Professional Education

  • Doctor of Philosophy, Ruprecht Karl Universitat Heidelberg (2014)
  • Diplom, J W Goethe Universitat Frankfurt (2008)

Stanford Advisors


All Publications

  • Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition CANCER CELL Kool, M., Jones, D. T., Jaeger, N., Northcott, P. A., Pugh, T. J., Hovestadt, V., Piro, R. M., Esparza, L. A., Markant, S. L., Remke, M., Milde, T., Bourdeaut, F., Ryzhova, M., Sturm, D., Pfaff, E., Stark, S., Hutter, S., Seker-Cin, H., Johann, P., Bender, S., Schmidt, C., Rausch, T., Shih, D., Reimand, J., Sieber, L., Wittmann, A., Linke, L., Witt, H., Weber, U. D., Zapatka, M., Koenig, R., Beroukhim, R., Bergthold, G., Van Sluis, P., Volckmann, R., Koster, J., Versteeg, R., Schmidt, S., Wolf, S., Lawerenz, C., Bartholomae, C. C., von Kalle, C., Unterberg, A., Herold-Mende, C., Hofer, S., Kulozik, A. E., von Deimling, A., Scheurlen, W., Felsberg, J., Reifenberger, G., Hasselblatt, M., Crawford, J. R., Grant, G. A., Jabado, N., Perry, A., Cowdrey, C., Croul, S., Zadeh, G., Korbel, J. O., Doz, F., Delattre, O., Bader, G. D., McCabe, M. G., Collins, V. P., Kieran, M. W., Cho, Y., Pomeroy, S. L., Witt, O., Brors, B., Taylor, M. D., Schueller, U., Korshunov, A., Eils, R., Wechsler-Reya, R. J., Lichter, P., Pfister, S. M. 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.

    View details for DOI 10.1016/j.ccr.2014.02.004

    View details for Web of Science ID 000333233400015

    View details for PubMedID 24651015

  • Epigenomic alterations define lethal CIMP-positive ependymomas of infancy NATURE MACK, S. C., Witt, H., Piro, R. M., Gu, L., Zuyderduyn, S., Stuetz, A. M., Wang, X., Gallo, M., Garzia, L., Zayne, K., Zhang, X., Ramaswamy, V., Jaeger, N., Jones, D. T., Sill, M., Pugh, T. J., Ryzhova, M., Wani, K. M., Shih, D. J., Head, R., Remke, M., Bailey, S. D., ZICHNER, T., Faria, C. C., Barszczyk, M., Stark, S., Seker-Cin, H., Hutter, S., Johann, P., Bender, S., HOVESTADT, V., Tzaridis, T., Dubuc, A. M., Northcott, P. A., Peacock, J., Bertrand, K. C., Agnihotri, S., Cavalli, F. M., Clarke, I., Nethery-Brokx, K., Creasy, C. L., Verma, S. K., Koster, J., Wu, X., Yao, Y., Milde, T., Sin-Chan, P., Zuccaro, J., Lau, L., Pereira, S., Castelo-Branco, P., Hirst, M., Marra, M. A., Roberts, S. S., Fults, D., Massimi, L., Cho, Y. J., van Meter, T., Grajkowska, W., Lach, B., Kulozik, A. E., von Deimling, A., Witt, O., Scherer, S. W., Fan, X., Muraszko, K. M., Kool, M., Pomeroy, S. L., Gupta, N., Phillips, J., Huang, A., Tabori, U., Hawkins, C., Malkin, D., Kongkham, P. N., Weiss, W. A., Jabado, N., Rutka, J. T., Bouffet, E., Korbel, J. O., Lupien, M., Aldape, K. D., Bader, G. D., Eils, R., Lichter, P., Dirks, P. B., Pfister, S. M., Korshunov, A., Taylor, M. D. 2014; 506 (7489): 445-?


    Ependymomas are common childhood brain tumours that occur throughout the nervous system, but are most common in the paediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic single nucleotide variants. Although devoid of recurrent single nucleotide variants and focal copy number aberrations, poor-prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype. Transcriptional silencing driven by CpG methylation converges exclusively on targets of the Polycomb repressive complex 2 which represses expression of differentiation genes through trimethylation of H3K27. CpG island methylator phenotype-positive hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically deregulated but genetically bland.

    View details for DOI 10.1038/nature13108

    View details for Web of Science ID 000332165100029

    View details for PubMedID 24553142

  • Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma NATURE GENETICS Jones, D. T., Hutter, B., Jaeger, N., Korshunov, A., Kool, M., Warnatz, H., Zichner, T., Lambert, S. R., Ryzhova, M., Dong Anh Khuong Quang, D. A., Fontebasso, A. M., Stuetz, A. M., Hutter, S., Zuckermann, M., Sturm, D., Gronych, J., Lasitschka, B., Schmidt, S., Seker-Cin, H., Witt, H., Sultan, M., Ralser, M., Northcott, P. A., Hovestadt, V., Bender, S., Pfaff, E., Stark, S., Faury, D., Schwartzentruber, J., Majewski, J., Weber, U. D., Zapatka, M., Raeder, B., Schlesner, M., Worth, C. L., Bartholomae, C. C., von Kalle, C., Imbusch, C. D., Radomski, S., Lawerenz, C., Van Sluis, P., Koster, J., Volckmann, R., Versteeg, R., Lehrach, H., Monoranu, C., Winkler, B., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A. E., Ebinger, M., Schuhmann, M. U., Cho, Y., Pomeroy, S. L., von Deimling, A., Witt, O., Taylor, M. D., Wolf, S., Karajannis, M. A., Eberhart, C. G., Scheurlen, W., Hasselblatt, M., Ligon, K. L., Kieran, M. W., Korbel, J. O., Yaspo, M., Brors, B., Felsberg, J., Reifenberger, G., Collins, V. P., Jabado, N., Eils, R., Lichter, P., Pfister, S. M. 2013; 45 (8): 927-U295

    View details for DOI 10.1038/ng.2682

    View details for Web of Science ID 000322374900018

  • Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations NATURE Pugh, T. J., Weeraratne, S. D., Archer, T. C., Krummel, D. A., Auclair, D., Bochicchio, J., Carneiro, M. O., Carter, S. L., Cibulskis, K., Erlich, R. L., Greulich, H., Lawrence, M. S., Lennon, N. J., McKenna, A., Meldrim, J., Ramos, A. H., Ross, M. G., Russ, C., Shefler, E., Sivachenko, A., Sogoloff, B., Stojanov, P., Tamayo, P., Mesirov, J. P., Amani, V., Teider, N., Sengupta, S., Francois, J. P., Northcott, P. A., Taylor, M. D., Yu, F., Crabtree, G. R., Kautzman, A. G., Gabriel, S. B., Getz, G., Jaeger, N., Jones, D. T., Lichter, P., Pfister, S. M., Roberts, T. M., Meyerson, M., Pomeroy, S. L., Cho, Y. 2012; 488 (7409): 106-110


    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, ?-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 ?-catenin signalling in medulloblastoma.

    View details for DOI 10.1038/nature11329

    View details for Web of Science ID 000307010700042

    View details for PubMedID 22820256

  • Dissecting the genomic complexity underlying medulloblastoma NATURE Jones, D. T., Jaeger, N., Kool, M., Zichner, T., Hutter, B., Sultan, M., Cho, Y., Pugh, T. J., Hovestadt, V., Stuetz, A. M., Rausch, T., Warnatz, H., Ryzhova, M., Bender, S., Sturm, D., Pleier, S., Cin, H., Pfaff, E., Sieber, L., Wittmann, A., Remke, M., Witt, H., Hutter, S., Tzaridis, T., Weischenfeldt, J., Raeder, B., Avci, M., Amstislavskiy, V., Zapatka, M., Weber, U. D., Wang, Q., Lasitschka, B., Bartholomae, C. C., Schmidt, M., von Kalle, C., Ast, V., Lawerenz, C., Eils, J., Kabbe, R., Benes, V., Van Sluis, P., Koster, J., Volckmann, R., Shih, D., Betts, M. J., Russell, R. B., Coco, S., Tonini, G. P., Schueller, U., Hans, V., Graf, N., Kim, Y., Monoranu, C., Roggendorf, W., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A. E., von Deimling, A., Witt, O., Maass, E., Roessler, J., Ebinger, M., Schuhmann, M. U., Fruehwald, M. C., Hasselblatt, M., Jabado, N., Rutkowski, S., von Bueren, A. O., Williamson, D., Clifford, S. C., McCabe, M. G., Collins, V. P., Wolf, S., Wiemann, S., Lehrach, H., Brors, B., Scheurlen, W., Felsberg, J., Reifenberger, G., Northcott, P. A., Taylor, M. D., Meyerson, M., Pomeroy, S. L., Yaspo, M., Korbel, J. O., Korshunov, A., Eils, R., Pfister, S. M., Lichter, P. 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 shows tremendous biological and clinical heterogeneity. 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 identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. 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, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 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 what are, to our knowledge, the first medulloblastoma fusion genes identified. 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 and 4 patients.

    View details for DOI 10.1038/nature11284

    View details for Web of Science ID 000307010700041

    View details for PubMedID 22832583

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