Analyzing The Pathways And Protein-protein Interaction Network Related To Nicotine Addiction

Objective: Nicotine is the major addictive substance in tobacco and it has broad effects on the central nervous system. Emerging evidence suggests that nicotine can alter the expression status of multiple molecular and biochemical pathways. However, the molecular mechanisms underlying nicotine addiction remain largely unclear. In this study, through using pathway enrichment and protein-protein interaction network(PPIN) analysis, we performed a systematic analysis on 220 nicotine addiction-related candidate genes(NAGenes) to identify the major signal pathways in the process of nicotine addiction, construct and analyze the PPIN associated with NAGenes, thereby made the foundation for understanding and constructing the molecular mechanisms underlying nicotine addiction.Methods: 1. Data source. In this study, 220 NAGenes were obtained via a multi-sourcebased gene prioritization approach. 2. GO enrichment analysis. Web Gestalt was used to identify the GO terms enriched in NAGenes, then the functional annotation clusters were determined by DAVID to comprehensively understand the major biological processes enriched in NAGenes. 3. Pathway and pathway crosstalk analysis. The significantly enrichment pathways were detected by IPA, then observing the interactions among significantly enriched pathways by crosstalk analysis, and visualizing the results using the software Cytoscape. 4. PPIN analysis. Calculate the global network topological measurements related to nicotine addiction to evaluate its topological properties and perform clustering analysis to intuitively observe the major biological functions included in the network. 5. Nicotine addiction-specific subnetwork. The subnetwork was extracted via the Steiner minimal tree algorithm and some new potential genes could be identified through the subnetwork.6. Nicotine addiction molecular network. A schematic molecular network was constructed for nicotine addiction via integrating the results from pathways and PPIN analysis.Results: 1. GO enrichment analysis. Multiple biological processes associated with neurodevelopment or synaptic transmission and molecular functions like ion channels activity or neurotransmitters activity were significantly enriched in NAGenes, such as synaptic transmission, transmission of nerve impulse, excitatory extracellular ligand-gated ion channel activity and neuron projection. 2. Pathway and pathway crosstalk analysis. These pathways related to neurotransmission system, immune system and metabolic process were significantly overrepresented for NAGenes, e.g., monoamine neurotransmitter receptors signaling, c AMP-mediated signaling, calcium signaling, G-protein coupled receptor signaling, synaptic long term potentiation/depression and dopamine degradation. Moreover, three pathways associated with retinoid X receptor(RXR), i.e., LPS/IL-1 mediated inhibition of RXR function, PXR/RXR activation and LXR/RXR activation, were also enriched in NAGenes. In addition, we found the circadian rhythm signaling was also in the enriched pathway list, supporting that there might be a link between nicotine addiction and abnormal or disrupted circadian rhythms. 3. PPIN analysis and the construction of nicotine addiction-specific subnetwork. As indicated by the results, the degree distributions of NAGenes were right-skewed in the context of human PPIN. Compared with alcohol addiction-related genes and cancer genes, the topological parameters(i.e., degree, clustering coefficient and closeness centricity) of NAGenes tended to be lower or more moderate, and the eccentricity centricity was opposite. Through the subnetwork analysis, we also found some novel promising genes such as CALM2, CAV1, CANX and PPP1 CA. 4. Molecular network of nicotine addiction. In the molecular network we constructed, we found some novel genes or pathways, e.g., MAPK, NF-κB, NF-κB signaling and MAPK signaling pathways. In addition, some feedback loops were also included in the molecular network and some loops interlinked with each other through Ca M and CAMKII.Conclusions: 1. The molecular mechanisms of nicotine addiction are extremely complex. The expression status of many genes would be altered when repeated exposure to nicotine, then such alteration mediated the biological processes related to neurotransmission, immune and metabolic and ultimately evoked the functional changes of nervous system. 2. Compared with alcohol addiction-related genes and cancer genes, NAGenes tended to be lower or moderate connections, might be less connected with each other and were more likely to be located at the margin of the PPIN. 3. Ca M and CAMKII played important roles in the induction of long term potentiation/depression, so they could be served as the potential targets in nicotine addiction irreversible characteristics research. 4. The results from our work provided valuable information for our construction of the molecular mechanisms underlying nicotine addiction and also suggested that the analysis methods we applied provided an efficient path to explore the molecular mechanisms of complex diseases.