Splicing is how cells turn long strands of RNA into shorter pieces called messenger RNA, which provide the template for the production of proteins.

While major splicing carries out 99.5% of this work, minor splicing is an indispensable process for the remaining 0.5% of genes, affecting about 700 of the 20,000 genes in the human genome.

The new research reveals that blocking minor splicing causes the accumulation of DNA damage in cancer cells and activates a key tumour suppressor pathway that leads to cell death. Remarkably, healthy cells are largely unaffected.

Although it affects only a small sub-set of genes, minor splicing is crucial for the correct expression of genes that drive cell growth and division – making it a potential Achilles’ heel for cancer cells.

Importantly, many of these genes are commonly hijacked by cancers driven by KRAS mutations, which are among the most frequent genetic changes found in solid tumours.

WEHI laboratory head Professor Joan Heath said scientists have long known that KRAS is central to many aggressive cancers but have struggled to turn that knowledge into broadly effective treatments.

“KRAS mutations come in a variety of flavours, making them extremely hard to treat, so even with decades of scientific effort there has been only limited progress so far,” Prof Heath said.

“But our approach is different. Instead of trying to target specific mutations that may only apply to a subset of patients, we’re disrupting a fundamental process that these fast-growing cancers rely on.

“This research offers a new way to tackle a problem that’s long resisted conventional approaches, with the potential to help a much wider group of patients.”

Using zebrafish and mouse models, as well as human lung cancer cells, the WEHI-led research is the first to demonstrate the impact of inhibiting minor splicing in in vivo models of solid tumours.

The study found reducing the activity of a protein encoded by the RNPC3 gene – an essential component of the minor splicing machinery – significantly slows tumour growth in liver, lung and stomach cancers.

“Just by halving the amount of this protein, we were able to significantly reduce tumour burden,” said Dr Karen Doggett, first author of the study.

“That’s a striking result, especially given how resilient these cancers usually are.”

The study also revealed that disrupting minor splicing triggers the p53 tumour suppressor pathway, a critical defence mechanism in the body’s fight against cancer.

Dubbed the ‘guardian of the genome’, the p53 protein responds to DNA damage by stalling cell division, initiating DNA repair or triggering cell death. This well-known pathway is frequently mutated or disabled in many cancers, allowing these cells to grow unchecked.

“Blocking minor splicing leads to DNA damage and activates this critical defensive response, which means cancers with a functional p53 pathway are likely to be especially vulnerable to this strategy,” Dr Doggett said.

“This opens the door to treatments that could be both more effective and less toxic, offering hope for patients with aggressive cancers that currently have limited options.”

To search for compounds that might inhibit minor splicing, the research team turned to the National Drug Discovery Centre headquartered at WEHI, with a screen of over 270,000 drug-like molecules identifying several promising hits.

“We’ve validated minor splicing as a compelling therapeutic target – now the challenge is to develop a drug compound that can safely and effectively inhibit it,” Prof Heath said.

The research draws on WEHI’s deep expertise in gene discovery and cancer biology, showcasing the power of collaboration across multiple labs and technologies.

“One of the strengths of this study is the breadth of models and tumour types we used,” Prof Heath said.

“We didn’t just test one kind of cancer or use one analysis method. This diversity in our approach gives us confidence that our strategy could be relevant across many forms of cancer, and not just in a narrow set of conditions.”

The research was supported by the National Health and Medical Research Council of Australia (NHMRC), Ludwig Institute for Cancer Research and National Institute of Neurological Disorders and Stroke.

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Header image: A section of liver tumour in a zebrafish shows liver cell DNA (cyan), cancer cells with KRAS activity (purple), and DNA damage (white). The study found that lowering a key protein involved in minor splicing causes DNA damage selectively in cancer cells, leading to the expression of the p53 tumour suppressor protein.