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

Publication date: 14 March 2016
Source:Cancer Cell, Volume 29, Issue 3
Author(s): Hye-Jung E. Chun, Emilia L. Lim, Alireza Heravi-Moussavi, Saeed Saberi, Karen L. Mungall, Mikhail Bilenky, Annaick Carles, Kane Tse, Inna Shlafman, Kelsey Zhu, Jenny Q. Qian, Diana L. Palmquist, An He, William Long, Rodrigo Goya, Michelle Ng, Veronique G. LeBlanc, Erin Pleasance, Nina Thiessen, Tina Wong, Eric Chuah, Yong-Jun Zhao, Jacquie E. Schein, Daniela S. Gerhard, Michael D. Taylor, Andrew J. Mungall, Richard A. Moore, Yussanne Ma, Steven J.M. Jones, Elizabeth J. Perlman, Martin Hirst, Marco A. Marra
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.

Teaser

Chun et al. perform integrated molecular analyses of extra-cranial malignant rhabdoid tumors (MRTs) and show that, although SMARCB1 loss drives nearly all MRTs, there are two subgroups of MRTs that are associated with patient age and differentially expressed genes.


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