Crunching cancer data to save lives

30 Jan 2025
Time to crunch some cancer data: Thanks to the Foundation data scientist Rafael Tubelleza is one of a number of data specialists working with Associate Professor Arutha Kulasinghe (right) to interpret and understand gargantuan amounts of cancer data of different cancers as a result of Arutha's research in spatial mapping of tumours.

Every year, around 165,000 Australians will hear the words ‘you have cancer.’ For some, their treatment journey is filled with hope and success, but for many others, it’s marked by ineffective therapies and heartbreaking outcomes.

So how can two people diagnosed with cancer have such different responses to treatment?

This is the exact question driving Associate Professor (A/Prof) Arutha Kulasinghe and his research team. As A/Prof Kulasinghe explained; “Therapeutics for cancer today are between $300,000 and $500,000 per patient per year, but they only work in 15 to 20% of patients.

“This means that in almost 80% of patients we are spending nearly half a million dollars on treatments that ultimately fail and could have adverse effects.”

The economic cost, along with the physical and emotional toll of ineffective therapies, highlights the urgent need for more targeted and effective solutions, solutions that Arutha and his team are striving to deliver.

In just five years, A/Prof Kulasinghe and his team have turned a $10,000 seed-grant into what could be the most promising advancement in our knowledge of cancer biology and targeting treatment: the field of spatial medicine.

This cutting-edge technology shows researchers how cancer cells interact within their environment: how tumours grow, spread, and respond to therapies. Insights that could change the way cancer care is approached, informing oncologists and clinicians about which treatments offer the best chance of survival for the patient.

“What we're trying to do is dial it back to fundamentally understand what's going on in each individual patient’s tumour,” Arutha explained.

“The only way to do that is by observing how individual tumour cells communicate with each other and the body’s own immune system.”

To achieve this, A/Prof Kulasinghe and his team take a patient’s tumour and profile it cell-by-cell to develop digital tumour maps.

“We don’t grind the tissue up to analyse it, instead, we stain it with a “paint-palette” of coloured biomarkers which light up the various proteins in the tissue,” he said.

“The colours reveal where exactly the aggressive tumour cells, the normal cells, and the immune cells are and how they’re interacting. For example, we can see which immune cells are actively killing the tumour and which immune cells are unable to detect it. This allows us to identify patterns within the tissue.”

After the paint is applied, the researchers can pinpoint where each cell exists in space, assigning an X, Y, and Z coordinate to every single cell. This level of detail allows for a remarkably intricate understanding of the tumour and its environment.

However, this is where the challenge lies. As A/Prof Kulasinghe explains,

“Once we’ve digitised the patient’s tumour, we now need to analyse the 5 million cells in space. Meaning, it’s no longer a biological challenge, it’s a computational challenge. How do we store this data? How do we analyse this data? And how do we create enough tissue data sets to identify patterns of drug-response and resistance?”

The scale of this challenge is overwhelming. Each slide that holds a cancerous tissue contains around 10 terabytes of data. To put that into perspective, the average laptop has a storage capacity of 250GB. In other words, you’d need the equivalent of 40 laptops to store the data from just one slide.

Given the complexity and scale of the data, 80% of Arutha’s lab functions as a dry lab, meaning it primarily consists of computational biologists and data scientists like Rafael Tubelleza.

“Once you've got those digital images of the tumours, you need to discuss the data with medical oncologists, pathologists, immunologists and computational biologists to interpret what it means,” he explained.

Arutha expressed his gratitude, to the donors of the PA Research Foundation as world-leading research wouldn’t be possible without their incredible generosity. Thanks to them the Foundation was able to provide further funding to the team to continue crunching the data and advancing their work.

However, the challenges and costs are worth it because the University of Queensland researcher and his team’s work is reaching all around the world through global initiatives like the Human Cell Atlas (HCA) and Human Tumour Atlas Network (HTAN), where he’ll be presenting data later this year on the efforts led in Australia.

“We’re building tissue atlases for lungs, livers, hearts, brains that are both normal and diseased. This becomes a global resource for the scientific and medical community, where we can contribute to efforts across the globe, from Africa to the US and Europe,” Arutha said.

“It’s powerful because now, we have a shared resource that any lab can analyse the same dataset. If generating this data is going to cost hundreds of thousands of dollars, we want people to be able to use that data. This Human Cell Atlas is a global consortium dedicated to creating cell atlases for every organ. It’s a really collaborative initiative.

“Once we've built these atlases, we can then analyse hundreds of patients that have responded to a drug and hundreds of patients that haven't responded to a drug from patient cohorts around the world. And so now you are identifying spatial patterns that differentiate your patient responder from your non responder.”

While the field of spatial medicine is relatively new, it is seen by many in the medical field as the future of cancer treatment. The goal of the research team is to build the evidence from patient cohort studies which will move into a clinical trial where therapies are selected based on individual tumour profiles.

To support Arutha’s research and pave the way for innovative solutions in cancer care, donate to the PA Research Foundation today. Your donation will help offer new hope to the thousands of Australians who face the uncertainty of cancer treatment each year.