2. Academic Validation
  3. SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors

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

  • Nat Commun. 2023 Dec 1;14(1):7762. doi: 10.1038/s41467-023-43498-3.
Ning Qing Liu # 1 2,  Irene Paassen # 3 4,  Lars Custers # 3 4,  Peter Zeller 4 5 6,  Hans Teunissen 1,  Dilara Ayyildiz 3 4,  Jiayou He 3 4,  Juliane Laura Buhl 3 4,  Eelco Wieger Hoving 3,  Alexander van Oudenaarden 4 5 6,  Elzo de Wit 7,  Jarno Drost 8 9
Affiliations

Affiliations

  • 1 Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
  • 2 Department of Hematology, Erasmus Medical Center (MC) Cancer Institute, Rotterdam, the Netherlands.
  • 3 Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
  • 4 Oncode Institute, Utrecht, the Netherlands.
  • 5 Hubrecht Institute-KNAW, Utrecht, the Netherlands.
  • 6 University Medical Center Utrecht, Utrecht, the Netherlands.
  • 7 Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands. e.d.wit@nki.nl.
  • 8 Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands. J.Drost@prinsesmaximacentrum.nl.
  • 9 Oncode Institute, Utrecht, the Netherlands. J.Drost@prinsesmaximacentrum.nl.
  • # Contributed equally.
PMID: 38040699 DOI: 10.1038/s41467-023-43498-3
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.

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