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SAGC Collaborative Projects



2023 saw the establishment of the South Australian node of the Australian Alliance for Indigenous Genomics (ALIGN), on the back of the successful 2021 Genomics Health Futures Mission grant to advance the benefits of Genomic Medicine for Aboriginal and Torres Strait Islander peoples.

Key priorities of the SA node, which is partially led by SAGC, revolve around extensive multi-omics analyses in the PROPHECY (Predicting Renal, Ophthalmic and Heart Events in the Aboriginal Community) study, Aboriginal-led policy development for Indigenous Genomics projects in SA and capacity development of a SA Indigenous genomics workforce. To help facilitate and guide this work, a South Australian Aboriginal Governance Committee has been established to provide Aboriginal insight and oversight into culturally safe genomics research practices so that we can work towards prioritising community benefit, health and wellbeing. The PROPHECY study is the largest longitudinal study of diabetes in Aboriginal Australians ever conducted. PROPHECY aims to understand why Aboriginal people get type II diabetes at a much younger age, and why they experience associated complications such as kidney disease and blindness at a much younger age than non-Aboriginal Australians.

A multi-omics approach will be applied to the PROPHECY study, encompassing DNA, RNA and methylome sequencing, as well as proteomics and metabolomics. Dr. Marlie Frank joined SAGC in 2023 as the SA Indigenous Genomics Coordinator. This is a joint appointment between SAGC and Aboriginal Health Equity, SAHMRI. Marlie has family connections through both the Kaurna and Yorta Yorta people and is an early career researcher, with a PhD in genomics, she will play a central role in co-ordinating activities, including sample analysis, workshops and scholarships as the representative of the SA node. Building an Indigenous genomics workforce and leaders of the future is a key priority for ALIGN in South Australia.


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People who have COVID-19 will excrete fragments of the SARS-CoV-2 virus through faecal waste or other bodily fluids into the wastewater stream through the sewerage system. A wastewater surveillance program therefore provides another mechanism through which community transmission can be monitored to complement clinical surveillance. The point of difference for wastewater surveillance is that it does not rely on clinical presentation by individuals. Wastewater surveillance will detect virus fragments from people who are weakly symptomatic or asymptomatic. The use of wastewater surveillance for detecting and quantifying the presence of SARS-CoV-2 virus fragments was expanded in 2022 to identify the variants of the virus circulating in the community in a manner that is independent of clinical presentation by individuals.

The aim was to provide a complementary source of information to analysis of variants detected from sequencing of clinical isolates. In South Australia, SA Water, SA Health and the SAGC ran a PCR-based screening wastewater surveillance program over the course of a year, whereby samples were collected from the major metropolitan wastewater treatment plants twice a week. These plants service about 65% of the SA population. PCR products from these samples were submitted to SAGC for sequencing. The resulting data produced was used by SA Health to assess changes in prevalence of variants and to monitor the appearance of new variants of concern (results are shown in the figure 1).

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Rapid vaccine development for pandemic preparedness

Emergence of COVID-19 and the ensuing pandemic has demonstrated the continued threat infectious diseases can pose to our health, economy, and lifestyle and highlighted the importance of vaccines as a countermeasure. COVID-19 vaccines were developed and approved in approximately 350 days, which was 5-10 times faster than ever before. However, even greater speed is needed, and 100-days for vaccine development is the current target. Achieving this goal will require a shift in current vaccine paradigms and development of new flexible, rapid, scalable technologies.

The Sementis viral vector vaccine platform (SCV) has been designed to deliver safe, versatile, and scale-able vaccines and is being positioned for pandemic preparedness. Sementis and the Experimental Therapeutics Laboratory at the University of South Australia (UniSA) have worked together to develop a multi-pathogen Chikungunya and Zika virus vaccine and a first-generation COVID-19 vaccine to demonstrate the immunogenicity of the vaccine platform and utility in infectious disease. UniSA has further collaborated with Sementis, as part of a broader global network to position the vaccine platform for pandemic preparedness. This included supporting the introduction of new technology to enable rapid construction and characterisation of new vaccines.

UniSA selected SAGC to provide genomic services to demonstrate vaccine quality and safety. The proximity of the UniSA and SAGC teams facilitated easy access to leading genomics services, expertise, and real-time knowledge sharing. This enabled UniSA to demonstrate the feasibility of rapid new vaccine construction and a suite of analytical tools for future vaccine development. This outcome supports the positioning of SCV for new vaccine readiness within 100 days of pandemic pathogen antigen identification. The services provided by SAGC, and accessibility to leading genomics capability will continue to support vaccine development in the Experimental Therapeutics Laboratory.

Professor John Hayball and Dr Tamara Cooper (Experimental Therapeutics Laboratory, UniSA) 

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Assessing the potential to use biological and chemical properties of the airborne fraction of soil for provenance assignment and forensic casework.

The airborne fraction of soil (dust) is both ubiquitous in nature and contains localised biological and chemical signatures, making it a potential medium for forensic intelligence. Metabarcoding of dust can yield biological communities unique to the site of interest, similarly, geochemical analyses can uncover elements and minerals within dust that can be matched to a geographic location. Combining these analyses presents multiple lines of evidence as to the origin of dust collected from items of interest. Dr. Jennifer Young is a DNA forensic technology research associate who lead a team where environmental dust samples were collected from belongings to determine whether bacterial and fungal communities in dust.

Dust and soil were collected from three sites with differing soil properties across South Australia. The resulting ITS and 16S sequencing data, generated at the SAGC, showed that it was possible to perform analysis from a single swabbed sample and that there were unique biological and chemical signatures between sites. When modelling bacterial and fungal diversity, Dr. Jennifer Young and team found samples were correctly predicted using dust 67% and 56% of the time and using soil 56% and 22% of the time for bacteria and fungi communities respectively. This proof-of-concept study found that metabarcoding of dust samples can generate bacteria and fungi community profiles that are unique to sites. While there is still a long way to go in this field, both metabarcoding and biogeochemical analyses of dust samples show potential for applications in forensic science.


Nicole R. Foster et. al, 2023, The secret hidden in dust: Assessing the potential to use biological and chemical properties of the airborne fraction of soil for provenance assignment and forensic casework, Forensic Science International: Genetics, Volume 67

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Chronic Visceral Pain and Irritable Bowel Syndrome

Irritable Bowel Syndrome (IBS) is a chronic disorder of the gastrointestinal tract affecting ~11% of the global population. Chronic visceral pain (CVP) is the most debilitating symptom associated with IBS. Despite this burden of disease, effective therapies for CVP associated with IBS are lacking. The first step in finding new treatments is understanding how pain from the gut is generated and transmitted to the brain via the microbiome-gut-brain axis and determining how these processes change in IBS. The Visceral Pain Research Group, led by Professor Stuart Brierley at SAHMRI is working in conjunction with SAGC to fill this knowledge gap. The goal is to identify changes in the molecular profile of precise cell types within the microbiome-gut-brain axis to determine how changes to these molecular profiles drive altered function and generate the abnormal pain signalling characteristic of IBS.

Using well-established models of IBS, in combination with state-of-the-art techniques (including genetic approaches, retrograde nerve tracing and FACS sorting), the Visceral Pain Research Group has isolated key cell types in the microbiome-gut-brain axis. The SAGC has created mRNA-Seq libraries from these single cell suspensions and have been sequencing them since the project’s inception. Together, we have processed more than a dozen experimental cohorts and are currently working through the bioinformatic analysis to interpret our results. With this ground-breaking project, we aim to identify novel targets and therapeutic strategies to relieve CVP, ultimately improving the quality of life of IBS patients.

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Novel Metabolic Therapies for Blood and Brain Cancer

The genes encoding isocitrate dehydrogenase 1 and 2 (IDH1/2) are mutated in brain cancer and leukaemia and drive the production of the oncometabolite (R)-2-hydroxyglutarate (R-2HG). However, specific differences between these two mutations with targetable implications have not been described. Dr Dan Thomas is a clinician and researcher who runs the Myeloid Metabolism Laboratory at SAHMRI. His team has recently discovered a novel susceptibility specifically for IDH1 mutation (mIDH1) by identifying the lipid synthesis enzyme ACC1 (acetyl CoA carboxylase 1) as a synthetic lethal target, published recently in Cancer Discovery and highlighted as one of the most important papers for 2023 by the European Cancer Association. By analyzing the metabolome of primary patient cells, his team identified a mIDH1-specific reduction in fatty acids compared to healthy progenitor cells that was not observed in IDH2-mutant cancer. Moreover, mIDH1 cells exhibited an increase in acyl-carnitine linked fatty acids destined for the mitochondria, indicating a switch to beta-oxidation. Overall, their data show that mIDH1 cancer cells have a higher dependency on both exogenous and de novo fatty acids than mIDH2 cancers.

This suggests that differences in intracellular localization between cytoplasmic IDH1 and mitochondrial IDH2 can have profound effects on metabolic phenotypes. These insights are important because it demonstrates novel targets for IDH1 mutant cancers beyond the production of the oncometabolite (R)-2-hydroxyglutarate, and offers hope for designing an ultra-precision approach encompassing diet and targeted therapy for cancer patients with IDH1, but not IDH2, mutant cancers. This is clinically relevant because emerging results from clinical trials testing mutant IDH inhibitors, such as ivosidenib, do not always result in tumour regression despite marked decreases in the oncometabolite. Dan's research suggests other metabolic dependencies beyond the Warburg effect, depending on somatic mutation context, such as mitochondrial-driven beta oxidation are also involved in cancer metabolism. This paper reinforces other recent studies supporting the notion that many cancers are not dependent on ATP or carbon supply for growth but are desperate for an adequate supply of re-usable NADPH (via NADH) and are prepared to sacrifice both de novo and exogenous fatty acids to guarantee this.

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130TB Data Generated
437 Researchers Supported
68 Grants Supported
12000 Samples Processed