Proteomics

“Proteomics” is the area of science dedicated to the large-scale study of proteins. In collaboration with medical oncologists Associate Professor Nick Pavlakis, Professor Stephen Clarke and others, we use cutting-edge technologies to examine how our proteins change when a person develops cancer, or how certain proteins change as patients are treated with different therapies.

Proteomics, the study of the proteome, is the next frontier in personalised medicine.

The proteome is the complete set of proteins present at a given time in a given cell or tissue.

Proteins make up about 42% of the dry weight of our bodies.

Proteomics Research Group Leader: Dr Sarah Hayes

Dr Hayes is a Post-doctoral Research Fellow whose research achievements have been recognised by a Cancer Institute NSW Research Scholar Award and Cancer Institute NSW Early Career Fellowship. Her expertise is in proteomics and a major focus of her research is the identification and verification of protein biomarkers for lung diagnosis, prognosis and response to treatment.  Her work is contributing to the growing field of research into personalised medicine and to our understanding of the effect of molecular cancer pathogenesis on treatment efficacy.

Projects

1. Investigating patterns of drug resistance in ALK rearranged non-small cell lung cancer

Dr Malinda Itchins, Dr Sarah Hayes, Dr Amanda Hudson, Prof Stephen Clarke, A/Prof Nick Pavlakis, and A/Prof Viive Howell

This is a largely non-smoking related lung cancer, characterised by a change to the ALK gene, often affecting a young and fit population. It behaves very differently to smoking related lung cancers and whilst very treatable with targeted therapy, resistance to such treatment is inevitable. Using proteomics, we want to identify the optimal method in which to sequence different cancer treatments in order to delay or overcome the development of resistance, with the ultimate goal of being able to apply the insights gained in the lab to ALK patient care.

Funding: NSW Health PhD Scholarship, 2017 and 2018 Sydney Vital Research Scholar Awards, Ilse Schnell Cancer Research Postgraduate Scholarship

2. Exploring methods to improve efficacy of immunotherapy in non-small cell lung cancer (NSCLC)

Dr Sarah Hayes, Dr Malmaruha Arasaratnam, Dr Kelly McKelvey, A/Prof Viive Howell and A/Prof Nick Pavlakis

Our research project is exploring methods to improve effectiveness of immune therapy in lung cancer. We will be looking to identify if there are proteins secreted in blood that can predict which patients respond well to immunotherapy and which do not benefit from this type of treatment. Using cutting-edge technologies, we hope to identify those key proteins that can help us to personalise patient treatments based on their molecular profile.

Funding: 2019 Ramsay Healthcare Research and Teaching Seed Funding

3. Laying the foundations for improved treatments for IDH-mutated glioma (brain cancer)

Ms Angela Cho, Dr Sarah Hayes, Dr Amanda Hudson, Dr Emily Colvin, A/Prof Michael Back, Prof Stephen Ackland (Hunter Medical Research Institute), A/Prof Helen Wheeler and A/Prof Viive Howell

Low grade gliomas are characterised by a relatively indolent clinical course and a good prognosis. However, these gliomas may recur as high grade gliomas, which are more aggressive and are difficult to treat. Our goal for this research is to better understand the mechanisms which may drive the change in behaviour of these tumours when they recur. To do this, we are comparing the proteomes of original low grade tumour and the aggressive, recurrent brain tumour to identify key proteins that are involved in the recurrence of this disease. Understanding how these tumours change over time and in response to therapy will lay the foundations for developing better treatments for this rare form of brain cancer.

Funding: Mark Hughes Foundation, Hunter Medical Research Institute, Sydney Neuro-Oncology Group and University of Sydney and Balnaves Foundation

4. Identification of biomarkers for Non-Small Cell Lung Cancer

Dr Sarah Hayes, Mrs Rozelle Harvie, Dr Amanda Hudson, Prof Stephen Clarke, A/Prof Nick Pavlakis and A/Prof Viive Howell

We are investigating whether certain tumour-specific molecular characteristics can be detected in minimally invasive samples, like blood, tissue biopsies or exhaled breath. We are ultimately hoping that this research can be used to assist in the earlier diagnosis of patients, prediction of patient prognosis or to help guide personalised cancer treatment selection.

Funding: 2018 Tour de Cure Scott Canner Early Career Fellowship and 2018 Fight for a Cure Early Career Fellowship

5. The exhaled breath condensate proteome: a promising source of biomarkers for lung cancer

Dr Sarah Hayes, Dr Ben Harris, Prof Stephen Clarke, A/Prof Nick Pavlakis, A/Prof Viive Howell

In recent years, there has been increasing interest in using exhaled breath as a tool for screening, diagnosing, and even monitoring diseases of the airway, including lung cancer. Changes in specific proteins found in exhaled breath of lung cancer patients may be an indication of the underlying cancer, presenting a potential screening technique for early detection of this disease. In this project, we are using cutting-edge mass spectrometry to comprehensively map proteins found in human breath from lung cancer patients to identify these proteins. This is the first time ever that the human lung cancer breath proteome (which we have termed the “breathome”) has been profiled by mass spectrometry.

Funding: 2018 Tour de Cure Scott Canner Early Career Fellowship and a 2018 Fight for a Cure Early Career Fellowship

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