Building blocks of molecular complexity: the neuronal cytoskeleton in health and disease

Lead Research Organisation: Birkbeck, University of London
Department Name: Biological Sciences

Abstract

Our brains are built from billions of specialised cells called neurons. The many complex tasks that our brains perform, including memory and thought, occur because neurons make connections with each other that allow them to communicate. Early in brain development, immature neurons are not connected to each other and must navigate to exactly the right position to correctly integrate into the brain's communication network. Healthy brain function throughout our lives depends on the connections between our neurons being well maintained. Severe human diseases can occur if neuron connectivity and operation breaks down at any stage: inaccurate neuron movement during brain development can cause epilepsy, intellectual disability and early death; incomplete maintenance of neuronal function as our brains mature into adulthood can cause neuropsychiatric illnesses including schizophrenia and mood disorders; and breakdown of neuronal function as we age can cause neurodegenerative disorders including amyotrophic lateral sclerosis and peripheral neuropathies. Work in my lab is seeking to understand the machinery that supports neuronal health during development and as we mature.

In the same way as our body has a skeleton that provides us with support and strength, neurons have a skeleton - called the cytoskeleton - which also gives them support and strength. The cytoskeleton is involved in many important aspects of neuronal life, and is part of the machinery that drives movement during development and maintenance of connectivity and signaling in mature neurons. Breakdown of the neuronal cytoskeleton is associated with developmental syndromes, neurodegenerative diseases and neuropsychiatric illness. Studying the cytoskeleton machinery is important so we can understand both how healthy neurons operate and how machinery malfunction causes disease.

This project will focus on a part of the cytoskeleton called microtubules. These are long cylindrical structures that act like scaffolding inside the neuron and also act as tracks along which molecular transport motors carry cargo within the neuron. The particular type of scaffolding and the particular type of cargo that is carried defines how the neuron functions. We would like to understand how the building blocks of this machinery are put together to help neurons undertake their many complex tasks within the brain. My research team studies the three-dimensional structure of microtubules, because knowing what they look like can help us understand how they work. We use a very powerful microscope called an electron microscope to take pictures of individual microtubules and then use computers to combine these pictures to calculate their three-dimensional shape. Using information from patients with diseases of the microtubule machinery, we will be able to locate disease-causing defects to particular machinery components.

In the future, this knowledge may allow us to target and repair the broken parts of the cytoskeleton machinery in diseased or damaged neurons. This could allow alleviation of symptoms associated with dementia, stroke and physical injury.

Technical Summary

The billions of neurons in the human brain require the microtubule (MT) cytoskeleton machinery to set up and maintain their diverse organisation and function. The importance of MTs for human health is reinforced because malfunction leads to diverse diseases of the nervous system. MTs are also critical in the context of brain repair therapies for treatment of physical injury or stroke. Investigation of the molecular operation and regulation of the MT cytoskeleton is thus essential to understand healthy neuronal diversity and function, and to characterise its disruption in disease. The aims of this research are to investigate the molecular building blocks of complexity in the neuronal MT machinery. We will dissect how heterogeneity in the MT subunits affects activities of MT-associated proteins and neuronal transport motors. We will investigate three families of important neuronal MT regulators - doublecortins, CAMSAPs, ensconsins - to elucidate the molecular mechanisms by which they regulate MTs and control cargo trafficking through interactions with motors. These components of the MT machinery will be reconstituted with increasing complexity to illuminate how their distinct molecular properties contribute to neuronal diversification and tuning. Cryo-electron microscopy enables unprecedented insight into cellular machinery and will be the major method used in the proposed research. Biochemical and biophysical assays will provide a functional context for our structural discoveries and allow us to test our hypotheses using protein engineering. To place our molecular discoveries in a cellular context, we will study the operation of the MT machinery in neurons using cryo-electron tomography. We will visualise the organisation of MTs in neurons and elucidate the impact of disruption of specific machinery components on them. Through this integrated programme of research, we will uncover regulatory mechanisms of the MT machinery with important implications for human health.

Planned Impact

Who will benefit from this research?
- Our academic and clinical project partners
- Patients with genetic disorders of neuronal development
- Patients with neuropsychiatric disorders
- Patients with brain damage due to mechanical injury, stroke or neurodegeneration
- UK economy
- The wider public
- Women in science

How will they benefit from this research?

The work described will lead to a greater understanding of essential mechanisms involved in human brain development, maintenance and repair. Disruption of components of the neuronal microtubule machinery cause human diseases including epilepsy, intellectual disability and peripheral neuropathy. Regularly sharing our findings with our academic and clinical partners will enable dissemination of our research and facilitate its scientific impact. The molecular insight that will arise from our studies will, first, contribute to improved diagnosis of particular syndromes associated with these diseases. There is emerging evidence that groups of symptoms cluster with particular types of mutations and our studies will provide greater clarity as to the molecular basis of these phenotypes. Once the molecular basis of these diseases are fully understood, novel treatments for these often devastating conditions can be contemplated. In the future, it is also hoped that the understanding that our work will bring concerning general mechanisms of neuronal development can be brought to bear on treatment of extremely common neurological phenomena such as brain injury, neurodegenerative diseases and stroke. I will engage charities working in this area - for example, Alzheimer's Society, Motor Neurone Disease Association, Mind, Stroke Association - as a route to engage with patient groups to talk about our research.

Science and technology is a key facet of global economy, and we will liaise with UCL Business (UCLB), who work with Birkbeck researchers on technology development and intellectual property matters, to maximise the impact of our discoveries. This will ultimately have benefits for the economic competitiveness of the UK. It is essential to retain talented young researchers in the UK, and the proposed research programme will provide an attractive research opportunity for excellent young scientists looking for multi-disciplinary and collaborative areas of discovery. In addition, transferable skills - such as time- and project management, presentation and collaboration, which can be applied in all employment sectors - will be acquired, particularly through transferable skills training within the Institute of Structural and Molecular Biology.

We will aim to make the discoveries of our research available not only to the academic community, but also to the general public. I have a proven track record of public communication of science. The appointed PDRAs and I will undertake to design web pages for my lab which are accessible for the general public and will seek to participate in other public understanding of science activities, for example by inviting sixth-form students to visit our lab and experience the day-to-day life of scientists. During the project period, I will arrange school visits to inspire future scientists by talking about the research in this programme. I will also work to advance gender equality in science, engineering and technology by targeting some of these impact actions in girls' schools.

Publications

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Title A microtubule RELION-based pipeline for cryo-EM image processing (MiRP) 
Description We created a pipeline designed for image processing and high-resolution reconstruction of cryo-electron microscopy microtubule datasets, based in the popular and user-friendly RELION image-processing package, Microtubule RELION-based Pipeline (MiRP). The pipeline uses a combination of supervised classification and prior knowledge about geometric lattice constraints in microtubules to accurately determine microtubule architecture and seam location. The presented method is fast and semi-automated, producing nearatomic resolution reconstructions with test datasets that contain a range of microtubule architectures and binding proteins. 
Type Of Material Model of mechanisms or symptoms - in vitro 
Year Produced 2019 
Provided To Others? Yes  
Impact Our image reconstruction procedures have been speeded up and are more robust. We know that others in the community have also tested our pipeline. 
URL https://github.com/moores-lab/MiRP
 
Title CAMSAP CKK MT models and reconstructions 
Description We deposited cryo-EM MT reconstructions and models generated in our Atherton et al, 2019, Nature Communications paper relating to the mechanism of CKK MT end recognition mechanism: The 13-protofilament and 14-protofilament HsCKK and NgCKK-MT models along with their corresponding electron density maps are deposited in the PDB. The PDB codes are as follows: 13-protofilament HsCKK-MT, PDB: 6QUS [https://www.rcsb.org/structure/6QUS], 14-protofilament HsCKK-MT, PDB: 6QVJ [https://www.rcsb.org/structure/ 6QVJ], 13-protofilament NgCKK-MT, PDB: 6QUY [https://www.rcsb.org/structure/6QUY], 14-protofilament NgCKK-MT, PDB: 6QVE [https://www.rcsb.org/structure/6QVE]. The EMDB codes (C1 reconstruction and symmetrised asymmetric unit) are as follows: 13-protofilament HsCKK-MT, EMDB-4643, 14-protofilament HsCKK-MT, EMDB-4654, 13-protofilament NgCKK-MT, EMDB-4644,14-protofilament NgCKKMT, EMDB-4650. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact We are not yet aware of any impact associated with these datasets. 
URL https://www.ebi.ac.uk/pdbe/emdb/empiar/
 
Title DCX MT models and reconstructions 
Description We deposited cryo-EM MT datasets calculated as part of the Manka and Moores NSMB publication in the publicly accessible EMDB and PDB databases: GMPCPP-DCX-MT (EMDB-3961, PDB 6EVW); GDP• Pi-DCX-MT (EMDB-3962, PDB 6EVX); GTP? S-DCX-MT (EMDB-3963, PDB 6EVY); GDP-DCX-MT (EMDB-3964, PDB 6EVZ); GDP-DCX-Taxol-MT (EMDB-3965, PDB 6EW0) 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Other researchers have used these data for further modelling of MT dynamics. 
URL https://www.ebi.ac.uk/pdbe/emdb
 
Title MT EMDB structure depositions 
Description We deposited cryo-EM MT reconstructions produced as part of the development of our MiRP tool in the publicly accessible EMDB database: 13 PF CKK-MT, EMD- 4643, 13 PF MKLP2-MT, EMD-10131 and 13 PF NDC-MT, EMD-10195 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact We are not yet aware of any impact associated with these datasets. 
URL https://www.ebi.ac.uk/pdbe/emdb
 
Title MT EMPIAR datasets 
Description We deposited cryo-EM MT datasets used in development of our MiRP tool in the publicly accessible EMPIAR database: CKK-MTs, code 465, MKLP2-MTs, code 467, NDC-MTs, code 10300. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact We are not yet aware of any impact associated with these datasets. 
URL https://www.ebi.ac.uk/pdbe/emdb/empiar/
 
Description Filmed a YouTube video about cryo-electron microscopy 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Following on from my BBC appearance, the Birkbeck External Relations team and I prepared a short YouTube video about cryo-electron microscopy ("What is Blobology?").
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=FIW18GmKzRA
 
Description Hosted class visit from local school 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact 30 pupils attended for a school visit to the research organisation, which sparked questions and discussions - both students and teachers spoke with us about the benefits of getting hands-on with equipment and elements of the scientific process, and also asked about opportunities available in higher education. We also discussed future joint activities.
Year(s) Of Engagement Activity 2019
 
Description Interview for local TV news 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Media (as a channel to the public)
Results and Impact BBC East Midlands sought an expert in cry-electron microscopy to appear on a local news segment - I went to Broadcasting House to record a short interview about this method.
Year(s) Of Engagement Activity 2019