-obesity treatment.

Selected recent publicationZhang L et al. The neuropeptide Y system: Pathological andimplications in obesity and cancer. Pharmacol Ther. 2011Jul:131(1):91-113.

Supervisor: Prof Herbert HerzogCo-Supervisor: Dr Lei Zhang andE: [email protected]: 02 9295 8296

17NEUROSCIENCE PROGRAM

Major techniques involved in this projectIndirect calorimetry, infrared imaging, stereotacticbrain injection, oral glucose tolerance test,intraperitoneal insulin test, dual-energy X-rayabsorptiometry, tissue dissection, in situ

hybridyzation, Western blotting,immunohistochemistry, various serum assays.

ProjectAltering Thermogenesis as Weight-loss Strategy.

Obesity-associated cardiovascular diseases anddiabetes are leading causes of death and areexpected to increase as the obesity epidemicworsens. Current weight-loss therapies mainlytarget reduction of energy intake, providing only atransient or partial solution with limitedeffectiveness. Alternatives are needed to combatthis problem and one potential promising approachis to target the other side of the energy balanceequation, energy expenditure.

The therapeutic potential of brown adipose tissue(BAT) in weight reduction via the regulation ofenergy expenditure has emerged as a conceivablypromising yet underexplored area. Whilst previouslybelieved to be small animal-specific and exclusivelyneonatal in mammals including humans, theabundance of functional BAT in adult humans hasbeen recently confirmed to be widespread bypositron emission tomography (PET) marking it apromising target for anti-obesity therapy. However,little is known about the control of BAT activity andfunction. BAT is the main tissue that harboursuncoupling protein 1 (UCP1), the major componentthat is responsible for mediating metabolicthermogenesis. Our preliminary data demonstratesthat elevated neuropeptide Y (NPY) levelsspecifically in the arcuate nucleus (ARC) of thehypothalamus, which is known to be a major driverfor marked reductions in energy expenditure, alsoinfluences UCP1 expression in the BAT.

We thus aim to investigate the specific role of theNPY system in integrating hypothalamic functionswith energy expenditure specifically focusing on BATactivity. To achieve this, we will utilise a set of noveland unique mouse models that allow for theneuron-type specific conditional deletion or over-expression of NPY in an inducible adult-onsetfashion. A wide range of laboratory techniques willbe employed, including but not limiting to in-situ

hybridisation, immunohistochemistry, high-sensitivity infrared thermal imaging, histological

examination, cell cultures, quantitative real time-PCR and Western blotting, to determine the keyregulators of thermogenesis and mitochondrialfunction and mechanistic central pathwayspossibly involved. All of the mouse models,methods and experimental paradigms are wellestablished in our laboratory as demonstrated byour extensive publication record on these topics inhighly ranked journals like Nature Medicine andCell Metabolism (1,2,3,4,5).

Results from this study will provide critical newinsights on NPY's role in the control of BAT-mediated energy expenditure. These results willalso provide valuable contributions to thedevelopment of potential therapeutics to increaseenergy expenditure, likely being a more effectiveway for the treatment of obesity.

Selected recent Publications1. Johnen H, Lin S, et al. Tumor-induced anorexia and weight loss are

mediated by the TGF-beta superfamily cytokine MIC-1. Nat Med.2007 Nov;13(11):1333-40.

2. Lin S, Shi YC, et al. Critical role of arcuate Y4 receptors and themelanocortin system in pancreatic polypeptide-induced reductionin food intake in mice. PLoS ONE. 2009;4(12):e8488.

3. Cox HM, Tough IR, et al. Peptide YY Is Critical forAcylethanolamine Receptor Gpr119-Induced Activation ofGastrointestinal Mucosal Responses. Cell Metab. 2010 Jun9;11(6):532-42.

4. Shi YC, Lin S, et al. NPY-neuron-specific Y2 receptors regulateadipose tissue and tranbecular bone but not cortical bonehomeostasis in mice. PloS ONE. 2010;5(6):e11361

5. Shi YC, Lin S, et al. Peripheral-specific Y2 receptor knockdownprotects mice from high-fat-induced obesity. Obesity. 2011 Nov;19(11): 2137-48

Supervisors: Dr Shu LinCo- Supervisor: Dr Yan ShiE: [email protected]: 02 9295 8291

ProjectInsulin Action in the Brain.

The prevalence of obesity has reached epidemiclevels and is further increasing at an alarming rate.Currently there are no effective therapeutictreatments for obesity, however it is generallyrecognised that any treatment must be associatedwith a reduction in energy intake, an increase inenergy expenditure or ideally both. Therefore,defining how the central nervous systemcoordinates information to regulate energy balanceis important for understanding the pathology ofobesity as well as for designing treatments tocombat this disease. Insulin is a potent anabolichormone, secreted by the pancreas in response to


the increase in blood glucose levels. Recently, insulinhas been reported to have effects not only in theperipheral tissues, but also in the brain to regulatesatiety and glucose and energy balance. Previousstudies from our lab and others have establishedthe importance of the central neuropeptides Y(NPY) system in the regulation of food intake andenergy expenditure, with hypothalamic NPY mRNAlevels elevated in several rodent models of obesity.Increased NPY levels contribute to the developmentof obesity in a two-fold way by increasing foodintake and also reducing energy expenditure.Although insulin is known to influence energybalance, the precise neuronal action andpopulation(s) of neurons that mediate insulin actionremains unknown. Thus, the major aim of thisproject is to understand and define the role ofinsulin in NPY neurons in the regulation of energyhomeostasis. This research will not only help to getmore mechanistic insights in the etiology of obesity,but also contribute to the precise understanding ofcentral insulin action in the NPY-ergic pathway inthe regulation of energy homeostasis.

Specific Aims_ To generate and characterise NPY-neuron specific

IR-deficient mice._ To investigate the molecular mechanisms by which

central insulin action regulates energyhomeostasis.

Summary of Techniques to be UsedConditional knockout mouse models, indirectcalorimetry, metabolic measurements, real-timePCR, in situ hybridisation, western blotting, patchclamp electrophysiology, immuno-histochemistry.

Supervisors: Prof Herbert Herzog:[email protected] Co-Supervisor: Dr Kim Loh E: [email protected]: 02 9295 8296

ProjectNon-coding RNA's and their role in obesity

Obesity is a major global public health concern, withAustralia being one of the most affected countries.Although great effort has been placed on identifyingtreatments for obesity and critical players andpathways that control appetite have beencharacterised, hardly any effective drugs are on the

market. Therefore there is a desperate need toidentify new alternative targets to treat obesity.One way to learn more about the critical pathwaysthat control food intake and energy homeostasis isby investigating naturally occurring mutations thatlead to obesity. The identification of the genemutation in the leptin gene that causes the massiveobesity in the ob/ob mouse was a landmarkdiscovery, which has and still provides us withimportant information about the control of thiscomplex system. While mutations in the leptin genein humans are actually very rare there are othergenetic variations that also lead to massive increasein appetite and the development of obesity thathave much higher frequencies like the one causingPrader-Willi-Syndrome (PWS), which is the mostcommon known genetic cause of obesity, with aprevalence of 1 in 25,000 to 1 in 10,000 live births.

PWS is characterised by severe infantile hypotoniawith poor suck and failure to thrive in the first 1 to2 years of life. This initial lack of feeding drivechanges then dramatically and subjects with PSWdevelop an obsession with food leading to an un-saturable appetite, which if not controlled, will leadto early-childhood onset obesity. PWS is due to theabsence of paternally expressed imprinted genes at15q11.2-q13. Interestingly, single deletion ofknown genes in this region in mice althoughshowing some effects related to the PWSphenotype, do not result in a phenotype that wouldresemble the classical features of overeating anddevelopment of obesity seen in human PWSsubjects. Importantly, several recent studies haveidentified subjects with PWS that have only micro-deletion in this locus on chromosome 15, but stillshow many of the major features such as increasedappetite and early onset of obesity characteristicfor this syndrome. The different deletions vary insize but all contain the entire 27 copies of theSNORD116 locus.

Astonishingly hardly anything is known on how thegenetic variations in Snord genes cause theincredible high-level of appetite and massiveobesity in affected individuals. Therefore the majoraim of this study is to identify the underlyingmechanism that leads to increased appetite andbody weight of a particular mutation in this PWSlocus, called Snord116 using various geneticallymodified mouse models.

Specific Aims_ Determine the effect of adult onset SNORD116

deficiency on food intake and energy homeostasis _ Investigate whether re-introduction of

SNORD116 can rescue the hyperphagia ofSNORD116 KO mice

_ Identification of SNORD116 down streamaffecter pathways

Supervisor: Prof Herbert HerzogE: [email protected]: 02 9295 8296


Project Anorexia Nervosa-The Starving Brain.

Anorexia nervosa is a debilitating disorder affectingas many as 1 in 100 young women. Approximately10% of people suffering with anorexia are male.

Without treatment, up to 25% of people withanorexia nervosa die. With treatment, about 20% ofpatients make only partial recoveries, remaining toofocused on food and weight to be able toparticipate fully in life. An additional 20% ofsufferers do not improve, even with treatment.They are seen repeatedly in emergency rooms,eating disorders programs and mental health clinics.Clearly, new treatments for anorexia nervosa aredesperately required.

The precise causes of anorexia nervosa areunknown, but environmental and psychologicalfactors often cited as playing a role. However,emerging evidence strongly suggests genetic causesfor anorexia nervosa. For instance, most peoplesimply cannot diet down to an unhealthily low bodyweight. That is because weight loss activates strongphysiological mechanisms that protect againstfurther weight loss. This 'famine reaction' istriggered by natural brain chemicals in a part of thebrain called the hypothalamus, with effects includeirrepressible hunger, lethargy and sharp reductionsin metabolic rate.

Paradoxically, people with anorexia nervosa do notdemonstrate these expected responses to weightloss, suggesting perturbations in the natural brainchemicals responsible for the famine reaction. If weunderstood exactly which chemicals in the brainwere responsible for mediating the famine reaction,how they worked, as well as how these moleculesare perturbed in anorexia nervosa, then we coulddevelop novel treatment strategies to target thephysical causes of this debilitating disorder, andpossibly therefore help people who do not respondto conventional treatments.

Using sophisticated genetic engineering techniques,we have developed mice with perturbations ingenes encoding substances that act on the brain tomediate the famine reaction, such as neuropeptideY, peptide YY, and dynorphins. Intriguingly, thesetransgenic mice demonstrate metabolic featurescharacteristic of people with anorexia nervosa,notably an enhanced ability to lose weight and burnbody fat. However, in order to fully investigate therole of these substances in the development andtreatment of anorexia nervosa, we need toinvestigate their effects on food intake and bodycomposition other eating related behaviours.

Supervisor: Prof Herbert HerzogE: [email protected]: 02 9295 8296

Inter-organ Signalling: A new level ofregulatory controlOur laboratory has a long-standing interest indefining the brain's role in controlling and co-ordinating peripheral tissue homeostasis. Usingsophisticated genetic studies in mice, we havedemonstrated that the hypothalamus regulatesthe behaviour of numerous organ systems, throughmodulation of specific neuropeptide pathways.

Our primary focus has been upon the powerful,multi-system responses that surround starvationand obesity, with a particular emphasis upon theneuropeptide Y (NPY ) system. NPY is one of themost powerful regulators of energy homoeostasisthroughout the body, and our group, incollaboration with the Eating Disorders Group, isamongst only a few in the world able to dissectthe activity of this crucial pathway, through uniqueanimal models made at the Garvan.

Using specific tissue responses, such as adipose,skeletal and pancreatic tissue, we have defined the mechanism whereby specific NPY pathwaysfrom the brain act within the periphery. Thesepathways are extremely potent, altering fat massby over 4-fold and the production of bone by 7-fold, as well as altering endocrine function throughaltered production or end-organ responses.Moreover, these signals are co-ordinated acrossmany organ systems, demonstrating a level ofintegration between organ systems, not fullyappreciated previously.

Excitingly, during the course of these studies, wehave uncovered unique signalling pathways, thatindicate an additional layer of communication notpreviously appreciated, acting between the organsthemselves. Endocrine regulation has typicallybeen viewed as a top-down process, from thehypothalamus via the pituitary to the circulation.Our research will focus upon emerging inter-tissuecommunications, defining entirely new signallingmolecules and axes of communication.

Our initial studies have identified actions entirelynovel to science. For example, using tissue-specificneuropeptide models, we have demonstratedbone's signalling to the brain to control its ownproduction, as well as bone's regulation of bothadipose and glucose homeostasis.


Post graduate projects within the lab will involveinvestigations of inter-organ communication,concerning, but not restricted to:_ Coordination of energy, skeletal and glucose

homeostasis _ Feedback signals from bone to brain_ Regulation of tumour cell growth by marrow and

skeletal tissue_ Consequences of chronic obesity/leptin resistance_ Neuropeptide regulation of central endocrine

function

These studies represent the forefront of ourunderstanding of how tissues communicate and co-ordinate their activities, and offer the potential forentirely new modalities for disease control. Everystudent within our lab has won at least oneinternational young investigator award for oralpresentation of their studies, and gone on tointernational positions. Our lab is integrated withmany others within the Institute, including ongoingclinical studies, and offers a rewarding, productiveand enjoyable experience for those eager to explorethis emerging field.

Supervisor: Dr Paul BaldockE: [email protected]: 02 9295 8244

Neurosignalling Group

Project 1Developing new therapies for mood disorders and schizophrenia.

BackgroundMood disorders (e.g. Bipolar disorder) andSchizophrenia are debilitating psychiatric illnessesthat severely impair people's lives. They affect200,000 Australians, are one of the leading causesof disability amongst young adults and cost thecommunity over $2 billion annually. One quarter ofyoung adult sufferers commit suicide, thereforethere is an urgent need to improve treatments formood disorder patients. Clear genetic orenvironmental causes have not been identified, soalternative strategies for developing noveltherapeutics are needed. Our approach is todetermine how current drug treatments work, sothat they can be improved. A key target of lithiumand other mood stabilisers is the important brainenzyme GSK3. This protein is essential for normal

development and healthy function of the brain,however it is 'hyperactivated' in Bipolar Disorder andSchizophrenia. This causes disruption of manycellular functions and impairs healthy brain function,although the pathways affected are not wellunderstood. Our goal is to discover targets of GSK3that directly lead to the development of mooddisorders and Schizophrenia, since these couldbecome more selective and potent drug targets forimproved treatment.

Project We performed a bioinformatic and biochemicalscreen to discover new targets of GSK3 in the brain.Surprisingly, we found a large cluster of GSK3targets associated with clathrin-mediatedendocytosis (CME), a process that is critical forefficient neurotransmission in the brain. Severalmood-stabilising drugs target CME, implicating it inthe pathogenesis of these disorders. Excitingly,several of these have already been geneticallyassociated with Bipolar and/or Schizophrenia,increasing the likelihood that they directlycontribute to the development of these disorders.This project will determine how GSK3 regulates themolecular function of these new targets, its affecton CME/neurotransmission in the brain and evaluatetheir potential to become novel therapeutic targets.This will be achieved using a variety of techniques,including protein biochemistry, recombinant DNAtechnology, immunoflourescence microscopy andprimary neuronal cell cultures. We will also usegenetically-modified flies to determine the role ofGSK3 targets on neurotransmission and behavioursassociated with mood disorders in a wholeorganism. This powerful technology is new to theGarvan Institute and will be performed incollaboration with the Pain Research Group lead byDr. Greg Neely. Opportunities exist to investigate10 new GSK3 targets already discovered, as well asthe opportunity to discover new targets.

Benefit Very little is known about the function of GSK3 andits targets, especially in the brains of mood disorderand Schizophrenic patients, providing greatopportunities for discovery. Many essential reagentshave already been generated and are ready for use,greatly expediting this research. The Garvan is anexceptionally well-equipped medical researchinstitute with state of the art facilities and modernlaboratories. Students in the Neurosignalling Groupwill be provided with attentive supervision, superiorresearch facilities, exposure to a wide range ofexperimental techniques and will participate innational/international conferences and collaborations.

Project 2 New transcription factors regulating neurogenesisand neuroplasticity: rewiring the brain.

BackgroundNeurogenesis is the production and incorporation ofnew neurons into existing circuits of the adult brain.This process promotes plasticity (ability of the brain


to rewire itself), facilitating learning and memorythroughout our lifetime. Neurogenesis is decreasedin several mental illnesses, including mood disorders,Alzheimer's disease and age-related cognitivedecline. Therefore, a fundamental knowledge of themechanisms controlling neurogenesis could lead tonew treatments that restore healthy mentalfunction or repair the brain following injury. Weperformed a genome-wide screen in Drosophila(fruit fly) using neuronal-specific RNAi knockdownto identify genes essential for neurogenesis andbrain development. We found that knockdown of 3transcription factors in fly neurons is lethal, clearlydemonstrating a cell fate and developmentalfunction in the brain. All 3 genes are associated withhuman diseases, although their role in braindevelopment has not yet been investigated.Opportunities exist in the Neurosignalling Group toinvestigate any one of these novel transcriptionfactors in brain development.

ProjectThis project will determine how the noveltranscription factors regulate neurogenesis, braindevelopment and behaviours associated withneurological disorders. More specifically, it will 1)determine how they regulate cell fate and behaviourin genetically-modified flies (collaboration with Dr.Greg Neely, Pain Research Group), and 2) determinethe biochemical mechanisms by which GSK3regulates their function. These goals will beachieved using a variety of techniques, includingprotein biochemistry, recombinant DNA technology,immunoflourescence microscopy and primaryneuronal cell cultures. This will provide valuableinsight into the mechanisms controllingneurogenesis and is likely to reveal new therapeuticavenues for improved treatment of mood disorders,Alzheimer's disease and age-related cognitive decline.

BenefitsMental health is a rapidly growing research field thathas recently become a health and research priorityin Australia and other developed nations. Manyessential reagents have already been generated andare ready for use, greatly expediting this research.The Garvan is an exceptionally well-equippedmedical research institute with state of the artfacilities and modern laboratories. Students in theNeurosignalling Group will be provided withattentive supervision, superior research facilities,exposure to a wide range of experimentaltechniques and will participate in national/international conferences and collaborations.

Supervisor: Dr Adam ColeNeurosignalling GroupE: [email protected]: 02 9295 8289

Bird and Swine Flu, Parkinson's Disease,Chronic PainThe focus of our group is to use a “systemsbiology” approach, combining fruit fly, mouse, andhuman genetics to identify novel conservedregulators of human disease. We are currentlyinvolved in using single nucleotide polymorphismgenotyping and next generation sequencingtechnologies to identify genes and rare mutationsthat contribute to human disease, which we thenvalidate in model organism and/or human cells.

Project 1Identification and validation of novel mutationsthat cause or modify Parkinson's disease (PD).

Therapies for neurodegenerative diseases, such asPD, represent an unmet clinical need. This projectis designed to rapidly identify novel drug targetsfor the treatment of PD. This project involvesanalysis of large genomic data sets followed byvalidation of these data in model organisms. Wehave access to novel PD genomics data and areinvolved in collaborative efforts to genotype andsequence samples from PD patients,asymptomatic close relatives, and control patients.We will then analyze these data within the contextof other genomics approaches to PD, followed byfunctional validation of these data using the fruitfly Drosophila melanogaster. In some cases thismay also involve the generation and phenotypingof transgenic mice when appropriate. Thesuccessful applicant will receive training in analysisof large genomics data sets and deep sequencingefforts, basic training in animal models of PD aswell as in vivo electrophysiology. Some previousexperience with sequence analysis or genomicsmodelling approaches will be preferred.

Project 2Prediction and validation of novel drugs fortreatment of PD.

This project is designed to directly identify newtherapeutic approaches (i.e. small molecules) forthe treatment of PD. This project is a mixture ofcomputational analysis of large genomic data setsand validation of these data in model organisms. Inthis project we will employ genomics approaches


to identify key genes involved in PD and will thenpredict small molecules that may target key PDgenes. Finally we will functionally evaluate a shortlist of candidate small molecules in fruit fly andmouse models of PD. The successful applicant willreceive training in analysis of large genomics datasets and deep sequencing efforts, basic training inanimal models of PD, as well as training in in vivoelectrophysiology, however some previousexperience with bioinformatics analysis orelectrophysiology will be preferred. At the end ofthis project we hope to have identified novel, FDAapproved therapeutics ready for trial in humanpatients with PD.

Project 3Identification and validation of novel mutationscausing severe chronic pain.

There is currently a lack of effective therapies totreat chronic pain diseases such as neuropathic pain.In this project, we will perform a genome-wideassociation study (GWAS) for chronic pain in fruitflies. These data will then be subject tobioinformatics analysis and compared to parallelunpublished human pain genomics approaches. Wewill then validate candidate GWAS loci using in vivotransgenic RNAi. Efforts will also be made toidentify key neural circuitry required for higher orderpain processing in the brain. The successful applicantwill receive training in delicate surgical manipulationof neural populations in live fruit flies as well as invivo electrophysiology.

Project 4Identification of novel drugs for the treatment ofhighly pathogenic influenza infections.

Highly pathogenic influenza, such as bird or swineflu, represents a major health concern and social riskto our society. The dangers of new highlypathogenic and transmissible influenza is clearlyexemplified by the pandemic of 1918, killing 50-100 million people or ~10% of those infected,resulting in the death of ~3% of the worldpopulation, and this devastating outbreak occurredbefore global air travel was commonplace. Despitemajor advances in medicine over the 20th century,

we are still extremely limited in our ability to treathighly pathogenic influenza infection, using most ofthe same strategies that were employed in 1918.We have a long-standing interest in host defence topathogens, and have developed a rapid, safe, invitro method for assessing the innate immuneresponse to bird and swine flu. In this project we willassess and model the innate immune response tobird/swine flu infection at the genomics level, anduse bioinformatics to predict key regulators ofinnate immunity. We will then identify candidatesmall molecule compounds predicted to block thesekey innate immune regulators and test thesecompounds for efficacy in suppressing the humaninnate immune reaction to influenza in vitro andeventually in mice as well. The successful applicantwill receive training in analysis of large genomicsdata sets and deep sequencing efforts, basictraining in handling human peripheral blood cells andinstruction in assessing innate immune responses toinfluenza in vitro (human) and in vivo (mice). Someprevious experience with bioinformatics analysis orbasic tissue culture will be preferred. At the end ofthis project we hope to have identified novel, FDAapproved therapeutics ready for trial in humanpatients with highly pathogenic influenza infections.

Recent publications1. Neely et al. A genome-wide Drosophila screen for heat nociception

identifies _2_3 as an evolutionarily conserved pain gene. Cell. 2010Nov 12;143(4):628-38.

2. Neely et al, A global in vivo Drosophila RNAi screen identifies NOT3as a conserved regulator of heart function. Cell. 2010 Apr2;141(1):142-53.(Cover).

3. Pospisilik et al, Drosophila genome-wide obesity screen revealshedgehog as a determin ant of brown versus white adipose cell fate.Cell. 2010 Jan 8;140(1):148-60.

4. Cronin et al, Genome-Wide RNAi Screen Identifies Genes Involved inIntestinal Pathogenic Bacterial Infection. Science. 2009 Jul17;325(5938):340-3.

5. Imai et al, Identification of oxidative stress and Toll-like receptor 4signaling as a key pathway of acute lung injury. Cell. 2008 Apr18;133(2):235-49.

6. Pospisilik et al, Targeted deletion of AIF decreases mitochondrialoxidative phosphorylation and protects from obesity and diabetes.Cell. 2007 Nov 2;131(3):476-91. (Cover).

Supervisor: Dr Greg NeelyPain Research GroupE: [email protected]: 02 9295 8297


Neurodegenerative Disorders ResearchPhD Studies in Dr Bryce Vissel's group allow you theopportunity to learn and develop cutting edgetechnologies and approaches that will contribute toa deeper understanding and treatment ofParkinson's disease, Alzheimer's disease or spinalcord disorders. The group uses sophisticatedapproaches to understand how synaptic dysfunctionleads to neurodegeneration and to identify potentialapproaches to reverse the disease process. Inaddition to studying mechanisms ofneurodegeneration, the group studies stem cells andthe mechanisms underlying regeneration in thenervous system. The goal of this work is to identifyapproaches that could drive recovery in the brain indiseases such as Parkinson's and Alzheimer'sdisease. All our projects will train you in a widerange of cutting edge approaches, includinganatomy, molecular biology, gene therapy,physiology, animal behaviour, cell culture, high endmicroscopy, surgery and so on. Our group is helpful,friendly and highly motivated. These are kinds ofstudies you could undertake:

Project 1Neural Regeneration Research and studies of StemCells in Parkinson's and Alzheimer's disease.

Students will have the opportunity to study neuralregeneration in our group. Adult neurogenesis is theprocess by which the brain generates new nervecells in the adult central nervous system (CNS) fromstem cells that naturally exist in the brain.Stimulating neurogenesis may potentially offer atherapeutic approach for neurodegenerativediseases such as Parkinson's disease, Alzheimer'sdisease, and spinal disorders. In our group, we areworking to identify mechanisms that regulate adultneurogenesis (neural repair mechanisms) in thenormal and diseased brain, to determine ifmanipulating these mechanisms may offertherapeutic potential. The students who areinterested in research projects in this area will learnadvanced techniques in the study of neurogenesisand neural stem cells. Techniques learned willinclude: (1)Stereotaxic survival surgery and genetherapy approaches, (2) Immunohistochemistrycombined with advanced confocal microscopy andstereology for analysis of regeneration. (3) Use of invitro cell systems, including neural stem cells, forstudying neurogenesis. (4) Behavioural testing todetermine the capacity for functional recovery inanimal models (5) molecular biology. Research into

mechanisms and role of neural regeneration is acutting edge area of research worldwide and theresearch has significant potential to lead toimportant discoveries.

Project 2The role of immune processes in Learning andMemory, and in Parkinson's and Alzheimer's disease.

Our lab's studies are identifying a criticallyimportant role for inflammatory processes in brainplasticity and disease. In our group, we areworking to identify mechanisms that regulate theinteraction between inflammatory cells andneurones in specific brain regions, with a view tounderstand how these mechanisms ultimately leadto normal bran function, or abnormal brainfunction in diseases such as Parkinson's andAlzheimer's disease. The students who areinterested in research projects in this area will learnadvanced techniques in the study ofneurodegeneration and neuroinflamation.Techniques learned will similarly include: (1)Stereotaxic survival surgery and gene therapyapproaches, (2) Immunohistochemistry combinedwith advanced confocal microscopy andstereology for analysis of regeneration. (3) Use ofin vitro cell systems. (4) Sophisticated learning andmemory and movement studies in mice (5)Molecular biology. Research into mechanisms androle of neurodegeneration and neuro-inflamation isanother cutting edge area of research worldwideand the research has significant potential to leadto important discoveries.

Project 3Post-transcriptional events that regulate neuralplasticity, memory and diseases.

We have recently identified RNA editing of specificneuronal RNAs as a novel mechanism that canaffect Parkinson's disease, Alzheimer's disease andbehaviour in mice. This is an exciting and novelproject that offers interesting possibilities forsignificant new insights into brain function. Theexperiments will use similar methods to thosedescribed for the projects above.

Supervisor: Dr Bryce VisselNeurodegenerative disorders researchE: [email protected]: 02 9295 8293

HEARING RESEARCH UNIT24

Project 1Tinnitus, hearing loss, and frequency organisationin the inferior colliculus.

Project 2Pathophysiology of hearing loss in the lateralsuperior olive.

Project 3Protection from noise trauma using anti-oxidants.

Our laboratory offers opportunities for students tostudy brain mechanisms of normal hearing so thatwe can better understand hearing loss and itsaccompanying brain abnormalities. In children,hearing loss impairs speech and languagedevelopment, which in turn undermines academicachievement. In adults, it has a negative impact onemployment opportunities and social functioning. Itcan create social isolation that develops intodepression, which in turn can lead to early onsetdementia. Many aspects of deteriorated hearing,such as listening to speech in a noisy background,cannot be explained solely on the basis of pathologyin the inner ear. Performance on these tasks is likelyaffected by neural reorganisation or deterioration inbrain circuits.

Studies of experimental animals have shown thatcongenital deafness results in abnormal auditorysynapses and pathologic alterations in centralauditory pathways. Disease, head trauma, ageing,drugs, and loud noise can cause hair cells to die.When hair cells die, they are gone forever and ourhearing diminishes. One way to think about hearingloss is that we lose resolution of our soundenvironment. When we are young, we have high-density auditory input to the brain. It is analogous tohaving high definition television for sight. Forreasons we can't explain, ageing typically causes haircells corresponding to high frequencies to die first.We might notice this loss when consonant soundsof speech, such as 's', 'f' and 'th', become difficult todistinguish. As receptor cells die, our soundenvironment “pixilates” and hearing loss worsens.You can hear sounds but the details are blurry. Manypeople wrongly assume that hearing loss can be

treated by simple amplification. In fact, hearing losshas many additional adverse symptoms; speechcomprehension in a noisy background is lost; tinnitusor ringing of the ears often emerges; andsometimes there is severe loudness distortion.Hearing loss is not just about volume. Increasing theloudness often does not improve auditoryperception; amplifying a fuzzy signal just gives you aloud fuzzy signal.

Projects will be designed using mice with variableexpressions of hearing loss and will experiment withintervention methods including hearing aids andacoustically enriched sound environments.Physiological and anatomical investigations willexamine changes in temporal processing andloudness perception and investigate thecorresponding changes in synaptic structure andorganisation of neural inputs to cells. Students willbe expected to learn techniques related to in vivosingle cell recordings, auditory brainstem responses,and otoacoustic emissions. Pathway tracing andimmunocytochemistry methods using light andelectron microscopy are also a normal part of thelab repertoire so that cell-to-cell circuits can bedescribed and structure-function relationshipsdetermined. These kinds of studies will focus on therelationship between hearing loss and synapticorganisation of the auditory system.

Supervisor: Prof David RyugoE: [email protected]: 02 9295 8288

25OSTEOPOROSIS & BONE BIOLOGY PROGRAM

Prof Peter Croucher Osteoporosis and Bone BiologyProgram Leader

Research at the Osteoporosis and Bone Biology Program is focused on understanding the causes anddevelopment of new treatments for major diseases of the skeleton, particularly osteoporosis and cancers,such multiple myeloma, and breast and prostate cancers that metastasise to bone. The latest cutting edgetechnology in genomics, proteomics and contemporary imaging approaches are being applied to addresscritical clinical questions in skeletal medicine. Students in the Program have made fundamental discoveriesthat are having a real impact in skeletal medicine. Garvan researchers were the first to show theimportance of genes in regulating the skeleton; have identified critical molecular pathways that regulatebone; and recently discovered the importance of neurological control of bone. Work undertaken at theGarvan has also led to the development of new approaches to predicting who will fracture their bones, anexample of laboratory discoveries being translated directly into the clinic for patient benefit. Research fromthe Osteoporosis and Bone Biology Program has been published in high ranking journals such as Nature,

Nature Genetics, Blood, JAMA, & N.Engl J. Med. PhD students participate and present their work at majorinternational scientific meetings and attracted numerous awards. Our postgraduate students are highlyregarded, gaining their own fellowships and have established their own independent scientific careers oftenat prestigious Institutes and Universities in the US, UK and Europe.

The Croucher lab's research interests are in themajor diseases of the skeletal system, particularly indiseases such as osteoporosis and tumours thatgrow in bone, including multiple myeloma, or thosethat metastasise to bone, such as breast andprostate cancer. Our research interests are inunderstanding the cellular and molecularmechanisms that lead to these conditions with theaim of developing new approaches for clinicalintervention. In recent years we have developednew screening tools that have allowed us to identifynew genes that control bone strength anddeveloped new approaches to increasing bonemass. We have also developed novel high-resolutionimaging technologies that allow us to visualiseindividual metastasis-initiating cells as they colonisethe skeleton. Building upon these discoveries we arenow Utilising the latest next generation genomictechnology, bioinformatic and systems biologyapproaches, and the latest high-resolution imagingto taking these projects forward. We have a numberof projects available in the following areas:

Project 1New gene targets for anabolic therapy inosteoporosis.

Treatments for osteoporosis prevents further boneloss but have a limited ability to restore bone massso patients continue to fracture. In collaborationwith Professor Graham William and Dr Duncan

Bassett at Imperial College London, we havescreened knockout mice from the Wellcome TrustSanger Institute Mouse Genetics Programme andidentified strains with increased bone strengthresulting from deletion of genes not previouslyknown to have a role in the skeleton. This projectwill establish the role of these pathways incontrolling bone strength and identify newtherapeutic targets for treating osteoporosis.

Project 2Targeting 'metastasis initiating cells' in breast andprostate cancer.

Bone metastases are a devastating clinicalconsequence for patients with breast and prostatecancer. The mechanisms leading to theirdevelopment are poorly defined, and approachesto prevention and treatment limited. We havedeveloped new high-resolution imagingtechnology that allows us to visualise the tumourinitiating cells, at a single cell resolution, in theskeleton. Projects in this area will use the latestimaging technology and next generation geneticand bioinformatic tools to establish a genetic andmolecular fingerprint of these tumour-initiatingcells and utilise this knowledge to develop newtherapeutic approaches to preventing thedevelopment of bone metastasis.

OSTEOPOROSIS & BONE BIOLOGY PROGRAM26

Project 3Defining the tumour initiating cells in multiplemyeloma.

Multiple myeloma is a B-cell neoplasmcharacterised by the growth of tumour cells in theskeleton and the development of a devastatingbone disease. We have developed novel in vivoimaging technology to study single myeloma cellsand their interactions with bone in vivo anddiscovered new molecules implicated in myelomabone disease. We will use this new technology andnext generation genetic and bioinformaticapproaches to define a genetic and molecularfingerprint of these cells, establish the role ofosteoblasts in regulating their behaviour and utilisethis knowledge to develop new therapeuticapproaches.

Supervisor: Prof Peter Croucher E: [email protected]: 02 9295 8243

Genetics and Epidemiology GroupOsteoporosis is a systemic skeletal diseasecharacterised by low bone mass and degenerativemicroarchitectural deterioration of bone tissuewhich consequently increase bone fragility andsusceptibility to fracture risk. The chance that a 50-year old woman has a hip fracture during herlifetime is about 12%, which is equivalent to orhigher than her risk of having breast cancer.Fracture is a serious event because it is associatedwith reduced life expectancy.

Our group is primarily interested in translationalscience of osteoporosis. We are interested inidentifying genetic and environmental risk factorsthat contribute to fracture susceptibility andmortality risk. We are actively working on theconcept of individualised prognosis of osteoporosisby using genes, hormones, bone turnover markers,and bone strength related parameters.

We have carried out genetic association studies,including participating in genomewide associationstudies (GWAS). We also perform a genome-widelinkage study to discover novel genes that areinvolved in the regulation of bone phenotypes andfracture risk. This line of research requires expertisein clinical medicine, genetics, and bioinformatics.

Specific projects included, but not limited to:

Poject 1Analysis of gene-gene and gene-environmentalinteractions on bone phenotypes.

Gene-gene interaction or epistasis is aphenomenon whereby the effect of one gene on aphenotype is modified by the presence of anothergene in the same or different chromosomes. Thepresence of epistasis presents a challenge in theanalysis of genetic association studies. We areinterested in an Bayesian approach to detect gene- phenotype association in human populations arenot sensitive enough to detect epistasis inosteoporosis phenotypes.

Poject 2Development of clinico-genetic prognosticmodels for individualising fracture risk.

We have developed a risk factor based model forpredicting fracture risk. We want to refine themodel by including genetic data. With a rapidimprovement in genotyping technology, nextgeneration of GWAS will be adding more variantsat a low frequency to cover as many SNPs aspossible. We are interested in the integration ofgenetic profiling into the existing prognostic modelto improve the predictive accuracy of fracture riskfor an individual.

Poject 3Development and validation of a compositeoutcome that captures all clinical aspects ofosteoporosis.

Patients with an existing fracture have anincreased risk of subsequent fracture andmortality. The hypothesis is that fracture, re-fracture, and mortality collectively provide abetter outcome that reflects the underlyingclinico-pathology of osteoporosis. The primary aimof this proposed project is therefore to develop a“composite outcome” for osteoporosis to capturefracture and its adverse outcomes.

27OSTEOPOROSIS & BONE BIOLOGY PROGRAM

Poject 4Role of biochemical markers of bone turnover inthe prognosis of fracture risk.

This project seeks to determine the short-termwithin-subject variability of bone turnover markers,and develop a sensitive longitudinal algorithm fordetermining the actual value for an individual andscreening for significant changes in those markerswithin an individual patient.

Poject 3Relationship between sarcopenia and osteoporosis.

Sarcopenia is a condition characterised by lossmuscle mass and reduced muscle strength. Thisproject is aimed at defining the gender-specificrelationship between muscle properties (i.e., musclemass, muscle strength, and muscle quality) andfragility fracture in men and women. The project willalso develop clinically based criteria for thediagnosis of sarcopenia that can be applied to thegeneral population.

ResourcesOur group is one of the world's leading osteoporosisresearch centres, with extensive experience in thegenetics of osteoporosis. Our work has beenpublished in Nature, Nature Genetics, New EnglandJournal of Medicine, Lancet, JAMA. More than 10papers from our group are among the highly citedpapers in the world. By joining our group, studentswill not just have access to leading experts, but alsoto extensive scientific resources, includingsophisticated genetic and bone analyticalequipments, and high performance computing.

Supervisor: Prof Tuan NguyenGenetics and Epidemiology GroupE: [email protected]: 02 9295 8277

Genetics & Epidemiology GroupNeuropeptide activity in the initiation andmaintenance of Anorexia Nervosa?

Anorexia nervosa (AN) is the most lethal psychiatriccondition, with up to 20% mortality over 20 years.Sadly, AN is an increasing health issue, with patientspresenting at younger ages and with increasingfrequency. To date, treatment options are severelylimited, however, recovery and survival rates aremarkedly improved (70% recovery at 12 months) ifrefeeding is included with normal psychiatric care.This is clear evidence for the importance ofrefeeding to this condition, formerly treated as apurely psychiatric disease.

Our laboratory, in collaboration with theNeuroscience Division, using genetic mouse models,has been instrumental in examining the action of afamily of neuropeptides, the Neuropeptide Y (NPY)system. These neuropeptides have been shown toexert powerful actions on fat and bone mass. Oneof the peripheral members of this family, PYY whichis produced in the gut in response to food intake, isan extremely powerful modulator of appetite andbone mass. It has been shown to be abnormal instates of altered body weight such as AnorexiaNervosa and obesity.

In Anorexia Nervosa, PYY is elevated which isconsistent with the loss of fat mass and bone massin these patients. It is our hypothesis that elevatedPYY alters the signalling of critical pathways in thebrain that control feeding, behaviour, hormoneproduction and bone mass, thereby producing acascade critical to the persistence and possibly evenaetiology of AN.

This project will combine both basic and clinicalaspects of research, the proportion of which can bealtered depending on the interests of the student.The basic research will dissect the central andperipheral actions of PYY in an effort to isolate atarget for therapeutic intervention. The clinicalresearch will involve collaboration with theChildren's Hospital at Westmead who have a largeintake of acute Anorexia Nervosa and all the tools in

OSTEOPOROSIS & BONE BIOLOGY PROGRAM28

place for assessment of changes in weight and bonein conjunction with serum levels of PYY among otherrelated hormones. There is also the potential for agenetic study examining the role of PYY in the firstdegree relatives of subjects with Anorexia Nervosa.

Supervisor: A/Prof Jackie CenterGenetics and Epidemiology GroupE: [email protected]: 02 9295 8271

Bisphosphonates are a “blockbuster” class of drugsused worldwide for the treatment of common bonediseases such as post-menopausal osteoporosis,cancer-induced bone loss and Paget's disease. Mylab is a world-leader in characterising how thesedrugs work at the cellular and molecular level. Wemade the breakthrough discovery a few years agothat most of these drugs work by inhibiting FPPsynthase, a critical enzyme involved in thebiosynthesis of cholesterol and a variety of lipidintermediates necessary for the lipid modification(prenylation) and hence normal function of essentialsignalling proteins. Several PhD projects will beavailable in my lab, addressing clinically importantquestions about the pharmacology and biologicalactions of these drugs and the role of prenylatedproteins in cancer cells.

Molecular Pharmacology Group

Project 1Modelling the Mevalonate Pathway in theTreatment of Bone Diseases.

In this project we will seek to understand: _ How inhibition of FPP synthase by bisphosphonate

drugs affects upstream and downstreammetabolites and enzymes of the mevalonatepathway, leading to adverse drug effects;

_ How different isoforms and modifications of theFPP synthase enzyme might affect theresponsiveness of patients to bisphosphonate drugs.

The accumulation of lipid metabolites directlyupstream of FPP synthase is the cause of acommon flu-like side-effect of bisphosphonatedrugs. A mathematical model of the pathway thatwe have developed will be tested, in well-established cell and organ culture models, to predictthe effect of bisphosphonates and other drugs on

lipid metabolites and enzyme expression using arange of molecular biology techniques includingmass spectrometry and quantitative PCR. Isoformsand newly-discovered post-translationalmodifications of FPP synthase, and their relevanceto differences in drug responsiveness betweenpatients, will be analysed using a variety of state-of-the-art next-generation sequencing,bioinformatic and proteomic approaches.

Project 2Proteomics and the Role of Prenylated Proteins inTumour Cells.

This project will: _ Optimise new, highly sensitive proteomic

techniques to identify lipid modified (prenylated)small GTPase signalling proteins.

_ Use these techniques to profile the expression ofprenylated small GTPases in normal cells andcancer cells and identify potential mechanismsinvolved in tumour growth and spread.

We have begun to develop an exciting newtechnique to identify prenylated proteins, utilisingbiochemical and 2D electrophoretic methods andmass spectrometry. Together with other state-of-the-art proteomic methods such as DIGE andSILAC, we have identified some changes in thelevels of prenylated Rab GTPases, involved invesicular trafficking, in cancer cells. This project willdevelop these observations to further study therole of Rab proteins and other small GTPases in thespread of tumour cells to the skeleton.

References1. Rogers, M.J., Crockett, J.C., Coxon, F.P., Monkkonen, J. (2011).

Biochemical and molecular mechanisms of action ofbisphosphonates. Bone 49 (S1), 34-41.

2. Itzstein C, Coxon FP, Rogers MJ. (2011). The regulation ofosteoclast function and bone resorption by small GTPases. Small

GTPases 2, 117-130. 3. Coxon, F.P., Taylor, A., Stewart, C.A., Baron, R., Seabra, M, Ebetino,

F.H. & Rogers, M.J. (2011). The gunmetal mouse reveals Rabgeranylgeranyl transferase to be the major molecular target ofphosphonocarboxylate analogues of bisphosphonates. Bone 49(S1), 111-121.

4. Roelofs, A.J., Jauhiainen, M., Mönkkönen, H., Rogers, M.J.,Mönkkönen, J. & Thompson, K. (2009). Zoledronic acid causesaccumulation of IPP/DMAPP selectively in peripheral bloodmonocytes due to efficient drug uptake. Br. J. Haematol. 144,245-50.

Supervisor: Dr Mike RogersE: [email protected]: 02 9295 8272

29GARVAN BIOINFORMATICS

and scientific literature databases. Very largedatasets from genome sequencing require highperformance computing infrastructure, and wehave recently installed such a system. Thesuccessful candidate will develop tools to harnessthis infrastructure.

Required BackgroundThese positions could be filled by students from a range of backgrounds, including bioinformatics,biochemistry, chemistry, physics, or computerscientists.

For the Genome Informatics a keen interest inbiology, and genome biology in particular is vital.Students with good scripting language skillsespecially in Python and the R-language would bean advantage, as would some familiarity with Java.An interest in GPGPU programming and map-reducetechniques like Hadoop would also be very helpful.

For the visualisation projects and an interest inusing data visualisation, human computerinteraction, usability, or design to address keychallenges in basic biomedical research. Ofparticular interest would be students with strongJavaScript or Java3D skills, as well as a stronginterest in using HTML 5 to build the next-generation of visualisation tools for analysingomics datasets for systems biology. There is alsoscope for students wishing to focus not on tooldevelopment, but on applying visualisationtechniques to data from various disease areas,possibly in collaboration with other groups at Garvan.

Supervisor: Dr Warren Kaplan and Dr SeánO'DonoghueE: [email protected] T: 02 9295 8146

In the last decade new technologies like massively parallel sequencing have transformed biology and medicalresearch from the study of individual genes or proteins to system-wide approaches. These technologiesprovide us with unprecedented insights into the biology of disease. However, they also generate enormousamounts of data and the role of Garvan's Informatics group is to make sense of these data. We do this onour locally housed data using high-performance computing methods, but as datasets have grown so largethat we cannot bring them in-house,we also mine them on remote locations. Much of what we do is thewriting of software to analyse the data, but because of its complexity we also use and develop innovativevisualisation methods to gain deeper insights into disease. We work very closely with bench scientists atGarvan who use our analyses to test hypotheses that we develop. Our students are an integral part ofachieving this vision. As bioinformatics is a new field with very few practitioners having been trained asbioinformaticians we look for talented individuals from the worlds of mathematics, physics, chemistry,computer-science and biology to achieve these aims.

General Research Project AreasThe sequencing of the human genome took 10years and cost almost $3 billion. Now withmassively parallel sequencing we're able tosequence a genome in days for only a few thousanddollars, and this has brought whole genomesequencing into the hands of individual researchersand have spawned the viability of genome medicine.From the time of the sequencing of the first humangenome over 10 years ago, genome biology has,and continues, to rewrite our understanding ofbiology, so that today we see the genome as anexquisitely regulated machine. We are interested inunderstanding this exquisite regulation in thecontext of diseases being studied at Garvan. Forfurther details contact [email protected].

The Garvan has recently started a new groupfocused on developing methods and tools forvisualising biological data. Jointly associated withCSIRO, the group focuses primarily on usingprinciples of usability, data visualisation, human-computer interfaces, and graphic design to developstate-of-the-art methods and tools that addresscutting edge challenges in biological and biomedicalresearch. A second focus of the team is on usingthese methods to analyse experimental datasets incollaboration with groups at the Garvan. Projectswill include the VIZBI initiative (http://vizbi.org), theReflect system for enhancing scientific literature(http://reflect.ws), and developing methods forintegrating macromolecular 3D structures withgenomics, proteomics, and other systems biologydata. For further details see http://odonoghuelab.org/.

Techniques UsedBioinformatics software development, graphicsdesign, 3D graphics, 3D animation, Human-computer interface development. Applications todata from genomics, proteomics, systems biology

Applications are submitted online at:www.garvan.org.au/education. All applicationsare considered by the Garvan Higher DegreesCommittee (HDC).

Closing dates for applications are: _ 31 October for admission in Semester 1

(March commencement)_ 30 April for admission in Semester 2

(July commencement)

Applications outside these times will only beconsidered in exceptional circumstances.

As Garvan is a not-for-profit organisation, it isunlikely that a research program would have thefunds to take on a postgraduate student withoutscholarship funding of some kind. However,there are many different sources of fundingavailable for postgraduate research students,such as UNSW APA, UIPA, IPRS and NHMRC.

Prospective students must also lodge anapplication for admission to UNSW online at:www.grs.unsw.edu.au/futurestudents/apply.html.As part of this process, you will need to haveagreed a potential research project with yoursupervisor.

Notes

garvan phd_projects_2013

Health & Medicine