A multiplexed proteomics approach to differentiate neurite outgrowth patterns.
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.
Liu
Tong
T
Center for Advanced Proteomics Research and Department of Biochemistry and Molecular Biology, UMDNJ-New Jersey Medical School, MSB E-609, Newark, NJ 07103, USA.
D'mello
Veera
V
Deng
Longwen
L
Hu
Jun
J
Ricardo
Michael
M
Pan
Sanqiang
S
Lu
Xiaodong
X
Wadsworth
Scott
S
Siekierka
John
J
Birge
Raymond
R
Li
Hong
H
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
C485833:JNJ460; D020932:Nerve Growth Factor; D016559:Tacrolimus