Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations

Abstract

Medulloblastomas are the most common malignant brain tumours in children. Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma on the basis of transcriptional and copy number profiles. Here we use whole-exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas have low mutation rates consistent with other paediatric tumours, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were newly identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR and LDB1. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant, but not wild-type, β-catenin. Together, our study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic β-catenin signalling in medulloblastoma.

Figure 1. Demographic characteristics, molecular subtypes and selected copy number alterations and somatic mutations across 92 medulloblastoma cases

Data tracks describing 92 medulloblastoma cases. Identifier: Unique name used to denote each case. Identifiers also link samples to those analyzed by Cho et al. Sex: males in blue, females in pink. Age: years of age at diagnosis binned as infants, children, or adults. Histology: pathology review of primary tissue specimen. Subtypes: based on copy number profiles derived from sequence or microarray data. Consensus subtypes from Taylor et al. Cho et al subtypes as published. Copy number alterations: Selected copy number alterations used to assign tumors to subtypes. Losses are blue. Gains are red. Somatic mutations: Gene names (HUGO symbols) grouped by functional category. MutSig gene names are in bold. Missense mutations are black, nonsense/splice site/indel mutations are orange, silent mutations are purple, and germline variants are green.

Figure 2. Location of mutations in histone methyltransferases, RNA helicases, and N-CoR complex-associated genes

Location of somatic mutations on linear protein domain models of genes from sets frequently mutated in medulloblastoma. All domain annotations are from UniProt and InterPro annotations. Diagrams were constructed using Domain Graph (DOG), version 2.0. a. Histone methyltransferase domains: red = SET, green = coiled-coil, blue = zinc-finger, and cyan=other. b. N-CoR complex-associated domains: purple = anti-parallel coiled-coil domains required for GPS2/NCOR2 (SMRT) interaction, yellow = other interaction domains as labeled: SANT domains binds DNA; CoRNR domains binds nuclear receptors; ANK repeats mediate a diversity of protein-protein interactions, and LIM-binding domains bind a common protein structural motif. c. RNA helicase domains: cyan = helicase and helicase-associated (InterPro), red = RNA-binding and RNA polymerase sigma factor (InterPro), blue = ATP binding site, and green = DEAD or DExH box motif. See Supplemental Table 1 for UniProt protein model identifiers.

Figure 3. Functional consequence of DDX3X point mutations

a, Three-dimensional model of the two recA-like domains of human DDX3X in complex with single-stranded RNA and a Mg-ATP analog. Displayed are the residues mutated in the N-terminal recA-like domain (R276K, D354H, R376C) and C-terminal recA-like domain (D506Y, R528H, R534H, P568L). Coloring: DDX3X residues 166–405 (light blue); DDX3X residues 406–582 (dark blue); single-stranded RNA (cyan); Mg-ATP analog (magenta and green). Molecular graphics images were produced using the University of San Francisco Chimera package (http://www.cgl.ucsf.edu/chimera). b, Mutant DDX3X potentiates mutant beta-catenin transactivation of TOPflash promoter. Represented is relative luciferase activity in 293T cells co-transfected with TOPflash reporter, FOPflash control, and either wild type or mutant DDX3Xs in combination with wild type or mutant beta-catenin. One-dimensional model of DDX3X displayed about bar graphs to illustrates the position of the mutations. c, Cell viability assays of medulloblastoma D425 cells stably transduced with either wild type or mutant DDX3X lentivirus in combination with either wild type or mutant beta-catenin lentivirus. For b and c, error bars depict the standard deviation of the mean from 5 replicate experiments performed for each condition. Student’s t-tests were performed to evaluate significance of differences in TOPflash intensity or cell proliferation value distributions as follows: increases with DDX3X alone vs. empty vector, increases with wtBetaCat vs. DDX3X alone, increases with mutBetaCat vs. DDX3X alone, and increases with mutBetaCat vs. wtBetaCat.