In a move that could revolutionize the development of new cancer treatments, researchers from the University of Newcastle and the Hunter Medical Research Institute (HMRI) have created the world's first virtual platform to host 3D copies of human cancer tissues.
Until now, tissue samples donated by patients have only been available on request from physical biobanks that are based locally. The process can take a few months for clearance and the samples are usually unable to be reused once examined. As a way of improving this scenario, a team led by Dr Jamie Flynn, Dr Antony Martin and Dr William Palmer has established The Virtual Biobank.
Lead researcher Dr Antony Martin tells us that the inspiration for the project came from an entirely different field.
"I was lucky enough to spend a few months working alongside CSIRO scientists who were undertaking a large project toward digitizing natural history collections of insects in 3D," says Dr Martin. "At the same time, my colleagues and I had made breakthroughs in 3D imaging of internal 3D microstructures and cells within cancer tissues obtained from physical biobanks. I thought, if they are doing this for insects, why not for these valuable cancer specimens?"
The online platform allows anyone with a computer to access virtual copies of tumor samples from the Hunter Cancer Biobank, as well as important clinical and molecular information.
"Physical human tissue specimens that are donated for research are stored in a decentralized manner without standardized metadata schema," explains Dr Martin. "This makes it difficult to access and compare specimens collected from different hospitals and different studies. By virtualizing de-identified specimens, we hope to reduce these barriers by making samples available online to researchers."
This unique online database, so far made up of 20 breast cancer samples, ensures that the physical sample remains intact and makes available information about rare cancers that would otherwise be restricted.
"Cancer research has become a computationally heavy undertaking and the more standardized datasets that are available, the more powerful the analysis and conclusions that can be drawn," says Dr Martin. "Until now, they could not visually see the microstructural changes that occur at different stages of cancer for example. Opening up this resource to anyone with an interest in medical research, including computational biologists around the world, will allow discoveries that we cannot yet imagine."
A crystal-clear perspective
To create these advanced 3D images, the researchers used a hand-built laser microscope, engineered in their 2016 study at the 3D Tissue Clearing and Lightsheet Microscope Facility, based at HMRI. Instead of analyzing a thin slice of the sample, the CLARITY light-sheet produces clear, detailed 3D images of the whole tissue at a cellular level in a process that only takes a few minutes.
Collaboration is key
Working with colleagues from the University of Newcastle's IT department and Library Research Services, the effectiveness of the shared database is enhanced through the use of embedded specialized software tools that would otherwise be too expensive for researchers to access.
"We really wanted to make The Virtual Biobank interactive and dynamic, so with lead developer, Dr Bill Pascoe, and the Academic Research Computing Support team (ARCS), we developed a software toolkit for other people to contribute additional information such as findings from their own investigations," Dr Martin says. "Users can also create full 3D images for free by simply uploading their own microscopy data to our 'Terastitcher Pipeline', eliminating the need for expensive commercial software that can ordinarily cost upwards of $50,000."
The Biobank also includes a "Tissue Tracker" that automatically collects metadata so that all new tissue samples can be cataloged and experiments easily replicated.
New opportunities
Although the Biobank is still in its early stages, the processes used by the team are applicable to any cancer tissue. In future studies, researchers hope to to extend its reach into new areas of cancer research and education, as well as facilitate cross-disciplinary interaction with engineering and computer sciences.
"We are excited about the possibilities that the combination of 3D imaging of specimens and virtual reality creates," says Dr Martin. "These are virtualized images of real biological specimens and viewing these in virtual reality would be a valuable educational tool. Above and beyond that, I can imagine a future where biopsies could be examined by experts remotely via virtual reality. Similarly, a surgeon could study real biopsies taken from historical case studies before performing a procedure and use these to help in patient decision processes before surgery."
Source: The University of Newcastle