Respiratory biology and drug delivery

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• Investigating the pathogenesis of COPD and severe asthma using next generation multiplexed proteomics and crosslinking mass spectrometry (XL-MS)

  In the field of respiratory disease, severe Asthma and Chronic Obstructive Pulmonary Disease (COPD) are the two greatest causes of morbidity resulting in severe breathing difficulties and illness, wheezing in asthma and often death in COPD. The recent COVID-19 pandemic has worsened the outcomes for patients with chronic respiratory disease. The result is an enormous ongoing cost both to individuals and health systems worldwide. The Center For Inflammation UTS / Centenary institute, led by Prof Hansbro has an internationally renowned track record in the development of human representative animal models to study severe asthma and COPD and is one of 4 Australian research institutes capable of studying in-vivo COVID-19 infections. By combining these established models together with advanced mass spectrometry-based proteomics, bulk and single cell RNA sequencing. This project aims to define the role that proteins play in the progression of the pathogenesis of COPD and Severe asthma and how they interact with the transcript.

  This project will focus on developing a rapid multiplex method for the analysis of proteoforms, using state of the art crosslinking mass spectrometry and 2D gel analysis. This will be combined with bulk and single cell RNA sequencing data to characterise how proteins are processed within cells after translation and how this is linked to the pathogenesis of COPD and severe asthma.

  Students will be working under the supervision of Post-Doctoral Fellow Dr Matthew O’Rourke at the UTS proteomics node and Prof Phil Hansbro at the Center For Inflammation, Centenary institute and have the opportunity to learn proteomic techniques such as crosslinking mass spectrometry (XL-MS) LCMS, protein extraction and purification and biomarker characterisation while working at the UTS PC2 laboratories. The successful candidate will also work closely with the Hansbro lab at the Centenary institute to develop reliable animal models for validation of key proteomic findings; combined with transcriptomics and whole genome sequencing, enabling them to combine all of these techniques to produce a comprehensive multi "omics" based thesis. Student will also be able to develop their skills in bioinformatics and the drafting and publication of peer reviewed publications. Further to this, students will have the opportunity to present their findings at internationally recognised conferences and participate in local meetings and academic workshops.     

• Which cells give rise to lung cancer?

  Lung cancer is a major cause of death worldwide and a disease in need of much better treatments. It is known that cigarette smoking is a causative factor in the vast majority of lung cancers, but much remains to be learnt about how it arises. The two most common types of lung cancer are adenocarcinoma (AdC) and squamous cell carcinoma (SCC). Although they resemble cells within the alveolar and airway compartments of the lung, respectively, the cell of origin of these distinct cancers has not been clearly established. Epithelial transition zones are found at the junctions of two types of epithelial tissues, such as where the airway epithelium meets the lung alveolar epithelium, and can give rise to cells of both tissues. In other organs, epithelial transition zones are hotspots for carcinomas and those that arise there are more aggressive.

  This project will investigate the epithelial transition zones within the lung, using markers known to be associated with them in other tissues, as well as markers of different types of lung epithelium. We will combine our established mouse models for lung cancer and cell lineage tracing to identify the cell of origin of AdC and SCC and examine both mouse human lung tissue for pre-malignant biological changes in lung epithelial transition cells. Structural and functional changes in their genes will be investigated to identify potential mechanisms for driving those biological changes.

  The candidate will gain experience in advanced microscopy, sequencing and general molecular biology methods.

• Investigating the host-pathogen interface of Mycobacterium abscessus infection

  Mycobacteria are a broad family of bacterial species broadly clustered into two major groups: Tuberculosis (TB) causing pathogens such as Mycobacterium tuberculosis, and non-tuberculous mycobacteria (NTM). NTM are a diverse group of bacteria, with over 200 species identified to date. Many of these species are environmental organisms found in soil and water sources and pose no risk to human health. However, some of these species are known to cause infections in immunocompromised individuals, or those with underlying structural or genetic abnormalities. The reported incidence of NTM infection is exponentially increasing in first-world countries, frequently surpassing new infections associated with TB, highlighting this emerging health crisis. Mycobacterium abscessus is a rapid-growing mycobacteria commonly associated with pulmonary and extra-pulmonary disease, particularly in those with chronic obstructive pulmonary disease (COPD) or cystic fibrosis (CF). M. abscessus is intrinsically resistant to many first-line antimycobacterial drugs, therefore making it increasingly difficult to treat and often associated with poor clinical outcomes and cure rates of approximately 40%. In the past decade, there has been a surge in our understanding of M. abscessus pathogenesis, however there is still limited understanding of both host and pathogen determinants controlling infection outcomes. In this project, we will dissect the host-pathogen interface of M. abscessus infection using a combination of cellular and animal models to identify novel pathogenic traits and host pathways required for infection. We will further explore host genetic determinants controlling M. abscessus infection using our world-leading mouse models of chronic respiratory disease. We will explore M. abscessus genetic signatures that are linked to diverse infection outcomes, and understand how these regulate the host-pathogen interface during infection. Finally, we will exploit these identified pathways to propose novel host-directed therapies that may lead to increased host clearance of M. abscessus infection.

• The Role of Mast Cell Proteases in Lung Infection

  S. pneumoniae, P. aeruginosa and Influenza A virus are 3 common respiratory pathogens responsible for extensive disease and mortality. S. pneumoniae is responsible for 25% of preventable child deaths, P. aeruginosa is a leading cause of hospital acquired infections whilst seasonal epidemics of Influenza infections result in half a million deaths per year.

  Mast cells, synonymous with allergy, are long lived tissue resident immune cells. They are strategically located in the lungs where they can detect pathogens and release numerous proinflammatory mediators to recruit additional cells or aid in direct killing of invading pathogens. For these reasons, they may be ideal targets for host-directed therapies to treat respiratory pathogens.

  Mature mast cells contain large granules filled with bioactive proteins including proteases, growth factors, immune signalling molecules and histamine. Following mast cell activation and subsequent degranulation these mediators are released from the cell. While it has been shown that mast cells are a critical part of the immune response to S. pneumoniae, P. aeruginosa and Influenza A infection, the role of specific mast cell proteases in infection and disease is unclear. It is likely that some proteases are responsible for helping to control pathogen burden, while others contribute to damaging inflammation.

  This project will use genetically modified mice that are deficient in specific mast cell proteins to dissect the role that mast cells play in the host response to lung infection. Understanding more about these host-pathogen interactions may identify new ways to treat respiratory diseases.

  Through this project you will gain skills in animal handling, in vivo and in vitro infection with viruses and bacteria, cell culture, flow cytometry and molecular biology techniques.

• How UV radiation damages the cornea

  Along with the skin, the cornea is the tissue most exposed to ultraviolet radiation (UVR) from sunlight. The outermost cells, which form a multilayered epithelium, absorb much of the UVR and must deal with its damaging effects to maintain a normal shape and clarity; otherwise, vision impairing conditions such as keratoconus and ocular cancers can arise. We have found that low levels of UVR, equivalent to 80 minutes of Sydney sunshine, cause corneal epithelial cells to increase proliferation and shedding from the surface, while maintaining tissue structure and clarity. However, chronic exposure to these low levels of UV radiation can contribute to a condition called keratoconus, which can require corneal transplants or lead to blindness if untreated.

  This project will investigate the signalling pathways by which corneal epithelia cells respond to UVR to cause keratoconus and the basic mechanisms by which epithelial stratification occurs. It will use advanced fluorescence microscopy of living corneas to visualise epithelial cells as they divide, migrate and stratify. The corneas from novel reporter strains of genetically modified mice will be used to locate and measure signalling responses in the living tissue, and probed with pathway-specific drugs to determine their importance.

• Developing new treatments for respiratory diseases such as asthma, COPD, fibrosis, infections and COVID-19

  Our focus is on investigating the development and progression of chronic respiratory diseases such as COPD, asthma, lung cancer and infections using mouse and human tissues. Our group is made of “clusters” who specialize in areas including 1) chronic respiratory disease in general, 2) bioinformatic analyses of genome-scale datasets, 3) epigenomics studies, 4) mitochondria, oxidative stress and immunometabolism, 5) microbiome studies, and 6) exosome studies of human and mouse tissues. We are also establishing our own COVID-19 PC3 laboratory.

  The main aims of the work involves investigating the pathogenesis and developing new treatments for respiratory diseases such as asthma, COPD, fibrosis, infections and COVID-19. Projects could involve the study of epigenetic (acetylation, methylation ), single cell sequencing/RNAseq, proteomics and multi-omics, bioinformatics, roles of innate immunity (Toll-like receptors IFNs, mast cells, inflammasomes), mitochondria/oxidative stress/immunometabolism /steroid responses and macrophage biology.

  Applicants must hold an undergraduate degree with at least a credit average (or equivalent) and have research experience through an Honours program (first class, or second class division one) or a Master’s degree by research in a relevant subject.

• New guardians of the mucosa: Cell and molecular characterisation of M cell biology

  The mucosa is the largest surface area in the body and forms the major protective barrier. It harbors a staggering 10-100 trillion micro-organisms. Consequently, it is both the primary portal through which infectious microbes enter the host and the pivotal first line of host defence. Disruption of this mucosal barrier results in the invasion of microbes into the host initiating a destructive cascade of inflammatory reactions. M cells are specialised intraepithelial cells that provide crucial links between microbes and antigens from the external environment and the host immune system. They act as the alarm system for mucosal surfaces of the gut and respiratory tract, and the pathways they initiate are essential for the rapid induction of responses against infectious challenge to maintain tissue homeostasis. Due to the rarity of M cells, to date, unravelling how they work has been intractable. This is despite the fact that M cells lay the foundation for mucosal immunity. A major road block to our understanding has been the lack of tools to probe these cells. We have developed novel reporter mice that now allow us to characterise the fundamental cellular and molecular biology of M cells and determine the pathways they employ to regulate immune function. We will use these systems to define how these cells and pathways work and what they contribute to host defence.

  The main questions we aim to address are:

  1.  What are the mechanisms regulating M cell number & function?
  2. What are the microbial signals that regulate the generation of natural & induced M cells?
  3. How are M cells molecularly wired?

• Elucidating the roles of steroid receptors in mitochondria

  Steroid hormones can be produced naturally by the body (such as oestrogen, progesterone and cortisol) or man-made (synthetic glucocorticoids eg. dexamethasone). They have effects on basic biological processes such as growth/death, metabolism and immune responses. This occurs at a molecular level as they activate steroid receptors and alter gene expression in cells. For example, the sex hormones oestrogen and progesterone oscillate at different stages of the menstrual cycle and during pregnancy, while a stress induced response results in the release of cortisol. The synthetic versions of these steroids are widely used in hormone replacement therapy, assisted reproduction and suppression of the inflammatory response.

  Mitochondria are a component of every living cell. They are involved in many cellular processes and their primary function is energy production. Whilst the effects of steroids interacting with steroid receptors in the cell’s nucleus is well understood, we have recently discovered that mitochondria also have steroid receptors and can shape immune responses by altering metabolism (i.e. immunometabolism). This opens up the possibility that mitochondria may be a second site of steroid receptor activity and may have major effects on biological processes.

  We hypothesise that mitochondrial steroid receptors play an important role in the immune response and cellular functions at different mucosal sites in the body. This occurs by changes in mitochondrial function and energy production that can result in inflammation.

  The aims of this project are to:

  1. characterise the effects of steroid hormones on mitochondrial function and metabolism in the lung.
  2. define the effects of steroid hormones on gene expression and the production of molecules involved in metabolism in lung cells.
  3. define the roles of steroid hormones in cells of the FRT and GIT.
  4. define the roles of steroid hormones in regulating mitochondrial function, immunometabolism and inflammation in response to environmental challenges in cells from different tissues.

  This study will elucidate the role that steroid hormones have at different sites in the body in mitochondria in different cells. This will substantially increase our knowledge of how steroid hormone exert their effects. This will lead to major benefits by improving the ways that steroid function can be manipulated. This would have major impacts on their use as treatments of humans and animals.

• Targeting bacteria as an early detection marker for lung cancer

  Lung cancer is the leading cause of cancer-related death world-wide and has a 5-year survival rate of 16%, which has remained unchanged in the last three decades. If we can detect lung cancer earlier, we can diagnose in the early stages of disease when the patients are eligible for curative surgery and improve this 5-year survival rate. Liquid biopsies are a minimally invasive method for lung cancer detection, however one of the main challenges for their use is the low yield of cell-free host DNA from plasma. By targeting the bacteria in the blood, which is approximately 150 times larger than the human genome, this challenge may be addressed. In a recent study, a ‘signature’ for the disrupted bacterial population relating to lung cancer has been found in the blood. This ‘signature’ can distinguish between healthy people and patients with lung cancer.

  We aim to identify bacteria-derived biomarkers of lung cancer in blood samples and assess the sensitivity of these biomarkers to detect the presence of early-stage lung cancer

  This research will be a laboratory-based PhD program however the candidate may be required to work in the clinical setting in order to retrieve clinical sample among other tasks. The candidate will gain extensive experience performing multi-omic analysis (metagenomics, metabolomic, proteomic and/or transcriptomic) on human biospecimens, and in developing and performing bioinformatic analysis. 

  From this PhD program, the candidate will identify a cancer-related bacterial signature in the blood as a novel biomarker to be used in a liquid biopsy for the early detection of lung cancer. Currently, only 16% of lung cancers are diagnosed in the early stage. In these patients, the 5-year survival rate is 56%. However, when lung cancer is diagnosed in later stages, the 5-year survival rate plummets to 5%, and more than half of these patients die within 12 months. This research will directly address this problem by creating a novel and sensitive liquid biopsy for the early detection of lung cancer.

• Investigating the metabolomic basis of the pathogenesis of COPD and COVID-19

  Disease (COPD) are the two greatest causes of morbidity resulting in severe breathing difficulties and illness, wheezing in asthma and often death in COPD. The recent COVID-19 pandemic has also worsened the outcomes for patients with chronic respiratory disease. The result is an enormous ongoing cost both to individuals and health systems worldwide. The CFI UTS / Centenary institute, led by Prof Hansbro has an internationally renowned track record in the development of human representative animal models to study severe asthma and COPD and is one of 4 Australian research institutes capable of studying in-vivo COVID- 19 infections.

  This project will focus on using state of the art mass spectrometry techniques to characterise the metabolomic features of COPD and COVID-19 and integrating that into ongoing proteomic and transcriptomic projects. Students will have the opportunity to learn the basics of mass spectrometry techniques such as LCMS, metabolite extraction and purification, and mass spectrometry imaging while working at the UTS PC2 laboratories. The successful candidate will be working under the supervision of Post-Doctoral Fellow Dr Matt O’Rourke at the UTS proteomics node and Prof Phil Hansbro at the Center For Inflammation, Centenary institute.  Students will gain hands on experience combining metabolomics data with transcriptomics and proteomics. The end result will be the creation of a multi "omics" based thesis.

  Students will also be able to develop their skills in bioinformatics, image analysis and the drafting and publication of peer reviewed publications. Further to this, students will have the opportunity to present their findings at internationally recognised conferences and participate in local meetings and academic workshops.