School research areas

Although metastasis is the foremost cause of cancer-related death, a specialized mechanism that reprograms anchorage dependency of solid tumour cells into circulating tumour cells (CTCs) during the metastatic cascade remains elusive. The Adherent-to-Suspension Transition (AST) has been proposed as a reprogramming of adherent cells into suspension cells via the aberrant induction of hematopoietic transcriptional regulators, which are hijacked by solid tumour cells to disseminate into CTCs.

Here we aim to investigate melanoma dissemination by using a synthetic epigenetic reprogramming approach to alter AST factors. The project will use mouse models and de novo metastatic patient specimens to uncover how Adherent-Suspension Plasticity (ASP) dictates anchorage plasticity during the dissemination and colonization process within the metastatic cascade.

Expected Outcomes and Impact: The results will uncover therapeutic strategies that target AST factors that can be deployed to abrogate CTC formation and suppress distant metastases specifically.

These findings will underscore an important early mechanism by which cancer cells spread and highlight novel targets for the development of anti-metastatic therapies.

Preferred applicant: We are seeking a highly motivated and diligent HDR applicant who has demonstrated the capacity to work independently. A background in cancer research, genetic engineering and molecular biology is required.

Highly desirable skills: Experience in working with animals and managing animal research ethics Experience with bioinformatics analysis using R, python and/or command line.

A scholarship may be available for this project. Applications close 12 June 2025.

Contact: Professor Elin Gray

Summary: Alzheimer’s disease (AD), the leading cause of dementia worldwide, is a complex disease with many
underlying genetic and environmental risk factors, resulting in inter‐individual variation in presentation
and trajectory. This project will utilise statistical and machine‐learning approaches to construct genetic
risk scores for improved genomic prediction of AD onset and progression.  Further, it will explore whether
modifiable lifestyle factors (e.g., physical activity, sleep) can mitigate genetic risk of AD, and identify the
stages along the disease trajectory where this effect is greatest. This study will help to identify individuals
likely to benefit from early pharmacological or non‐pharmacological (i.e., lifestyle) interventions, which
may delay or prevent disease onset.

Preferred applicant:

We are looking for applicants with a high level of achievement, including an Honours or Masters by
Research degree. Alternatively, a Masters by Coursework in a highly desired area (e.g. bioinformatics, data
science, statistical genetics) with demonstrable research experience (e.g. research publications). The
ideal candidate will have experience in statistical analysis and genetics, excellent organisational and
communication skills, and a strong understanding of research methods.  Well‐developed skills in the use
of R statistical software and previous experience in the use of software for analysis of genetic data and
construction of genetic risk scores (e.g. PLINK, PRSice) are highly desirable.

Contact: Dr Eleanor O'Brien

A scholarship may be available for this project. Applications close 12 June 2025.

Summary: Adoptive cell therapy (ACT) with tumor‐infiltrating lymphocytes (TIL) has demonstrated durable responses
in patients with solid malignancies, particularly for cutaneous melanoma.  Through collaboration with the
Harry Perkins Institute of Medical Research and Centre for Tissue Therapy WA, our team will deliver a TIL
ACT treatment called Perkileucel. This cell therapy will be manufactured in Therapeutic Goods
Administration (TGA)‐accredited laboratories in Perth, and a clinical trial will open at the end of 2024. The
PhD project aims to evaluate biomarkers in blood and tumor tissue to identify predictors of response to
TIL ACT and monitor the patient's response to treatment.

Preferred applicant:  We are looking for a motivated applicant who aspires to make a difference to cancer patients through the
application of translational research, with background knowledge of immunology and molecular biology.  
The following attributes are desirable:
* Experience in statistics and machine learning, and
* Excellent organisational, problem‐solving and project management skills.

Internship opportunity through iPREP Biodesign which is based on an application process.

Contact: Professor Elin Gray

A scholarship may be available for this project. Applications close 12 June 2025.

Summary: Immune checkpoint blockade (ICB) inhibits tumour immune escape and has significantly advanced cancer therapy, in particular for melanoma and lung cancer. However, ICB benefits only a minority of patients treated and may lead to many immune-related adverse events. Therefore, identifying factors that can predict treatment outcomes, enhance synergy with ICB, and mitigate immune-related adverse events is urgently needed. Tertiary lymphoid structures (TLS) are ectopic lymphoid tissues that arise within or around a tumour and have been found to be associated with better prognosis and improved clinical outcomes after ICB therapy. TLS are dynamic structures where various immune cell subpopulations interact. These interactions can influence the overall immune response, either promoting or inhibiting tumour growth depending on the context. TLS facilitate the maturation of immune cells, including T cells and B cells, which are essential for mounting an effective anti-tumour response. However, the precise mechanisms and signals that initiate and regulate the formation of TLS are not fully understood. Moreover, although TLS are associated with better outcomes in immunotherapy, the exact ways they interact with different types of immunotherapies and how they can be manipulated to improve treatment responses need to be researched.

Our team has shown that a B-cell signature, referred, can be detected in the plasma of patients with improved clinical outcomes after ICB therapy, which overlaps with reported TLS gene expression signatures. The proposed PhD project will aim to:

1. To develop a murine model for the induction of TLS
2. To evaluate the evolution of the B-cell signature relative to TLS maturity
3. To analyse TLS and TME contexture, relative to B cell subpopulations and antigenic specificities.

Expected Outcomes and Impact: The results will underscore the aetiology of the B-cell signature observed in plasma relative to TLS formation and maturation. The study aims to uncover the role of B-cells in orchestrating the anti-tumour immune response and may reveal therapeutic strategies to enhance this response or enhance the activity of ICB.

Preferred applicant: We are seeking a highly motivated and diligent HDR applicant who has demonstrated the capacity to work independently. A background and interest in immunology and cancer research is required.

Highly desirable skills: Experience in working with animals and managing animal ethics, Experience in Windows and Linux operating systems, Experience with bioinformatics analysis using R, python and command line

Contact: Professor Elin Gray

A Scholarship may be available for this project. Applications close 12 June 2025.

Melanoma treatment has been revolutionised by the advent of immune check point inhibitors (ICIs). However, only 50% of patients will respond to the treatment. A promising alternative for those who ICI is ineffective is tumour infiltrating lymphocyte (TIL) therapy, an innovative form of immunotherapy that involves extraction, expansion and infusion of a patient’s specific immune cells (T cells). In an Australian first, the PERTIL trial, led by Prof Elin Gray, will be treating ICI resistant melanoma patients with TIL therapy. Predicting who will benefit from TIL therapy will be an important complementary work to the PERTIL trial.

Our team has shown the value of circulating tumour DNA (ctDNA) as a blood-based biomarker for melanoma. Plasma-derived ctDNA can be distinguished from normal cell free DNA (cfDNA) by differences in biology, including fragment length and tumour-induced DNA lesions. Thus, this project will leverage ctDNA genomics and bioinformatics to predict patients that would benefit from TIL therapy.

Specific Aims: 1) Construct a machine learning model of cfDNA features which can predict response to TIL therapy at baseline. 2) Longitudinally monitor patients for markers of treatment response and resistance using cfDNA.

Expected Outcomes and Impact: The development of a novel biomarker that could be used to predict which patients will benefit from TIL therapy. The successful completion of the project will provide clinicians with more information regarding the success of TIL therapy prior to administration.

Preferred applicant: We are looking for a HDR applicant with extensive wet lab experience in cfDNA extraction, library preparation and next generation sequencing. We also expect that the student is proficient in both windows and linux operating systems, as well as having previous experience with bioinformatics analysis using R, python and command line.

Contact: Dr Aaron Beasley

This project aims to explore the expectations and perceptions of what a genetic test can provide from the perspective of people seeking out private genetic testing. Exploring what people perceive genetic testing can do will allow for a greater understanding of the gap between current technology and expectations (Masters by Research project).

Contact: Professor Simon Laws

This project aims to examine patient satisfaction with private genetic counselling services across all areas of service, i.e. familial cancer, reproduction, adult, paediatrics and pharmacogenomics. Demonstrating patient perspectives and satisfaction may drive change within the industry leading to better healthcare outcomes in genetic health of the population (Masters by research project).

Contact: Professor Simon Laws

Leveraging extensive existing genome wide genetic and longitudinal clinical phenotype (brain imaging, cognition) data combined with bioinformatic approaches, this program of research will further our understanding of the genetic contributions to Alzheimer's disease development and progression.

Contact: Professor Simon laws

Leveraging extensive longitudinal epigenetic (genome wide methylation) and clinical phenotype (brain imaging, cognition) data combined with bioinformatic approaches, this project will contribute significantly to understanding epigenetic changes that occur during the development and progression of Alzheimer’s disease.

Contact: Professor Simon Laws

This research program investigates the interaction of genetics and lifestyle/modifiable risk factors (sleep, physical activity, diet, and metabolic factors) in the context of Alzheimer's Disease with the aim of furthering our understanding of gene-lifestyle interactions (Lifestyle Genomics (LGx)) and development of individualised lifestyle interventions and preventative strategies.

Contact: Professor Simon Laws

The overarching aim of this study is to assess the clinical utility of blood derived biomarkers such as circulating tumour cells (CTCs), circulating tumour DNA (ctDNA) and extracellular vesicles for predicting and monitoring response to immune checkpoint blockade in melanoma and lung cancer. It is expected that a suitable candidate has a background in bioinformatic analysis.

Contact: Professor Elin Gray

Uveal melanoma is the deadliest form of eye cancer that frequently metastasises to the liver. Loss of BRCA1-associated protein 1 (BAP1) is associated with elevated risks of metastasis of uveal melanoma. Currently, there is lack of effective treatment options for metastatic uveal melanoma. The research project aims to characterise interactions between BAP1-deficient or BAP1 wild-type uveal melanoma with liver cells and to also investigate the efficacy of a dual HDAC/PI3K inhibitor in preclinical uveal melanoma models.

Contact: Dr Vivian Chua

Contact: Dr Pauline Zaenker

Contact: Dr Xingang Li

This ongoing research project aims to develop precise screening and diagnostic N-glycan biomarker panels, over multiple complex phenotypes, and the investigation of their inter- and intra-population validity.

Contact: Professor Wei Wang

The group are one of the founding members of the Human Glycome Project. The N-glycome may be able to stratify individuals who are at risk of developing more serious chronic diseases, during a window where changed behaviours may have the greatest impact.

Contact: Professor Wei Wang

The group has ongoing research focusing on Suboptimal Health Status in diverse populations differing in age range, socioeconomic status, ethnicity and lifestyle behaviours.

Contact: Professor Wei Wang