Molecular classification of a complex structural rearrangement of the RB1 locus in an infant with sporadic, isolated, intracranial, sellar region retinoblastoma

Kathleen M. Schieffer, Alexander Z. Feldman, Esko A. Kautto, Sean McGrath, Anthony R. Miller, Maria Elena Hernandez-Gonzalez, Stephanie LaHaye, Katherine E. Miller, Daniel C. Koboldt, Patrick Brennan, Benjamin Kelly, Amy Wetzel, Vibhuti Agarwal, Margaret Shatara, Suzanne Conley, Diana P. Rodriguez, Rolla Abu-Arja, Ala Shaikhkhalil, Matija Snuderl, Brent A. OrrJonathan L. Finlay, Diana S. Osorio, Annie I. Drapeau, Jeffrey R. Leonard, Christopher R. Pierson, Peter White, Vincent Magrini, Elaine R. Mardis, Richard K. Wilson, Catherine E. Cottrell, Daniel R. Boué

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Abstract

Retinoblastoma is a childhood cancer of the retina involving germline or somatic alterations of the RB Transcriptional Corepressor 1 gene, RB1. Rare cases of sellar-suprasellar region retinoblastoma without evidence of ocular or pineal tumors have been described. A nine-month-old male presented with a sellar-suprasellar region mass. Histopathology showed an embryonal tumor with focal Flexner-Wintersteiner-like rosettes and loss of retinoblastoma protein (RB1) expression by immunohistochemistry. DNA array-based methylation profiling confidently classified the tumor as pineoblastoma group A/intracranial retinoblastoma. The patient was subsequently enrolled on an institutional translational cancer research protocol and underwent comprehensive molecular profiling, including paired tumor/normal exome and genome sequencing and RNA-sequencing of the tumor. Additionally, Pacific Biosciences (PacBio) Single Molecule Real Time (SMRT) sequencing was performed from comparator normal and disease-involved tissue to resolve complex structural variations. RNA-sequencing revealed multiple fusions clustered within 13q14.1-q21.3, including a novel in-frame fusion of RB1-SIAH3 predicted to prematurely truncate the RB1 protein. SMRT sequencing revealed a complex structural rearrangement spanning 13q14.11-q31.3, including two somatic structural variants within intron 17 of RB1. These events corresponded to the RB1-SIAH3 fusion and a novel RB1 rearrangement expected to correlate with the complete absence of RB1 protein expression. Comprehensive molecular analysis, including DNA array-based methylation profiling and sequencing-based methodologies, were critical for classification and understanding the complex mechanism of RB1 inactivation in this diagnostically challenging tumor.

Original languageEnglish
Article number61
JournalActa Neuropathologica Communications
Volume9
Issue number1
DOIs
StatePublished - Dec 2021

Keywords

  • DNA array-based methylation
  • Intracranial retinoblastoma
  • PacBio
  • RB1
  • SMRT sequencing
  • Sellar-suprasellar retinoblastoma
  • Structural variation

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