Bioinformatics facility gain access to groundbreaking spatial technology, deep dive into organoids

reNEW Melbourne’s Bioinformatics Facility, managed by A/Prof Mirana Ramialison, was recently awarded a grant to access to BGI’s Stereo-seq technology.

This was awarded through Spatial Temporal Omics Consortium (STOC), an open collaborative research initiative established to unite, organize, advance, and share global scientific efforts in spatiotemporal omics to solve the mysteries of life.

The grant gives researchers early access to ground-breaking spatial transcriptomics technology Stereo-seq (SpaTial Enhanced REsolution Omics-Sequencing). This technology is one of the few spatial transcriptomics technologies that can be used for 3D models of human tissue, called organoids.

This technology is not currently available for purchase.

reNEW Melbourne expertise
reNEW Melbourne, located at the Murdoch Children’s Research Institute, is well placed to use this ground-breaking technology.

reNEW Melbourne hosts a unique combination of laboratories that are world-leaders in generating organoids of different organs and tissues: brain, heart, kidney, lung, muscle and blood.

Organoids are three dimensional models of organs and tissues and overcome many of the limitations of animal models or two dimensional cell cultures. As organoids can be cultured from genetically engineered stem cells and patient cells, they offer flexibility in reproducing different genetic causes of disease development. They can also represent different stages of development.

In parallel, reNEW Melbourne has the bioinformatics resources for analysis and deciphering this complex data. The Transcriptomics & Bioinformatics lab, also led by Ramialison, has experience working with spatially resolved transcriptomics data. The lab is spearheading the effort within the Murdoch Children’s to establish spatial transcriptomics as a more routine and accessible experiment.

Strengthening reNEW through comprehensive atlas
With this grant, the Bioinformatics Facility propose to generate a transcriptome-wide spatial atlas of the reNEW Melbourne organoids, capturing data across the different areas of the body that reNEW Melbourne are experts in.

By placing thin slices of the organoids on specialised slides and performing mRNA sequencing, the location, or spatial information, of each gene’s expression can be obtained. This gives an accurate map of all the different types of cells within each organoid.

“This can serve as a reference base for future studies that use organoids to model different disease, to investigate the cause of disease, or when screening drug compounds for novel treatments”, said Natalie Charitakis, a PhD student in the Transcriptomics & Bioinformatics and Heart Regeneration and Disease labs and a lead investigator in the grant.

The long-term goal of the Facility is to make the atlas accessible to all researchers across all the reNEW nodes

“Through this atlas, not only will we learn about each organoid type, but we can gain new insights about core principles of organoid formation”, said Ramialison.

“This work will promote the use of organoid models to fast-forward our understanding of human development and disease.”

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