Spatial conversations

Raymond completed his PhD at the University of Hong Kong before joining the lab of Jane Visvader and Geoff Lindeman at Walter and Eliza Hall Institute in 2017. He is currently a Senior Research Officer with joint appointment across Imaging, Genomics, and Edwin Hawkins laboratories. He leads the implementation of spatial multi-omics technologies at WEHI and is heavily involved in technology benchmarking projects. His research focuses on studying the role of bone marrow microenvironment in cancer development using spatial omics technologies.

Mai La is a post-doctoral researcher at the University of Melbourne Centre for Cancer Research. She completed her PhD in stem cell biology at Monash University in 2021. Since joining the University of Melbourne in 2022, Mai has been investigating pancreatic cancer under the guidance of Prof. Sean Grimmond and A/Prof. Fernando Rossello. Her research focuses on employing multi-omics approaches, including genomics and transcriptomics, to unravel the intricate molecular mechanisms of pancreatic cancer. Mai’s work aims to enhance our understanding of this challenging disease and contribute to the development of targeted therapeutic strategies.

Dr Alexander Combes (PhD) is internationally recognised for pioneering advanced imaging and single cell approaches to investigate kidney development and disease in mouse models and human kidney organoids. He has 54 publications in the field (>3,837 citations, H-index 31) including first/last author papers in Developmental Cell, Nature Protocols, Elife, Genome Medicine, and top journals in the field like Kidney International (IF 18). His profile is evidenced by invited reviews in Nat Rev Nephrol and Genes and Development, invited talks at top kidney meetings ASN Kidney week USA, RenalToolBox UK, and publications with prominent nephrologists in the USA and Europe. He is funded to investigate the fundamental mechanisms of kidney development through the ARC, and to model disease in human kidney organoids through Therapeutic Innovation Australia and the Medical Research Future Fund.

Awarded a PhD at the University of Queensland (UQ), Dr Combes undertook postdoctoral studies with developmental biologist and kidney organoid pioneer Professor Melissa Little. During this time, he spent several years working closely with teams in Oxford, Harvard, and other prestigious institutes in the USA, and was awarded highly competitive fellowships and funding through ARC, NHMRC, and international organisations. His current work continues to explore the fundamental mechanisms of kidney development and explores the potential of human kidney organoids for disease modelling and drug screening in acute kidney injury, which affects over 13 million people each year and lacks targeted therapies.

Saskia Freytag is a laboratory head in the Personalised Oncology Division at Walter and Eliza Hall Institute for Medical Research. Together with Dr Sarah Best and Dr Jim Whittle, Saskia co-leads the Brain Cancer Research Laboratory within the Brain Cancer Centre, where she leads the Bioinformatics arm. Her group uses cutting-edge single cell and spatial omics technologies to improve surgical methods, understand resistance mechanisms, and identify novel treatment strategies. Saskia has a PhD in Statistical Genetics from Georg-August University in Göttingen (Germany), followed by postdoctoral positions at WEHI and the Harry Perkins Institute of Medical Research in Perth. Saskia has been supported by funding from Carrie’s Beanies for Brain Cancer (CB4BC), Cancer Australia, Cancer Council Victoria, the MRFF and the NHMRC. In addition to her research career, Dr Freytag is deeply committed to fostering community and promoting inclusivity in science. She chairs the Code of Conduct Committee of the international Bioconductor Project and served as the ambassador for the Australian Mathematical Science Institute’s CHOOSEMATHS program from 2016 to 2018.

Understanding molecular and structural heterogeneity in tissues is a key component of studying health and disease. Indeed, making progress towards new treatments for a deadly, progressive disease like idiopathic pulmonary fibrosis requires genetic and molecular analysis at high cellular and spatial resolution. Happily, modern ‘omics technologies provide the ability to characterise genetic and other high-dimensional molecular states at single-cell resolution, now also with spatial context. Rich, complex datasets are exciting, but bring with them deep challenges for winnowing the wheat from the chaff to answer biological questions of interest. In this talk, I will discuss using “traditional” statistical and recently developed deep learning approaches to spatial transcriptomic data in diseased and healthy lungs. I will present our use of graph neural network models (among other approaches) to characterise the molecular basis for tissue niche structure in lung fibrosis using 10x Xenium data on 45 lung samples. This analysis offers new insights into the spatial heterogeneity of gene expression in healthy and fibrotic regions of the lung and identifies “early transition” regions from healthy to disease states as the most promising area for clinical intervention.

Dr Lipin Loo is the Group Leader in RNA therapies and a co-Leader of the Single Cell and Spatial Biology node at the Charles Perkins Centre, University of Sydney. Utilising genetic screens and single-cell/spatial transcriptomics, Lipin aims to identify and map transcriptional changes underlying pathophysiological conditions such as chronic pain and neuropathy. Elucidating these orchestrated transcriptional changes will have a far-ranging impact on our understanding of disease-causing aberrations and instruct our strategies in restoring normal function in diseased cells.

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