The future is 3D: Computational Biologist Dr Anna Trigos is transforming how we see cancer
28 January 2025
Dr Anna Trigos is a Group Leader in the Computational Biology Program at Peter Mac, and leader of the Trigos Lab. She has received a Foundation Grant from Peter MacCallum Cancer Foundation for her project, The future is in 3D: developing new workflows and computational methods to study cancer in 3D.
“The complexity of cancer biology has always amazed me”, Anna says. “Regardless of how much you learn, discover or understand, it always feels like just the beginning.”
In Anna’s first research project as an undergraduate biology student, she was tasked with exploring how one tiny molecule was controlled by another to support nerve regeneration. She recalls spending hours trying to understand why this single molecule, among the hundreds of thousands of others, was special.
This was a pivotal moment for Anna, who realised it was impossible for the human brain to remember all 20,000 gene names and the myriad pathways in which they’re all involved. She didn’t know it at the time, but it set her on a path to become a computational biologist.
“As a cancer researcher in computational biology, data is our bread and butter – not pipettes!” Anna explains.
“People think of different things when you say data – numbers, digits, storage. But to me, it represents an undiscovered world of networks and patterns. One small change in one corner of a complex network could have a cascade effect and disrupt the entire system, transforming a normal cell to a cancer cell. This is the common thread through all the projects I work on. I try to define the ‘rules’ that govern a system.”
In her first computational project, Anna’s team investigated whether cancer cells function differently from normal cells by acting more like single-cell organisms, such as bacteria, rather than relying on being part of an organ. To explore this idea, they focused on gene activity, examining which genes are activated in cancer at any point in time.
They searched for patterns across 20,000 genes in 10,000 samples, totalling 200 million data points, and uncovered an underlying network where key interactions were disrupted by mutations. This discovery offered valuable new insights into the fundamental biological processes that drive cancer.
Networks of connections between genes involved in cancer, such as this one, often look like flowers. A coincidence, or a hidden pattern?
Today, Anna leads the Trigos Lab, which is focused on understanding cancer evolution and cancer ecosystems through the analysis of “omics” data and the application of computational methods.
Omics data refers to large-scale data generated from various biological fields that study different components of living organisms at a molecular level. Each type of “omics” focuses on a different aspect of biology, such as genomics (genes), transcriptomics (RNA), proteomics (proteins), metabolomics (metabolites), epigenomics (gene regulation).
Anna’s team is working to uncover how different omics layers adapt and co-evolve as an ecosystem to drive cancer development, progression, and resistance to therapy.
“We are currently in the era of big data in biology and medicine, and one of the biggest challenges is integrating data across different biological levels. For example, we need to understand how genetic changes at the DNA level impact cells, tissues, and entire organisms, and ultimately determine factors like disease aggressiveness, treatment response, and prognosis.”
“The key question is: how do these biological systems interact and influence each other? What are the overarching rules or patterns that govern how these systems function together? Understanding these connections is crucial for advancing our knowledge and improving patient care.”
As an undergraduate, Anna wondered if humans could ever truly understand biological systems, or if it was simply too complex. Now, she says, “No, we just need the right mindset, questions and tools. We just need computational biology.”
Anna has received a Foundation Grant to develop new computational methods to study cancer in 3D. It will be one of the first projects in Australia to produce 3D spatial tumour models, enabling scientists to capture the true biology of tumours and accelerate the discovery of new cancer cures.
