Differential Expression of Genes for Ubiquitin Ligases in Medulloblastoma Subtypes

The Cerebellum
Jerry Vriend, Robert B Tate

Abstract

Using publically available datasets on gene expression in medulloblastoma (MB) subtypes, we selected genes for ubiquitin ligases and identified statistically those that best predicted each of the four major MB subgroups as separate disease entities. We identify a gene coding for an ubiquitin ligase, ZNRF3, whose overexpression alone can predict the WNT subgroup for 100% in the Pfister dataset. For the SHH subgroup, we identify a gene for a regulatory subunit of the protein phosphatase 2A (PP2A), PPP2R2C, as the major predictor among the E3 ligases genes. The ubiquitin and ubiquitin-like conjugation database (UUCD) lists PPP2R2C as coding for a Cullin Ring ubiquitin ligase adaptor. For group 3 MBs, the best ubiquitin ligase predictor was PPP2R2B, a gene which codes for another regulatory subunit of the PP2A holoenzyme. For group 4, the best E3 gene predictors were MID2, ZBTB18, and PPP2R2A, which codes for a third PP2A regulatory subunit. Heatmap analysis of the E3 gene data shows that expression of ten genes for ubiquitin ligases can be used to classify MBs into the four major consensus subgroups. This was illustrated by analysis of gene expression of ubiquitin ligases of the Pfister dataset and confirmed in the dataset of Cava...Continue Reading

References

May 2, 2001·Genes & Development·W P Tansey
May 16, 2001·Biochemical and Biophysical Research Communications·W ZhangX Cao
Jul 13, 2002·International Journal of Cancer. Journal International Du Cancer·Alain LatilOlivier Cussenot
May 29, 2003·Molecular Cell·So Young KimWilliam P Tansey
Jul 9, 2004·Genome Biology·Hui-Chuan Huang, Peter S Klein
Jul 17, 2004·Cancer Research·Julien MazieresDavid M Jablons
Nov 17, 2005·Molecular and Cellular Biology·Scott Stewart, Guowei Fang
Dec 14, 2005·International Review of Cytology·Sally P Wheatley, Iain A McNeish
Jul 11, 2006·BMC Cell Biology·Jeremy T Blitzer, Roel Nusse
Nov 28, 2007·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Melissa R JunttilaJukka Westermarck
Apr 24, 2008·Genes to Cells : Devoted to Molecular & Cellular Mechanisms·So MaezawaOsamu Koiwai
Jan 24, 2009·Proceedings of the National Academy of Sciences of the United States of America·Pierre-Olivier FrappartPeter J McKinnon
Jul 1, 2007·Cell Adhesion & Migration·Anna A Sablina, William C Hahn
Sep 17, 2009·Journal of Cell Science·Cordula Surmann-SchmittMichael Stock
Oct 13, 2009·Molecular Cell·Mei KongCraig B Thompson
Dec 4, 2009·Proceedings of the National Academy of Sciences of the United States of America·Qing ZhangJin Jiang
Dec 17, 2009·The Journal of Cell Biology·Chad G PearsonMark Winey
Feb 16, 2010·Molecular and Cellular Biology·Xiaohui WenSuzie J Scales
May 13, 2010·Proceedings of the National Academy of Sciences of the United States of America·Eunice Y LeeMatthew P Scott
May 28, 2010·Cell Cycle·Gianluca CanettieriAlberto Gulino
Sep 9, 2010·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Paul A NorthcottMichael D Taylor
Nov 26, 2010·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Yoon-Jae ChoScott L Pomeroy
Dec 15, 2010·Nature Reviews. Drug Discovery·Lynn BedfordJames E Brownell
Jun 3, 2011·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Marc RemkeAndrey Korshunov
Jul 12, 2011·Nature Structural & Molecular Biology·Tomas MalinauskasE Yvonne Jones

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Methods Mentioned

BETA
ubiquitination
GTPase

Software Mentioned

R2 analysis and visualization platform
R2
R2 GAVP )

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