In Silico Model-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology

Abstract

Objective: Deficient brain-derived neurotrophic factor (BDNF) is one of the important mechanisms underlying the neuroplasticity abnormalities in schizophrenia. Aberration in BDNF signaling pathways directly or circuitously influences neurotransmitters like glutamate and gamma-aminobutyric acid (GABA). For the first time, this study attempts to construct and simulate the BDNF-neurotransmitter network in order to assess the effects of BDNF deficiency on glutamate and GABA.

Methods: Using CellDesigner, we modeled BDNF interactions with calcium influx via N-methyl-D-aspartate receptor (NMDAR)- Calmodulin activation; synthesis of GABA via cell cycle regulators protein kinase B, glycogen synthase kinase and β-catenin; transportation of glutamate and GABA. Steady state stability, perturbation time-course simulation and sensitivity analysis were performed in COPASI after assigning the kinetic functions, optimizing the unknown parameters using random search and genetic algorithm.

Results: Study observations suggest that increased glutamate in hippocampus, similar to that seen in schizophrenia, could potentially be contributed by indirect pathway originated from BDNF. Deficient BDNF could suppress Glutamate decarboxylase 67-mediated GABA synthesis. Further, deficient BDNF corresponded to impaired transport via vesicular glutamate transporter, thereby further increasing the intracellular glutamate in GABAergic and glutamatergic cells. BDNF also altered calcium dependent neuroplasticity via NMDAR modulation. Sensitivity analysis showed that Calmodulin, cAMP response element-binding protein (CREB) and CREB regulated transcription coactivator-1 played significant role in this network.

Conclusion: The study presents in silicoquantitative model of biochemical network constituting the key signaling molecules implicated in schizophrenia pathogenesis. It provides mechanistic insights into putative contribution of deficient BNDF towards alterations in neurotransmitters and neuroplasticity that are consistent with current understanding of the disorder.

Keywords: Brain-derived neurotrophic factor; Computer simulation; Neuronal plasticity; Neurotransmitter agents; Schizophrenia; Signal transduction.

Fig. 1

Important components of the brain-derived neurotrophic factor (BDNF) network. Major conceptual components are shown. The nodes colored in red represent entities reported to be altered in schizophrenia. Edges represent interactions between the nodes and flow of signals, initiated by BDNF. TrkB, tropomycin-related kinase; AKT, protein kinase B; NMDAR, N-methyl-D-aspartate receptor; PLC, phoshpholipase C; GABA, gamma-aminobutyric acid; CAM-II, Ca²⁺/calmodulin-dependent protein kinase II; CREB, cAMP response element-binding protein.

Fig. 2

Workflow of the study methodology. (A) Multiple databases like Panther pathway, Reactome and BioModels were used for building model sub-components. (B) System Biology Markup Language (SBML) squeezer was used to generate the kinetic laws. Initial values were defined from BioGPS database. (C) The SBML model was imported in COPASI. Global constants were defined from BRENDA and DOQCS. Unavailable values were optimized after assigning parameters and defining ordinary differential equations. Analyses included steady state stability, perturbation time-course simulation and sensitivity analysis.

Fig. 3

Network fabricated in CellDesigner. Components of the modeled network were (A) calcium influx: Ca2+ influx and NMDAR activation by glutamate and brain-derived neurotrophic factor (BDNF); activation of CREB pathway by triggering calmodulin. (B) Protein kinase B/AKT pathway: Regulates apoptosis, stimulates cell cycle regulatory molecules and promotes gamma-aminobutyric acid (GABA) synthesis via AKT pathway. (C) Glutamate formation: Formation via glutminase and activation of glutamate transport via BDNF-tropomycin-related kinase B (TrkB) mediated PLC-γ pathway. (D) GABA formation: Conversion of glutamate to GABA via β-catenin and glutamic acid decarboxylase (GAD) 67; transportation of GABA via BDNF-TrkB interaction with VGAT. NMDAR, N-methyl-D-aspartate receptor; CREB, cAMP response element-binding protein; AKT, protein kinase B; PLC, phospholipase C; VGAT, vesicular GABA transporter.

Fig. 4

Time course plot for gamma-aminobutyric acid (GABA). Short term effect of brain-derived neurotrophic factor (BDNF) on GABA: time course of 100 seconds with 5,000 intervals of 0.02 seconds depicted on log scale. *Activated; red arrow, inhibition; green arrow, activation. TrkB, tropomycin-related kinase B; AKT, protein kinase B; GSK3-β, glycogen synthase kinase 3; CTNNB1, catenin beta-1; GAD67, glutamic acid decarboxylase 67.

Fig. 5

Time course plot for gluamate. Short term effect of brain-derived neurotrophic factor (BDNF) on glutamate: time course of 100 seconds with 5,000 intervals of 0.02 seconds depicted on log scale. *Activated; green arrow, activation. TrkB, tropomycin-related kinase B; PLC, phopholipase C; VGLUT, vesicular glutamate transporter.

Fig. 6

Effects of brain-derived neurotrophic factor (BDNF) perturbations. Time course plots on log-linear scale at varying BDNF concentrations for (A) PLC-γ, (B) AKT, (C) glutamate in GABAergic cell, (D) glutamate in glutamatergic cell, (E) GABA extracellular, and (F) AKT for 100 seconds with 5,000 intervals of 0.02 seconds. Colors of the lines from dark to light pink correspond to the percentage of initial BDNF concentration with respect to database derived expression levels in temporal lobe, i.e., 100%, 75%, 50%, and 10% respectively. PLC, phospholipase C; AKT, protein kinase B; GABA, gamma-aminobutyric acid; NMDAR, N-methyl-D-aspartate receptor.

Fig. 7

Sensitivity analysis. Bar plot of the sensitivity analysis: x axis displays the species and y axis shows sensitivity. In addition to BDNF-TrkB, calcium, calmodulin, CRTC1 and CREB show high sensitivity. AKT, protein kinase B; BDNF, brain-derived neurotrophic factor; CAM2, Ca²⁺/calmodulin-dependent protein kinase II; CREB, cAMP response element-binding protein; CRTC1, CREB-regulated transcription coactivator 1; CTNNB1, catenin beta-1; GAD67, glutamic acid decarboxylase 67; GSK3, glycogen synthase kinase 3; NMDAR, N-methyl-D-aspartate receptor; PIP2, phosphatidylinositol 4,5-bisphosphate; PLC, phospholipase C; PPP3, protein phosphatase 3; TrkB, tropomycin related kinase B; vGAT, vesicular GABA transporter; VGLUT, vesiccular glutamate transporter.