Early lung damage mapped in children with cystic fibrosis

Melbourne researchers have mapped how lung damage begins early in life for children with cystic fibrosis, providing new insights that will help reshape future care.

The research team, led by Murdoch Children’s Research Institute (MCRI) and the Peter MacCallum Cancer Centre, has created the largest-ever lung atlas of the lower airways in young cystic fibrosis patients, offering new clues into preventing long-term disease.

MCRI Associate Professor Melanie Neeland said the findings showed that immune abnormalities in cystic fibrosis patients were already well established by early childhood, with current treatments failing to protect the lungs from irreversible damage.

Image: Associate Professor Melanie Neeland

How was the lung atlas created?

The team analysed more than 190,000 individual cells from 45 lung samples taken from 37 children treated at The Royal Children’s Hospital (RCH) for cystic fibrosis, aged five months to six years. Using advanced single-cell sequencing and protein analysis, they identified 43 distinct types of immune and epithelial cells, building a detailed cellular map of the developing lung.

The research was supported by the Chan Zuckerberg Initiative, reflecting their interest in studying how cells operate to better understand why disease happens and how to correct it.

Published in Mucosal Immunology, the study found that even in preschool-aged children with cystic fibrosis, their key immune cells, especially macrophages, aren’t strong enough to help fight off infections. These cells displayed abnormal activity in several important biological pathways, including those involved in inflammation, cholesterol regulation and tissue scarring linked to lung fibrosis.

Importantly, these abnormalities were more pronounced in children who had already begun developing bronchiectasis, a form of irreversible lung damage that can lead to lifelong breathing problems.

Children with cystic fibrosis often face persistent lung infections due to thick mucus in their airways. In Australia, about 1,600 children have cystic fibrosis with one baby born with the condition every four days.

Critical window identified for anti-inflammatory treatments

The researchers also examined the effects of commonly used cystic fibrosis medications that focus on the condition’s underlying genetic defect.

Associate Professor Neeland said despite major advances in treating cystic fibrosis, the findings suggested that targeted anti‑inflammatory treatments may be necessary alongside current medications to prevent permanent lung damage.

“We discovered immune dysfunction in the lungs begins in the preschool years and persists despite current breakthrough therapies,” she said.

“Although these therapies have been considered highly effective treatments, our findings in children suggest their impact on lung disease may not be as good as once predicted “

“This suggests that early intervention strategies that combine these medications with targeted anti-inflammatory therapies could help prevent lung damage. These findings provide a powerful new resource, highlighting a critical window for intervention.”

MCRI Associate Professor Shivanthan Shanthikumar, who is also a Paediatric Respiratory Specialist at the RCH, said, “The study shows there’s still a long way to go to ensure people with cystic fibrosis can live unaffected by the disease. It also highlights the importance of studying lung disease in preschool children, who are often overlooked in research that focuses on adults.”

Image: Associate Professor Shivanthan Shanthikumar

Life-changing impact of taking part in clinical trials

Lewis, 12, who has cystic fibrosis, has previously participated in MCRI trials with one transforming how early life lung disease in cystic fibrosis is viewed.

Lewis, (pictured above with MCRI Dr Louis Perriman), recently also visited MCRI for a tour of the lung stem cell medicine lab.

Mum Justine said the cystic fibrosis research had been transformative and encouraged other families to enrol in clinical trials. To help find new treatments, MCRI researchers have also grown human lung stem cell models in the lab to screen thousands of existing medicines to see if any might be effective against cystic fibrosis. 

“We have taken part in research before and would do it again in a heartbeat if it helps other children,” Justine said. “The only reason Lewis has access to life-changing medications is because a team of researchers somewhere proved that they work.

Image: Lewis, 12, has cystic fibrosis

“We were encouraged early on by his doctors to not keep Lewis in a bubble, so with the help of different treatments, he can still play sport and thrive in outdoor activities.”

Read more about Lewis’ experience with cystic fibrosis.

Researchers from the University of Melbourne, The Royal Children’s Hospital, Walter and Eliza Hall Institute of Medical Research, Garvan Institute of Medical Research and the University of New South Wales also contributed to the research.

Banner image credit: David Caird, courtesy of News Corp

Publication

Jovana Maksimovic, Shivanthan Shanthikumar, George Howitt, Gunjan Dixit, Peter F Hickey, Casey Anttila, Daniel V. Brown, Liam Gubbels, Anne Senabouth, Daniela Amann-Zalcenstein, Joseph E. Powell, Sarath C. Ranganathan, Alicia Oshlack and Melanie R. Neeland. ‘Single-cell profiling of BAL in preschool cystic fibrosis reveals macrophage dysregulation and ivacaftor-modified inflammatory programs in the early life lung,’ Mucosal Immunology. DOI: 10.1016/j.mucimm.2026.03.012

*The content of this communication is the sole responsibility of MCRI and does not reflect the views of the NHMRC.

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Associate Professor Melanie Neeland, MCRI Team Leader, Respiratory

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About Murdoch Children’s Research Institute

Murdoch Children’s Research Institute (MCRI) is one of the world’s top three child health research institutes, dedicated to improving the health of children and adolescents in Australia and around the world. In 2026 MCRI celebrates its 40th anniversary, marking four decades of transforming child health through research, discovery and innovation. Its breakthroughs have improved diagnosis, informed global vaccine strategies, advanced precision medicine, and continue to redefine what’s possible for sick children. MCRI is one of the only research institutes in Australia to offer genetic testing to help families find answers for children with previously undiagnosed conditions.

Funding

The study was funded by the Chan Zuckerberg Initiative (Inflammation Network), National Health and Medical Research Council of Australia Synergy Grant (1183640), Investigator Grant to AO (1196256), Investigator Grant to JM (2026098), and a Vertex Mentored Research Innovation Award. S.S is supported by a clinician-scientist fellowship from the Melbourne Children’s Campus.