title: A germline mutation of CDKN2A and a novel RPLP1-C19MC fusion detected in a rare melanotic neuroectodermal tumor of infancy: a case report.
abstract: Melanotic neuroectodermal tumor of infancy (MNTI) is exceptionally rare and occurs predominantly in the head and neck (92.8 % cases). The patient reported here is only the eighth case of MNTI presenting in an extremity, and the first reported in the fibula.
  
  
  
  A 2-month-old female presented with a mass arising in the fibula. Exhaustive genomic, transcriptomic, epigenetic and pathological characterization was performed on the excised primary tumor and a derived cell line. Whole-exome analysis of genomic DNA from both the tumor and blood indicated no somatic, non-synonymous coding mutations within the tumor, but a heterozygous, unique germline, loss of function mutation in CDKN2A (p16(INK4A), D74A). SNP-array CGH on DNA samples revealed the tumor to be euploid, with no detectable gene copy number variants. Multiple chromosomal translocations were identified by RNA-Seq, and fusion genes included RPLP1-C19MC, potentially deregulating the C19MC cluster, an imprinted locus containing microRNA genes reactivated by gene fusion in embryonal tumors with multilayered rosettes. Since the presumed cell of origin of MNTI is from the neural crest, we also compared gene expression with a dataset from human neural crest cells and identified 185 genes with significantly different expression. Consistent with the melanotic phenotype of the tumor, elevated expression of tyrosinase was observed. Other highly expressed genes encoded muscle proteins and modulators of the extracellular matrix. A derived MNTI cell line was sensitive to inhibitors of lysine demethylase, but not to compounds targeting other epigenetic regulators.
  
  
  
  In the absence of somatic copy number variations or mutations, the fully transformed phenotype of the MNTI may have arisen in infancy because of the combined effects of a germline CDKN2A mutation, tumor promoting somatic fusion genes and epigenetic deregulation. Very little is known about the etiology of MNTI and this report advances knowledge of these rare tumors by providing the first comprehensive genomic, transcriptomic and epigenetic characterization of a case.
authors: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK.
authors: David J
authors: DJ
authors: Barnes
authors: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK.
authors: Edward
authors: E
authors: Hookway
authors: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK.
authors: Nick
authors: N
authors: Athanasou
authors: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK.
authors: Takeshi
authors: T
authors: Kashima
authors: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK.
authors: Udo
authors: U
authors: Oppermann
authors: Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK.
authors: Simon
authors: S
authors: Hughes
authors: Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK.
authors: Daniel
authors: D
authors: Swan
authors: Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK.
authors: Dietrich
authors: D
authors: Lueerssen
authors: Oxford Gene Technology Ltd, Begbroke Science Park, Begbroke Hill, Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK.
authors: John
authors: J
authors: Anson
authors: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Nuffield Orthopaedic Centre, Windmill Road, Headington, Oxford, OX3 7HE, UK. bass.hassan@path.ox.ac.uk.|Tumour Growth Group, Oxford Molecular Pathology Institute, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK. bass.hassan@path.ox.ac.uk.
authors: A Bassim
authors: AB
authors: Hassan
mesh_terms: D001859:Bone Neoplasms / Q000235:genetics*; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050763:Cyclin-Dependent Kinase Inhibitor p18 / Q000235:genetics*; D005260:Female; D005360:Fibula / Q000473:pathology*; D015972:Gene Expression Regulation, Neoplastic; D018095:Germ-Line Mutation; D006801:Humans; D007223:Infant; D017600:Neuroectodermal Tumor, Melanotic / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D010750:Phosphoproteins / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: C000614131:CDKN2A protein, human; D019941:Cyclin-Dependent Kinase Inhibitor p16; D050763:Cyclin-Dependent Kinase Inhibitor p18; D015514:Oncogene Proteins, Fusion; D010750:Phosphoproteins; D012269:Ribosomal Proteins; C035690:ribosomal phosphoprotein P1
keywords: Germline CDKN2A mutation; Melanotic Neuroectodermal Tumor of Infancy; RNA-Seq; RPLP1-C19MC fusion gene; Sensitivity to lysine demethylase inhibitors