title: A multiplexed proteomics approach to differentiate neurite outgrowth patterns.
abstract: We report here a method for proteomics pattern discovery by utilizing a self-organizing map approach to analyze data obtained from a novel multiplex iTRAQ proteomics method. Through the application of this technique, we were able to delineate the early molecular events preceding dorsal root ganglia neurite outgrowth induced by either nerve growth factor (NGF) or an immunophilin ligand, JNJ460. Following pattern analysis we discovered that each neurotrophic agent promoted mostly distinct increases in protein expression with few overlapping patterns. In the NGF-treated group, proteins possessing "biosynthesis function" (p < 0.002) and "ribosome localization" (p < 0.0003) were increased, while proteins promoting "organogenesis" (p < 0.004) and related "signal transduction" (p < 0.008) functions were notably increased in the JNJ460-treated group. This study suggests that the properties of neurite outgrowth triggered by NGF and JNJ460 can be distinguished at the proteome level. Multiplexed proteomics analysis, along with pattern discovery bioinformatics tools, has the capability to differentiate subtle neuroproteomics patterns.
authors.affiliation: Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, MSB E-609, Newark, NJ 07103, USA.
authors.forename: Tong
authors.initials: T
authors.lastname: Liu
authors.forename: Veera
authors.initials: V
authors.lastname: D'mello
authors.forename: Longwen
authors.initials: L
authors.lastname: Deng
authors.forename: Jun
authors.initials: J
authors.lastname: Hu
authors.forename: Michael
authors.initials: M
authors.lastname: Ricardo
authors.forename: Sanqiang
authors.initials: S
authors.lastname: Pan
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Lu
authors.forename: Scott
authors.initials: S
authors.lastname: Wadsworth
authors.forename: John
authors.initials: J
authors.lastname: Siekierka
authors.forename: Raymond
authors.initials: R
authors.lastname: Birge
authors.forename: Hong
authors.initials: H
authors.lastname: Li
mesh_terms: D000818:Animals; D015153:Blotting, Western / Q000379:methods; D002454:Cell Differentiation / Q000187:drug effects / Q000502:physiology*; D019295:Computational Biology / Q000379:methods; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D005727:Ganglia, Spinal / Q000166:cytology; D051379:Mice; D008810:Mice, Inbred C57BL; D020932:Nerve Growth Factor / Q000494:pharmacology; D016501:Neurites / Q000187:drug effects / Q000378:metabolism*; D009474:Neurons / Q000166:cytology / Q000187:drug effects / Q000502:physiology*; D040901:Proteomics / Q000379:methods*; D016559:Tacrolimus / Q000031:analogs & derivatives / Q000494:pharmacology; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: C485833:JNJ460; D020932:Nerve Growth Factor; D016559:Tacrolimus