Multiscale Computational Tools for Optogenetics

Optogenetics is a new tool in which light-sensitive ion channels ('opsins') are genetically inserted into cell membranes. This allows for the precise spatial and temporal optical stimulation of excitable cells such as neural ensembles, as well as modulation of signalling cascades, and has numerous applications which are only beginning to be explored. Apart from becoming a key technology for neuroscience and deconstruction of brain circuits, applications are rapidly emerging throughout biology: e.g. control of cardiac cells, sensing and monitoring cellular activities, optical control of cell signalling pathways, using light to destroy proteins and cells [1] etc. The field of optogenetics has the potential to be one of the most important new techniques for many years and it was declared the Method of the Year for 2010 by Nature Methods [2].

There are several families of opsins, each of which has unique temporal and spectral properties. There is a substantial effort to characterize opsins for each cell population, and a continual drive to improve their efficacy. While the effect of an opsin can be quantified at the level of individual cells (e.g. neurons), it currently remains practically impossible to experimentally test each opsin for each cell type or biological system of interest. This significantly limits the effectiveness of optogenetics as a biological tool.

The aim of this project is to develop multiscale computational tools for optogenetics. Firstly, we will develop a tool for characterizing opsins, allowing us to link from the underlying biophysical photocycle that defines kinetic model of opsins (molecular-complex scale). Consequently this will allow us to obtain a functional understanding of each opsin and hence guide not only opsin choice for a given system, but potentially also guide opsin development. Secondly, we will build software to transform the biophysical model into computational formats for use in commonly used neural simulation tools. This will be done at the levels of single cell/compartment and cell networks. This will allow the inclusion of realistic models of optogenetics in existing simulations, allowing the use of virtual opsins to identify the correct experimental opsin choice. Together, these tools will improve the use of optogenetics as an effective and refined tool, enabling its potential to transform the biological sciences.

This project will deliver three software packages:
1. Software that when given current and voltage traces of system, will generate kinetic state-model.
2. Software modules for implementation of opsins in NEURON platform.
3. Software module for description of opsin in a point neuron scheme implemented in NEST.

Methodology:
1. Modelling of opsin kinetics. The dynamics of the ChR2 photocurrents can be accurately reproduced using a four-state kinetic model. We plan to expand this approach to all other opsins and describe their photocycles with an N-state functional model. The dynamics of this process can be described with a set of linear, non-stationary rate equations.

2. Modelling of opsin currents. Hodgkin-Huxley paradigm of neuronal simulation will be used. The photocurrent will be expressed as a function of light intensity (L), time (t) and membrane voltage (V).

3. Characterisation of opsin kinetics. On the bases of the input illumination parameters and the measured photocurrent traces in the voltage clamp arrangement a set of values for the transition rate coefficients will be established through curve fitting and optimization process. For the points 1-3 we will use MATLAB.

4. NEURON platform implementation. Each opsin model will be implemented in NEURON via a new mechanism called opsin.mod. The concrete mechanism of implementation will be as a POINT PROCESS module with an ELECTRODE CURRENT. The rate equation scheme that describes opsin's photocycle has a very simple description in the KINETIC block of NEURON.

5. NEST platform implementation. For network level suites, the so-called point neuron models will be considered and appropriate simplified model version of opsins will be developed which will be compatible with NEST platform first.

6. Validation. The proposed software tools will be tested and validated using the experimental results for ChR2 and ArchT from experiments to be conducted at the Simon Schultz lab (Co-I).

The first circle of beneficiaries will be the project participants and other colleagues at Imperial working in the area of optogenetics, neurosciences and traumatic brain injury. At the moment we collaborate within a Network of Excellence funded by the Wellcome Trust Institutional Strategic Support Fund. Specifically this network was built around the theme of optogenetic manipulation of injured neural circuits and apart from the PI and Co-I of this project participants are Prof William Wisden (Life Sciences), Dr Vicenzo De Paola (Medicine) and Dr Daniel Sharp (Medicine).

The proposed computational tools will have an immediate impact on the academic community engaged in the development and applications of optogenetics. There are more than a hundred groups around the world which currently use optogenetics in their research. The specific beneficiaries and how they will benefit are listed in the Academic beneficiaries section.

There will also be a strong impact on the careers of the researchers involved as well as for the Institute of Biomedical Engineering and Imperial College in further developing, strengthening and consolidating its position in the optogenetics area with particular emphasis on computational modelling and neurotechnology applications, such as retinal prosthesis. This project has the potential to significantly support the development of a new generation of retinal implants, which is of strategic importance to us. The long term impact is the potential to enhance quality of life and health of blind people. Recently several groups (including us) have started to investigate the idea of using optogenetics for a retinal prosthesis by targeted expression of ChR2 in retinal ganglion cells or NpHR in photoreceptors (somas often remain functional although the outer segment degenerates causing blindness). In order to create a complete system we need to engineer an illumination system and for that purpose it is instrumental to have some simulation tool to calculate the light pulses' duration and intensity. We have two patent applications regarding such a system and in both cases the system design relies on computational optogenetics.

Optical neural stimulation pushes the boundaries of fusing engineering with biology and the results will be groundbreaking, potentially finally bringing implantable stimulation into mainstream medicine. This will offer a breakthrough in the treatment of serious medical conditions affecting a significant number of people globally, such as treatment-resistant epilepsy, Parkinson's disease, severe obesity and clinical depression, which are considered to be practically incurable today. We note here that this would be a long term goal since optogenetics relies on the gene technology which is still not developed for human subject in the case of microbial opsins. Anyway our research and developed tools could have significant impact in the area of neural prostheses, so the targeted long term beneficiaries will be disabled people, in particular those who suffer from deafness, blindness, or balancing problems, as well as the people with severe types of depression or Parkinson's disease.

To ensure that the potential beneficiaries have the opportunity to benefit from this research we will: (a) make the developed computational tools publicly available (NEURON DB and our web site), (b) publish the results and present at conferences, and communicate with our external collaborators specified in the track record, (c) make contacts with leading neural prosthesis design and manufacturing firms, to discuss the potential use of the techniques (more in the pathways to Impact document).