New software tool could help better understand childhood cancer

New cutting-edge software developed in Melbourne can help uncover how the most common heart tumour in children forms and changes. And the technology has the potential to further our understanding of other childhood diseases, according to a new study.

The research, led by Murdoch Children’s Research Institute (MCRI) and published in Genome Biology, found the software, VR-Omics, can identify previously undetected cell activities of cardiac rhabdomyoma, a type of benign heart tumour.

Developed by MCRI’s Professor Mirana Ramialison, VR-Omics is the first tool capable of analysing and visualising data in both 2D and 3D virtual reality environments. The innovative technology aims to analyse the spatial genetic makeup of human tissue to better understand a specific disease.

Image: Professor Mirana Ramialison

Cardiac rhabdomyoma, usually detected during pregnancy or infancy, doesn’t cause health problems in most cases. But in some babies and children the tumours can grow and block blood flow to vital organs, causing respiratory distress, irregular heartbeat, obstructions and heart failure.

“When the tumours cause severe health complications, treatment options are limited and include surgically removing part of the heart, which may lead to further complications and death,” Professor Ramialison said. Unfortunately, it’s not well understood why these tumours form.”

To challenge her new software, Professor Ramialison and her team, including Denis Bienroth and Natalie Charitakis, analysed heart tissue from three children in Melbourne with cardiac rhabdomyoma. In a breakthrough, the research uncovered specific underlying features of the tumour that hadn’t been identified previously.

Image: Denis Bienroth

Professor Ramialison said the VR-Omics tool would help researchers to gain a better insight into the disease.

“VR-Omics generates 3D visualisations of the cells within human tissue based on large collections of patient data,” she said. This could allow for greater analysis of human tissue compared to other methods.”

Professor Ramialison also benchmarked the software against existing state-of-the-art methods, finding it performed better in all analysis steps.

mage: Natalie Charitakis

“VR-Omics has a unique capacity to analyse large datasets, which allows it to explore new biological mechanisms in rare tissue sections, like those from cardiac rhabdomyoma,” she said. The technology will enable more biological discoveries that could help better understand many childhood conditions.”

Researchers from the Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine (CardioRegen), the University of Konstanz in Germany, Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Melbourne and Monash University also contributed to the findings.

Watch a video of the VR-Omics software

Publication

Denis Bienroth, Natalie Charitakis, Dillon Wong, Yunhan C. Zhang, Sabrina Jaeger-Honz, Jialin Ding, Kevin I. Watt, Julian Stolper, Hazel Chambers-Smith, Duncan MacGregor, Bronwyn Christiansen, Celine Vivien, Adam T. Piers, Lisa N. Waylen, Lucas B. Hoffmann, Jessica Tang, Hue M. La, Mei R. M. Du, Monika Mohenska, Jose M. Polo, Sean Grimmond, Ethan Scott, Fernando J. Rossello, Enzo R. Porrello, Karsten Klein, Hieu T. Nim, David A. Elliott, Falk Schreiber and Mirana Ramialison. ‘Automated integration of multi‑slice spatial transcriptomics data in 2D and 3D using VR‑Omics,’ Genome Biology. DOI: 10.1186/s13059-025-03630-6

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Mirana Ramialison, MCRI Group Leader, Transcriptomics and Bioinformatics

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About Murdoch Children’s Research Institute

The Murdoch Children's Research Institute (MCRI) is the largest child health research institute in Australia committed to making discoveries and developing treatments to improve child and adolescent health in Australia and around the world. They are pioneering new treatments, trialling better vaccines and improving ways of diagnosing and helping sick babies, children and adolescents. It is one of the only research institutes in Australia to offer genetic testing to find answers for families of children with previously undiagnosed conditions.

Funding

Mirana Ramialison and Hieu T. Nim are supported by an NHMRC Ideas Grant (APP1180905). Professor Ramialison is funded by a Heart Foundation Future Leader Fellowship. Natalie Charitakis is supported a 10x-Millenium Science’s Spatial Pioneer fellowship. Additional infrastructure funding to Murdoch Children's Research Institute was provided by the NHMRC Independent Research Institute Infrastructure Support Scheme. The Australian Regenerative Medicine Institute is supported by grants from the Victorian Government and the Australian Government. The Novo Nordisk Foundation Center for Stem Cell Medicine is supported by Novo Nordisk Foundation grants (NNF21CC0073729).