Uncovering the origins of malignant rhabdoid tumors

HINXTON, UK & UTRECHT, The Netherlands—Researchers at the Wellcome Sanger Institute, the Princess Máxima Center for Pediatric Oncology, and their collaborators have discovered the first proof of the origin of malignant rhabdoid tumor (MRT), a rare childhood cancer. The study, which has been published in Nature Communications, found that MRT arises from developmental cells in the neural crest whose maturation is blocked by a genetic defect. The team also identified two drugs that might be used to overcome this block and resume normal development, bringing hope of new treatments for the disease.

“To be able to identify where malignant rhabdoid tumor comes from for the first time is an important step in being able to treat this disease, but to confirm that it is possible to overcome the genetic flaw that can cause these tumors is incredibly exciting,” stated Dr. Jarno Drost, co-lead author of the study from the Princess Máxima Center for Pediatric Oncology. “The fact that two drugs already exist that we think can be used to treat the disease gives us hope that we can improve outcomes for children diagnosed with MRT.”

Malignant rhabdoid tumor is a rare soft tissue cancer that predominantly affects infants. Although these tumors can arise in any part of the body, they usually form in the kidneys and the brain. MRT is one of the childhood cancers with the poorest outcomes. The rarity of MRT, combined with its aggressiveness, makes clinical trials extremely difficult to put together. Until now the origin of MRT has been unknown, and no reliably effective treatment currently exists. 

This new study sought to discover the root of MRT, in the hope of identifying new treatments for the disease. Researchers sequenced whole genomes in two cases of MRT at the Wellcome Sanger Institute, alongside corresponding normal tissues. The team then conducted phylogenetic analyses of the somatic mutations in the diseased and healthy tissue, in order to reconstruct the timeline of normal and abnormal development.

The analyses confirmed that MRT develops from progenitor cells on their way to becoming Schwann cells — a cell type found in the neural crest — due to a mutation in the SMARCB1 gene. This mutation blocks the normal development of these cells, which can then go on to form MRT.

Researchers at the Princess Máxima Center inserted the intact SMARCB1 gene into patient-derived MRT organoids to successfully overcome the maturation block that had prevented normal development and led to cancer. Based on single-cell mRNA analyses and predictions made from these experiments, the researchers then identified two existing medicines that can overcome the maturation block, and could potentially be used to treat children with MRT.

“It is fantastic to see this collaborative research bearing highly translatable outcomes in a childhood cancer with a currently poor prognosis. It emphasizes the significant benefit of a national tumor banking system, that allows collection of rarer tumors and, in turn, the best use of such precious tissue through agreement of the CCLG Biological Studies committee that oversees this resource,” noted Professor Richard Grundy, chair of the Children’s Cancer and Leukaemia Group. “For this to result in such a meaningful outcome gives new hope to children with malignant rhabdoid tumor.”

“We began our enquiry into the origins of malignant rhabdoid tumors in late 2019, so we have gone from hypothesis to discovery of origin to possible treatments for the disease in just over a year,” pointed out Dr. Sam Behjati, co-lead author of the study from the Wellcome Sanger Institute. “This was possible due to all the leading-edge tools available to us, from organoid technology to single-cell mRNA sequencing to drug screen databases. I hope this study will serve as the blueprint for discovering the origin of other childhood cancers, and ultimately lead to better outcomes for children affected by these awful diseases.”