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SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors

Author

Listed:
  • Ning Qing Liu

    (Netherlands Cancer Institute
    Erasmus Medical Center (MC) Cancer Institute)

  • Irene Paassen

    (Princess Máxima Center for Pediatric Oncology
    Oncode Institute)

  • Lars Custers

    (Princess Máxima Center for Pediatric Oncology
    Oncode Institute)

  • Peter Zeller

    (Oncode Institute
    Hubrecht Institute-KNAW
    University Medical Center Utrecht)

  • Hans Teunissen

    (Netherlands Cancer Institute)

  • Dilara Ayyildiz

    (Princess Máxima Center for Pediatric Oncology
    Oncode Institute)

  • Jiayou He

    (Princess Máxima Center for Pediatric Oncology
    Oncode Institute)

  • Juliane Laura Buhl

    (Princess Máxima Center for Pediatric Oncology
    Oncode Institute)

  • Eelco Wieger Hoving

    (Princess Máxima Center for Pediatric Oncology)

  • Alexander Oudenaarden

    (Oncode Institute
    Hubrecht Institute-KNAW
    University Medical Center Utrecht)

  • Elzo Wit

    (Netherlands Cancer Institute)

  • Jarno Drost

    (Princess Máxima Center for Pediatric Oncology
    Oncode Institute)

Abstract

Malignant rhabdoid tumor (MRT) is a highly malignant and often lethal childhood cancer. MRTs are genetically defined by bi-allelic inactivating mutations in SMARCB1, a member of the BRG1/BRM-associated factors (BAF) chromatin remodeling complex. Mutations in BAF complex members are common in human cancer, yet their contribution to tumorigenesis remains in many cases poorly understood. Here, we study derailed regulatory landscapes as a consequence of SMARCB1 loss in the context of MRT. Our multi-omics approach on patient-derived MRT organoids reveals a dramatic reshaping of the regulatory landscape upon SMARCB1 reconstitution. Chromosome conformation capture experiments subsequently reveal patient-specific looping of distal enhancer regions with the promoter of the MYC oncogene. This intertumoral heterogeneity in MYC enhancer utilization is also present in patient MRT tissues as shown by combined single-cell RNA-seq and ATAC-seq. We show that loss of SMARCB1 activates patient-specific epigenetic reprogramming underlying MRT tumorigenesis.

Suggested Citation

  • Ning Qing Liu & Irene Paassen & Lars Custers & Peter Zeller & Hans Teunissen & Dilara Ayyildiz & Jiayou He & Juliane Laura Buhl & Eelco Wieger Hoving & Alexander Oudenaarden & Elzo Wit & Jarno Drost, 2023. "SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43498-3
    DOI: 10.1038/s41467-023-43498-3
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