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1.  Active medulloblastoma enhancers reveal subgroup-specific cellular origins 
Nature  2016;530(7588):57-62.
Medulloblastoma is a highly malignant paediatric brain tumour, often inflicting devastating consequences on the developing child. Genomic studies have revealed four distinct molecular subgroups with divergent biology and clinical behaviour. An understanding of the regulatory circuitry governing the transcriptional landscapes of medulloblastoma subgroups, and how this relates to their respective developmental origins, is lacking. Using H3K27ac and BRD4 ChIP-Seq, coupled with tissue-matched DNA methylation and transcriptome data, we describe the active cis-regulatory landscape across 28 primary medulloblastoma specimens. Analysis of differentially regulated enhancers and super-enhancers reinforced inter-subgroup heterogeneity and revealed novel, clinically relevant insights into medulloblastoma biology. Computational reconstruction of core regulatory circuitry identified a master set of transcription factors, validated by ChIP-Seq, that are responsible for subgroup divergence and implicate candidate cells-of-origin for Group 4. Our integrated analysis of enhancer elements in a large series of primary tumour samples reveals insights into cis-regulatory architecture, unrecognized dependencies, and cellular origins.
PMCID: PMC5168934  PMID: 26814967
3.  Toward understanding and exploiting tumor heterogeneity 
Nature medicine  2015;21(8):846-853.
The extent of tumor heterogeneity is an emerging theme that researchers are only beginning to understand. How genetic and epigenetic heterogeneity affects tumor evolution and clinical progression is unknown. The precise nature of the environmental factors that influence this heterogeneity is also yet to be characterized. Nature Medicine, Nature Biotechnology and the Volkswagen Foundation organized a meeting focused on identifying the obstacles that need to be overcome to advance translational research in and tumor heterogeneity. Once these key questions were established, the attendees devised potential solutions. Their ideas are presented here.
PMCID: PMC4785013  PMID: 26248267
4.  Immortalization capacity of HPV types is inversely related to chromosomal instability 
Oncotarget  2016;7(25):37608-37621.
High-risk human papillomavirus (hrHPV) types induce immortalization of primary human epithelial cells. Previously we demonstrated that immortalization of human foreskin keratinocytes (HFKs) is HPV type dependent, as reflected by the presence or absence of a crisis period before reaching immortality. This study determined how the immortalization capacity of ten hrHPV types relates to DNA damage induction and overall genomic instability in HFKs.
Twenty five cell cultures obtained by transduction of ten hrHPV types (i.e. HPV16/18/31/33/35/45/51/59/66/70 E6E7) in two or three HFK donors each were studied.
All hrHPV-transduced HFKs showed an increased number of double strand DNA breaks compared to controls, without exhibiting significant differences between types. However, immortal descendants of HPV-transduced HFKs that underwent a prior crisis period (HPV45/51/59/66/70-transduced HFKs) showed significantly more chromosomal aberrations compared to those without crisis (HPV16/18/31/33/35-transduced HFKs). Notably, the hTERT locus at 5p was exclusively gained in cells with a history of crisis and coincided with increased expression. Chromothripsis was detected in one cell line in which multiple rearrangements within chromosome 8 resulted in a gain of MYC.
Together we demonstrated that upon HPV-induced immortalization, the number of chromosomal aberrations is inversely related to the viral immortalization capacity. We propose that hrHPV types with reduced immortalization capacity in vitro, reflected by a crisis period, require more genetic host cell aberrations to facilitate immortalization than types that can immortalize without crisis. This may in part explain the observed differences in HPV-type prevalence in cervical cancers and emphasizes that changes in the host cell genome contribute to HPV-induced carcinogenesis.
PMCID: PMC5122336  PMID: 26993771
arrayCGH; high-risk HPV; E6/E7; transformation; chromothripsis
5.  Negative Selection and Chromosome Instability Induced by Mad2 Overexpression Delay Breast Cancer but Facilitate Oncogene-Independent Outgrowth 
Cell Reports  2016;15(12):2679-2691.
Chromosome instability (CIN) is associated with poor survival and therapeutic outcome in a number of malignancies. Despite this correlation, CIN can also lead to growth disadvantages. Here, we show that simultaneous overexpression of the mitotic checkpoint protein Mad2 with KrasG12D or Her2 in mammary glands of adult mice results in mitotic checkpoint overactivation and a delay in tumor onset. Time-lapse imaging of organotypic cultures and pathologic analysis prior to tumor establishment reveals error-prone mitosis, mitotic arrest, and cell death. Nonetheless, Mad2 expression persists and increases karyotype complexity in Kras tumors. Faced with the selective pressure of oncogene withdrawal, Mad2-positive tumors have a higher frequency of developing persistent subclones that avoid remission and continue to grow.
Graphical Abstract
•Mad2 overexpression leads to mitotic arrest, cell delamination, and cell death•High Mad2 levels delay oncogene-induced mammary tumorigenesis•Mad2 overexpression increases chromosome instability prior to and during tumor growth•Elevated Mad2 levels facilitate the development of oncogene-independent subclones
Rowald et al. report that Mad2 overexpression in the mammary gland results in mitotic arrest, chromosome missegregation, and cell depletion, causing a delay in KrasG12D-driven mammary tumorigenesis. After oncogene silencing, however, Mad2-positive tumors show a frequent occurrence of persistent tumor subclones that do not regress.
PMCID: PMC4920917  PMID: 27292643
6.  Next-generation sequencing-based detection of germline L1-mediated transductions 
BMC Genomics  2016;17:342.
While active LINE-1 (L1) elements possess the ability to mobilize flanking sequences to different genomic loci through a process termed transduction influencing genomic content and structure, an approach for detecting polymorphic germline non-reference transductions in massively-parallel sequencing data has been lacking.
Here we present the computational approach TIGER (Transduction Inference in GERmline genomes), enabling the discovery of non-reference L1-mediated transductions by combining L1 discovery with detection of unique insertion sequences and detailed characterization of insertion sites. We employed TIGER to characterize polymorphic transductions in fifteen genomes from non-human primate species (chimpanzee, orangutan and rhesus macaque), as well as in a human genome. We achieved high accuracy as confirmed by PCR and two single molecule DNA sequencing techniques, and uncovered differences in relative rates of transduction between primate species.
By enabling detection of polymorphic transductions, TIGER makes this form of relevant structural variation amenable for population and personal genome analysis.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-016-2670-x) contains supplementary material, which is available to authorized users.
PMCID: PMC4862182  PMID: 27161561
Retrotransposon; L1; Transductions; NGS; Bioinformatics; Genome; Genetics; Primates; Single-molecule sequencing
7.  Comprehensive genomic profiles of small cell lung cancer 
George, Julie | Lim, Jing Shan | Jang, Se Jin | Cun, Yupeng | Ozretić, Luka | Kong, Gu | Leenders, Frauke | Lu, Xin | Fernández-Cuesta, Lynnette | Bosco, Graziella | Müller, Christian | Dahmen, Ilona | Jahchan, Nadine S. | Park, Kwon-Sik | Yang, Dian | Karnezis, Anthony N. | Vaka, Dedeepya | Torres, Angela | Wang, Maia Segura | Korbel, Jan O. | Menon, Roopika | Chun, Sung-Min | Kim, Deokhoon | Wilkerson, Matt | Hayes, Neil | Engelmann, David | Pützer, Brigitte | Bos, Marc | Michels, Sebastian | Vlasic, Ignacija | Seidel, Danila | Pinther, Berit | Schaub, Philipp | Becker, Christian | Altmüller, Janine | Yokota, Jun | Kohno, Takashi | Iwakawa, Reika | Tsuta, Koji | Noguchi, Masayuki | Muley, Thomas | Hoffmann, Hans | Schnabel, Philipp A. | Petersen, Iver | Chen, Yuan | Soltermann, Alex | Tischler, Verena | Choi, Chang-min | Kim, Yong-Hee | Massion, Pierre P. | Zou, Yong | Jovanovic, Dragana | Kontic, Milica | Wright, Gavin M. | Russell, Prudence A. | Solomon, Benjamin | Koch, Ina | Lindner, Michael | Muscarella, Lucia A. | la Torre, Annamaria | Field, John K. | Jakopovic, Marko | Knezevic, Jelena | Castaños-Vélez, Esmeralda | Roz, Luca | Pastorino, Ugo | Brustugun, Odd-Terje | Lund-Iversen, Marius | Thunnissen, Erik | Köhler, Jens | Schuler, Martin | Botling, Johan | Sandelin, Martin | Sanchez-Cespedes, Montserrat | Salvesen, Helga B. | Achter, Viktor | Lang, Ulrich | Bogus, Magdalena | Schneider, Peter M. | Zander, Thomas | Ansén, Sascha | Hallek, Michael | Wolf, Jürgen | Vingron, Martin | Yatabe, Yasushi | Travis, William D. | Nürnberg, Peter | Reinhardt, Christian | Perner, Sven | Heukamp, Lukas | Büttner, Reinhard | Haas, Stefan A. | Brambilla, Elisabeth | Peifer, Martin | Sage, Julien | Thomas, Roman K.
Nature  2015;524(7563):47-53.
We have sequenced the genomes of 110 small cell lung cancers (SCLC), one of the deadliest human cancers. In nearly all the tumours analysed we found bi-allelic inactivation of TP53 and RB1, sometimes by complex genomic rearrangements. Two tumours with wild-type RB1 had evidence of chromothripsis leading to overexpression of cyclin D1 (encoded by the CCND1 gene), revealing an alternative mechanism of Rb1 deregulation. Thus, loss of the tumour suppressors TP53 and RB1 is obligatory in SCLC. We discovered somatic genomic rearrangements of TP73 that create an oncogenic version of this gene, TP73Δex2/3. In rare cases, SCLC tumours exhibited kinase gene mutations, providing a possible therapeutic opportunity for individual patients. Finally, we observed inactivating mutations in NOTCH family genes in 25% of human SCLC. Accordingly, activation of Notch signalling in a pre-clinical SCLC mouse model strikingly reduced the number of tumours and extended the survival of the mutant mice. Furthermore, neuroendocrine gene expression was abrogated by Notch activity in SCLC cells. This first comprehensive study of somatic genome alterations in SCLC uncovers several key biological processes and identifies candidate therapeutic targets in this highly lethal form of cancer.
PMCID: PMC4861069  PMID: 26168399
8.  An integrated map of structural variation in 2,504 human genomes 
Sudmant, Peter H. | Rausch, Tobias | Gardner, Eugene J. | Handsaker, Robert E. | Abyzov, Alexej | Huddleston, John | Zhang, Yan | Ye, Kai | Jun, Goo | Fritz, Markus Hsi-Yang | Konkel, Miriam K. | Malhotra, Ankit | Stütz, Adrian M. | Shi, Xinghua | Casale, Francesco Paolo | Chen, Jieming | Hormozdiari, Fereydoun | Dayama, Gargi | Chen, Ken | Malig, Maika | Chaisson, Mark J.P. | Walter, Klaudia | Meiers, Sascha | Kashin, Seva | Garrison, Erik | Auton, Adam | Lam, Hugo Y. K. | Mu, Xinmeng Jasmine | Alkan, Can | Antaki, Danny | Bae, Taejeong | Cerveira, Eliza | Chines, Peter | Chong, Zechen | Clarke, Laura | Dal, Elif | Ding, Li | Emery, Sarah | Fan, Xian | Gujral, Madhusudan | Kahveci, Fatma | Kidd, Jeffrey M. | Kong, Yu | Lameijer, Eric-Wubbo | McCarthy, Shane | Flicek, Paul | Gibbs, Richard A. | Marth, Gabor | Mason, Christopher E. | Menelaou, Androniki | Muzny, Donna M. | Nelson, Bradley J. | Noor, Amina | Parrish, Nicholas F. | Pendleton, Matthew | Quitadamo, Andrew | Raeder, Benjamin | Schadt, Eric E. | Romanovitch, Mallory | Schlattl, Andreas | Sebra, Robert | Shabalin, Andrey A. | Untergasser, Andreas | Walker, Jerilyn A. | Wang, Min | Yu, Fuli | Zhang, Chengsheng | Zhang, Jing | Zheng-Bradley, Xiangqun | Zhou, Wanding | Zichner, Thomas | Sebat, Jonathan | Batzer, Mark A. | McCarroll, Steven A. | Mills, Ryan E. | Gerstein, Mark B. | Bashir, Ali | Stegle, Oliver | Devine, Scott E. | Lee, Charles | Eichler, Evan E. | Korbel, Jan O.
Nature  2015;526(7571):75-81.
Structural variants (SVs) are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight SV classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype-blocks in 26 human populations. Analyzing this set, we identify numerous gene-intersecting SVs exhibiting population stratification and describe naturally occurring homozygous gene knockouts suggesting the dispensability of a variety of human genes. We demonstrate that SVs are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of SV complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex SVs with multiple breakpoints likely formed through individual mutational events. Our catalog will enhance future studies into SV demography, functional impact and disease association.
PMCID: PMC4617611  PMID: 26432246
9.  Genomics and drug profiling of fatal TCF3-HLF-positive acute lymphoblastic leukemia identifies recurrent mutation patterns and therapeutic options 
Nature genetics  2015;47(9):1020-1029.
TCF3-HLF-fusion positive acute lymphoblastic leukemia (ALL) is currently incurable. Employing an integrated approach, we uncovered distinct mutation, gene expression, and drug response profiles in TCF3-HLF-positive and treatment-responsive TCF3-PBX1-positive ALL. Recurrent intragenic deletions of PAX5 or VPREB1 were identified in constellation with TCF3-HLF. Moreover somatic mutations in the non-translocated allele of TCF3 and a reduction of PAX5 gene dosage in TCF3-HLF ALL suggest cooperation within a restricted genetic context. The enrichment for stem cell and myeloid features in the TCF3-HLF signature may reflect reprogramming by TCF3-HLF of a lymphoid-committed cell of origin towards a hybrid, drug-resistant hematopoietic state. Drug response profiling of matched patient-derived xenografts revealed a distinct profile for TCF3-HLF ALL with resistance to conventional chemotherapeutics, but sensitivity towards glucocorticoids, anthracyclines and agents in clinical development. Striking on-target sensitivity was achieved with the BCL2-specific inhibitor venetoclax (ABT-199). This integrated approach thus provides alternative treatment options for this deadly disease.
PMCID: PMC4603357  PMID: 26214592
acute lymphoblastic leukemia; leukemia xenograft model; next generation sequencing; drug resistance; drug activity profiling; TCF3-PBX1; TCF3-HLF; leukemic stem cell; integrative; genomics; BCL2; BH3-mimetics; venetoclax; ABT-199; cytarabine; vincristine; glucocorticoids; prednisone; dexamethasone; mTOR inhibitor; anthracycline; bortezomib; HSP90; AUY922; panobinostat
10.  Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks 
Current Biology  2016;26(1):38-51.
Embryogenesis is remarkably robust to segregating mutations and environmental variation; under a range of conditions, embryos of a given species develop into stereotypically patterned organisms. Such robustness is thought to be conferred, in part, through elements within regulatory networks that perform similar, redundant tasks. Redundant enhancers (or “shadow” enhancers), for example, can confer precision and robustness to gene expression, at least at individual, well-studied loci. However, the extent to which enhancer redundancy exists and can thereby have a major impact on developmental robustness remains unknown. Here, we systematically assessed this, identifying over 1,000 predicted shadow enhancers during Drosophila mesoderm development. The activity of 23 elements, associated with five genes, was examined in transgenic embryos, while natural structural variation among individuals was used to assess their ability to buffer against genetic variation. Our results reveal three clear properties of enhancer redundancy within developmental systems. First, it is much more pervasive than previously anticipated, with 64% of loci examined having shadow enhancers. Their spatial redundancy is often partial in nature, while the non-overlapping function may explain why these enhancers are maintained within a population. Second, over 70% of loci do not follow the simple situation of having only two shadow enhancers—often there are three (rols), four (CadN and ade5), or five (Traf1), at least one of which can be deleted with no obvious phenotypic effects. Third, although shadow enhancers can buffer variation, patterns of segregating variation suggest that they play a more complex role in development than generally considered.
•Regulation by shadow enhancers is pervasive and complex during embryonic development•The vast majority of genes have more than two enhancers with similar activity•Shadow enhancers buffer genetic variation within a population, but yet appear conserved•Evolutionary analyses suggest that they play complex and fundamental roles in development
Cannavò et al. examine redundant (shadow) enhancers genome wide, finding that the majority of loci have more than two elements with similar activity. Evolutionary analyses show evidence of pervasive stabilizing selection and an ability to buffer mutations, suggesting that shadow enhancers have complex and fundamental roles in developmental networks
PMCID: PMC4712172  PMID: 26687625
enhancer; redundancy; shadow enhancer; robustness; transcriptional networks; development
11.  Exome sequencing of osteosarcoma reveals mutation signatures reminiscent of BRCA deficiency 
Nature Communications  2015;6:8940.
Osteosarcomas are aggressive bone tumours with a high degree of genetic heterogeneity, which has historically complicated driver gene discovery. Here we sequence exomes of 31 tumours and decipher their evolutionary landscape by inferring clonality of the individual mutation events. Exome findings are interpreted in the context of mutation and SNP array data from a replication set of 92 tumours. We identify 14 genes as the main drivers, of which some were formerly unknown in the context of osteosarcoma. None of the drivers is clearly responsible for the majority of tumours and even TP53 mutations are frequently mapped into subclones. However, >80% of osteosarcomas exhibit a specific combination of single-base substitutions, LOH, or large-scale genome instability signatures characteristic of BRCA1/2-deficient tumours. Our findings imply that multiple oncogenic pathways drive chromosomal instability during osteosarcoma evolution and result in the acquisition of BRCA-like traits, which could be therapeutically exploited.
Osteosarcomas are a heterogenous group of tumours and little is known about how these tumours evolve. Here, Kovac et al. use exome sequencing and discover that although no driver gene explains the majority of these tumours, they are characterized by specific mutation signatures and genomic instability typical of BRCA1/2-deficient tumours.
PMCID: PMC4686819  PMID: 26632267
12.  Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms 
Nature communications  2015;6:7256.
Investigating genomic structural variants at basepair resolution is crucial for understanding their formation mechanisms. We identify and analyze 8,943 deletion breakpoints in 1,092 samples from the 1000 Genomes Project. We find breakpoints have more nearby SNPs and indels than the genomic average, likely a consequence of relaxed selection. By investigating the correlation of breakpoints with DNA methylation, Hi-C interactions, and histone marks and the substitution patterns of nucleotides near them, we find that breakpoints with the signature of non-allelic homologous recombination (NAHR) are associated with open chromatin. We hypothesize that some NAHR deletions occur without DNA replication and cell division, in embryonic and germline cells. In contrast, breakpoints associated with non-homologous (NH) mechanisms often have sequence micro-insertions, templated from later replicating genomic sites, spaced at two characteristic distances from the breakpoint. These micro-insertions are consistent with template-switching events and suggest a particular spatiotemporal configuration for DNA during the events.
PMCID: PMC4451611  PMID: 26028266
13.  Assembly and diploid architecture of an individual human genome via single-molecule technologies 
Nature methods  2015;12(8):780-786.
We present the first comprehensive analysis of a diploid human genome that combines single-molecule sequencing with single-molecule genome maps. Our hybrid assembly markedly improves upon the contiguity observed from traditional shotgun sequencing approaches, with scaffold N50 values approaching 30 Mb, and we identified complex structural variants (SVs) missed by other high-throughput approaches. Furthermore, by combining Illumina short-read data with long reads, we phased both single-nucleotide variants and SVs, generating haplotypes with over 99% consistency with previous trio-based studies. Our work shows that it is now possible to integrate single-molecule and high-throughput sequence data to generate de novo assembled genomes that approach reference quality.
PMCID: PMC4646949  PMID: 26121404
Neuro-Oncology  2014;16(Suppl 5):v170-v171.
Medulloblastoma (MB) is the most common malignant brain tumor in children. Genomic studies have identified four molecular subgroups: WNT, SHH, Group 3, and Group 4. Among these, Group 3 tumors are the most aggressive and the most frequently fatal. Aside from amplification or overexpression of the MYC oncogene (which is insufficient for tumorigenesis on its own), oncogenic drivers for Group 3 MB remain largely unidentified. Recently, whole genome sequencing of primary MB samples identified a series of disparate genomic structural variants restricted to Groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 and GFI1B. Using an orthotopic transplantation model, we show that Gfi1 and Gfi1B can cooperate strongly with Myc to transform neural stem cells and drive MB formation in mice. The resulting tumors are highly invasive and proliferative, and exhibit histological and molecular characteristics consistent with human Group 3 MB. These studies suggest that Gfi1 and Gfi1B may be important drivers of tumorigenesis in Group 3 MB. Our ongoing studies are focused on understanding the molecular mechanisms by which Gfi1 and Gfi1B contribute to tumor formation. Specifically, we are using proteomic approaches to examine the cofactors that bind to Gfi proteins and mediate their effects, and a combination of expression profiling and chromatin immunoprecipitation-sequencing (ChIP-Seq) to identify the molecular targets of these transcription factors in MB. In addition, we have created conditional Gfi1-expressing mice to determine whether these proteins are required for tumor maintenance. Finally, we are using cells from our animal models to identify therapeutic agents that inhibit the growth of Gfi-activated tumors in vitro and in vivo. These studies will provide key insights into the biology of Group 3 MB and help identify novel approaches to therapy.
PMCID: PMC4218492
15.  A novel autosomal recessive TERT T1129P mutation in a dyskeratosis congenita family leads to cellular senescence and loss of CD34+ hematopoietic stem cells not reversible by mTOR-inhibition 
Aging (Albany NY)  2015;7(11):911-927.
The TERT gene encodes for the reverse transcriptase activity of the telomerase complex and mutations in TERT can lead to dysfunctional telomerase activity resulting in diseases such as dyskeratosis congenita (DKC). Here, we describe a novel TERT mutation at position T1129P leading to DKC with progressive bone marrow (BM) failure in homozygous members of a consanguineous family. BM hematopoietic stem cells (HSCs) of an affected family member were 300-fold reduced associated with a significantly impaired colony forming capacity in vitro and impaired repopulation activity in mouse xenografts. Recent data in yeast suggested improved cellular checkpoint controls by mTOR inhibition preventing cells with short telomeres or DNA damage from dividing. To evaluate a potential therapeutic option for the patient, we treated her primary skin fibroblasts and BM HSCs with the mTOR inhibitor rapamycin. This led to prolonged survival and decreased levels of senescence in T1129P mutant fibroblasts. In contrast, the impaired HSC function could not be improved by mTOR inhibition, as colony forming capacity and multilineage engraftment potential in xenotransplanted mice remained severely impaired. Thus, rapamycin treatment did not rescue the compromised stem cell function of TERTT1129P mutant patient HSCs and outlines limitations of a potential DKC therapy based on rapamycin.
PMCID: PMC4694062  PMID: 26546739
TERT; TERC; mTOR; rapamycin; sirolimus; senescence
16.  A cell-based model system links chromothripsis with hyperploidy 
Molecular Systems Biology  2015;11(9):828.
A remarkable observation emerging from recent cancer genome analyses is the identification of chromothripsis as a one-off genomic catastrophe, resulting in massive somatic DNA structural rearrangements (SRs). Largely due to lack of suitable model systems, the mechanistic basis of chromothripsis has remained elusive. We developed an integrative method termed “complex alterations after selection and transformation (CAST),” enabling efficient in vitro generation of complex DNA rearrangements including chromothripsis, using cell perturbations coupled with a strong selection barrier followed by massively parallel sequencing. We employed this methodology to characterize catastrophic SR formation processes, their temporal sequence, and their impact on gene expression and cell division. Our in vitro system uncovered a propensity of chromothripsis to occur in cells with damaged telomeres, and in particular in hyperploid cells. Analysis of primary medulloblastoma cancer genomes verified the link between hyperploidy and chromothripsis in vivo. CAST provides the foundation for mechanistic dissection of complex DNA rearrangement processes.
PMCID: PMC4592670  PMID: 26415501
chromothripsis; hyperploidy; DNA rearrangements; telomere damage; transformation
17.  Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma 
Northcott, Paul A | Lee, Catherine | Zichner, Thomas | Stütz, Adrian M | Erkek, Serap | Kawauchi, Daisuke | Shih, David JH | Hovestadt, Volker | Zapatka, Marc | Sturm, Dominik | Jones, David TW | Kool, Marcel | Remke, Marc | Cavalli, Florence | Zuyderduyn, Scott | Bader, Gary | VandenBerg, Scott | Esparza, Lourdes Adriana | Ryzhova, Marina | Wang, Wei | Wittmann, Andrea | Stark, Sebastian | Sieber, Laura | Seker-Cin, Huriye | Linke, Linda | Kratochwil, Fabian | Jäger, Natalie | Buchhalter, Ivo | Imbusch, Charles D | Zipprich, Gideon | Raeder, Benjamin | Schmidt, Sabine | Diessl, Nicolle | Wolf, Stephan | Wiemann, Stefan | Brors, Benedikt | Lawerenz, Chris | Eils, Jürgen | Warnatz, Hans-Jörg | Risch, Thomas | Yaspo, Marie-Laure | Weber, Ursula D | Bartholomae, Cynthia C | von Kalle, Christof | Turányi, Eszter | Hauser, Peter | Sanden, Emma | Darabi, Anna | Siesjö, Peter | Sterba, Jaroslav | Zitterbart, Karel | Sumerauer, David | van Sluis, Peter | Versteeg, Rogier | Volckmann, Richard | Koster, Jan | Schuhmann, Martin U | Ebinger, Martin | Grimes, H. Leighton | Robinson, Giles W | Gajjar, Amar | Mynarek, Martin | von Hoff, Katja | Rutkowski, Stefan | Pietsch, Torsten | Scheurlen, Wolfram | Felsberg, Jörg | Reifenberger, Guido | Kulozik, Andreas E | von Deimlmg, Andreas | Witt, Olaf | Eils, Roland | Gilbertson, Richard J | Korshunov, Andrey | Taylor, Michael D | Lichter, Peter | Korbel, Jan O | Wechsler-Reya, Robert J | Pfister, Stefan M
Nature  2014;511(7510):428-434.
Summary Paragraph
Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation, and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoural heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and Group 4 subgroup medulloblastomas account for the majority of paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to Groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family protooncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1/GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate ‘enhancer hijacking’ as an efficient mechanism driving oncogene activation in a childhood cancer.
PMCID: PMC4201514  PMID: 25043047
18.  Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition 
Kool, Marcel | Jones, David T.W. | Jäger, Natalie | Northcott, Paul A. | Pugh, Trevor J. | Hovestadt, Volker | Piro, Rosario M. | Esparza, L. Adriana | Markant, Shirley L. | Remke, Marc | Milde, Till | Bourdeaut, Franck | Ryzhova, Marina | Sturm, Dominik | Pfaff, Elke | Stark, Sebastian | Hutter, Sonja | Şeker-Cin, Huriye | Johann, Pascal | Bender, Sebastian | Schmidt, Christin | Rausch, Tobias | Shih, David | Reimand, Jüri | Sieber, Laura | Wittmann, Andrea | Linke, Linda | Witt, Hendrik | Weber, Ursula D. | Zapatka, Marc | König, Rainer | Beroukhim, Rameen | Bergthold, Guillaume | van Sluis, Peter | Volckmann, Richard | Koster, Jan | Versteeg, Rogier | Schmidt, Sabine | Wolf, Stephan | Lawerenz, Chris | Bartholomae, Cynthia C. | von Kalle, Christof | Unterberg, Andreas | Herold-Mende, Christel | Hofer, Silvia | Kulozik, Andreas E. | von Deimling, Andreas | Scheurlen, Wolfram | Felsberg, Jörg | Reifenberger, Guido | Hasselblatt, Martin | Crawford, John R. | Grant, Gerald A. | Jabado, Nada | Perry, Arie | Cowdrey, Cynthia | Croul, Sydney | Zadeh, Gelareh | Korbel, Jan O. | Doz, Francois | Delattre, Olivier | Bader, Gary D. | McCabe, Martin G. | Collins, V. Peter | Kieran, Mark W. | Cho, Yoon-Jae | Pomeroy, Scott L. | Witt, Olaf | Brors, Benedikt | Taylor, Michael D. | Schüller, Ulrich | Korshunov, Andrey | Eils, Roland | Wechsler-Reya, Robert J. | Lichter, Peter | Pfister, Stefan M.
Cancer cell  2014;25(3):393-405.
Smoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream MYCN and GLI2 amplifications and frequent TP53 mutations, often in the germline, all of which were rare in infants and adults. Functional assays in different SHH-MB xenograft models demonstrated that SHH-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant.
PMCID: PMC4493053  PMID: 24651015
Neuro-Oncology  2014;16(Suppl 3):iii24.
BACKGROUND: Genomics has illuminated the extensive intertumoural heterogeneity of medulloblastoma and identified at least four distinct molecular subgroups of the disease. Group 3 and Group 4 subgroup medulloblastomas account for the majority of pediatric cases, yet, oncogenic drivers for these subtypes remain poorly understood. Exome and genome sequencing studies have confirmed a paucity of recurrent gene-level mutations in Group 3 and Group 4, suggesting that alternative oncogenic mechanisms must account for the large fraction of cases that cannot currently be explained by single-nucleotide variants or insertions/deletions alone. METHODS: Analysis of whole-genome sequencing data consisting of 128 primary Group 3 and Group 4 medulloblastoma samples facilitated a systematic, high-resolution screen for chromosomal breakpoints recurrently targeting novel medulloblastoma drivers by structural variation. A non-overlapping set of 22 medulloblastomas was sequenced by long-range paired-end mapping in order to validate structural variants observed in our discovery cohort. Select cases of interest were also investigated at the epigenome-level using a combination of whole-genome bisulphite sequencing and enhancer histone mark ChIP-sequencing. RESULTS: Our systematic analysis of structural variants identified highly disparate genomic structural rearrangements, restricted to Groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family proto-oncogenes, GFI1 & GFI1B. Diverse mechanisms of structural variation, including duplications, deletions, inversions, translocations, and other complex genomic variants were observed in nearly all GFI1/1B-activated cases. Comprehensive characterization of these structural variants established that GFI1/GFI1B expression becomes activated through relocation of their coding sequences to genomic regions of transcriptionally active chromatin. Functional analyses performed in mice confirmed the oncogenicity of Gfi1/Gfi1b in the context of medulloblastoma and demonstrated apparent synergy between both of these candidates and the c-Myc oncogene. CONCLUSIONS: These studies establish GFI1 and GFI1B as novel, highly prevalent medulloblastoma oncogenes specifically active in Group 3 and Group 4. Given their high frequencies of activation, GFI1 and GFI1B represent excellent candidates for prioritization of molecularly targeted therapy aimed at treatment of a significant proportion of Group 3 and Group 4 medulloblastoma patients. SECONDARY CATEGORY: Pediatrics.
PMCID: PMC4144586
20.  Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma 
Jones, David T.W. | Hutter, Barbara | Jäger, Natalie | Korshunov, Andrey | Kool, Marcel | Warnatz, Hans-Jörg | Zichner, Thomas | Lambert, Sally R. | Ryzhova, Marina | Quang, Dong Anh Khuong | Fontebasso, Adam M. | Stütz, Adrian M. | Hutter, Sonja | Zuckermann, Marc | Sturm, Dominik | Gronych, Jan | Lasitschka, Bärbel | Schmidt, Sabine | Şeker-Cin, Huriye | Witt, Hendrik | Sultan, Marc | Ralser, Meryem | Northcott, Paul A. | Hovestadt, Volker | Bender, Sebastian | Pfaff, Elke | Stark, Sebastian | Faury, Damien | Schwartzentruber, Jeremy | Majewski, Jacek | Weber, Ursula D. | Zapatka, Marc | Raeder, Benjamin | Schlesner, Matthias | Worth, Catherine L. | Bartholomae, Cynthia C. | von Kalle, Christof | Imbusch, Charles D. | Radomski, Sylwester | Lawerenz, Chris | van Sluis, Peter | Koster, Jan | Volckmann, Richard | Versteeg, Rogier | Lehrach, Hans | Monoranu, Camelia | Winkler, Beate | Unterberg, Andreas | Herold-Mende, Christel | Milde, Till | Kulozik, Andreas E. | Ebinger, Martin | Schuhmann, Martin U. | Cho, Yoon-Jae | Pomeroy, Scott L. | von Deimling, Andreas | Witt, Olaf | Taylor, Michael D. | Wolf, Stephan | Karajannis, Matthias A. | Eberhart, Charles G. | Scheurlen, Wolfram | Hasselblatt, Martin | Ligon, Keith L. | Kieran, Mark W. | Korbel, Jan O. | Yaspo, Marie-Laure | Brors, Benedikt | Felsberg, Jörg | Reifenberger, Guido | Collins, V. Peter | Jabado, Nada | Eils, Roland | Lichter, Peter | Pfister, Stefan M.
Nature genetics  2013;45(8):927-932.
Pilocytic astrocytoma, the most common childhood brain tumor1, is typically associated with mitogen-activated protein kinase (MAPK) pathway alterations2. Surgically inaccessible midline tumors are therapeutically challenging, showing sustained tendency for progression3 and often becoming a chronic disease with substantial morbidities4.
Here we describe whole-genome sequencing of 96 pilocytic astrocytomas, with matched RNA sequencing (n=73), conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. We identified recurrent activating mutations in FGFR1 and PTPN11 and novel NTRK2 fusion genes in non-cerebellar tumors. New BRAF activating changes were also observed. MAPK pathway alterations affected 100% of tumors analyzed, with no other significant mutations, indicating pilocytic astrocytoma as predominantly a single-pathway disease.
Notably, we identified the same FGFR1 mutations in a subset of H3F3A-mutated pediatric glioblastoma with additional alterations in NF15. Our findings thus identify new potential therapeutic targets in distinct subsets of pilocytic astrocytoma and childhood glioblastoma.
PMCID: PMC3951336  PMID: 23817572
21.  Subgroup specific structural variation across 1,000 medulloblastoma genomes 
Northcott, Paul A | Shih, David JH | Peacock, John | Garzia, Livia | Morrissy, Sorana | Zichner, Thomas | Stütz, Adrian M | Korshunov, Andrey | Reimand, Juri | Schumacher, Steven E | Beroukhim, Rameen | Ellison, David W | Marshall, Christian R | Lionel, Anath C | Mack, Stephen | Dubuc, Adrian | Yao, Yuan | Ramaswamy, Vijay | Luu, Betty | Rolider, Adi | Cavalli, Florence | Wang, Xin | Remke, Marc | Wu, Xiaochong | Chiu, Readman YB | Chu, Andy | Chuah, Eric | Corbett, Richard D | Hoad, Gemma R | Jackman, Shaun D | Li, Yisu | Lo, Allan | Mungall, Karen L | Nip, Ka Ming | Qian, Jenny Q | Raymond, Anthony GJ | Thiessen, Nina | Varhol, Richard J | Birol, Inanc | Moore, Richard A | Mungall, Andrew J | Holt, Robert | Kawauchi, Daisuke | Roussel, Martine F | Kool, Marcel | Jones, David TW | Witt, Hendrick | Fernandez-L, Africa | Kenney, Anna M | Wechsler-Reya, Robert J | Dirks, Peter | Aviv, Tzvi | Grajkowska, Wieslawa A | Perek-Polnik, Marta | Haberler, Christine C | Delattre, Olivier | Reynaud, Stéphanie S | Doz, François F | Pernet-Fattet, Sarah S | Cho, Byung-Kyu | Kim, Seung-Ki | Wang, Kyu-Chang | Scheurlen, Wolfram | Eberhart, Charles G | Fèvre-Montange, Michelle | Jouvet, Anne | Pollack, Ian F | Fan, Xing | Muraszko, Karin M | Gillespie, G. Yancey | Di Rocco, Concezio | Massimi, Luca | Michiels, Erna MC | Kloosterhof, Nanne K | French, Pim J | Kros, Johan M | Olson, James M | Ellenbogen, Richard G | Zitterbart, Karel | Kren, Leos | Thompson, Reid C | Cooper, Michael K | Lach, Boleslaw | McLendon, Roger E | Bigner, Darell D | Fontebasso, Adam | Albrecht, Steffen | Jabado, Nada | Lindsey, Janet C | Bailey, Simon | Gupta, Nalin | Weiss, William A | Bognár, László | Klekner, Almos | Van Meter, Timothy E | Kumabe, Toshihiro | Tominaga, Teiji | Elbabaa, Samer K | Leonard, Jeffrey R | Rubin, Joshua B | Liau, Linda M | Van Meir, Erwin G | Fouladi, Maryam | Nakamura, Hideo | Cinalli, Giuseppe | Garami, Miklós | Hauser, Peter | Saad, Ali G | Iolascon, Achille | Jung, Shin | Carlotti, Carlos G | Vibhakar, Rajeev | Ra, Young Shin | Robinson, Shenandoah | Zollo, Massimo | Faria, Claudia C | Chan, Jennifer A | Levy, Michael L | Sorensen, Poul HB | Meyerson, Matthew | Pomeroy, Scott L | Cho, Yoon-Jae | Bader, Gary D | Tabori, Uri | Hawkins, Cynthia E | Bouffet, Eric | Scherer, Stephen W | Rutka, James T | Malkin, David | Clifford, Steven C | Jones, Steven JM | Korbel, Jan O | Pfister, Stefan M | Marra, Marco A | Taylor, Michael D
Nature  2012;488(7409):49-56.
Medulloblastoma, the most common malignant pediatric brain tumour, is currently treated with non-specific cytotoxic therapies including surgery, whole brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, prior attempts to identify targets for therapy have been underpowered due to small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup enriched. The most common region of focal copy number gain is a tandem duplication of the Parkinson’s disease gene SNCAIP, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1 that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGFβ signaling in Group 3, and NF-κB signaling in Group 4 suggest future avenues for rational, targeted therapy.
PMCID: PMC3683624  PMID: 22832581
22.  ICGC PedBrain: Dissecting the genomic complexity underlying medulloblastoma 
Jones, David TW | Jäger, Natalie | Kool, Marcel | Zichner, Thomas | Hutter, Barbara | Sultan, Marc | Cho, Yoon-Jae | Pugh, Trevor J | Hovestadt, Volker | Stütz, Adrian M | Rausch, Tobias | Warnatz, Hans-Jörg | Ryzhova, Marina | Bender, Sebastian | Sturm, Dominik | Pleier, Sabrina | Cin, Huriye | Pfaff, Elke | Sieber, Laura | Wittmann, Andrea | Remke, Marc | Witt, Hendrik | Hutter, Sonja | Tzaridis, Theophilos | Weischenfeldt, Joachim | Raeder, Benjamin | Avci, Meryem | Amstislavskiy, Vyacheslav | Zapatka, Marc | Weber, Ursula D | Wang, Qi | Lasitschka, Bärbel | Bartholomae, Cynthia C | Schmidt, Manfred | von Kalle, Christof | Ast, Volker | Lawerenz, Chris | Eils, Jürgen | Kabbe, Rolf | Benes, Vladimir | van Sluis, Peter | Koster, Jan | Volckmann, Richard | Shih, David | Betts, Matthew J | Russell, Robert B | Coco, Simona | Tonini, Gian Paolo | Schüller, Ulrich | Hans, Volkmar | Graf, Norbert | Kim, Yoo-Jin | Monoranu, Camelia | Roggendorf, Wolfgang | Unterberg, Andreas | Herold-Mende, Christel | Milde, Till | Kulozik, Andreas E | von Deimling, Andreas | Witt, Olaf | Maass, Eberhard | Rössler, Jochen | Ebinger, Martin | Schuhmann, Martin U | Frühwald, Michael C | Hasselblatt, Martin | Jabado, Nada | Rutkowski, Stefan | von Bueren, André O | Williamson, Dan | Clifford, Steven C | McCabe, Martin G | Collins, V. Peter | Wolf, Stephan | Wiemann, Stefan | Lehrach, Hans | Brors, Benedikt | Scheurlen, Wolfram | Felsberg, Jörg | Reifenberger, Guido | Northcott, Paul A | Taylor, Michael D | Meyerson, Matthew | Pomeroy, Scott L | Yaspo, Marie-Laure | Korbel, Jan O | Korshunov, Andrey | Eils, Roland | Pfister, Stefan M | Lichter, Peter
Nature  2012;488(7409):100-105.
Medulloblastoma is an aggressively-growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and displays tremendous biological and clinical heterogeneity1. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life.
Four tumour subgroups with distinct clinical, biological and genetic profiles are currently discriminated2,3. WNT tumours, displaying activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens4. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis2. Group 3 & 4 tumours are molecularly less well-characterised, and also present the greatest clinical challenges2,3,5. The full repertoire of genetic events driving this distinction, however, remains unclear.
Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs. Tetraploidy was identified as a frequent early event in Group 3 & 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA-sequencing confirmed these alterations, and revealed the expression of the first medulloblastoma fusion genes. Chromatin modifiers were frequently altered across all subgroups.
These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 & 4 patients.
PMCID: PMC3662966  PMID: 22832583
23.  The Genomic and Transcriptomic Landscape of a HeLa Cell Line 
G3: Genes|Genomes|Genetics  2013;3(8):1213-1224.
HeLa is the most widely used model cell line for studying human cellular and molecular biology. To date, no genomic reference for this cell line has been released, and experiments have relied on the human reference genome. Effective design and interpretation of molecular genetic studies performed using HeLa cells require accurate genomic information. Here we present a detailed genomic and transcriptomic characterization of a HeLa cell line. We performed DNA and RNA sequencing of a HeLa Kyoto cell line and analyzed its mutational portfolio and gene expression profile. Segmentation of the genome according to copy number revealed a remarkably high level of aneuploidy and numerous large structural variants at unprecedented resolution. Some of the extensive genomic rearrangements are indicative of catastrophic chromosome shattering, known as chromothripsis. Our analysis of the HeLa gene expression profile revealed that several pathways, including cell cycle and DNA repair, exhibit significantly different expression patterns from those in normal human tissues. Our results provide the first detailed account of genomic variants in the HeLa genome, yielding insight into their impact on gene expression and cellular function as well as their origins. This study underscores the importance of accounting for the strikingly aberrant characteristics of HeLa cells when designing and interpreting experiments, and has implications for the use of HeLa as a model of human biology.
PMCID: PMC3737162  PMID: 23550136
genomics; transcriptomics; HeLa cell line; resource; variation
24.  Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations 
Cell  2012;148(1-2):59-71.
Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.
PMCID: PMC3332216  PMID: 22265402

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