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Projects

Examples of projects that have been completed using the genomics and/or bioinformatics services provided by the SAGC.
-used to indicate the calibre of projects carried out and the many and varied methodological and analysis approaches that can be taken

COVID-19 and its long-term effects on the immune system

Coronavirus Disease 2019 (COVID-19) is caused by a highly infectious respiratory virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and is responsible for the ongoing global pandemic. While the death toll from COVID-19 has been devasting (>4 million as of 9 July 2021 according to the Johns Hopkins University Coronavirus Resource Center), the vast majority of those infected fortunately do recover. Nevertheless, it is now increasingly apparent that recovered individuals, even those who had mild COVID-19, can suffer from persistent symptoms for many months after infection. Popularly referred to as ‘long COVID’, symptoms globally resemble similar post-infectious syndromes, such as Ebola and SARS-CoV-1, and suggest that there may be a long-lasting dysregulation of the immune response in individuals recovering from COVID-19.  

Professor David Lynn and his team approached the SAGC in order to utilise RNA-Sequencing to better understand long COVID at a transcriptional level in 69 individuals recovering from mild, moderate, severe and critical COVID-19. Following sample collection at 12, 16 and 24-weeks post-infection, the SAGC utilised state-of-the-art methods and sequencing technology to generate approximately 68.2 million individual sequences per sample from 138 blood samples. Through the SAGC’s involvement, an increased understanding was obtained about the effects of COVID-19 at a gene expression level, with evidence that patients suffering from long COVID were transcriptionally different up to 24 weeks post-infection.  

 

Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infection

Professor David Lynn and team
BMC Medicine | 2021 

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Integration of DNA methylation and gene expression in the horse placenta

The placenta is the fetomaternal interface, which is essential for fetal growth and survival, playing a central role in the health of both the fetus and its mother. The dynamic gene expression during pregnancy dramatically contributes to the correct functionality of this temporary tissue. The epitheliochorial placenta of the horse is a valuable resource to understand parent-of-origin expression due to minimal bias associated with remnants of maternal tissue compared to other eutherian mammals. This study identified genes whose transcription is biased to either the paternal or maternal chromosome in the equine placenta. Overall, this study, which was published in the Proceedings of the National Academy of Sciences USA, contributes to a better understanding of regulatory processes in placental function, evolution, and disease, using horses as a model for eutherian mammals’ placenta.  

Our partners were specifically interested in how parent-of-origin expression comes about in horses, and how methylation acts on the DNA during imprinting. DNA methylation analysis, outside of well sampled or model organisms, can often be difficult due to poor reference genomes. The SAGC team was brought in as a consultant due it our previous expertise in using Epigenetic approaches for model organisms, such as the plant fungus Botrytis cinerea and the commercial fruit crop grapevine (Vitis vinifera). The SAGC was able to validate the DNA methylation analysis (in the absence of phasing information) and RNA expression work. Currently there is limited information about how the expression of paternal and maternal allele’s impact the development of the placenta, a crucial element in long-term health of placental animals.  

 

Parental bias in expression and interaction of genes in the equine placenta

Professor Barry Ball and team
PNAS | 2021 

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Underpinning the cellular mechanisms of atherosclerosis using single cell analysis

Atherosclerosis is a complex vascular condition associated with aging, and a major cause of mortality worldwide. It involves a build-up of a "plaque" consisting of fats, cholesterol, and other substances on and within the artery walls, resulting in restricted blood flow and an increased risk of blood clots and heart attacks. At the cellular level, atherosclerosis involves a diverse range of cell types interacting in complex ways to produce inflammation, however the mechanisms causing inflammation are not well understood. Current therapeutic approaches treat symptoms like high-cholesterol and high blood pressure, without addressing the underlying causes of cellular dysfunction. They also do not fully account for specific environmental and genetic factors in different individuals. A deeper understanding of the cell types involved, and their activities is therefore required to develop more targeted therapeutic strategies for atherosclerosis.  

Single cell RNA-seq sequencing (scRNA-seq) technology has recently been gaining traction for understanding complex diseases like atherosclerosis, while bringing us closer to the idea of using a "precision medicine" approach to treat underlying cellular causes of the condition. Associate Professor Peter Psaltis approached the SAGC about using scRNA-seq technology to facilitate a better understanding of atherosclerosis mechanisms in the heart and aorta at the cellular level. Previous research conducted by Associate Professor Peter Psaltis identified a rare "progenitor" cell population in mice that appeared critical to a known mechanism that leads to atherosclerosis. Using state-of-the-art-methods, the SAGC carried out scRNA-seq and analysis to characterise the different cell-types present in the heart and the aorta in unprecedented detail, contributing to an improved understanding of the cellular mechanisms underpinning atherosclerosis.  

 

Vasculogenic properties of adventitial Sca-1+CD45+ progenitor cells in mice: a potential source of vasa vasorum in atherosclerosis

Professor Peter Psaltis and team
Scientific Reports | 2019

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Art versus science

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Dr Helen Pynor (Australian Network for Art & Technology SAHMRI resident) and Dr Jimmy Breen (SAGC Bioinformatics Platform Lead) have joined forces to explore the ideas around the body’s porosity, the way the body ‘leaks’ out into the world in ways we don’t necessarily think about, and the part DNA plays in that story.

Helen says “I was aware that we shed DNA that’s in our skin cells, as we go about our daily lives, but was fascinated to learn from Jimmy that we breathe DNA out in the vapour that comes out of our lungs. It’s fascinating to me that this molecule, DNA, that we regard as central to our biological identity and is tucked away securely in cell nuclei, is casually emitted by us each time we exhale, and that we are, of course, also breathing in the DNA of others. There’s something humorously promiscuous about this, but also materially and philosophically intriguing. It also has resonances for the Covid world we’re living in.”

Dr Pynor’s residency at SAHMRI will culminate in a body of research that will take the form of a written piece and a series of artworks.

The artwork generated from this research will include a video work, still photographic images, a kinetic sculpture involving exhaled water vapour, and the DNA genomic data itself.

The kinetic sculpture tests the collection of a shared breath sample using an R-Tube device. The exhaled DNA is then extracted, analysed and sequenced.

Dr Breen has worked closely with Dr Pynor throughout her residency to bring her project to life.

“The collaboration with Jimmy has been enormously valuable,” Dr Pynor said.

“With my own prior background in molecular biology, I feel we’ve formed an extremely productive and generative collaboration.”

“Jimmy’s experience has greatly expanded my own understandings.”

Promoting the collaboration is ANAT, an Adelaide-based agency facilitating the uptake of artists into science and technology sectors.

For over 30 years, ANAT has been identifying opportunities for artists to contribute to scientific innovation.

Dr Pynor said she is grateful for the opportunity.

“We hope the new work will stimulate philosophical reflection and expand viewers’ perception of life and its endlessly reiterating exchanges,” she said.

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