Kolarich Group

Supervisors and collaborators: Assoc Prof Daniel Kolarich and Prof Chamindie Punyadeera

Head and neck squamous cell carcinomas (HNSCC) are the seventh most common form of malignancy and are responsible for 3–4% of cancer-related deaths globally. 50% of patients with HNSCC succumb to their disease within 5 years of diagnosis. Therefore, early detection, is an unmet clinical need.

In-depth molecular profiling of circulating extracellular vesicles (EVs) provides a promising avenue to identify tumour, stage and cancer-type specific molecular features that can deliver vital diagnostic information. EVs can easily be isolated and enriched by non-invasive sampling, such as the use of saliva, providing a fast and efficient avenue for developing non-invasively, biomarkers of clinical relevance.

Building upon our already established and successful collaboration and expertise available between the Kolarich (proteomics, glycomics and cancer glycobiology) and Punyadeera (patient recruitment, liquid biopsy and cancer genomics) groups this project aims to integrate existing multi-omics platforms to comprehensively characterise EVs and their cargo (proteins and glycoproteins) in saliva from HNSCC patients and matched healthy controls. This will enable us to identify novel early-stage markers for HNSCC, and the developed methodologies that can act as a blue-print for studying EVs from other body fluids relevant for different cancer types.

The outcomes from this project will have a high translational potential and will deliver novel insights into the glycobiology of HNSCC.

Supervisors: Dr Chris Day, Prof Joe Tiralongo, Dr Alison Peel & Assoc Prof Daniel Kolarich

Glycomics, glycoproteomics, infection, evolution, zoonotic disease

Animals such as bats are considered prime hosts for zoonotic diseases before they "jump" to humans. Viruses such as influenza or COVID-19 are known to infect different host species, where they can gain novel functions and increase their virulence.

The cell surface of mucosal barriers in the respiratory tract plays a fundamental role in this interplay. This cell surface, but also any body fluid proteins are extensively modified with species specific sugars called glycans. These glycans build a universal language used by cells but also abused by pathogens. Though eukaryotic organisms share one alphabet, evolution made them speak multiple different languages and dialects. We have developed glycomics & glycoproteomics tools to translate these languages and uncover how pathogens learned to speak and interpret glyco-languages between different species. Understanding this relationship is crucial as viral, bacterial and parasite pathogens have developed elaborate strategies to jump between hosts – and many of these strategies involve cell surface glycans. The influenza virus is just one fairly well understood example that uses this strategy.

As part of this project several student projects are available that include 1.) characterisation of the plasma/serum glycome across several vertebrae species; 2.) investigation and understanding cross-species recognition of pathogen adhesins; 3.) novel, cutting-edge science to understand the role of glycosylation and infection in flying foxes;

4.) working in and with an interdisciplinary and international team delivering first-hand knowledge and skills in a variety of biochemical and immunological skills and techniques.

The outcomes of these highly collaborative (across Griffith, national and international partners) projects will provide novel clues how infectious diseases can spread and uncover novel targets to stop their distribution and uncover novel biology in animal species of primary interest for the distribution of zoonotic pathogens. Students will be introduced to biochemistry and immunology laboratory workflows that include (but are not limited to) SDS-PAGE, Western blotting, Proteomics and Glycomics sample preparation, acquisition and data analyses and gain general knowledge in Biochemistry, Glycobiology and Immunology.

Techniques: mass spectrometry, glycomics, proteomics, microarray, Immunoglobulins, protein purification, immunological techniques.

Supervisors: Dr Larissa Dirr, Dr Alpesh Malde, Prof Joe Tiralongo, Prof Mark von Itzstein, Assoc Prof Daniel Kolarich

Glycoproteomics, biochemistry, signaling, protein structure

Receptor glycoproteins are highly important signalling molecules in controlling cell communication and interaction. Dysregulation of these signalling pathways is frequently associated with diseases such as cancer and chronic inflammatory conditions. However, the role their glycosylation plays for protein structure and interaction is still poorly understood.

Type III family of receptor tyrosine kinases such as c-KIT (also known as SCF receptor or CD117 PDGF-receptor-a and b, CSF-1 receptor and the FLT3 receptor play a vital role in the pathogenesis across different types of cancer.

As part of a larger project a variety of student projects are available that include aspects of mass spectrometry applications (proteomics, glycomics and glycoproteomics) next to protein structure, cell culture, Western Blot, electrophoresis and other standard biochemistry techniques. In combination these techniques are being employed to characterise and modulate the glycosylation of these important signalling molecules to understand how protein-specific glycosylation impacts protein function and cell signalling. This knowledge will provide opportunities for developing novel therapeutic strategies targeting these receptor proteins. As part of this project, students will be introduced to biochemistry laboratory workflows that include (but not limited to) SDS-PAGE, Western blotting, Proteomics and Glycomics sample preparation, acquisition and data analyses and gain general knowledge in Biochemistry and Glycobiology.

Techniques: mass spectrometry, glycomics, proteomics, cell culture, Western blotting, protein structure, basic biochemical workflows.

Supervisors: Dr Arun Everest-Dass, Assoc Prof Chamindie Punyadeera, Prof Mark von Itzstein & Assoc Prof Daniel Kolarich

Glycomics, proteomics, cancer, cancer-biomarkers, cancer microenvironment, cancer diagnostics, multi-omics

Understanding cancer and patient-specific dynamics of protein glycosylation holds enormous yet unmined potential for cancer precision medicine. Glycosylation is a dynamic protein post translational modification in which defined sugars (so called glycans) are attached to proteins by highly individual biosynthetic pathways. Human blood groups are one example of the individuality and clinical relevance of protein glycosylation, as specific glycans form the molecular basis of the human ABO blood group system. About 2 % of human genes are dedicated to biosynthetic pathways of this glycosylation machinery. Genomics and transcriptomics can provide some information about the presence or absence of glycosylation-relevant genes. However, the biosynthetic events that regulate the glycosylation machinery are beyond direct genomic and transcriptional regulation. Glycomics and glycoproteomics approaches thus are the only technologies that can be employed to sequence the cancer glycocode.

In close collaboration with national and international clinical partners we are studying cancer glycocode to understand why cancer forms, what makes individual cancers specific and to identify the weak points that allow us to develop novel strategies to fight cancer. With a focus on cancers such as Leukaemia, Prostate cancer, Melanoma, Ovarian cancer, Head & Neck Cancer or Colon cancer we use highly sensitive and selective glycan/glycoprotein sequencing tools to study cell surface glycoconjugates and their role in pathological processes. One technology involves cutting-edge Laser capture Microdissection that allows the specific cutting of cancer cells from tissue that has revolutionised how we can read the language of cancer. As part of the Australian Centre for Cancer Glycomics (A2CG) we are now systematically applying our glycan-sequencing technologies to sequence cancer glycomes in a variety of cancers.

Be part of the cancer glyco-revolution. A number of student projects are available supporting this important endeavour that will result in a new generation of diagnostic and prognostic cancer markers. As part of this project, students will be introduced to biochemistry laboratory workflows that include (but not limited to) SDS-PAGE, Western blotting, Proteomics and Glycomics sample preparation, acquisition and data analyses and gain general knowledge in Biochemistry and Glycobiology. They will work in an interdisciplinary and multi-national team at the direct interface between the clinic and the research lab.

Techniques: mass spectrometry, glycomics, proteomics, Western blotting, Laser Capture Microdissection microscopy, basic biochemical workflows

Supervisors: Prof Nicolle Packer, Prof Riccardo Dolcetti, Prof Mark von Itzstein & Assoc Prof Daniel Kolarich

Glycoproteomics, cancer biology, Understanding cancer immunotherapy

Cancer therapies have experienced a tremendous revolution with the introduction of therapies that use monoclonal antibodies that specifically target cancer cell surface targets and immune-checkpoint receptors. More than 95% of the protein receptors targeted by these immunotherapy agents are in fact glycoproteins, but to date the impact of receptor glycosylation in precision medicine is still not understood.

In this close collaboration with colleagues from the Peter MacCallum Cancer Centre students will be introduced to biochemistry and immunology laboratory workflows that include (but not limited to) SDS-PAGE, Western blotting, Proteomics and Glycomics sample preparation, acquisition and data analyses and gain general knowledge in Biochemistry and Glycobiology. Cancers that are being targeted in this project include Leukaemia, prostate cancer, melanoma, Head & Neck Cancer, Hepatocellular carcinoma or Colon cancer are investigated.

Techniques: mass spectrometry, glycomics, proteomics, cell culture, Western blotting, basic biochemical workflows

Supervisors: Dr Thomas Ve, Dr Yun Shi & Assoc Prof Daniel Kolarich

Structural Biology, Biochemistry, Microbiology, Innate Immunity

In both animals and plants TIR domain enzymes have important immune functions. While bacterial TIR proteins have long been recognised, their biochemistry and function remain poorly understood. Some TIR domain containing proteins with NAD+ cleavage activity have been reported to be involved in (i) subversion of host innate immunity (4) and (ii) in antiphage defence systems, but the mechanism of how these proteins utilise NAD+ and its metabolites to modulate the immune system, or provide resistance against phage infection has not yet been explored. As the bacterial TIR domain family is widespread and highly sequence diverse the characterised NAD+ cleaving bacterial TIR domains is likely to only comprise a small fraction of this family’s enzyme diversity and a kingdom wide analysis of them will allow systematic identification of new bacterial signalling nucleotides as well as potential agonists/antagonists of the innate immune system in animals and plants. Mechanistic understanding of bacterial defence systems has previously led to the development of revolutionary biotechnological tools such as restriction enzymes and CRISPR-Cas. Understanding the mechanism of new defence systems such as the ones containing TIR domains may facilitate strategies for developing new useful molecular tools.

This multidisciplinary project can include work on one, or several, topic, including: (i) Characterise the structural basis of TIR domain NADase activity; (ii) Explore the diversity of nucleotide signals produced by bacterial TIR domain containing proteins (iii) Identify the mechanisms that regulate TIR domain NADase activity; and (iv) Define the interactome of TIR domain produced nucleotide signals.

Techniques: X-ray Crystallography, Cryo-EM, NMR, Enzyme assays, HPLC, mass spectrometry.