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Spatial omics sparks a science revolution 

This article featured in Illuminate Newsletter Summer ‘23
Key Researchers
Division Head
Black and white photo of Verena Wimmer
Senior Research Scientist
Senior Research Scientist (Technology)
Raymond Yip in spatial omics labs

In the 19th century, the microscope illuminated the world of infectious diseases. In the 20th century, advances in DNA sequencing unlocked profound insights into the molecular basis of disease. Now, spatial omics is ushering us into a whole new era of discovery and WEHI is poised to lead the way.

This emerging field, powered by cutting-edge technologies, studies cells within their natural, undisturbed location inside tissue. Spatial omics can scrutinise thousands of variables and visualise cellular interactions like never before.

WEHI leads the way

In the last few years, WEHI has invested in a number of spatial omics technologies, including some of the first of their kind in Australia. These leverage WEHI’s strong expertise in microscopy and genomics, but also the outstanding skills of our scientists in bioinformatics and computational biology.

MERSCOPE, one of the world’s leading single-cell spatial transcriptomics technologies, is a powerful tool combining automated microscopy with a system that moves fluids around.

This technique, together with tagging of RNA molecules, allows for hundreds of genes to be detected and analysed within a tissue sample. It does this at sub-cellular resolution and keeps the cells undisturbed in their native location.

Professor Tony Papenfuss, theme leader  for  Computational Biology, believes that adding this capacity to WEHI’s laboratories will propel ‘the world of science’ more quickly towards solving intricate challenges in some of the most complex disease areas including cancer, immune disorders and neurogenerative conditions.

“Spatial omics has the potential to transform our scientific understanding of many diseases and crack open previously unimaginable solutions for their treatment and prevention,” says Prof Papenfuss.

Head of the Advanced Technology and Biology division, Associate Professor Kelly Rogers OAM, says WEHI’s unique strength in the world of spatial omics lies in its seamless integration of the interdisciplinary expertise (imaging, genomics and bioinformatics) required to excel in this rapidly emerging area.

“Having this powerful trio under the one roof sets us apart. It allows us to innovate and generate data within a competitive timeframe, putting WEHI at the forefront of this fast-evolving field,” says Assoc Prof Rogers.

Xenium, the first to be installed in Australia, is a cutting-edge spatial omics instrument at WEHI. By visualising millions of gene products and applying bioinformatics analysis, cell types can be colour-coded for deeper exploration of tissue, like cancer's cellular and molecular makeup.
Xenium is another of WEHI’s next-generation spatial omics instruments, also the first of its kind installed in Australia. By visualising millions of gene products and applying bioinformatics analysis, cell types can be colour-coded for deeper exploration of tissue.
Opening eyes to a new frontier

Spatial biology has emerged only in the last few years, prompted by numerous technological advances.

The most powerful aspect of spatial omics is its ability to assess the spatial context of a range of molecules within cells – such as proteins and mRNA – to understand how the cells interact and relate to each other within the three-dimensional structure of an organ.

WEHI’s 3D imaging specialist Dr Verena Wimmer explains how this new way of viewing networks within tissues is uncovering the hidden workings of disease.

“Cells exist in complex communication networks within tissue. Spatially they are organised into 3D ‘neighbourhoods’, which underpin their biological activity,” she says.

“For decades, investigating the cell types present in a given tissue on a molecular level required ‘destruction’ of these neighbourhoods – losing valuable information about the spatial relationship between different molecules and cells.

“Spatial omics is allowing us to map these ‘neighbourhoods’ with unprecedented detail and scale for the first time.”

Limitless horizons

Recognised by Nature as the “method of the year” in 2020, spatial omics has the potential to revolutionise entire areas of medical research.

Dr Daniela Zalcenstein, a specialist in single cell genomics at WEHI, agrees that the applications for spatial omics are endless.

“We are still on the cusp of grasping its full potential, but its use in translational and clinical research is incredibly versatile.”

Recent studies at WEHI have already revealed how spatial omics is changing the face of medical research:

  • Cancer: Currently, an individual’s response to a cancer drug cannot be reliably predicted. Spatial omics reveals predictive opportunities for immunotherapy resistance, allowing for better guided treatment decisions.
  • Vaccination and immunity: Vaccines generate memory cells for long-term pathogen recognition. Spatial omics is understanding the cell-to-cell ‘conversations’ crucial for immune memory, potentially revolutionising vaccine creation.
  • Brain disease: Over 5000 complex cell types are organised and communicate in the brain. Understanding these sophisticated connections in a spatial context is unlocking the secrets of degenerative diseases like Parkinson’s and dementia.

Spatial omics at WEHI is a collaboration between the genomics, imaging, bioinformatics and histology facilities. These teams are committed to being at the forefront of spatial omics technology and methods, including spatial transcriptomics and spatial proteomics 

They believe the future is bright for spatial omics and that today’s high-tech instruments and methods are only just the tip of the iceberg in terms of its scope.

Banner image: MERSCOPE, funded by the Barrie Dalgleish Centre for Myeloma and Related Blood Cancers and the first to be installed in Australia, helps researcher Dr Raymond Yip study the physical and chemical communications among distinct cell types.

First published on 29 November 2023
This article featured in Illuminate Newsletter Summer ‘23
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