Abstract
Angiocentric gliomas are pediatric low-grade gliomas (PLGGs) without known recurrent genetic drivers. We performed genomic analysis of new and published data from 249 PLGGs, including 19 angiocentric gliomas. We identified MYB-QKI fusions as a specific and single candidate driver event in angiocentric gliomas. In vitro and in vivo functional studies show that MYB-QKI rearrangements promote tumorigenesis through three mechanisms: MYB activation by truncation, enhancer translocation driving aberrant MYB-QKI expression and hemizygous loss of the tumor suppressor QKI. To our knowledge, this represents the first example of a single driver rearrangement simultaneously transforming cells via three genetic and epigenetic mechanisms in a tumor.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Accession codes
References
Ramkissoon, L.A. et al. Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1. Proc. Natl. Acad. Sci. USA 110, 8188–8193 (2013).
Zhang, J. et al. Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas. Nat. Genet. 45, 602–612 (2013).
Wang, M. et al. Monomorphous angiocentric glioma: a distinctive epileptogenic neoplasm with features of infiltrating astrocytoma and ependymoma. J. Neuropathol. Exp. Neurol. 64, 875–881 (2005).
Lellouch-Tubiana, A. et al. Angiocentric neuroepithelial tumor (ANET): a new epilepsy-related clinicopathological entity with distinctive MRI. Brain Pathol. 15, 281–286 (2005).
Jones, D.T.W. et al. Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat. Genet. 45, 927–932 (2013).
Klempnauer, K.H., Bonifer, C. & Sippel, A.E. Identification and characterization of the protein encoded by the human c-myb proto-oncogene. EMBO J. 5, 1903–1911 (1986).
Klempnauer, K.H., Gonda, T.J. & Bishop, J.M. Nucleotide sequence of the retroviral leukemia gene v-myb and its cellular progenitor c-myb: the architecture of a transduced oncogene. Cell 31, 453–463 (1982).
Ness, S.A., Marknell, A. & Graf, T. The v-myb oncogene product binds to and activates the promyelocyte-specific mim-1 gene. Cell 59, 1115–1125 (1989).
Sakura, H. et al. Delineation of three functional domains of the transcriptional activator encoded by the c-myb protooncogene. Proc. Natl. Acad. Sci. USA 86, 5758–5762 (1989).
Gonda, T.J., Buckmaster, C. & Ramsay, R.G. Activation of c-myb by carboxy-terminal truncation: relationship to transformation of murine haemopoietic cells in vitro. EMBO J. 8, 1777–1783 (1989).
Hu, Y.L., Ramsay, R.G., Kanei-Ishii, C., Ishii, S. & Gonda, T.J. Transformation by carboxyl-deleted Myb reflects increased transactivating capacity and disruption of a negative regulatory domain. Oncogene 6, 1549–1553 (1991).
Press, R.D., Reddy, E.P. & Ewert, D.L. Overexpression of C-terminally but not N-terminally truncated Myb induces fibrosarcomas: a novel nonhematopoietic target cell for the myb oncogene. Mol. Cell. Biol. 14, 2278–2290 (1994).
Grässer, F.A., Graf, T. & Lipsick, J.S. Protein truncation is required for the activation of the c-myb proto-oncogene. Mol. Cell. Biol. 11, 3987–3996 (1991).
GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).
Malaterre, J. et al. c-Myb is required for neural progenitor cell proliferation and maintenance of the neural stem cell niche in adult brain. Stem Cells 26, 173–181 (2008).
Friedrich, V.L. Jr. The myelin deficit in quacking mice. Brain Res. 82, 168–172 (1974).
Yin, D. et al. High-resolution genomic copy number profiling of glioblastoma multiforme by single nucleotide polymorphism DNA microarray. Mol. Cancer Res. 7, 665–677 (2009).
Zhao, Y. et al. The tumor suppressing effects of QKI-5 in prostate cancer: a novel diagnostic and prognostic protein. Cancer Biol. Ther. 15, 108–118 (2014).
Bian, Y. et al. Downregulation of tumor suppressor QKI in gastric cancer and its implication in cancer prognosis. Biochem. Biophys. Res. Commun. 422, 187–193 (2012).
Zack, T.I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).
Wu, J., Zhou, L., Tonissen, K., Tee, R. & Artzt, K. The quaking I-5 protein (QKI-5) has a novel nuclear localization signal and shuttles between the nucleus and the cytoplasm. J. Biol. Chem. 274, 29202–29210 (1999).
Gao, R. et al. A unifying gene signature for adenoid cystic cancer identifies parallel MYB-dependent and MYB-independent therapeutic targets. Oncotarget 5, 12528–12542 (2014).
Mansour, M.R. et al. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science 346, 1373–1377 (2014).
Northcott, P.A. et al. Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature 511, 428–434 (2014).
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
Menzel, S. et al. The HBS1L-MYB intergenic region on chromosome 6q23.3 influences erythrocyte, platelet, and monocyte counts in humans. Blood 110, 3624–3626 (2007).
Bachoo, R.M. et al. Epidermal growth factor receptor and Ink4a/Arf: convergent mechanisms governing terminal differentiation and transformation along the neural stem cell to astrocyte axis. Cancer Cell 1, 269–277 (2002).
Wang, Y., Vogel, G., Yu, Z. & Richard, S. The QKI-5 and QKI-6 RNA binding proteins regulate the expression of microRNA 7 in glial cells. Mol. Cell. Biol. 33, 1233–1243 (2013).
Chen, A.-J. et al. STAR RNA-binding protein Quaking suppresses cancer via stabilization of specific miRNA. Genes Dev. 26, 1459–1472 (2012).
Ji, S. et al. miR-574-5p negatively regulates Qki6/7 to impact β-catenin/Wnt signalling and the development of colorectal cancer. Gut 62, 716–726 (2013).
Bandopadhayay, P. et al. BET bromodomain inhibition of MYC-amplified medulloblastoma. Clin. Cancer Res. 20, 912–925 (2014).
Delmore, J.E. et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904–917 (2011).
Chipumuro, E. et al. CDK7 inhibition suppresses super-enhancer–linked oncogenic transcription in MYCN-driven cancer. Cell 159, 1126–1139 (2014).
D'Alfonso, T.M. et al. MYB-NFIB gene fusion in adenoid cystic carcinoma of the breast with special focus paid to the solid variant with basaloid features. Hum. Pathol. 45, 2270–2280 (2014).
Persson, M. et al. Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck. Proc. Natl. Acad. Sci. USA 106, 18740–18744 (2009).
Stephens, P.J. et al. Whole exome sequencing of adenoid cystic carcinoma. J. Clin. Invest. 123, 2965–2968 (2013).
Danan-Gotthold, M. et al. Identification of recurrent regulated alternative splicing events across human solid tumors. Nucleic Acids Res. 43, 5130–5144 (2015).
Conn, S.J. et al. The RNA binding protein quaking regulates formation of circRNAs. Cell 160, 1125–1134 (2015).
Lu, W. et al. QKI impairs self-renewal and tumorigenicity of oral cancer cells via repression of SOX2. Cancer Biol. Ther. 15, 1174–1184 (2014).
Crompton, B.D. et al. The genomic landscape of pediatric Ewing sarcoma. Cancer Discov. 4, 1326–1341 (2014).
Kieran, M.W. et al. Absence of oncogenic canonical pathway mutations in aggressive pediatric rhabdoid tumors. Pediatr. Blood Cancer 59, 1155–1157 (2012).
Beroukhim, R. et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc. Natl. Acad. Sci. USA 104, 20007–20012 (2007).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
Chiang, D.Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99–103 (2009).
Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).
Robinson, J.T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Lawrence, M.S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495–501 (2014).
Drier, Y. et al. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res. 23, 228–235 (2013).
Chapman, M.A. et al. Initial genome sequencing and analysis of multiple myeloma. Nature 471, 467–472 (2011).
Torres-García, W. et al. PRADA: pipeline for RNA sequencing data analysis. Bioinformatics 30, 2224–2226 (2014).
Craig, J.M. et al. DNA fragmentation simulation method (FSM) and fragment size matching improve aCGH performance of FFPE tissues. PLoS One 7, e38881 (2012).
Firestein, R. et al. CDK8 is a colorectal cancer oncogene that regulates β-catenin activity. Nature 455, 547–551 (2008).
Bergthold, G. et al. Expression profiles of 151 pediatric low-grade gliomas reveal molecular differences associated with location and histological subtype. Neuro-oncol. 17, 1486–1496 (2015).
Sievert, A.J. et al. Paradoxical activation and RAF inhibitor resistance of BRAF protein kinase fusions characterizing pediatric astrocytomas. Proc. Natl. Acad. Sci. USA 110, 5957–5962 (2013).
Reynolds, B.A. & Weiss, S. Generation of neurons and astrocytes from isolated cells of the adult mammalian central nervous system. Science 255, 1707–1710 (1992).
Bolstad, B.M., Irizarry, R.A., Astrand, M. & Speed, T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193 (2003).
Gould, J., Getz, G., Monti, S., Reich, M. & Mesirov, J.P. Comparative gene marker selection suite. Bioinformatics 22, 1924–1925 (2006).
Garber, M. et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol. Cell 47, 810–822 (2012).
Etchegaray, J.-P. et al. The histone deacetylase SIRT6 controls embryonic stem cell fate via TET-mediated production of 5-hydroxymethylcytosine. Nat. Cell Biol. 17, 545–557 (2015).
Bengtsen, M. et al. c-Myb binding sites in haematopoietic chromatin landscapes. PLoS One 10, e0133280 (2015).
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Quintana, A.M., Liu, F., O'Rourke, J.P. & Ness, S.A. Identification and regulation of c-Myb target genes in MCF-7 cells. BMC Cancer 11, 30 (2011).
Zhao, L. et al. Integrated genome-wide chromatin occupancy and expression analyses identify key myeloid pro-differentiation transcription factors repressed by Myb. Nucleic Acids Res. 39, 4664–4679 (2011).
Zhu, J. et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642–654 (2013).
Chapuy, B. et al. Discovery and characterization of super-enhancer–associated dependencies in diffuse large B cell lymphoma. Cancer Cell 24, 777–790 (2013).
Acknowledgements
We thank and acknowledge the Dana-Farber Harvard Cancer Center/Pediatric Low-Grade Astrocytoma Consortium and the Children's Brain Tumor Tissue Consortium, including additional participating sites: Ann and Robert Lurie Children's Hospital, Seattle Children's Hospital and Children's Hospital of Pittsburgh for sample contribution, members of the Genomic Platform and Firehose Team at the Broad Institute for assistance with genomic sequencing and analysis, the Neuro-Histology laboratories of Boston Children's Hospital and Brigham and Women's Hospital, H. Homer (Brigham and Women's Hospital) for technical assistance with FISH, and members of the Ligon, Resnick and Beroukhim laboratories for useful discussions.
We acknowledge the following funding sources: A Kids' Brain Tumor Cure Foundation Pediatric Low-Grade Astrocytoma Foundation (P.B., K.L.L., R.B., M.W.K., L.G., C.D.S. and A.C.R.), US National Institutes of Health grant R01NS085336 (A.C.R., A.J.W., P.B.S. and M. Santi), Voices Against Brain Cancer (A.C.R.), the Children's Brain Tumor Foundation (A.C.R. and A.J.W.), the Stop and Shop Pediatric Brain Tumor Program (P.B. and M.W.K.), the Path to Cure Foundation (K.L.L.), US National Institutes of Health grant PO1CA142536 (C.D.S., K.L.L. and R.B.), St. Baldrick's Foundation (P.B.), the American Brain Tumor Association (L.A.R.), the Team Jack Foundation (P.B., M.W.K., R.B. and L.G.), the Andrysiak Fund for LGG (M.W.K.), a Broad Institute Scientific Projects to Accelerate Research and Collaboration (SPARC) grant (A.G.), the Jared Branfman Sunflowers for Life Fund for Pediatric Brain and Spinal Cancer Research (P.B., R.B. and S. Santagata), the Sontag Foundation (K.L.L. and R.B.), the Nuovo-Soldati Foundation (G.B.), the Philippe Foundation (G.B.), Fondation Etoile de Martin (J.G.), the Damon Runyon-Sohn Pediatric Fellowship Award (A.J.W.), a Hyundai Scholar Grant (A.J.W.), the Bear Necessities Pediatric Cancer Foundation (A.J.W. and A.C.R.), the Rally Foundation for Childhood Cancer Research (A.J.W.), National Institute of Neurological Disorders and Stroke (NINDS) grant K08NS087118 (S.H.R.), the Pediatric Brain Tumor Foundation (R.B. and P.B.), Thea's Star of Hope (A.C.R. and A.J.W.), the Hungarian Brain Research Program, grant KTIA_13_NAP-A-V/3, the Janos Bolyai Scholarship of the Hungarian Academy of Sciences (A.K.), NINDS grant 1R01NS091620 (D.A.H.-K.), the Nancy and Stephen Grand Philanthropic Fund (D.A.H.-K.) and the Pediatric Low-Grade Astrocytoma Foundation (D.A.H.-K.).
Finally, we thank and acknowledge the many children and families affected by PLGGs for their generous contributions to this research.
Author information
Authors and Affiliations
Contributions
P.B., L.A.R., P.J., G.B., K.L.L., R.B. and A.C.R. designed research. P.B., L.A.R., P.J., G.B., H.J.H., Y.Z., N.C., A.S., K.B., R.E.H., M. Santi, A.M.B., M. Scagnet, S.M., D.A.H., J.J.P., A.J.W., P.B.S., J.W., R.Z., S.E.S., L.U., R.O'R., W.J.G., K.P., S.H.R., Y.J.K., D.K., B.R.P., A.G.-Y., P.M.H., A.F., H.M., A.A.T., S. Seepo, M.D., P.V.H., D.C.B., S.P., C.H., U.T., A.K., L.B., P.C.B., C.E., F.J.R., D.A.H., D.A.H.-K., S. Santagata, C.D.S., J.E.B., N.J., A.G., J.G., A.H.L., L.G., M.W.K., K.L.L., R.B. and A.C.R. completed the research. P.B., L.A.R., P.J., G.B., J.W., H.J.H., Y.Z., A.J.W., P.B.S., R.Z., A.F., S.E.S., W.J.G., S.H.R., S. Santagata, A.G., J.E.B., A.H.L., A.C.R., K.L.L. and R.B. analyzed the data. J.W., P.V., M.P., D.C.B., C.G., S.P., C.H., U.T., A.K., L.B., P.C.B., C.E., M. Santi, A.M.B., M. Scagnet, S.M., D.A.H., D.A.H.-K., J.J.P., F.J.R., S. Santagata, N.J., A.G., J.G., A.H.L. and L.G. contributed new reagents, algorithms and/or samples. P.B., L.A.R., P.J., G.B., K.L.L., R.B. and A.C.R. wrote the manuscript. K.L.L., R.B. and A.C.R. supervised the study. All authors reviewed, edited and approved the manuscript.
Corresponding authors
Ethics declarations
Competing interests
The Dana-Farber Cancer Institute has licensed drug-like derivatives of JQ1 prepared in the Bradner laboratory to Tensha Therapeutics for clinical translation as cancer therapeutics. The Dana-Farber Cancer Institute and J.E.B. have been provided minor equity shares in Tensha Therapeutics.
Integrated supplementary information
Supplementary Figure 1 Significant regions of recurrent copy number alterations in PLGG.
GISTIC q values for amplifications (left) and deletions (right) are plotted across the genome.
Supplementary Figure 2 Driver genomic alterations in PLGGs.
Co-mutation plot of the driver alterations identified in 54 PLGGs profiled with WES and/or array CGH.
Supplementary Figure 3 MYB-QKI binding and transcriptional effects.
(a) Identified MYB-QKI binding peaks at MYB in mNSCs over-expressing MYB-QKI. (b) Expression of MYB, truncated MYB, MYB-QKI and truncated QKI in the cell lines used in mim-1 promoter assays. (c) Linear increases in mim-1 promoter activity with increases in MYB-QKI expression. (d) Enrichment of MYB pathway activation in normal brain, PLGGs without MYB-QKI and angiocentric gliomas with MYB-QKI. Values represent mean expression ± s.e.m.
Supplementary Figure 4 H3K27ac enhancer profiling of the 3′ region of QKI in a human angiocentric glioma.
H3K27ac enhancer peaks are associated with QKI in angiocentric glioma.
Supplementary Figure 5 H3K27ac enhancer formation at MYB in PLGGs.
H3K27ac enhancer formation at the MYB promoter in two human MYB-QKI angiocentric gliomas (top tracks) and a BRAF-altered pilocytic astrocytoma (lower track).
Supplementary Figure 6 Expression of MYB-QKI in HEK293T, NIH3T3 and mNSCs.
(a) MYB promoter activation in HEK293T and NIH3T3 cells with and without expression of MYB-QKI. (b) Exogenous expression of MYB-QKI and truncated MYB in NIH3T3 cells and mNSCs via retroviral transduction. (c) Representative OLIG2 and GFAP immunohistochemical analysis of tumors from mNSCs overexpressing truncated MYB, MYBQKI5 and MYB-QKI as compared to eGFP controls. Positive staining for both OLIG2 and GFAP is observed in a subset of tumor cells in tumors generated from truncated MYB or MYB-QKI5 overexpression, whereas tumors formed by MYB-QKI6 overexpression are negative for OLIG2 and have low levels of GFAP expression. Scale bars, 50 microns.
Supplementary Figure 7 Oncogenic activity of MYB-QKI.
(a) Number of colonies of NIH3T3 cells expressing MYB, MYB-QKI or a vector control in soft agar (left) and representative images (right). NIH3T3 cells overexpressing BRAF-V600E are shown as a positive control. The mean of three replicate measurements is shown. Error bars, s.e.m. (b) Table of tumor penetrance from both NIH3T3 and mNSC models with overall P < 0.001.
Supplementary Figure 8 Suppression of wild-type Qk in mouse neural stem cells expressing MYB-QKI.
(a) Suppression of wild-type Qk in mouse NSCs expressing MYB-QKI following infection with shQKI vectors (or shLacZ control). (b) Proliferation of mNSCs overexpressing eGFP, truncated MYB or MYB-QKI with suppression of wild-type Qk over 5 d in pool 4 (values represent the means of five replicate measurements with s.e.m.). Expression of wild-type Qk relative to shLacZ control is shown. (c) shQk signature defined following suppression of wild-type Qk in mNSCs that overexpress MYB-QKI6.
Supplementary Figure 9 MYB ChIP-seq binding to MYB target genes.
Binding of MYB to MYB target genes in K562 cells using the Abcam 45150 antibody.
Supplementary Figure 10 Validation of MYB ChIP-seq data.
(a) Top four enriched DNA-binding motifs in MYB ChIP-seq peaks obtained from mNSCs overexpressing MYB-QKI. (b) MYB DNA-binding motifs. (c) Venn diagrams showing overlap of the MYB-QKI peaks identified (P-value threshold = 1 × 10–6) as compared to those reported in Zhao et al. and Quintana et al. The P values shown were calculated by χ2 test with Yates correction. Of 2,879 genes identified in our set, 20% (Zhao) and 42% (Quintana) were also identified in the other studies.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–10 and Supplementary Note. (PDF 1378 kb)
Supplementary Table 1
PLGGs included in analysis, including tumor demographics, method of profiling and driver alterations identified (XLSX 28 kb)
Supplementary Table 2
GISTIC amplification peaks (TXT 4 kb)
Supplementary Table 3
GISTIC deletion peaks (TXT 1 kb)
Supplementary Table 4
Differentially expressed genes in neural stem cells expressing eGFP, MYBtr or MYB-QKI (XLSX 6262 kb)
Supplementary Table 5
Gene-Set Enrichment Analysis in neural stem cells expressing eGFP, MYBtr or MYB-QKI (XLS 344 kb)
Supplementary Table 6
Differentially expressed genes in neural stem cells expressing MYB-QKI with shLacZ or shQk (XLSX 3420 kb)
Supplementary Table 7
miRNAs that are differentially expressed in mNSCs expressing MYB-QKI following suppression of wild type Qk (XLSX 37 kb)
Supplementary Table 8
MYB promoter sequence and shQk clones used in experiments (XLSX 21 kb)
Supplementary Table 9
PCR primers used in experiments (XLSX 41 kb)
Supplementary Table 10
ChIP-seq peaks (P = 1.0 × 10-6) identified following MYB ChIPseq in mNSC over-expressing MYBQKI5. Peaks that contain a MYB binding motif (fragment size used in analysis = 200 bp) are shown in the columns labeled MYBL1 or MYB (XLS 2137 kb)
Rights and permissions
About this article
Cite this article
Bandopadhayay, P., Ramkissoon, L., Jain, P. et al. MYB-QKI rearrangements in angiocentric glioma drive tumorigenicity through a tripartite mechanism. Nat Genet 48, 273–282 (2016). https://doi.org/10.1038/ng.3500
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng.3500
This article is cited by
-
RNA splicing dysregulation and the hallmarks of cancer
Nature Reviews Cancer (2023)
-
A novel EWSR1-MYB fusion in an aggressive advanced breast adenoid cystic carcinoma with mixed classical and solid-basaloid components
Virchows Archiv (2023)
-
DIPG-like MYB-altered diffuse astrocytoma with durable response to intensive chemotherapy
Child's Nervous System (2023)
-
From modulation of cellular plasticity to potentiation of therapeutic resistance: new and emerging roles of MYB transcription factors in human malignancies
Cancer and Metastasis Reviews (2023)
-
Treatment of Pediatric Low-Grade Gliomas
Current Neurology and Neuroscience Reports (2023)
