Labs

Human cancers harbour defects in processes that inhibit or enhance tumour growth, so-called tumour suppressor and oncogenes. Importantly, these abnormalities render the tumour cells resistant to many therapies.

Our research is focused on understanding how cancers develop and finding new therapy approaches, including targeted drugs as well as immune therapies to treat these cancers.

We aim to identify novel genes involved in the development of normal and malignant haematopoiesis. We are using in vivo CRISPR approaches to systematically identify new candidate genes, with the ultimate goal of using these targets as novel anti-cancer therapies.

We have recently also started to understand the mechanisms of therapy resistance in cancers and how we can overcome this by reducing the fitness of the cancer cells or enhancing immune therapies using different CRISPR approaches.

Identification of tumour immune evasion mechanisms

Cancer immune evasion is a major hurdle in for the success of current immunotherapies, both in the context of adoptive cellular therapy (ACT) and immune checkpoint blockade. Despite the clinical success of diverse immunotherapies, many patients do not respond or ultimately relapse, likely due to tumours evolving to escape sufficient recognition by the immune system. Although considerable progress has been made in understanding how cancers evade immunity, measures to counteract tumour immune escape are lacking. We employ cutting-edge screening mechanisms to identify tumour immune evasion mechanisms and avenues to sensitise tumour cells to T cell-mediated killing.

Genetic/epigenetic control of effective anti-tumour T cell responses

Despite the success of adoptive cellular therapy (ACT) in the context of haematological malignancies, response rates against solid malignancies are poor, likely due to tumour-associated immunosuppression and subsequent T cell exhaustion. Indeed, it is becoming clear that the failure of T cells to elicit a successful and long-term anti-tumour immune response is controlled by transcriptional, epigenetic and post-translational modifications. However, our current understanding of the molecules involved in these processes is limited. We use cutting-edge technology including in vitro and in vivo CRISPR screens, high throughput drug screens and novel single cell sequencing protocols to identify novel underlying molecular mechanisms leading to T cell dysfunction in cancer and identify mechanisms to improve T cell function in this context. We employ a variety of pre-clinical models of CAR T cell therapy and re-directed TCR T cell therapy to validate novel immunotherapy targets for translation into the clinic.

Identification of novel immunotherapy approaches.

High-throughput screening has been a staple in drug discovery in recent decades. Target-based drug discovery relies heavily on singular readouts such as reporter gene expression or perturbation of enzymatic activity in response to small molecule treatment. However, with a recent renewed focus on phenotypic based drug discovery, there is an increased interest in more comprehensive and less biased screening methods that combine aspects of both target-based and phenotypic screening, such as RNA-seq. To complement our genetic screens, we also perform high-throughput drug screens for agents that promote favourable states of T cell differentiation for anti-tumour immunity and agents that increase the immunogenicity of cancer cells. Importantly, identification of such agents would allow us to enhance current immunotherapy approaches.

Tumour infiltrating regulatory T cells

Our body’s immune system can recognise and effectively eliminate tumours. To escape immune attack, tumours hijack a specialised immune cell population known as regulatory T cells (Tregs), which potently suppresses anti-tumour immune cells to promote tumour growth. Targeting Tregs, therefore, is an attractive strategy to revert immune suppression in tumours and boost the function of anti-tumour immune cells. Our laboratory aims to discover transcriptional and epigenetic mechanisms employed by Tregs to infiltrate tumours in vital organs such as the gut, lung, liver and brain. These mechanisms will be harnessed to target Tregs for the treatment of solid tumours.

Stromal-immune cell crosstalk

Tumour microenvironment is composed of actively proliferating tumour cells, stromal cells, blood vessels and a plethora of immune cells. Stromal cells are known to produce a variety of growth factors and immunomodulatory molecules that directly shapes the immune landscape of tumours. We use cutting-edge molecular tools and microscopy to understand the molecular makeup of stromal cells in diverse tissues and tumours as well as their crosstalk with immune cells, in particular Tregs.

Metabolic regulation of tumour immunity

Cellular metabolism is critical for the differentiation, growth and function of tumour cells and immune cells. Metabolic intermediates serve as catalysts for several cellular processes including gene transcription. Systemic metabolic changes also influence anti-tumour immune responses and immunotherapy outcomes. Our laboratory aims to understand how cellular metabolism and tumour derived ‘oncometabolites’ shape the transcriptional landscape of tumour infiltrating immune cells. We also investigate how changes in systemic metabolism affects anti-tumour immunity and immunotherapy outcomes.

Eph receptors

Eph receptors are cell surface proteins that guide cell migration by binding to other cell-bound proteins (ephrins) on adjacent cells, thereby controlling cell-cell adhesion. Ephs coordinate cell movement during normal development of tissue and organ boundaries, and the vascular and neural networks. They are generally scarce in adults but reappear in cancers, where they are often on early ‘progenitor’ cell types, associated with blood vessel formation, and tumour cell invasion and spread.

EphA3 is a particular focus, which we investigate in tumour models, using ‘knock-down’ mice or by treatment with a specific antibody we helped develop, with the aid of drug payloads to specifically target the tumour microenvironment.

ADAM metalloproteases

ADAM metalloproteases (or ADAMs) are cell membrane-bound proteases that shed a range of other membrane proteins, regulating the activity of diverse cell surface receptors. These include Ephs and other receptors controlling cancer cell growth, drug resistance, and invasion and spread to other tissues. ADAMs also play an important role in the tumour microenvironment and in inflammation.

ADAM10 and 17 are of particular interest and we are investigating their function in tumours, as well as developing antibodies and antibody-drug conjugates as potential new therapies.

Targeting Strategies in Cancer

We have identified a series of molecules selectively expressed on cancer cells, and in the tumour microenvironment, that can be targeted for cancer therapy. This includes conformationally exposed receptor epitopes, such as found on the Epidermal Growth Factor Receptor (EGFR) and which led to the development of mAb806 and our first-in-human trials of this molecule. Our research findings have provided a new paradigm in antibody-based targeting and therapy of solid tumours. This work has expanded to incorporate structure-function studies of additional novel antibodies we have developed that target cell surface receptors and tumour microenvironment in tumours, as well as investigating mechanisms of resistance to antibody therapeutics, and targeting key molecules involved in sustaining the tumour microenvironment.

Antibody Engineering

We have developed techniques for generation and humanisation of antibodies. Recent molecular engineering, structural and modelling approaches in our laboratory have defined novel Fc:FcRn and Fc:FcγR interactions, which result in improved immune effector function and bioavailability of humanised antibodies. We have also developed strategies to deliver payloads specifically to tumours through conjugation of drugs, toxins and isotopes to recombinant antibodies, peptides and nanoparticles, both in preclinical models and more recently in clinical trials in cancer patients. These studies are showing encouraging results in patients with cancers of the brain, colon and breast, as well as other solid tumours.

Tumour Payload Delivery

The development of recombinant antibodies for cancer therapy has emerged as one of the most promising areas in oncology therapeutics, both as single agents, and for payload delivery. The concept of being able to deliver toxins through antibody-drug conjugates, or radiotherapy by antibody-radioisotope conjugates targeting the payload to sites of disease, are exciting and promising approaches that we are exploring preclinically and clinically with antibodies developed in our laboratory.

Novel Metabolic Tracers

An exciting recent development in the molecular imaging of cancer comes from the identification of critical biochemical pathways responsible for tumour growth and metastasis, and immune targets which can be exploited for therapy, which can be imaged with novel SPECT and positron emission tomography (PET) tracers. Taking the discovery of novel metabolic tracers in the laboratory to clinical trials is a major focus of our molecular imaging / PET research program and is leading to a deeper understanding of tumour biology and therapy response.

Our goal is to understand cancer at a single cell level to advance cancer biomarker discovery and translation

Our laboratory specialises in using innovative single cell techniques to deconstruct tissue samples and reveal the genetic architecture of individual cells. This allows us to study heterogeneity in a range of cancers, including breast cancer, and address key biological questions:

• How intra-tumoural heterogeneity drives tumour progression and metastasis in aggressive cancers?
• What role do the tumour microenvironment play during metastasis?
• How can we effectively monitor metastatic disease progression and prevent cancer recurrence?
• Which premalignant molecular alterations are involved in breast tumorigenesis and can rare aberrant cell populations be identified for target biomarker discovery?
• How single cell transcriptomics can be utilised to improve personalised treatment for cancer patients?

Isolation and characterisation of circulating tumour cells

Liquid biopsies, which capture circulating tumour cells in the blood, are a useful, non-invasive way of monitoring tumour spread and drug response. Our laboratory studies the diversity and biological properties of cancer cells captured in blood. This helps improve the diagnosis of patients, predict drug response and, in the longer term, develop cancer treatments personalised to a patient’s specific cancer.  

Follow tumour progression using cellular tracking

Each cell collected from a patient’s tumour can be labelled with tags or ‘barcodes’, allowing us to determine which subpopulations of cells in the tumour contribute to metastasis, organ specificity and drug-resistance. We are particularly interested in the effect of different microenvironments or ‘niches’ on the survival of cancer cells and the progression of disease.

Test new drugs in advanced models of metastatic breast cancer

Our laboratory is interested in developing ways to test the effect of various drugs on the survival of circulating tumour cells or metastasis. In particular, we focus on testing the effect of new targeted therapies on metastatic progression.

Develop a novel method for quantifying scRNA-seq data.

Single-cell RNA sequencing (scRNA-seq) has transformed the field of biomedical research. The 10x Genomics scRNA-seq technology is capable of sequencing the expression of thousands of genes in hundreds of thousands of individual cells simultaneously. Quantifying UMI (Unique Molecular Identifier) data generated from this technology is challenging because of the large volume of the data and the complexity of quantification. We are developing a new algorithm for accurate and efficient quantification of data from this technology. The successful development of this new bioinformatics tool will significantly reduce the data analysis time and improve the accuracy of gene expression quantification.

Develop a new method for mapping long sequencing reads

Long-read sequencing technologies, such as Nanopore and PacBio, have the potential to sequence whole gene transcript and discover long-range genomic mutations among other applications. A significant challenge for analysing long-read data is the read mapping which aligns each read to a reference genome. This is a critical step for successfully identifying full gene transcripts and detecting breakpoints of long-range mutations. We will expand the ‘seed-and-vote’ read mapping paradigm we successfully developed for mapping short reads, to develop a new method for long-read mapping. The successful development of this new tool is likely to result in discovery of new gene transcripts and mutations in diseases such as cancer.

Reconstruct a gene regulatory network to elucidate the differentiation of CD8+ T cells

Understanding the molecular mechanisms underlying the differentiation of CD8+ T cells will not only generate new knowledge in the field of immunity but is also important for the development of new strategies for improved immunotherapy. We will utilise omics data generated for mouse with chronic infection to reconstruct a gene regulatory network (GRN) containing interaction of key transcription factors and target genes to elucidate how differentiation of CD8+ cells are delicately regulated. We will then investigate how this GRN is perturbed in metastatic breast cancer using a mouse model of this disease and also cancer patient sequencing data available in the The Cancer Genome Atlas (TCGA) database. An outcome of this study will be a gene signature that can be used to predict which metastatic breast cancer patients will respond to immunotherapy.

Provide bioinformatics support to biology labs

Modern biomedical research makes use of powerful sequencing technologies such as single-cell RNA sequencing technologies. Bioinformatics support for fast and accurate analysis of sequencing data is important for the success of such research. Our lab collaborates with almost all the labs at ONJCRI to provide strong support for their bioinformatics needs. We specialize in analysing data generated from a range of sequencing technologies including bulk RNA-seq, single-cell RNA-seq, single-cell TCR-seq, ChIP-seq, ATAC-seq etc. We are also experienced in analysing public datasets generated by large consortia such as TCGA. We have contributed to many discoveries made in projects related to a wide range of cancer such as GI cancer, breast cancer and brain cancer.

We have identified several genes that regulate the metastatic process. By understanding how these genes act to control metastasis, we can develop effective therapies which directly target these genes or other genes controlled by these metastasis regulators. Another important aspect of our research is to examine human breast cancer tissues for evidence that the gene identified in our preclinical models is also relevant in the human disease.

Metastasis Regulating Genes

We have shown that some of the genes we have identified, including caveolin-1, microRNA-200 and BMP4, are able to suppress metastasis. With BMP4, we have found that its metastasis suppressing activity is in part through the inhibition of G-CSF, which controls the mobilisation and differentiation of neutrophils. In the presence of a tumour, the activity of neutrophils can be changed from infection fighting to supporting the spread of cancer cells to other organs, such as the lung. This led to our demonstration in our preclinical models that blocking the mobilisation of neutrophils can reduce metastasis. We are now probing more deeply to understand how neutrophil function is altered by factors released from tumours and the relevance of this to patients with breast cancer.

Much of our research is focused on immune regulation of metastasis by the innate immune system (including macrophages and neutrophils), but some of the other genes we have identified appear to act directly on the tumour cells to prevent their ability to metastasise.

Metastatic Dormancy

Breast cancer is noted for the long latency between diagnosis and therapy for the primary cancer and development of secondary cancers, which can cause ongoing anxiety for patients fearing a recurrence. We are investigating how tumour cells can disseminate from the primary tumour and remain alive but clinically undetectable for many years, and how they start expanding into life-threatening cancers in some patients. We are seeking therapies that prevent the expansion of these dormant cancer cells into new tumours.

Drug Discovery and Delivery

We have collaborated with Dr Ian Street and the Walter and Eliza Hall Institute drug discovery team to identify small molecules that can be developed into drugs to combat metastatic disease. We also work with the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology (Monash University) to improve drug delivery to tumours using nanoparticle technology.

Apoptosis

Cellular fate is controlled by multiple molecular pathways. The most studied is apoptosis, a form of programmed cell death used by all multicellular organisms to eliminate cells which are damaged, no longer needed or which might become a threat to the organism. This process is often deregulated in cancer cells allowing them to survive and proliferate when otherwise they should be eliminated.

BH3 mimetics

Dysfunctional apoptosis can cause or accelerate cancer development, but also underlies resistance to common cancer treatment approaches such as chemotherapy. Members of a particular family of proteins (the “BCL-2” proteins) are critical regulators of apoptosis. Recently, a new class of drugs called “BH3 mimetics” have been developed to target some BCL-2 proteins and activate apoptosis, leading to tumour cell death. One of these drugs is now being used in the clinic to treat some blood cancers, and others are under extensive investigation, including by our lab.

Autophagy

Autophagy is predominantly a process that enables cells to survive under stressful conditions such as when nutrients are in short supply. Like apoptosis, it can also become dysfunctional in cancer. Under some circumstance, proteins that regulate autophagy can also interact with those involved in apoptosis. This is a particular interest of our lab as it might have important implications for how cancer cell survive abnormally.