title: Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways.
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.
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Hye-Jung E
authors.initials: HE
authors.lastname: Chun
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Emilia L
authors.initials: EL
authors.lastname: Lim
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Alireza
authors.initials: A
authors.lastname: Heravi-Moussavi
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Saeed
authors.initials: S
authors.lastname: Saberi
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Karen L
authors.initials: KL
authors.lastname: Mungall
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Mikhail
authors.initials: M
authors.lastname: Bilenky
authors.affiliation: Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Annaick
authors.initials: A
authors.lastname: Carles
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Kane
authors.initials: K
authors.lastname: Tse
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Inna
authors.initials: I
authors.lastname: Shlafman
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Kelsey
authors.initials: K
authors.lastname: Zhu
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Jenny Q
authors.initials: JQ
authors.lastname: Qian
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Diana L
authors.initials: DL
authors.lastname: Palmquist
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: An
authors.initials: A
authors.lastname: He
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: William
authors.initials: W
authors.lastname: Long
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Goya
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Michelle
authors.initials: M
authors.lastname: Ng
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Veronique G
authors.initials: VG
authors.lastname: LeBlanc
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Erin
authors.initials: E
authors.lastname: Pleasance
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Nina
authors.initials: N
authors.lastname: Thiessen
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Tina
authors.initials: T
authors.lastname: Wong
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Eric
authors.initials: E
authors.lastname: Chuah
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Yong-Jun
authors.initials: YJ
authors.lastname: Zhao
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Jacquie E
authors.initials: JE
authors.lastname: Schein
authors.affiliation: Office of Cancer Genomics, National Cancer Institute, US National Institutes of Health, Bethesda, MD 20892, USA.
authors.forename: Daniela S
authors.initials: DS
authors.lastname: Gerhard
authors.affiliation: The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.
authors.forename: Michael D
authors.initials: MD
authors.lastname: Taylor
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Mungall
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Moore
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
authors.forename: Yussanne
authors.initials: Y
authors.lastname: Ma
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
authors.forename: Steven J M
authors.initials: SJM
authors.lastname: Jones
authors.affiliation: Department of Pathology and Laboratory Medicine, Lurie Children's Hospital, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL 60611, USA.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Perlman
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
authors.forename: Martin
authors.initials: M
authors.lastname: Hirst
authors.affiliation: Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada. Electronic address: mmarra@bcgsc.ca.
authors.forename: Marco A
authors.initials: MA
authors.lastname: Marra
mesh_terms: D045744:Cell Line, Tumor; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D015870:Gene Expression / Q000235:genetics; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D006657:Histones / Q000235:genetics; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D018335:Rhabdoid Tumor / Q000235:genetics*; D000071796:SMARCB1 Protein; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome / Q000235:genetics
chemical_list: D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D006657:Histones; D035683:MicroRNAs; D000071796:SMARCB1 Protein; C513266:SMARCB1 protein, human; D014157:Transcription Factors