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Germline Elongator mutations in Sonic Hedgehog medulloblastoma

Sebastian M. Waszak, Robinson Giles W, Brian L. Gudenas, Kyle S. Smith, Antoine Forget, Marija Kojic, Jesus Garcia-Lopez, Jennifer Hadley, Kayla V. Hamilton, Emilie Indersie, Ivo Buchhalter, Jules Kerssemakers, Natalie Jäger, Tanvi Sharma, Tobias Rausch, Marcel Kool, Dominik Sturm, David T. W. Jones, Aksana Vasilyeva, Ruth G. Tatevossian, Geoffrey Neale, Bérangère Lombard, Damarys Loew, Joy Nakitandwe, Michael Rusch, Daniel C. Bowers, Anne Bendel, Sonia Partap, Murali Chintagumpala, John Crawford, Nicholas G. Gottardo, Amy Smith, Christelle Dufour, Stefan Rutkowski, Tone Eggen, Finn Wesenberg, Kristina Kjaerheim, Maria Feychting, Birgitta Lannering, Joachim Schüz, Christoffer Johansen, Tina V. Andersen, Martin Röösli, Claudia E. Kuehni, Michael Grotzer, Marc Remke, Stéphanie Puget, Kristian W. Pajtler, Till Milde, Olaf Witt, Marina Ryzhova, Andrey Korshunov, Brent A. Orr, David W. Ellison, Laurence Brugieres, Peter Lichter, Kim E. Nichols, Amar Gajjar, Brandon J. Wainwright, Olivier Ayrault, Jan O. Korbel (), Paul A. Northcott () and Stefan M. Pfister ()
Additional contact information
Sebastian M. Waszak: Genome Biology Unit
Robinson Giles W: St Jude Children’s Research Hospital
Brian L. Gudenas: St Jude Children’s Research Hospital
Kyle S. Smith: St Jude Children’s Research Hospital
Antoine Forget: Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021
Marija Kojic: University of Queensland
Jesus Garcia-Lopez: St Jude Children’s Research Hospital
Jennifer Hadley: St Jude Children’s Research Hospital
Kayla V. Hamilton: St Jude Children’s Research Hospital
Emilie Indersie: Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021
Ivo Buchhalter: German Cancer Research Center (DKFZ)
Jules Kerssemakers: German Cancer Research Center (DKFZ)
Natalie Jäger: Hopp Children’s Cancer Center Heidelberg (KiTZ)
Tanvi Sharma: Hopp Children’s Cancer Center Heidelberg (KiTZ)
Tobias Rausch: Genome Biology Unit
Marcel Kool: Hopp Children’s Cancer Center Heidelberg (KiTZ)
Dominik Sturm: Hopp Children’s Cancer Center Heidelberg (KiTZ)
David T. W. Jones: Hopp Children’s Cancer Center Heidelberg (KiTZ)
Aksana Vasilyeva: St Jude Children’s Research Hospital
Ruth G. Tatevossian: St Jude Children’s Research Hospital
Geoffrey Neale: St Jude Children’s Research Hospital
Bérangère Lombard: Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique
Damarys Loew: Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique
Joy Nakitandwe: St Jude Children’s Research Hospital
Michael Rusch: St Jude Children’s Research Hospital
Daniel C. Bowers: University of Texas Southwestern Medical School
Anne Bendel: Children’s Hospitals and Clinics of Minnesota
Sonia Partap: Stanford University
Murali Chintagumpala: Baylor College of Medicine
John Crawford: University of California San Diego and Rady Children’s Hospital
Nicholas G. Gottardo: Telethon Kids Institute
Amy Smith: Arnold Palmer Hospital Center for Children’s Cancer
Christelle Dufour: Université Paris-Saclay, Department of Pediatric and Adolescent Oncology
Stefan Rutkowski: University Medical Center Hamburg-Eppendorf
Tone Eggen: The Cancer Registry of Norway, Majorstuen
Finn Wesenberg: Institute of Population-Based Cancer Research
Kristina Kjaerheim: Institute of Population-Based Cancer Research
Maria Feychting: Karolinska Institutet
Birgitta Lannering: University of Gothenburg, The Queen Silvia Children’s Hospital
Joachim Schüz: International Agency for Research on Cancer (IARC)
Christoffer Johansen: Rigshospitalet, University of Copenhagen
Tina V. Andersen: University of Basel
Martin Röösli: Institute of Social and Preventive Medicine University of Bern
Claudia E. Kuehni: Institute of Social and Preventive Medicine University of Bern
Michael Grotzer: University Children’s Hospital of Zurich
Marc Remke: University Hospital Düsseldorf
Stéphanie Puget: Necker Hospital, Université de Paris
Kristian W. Pajtler: Hopp Children’s Cancer Center Heidelberg (KiTZ)
Till Milde: Hopp Children’s Cancer Center Heidelberg (KiTZ)
Olaf Witt: Hopp Children’s Cancer Center Heidelberg (KiTZ)
Marina Ryzhova: Burdenko Neurosurgical Institute
Andrey Korshunov: German Cancer Research Center (DKFZ)
Brent A. Orr: St Jude Children’s Research Hospital
David W. Ellison: St Jude Children’s Research Hospital
Laurence Brugieres: Université Paris-Saclay, Department of Pediatric and Adolescent Oncology
Peter Lichter: German Cancer Research Center Heidelberg (DKFZ)
Kim E. Nichols: St Jude Children’s Research Hospital
Amar Gajjar: St Jude Children’s Research Hospital
Brandon J. Wainwright: University of Queensland
Olivier Ayrault: Université Paris Sud, Université Paris-Saclay, CNRS UMR 3347, INSERM U1021
Jan O. Korbel: Genome Biology Unit
Paul A. Northcott: St Jude Children’s Research Hospital
Stefan M. Pfister: Hopp Children’s Cancer Center Heidelberg (KiTZ)

Nature, 2020, vol. 580, issue 7803, 396-401

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41586-020-2164-5

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