Acta Neuropathol DOI 10.1007/s00401-014-1297-8
Original Paper
Genomic and transcriptomic analyses match medulloblastoma mouse models to their human counterparts Julia Pöschl · Sebastian Stark · Philipp Neumann · Susanne Gröbner · Daisuke Kawauchi · David T. W. Jones · Paul A. Northcott · Peter Lichter · Stefan M. Pfister · Marcel Kool · Ulrich Schüller
Received: 8 April 2014 / Revised: 8 May 2014 / Accepted: 19 May 2014 © Springer-Verlag Berlin Heidelberg 2014
Abstract Medulloblastoma is a malignant embryonal brain tumor with highly variable outcome. In order to study the biology of this tumor and to perform preclinical treatment studies, a lot of effort has been put into the generation of appropriate mouse models. The usage of these models, however, has become debatable with the advances in human medulloblastoma subgrouping. This study brings together multiple relevant mouse models and matches genetic alterations and gene expression data of 140 murine tumors with 423 human medulloblastomas in a global way. Using AGDEX analysis and k-means clustering, we show that the Blbp-cre::Ctnnb1(ex3)Fl/+Trp53Fl/Fl mouse model fits well to human WNT medulloblastoma, and that, among various Myc- or Mycn-based mouse medulloblastomas, tumors in Glt1-tTA::TRE-MYCN/Luc mice proved to be
most specific for human group 3 medulloblastoma. None of the analyzed models displayed a significant match to group 4 tumors. Intriguingly, mice with Ptch1 or Smo mutations selectively modeled SHH medulloblastomas of adulthood, although such mutations occur in all human age groups. We therefore suggest that the infantile or adult gene expression pattern of SHH MBs are not solely determined by specific mutations. This is supported by the observation that human medulloblastomas with PTCH1 mutations displayed more similarities to PTCH1 wild-type tumors of the same age group than to PTCH1-mutated tumors of the other age group. Together, we provide novel insights into previously unrecognized specificity of distinct models and suggest these findings as a solid basis to choose the appropriate model for preclinical studies on medulloblastoma.
M. Kool and U. Schüller are co-senior authors.
Keywords WNT · SHH · Medulloblastoma · Gene expression profile · Mutations · Mouse model
Electronic supplementary material The online version of this article (doi:10.1007/s00401-014-1297-8) contains supplementary material, which is available to authorized users. J. Pöschl · U. Schüller (*) Center for Neuropathology and Prion Research, Ludwig-Maximilians-University, Feodor‑Lynen‑Strasse 23, 81377 Munich, Germany e-mail: [email protected]‑muenchen.de; [email protected] S. Stark · S. Gröbner · D. Kawauchi · D. T. W. Jones · P. A. Northcott · S. M. Pfister · M. Kool Division of Pediatric Neuroncology (B062), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany e-mail: [email protected]
P. Neumann Department of Informatics, Technical University, Munich, Germany P. Lichter Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany S. M. Pfister Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
S. Stark Department of General Pediatrics, Heidelberg University Hospital, Heidelberg, Germany
13
Acta Neuropathol
Introduction
Materials and methods
For decades, medulloblastoma was recognized as a malignant embryonal brain tumor with particularly poor prognosis. Affected patients were treated with surgery, chemotherapy and—depending on their age—radiotherapy. In the era of personalized medicine, this image has changed dramatically. Medulloblastoma is now acknowledged as a group of at least four major tumor types that significantly differ from each other with respect to genetics, epigenetics, gene expression, histology, and clinical outcome [17, 32, 33]. This knowledge requires stratified therapeutic approaches that refer to each tumor subgroup and to each tumor’s genetics, which can vary even within one subgroup. Therefore, the use of mouse models to study a tumor’s biology or to perform preclinical trials has to be carefully adapted to the tumor subgroup that is planned to be investigated or targeted [22]. Ptch1+/− mice, for instance, that develop medulloblastoma due to the constitutive activation of the Sonic hedgehog (Shh) pathway [9], have to be considered unsuitable for investigations that do not refer to medulloblastoma of the SHH subgroup. Hence, approximately 70 % of human medulloblastoma cases are not covered by this model [17]. More strictly, Ptch1+/− mice may even be unsuitable to model medulloblastoma that do not carry PTCH1 mutations, which account for approximately 85 % of any medulloblastomas [14]. Meanwhile, a variety of additional transgenic mice has been generated that were suggested as models for ‘medulloblastoma’. However, until recently, neither the technology nor a large enough cohort size of thoroughly analyzed human medulloblastoma samples was available to comprehensively categorize and validate the generated mouse models with respect to the growing diversity of human medulloblastoma. This study brings together genome-wide sequencing data and gene expression profiles from 47 and 423 human medulloblastomas, respectively. These data are used as a reference to precisely match existing mouse models to subgroups of the human disease. This said, we acknowledge the commonly accepted four molecular groups of human medulloblastoma (WNT, SHH, Group 3 and Group 4) [47], but we also take into account newly identified subgroups within the cohort of SHH patients, i.e., SHH tumors that arise in infants and SHH tumors that arise in adults [31]. Based on our approach, this study indicates a substantial lack of reliable models for Group 4 medulloblastoma, but reveals surprising details on a number of genetically engineered mice that model human SHH medulloblastoma. Results from whole genome sequencing of mouse and human tumors demonstrate that the genetic make-up is not the single driver of a tumor’s gene expression profile, which determines molecular medulloblastoma classification.
Human tissue samples
13
Snap frozen human tissue samples were reviewed by experienced neuropathologists and examined for tumor content. Samples were excluded from analysis when
Original Paper
Genomic and transcriptomic analyses match medulloblastoma mouse models to their human counterparts Julia Pöschl · Sebastian Stark · Philipp Neumann · Susanne Gröbner · Daisuke Kawauchi · David T. W. Jones · Paul A. Northcott · Peter Lichter · Stefan M. Pfister · Marcel Kool · Ulrich Schüller
Received: 8 April 2014 / Revised: 8 May 2014 / Accepted: 19 May 2014 © Springer-Verlag Berlin Heidelberg 2014
Abstract Medulloblastoma is a malignant embryonal brain tumor with highly variable outcome. In order to study the biology of this tumor and to perform preclinical treatment studies, a lot of effort has been put into the generation of appropriate mouse models. The usage of these models, however, has become debatable with the advances in human medulloblastoma subgrouping. This study brings together multiple relevant mouse models and matches genetic alterations and gene expression data of 140 murine tumors with 423 human medulloblastomas in a global way. Using AGDEX analysis and k-means clustering, we show that the Blbp-cre::Ctnnb1(ex3)Fl/+Trp53Fl/Fl mouse model fits well to human WNT medulloblastoma, and that, among various Myc- or Mycn-based mouse medulloblastomas, tumors in Glt1-tTA::TRE-MYCN/Luc mice proved to be
most specific for human group 3 medulloblastoma. None of the analyzed models displayed a significant match to group 4 tumors. Intriguingly, mice with Ptch1 or Smo mutations selectively modeled SHH medulloblastomas of adulthood, although such mutations occur in all human age groups. We therefore suggest that the infantile or adult gene expression pattern of SHH MBs are not solely determined by specific mutations. This is supported by the observation that human medulloblastomas with PTCH1 mutations displayed more similarities to PTCH1 wild-type tumors of the same age group than to PTCH1-mutated tumors of the other age group. Together, we provide novel insights into previously unrecognized specificity of distinct models and suggest these findings as a solid basis to choose the appropriate model for preclinical studies on medulloblastoma.
M. Kool and U. Schüller are co-senior authors.
Keywords WNT · SHH · Medulloblastoma · Gene expression profile · Mutations · Mouse model
Electronic supplementary material The online version of this article (doi:10.1007/s00401-014-1297-8) contains supplementary material, which is available to authorized users. J. Pöschl · U. Schüller (*) Center for Neuropathology and Prion Research, Ludwig-Maximilians-University, Feodor‑Lynen‑Strasse 23, 81377 Munich, Germany e-mail: [email protected]‑muenchen.de; [email protected] S. Stark · S. Gröbner · D. Kawauchi · D. T. W. Jones · P. A. Northcott · S. M. Pfister · M. Kool Division of Pediatric Neuroncology (B062), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany e-mail: [email protected]
P. Neumann Department of Informatics, Technical University, Munich, Germany P. Lichter Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany S. M. Pfister Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
S. Stark Department of General Pediatrics, Heidelberg University Hospital, Heidelberg, Germany
13
Acta Neuropathol
Introduction
Materials and methods
For decades, medulloblastoma was recognized as a malignant embryonal brain tumor with particularly poor prognosis. Affected patients were treated with surgery, chemotherapy and—depending on their age—radiotherapy. In the era of personalized medicine, this image has changed dramatically. Medulloblastoma is now acknowledged as a group of at least four major tumor types that significantly differ from each other with respect to genetics, epigenetics, gene expression, histology, and clinical outcome [17, 32, 33]. This knowledge requires stratified therapeutic approaches that refer to each tumor subgroup and to each tumor’s genetics, which can vary even within one subgroup. Therefore, the use of mouse models to study a tumor’s biology or to perform preclinical trials has to be carefully adapted to the tumor subgroup that is planned to be investigated or targeted [22]. Ptch1+/− mice, for instance, that develop medulloblastoma due to the constitutive activation of the Sonic hedgehog (Shh) pathway [9], have to be considered unsuitable for investigations that do not refer to medulloblastoma of the SHH subgroup. Hence, approximately 70 % of human medulloblastoma cases are not covered by this model [17]. More strictly, Ptch1+/− mice may even be unsuitable to model medulloblastoma that do not carry PTCH1 mutations, which account for approximately 85 % of any medulloblastomas [14]. Meanwhile, a variety of additional transgenic mice has been generated that were suggested as models for ‘medulloblastoma’. However, until recently, neither the technology nor a large enough cohort size of thoroughly analyzed human medulloblastoma samples was available to comprehensively categorize and validate the generated mouse models with respect to the growing diversity of human medulloblastoma. This study brings together genome-wide sequencing data and gene expression profiles from 47 and 423 human medulloblastomas, respectively. These data are used as a reference to precisely match existing mouse models to subgroups of the human disease. This said, we acknowledge the commonly accepted four molecular groups of human medulloblastoma (WNT, SHH, Group 3 and Group 4) [47], but we also take into account newly identified subgroups within the cohort of SHH patients, i.e., SHH tumors that arise in infants and SHH tumors that arise in adults [31]. Based on our approach, this study indicates a substantial lack of reliable models for Group 4 medulloblastoma, but reveals surprising details on a number of genetically engineered mice that model human SHH medulloblastoma. Results from whole genome sequencing of mouse and human tumors demonstrate that the genetic make-up is not the single driver of a tumor’s gene expression profile, which determines molecular medulloblastoma classification.
Human tissue samples
13
Snap frozen human tissue samples were reviewed by experienced neuropathologists and examined for tumor content. Samples were excluded from analysis when
