Virtual presynaptic nerve terminal: a computational tool for studying synaptic transmitter release in health and disease

Synaptic transmission forms the basis of neuronal communication in the brain. When an action potential invades a presynaptic structure (known as a bouton or terminal) it depolarises the presynaptic membrane, which activates Ca2+ channels leading to an influx of Ca2+ ions into the nerve terminal. This Ca2+ influx triggers fast fusion of synaptic vesicles (SV) filled with neurotransmitters. Neurotransmitters quickly diffuse towards the postsynaptic neuron, where they bind to specific receptors and evoke further electrical and/or chemical signalling. The efficiency of the whole process is ensured by the precise timing of the Ca2+ signal and SV fusing. Although the general molecular mechanism of transmitter release is well established, the precise regulation of vesicular release process at different synapses remains incompletely resolved.
The main difficulty studying this regulation at the level of single synapses is that the majority of presynaptic boutons in the brain are very small, and as a result the experimental techniques are confronted with serious limitations. Data-constrained realistic computational models of presynaptic structures are therefore essential tools that allow one to complement the limitations of experimental approaches and to quantitatively predict the behaviour of nerve terminals during physiological neuronal activity. At present, the use of computational models is impeded because of the absence of a unified modelling framework of the presynaptic terminal that would allow research laboratories with limited mathematical/computational expertise to implement a realistic model for their experimental data.
In this project we propose to develop such a unified computational framework model of a presynaptic terminal, which will allow the neuroscience community to explore mechanisms of Ca2+-driven transmitter release that cannot be directly determined experimentally. We will use the powerful software platform Virtual Cell (http://vcell.org/) for implementing and simulating our three-dimensional computational model. The model will include the key functional presynaptic elements that are known to be important in shaping transmitter release dynamics.
Different types of synapses in the central nervous system have diverse structural and molecular organisation that leads to their distinct functional properties. During the project we will apply our implemented framework to investigate a number of scientific questions in collaboration with a group of world-leading experimental laboratories (end-users) both in the UK and abroad. In particular, we will adapt our computational framework to model several canonical synapse-types and then will systematically study how individual presynaptic elements regulate synaptic transmitter release both in health and disease. Models in each project will be constrained and tuned using existing and novel experimental data from the end-user laboratories.
We anticipate that our results will provide novel quantitative insights into the regulation of transmitter release and will have an immediate impact in facilitating the experimental work in the end-user laboratories. We will also apply the developed models to investigate in silico the mechanisms of presynaptic bouton dysfunctions in collaboration with clinical and experimental colleagues in UCL Queen Square Institute of Neurology. In particular, we will focus on presynaptic channelopathies - episodic neurological disorders caused by mutations in presynaptic ion channels (including some forms of migraine, epilepsy and ataxias). At the end of the project, our validated computational framework will be released to the public domain for the research community together with a user-friendly manual explaining how individual modelling blocks can be run, linked, and modified to address a particular research question. This will provide a powerful resource for other experimental laboratories, particularly the ones that lack modelling expertise.

The principal difficulty in studying the regulation of transmitter release is that the majority of presynaptic boutons in the brain are small (~1 micron, comparable to the diffraction limit of conventional optical microscopy ~300 nm). Data-constrained realistic computational models of presynaptic terminals are therefore essential tools that bypass the limitations of experimental approaches. Here we propose to develop a unified framework to model presynaptic terminal function, which will allow neuroscientists to explore the mechanisms of Ca2+-driven transmitter release that cannot be directly determined experimentally. We will incorporate in the model the following key functional presynaptic elements: (i) the morphological structure of a presynaptic terminal (3D geometry, distributions of voltage-gated calcium channels (VGCCs) and release ready synaptic vesicles (SVs)); (ii) pre-defined VGCC kinetic models; (iii) Ca2+ diffusion, buffering and extrusion mechanisms; (iv) intracellular Ca2+ stores (v) Ca2+ activation of SV exocytosis and replenishment. During the project, we will collaborate with a group of world-leading laboratories specialising in synaptic physiology. This will allow us to develop experimentally constrained models of several canonical presynaptic terminals and to investigate how the complex interplay among distinct functional presynaptic components regulates transmitter release and use-dependent plasticity in different synapses. We will also use the model to investigate in silico the mechanisms of presynaptic channelopathies, with a particular focus on some forms of migraine, epilepsy and ataxias caused by mutations in presynaptic Cav2.1 (P/Q-type) VGCCs and Kv1.1 potassium channels. We anticipate that the release of the unified presynaptic model to the public domain will provide a powerful, currently unavailable resource, which will facilitate experimental research in the field of synaptic physiology.

(1) Impact to general knowledge. An important step towards gaining insights into both normal and abnormal physiological brain functions involves understanding the precise regulation of transmitter release and synaptic plasticity in diverse types of central synapses. Therefore, our study, which is focused on the development of novel computational tools for neurophysiologists to be used for understanding synaptic function, has the potential for major long-term impacts on human well-being. The project will produce direct impact by: (i) providing the scientific communities of experimentalists and theoreticians with a unified computational framework which will allow them to explore mechanisms of Ca2+-driven transmitter release that cannot be directly determined experimentally; (ii) generating fundamental scientific knowledge about Ca2+-driven transmitter release mechanisms in health and disease. The immediate beneficiaries will be synaptic physiologists from the laboratories of our primary end-users involved in the project and from other experimental groups, as well as computational neuroscientists interested in realistic, experimentally constrained spatial models. We plan to support this computational resource beyond the duration of the grant and thereby we expect to see more end-users starting to utilise it in their research laboratories. Therefore we anticipate that this project will have a long-term gradually increasing impact on the research programmes of the aforementioned beneficiaries.

(2) Potential clinical and patient impact. We anticipate that this project has the potential to have a significant long-term impact on the development of new treatments for paroxysmal neurological disorders. Ion channels underlie neuronal excitability and all brain activity. Although they are implicated in the manifestations of almost all neurological and neuropsychiatric diseases, the most direct evidence for the pathophysiological importance of ion channels comes from genetic mutations that disrupt their normal function (channelopathies). Channelopathies are known to cause a range of neurological disorders including migraine, cerebellar ataxia and epilepsy. An important step toward our understanding of the mechanisms of these diseases (and subsequently developing new treatments) is in deciphering how particular channelopathies disrupt neurotransmission in different types of synapses. Thus, our computational framework represents an ideal tool for exploring channelopathies through in-silico experiments. In particular, one of the goals of this project is to investigate the mechanisms of two important channelopathies that affects presynaptic signalling: Familial Hemiplegic Migraine Type 1 and Episodic Ataxia Type 1. We anticipate that the use of our model will provide unparalleled insights into the understanding of these diseases and also other types of paroxysmal neurological disorders, most notably epilepsy and migraine. Epilepsy has a prevalence of 4-10 in 1000 people and accounts for 20% of all neurological consultations, and it is increasingly believed that idiopathic forms of this group of diseases are caused in large part by polygenic ion channel disturbances. Migraine affects 10% of the population, and represents a major burden to society and to the individual.

(3) Skills for staff on project. The involved staff (a PDRA and a PhD student funded by the Department of Computer Science at Warwick) will gain extremely valuable experience in mathematical modelling, computational implementation, data- driven model validation, and systematic investigation of complex multi-scale presynaptic mechanisms, combined with interdisciplinary and exposure to advanced experimental techniques. We anticipate that the skills earned during this project will make the involved researchers especially competitive for future positions.