Identification of Novel Signal Transduction, Immune Function, and Oxidative Stress Genes and Pathways by Topiramate for Treatment of Methamphetamine Dependence Based on Secondary Outcomes

Abstract

Background: Topiramate (TPM) is suggested to be a promising medication for treatment of methamphetamine (METH) dependence, but the molecular basis remains to be elucidated.

Methods: Among 140 METH-dependent participants randomly assigned to receive either TPM (N = 69) or placebo (N = 71) in a previously conducted randomized controlled trial, 50 TPM- and 49 placebo-treated participants had a total 212 RNA samples available at baseline, week 8, and week 12 time points. Following our primary analysis of gene expression data, we reanalyzed the microarray expression data based on a latent class analysis of binary secondary outcomes during weeks 1-12 that provided a classification of 21 responders and 31 non-responders with consistent responses at both time points.

Results: Based on secondary outcomes, 1,381, 576, 905, and 711 differentially expressed genes at nominal P values < 0.05 were identified in responders versus non-responders for week 8 TPM, week 8 placebo, week 12 TPM, and week 12 placebo groups, respectively. Among 1,381 genes identified in week 8 TPM responders, 359 genes were identified in both week 8 and week 12 TPM groups, of which 300 genes were exclusively detected in TPM responders. Of them, 32 genes had nominal P values < 5 × 10^-3 at either week 8 or week 12 and false discovery rates < 0.15 at both time points with consistent directions of gene expression changes, which include GABARAPL1, GPR155, and IL15RA in GABA receptor signaling that represent direct targets for TPM. Analyses of these 300 genes revealed 7 enriched pathways belonging to neuronal function/synaptic plasticity, signal transduction, inflammation/immune function, and oxidative stress response categories. No pathways were enriched for 72 genes exclusively detected in both week 8 and week 12 placebo groups.

Conclusion: This secondary analysis study of gene expression data from a TPM clinical trial not only yielded consistent results with those of primary analysis but also identified additional new genes and pathways on TPM response to METH addiction.

Keywords: clinical trial; gene expression profiling; methamphetamine dependence; microarray analysis; topiramate.

Figure 1

Volcano plots depicting log₂(Fold Change) (x-axis) and −log₁₀(P value) (y-axis) for genes of (A) week 8 topiramate (TPM) and (B) week 12 TPM groups. Genes with 0.01 ≤ P values < 0.05 and P values < 0.01 were shown by green and red colors, respectively. Five most statistically significant genes for each group were shown in pink color. Genes with P values < 5 × 10⁻³ and |Fold Change|s > 1.40 for both week 8 and week 12 TPM groups were underlined, and shown in blue color [except in (B), SASH1 was shown in pink color, because this gene was among top five]. For each group, if a gene was detected by both ordinary Student’s t-test and empirical Bayes moderated t-test at a nominal P value < 0.05, that gene’s corresponding symbol was highlighted in bold font. (A) ITGB5 is not in bold font, and all other gene symbols were in bold font; (B) SASH1 and PML are not in bold font, and all other gene symbols were in bold font.

Figure 2

Enriched PI3K/AKT signaling pathway, identified by Ingenuity Pathway Analysis based on 300 differentially expressed genes (nominal P values < 0.05) detected exclusively in both week 8 and week 12 topiramate (TPM) groups. Symbols with a single border indicate single genes. Those with a double border indicate complexes of genes or the possibility that alternative genes might act in the pathway. Red color symbols indicate upregulated gene clusters, and green color symbols represent downregulated gene clusters. At both time points, GYS1, HSP90B1, NFKBIE, PPP2R5D, RRAS, and TP53 were consistently downregulated, and PTEN was consistently upregulated. If a gene was detected by both the ordinary Student’s t-test and the empirical Bayes moderated t-test in either the week 8 TPM group or week 12 TPM group, that gene’s corresponding symbol was highlighted in bold font.

Figure 3

Molecular interaction network revealed by Ingenuity Pathway Analysis detected exclusively for both week 8 and week 12 topiramate (TPM) groups. Solid lines represent direct interactions, and dashed lines represent indirect interactions, with or without filled arrows indicating functional interaction or physical association, respectively. A line with a terminal bar indicates inhibition, whereas filled arrows that are preceded by a terminal bar indicate inhibition as well as functional interaction. Each node’s shape indicates the class of molecule: horizontal ovals are transcription regulators, vertical rectangles are G-protein-coupled receptors, triangles are phosphatases, inverted triangles are kinases, horizontal diamonds are peptidases, double circles are complexes/groups, and single circles are other types of biological molecules. Lines starting and finishing on the same node indicate self-regulation. Arrowheads indicate the directionality of relationship. Nodes are colored according to extent of differential expression, with up- and downregulation represented by red and green colors, respectively. For each group, if a gene was detected by both ordinary Student’s t-test and empirical Bayes moderated t-test at a nominal P value < 0.05, that gene’s corresponding symbol was highlighted in bold font. (A) Week 8 TPM (CENTA1, CHST14, CTDSPL, CTNND1, DTX1, DVL3, MAFK, NFIC, POU2AF1, PSMD1, and TCF3 were downregulated and BPGM, CSNK1A1, CXCR4, MAPK14, PLEKHF2, PSMB2, PTEN, and SRPK1 were upregulated, respectively); and (B) week 12 TPM (CENTA1, CHST14, CTNND1, DTX1, DVL3, MAFK, NFIC, POU2AF1, PSMB2, PSMD1, and TCF3 were downregulated and BPGM, CSNK1A1, CTDSPL, CXCR4, MAPK14, PLEKHF2, PTEN, and SRPK1 were upregulated, respectively).

Figure 4

An integrated model of biological pathways related to topiramate (TPM) treatment for methamphetamine (METH) addiction. The joint effects of TPM and METH act on several molecular pathways that eventually lead to modulations of neuroplasticity and neurotoxicity/neurodegeneration, which results in abstinence and reduction of METH use. Pathways enriched exclusively in TPM responder groups at weeks 8 and 12 are highlighted in gray.