A multiplexed proteomics approach to differentiate neurite outgrowth patterns

Tong Liu, Veera D'mello, Longwen Deng, Jun Hu, Michael Ricardo, Sanqiang Pan, Xiaodong Lu, Scott Wadsworth, John Siekierka, Raymond Birge, Hong Li

Research output: Contribution to journalArticleResearchpeer-review

13 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)22-29
Number of pages8
JournalJournal of Neuroscience Methods
Volume158
Issue number1
DOIs
StatePublished - 15 Nov 2006

Fingerprint

Nerve Growth Factor
Proteomics
Immunophilins
Organogenesis
Spinal Ganglia
Protein Biosynthesis
Proteome
Computational Biology
Ribosomes
Signal Transduction
Proteins
Ligands
JNJ460
Neuronal Outgrowth

Keywords

  • Immunophilin ligand
  • Mass spectrometry
  • Nerve growth factor
  • Proteomic pattern
  • SOM analysis
  • iTRAQ

Cite this

Liu, Tong ; D'mello, Veera ; Deng, Longwen ; Hu, Jun ; Ricardo, Michael ; Pan, Sanqiang ; Lu, Xiaodong ; Wadsworth, Scott ; Siekierka, John ; Birge, Raymond ; Li, Hong. / A multiplexed proteomics approach to differentiate neurite outgrowth patterns. In: Journal of Neuroscience Methods. 2006 ; Vol. 158, No. 1. pp. 22-29.
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Liu, T, D'mello, V, Deng, L, Hu, J, Ricardo, M, Pan, S, Lu, X, Wadsworth, S, Siekierka, J, Birge, R & Li, H 2006, 'A multiplexed proteomics approach to differentiate neurite outgrowth patterns', Journal of Neuroscience Methods, vol. 158, no. 1, pp. 22-29. https://doi.org/10.1016/j.jneumeth.2006.05.010

A multiplexed proteomics approach to differentiate neurite outgrowth patterns. / Liu, Tong; D'mello, Veera; Deng, Longwen; Hu, Jun; Ricardo, Michael; Pan, Sanqiang; Lu, Xiaodong; Wadsworth, Scott; Siekierka, John; Birge, Raymond; Li, Hong.

In: Journal of Neuroscience Methods, Vol. 158, No. 1, 15.11.2006, p. 22-29.

Research output: Contribution to journalArticleResearchpeer-review

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AU - D'mello, Veera

AU - Deng, Longwen

AU - Hu, Jun

AU - Ricardo, Michael

AU - Pan, Sanqiang

AU - Lu, Xiaodong

AU - Wadsworth, Scott

AU - Siekierka, John

AU - Birge, Raymond

AU - Li, Hong

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N2 - 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.

AB - 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.

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