1
|
Waszak SM, Robinson GW, Gudenas BL, Smith KS, Forget A, Kojic M, Garcia-Lopez J, Hadley J, Hamilton KV, Indersie E, Buchhalter I, Kerssemakers J, Jäger N, Sharma T, Rausch T, Kool M, Sturm D, Jones DTW, Vasilyeva A, Tatevossian RG, Neale G, Lombard B, Loew D, Nakitandwe J, Rusch M, Bowers DC, Bendel A, Partap S, Chintagumpala M, Crawford J, Gottardo NG, Smith A, Dufour C, Rutkowski S, Eggen T, Wesenberg F, Kjaerheim K, Feychting M, Lannering B, Schüz J, Johansen C, Andersen TV, Röösli M, Kuehni CE, Grotzer M, Remke M, Puget S, Pajtler KW, Milde T, Witt O, Ryzhova M, Korshunov A, Orr BA, Ellison DW, Brugieres L, Lichter P, Nichols KE, Gajjar A, Wainwright BJ, Ayrault O, Korbel JO, Northcott PA, Pfister SM. Germline Elongator mutations in Sonic Hedgehog medulloblastoma. Nature 2020; 580:396-401. [PMID: 32296180 PMCID: PMC7430762 DOI: 10.1038/s41586-020-2164-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/30/2020] [Indexed: 12/13/2022]
Abstract
Cancer genomics has revealed many genes and core molecular processes that contribute to human malignancies, but the genetic and molecular bases of many rare cancers remains unclear. Genetic predisposition accounts for 5 to 10% of cancer diagnoses in children1,2, and genetic events that cooperate with known somatic driver events are poorly understood. Pathogenic germline variants in established cancer predisposition genes have been recently identified in 5% of patients with the malignant brain tumour medulloblastoma3. Here, by analysing all protein-coding genes, we identify and replicate rare germline loss-of-function variants across ELP1 in 14% of paediatric patients with the medulloblastoma subgroup Sonic Hedgehog (MBSHH). ELP1 was the most common medulloblastoma predisposition gene and increased the prevalence of genetic predisposition to 40% among paediatric patients with MBSHH. Parent-offspring and pedigree analyses identified two families with a history of paediatric medulloblastoma. ELP1-associated medulloblastomas were restricted to the molecular SHHα subtype4 and characterized by universal biallelic inactivation of ELP1 owing to somatic loss of chromosome arm 9q. Most ELP1-associated medulloblastomas also exhibited somatic alterations in PTCH1, which suggests that germline ELP1 loss-of-function variants predispose individuals to tumour development in combination with constitutive activation of SHH signalling. ELP1 is the largest subunit of the evolutionarily conserved Elongator complex, which catalyses translational elongation through tRNA modifications at the wobble (U34) position5,6. Tumours from patients with ELP1-associated MBSHH were characterized by a destabilized Elongator complex, loss of Elongator-dependent tRNA modifications, codon-dependent translational reprogramming, and induction of the unfolded protein response, consistent with loss of protein homeostasis due to Elongator deficiency in model systems7-9. Thus, genetic predisposition to proteome instability may be a determinant in the pathogenesis of paediatric brain cancers. These results support investigation of the role of protein homeostasis in other cancer types and potential for therapeutic interference.
Collapse
Affiliation(s)
- Sebastian M Waszak
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Giles W Robinson
- Department of Oncology, Division of Neuro-Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brian L Gudenas
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kyle S Smith
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Antoine Forget
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Marija Kojic
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Jesus Garcia-Lopez
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jennifer Hadley
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kayla V Hamilton
- Department of Oncology, Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Emilie Indersie
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Ivo Buchhalter
- Omics IT and Data Management Core Facility (W610), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jules Kerssemakers
- Omics IT and Data Management Core Facility (W610), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tanvi Sharma
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Dominik Sturm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T W Jones
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Pediatric Glioma Research Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aksana Vasilyeva
- Cancer Center Administration, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ruth G Tatevossian
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Geoffrey Neale
- Hartwell Center, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Paris, France
| | - Joy Nakitandwe
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Michael Rusch
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel C Bowers
- Division of Pediatric Hematology-Oncology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Anne Bendel
- Department of Pediatric Hematology and Oncology, Children's Hospitals and Clinics of Minnesota, Minnesota, MN, USA
| | - Sonia Partap
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | | | - John Crawford
- Department of Neurosciences, University of California San Diego and Rady Children's Hospital, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego and Rady Children's Hospital, San Diego, CA, USA
| | - Nicholas G Gottardo
- Department of Paediatric and Adolescent Oncology/Haematology, Perth Children's Hospital and Brain Tumour Research Programme, Telethon Kids Institute, Perth, Western Australia, Australia
| | - Amy Smith
- Arnold Palmer Hospital Center for Children's Cancer, Orlando, FL, USA
| | - Christelle Dufour
- Gustave Roussy, Université Paris-Saclay, Department of Pediatric and Adolescent Oncology, Villejuif, France
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tone Eggen
- The Cancer Registry of Norway, Majorstuen, Oslo, Norway
| | - Finn Wesenberg
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
| | - Kristina Kjaerheim
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
| | - Maria Feychting
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Lannering
- Department of Pediatrics, University of Gothenburg, The Queen Silvia Children's Hospital, Gothenburg, Sweden
| | - Joachim Schüz
- Section of Environment and Radiation, International Agency for Research on Cancer (IARC), Lyon, France
| | - Christoffer Johansen
- Oncology Clinic, Finsen Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Tina V Andersen
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Martin Röösli
- Swiss Childhood Cancer Registry, Institute of Social and Preventive Medicine University of Bern, Bern, Switzerland
| | - Claudia E Kuehni
- Swiss Childhood Cancer Registry, Institute of Social and Preventive Medicine University of Bern, Bern, Switzerland
- Department of Paediatric Haematology and Oncology, University Children's Hospital, Bern, Switzerland
| | - Michael Grotzer
- University Children's Hospital of Zurich, Zurich, Switzerland
| | - Marc Remke
- Department of Pediatric Oncology, Hematology, and Clinical Immunology, Medical Faculty, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Stéphanie Puget
- Department of Pediatric Neurosurgery, Necker Hospital, Université de Paris, Paris, France
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Olaf Witt
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Pediatric Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marina Ryzhova
- Department of Neuropathology, Burdenko Neurosurgical Institute, Moscow, Russia
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital, Heidelberg, Germany
| | - Brent A Orr
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - David W Ellison
- Department of Pathology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Laurence Brugieres
- Gustave Roussy, Université Paris-Saclay, Department of Pediatric and Adolescent Oncology, Villejuif, France
| | - Peter Lichter
- Division of Molecular Genetics, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Kim E Nichols
- Department of Oncology, Division of Cancer Predisposition, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Amar Gajjar
- Department of Oncology, Division of Neuro-Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon J Wainwright
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Olivier Ayrault
- Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021, Orsay, France
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
| | - Paul A Northcott
- Department of Developmental Neurobiology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Stefan M Pfister
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany.
| |
Collapse
|