Modelling cortical network development at the cellular scale and disruption by Mecp2 deficiency.

Lead Research Organisation: University of Cambridge
Department Name: Physiology Development and Neuroscience

Abstract

Disruption to the refinement of brain connectivity during early postnatal development can have profound effects on cognitive functions. In Rett syndrome, young girls develop normally for the first 6-18 months-of-age followed by regression of cognitive, language, social, sensory and motor abilities. In 95% of cases, Rett syndrome is caused by loss-of-function mutations in the chromatin-remodeller MECP2 (Chahrour & Zoghbi, 2007). However, there are no treatments available for Rett syndrome, and further understanding of the neurophysiological consequences of MeCP2 deficiency is needed.
Mecp2-deficient mice also show regression of behavioural, sensory and motor function following an initially normal development. Thus, Mecp2-deficient mice provide a useful way of modelling pathological processes in order to identify innovative targets for treatment of Rett syndrome.
Electrophysiological recordings have previously shown cell-type specific effects of Mecp2 deficiency - inhibitory Parvalbumin-expressing (PV) cells develop prematurely whereas excitatory pyramidal neurons show delayed development (Mierau et al., 2016). This may contribute to disruption of the excitatory/inhibitory (EI) balance in the cortex during a critical developmental period (Goffin & Zhou, 2012). However, the downstream effects on network function are unknown.
The goal of my interdisciplinary PhD research will be to assess developmental network-level defects due to Mecp2 deficiency and how specific excitatory and inhibitory cells contribute to this pathology. To do this, I will record spontaneous activity in cultured cortical cells using MEAs before applying various computational methods for detecting spiking and bursting activity. Following this I will characterise the effects of Mecp2 deficiency in terms of more detailed network features including clustering, path length and small-world topology (derived from graph theory). I will then apply machine learning classification in order to determine the primary features of Mecp2-efficient networks. I have set the following aims:
1. Assess changes network measures (such as at sequential time points and compare this development between wild-type and Mecp2-deficient cultures. This will elucidate to how Mecp2 deficiency affects network-level parameters during development. I will include a comparison of different burst detection methods.
2. Compare the contribution of PV cell-mediated inhibition to the development of network connectivity in wild-type and Mecp2-deficicient cultures. I will employ an optogenetic approach using Mecp2-deficient mice that express a light-silencing channel (archaerhodopsin) selectively in PV cells. This will enable me to silence PV cells during MEA recordings and assess changes in network activity.
3. As Mecp2 deficiency accelerates PV cell maturation, the final aim will be to test whether preventing this process may recover network function by restoring the excitatory-inhibitory balance in the network. I will use chronic, intermittent silencing of PV cells through optogenetic manipulation.
I hypothesise that Mecp2-deficient cultures will show hyper-activity and hyper-connectivity. This may be shown by an reduced characteristic path length and an increased clustering coefficient. These findings would suggest that Mecp2 deficiency leads to a alterations in both local and global information-processing efficiency. Additionally, I hypothesise that optogenetic manipulations PV cells will show that decreasing PV cell activity alters neuronal activity such that overall network synchrony is reduced. Furthermore, chronic intermittent silencing of PV cells in Mecp2-deficient cultures may ameliorate these differences between Mecp2-deficient and wild-type cultures. This would have implications for the treatment of Rett Syndrome by suggesting premature PV cell activity as a target for therapeutic interventions.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
MR/N013433/1 01/10/2016 30/04/2026
2274263 Studentship MR/N013433/1 01/10/2019 30/09/2023 Alexander Dunn
 
Description Generative principles underpinning neocortical neuronal network topology in vitro 
Organisation ETH Zurich
Country Switzerland 
Sector Academic/University 
PI Contribution Conception of the overall project idea--applying generative model to cellular scale cortical networks; pilot study applying functional connectivity analyses from our group, combined with generative modelling analyses from MRC CBU group to recordings from ETH Zurich group. Designing of experiments to validate models e.g. using gabazine-treated cortical cultures of a given concentration at a specific time point and characterization of electrophysiological activity. Further running of generative models and creation of some figures or parts of figures for manuscript (final draft nearly ready to be submitted for preprint). Some manuscript section writing and reviewing of whole manuscript.
Collaborator Contribution Culturing of rodent and human iPSC cortical networks (ETH). Running of simulations (ETH and CBU). Creation of figures or parts of figures for manuscript (CBU and ETH). Statistical analyses (CBU and ETH). ETH carrying out all experiments, spike detection and spike sorting analyses. CBU doing most simulations, figure creation, statistical analyses and manuscript drafting.
Impact Multi-disciplinary--electrophysiology and computational modelling of networks. Outputs include insights into the utility of spike sorting, and improvement of generative modelling approach as it had to be adapted to ephys data. Insight into role of GABA in implementation of neuronal network developmental principles. Manuscript to be submitted for pre print in the next two months.
Start Year 2020
 
Description Generative principles underpinning neocortical neuronal network topology in vitro 
Organisation Medical Research Council (MRC)
Department MRC Cognition and Brain Sciences Unit
Country United Kingdom 
Sector Academic/University 
PI Contribution Conception of the overall project idea--applying generative model to cellular scale cortical networks; pilot study applying functional connectivity analyses from our group, combined with generative modelling analyses from MRC CBU group to recordings from ETH Zurich group. Designing of experiments to validate models e.g. using gabazine-treated cortical cultures of a given concentration at a specific time point and characterization of electrophysiological activity. Further running of generative models and creation of some figures or parts of figures for manuscript (final draft nearly ready to be submitted for preprint). Some manuscript section writing and reviewing of whole manuscript.
Collaborator Contribution Culturing of rodent and human iPSC cortical networks (ETH). Running of simulations (ETH and CBU). Creation of figures or parts of figures for manuscript (CBU and ETH). Statistical analyses (CBU and ETH). ETH carrying out all experiments, spike detection and spike sorting analyses. CBU doing most simulations, figure creation, statistical analyses and manuscript drafting.
Impact Multi-disciplinary--electrophysiology and computational modelling of networks. Outputs include insights into the utility of spike sorting, and improvement of generative modelling approach as it had to be adapted to ephys data. Insight into role of GABA in implementation of neuronal network developmental principles. Manuscript to be submitted for pre print in the next two months.
Start Year 2020
 
Title MEA spiking activity viewer 
Description Can open a micro electrode array recording and it will automatically detect spike times and plot the data for you, before doing complex graph analyses. The user has a GUI to change the settings. The app implementation was designed by Timothy Sit, our UCL collaborator. Based on code and ideas coming from Timothy and others in our group including myself. Trialed and tested by myself and others on data recorded by Susanna Mierau and myself. 
Type Of Technology Webtool/Application 
Year Produced 2021 
Impact New users of MEAs with little/no coding experience can view the nature of recordings instantaneously. 
URL https://spike-network-viewer.herokuapp.com/spike-network-viewer