Integrated proteomic and transcriptomic-based approaches to identifying signature biomarkers and pathways for elucidation of Daoy and UW228 subtypes

Roger Higdon, Jessie Kala, Devan Wilkins, Julia Fangfei Yan, Manveen K. Sethi, Liang Lin, Siqi Liu, Elizabeth Montague, Imre Janko, John Choiniere, Natali Kolker, William S. Hancock, Eugene Kolker, Susan Fanayan*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
8 Downloads (Pure)

Abstract

Medulloblastoma (MB) is the most common malignant pediatric brain tumor. Patient survival has remained largely the same for the past 20 years, with therapies causing significant health, cognitive, behavioral and developmental complications for thosewho survive the tumor. In this study, we profiled the total transcriptome and proteome of two established MB cell lines, Daoy and UW228, using high-throughput RNA sequencing (RNA-Seq) and label-free nano-LC-MS/MS-based quantitative proteomics, coupled with advanced pathway analysis. While Daoy has been suggested tobelong to the sonic hedgehog (SHH) subtype, the exact UW228 subtype is not yet clearly established. Thus, a goal of this study was to identify protein markers and pathways that would help elucidate their subtype classification. A number of differentially expressed genes and proteins, including a number of adhesion, cytoskeletal and signaling molecules, were observed between the two cell lines. While several cancer-associated genes/proteins exhibited similar expression across the two cell lines, upregulation of a number of signature proteins and enrichment of key components of SHH andWNT signaling pathways were uniquely observed in Daoy and UW228, respectively. The novel information on differentially expressed genes/proteins and enriched pathways provide insights into the biology of MB, which could help elucidate their subtype classification.

Original languageEnglish
Article number5
Pages (from-to)1-16
Number of pages16
JournalProteomes
Volume5
Issue number1
DOIs
Publication statusPublished - Mar 2017

Bibliographical note

Copyright the Author(s) 2017. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

Keywords

  • medulloblastoma
  • Daoy
  • UW228
  • SHH subtype
  • WNT subtype
  • transcriptome
  • proteome

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