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Spatial omics

This emerging field, powered by innovative new technologies, is unveiling cellular communication networks at unprecedented scale, enabling us to visualise the inner workings of the body like never before.

What is spatial omics?

Spatial omics is an innovative new way to do science, powered by creative methods and advanced technical solutions. It explores cells in tissue samples, without disturbing how they would be naturally positioned in the body

Spatial omics is revealing an entirely new dimension of knowledge around the intricate world of cells within tissues.  

These breakthrough technologies allow for the analysis of intact tissue sections in never-before-seen detail. Spatial omics shows which genes are active in a given cell. This allows scientists to identify the type of cell, understand what the cell is doing and how it communicates with its neighbours.

Spatial omics at WEHI

  • Unveiling insights: Spatial omics uncovers molecular cell types, aiding disease understanding, predicting treatment responses, advancing vaccines and decoding complex spatial environments within tissues, such as the brain.
  • Revolutionising science: Spatial omics is transforming medical research by visualising mRNA and proteins within cells, in their native location within tissue at a biomolecular level. It allows us to compare what cells are doing in addition to their location. It is far superior to previous methods that compromised or ‘destroyed’ cellular locations.
  • Cutting-edge tools: Using molecular barcoding, cutting-edge automated microscopes and next-generation sequencing to understand cell communication, spatial omics is opening up new pathways for scientific discovery.
  • WEHI thought-leaders: WEHI has installed some of the first spatial omics technologies in Australia, foreseeing their potential for breakthroughs in global health solutions.
  • Unique strength: Alongside an established histology facility, WEHI has all three pillars of spatial omics (imaging, genomics and bioinformatics) under the one roof. This allows us to innovate and generate data within a competitive timeframe, through seamless integration.

Unlocking a hidden world

Progressive science needs excellent tools. Spatial omics uses cutting-edge technologies to detect up to thousands of mRNAs and proteins in tissue to understand the complex ways that cells interact and work together in organisms.

In simple terms, it explores cells in tissue samples, without disturbing how they would be naturally positioned in the body.

Specifically, spatial omics enables an unprecedented analysis of cells in their native environment. It surpasses previous techniques by keeping the tissue sample intact while collecting complex information about the spatial relationship between different molecules and cells.

“Spatial omics is like opening a portal to a whole new dimension, which allows us to see glimpses of ‘conversations’ between cells that have been hidden until now.”
– Associate Professor Marie-Liesse Asselin-Labat, Chair, Spatial Omics Strategy, WEHI
WEHI’s MERSCOPE platform is one of the world’s leading single-cell spatial transcriptomics technologies. It can ‘light up’ a subset of gene products, labelling distinct immune cell types such as T and B cells. This helps study the physical and chemical communications amongst them, generating new knowledge on how our body fights infection.
Above: WEHI’s MERSCOPE platform is one of the world’s leading single-cell spatial transcriptomics technologies. It can ‘light up’ a subset of gene products, labelling distinct immune cell types such as T and B cells. This helps study the physical and chemical communications amongst them, generating new knowledge on how our body fights infection.

WEHI leading the way

WEHI has taken the lead in being the first to bring several of these next generation spatial omics technologies to Australia.

Adding this capacity to our laboratories will propel us more quickly towards solving some of the most intricate global health challenges.

“Spatial omics has the potential to transform our scientific understanding of many diseases and crack open previously unimaginable solutions for their treatment and prevention.”
– Professor Tony Papenfuss,  Computational Biology Theme Leader, WEHI
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.
Above: 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.

WEHI’s strength – seamless integration

In the world of spatial omics, WEHI’s unique strength lies in its seamless integration of 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.”
– Associate Professor Kelly Rogers OAM, Head, Advanced Technology and Biology division, WEHI

Having expertise across these pivotal areas creates a fully integrated research environment. Our ability to facilitate workflows across platforms means we can integrate all three key areas of spatial omics:

  • genomics sequencing methods for unbiased discovery
  • high-resolution imaging approaches supported by the Centre for Dynamic Imaging to validate and refine initial findings
  • bioinformatics to develop new methods to analyse and integrate data generated on these diverse platforms.

This unique set-up, coupled with an inhouse state-of-the art histology laboratory, offers seamless end-to-end solutions, with immediate feedback and fast turn-around times.

Revealing the body’s hidden secrets

Uniquely, spatial omics reveals how cells are organised within tissue. This information is important because cells function and communicate in three-dimensional neighbourhoods.

For decades, investigating cells in tissue samples required a compromise. A biased approach could look at a small number of known markers within the spatial context. An unbiased approach could look at many markers in individual cells, but their locations would be ‘destroyed’, losing critical information about the spatial relationship between molecules and cells.

Spatial omics instruments show a richer view of intact tissue samples. These perspectives are revealing crucial insights about how cells interact in healthy and diseased tissue.

MIBIscope, run by Dr Claire Marceaux, the first installed in Australia, is a cutting-edge spatial proteomic platform available at WEHI.
Above: MIBIscope, the first installed in Australia, run by Dr Claire Marceaux, allows single-cell spatial proteomic analysis.

Spatial omics has the potential to empower the next generation of scientific discoveries, uncovering the hidden workings of diseases.

What makes these high-tech instruments revolutionary is that they allow scientists to scrutinise thousands of simultaneous variables and understand cellular interactions. This is helping to uncover the underlying causes of diseases, so that we can find better treatments sooner.

How it helps science

Inside our bodies, cells make up complex tissues. It’s not just what each cell is made of that matters, but also where it is located. This location plays a huge role in how a tissue works, and also in understanding what might go wrong when a disease develops.

“Spatial omics is the new frontier in medical research. It will take us to places we have never imagined in science discovery.”
– Dr Rory Bowden, Head, Genomics Laboratory, WEHI

Spatial omics in action

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

Cancer: predicting treatment response

  • 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: advancing vaccine design

  • 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: unveiling complex networks

  • 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.

WEHI’s spatial omics technologies

WEHI’s commitment to excellence is evident in its first to market position in spatial omics technologies and methods, including spatial transcriptomics and spatial proteomics.

In recent years, WEHI has invested in several next generation spatial omics and imaging systems within our Centre for Dynamic Imaging and the Advanced Genomics Facility including:

Spatial omics at WEHI is a collaboration between the genomics, imaging, bioinformatics and histology facilities. Come chat with us to explore applying this state-of-the-art technology to your research.
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Illuminate Summer 2023
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