Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

Chun, H. J.; Lim, E. L.; Heravi-Moussavi, A.; Saberi, S.; Mungall, K. L.; Bilenky, M.; Carles, A.; Tse, K.; Shlafman, I.; Zhu, K.; Qian, J. Q.; Palmquist, D. L.; He, A.; Long, W.; Goya, R.; Ng, M.; LeBlanc, V. G.; Pleasance, E.; Thiessen, N.; Wong, T.; Chuah, E.; Zhao, Y. J.; Schein, J. E.; Gerhard, D. S.; Taylor, M. D.; Mungall, A. J.; Moore, R. A.; Ma, Y.; Jones, S. J.; Perlman, E. J.; Hirst, M.; Marra, M. A.

Cancer Cell. 2016 Mar 16; 29(3):394-406

Abstract

Malignant rhabdoid tumors (MRTs) are rare lethal tumors of childhood that most commonly occur in the kidney and brain. MRTs are driven by SMARCB1 loss, but the molecular consequences of SMARCB1 loss in extra-cranial tumors have not been comprehensively described and genomic resources for analyses of extra-cranial MRT are limited. To provide such data, we used whole-genome sequencing, whole-genome bisulfite sequencing, whole transcriptome (RNA-seq) and microRNA sequencing (miRNA-seq), and histone modification profiling to characterize extra-cranial MRTs. Our analyses revealed gene expression and methylation subgroups and focused on dysregulated pathways, including those involved in neural crest development.

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