The search for molecular markers in a gene-orphan case study of a pediatric spinal cord pilocytic astrocytoma

Carolina Martinelli, Fabio Gabriele, Federico Manai, Roberto Ciccone, Francesca Novara, Elisabetta Sauta, Riccardo Bellazzi, Monica Patane, Isabella Moroni, Rosina Paterra, Sergio Comincini

Research output: Contribution to journalArticlepeer-review

Abstract

Background/Aim: We herein presented a case of pediatric spinal cord pilocytic astrocytoma diagnosed on the basis of histopathological and clinical findings. Materials and Methods: Given the paucity of data on genetic features for this tumor, we performed exome, array CGH and RNA sequencing analysis from nucleic acids isolated from a unique and not repeatable very small amount of a formalin-fixed, paraffin-embedded (FFPE) specimen. Results: DNA mutation analysis, comparing tumor and normal lymphocyte peripheral DNA, evidenced few tumor-specific single nucleotide variants in DEFB119, MUC5B, NUDT1, LTBP3 and CPSF3L genes. Differently, tumor DNA was not characterized by for the main pilocytic astrocytoma gene variations, including BRAFV600E. An inframe trinucleotides insertion involving DLX6 or lnc DLX6-AS1 genes was scored in 44.9% of sequenced reads; the temporal profile of this variation on the expression of DLX-AS1 was investigated in patient`s urine-derived exosomes, reporting no significant variation in the one-year molecular follow-up. Array CGH identified a tumor microdeletion at the 6q25.3 chromosomal region, spanning 1,01 Mb and comprising ZDHHC14, SNX9, TULP4 and SYTL3 genes. The expression of these genes did not change in urine-derived exosomes during the one-year investigation period. Finally, RNAseq did not reveal any of the common pilocytic BRAF-KIAA1549 genes fusion events. Conclusion: To our knowledge, the present report is one of the first described gene-orphan case studies of a pediatric spinal cord pilocytic astrocytoma.

Original languageEnglish
Pages (from-to)117-130
Number of pages14
JournalCancer Genomics and Proteomics
Volume17
Issue number2
DOIs
Publication statusPublished - 2020

Keywords

  • Bioinformatics
  • Chromosomal abnormalities
  • DNA mutations
  • Exome analysis
  • Pediatric astrocytic tumors

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics
  • Cancer Research

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