Childhood kidney cancer has millions of genetic changes, opening door to possible treatments

Researchers have uncovered that some childhood cancers have a substantially higher number of DNA changes than previously thought, changing the way we view children’s tumours and possibly opening up new or repurposed treatment options.

Concentrating on a type of childhood kidney cancer, known as Wilms tumour, an international team genetically sequenced multiple tumours at a resolution that was previously not possible. This collaboration included researchers at the Wellcome Sanger Institute, University of Cambridge, Princess Máxima Center for Pediatric Oncology, the Oncode Institute in the Netherlands, Great Ormond Street Hospital, and Cambridge University Hospitals NHS Foundation Trust.

They uncovered many more genetic changes per cancer cell than expected, adding up to millions of changes per tumour. This suggests that some childhood tumours could be eligible for treatments such as immunotherapy.

In the study, published today (29 May) in Nature Communications, the team also describes a single, spontaneous genetic change that causes a rare type of Wilms tumour, which children are born with, and that this change happens early during development in the womb. They found that these tumours have a particular appearance under the microscope and genetic profile, implying that it could be possible, in the future, to develop personalised therapeutics and tailor clinical plans for those with this genetic change.

This research challenges the widely held notion that childhood cancers have a very low number of genetic changes and instead suggests that there could be effective adult treatments that could be adapted for childhood tumours in the future.

Wilms tumour is a type of kidney cancer that largely affects children under the age of five. In the UK, about 85 children are diagnosed with Wilms tumour every year¹.

Previously, it was thought that childhood cancer tumours, like those in Wilms tumour, had a low number of genetic changes, also called genetic variants.  

To investigate how and why these tumours present so early in life, the team at the Sanger Institute and their collaborators applied the latest genomic sequencing techniques to understand more about how and when these genetic changes occurred.

Bulk whole genome sequencing methods allow researchers to find genetic changes that are shared by all the cells in the tumour. While this can work well for adult tumours, as the cells have had more time to develop, childhood tumours have fewer shared genetic changes, meaning that the large number of mutations that are not shared by all cells are missed.

To overcome this, the team used two cutting-edge techniques: nanorate sequencing², otherwise known as nanoseq, and whole-genome sequencing of single-cell-derived organoids³ to study kidney tumours at much higher resolution. These methods allow scientists to find genetic changes that might be present in just a single cell of a cancer.

The team used these methods to genetically sequence Wilms tumour samples from four children, aged up to six months. They found that a single cancer cell had an additional 72 to 111 genetic changes on top of the ones already identified via bulk whole genome sequencing methods⁴. This means that when the overall number of cells in the tumour is taken into consideration, there are most likely millions of genetic changes per tumour overall, not the low numbers that were previously thought.

Alongside changing our understanding of childhood tumours, this new finding could also have implications for treatment. The researchers suggest that with this number of possible genetic changes, it’s likely that tumours could become resistant to treatments quicker, or that some drugs might not work at all.

However, this discovery could also mean that childhood tumours are better candidates for existing treatments that are currently used for adult tumours, such as immunotherapies⁵.

The team also traced the evolution of the tumours in three children and uncovered a new mutation that causes Wilms tumour. This single change in the FOXR2 gene was found to happen while the kidney was developing in the womb, and is associated with a particular appearance of the tumour under the microscope and a specific set of RNA changes. Researchers suggest that this could be used to identify these tumours and that, one day, it may be possible to develop specific personalised treatment for certain genetic profiles in Wilms tumour.

Dr Henry Lee-Six, co-first author at the Wellcome Sanger Institute, said: “Widespread sequencing methods are incredibly useful for a large number of cancer tumours, especially in adults. However, they fail to capture the true genetic complexity of cancers, particularly those that occur in the youngest children. With these latest genomic sequencing techniques, we can now see a much more detailed picture of Wilms tumour, which can occur in newborns. This could help us understand this condition in more detail, and may change the way we view and treat childhood tumours as a whole.”

Dr Jarno Drost, co-senior author at the Princess Máxima Center for Pediatric Oncology and the Oncode Institute in the Netherlands, said: “Being able to trace the evolution of a tumour can uncover crucial information about how and why it develops. In this study, we uncovered a single genetic change that occurred during development and caused this subset of Wilms tumour. Treatment for Wilms tumour has to carefully balance treating the tumour and lowering the risk of recurrence, while minimising the impact this can have on a young child’s quality of life and their family. By understanding the genetic changes that cause tumours, and in this case, identifying different genetic subsets, it could lead to more targeted treatment options, something that every child deserves.”  

Professor Sam Behjati, co-senior author at the Wellcome Sanger Institute and Cambridge University Hospitals NHS Foundation Trust, said: “It has been a widely held belief that childhood tumours had much lower numbers of genetic changes than adult tumours. However, thanks to the development of new genomic sequencing tools, we have been able to show that, at least in these cases, it is not true. Our findings suggest that childhood tumours have at least four times more genetic changes per cell than expected, which adds millions more changes per tumour, highlighting that what we could see before was just the tip of the iceberg. This has implications for both childhood kidney cancer and possibly other childhood tumours. If we understand childhood cancer fully, we can develop new ways to treat it or repurpose existing treatments to get options to those who need them as quickly as possible.”

ENDS

Contact details:

Rachael Smith

Press Office

Wellcome Sanger Institute

Cambridge, CB10 1SA

07827979492 / 07748379849

Email: press.office@sanger.ac.uk

Notes to Editors:

1. Cancer Research UK. Wilms tumour (nephroblastoma) web page. Available at: https://www.cancerresearchuk.org/about-cancer/childrens-cancer/wilms-tumour/about [Last accessed: March 2025]
2. Nanorate sequencing is a new genomic sequencing method that attaches markers to both strands of DNA, compared to bulk sequencing methods that attach a marker to one of the strands. The two strands can be sequenced independently and the results compared. This allows for much more accurate sequencing, allowing the detection of extremely rare mutations. 
3. Whole-genome sequencing of single-cell-derived organoids is a method where an organoid is grown from a single cell of a sample, meaning that all cells in the organoid share the set of genetic changes that were present in the original sampled cell. Whole-genome sequencing is then applied to the organoid to capture the genetic changes of a single cell.  
4. Bulk whole genome sequencing of the tumours found between 30 and 61 genetic changes per tumour.   
5. Immunotherapies harness the body's immune system to destroy the cancer cells, and can be very effective. A high amount of genetic changes is linked to the success of immunotherapy, and therefore, it was thought that many childhood tumours were not eligible. 

Publication:

H. Lee-Six, T. D. Treger, M. Dave, et al. (2025) ‘High-resolution clonal architecture of hypomutated Wilms tumours’. Nature Communications. DOI: 10.1038/s41467-025-59854-4

Funding:

This research was part-funded by Wellcome, the Little Princess Trust, the European Research Council and a Dutch Cancer Society (KWF)/Alpe d’HuZes Bas Mulder Award. A full acknowledgement list can be found on the publication.

Selected websites:

The Wellcome Sanger Institute

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About the Princess Máxima Center for pediatric oncology

When a child is seriously ill from cancer, only one thing matters: a cure.

Every year, 600 children in the Netherlands are diagnosed with cancer. Sadly, one in four of these children dies. That is why in the Princess Máxima Center for pediatric oncology, we work together with passion and without limits every day to improve the survival rate and quality of life of children with cancer. Now, and in the long term. Because children have their whole lives ahead of them.

The Princess Máxima Center is no ordinary hospital, but a research hospital. All children with cancer in the Netherlands are treated here, and it’s where all research into childhood cancer in the country takes place. This makes the Princess Máxima Center the largest pediatric cancer center in Europe. More than 900 healthcare professionals and 450 scientists work closely with Dutch and international hospitals to find better treatments and new perspectives for a cure.

In this way, we offer children today the best possible care, and we take important steps to improve survival for children who cannot not yet be cured.

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