Dust Diseases Board Fellowships and Scholarships

Chief Investigator

Dr Jonathan Chee

Organisation

University of Western Australia

Awarded funding

$240,000 (3 years)

Immune checkpoint therapies (ICT) that target programmed death (PD)-1, PD ligand (PD-L)1, and cytotoxic T lymphocyte-associated antigen (CTLA)-4 have revolutionized treatment of some advanced cancers, occasionally leading to durable responses.

ICT is changing how oncologists approach mesothelioma treatment (Baas et al. Lancet 2021). Our recent positive phase II DREAM clinical trial also showed promising activity in mesothelioma patients that received anti-PD-L1 antibody durvalumab in combination with cisplatin and pemetrexed chemotherapy (chemo-ICT) (Nowak et al. Lancet Oncology 2021). However, only a subset of patients benefit from ICT or chemo-ICT. Furthermore, there are financial costs and toxicities that come with ICT.

Dr Chee's research aims to investigate the immunological mechanisms that underlie successful anti-tumour responses in patients treated with chemo-ICT. Mechanistic understanding of therapeutic response will accelerate the development of predictive biomarkers. Not all patients benefit; an accurate predictive biomarker of response will help oncologists stratify patients, and develop new treatment strategies for those unlikely to respond. Dr Chee's research addresses this unmet need for a biomarker of response, and develops novel strategies to improve therapy responses for patients with mesothelioma.

Theme 1.  Identifying immune biomarkers of response to chemo-ICT in mesothelioma.

As ICT removes the suppression imposed on the anti-tumour immune response, I posit that changes in immune cells can act as biomarkers of response. I will characterise individual immune cells from longitudinal peripheral blood and pleural effusion samples collected from our DREAM clinical trial with high throughput single cell sequencing. Using novel network and time-series analysis of sequencing data, we previously identified biomarkers of response, and druggable targets that improved ICT responses in murine mesothelioma. I will use these established approaches to identify changes in immune cells gene expression that will be predictive of chemo-ICT response. If successful, results from my project could impact the design of biomarker studies in the 480 patient international phase 3 study (DREAM3R), which is co-led by Prof Nowak. This is an unparalleled opportunity to impact patients affected by dust related cancers both locally and internationally.

Theme 2.  Targeted epigenetic modification to improve mesothelioma responses to ICT

The second theme develops novel strategies to improve ICT responses. In collaboration with A/Prof Blancafort, I will develop state of the art Epi-CRISPR technology that precisely reprograms the epigenetic state of target genes within cells. Using Epi-CRISPR, I will upregulate or repress immune-related genes that will improve the immunogenicity of mesothelioma tumours. Targets will be identified from published studies, or from DREAM clinical data. Epi-CRISPR will be tested in vitro, and in vivo in preclinical mesothelioma models treated with ICT.

Targeted delivery of Epi-CRISPR to mesothelioma tumours in vivo can be achieved by designer liposomes and nanoparticles, which are ongoing areas of research by the collaborative team. Cancer targeting CRISPR based technologies are currently being assessed in phase I clinical trials, highlighting the feasibility of testing this approach. If successful, the NCARD team has the necessary technical and clinical trial expertise to move this precision based therapy into further preclinical studies and eventually clinical trials.

Chief Investigator

Dr Christina Begka

Organisation

Monash University

Awarded funding

$240,000 (3 years)

The problem. Silicosis is a devastating progressive fibrotic lung disease initiated by inhalation of silica dust. Although new regulations in NSW for preventing occupational exposure to silica are about to be put in place (as of July 1 2020), the burden of this disease is under-appreciated and individuals previously exposed to silica through dry-cutting practices in NSW and throughout Australia will still be presenting with lung fibrosis for years to come.

Current known cases merely reflect the “tip of the iceberg” of this emerging public health emergency. Currently, there is no known pharmacological treatment, and there is a paucity of data to help inform clinical decisions on treatment.

Our goals

Utilizing a new animal model of silicosis, the goal of this project is to ascertain whether two highly translational interventions could hold potential for treatment of people suffering from silicosis, specifically:

• whether targeted broncho-alveolar lavage is effective at removing silica from the airways and consequently reducing disease progression, and
• whether removing silica-ladened macrophages and restoring healthy airway macrophage populations re-establishes lung health.

A novel model system

Dr. Begka has established a world-first mouse model of lung silicosis, where through the use of a miniaturized endoscope, equipped with a camera and irrigation channel, a dose of silica can be delivered directly to a single lung lobe. This results in the development of silica pathophysiology and fibrotic nodules only in the selected lobe, while the counter lobe remains unaffected and provides an internal control for the model and interventions to be tested.

Aim 1

Therapeutic intervention by segmental broncho-alveolar lavage (BAL) for the removal of silica dust. We hypothesize that by reducing the burden of silica in the airways we will reduce disease severity and progression. In our new model, we can perform lobe-specific lavage to remove both silica particles and “foamy” macrophages, characteristic of alveolar proteinosis and silicosis. We will wash distinct lung lobes at different stages of disease, and track the impact of this intervention on disease development, using a NanoPET/CT small animal scanner, and lung function. In addition, we have established a multi-omics (lipidome, metabolome, RNAseq) analysis pipeline that allows in-depth analysis of disease causing pathways.

Aim 2

Targeting airway macrophages to restore lung health. Dysregulated macrophage functionality in the airways could drive disease pathology in silicosis. We will induce silicosis throughout the lung, then pharmacologically remove macrophages in a single lobe, followed by repopulation of that lobe with healthy macrophages. Disease progression in the individual lobes will be monitored as in Aim 1.

Outcomes

Our evaluation of the use of lung lavages and macrophage restoration strategies is not only novel but, by design, highly translational. Clinically, lung lavage is a viable, albeit yet to be implemented therapy for lung silicosis. Similarly, restoration of macrophage populations is feasible with clinically approved drugs. Data yielded from our unique model system will provide the much-needed platform for clinical studies and holds the potential to make a substantial impact on patient care in the medium term.

Chief Investigator

Dr Anna Yeung

Organisation

Woolcock Institute of Medical Research

Awarded funding

$240,000 (3 years)

Silicosis is an incurable lung disease caused by inhaled crystalline silica dust whereby prolonged exposure manifests into nodular lesions and chronic inflammation in the lungs. Historically coal and gold miners were the most common occupations affected by silicosis, which can develop from chronic (more than 10 years) exposure to moderate levels of respirable crystalline silica (RCS).

In recent years however, Australia has seen a dramatic rise in the number of cases of acute silicosis, especially among young stonemasons and builders, which have been linked to the increase use of engineered stone – a popular material used in kitchen and bathroom benchtops. Cutting, sanding and drilling into stone materials generate large amounts of dust, such high exposure levels of RCS vastly reduces the timeframe for the onset of silicosis down to five years, and in extreme cases onset can occur after a few months.

Although safe work practices such as adequate ventilation, using wet cutting techniques and wearing protective masks are in place to reduce exposure to RCS, however may be ignored or perhaps unable to be implemented. As such, the current proposal aims to increase the understanding of how RCS cause damage to the lung epithelium using cellular models and looking at the physiological impacts. Ultimately this work aims to affect policy to reduce RCS exposure and improve the safety of workers.

The project will look at four specific aims:

Aim 1

Investigating the size of RCS particles and the duration of time that particles remain in the air following wet and dry cutting in well-ventilated and non-ventilated rooms. The project will utilize an Andersen Cascade Impactor designed to capture particles, and a laser particle counter to enumerate particle size and number generated under different cutting conditions.

Aim 2

Investigate the toxicity effects of different sized RCS particles on macrophage uptake and airway epithelial cell toxicity. Blood-derived macrophages and airway epithelial cells differentiated at air liquid interface will be exposed to different sized RCS particles. Dr Yeung will measure particle uptake by macrophages - a process thought to play an important role in silicosis disease progression, and also measure toxicity effects on airway epithelium. The outcome of this aim will show whether some particle fractions are more toxic than others.

Aim 3

Determine the effectiveness of cheaper protective masks (50 cents - $1.50) in the protection against harmful RCS particles. Dr Yeung has identified a number of N95 respirators that are inexpensive. Dr Yeung would like to evaluate their effectiveness against high-level exposures to RCS (some N95 respirators easily clog up, leading to workers removing), and then engage with major suppliers of manufactured stone products to see if such respirators could be supplied with their products.

Aim 4

Develop multi-language information pamphlets (English, Chinese, Arabic) in consultation with stonemasons and contractors. Many people with silicosis in the building industry come from non-English speaking backgrounds, and are not aware of the dangers of RCS. Therefore, much like the images placed on cigarettes we aim to produce similar warnings labels that could be placed on cutting discs.

Chief Investigator

Dr Amber Louw

Organisation

Institute for Respiratory Health

Awarded funding

$120,000 (3 years)

Malignant pleural mesothelioma (MPM) is an aggressive cancer caused by asbestos that is universally fatal. Two of the most frequently mutated genes in MPM are BRCA1-associated protein 1 (BAP1) and cyclin-dependent kinase inhibitor 2A (CDKN2A). My research aims to evaluate the biological and clinical consequences of these genetic changes commonly seen in MPM through three avenues.

1. Understanding the biological consequences of these genetic changes: Up to 76 per cent of MPM have BAP1 loss while more than half demonstrate homozygous deletion of CDKN2A. The biological consequences of these losses have not been fully characterised. We will use established primary MPM cell lines from clinical samples with different BAP1 and CDKN2A expression profiles to determine: the cell proliferation and migration rates of these cell lines, determine the sensitivity of these cell lines to chemotherapeutic agents routinely used clinically (in other words pemetrexed, cisplatin and gemcitabine) and agents previously reported to be effective in the absence of BAP1 expression (in other words the PARP inhibitor olaparib in combination with a PI3K-mTOR inhibitor).
2. Understanding the frequency of BAP1 and CDKN2A loss in an Australian cohort: Since January 2015 to December 2018, 200 patients have been diagnosed with MPM at PathWest, Nedlands. The average age of patients is 72 years and 80 per cent are male. BAP1 protein expression by immunohistochemistry (IHC) and CDKN2A status by fluorescence in-situ hybridisation (FISH) has been assessed for a subset of these cases. We propose to determine the frequency of BAP1 loss of protein expression by IHC and homozygous deletion of CDKN2A by FISH in this cohort where sufficient material is available.
3. Correlating these genetic changes with clinical and epidemiological data: For MPM cases where tumour BAP1 and CDKN2A status has been determined (in 1 and 2) we will correlate expression profiles with patient survival from diagnosis; cancer history; asbestos and tobacco–exposure data; and clinical response to chemotherapy. Survival data and the incidence of other cancers in this population is available through the Western Australian Mesothelioma Registry (WAMR) which maintains a comprehensive, validated record of MPM cases for the State. Asbestos and tobacco exposure data is available for a subset of MPM cases enrolled on the Genetic Understanding of Asbestos Related Disease (GUARD) study, (Prof Creaney is a CI on this study). Clinical response to chemotherapy data is available for a subset of cases who have previously consented to be part of the Tumour Immunology Group – National Centre of Asbestos Disease biobank (managed by Prof Creaney).

Results from this research will provide valuable information regarding the frequency of these genetic changes in an Australian cohort. Preliminary data examining BAP1 IHC and CDKN2A FISH in the pathological assessment of difficult cases suggests that these may be valuable in the diagnostic pathway. Results may also have clinical significance for patients, in that predicting prognosis impacts treatment selection. Additionally, molecular profiling of patients likely to respond to a given agent may improve treatment planning. Improved understanding of the underlying genetic events in MPM may lead to development of new treatment strategies.

Chief Investigator

Mr Joel Kidman

Organisation

University of Western Australia

Awarded funding

$120,000 (3 years)

Malignant mesothelioma is an aggressive and incurable cancer caused by asbestos. Standard treatment of chemotherapy is predominantly palliative with patients having a median survival of approximately 12 months. This poor prognosis highlights the need to develop new therapies. Immunotherapies, such as immune checkpoint blockade (ICPB, anti-PD-L1/CTLA-4) have transformed the treatment modalities of other cancers such as melanoma and non-small cell lung cancer, with long-term tumour regression observed in approximately 20 per cent of treated patients.

ICPB treatments for mesothelioma are currently being assessed by other research groups and ourselves, with responses similarly observed in a small proportion of treated patients. It is unknown why only a minority of patients respond to ICPB, but others do not.

The project aims to understand mechanisms that underlie successful responses to ICPB by characterising features of the immune system in responding and non-responding individuals. To achieve this, Joel will utilise unique preclinical models, novel technologies such as immuno-sequencing, network biology and machine learning to help me unravel this complex question.

This project is significant because they will develop a predictor of response to treatment outcomes for mesothelioma patients. There is currently no single accurate biomarker that will predict immunotherapy response. Having a biomarker will aid clinicians in tailoring treatment plans, saving time, costs and preventing side effects. Furthermore, in-depth understanding of therapy mechanisms will help develop novel ways of converting non-responders into responders.

Joel's focus is on T cell receptors (TCR), as T cells are a group of immune cells pivotal in CPB responses. The hallmark of T cell function is antigen-specificity, which is determined by a diverse set of antigen receptors. Notably, the collection (repertoire) of TCRs in any given individual is highly different, and Joel hypothesizes this difference is why some patients respond to therapy but others do not, and novel network analysis of TCRs provides a biomarker of response to therapy.

The project aims are:

1. To characterise features of the T cell repertoire that change over time in responding and non-responding animals to ICPB.
2. To develop novel computational analyses of T cell sequencing data that will generate a biomarker of response to ICPB. Joel will utilise an established preclinical model that closely mimics ICPB responses observed in the clinic.

Joel will use cutting-edge sequencing technology to exhaustively characterise the T cell repertoire. Data sets produced by T cell repertoire sequencing require novel analysis methods beyond the standard methods that are currently used. Joel will apply novel network analysis, machine learning, and mathematical modelling in my analysis workflow to provide a rigorous understanding of nuanced differences in T cell repertoire over time.

These methods may provide insight that were not previously obtainable from traditional data modelling. Joel will subsequently validate my approach using serial blood samples from mesothelioma patients undergoing ICPB and chemotherapy. All patients outcomes are blinded, and Joel will determine if TCR analysis can reliably differentiate patient outcomes, and if so, at what time point can the effect a mesothelioma patients treatment be known.