Convergent transcriptomics and proteomics of environmental enrichment and cocaine identifies novel therapeutic strategies for addiction

Yafang Zhang, Elizabeth J. Crofton, Xiuzhen Fan, Dingge Li, Fanping Kong, Mala Sinha, Bruce A. Luxon, Heidi Spratt, Cheryl F. Lichti, Thomas Green

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Transcriptomic and proteomic approaches have separately proven effective at identifying novel mechanisms affecting addiction-related behavior; however, it is difficult to prioritize the many promising leads from each approach. A convergent secondary analysis of proteomic and transcriptomic results can glean additional information to help prioritize promising leads. The current study is a secondary analysis of the convergence of recently published separate transcriptomic and proteomic analyses of nucleus accumbens (NAc) tissue from rats subjected to environmental enrichment vs. isolation and cocaine self-administration vs. saline. Multiple bioinformatics approaches (e.g. Gene Ontology (GO) analysis, Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA)) were used to interrogate these rich data sets. Although there was little correspondence between mRNA vs. protein at the individual target level, good correspondence was found at the level of gene/protein sets, particularly for the environmental enrichment manipulation. These data identify gene sets where there is a positive relationship between changes in mRNA and protein (e.g. glycolysis, ATP synthesis, translation elongation factor activity, etc.) and gene sets where there is an inverse relationship (e.g. ribosomes, Rho GTPase signaling, protein ubiquitination, etc.). Overall environmental enrichment produced better correspondence than cocaine self-administration. The individual targets contributing to mRNA and protein effects were largely not overlapping. As a whole, these results confirm that robust transcriptomic and proteomic data sets can provide similar results at the gene/protein set level even when there is little correspondence at the individual target level and little overlap in the targets contributing to the effects.

Original languageEnglish (US)
Pages (from-to)254-266
Number of pages13
JournalNeuroscience
Volume339
DOIs
StatePublished - Dec 17 2016

Fingerprint

Cocaine
Proteomics
Proteins
Self Administration
Messenger RNA
Therapeutics
Genes
Peptide Elongation Factors
rho GTP-Binding Proteins
Gene Ontology
Ubiquitination
Nucleus Accumbens
Glycolysis
Computational Biology
Ribosomes
Adenosine Triphosphate

Keywords

  • addiction
  • cocaine
  • environmental enrichment
  • proteomics
  • self-administration
  • transcriptomics

ASJC Scopus subject areas

  • Neuroscience(all)

Cite this

Convergent transcriptomics and proteomics of environmental enrichment and cocaine identifies novel therapeutic strategies for addiction. / Zhang, Yafang; Crofton, Elizabeth J.; Fan, Xiuzhen; Li, Dingge; Kong, Fanping; Sinha, Mala; Luxon, Bruce A.; Spratt, Heidi; Lichti, Cheryl F.; Green, Thomas.

In: Neuroscience, Vol. 339, 17.12.2016, p. 254-266.

Research output: Contribution to journalArticle

Zhang, Yafang ; Crofton, Elizabeth J. ; Fan, Xiuzhen ; Li, Dingge ; Kong, Fanping ; Sinha, Mala ; Luxon, Bruce A. ; Spratt, Heidi ; Lichti, Cheryl F. ; Green, Thomas. / Convergent transcriptomics and proteomics of environmental enrichment and cocaine identifies novel therapeutic strategies for addiction. In: Neuroscience. 2016 ; Vol. 339. pp. 254-266.
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