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n2:pmcid
PMC0
bibo:doi
10.1038%2Fnature11213
n5:contains
_:vb16663384 _:vb16663404 _:vb16663394 _:vb16663398
Subject Item
_:vb16663384
rdf:type
n5:Section
dc:title
discussion
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_:vb16663388 _:vb16663389 _:vb16663390 _:vb16663391 _:vb16663385 _:vb16663386 _:vb16663387 _:vb16663392 _:vb16663393
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_:vb16663385
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Further epigenetic studies will be required to uncover the identity of these genes, but evidence suggests these may include OTX2, MYC and MYCN>>44<<,45. Since amplification of these genes was detected almost exclusively in subgroup-3 and 4 tumours that lacked mutations in KDM6A, CHD7 or ZMYM3, it is tempting to speculate that these genetic alterations target common transforming
n2:mentions
n3:18483221
Subject Item
_:vb16663386
rdf:type
n2:Context
rdf:value
Further epigenetic studies will be required to uncover the identity of these genes, but evidence suggests these may include OTX2, MYC and MYCN44,>>45<<. Since amplification of these genes was detected almost exclusively in subgroup-3 and 4 tumours that lacked mutations in KDM6A, CHD7 or ZMYM3, it is tempting to speculate that these genetic alterations target common transforming pathways.
n2:mentions
n3:19333393
Subject Item
_:vb16663387
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A recent study detected recurrent mutations in three other chromatin remodelers in medulloblastoma>>42<<: SMARCA4, MLL2 and MLL3, but this study did not include details of tumour subgroup. Here, we show that mutations in SMARCA4, CREBBP, TRRAP and MED13 are enriched in WNT-subgroup medulloblastomas; thereby uncovering potential cooperative
n2:mentions
n3:21163964
Subject Item
_:vb16663388
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Thus, disruptions in the epigenetic machinery of medulloblastoma are likely to be subgroup specific and may cooperate with other oncogenic mutations. The low incidence of MLL2 mutations detected in our study relative to Parsons et al.,>>42<< likely reflects differences the our study populations (see Supplementary Results).
n2:mentions
n3:21163964
Subject Item
_:vb16663389
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Although medulloblastoma is more prevalent in males, especially subgroup-3 and 4 disease>>46<<, the reason for this sex bias is unknown. One potential explanation is the location of medulloblastoma oncogenes or tumour suppressor genes on chromosome X47.
n2:mentions
n3:20823417
Subject Item
_:vb16663390
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One potential explanation is the location of medulloblastoma oncogenes or tumour suppressor genes on chromosome X>>47<<. Three of the most recurrently mutated genes detected in our study are located on chromosome X, of which two (ZMYM3 and KDM6A) were observed almost exclusively in males. Mutation of these genes might explain some of the male sex-bias in
n2:mentions
n3:15286741
Subject Item
_:vb16663391
rdf:type
n2:Context
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Three of four female medulloblastomas carried heterozygous mutations in DDX3X that escapes X inactivation>>25<< and our functional data indicate that mutations in this gene provide a proliferative advantage to LRLPs that generate these tumours.
n2:mentions
n3:20363980
Subject Item
_:vb16663392
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Mutations that activate PIK3CA and DDX3X in WNT-subgroup tumors might also be targeted with novel therapeutic strategies>>48<<,49. Future clinical trials of drugs that target these mutant proteins must recruit the appropriate patient populations, since we show mutations display subgroup-specificity in medulloblastoma. Our accurate mouse models of WNT, SHH and
n2:mentions
n3:18270573
Subject Item
_:vb16663393
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Mutations that activate PIK3CA and DDX3X in WNT-subgroup tumors might also be targeted with novel therapeutic strategies48,>>49<<. Future clinical trials of drugs that target these mutant proteins must recruit the appropriate patient populations, since we show mutations display subgroup-specificity in medulloblastoma. Our accurate mouse models of WNT, SHH and
n2:mentions
n3:19629070
Subject Item
_:vb16663394
rdf:type
n5:Section
dc:title
methods summary
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_:vb16663396 _:vb16663397 _:vb16663395
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_:vb16663395
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Whole genome sequencing (WGS) and analysis of WGS data were performed as previously described>>50<<. Details of sequence coverage, custom capture and other validation procedures are provided in Supplementary Information (Supplementary Tables 12-15). Sequence and SNP array data were deposited in dbGaP (dbGaP accession number: phs000409,
n2:mentions
n3:22237106
Subject Item
_:vb16663396
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Reverse transcriptase Real Time-PCR analysis of genes targeted in mouse LRLPs by shRNAs were performed as described previously>>32<<. LRLPs were isolated and transduced with indicated lentiviruses in stem cell cultures or targeted in utero with shRNAs or mutant cDNA sequences by electroporation as described (Supplementary Information)5. Mice harbouring a cre-inducible
n2:mentions
n3:16567768
Subject Item
_:vb16663397
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LRLPs were isolated and transduced with indicated lentiviruses in stem cell cultures or targeted in utero with shRNAs or mutant cDNA sequences by electroporation as described (Supplementary Information)>>5<<. Mice harbouring a cre-inducible Pik3caE545K allele were generated using homologous recombination: A lox-puro-STOP-lox cassette was introduced immediately upstream of the exon containing the initiation codon, exon 9 was replaced with an
n2:mentions
n3:21150899
Subject Item
_:vb16663398
rdf:type
n5:Section
dc:title
novel copy number variations, structural alterations and heritable mutations are rare in medulloblastoma
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_:vb16663400 _:vb16663401 _:vb16663402 _:vb16663403 _:vb16663399
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_:vb16663399
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We detected expected>>2<< gains of MYC, MYCN and OTX2 in subgroup-3 and 4, but no novel recurrent amplifications (Figure 1, Supplementary Figure 12, Supplementary Table 7).
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n3:22134537
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_:vb16663400
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n2:Context
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In keeping with recent reports>>9<<, high-level amplification of MYCN in subgroup-3 sample #16 (sample numbering as Figure 1) was generated by chromothripsis; although chromothripsis was observed infrequently (n=2/37 of ‘discovery cohort’; Supplementary Figure 13).
n2:mentions
n3:22265402
Subject Item
_:vb16663401
rdf:type
n2:Context
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Focal homo- or heterozygous deletion of genes previously implicated in medulloblastoma were also detected (e.g., PTCH1, PTEN, Figure 1)>>10<<,11 but novel recurrent focal deletions were rare.
n2:mentions
n3:20520772
Subject Item
_:vb16663402
rdf:type
n2:Context
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Focal homo- or heterozygous deletion of genes previously implicated in medulloblastoma were also detected (e.g., PTCH1, PTEN, Figure 1)10,>>11<< but novel recurrent focal deletions were rare.
n2:mentions
n3:8681379
Subject Item
_:vb16663403
rdf:type
n2:Context
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Although germline mutations in TP53, PTCH1, APC, and CREBBP, predispose to medulloblastoma>>11<<-14, only 23 mutations previously associated with cancer were detected in ‘discovery cohort’ germlines:
n2:mentions
n3:8681379 n3:7661930 n3:11741116 n3:1978757
Subject Item
_:vb16663404
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n5:Section
dc:title
novel recurrent sequence mutations target distinct medulloblastoma subgroups
n5:contains
_:vb16663412 _:vb16663413 _:vb16663414 _:vb16663415 _:vb16663408 _:vb16663409 _:vb16663410 _:vb16663411 _:vb16663420 _:vb16663421 _:vb16663422 _:vb16663423 _:vb16663416 _:vb16663417 _:vb16663418 _:vb16663419 _:vb16663405 _:vb16663406 _:vb16663407 _:vb16663428 _:vb16663429 _:vb16663430 _:vb16663431 _:vb16663424 _:vb16663425 _:vb16663426 _:vb16663427 _:vb16663436 _:vb16663437 _:vb16663438 _:vb16663432 _:vb16663433 _:vb16663434 _:vb16663435
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_:vb16663405
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The H3K27 trimethyl mark (H3K27me3) represses lineage specific genes in stem cells (Supplementary Figure 8)>>15<<. H3K27me3 is written by the polycomb repressive complex 2 (PRC2) that includes the methylase EZH216,17, and erased during differentiation by the demethylase KDM6A18.
n2:mentions
n3:17603471
Subject Item
_:vb16663406
rdf:type
n2:Context
rdf:value
H3K27me3 is written by the polycomb repressive complex 2 (PRC2) that includes the methylase EZH>>216<<,17, and erased during differentiation by the demethylase KDM6A18.
n2:mentions
n3:12351676
Subject Item
_:vb16663407
rdf:type
n2:Context
rdf:value
H3K27me3 is written by the polycomb repressive complex 2 (PRC2) that includes the methylase EZH216,>>17<<, and erased during differentiation by the demethylase KDM6A18.
n2:mentions
n3:12408863
Subject Item
_:vb16663408
rdf:type
n2:Context
rdf:value
H3K27me3 is written by the polycomb repressive complex 2 (PRC2) that includes the methylase EZH216,17, and erased during differentiation by the demethylase KDM6A>>18<<. As H3K27me3 is erased, chromatin remodelers recruited to H3K4me3 promote differentiation e.g., CHD719,20. This process is tightly controlled during development and deregulated in cancers: EZH2 is mutated in lymphomas21, and upregulated
n2:mentions
n3:17713478
Subject Item
_:vb16663409
rdf:type
n2:Context
rdf:value
As H3K27me3 is erased, chromatin remodelers recruited to H3K4me3 promote differentiation e.g., CHD>>719<<,20. This process is tightly controlled during development and deregulated in cancers: EZH2 is mutated in lymphomas21, and upregulated in breast22 and prostate23 cancer; while biallelic inactivation of KDM6A (Xp11.2) or KDM6A and its
n2:mentions
n3:19251738
Subject Item
_:vb16663410
rdf:type
n2:Context
rdf:value
As H3K27me3 is erased, chromatin remodelers recruited to H3K4me3 promote differentiation e.g., CHD719,>>20<<. This process is tightly controlled during development and deregulated in cancers: EZH2 is mutated in lymphomas21, and upregulated in breast22 and prostate23 cancer; while biallelic inactivation of KDM6A (Xp11.2) or KDM6A and its paralog
n2:mentions
n3:20804967
Subject Item
_:vb16663411
rdf:type
n2:Context
rdf:value
This process is tightly controlled during development and deregulated in cancers: EZH2 is mutated in lymphomas>>21<<, and upregulated in breast22 and prostate23 cancer; while biallelic inactivation of KDM6A (Xp11.2) or KDM6A and its paralog UTY (Yq11), occurs in adult female and male cancers, respectively24.
n2:mentions
n3:20081860
Subject Item
_:vb16663412
rdf:type
n2:Context
rdf:value
This process is tightly controlled during development and deregulated in cancers: EZH2 is mutated in lymphomas21, and upregulated in breast22 and prostate>>23<< cancer; while biallelic inactivation of KDM6A (Xp11.2) or KDM6A and its paralog UTY (Yq11), occurs in adult female and male cancers, respectively24.
n2:mentions
n3:12374981
Subject Item
_:vb16663413
rdf:type
n2:Context
rdf:value
in cancers: EZH2 is mutated in lymphomas21, and upregulated in breast22 and prostate23 cancer; while biallelic inactivation of KDM6A (Xp11.2) or KDM6A and its paralog UTY (Yq11), occurs in adult female and male cancers, respectively>>24<<.
n2:mentions
n3:19330029
Subject Item
_:vb16663414
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n2:Context
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The single female with a KDM6A splice site mutation deleted the second allele that escapes X inactivation>>25<< (subgroup-4 #15), and 57% (n=4/7) of KDM6A-mutant male medulloblastomas deleted chromosome Y, compared with only 6% (n=3/51) of male, KDM6A wild-type tumours (P<0.005, Fisher’s exact; Figure 1).
n2:mentions
n3:20363980
Subject Item
_:vb16663415
rdf:type
n2:Context
rdf:value
Subgroup-3 and 4 medulloblastomas also gained and overexpressed EZH2 (7q35-34) that writes H3K27me3, and contained novel inactivating mutations in effectors and regulators of the H3K4me3 mark>>26<< (Figure 2a; Supplementary Figure 8). Gain of 7q was significantly enriched among subgroup-3 and 4 medulloblastomas (P<0.005 Fisher’s exact) and correlated directly with EZH2 expression.
n2:mentions
n3:17320161
Subject Item
_:vb16663416
rdf:type
n2:Context
rdf:value
ZMYM3 (Xq13.1) that participates in a protein complex with KDM1A to regulate gene expression at the H3K4me3 mark>>27<< was targeted by novel frameshift, nonsense and missense mutations in three male subgroup-4 medulloblastomas.
n2:mentions
n3:16079794
Subject Item
_:vb16663417
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n2:Context
rdf:value
Relatively low levels of H3K27me3 were detected in LRLPs and committed GNPs that generate WNT and SHH-subgroup medulloblastomas respectively>>3<<-5, potentially explaining why mutations that preserve this epigenetic mark are absent from these tumours.
n2:mentions
n3:21150899 n3:18691548 n3:18691547
Subject Item
_:vb16663418
rdf:type
n2:Context
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We recently showed that subgroup-3 medulloblastomas arise from a rare fraction of cerebellar progenitors>>6<<. We are currently investigating if these progenitors are found among the H3K27me3 positive cells seen in the external germinal layer (Figure 2b).
n2:mentions
n3:22340591
Subject Item
_:vb16663419
rdf:type
n2:Context
rdf:value
We are currently investigating if these progenitors are found among the H3K27me>>3<< positive cells seen in the external germinal layer (Figure 2b).
n2:mentions
n3:18691547
Subject Item
_:vb16663420
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n2:Context
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CTNNB1, the principal effector of the WNT pathway, forms a transcription factor with the T cell factor/lymphoid enhancer factor (TCF/LEF)>>28<<. The c-terminus of CTNNB1 then recruits a series of protein complexes that remodel chromatin and promote transcription at WNT-responsive genes (Supplementary Figure 8). These include: histone acetyltransferases (e.g., CREBBP and
n2:mentions
n3:19305417
Subject Item
_:vb16663421
rdf:type
n2:Context
rdf:value
These include: histone acetyltransferases (e.g., CREBBP and TRRAP-TIP60 complexes)>>28<<,29; ATPases of the SWI/SNF family (e.g., SMARCA4)30; and the Mediator complex that coordinates RNA polymerase II placement (e.g., MED13)31.
n2:mentions
n3:19305417
Subject Item
_:vb16663422
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n2:Context
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These include: histone acetyltransferases (e.g., CREBBP and TRRAP-TIP60 complexes)28,>>29<<; ATPases of the SWI/SNF family (e.g., SMARCA4)30; and the Mediator complex that coordinates RNA polymerase II placement (e.g., MED13)31.
n2:mentions
n3:10775268
Subject Item
_:vb16663423
rdf:type
n2:Context
rdf:value
These include: histone acetyltransferases (e.g., CREBBP and TRRAP-TIP60 complexes)28,29; ATPases of the SWI/SNF family (e.g., SMARCA4)>>30<<; and the Mediator complex that coordinates RNA polymerase II placement (e.g., MED13)31.
n2:mentions
n3:11532957
Subject Item
_:vb16663424
rdf:type
n2:Context
rdf:value
As expected, >70% (n=8/11) of WNT-medulloblastomas contained mutations that stabilise CTNNB1 (Figure 1 and Supplementary Figure 8; P<0.0001, Fishers exact)>>32<<,33. A single subgroup-3 case (#5) also mutated CTNNB1, but this mutation has not been reported in cancer, did not upregulate nuclear CTNNB1 (Figure 1) and is of unclear significance. Remarkably, six WNT-subgroup medulloblastomas mutated
n2:mentions
n3:16567768
Subject Item
_:vb16663425
rdf:type
n2:Context
rdf:value
As expected, >70% (n=8/11) of WNT-medulloblastomas contained mutations that stabilise CTNNB1 (Figure 1 and Supplementary Figure 8; P<0.0001, Fishers exact)32,>>33<<. A single subgroup-3 case (#5) also mutated CTNNB1, but this mutation has not been reported in cancer, did not upregulate nuclear CTNNB1 (Figure 1) and is of unclear significance. Remarkably, six WNT-subgroup medulloblastomas mutated
n2:mentions
n3:18769486
Subject Item
_:vb16663426
rdf:type
n2:Context
rdf:value
CDH1 sequesters CTNNB1 at the cell membrane>>34<<, and mutations that disrupt this interaction promote WNT signaling in adult cancers35,36.
n2:mentions
n3:10085258
Subject Item
_:vb16663427
rdf:type
n2:Context
rdf:value
CDH1 sequesters CTNNB1 at the cell membrane34, and mutations that disrupt this interaction promote WNT signaling in adult cancers>>35<<,36. The functional consequences of CDH1R63G and CDH1V329F remain to be determined, but their restriction to WNT-subgroup tumours; mutual exclusivity with CTNNB1 mutations; and adjacency to residues mutated in breast cancer (http://www.
n2:mentions
n3:8075649
Subject Item
_:vb16663428
rdf:type
n2:Context
rdf:value
CDH1 sequesters CTNNB1 at the cell membrane34, and mutations that disrupt this interaction promote WNT signaling in adult cancers35,>>36<<. The functional consequences of CDH1R63G and CDH1V329F remain to be determined, but their restriction to WNT-subgroup tumours; mutual exclusivity with CTNNB1 mutations; and adjacency to residues mutated in breast cancer (http://www.sanger.
n2:mentions
n3:8033105
Subject Item
_:vb16663429
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n2:Context
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We showed previously that mutant Ctnnb1 initiates WNT-subgroup medulloblastoma by arresting the migration of LRLPs from the embryonic dorsal brainstem to the pontine grey nucleus (PGN)>>5<<. Therefore, to test if disruption of CDH1 might substitute for mutant CTNNB1 in medulloblastoma, we used shRNAs to knock down Cdh1 in embryonic day (E) 14.5 mouse LRLPs (Figure 3a to c).
n2:mentions
n3:21150899
Subject Item
_:vb16663430
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n2:Context
rdf:value
DDX3X regulates several critical cell processes including chromosome segregation>>37<<, cell cycle progression38, gene transcription and translation39.
n2:mentions
n3:21730191
Subject Item
_:vb16663431
rdf:type
n2:Context
rdf:value
DDX3X regulates several critical cell processes including chromosome segregation37, cell cycle progression>>38<<, gene transcription and translation39.
n2:mentions
n3:20837705
Subject Item
_:vb16663432
rdf:type
n2:Context
rdf:value
DDX3X regulates several critical cell processes including chromosome segregation37, cell cycle progression38, gene transcription and translation>>39<<. Previously reported cancer associated mutations in DDX3X disrupt the ATPase activity of the protein, but seven of eight mutations identified in our series clustered in the DEAD-box domain (Supplementary Information; Supplementary Figure
n2:mentions
n3:19782656
Subject Item
_:vb16663433
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Indeed, the wild-type allele of DDX3X that escapes X inactivation>>25<< was retained by two of three DDX3X-mutant female medulloblastomas, and knock-down of Ddx3x halved the self-renewal rate of mouse LRLPs, suggesting this protein is important for the proliferation and/or maintenance of the LRLP lineage
n2:mentions
n3:20363980
Subject Item
_:vb16663434
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Although PIK3CA mutations are common in adult cancers>>40<< and reported in medulloblastoma41, their role in tumourigenesis remains controversial.
n2:mentions
n3:15016963
Subject Item
_:vb16663435
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Although PIK3CA mutations are common in adult cancers40 and reported in medulloblastoma>>41<<, their role in tumourigenesis remains controversial.
n2:mentions
n3:15289301
Subject Item
_:vb16663436
rdf:type
n2:Context
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Mice harboring Pik3caE545K or Pik3caE545K and Tp53flx/flx were bred with Blbp-Cre that drives efficient recombination in LRLPs>>5<<. Blbp-Cre ; Pik3caE545K mice, with or without Tp53flx/flx, survived tumour free for a median of 212 days with no evidence of aberrant LRLP migration (Figure 4a and data not shown). In stark contrast, 100% (n=11/11) of Blbp-Cre ;
n2:mentions
n3:21150899
Subject Item
_:vb16663437
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These tumours contained mutations in MLL2, TP53, and PTEN that have been reported previously in medulloblastoma>>42<<; but these mutations occur in other subgroups and are not known to activate SHH signals.
n2:mentions
n3:21163964
Subject Item
_:vb16663438
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Disruption of GABAA receptors can enhance neural stem cell proliferation>>43<<, suggesting these mutations might deregulate the proliferation of GNPs that generate SHH-subgroup medulloblastomas.
n2:mentions
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