Dataset Information

Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma.

ABSTRACT: Olfactory neuroblastoma (ONB) is a rare malignant neoplasm arising in the upper portion of the sinonasal cavity. To better understand the genetic bases for ONB, here we perform whole exome and whole genome sequencing as well as single nucleotide polymorphism array analyses in a series of ONB patient samples. Deletions involving the dystrophin (DMD) locus are found in 12 of 14 (86%) tumors. Interestingly, one of the remaining tumors has a deletion in LAMA2, bringing the number of ONBs with deletions of genes involved in the development of muscular dystrophies to 13 or 93%. This high prevalence implicates an unexpected functional role for genes causing hereditary muscular dystrophies in ONB.

SUBMITTER: Gallia GL

PROVIDER: S-EPMC6303314 | biostudies-other | 2018 Dec

REPOSITORIES: biostudies-other

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Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma.

Gallia Gary L GL Zhang Ming M Ning Yi Y Haffner Michael C MC Batista Denise D Binder Zev A ZA Bishop Justin A JA Hann Christine L CL Hruban Ralph H RH Ishii Masaru M Klein Alison P AP Reh Douglas D DD Rooper Lisa M LM Salmasi Vafi V Tamargo Rafael J RJ Wang Qing Q Williamson Tara T Zhao Tianna T Zou Ying Y Meeker Alan K AK Agrawal Nishant N Vogelstein Bert B Kinzler Kenneth W KW Papadopoulos Nickolas N Bettegowda Chetan C

Nature communications 20181221 1

Olfactory neuroblastoma (ONB) is a rare malignant neoplasm arising in the upper portion of the sinonasal cavity. To better understand the genetic bases for ONB, here we perform whole exome and whole genome sequencing as well as single nucleotide polymorphism array analyses in a series of ONB patient samples. Deletions involving the dystrophin (DMD) locus are found in 12 of 14 (86%) tumors. Interestingly, one of the remaining tumors has a deletion in LAMA2, bringing the number of ONBs with deleti ...[more]

PMID: 30575736

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Project description:Neuroblastoma (NB) is a heterogeneous pediatric tumor. To better understand the biological pathways involved in the development of high-risk neuroblastoma, we performed parallel global protein and mRNA expression profiling on NB tumors of stage 4 MYCN-amplified (4+) and stage 1 MYCN-not-amplified (1-) using isotope-coded affinity tags (ICAT) and Affymetrix U133plus2 microarray, respectively. A total of 1461 proteins represented by 2 or more peptides were identified from the quantitative ICAT analysis, of which 433 and 130 proteins are up- or down-regulated, respectively, in 4+ tumor compared to the 1- tumor. Pathway analysis of the differentially expressed proteins showed the enrichment of glycolysis, DNA replication and cell cycle processes in the up-regulated proteins and cell adhesion, nervous system development and cell differentiation processes in the down-regulated proteins in 4+ tumor; suggesting a less mature neural and a more invasive phenotype of 4+ tumor. Myc targets and ribosomal proteins are overrepresented in the 4+ tumors as expected; functional gene sets reported to be enriched in neural and embryonic stem cells are significantly enriched in the 4+ tumor, indicating the existence of a stemness signature in MYCN-amplified stage 4 tumor. In addition, protein and mRNA expression are moderately correlated (r = 0.51, p < 0.0001), as approximately half of the up-regulated proteins in 4+ tumor have elevated mRNA level (n = 208), and one-third of down-regulated proteins have lower mRNA expression (n = 47). Further biological network analysis revealed that the differentially expressed proteins closely interact with other proteins of known networks; the important role of MYCN is confirmed and other transcription factors identified in the network may have potential roles in the biology of NB tumor. We used global genomic and proteomic analysis to identify biologically relevant proteins and pathways important to NB progression and development that may provide new insights into the biology of advanced neuroblastoma.

Dataset Information

Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma.

Publications

Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma.

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