Understanding how PAR proteins cooperate to establish cell polarity (New Investigator)

Lead Research Organisation: Newcastle University
Department Name: Biosciences Institute

Abstract

To generate an organism from an initially symmetric one-cell embryo, cells divide and lose their initial symmetry, acquiring structural and functional differences through a process termed cell polarisation. A crucial step in the polarisation of animal cells is the distribution of conserved polarity effectors to discrete domains on the cell surface. From their asymmetric position these key proteins control important events that build an organism, including the generation of the plethora of cell types needed, the organization of tissues into organs and the establishment of embryonic axes that lay the bases for the architectural plan of an animal. Therefore, when the position and function of these polarity effectors is impaired a wide range of diseases can arise including cancer.

What ensures the correct localisation and function of these polarity proteins? We recently identified a new way of regulation for these polarity effectors. We found that, like in a manufacturing factory, there is a division of labour for the polarity proteins that will specify a cell domain. They group themselves into distinct protein-complexes, which become specialised in a given function. For the proteins we studied we found that there are at least two distinct protein-complexes, one specialised in the asymmetric distribution of the polarity proteins and the other focused on their activation. A very tight functional coordination between these protein-complexes is required to generate an asymmetric and active domain of polarity proteins that will polarise cells, allowing the development of an organism. We do not know how this important cooperation is achieved; therefore we propose innovative cell biology techniques to identify the players involved and their modes of action.

By understanding how cells are polarised we will give insight into key aspects of human embryo development and we will pinpoint events that can go wrong and cause disease. Thus it is important that we identify the mechanisms that control correct cell polarisation; understanding this will, in the long-term, provide new avenues in the design of drugs that can correct errors in these mechanisms of control.

Technical Summary

To generate a complex, highly structured organism from a symmetric one-cell embryo, cells undergo genetically-encoded programs where as they divide they acquire structural and functional differences through a process termed cell polarisation. A crucial step in the polarisation of animal cells is the localisation of conserved polarity effectors, among them the PAR proteins, to discrete membrane domains on the cell surface. When these processes are impaired, developmental disorders can arise including cancer.

We recently discovered an important layer of regulation for PAR proteins (Rodriguez et al DevCell 2017). PARs generally define two membrane domains within polarising cells, i.e. antero-posterior for the asymmetrically dividing C.elegans zygote (one-cell embryo) or apico-basal for epithelial cells. We have found that the set of PARs that define the anterior zygote actually work as two distinct protein complexes that cooperate to polarise the zygote. These PAR complexes have different functions; one focuses on sensing cues to become asymmetrically localised and the other on activating the main signaling component, aPKC kinase. Coupling of these complexes is strictly necessary to generate an asymmetric and active domain of aPKC, which will signal the zygotes' asymmetric division, leading to the soma and germline lineage. We found that aPKC activity is required to functionally couple these complexes and the goal of this project will be to understand how aPKC achieves this important task. We will identify aPKC substrates and the mechanisms that regulate this dynamic cooperation between PAR protein complexes.

By elucidating the fundamental principles that govern the asymmetric organization and function of polarity effectors we will understand a process that sits at the heart of many important developmental biology events. We expect our research to provide new avenues for drug design strategies in different developmental disorders.

Planned Impact

Our research will reveal the fundamental principles of how PAR proteins, key regulators of cell polarity, coordinate their tasks to generate specialised domains within cells. This polarisation of cells is critical to many aspects of embryo development, including asymmetric cell division, tissue formation, neuronal development, cell migration and embryos axis establishment. Given that cell polarity sits at the heart of a wide range of cell biological processes, which are all important for the development of humans, we expect our findings to be of broad popular interest.

The most immediate impact will be in the SCIENTIFIC COMMUNITIES described under academic beneficiaries (cell and developmental biology, cell polarity, cell division, cell fate, cytoskeleton dynamics, stem cell biology, signaling and developmental disorders), mainly through collaborations, participation at conferences and publication in high impact open access journals. We will ensure wide dissemination of the data, reagents and methods generated to the UK and international research community.

In the long term because cell polarity is crucial to most developmental processes, we expect that by understanding the fundamental mechanisms that regulate polarity we will find aspects that can go wrong in developmental disorders. This will allow the development of novel therapeutic strategies, impacting on the PHARMACEUTICAL AND PUBLIC HEALTH SECTOR. Currently inhibitors of aPKC (the PAR signaling component focus of our studies) are being tested as drugs against cancer and nervous system disorders. Indeed, in our previous publication we have characterised an aPKC inhibitor developed by Cancer Research Technology Limited. Our future mass spectrometry analyses and genetic screens (AIMs1&2 from research proposal) will identify aPKC substrates and regulators that in a similar way can be putative therapeutic targets for cancer or other developmental disorders. I will meet annually with the Business Development at Newcastle University to examine the possibilities for application and commercialization of our research. Commercially exploitable intellectual property (IP) will be assessed prior to publication.

The cutting edge research techniques developed during this project in mass spectrometry and live cell super-resolution imaging, will directly benefit Newcastle proteomics facility and the Bio-imaging unit. In particular, our work will help validate and commercialise the iSIM super-resolution imaging technology benefiting the developer, a local LIFE SCIENCE TECHNOLOGY company (VisiTech International, Sunderland). In addition, our methods and tools will be immediately shared with members of the University and our collaborators.

The RA working on the project will benefit from innovative technical skills and research experience. This work will also benefit other members of the Cell Division Biology Group, including PhD and master students, through exposure to new techniques and research areas. Thus, this grant will contribute towards UK SCIENCE through developing expertise and training skilled researchers that will be highly employable in public and private research sectors, increasing capacity in growing research areas.

During the course of this project we will take opportunities to engage with the GENERAL PUBLIC. I have a demonstrated interest in presenting my work to the public, having been involved in outreach activities with schools, science festivals and patients. During this project the RA and I will participate in the organization and delivery of "Soap Box Science" events in central Newcastle, and "Meet the Scientist" days focusing on C.elegans research and cell division at the International Centre for Life museum. All of these will be invaluable opportunities to attract public attention towards our research interests, which will be supported by press releases from our work (university website, local and national press) and the use of social media.

Publications

10 25 50
 
Description Here we set to identify how protein complexes cooperate in the creation of cellular asymmetries that are key to most cellular functions. The C.elegans nematode one-cell stage embryo undergoes an asymmetric cell division that kicks off the somatic versus germline lineages. This division is regulated by the asymmetric distribution of PAR-protein complexes, the activity and membrane organisation of which are reliant on the activity of the kinase, aPKC (see our review, URL below). However, how aPKC regulates its own dynamics and that of PAR complex formation and dissolution is still not understood.

In Aim.1 we proposed to identify aPKC substrates to get a better understanding of aPKC function. Two approaches have been undertaken:
1) Unbiased phosphoproteomics approach leading to the identification of aPKC substrates key in embryo development.
o Progress/findings: We have developed a protocol to obtain early embryo protein extracts with and without aPKC activity and through phosphoproteomics have identified 159 candidate targets of aPKC. We have prioritised the study of 60 candidates most likely to be direct substrates of aPKC and to present an embryonic developmental role. 22 of these 60 candidates regulate the one-cell stage embryo asymmetric cell division, including 8 genes involved in PAR complex formation. We are currently determining how aPKC phosphorylation could regulate the function of these genes.
2) Candidate approach following our previous data proposing that the small GTPase CDC-42 is an aPKC substrate.
o Progress/findings: We have evidence that aPKC phosphorylation of CDC-42 can disrupt aPKC interaction with CDC-42 and in turn, promote the membrane release of the PAR complex aPKC/PAR-6/CDC-42. In this way aPKC can restrict its own domain of action, contributing to PAR asymmetry.

In Aim.2 we planned to pinpoint the mechanisms by which active aPKC becomes asymmetrically localised. Our preliminary data in Aim.1 "candidate approach," indicates a possible mechanism that could at least partially explain how aPKC activity is spatially restricted. Given COVID-derived timing restrictions, we have decided to progress further Aim1.2 prior to starting experiments proposed in Aim.2.2.

Aim.3's goal is to characterise at nano-scale resolution the dynamics of asymmetrically localised PAR proteins and to study how these dynamics are altered in absence of aPKC activity.
o Progress/findings: In collaboration with Adam Wollman we have built a fast acquisition super-resolution TIRF microscope. This microscope in combination with bespoken computational tools, have allowed us for the first time to track and extract meaningful biological data from PAR-6 and PAR-3 protein dynamics in wild-type embryos, aPKC kinase-dead mutants and upon removal of PAR-3 or CDC-42. Our results indicate a tug of war between aPKC/PAR-3 and CDC-42 in the generation of PAR asymmetry. aPKC/PAR-3 reduce PAR-6 random mobility at the plane of the membrane and promote PAR-6 active transport towards the anterior of the zygote through actomyosin dependent flows. Whereas CDC-42 does the opposite, promotes PAR-6 random mobility and reduces PAR-3 ability to mediate anterior PAR asymmetry, by limiting the recruitment of PAR-6 to PAR-3 clusters, which are required to sense actomyosin flows. We are submitting these results for publication and using preliminary data obtained in this grant to support new grant applications.
Exploitation Route - Our phosphoproteomics protocols and datasets will be useful to academic and pharmaceutical researchers identifying kinase substrates using this approach.
- C.elegans strains and protocols have been shared with our collaborators. Once published strains will be available through CGC (CGC,https://cgc.umn.edu/). I predict interest from research scientists, academics, and the biotech industry.
- The development of user-friendly tools for single-particle tracking, has been useful for the training of undergraduates on computational methods. Our tools will also benefit other academic labs and biotechnology industries, wanting to expand their research into nano-scale tracking of proteins.
- Our results on how aPKC could be restricting its domain of action and controlling PAR dynamics, have been communicated to our collaborators influencing their research. In addition, in 2021 and 2023 our work has been presented at scientific meetings (Dynamic Cell IV, EMBO Cell polarity and membrane dynamics and International C.elegans meeting) favouring discussions and collaborations. The most immediate impact has been on researchers with an interest in developmental biology and cell polarity. Given that cell polarity and aPKC sit at the heart of cell biological processes, which are important to human development, we expect our findings to be of interest to biomedical research.
Sectors Education,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Transport,Other

URL https://royalsocietypublishing.org/doi/abs/10.1098/rstb.2019.0555
 
Description Our findings have been exposed to pupils in primary schools in Newcastle Our finding have been part of university lectures at Newcastle University Our findings have been presented and discussed at national and international scientific meetings (Cell polarity and membrane dynamics EMBO, International C. elegans meeting GSA, Dynamic cell Biochemical Society) Our findings and developed methods are also part of future grants where we propose to expand into new areas of research (BBSRC pioneer award)
First Year Of Impact 2023
Sector Education
Impact Types Cultural

 
Description BBSRC DTP studentship (2019-2023)_Revealing the dynamic mechanisms by which protein complexes cooperate to establish cell polarity
Amount £136,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2019 
End 09/2023
 
Description Understanding the molecular and biophysical mechanisms that drive cell contact re-establishment after division
Amount £136,000 (GBP)
Funding ID 2577765 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2021 
End 01/2025
 
Title Labelling of C. elegans zygotes with HaloTag dyes for more stable detection of recombinant HaloTagged proteins. 
Description We have established a protocol for embryo extraction and incubation with JF549 and JF646 dyes (provided by Janelia Farms), that allows for rapid and stable uptake. 
Type Of Material Technology assay or reagent 
Year Produced 2022 
Provided To Others? Yes  
Impact This work has greatly impacted our research and that of collaborators as we are currently able to detect and track with precision very dynamic PAR proteins 
 
Title New C. elegans strain: aPKC temperature sensitive mutant (ne4246) crossed with PAR3::GFP and PAR-6::HaloTag 
Description This strain allows very sensitive detection and tracking of fast PAR-6 single-molecules in combination with PAR-3 molecules, in a mutant strain that lacks aPKC activity. PAR-6 molecules are labelled with Janelia Farm JFX-549 dye. 
Type Of Material Biological samples 
Year Produced 2021 
Provided To Others? Yes  
Impact We have shared this strain with collaborators and will be deposited in CGC (https://cgc.umn.edu/). This strain has improved our detections of PAR-6, gaining a better understanding of PAR-6 dynamics. We have found that previous studies (including ours) were biased towards the detection of slower and more stable particles. 
 
Title New C. elegans strain: aPKC temperature sensitive mutant (ne4246) crossed with eGFP::PAR-3b and PAR-6::mCherry 
Description We have crossed the aPKC temperature-sensitive mutant with a reporter strain for PAR-3 and PAR-6. This strain will allow us to characterise live and in super-resolution the dynamics of polarity proteins when aPKC kinase activity is inhibited. 
Type Of Material Biological samples 
Year Produced 2020 
Provided To Others? Yes  
Impact Initial characterisation of this strain under TIRF microscopy has identified the need to label PAR-6 with a brighter and more stable dye. We are currently crossing the aPKC temperature-sensitive mutant with a PAR3::GFP and PAR-6::HaloTag, in order to label PAR-6 with the Janelia Farm dye JF549. We have shared this strain with collaborators and will be deposited in CGC (https://cgc.umn.edu/) 
 
Title New C. elegans strains: CDC-42::GFP reporter strains also expressing a membrane-tethered nanobody against GFP 
Description We have generated a research tool to test if CDC-42 phosphorylation on S71 alters in vivo the interaction of CDC-42 with other PAR proteins. C. elegans CDC-42 reporters (wildtype or phosphomimetic CDC-42(S71E) mutant) have been crossed to a strain expressing a membrane-tethered nanobody against GFP. Therefore, in these strains we force the membrane localisation of CDC-42 reporters at sites where CDC-42 is normally not present. In this experimental condition, we can investigate if these CDC-42 reporters can recruit other PAR proteins. Preliminary results indicate that whereas the wildtype CDC-42 can recruit aPKC to the membrane, the phosphomimetic CDC-42 mutant cannot. ****UPDATE 2022**** We have also created a strain where the non-phosphorylatable form of CDC-42 (S71A) is brought to the membrane using the same technique described above (membrane-tethered nanobody against GFP). This strain was a required control for our experiment. 
Type Of Material Biological samples 
Year Produced 2021 
Provided To Others? No  
Impact The most immediate effect is on the development of our project. Using this tool we are now able to test if CDC-42 phosphorylation on S71 alters in vivo the interaction of CDC-42 with other PAR proteins. We have observed that the phosphomimetic form of CDC-42 (S71E) disrupts CDC-42 interaction with aPKC. These results once published will impact a large research community, given that CDC-42 is a small GTP involved in the structure and function of many cell types, including embryonic, migrating, neuronal and epithelial cells. Once published the strains will be deposited in CGC (https://cgc.umn.edu/). 
 
Title New C. elegans strains: phosphomimetic and non-phosphorylatable mutants of aPKC putative targets 
Description Using CRISPR/Cas9 technology we are generating phosphomimetic and non-phosphorylatable forms of putative substrates of aPKC that have a role in the C. elegans zygote (22 identified, 12 generates thus far) and will generate GFP reporter lines of those which phospho-mutants show an early embryo phenotype. 
Type Of Material Biological samples 
Year Produced 2023 
Provided To Others? No  
Impact Strains and initial phenotypes will be reported at the international C. elegans meeting in June and strains will be made available to collaborators. 
 
Title Optimised detection of aPKC targets 
Description We are currently trying to establish a throughput protocol to detect direct targets (substrates) of aPKC. Briefly, using our phosphoproteomics aimed at identifying potential aPKC targets, we will select a list of those best hits (showing biggest phosphorylation difference between wild-type and loss of aPKC activity) that present predicted aPKC phosphorylation sites and when knock-down lead to polarity defects in the zygote. We will generate GFP lines of selected candidates with the aim to study their localisation but most importantly to pull them down with GFP-nano beads, and run gel retardation assays (PhosTag) to determine if the presence (over-activation) or absence of aPKC leads to changes in their phosphorylation state. This will help us determine if the candidates are substrates of aPKC. ***UPDATE 2023*** Our comprehensive phosphoproteomic comparison between aPKC-inhibited and control embryos to determine aPKC substrates, revealed 159 targets that contained potential aPKC phosphosites. Through bioinformatic scoring of these genes according to: their GO term, aPKC motif match and fold change in phosphorylation, the 159 genes were narrowed down to 60 genes. To identify which of these selected putative substrates have roles in the one-cell embryo, an RNAi phenotypic screen was undertaken which has identified 22 genes with early embryo phenotypes. We are generating phosphomimetic and non-phosphorylatable forms of these putative substrates of aPKC and will generate GFP reporter lines of those which phospho-mutants show an early embryo phenotype. 
Type Of Material Technology assay or reagent 
Year Produced 2022 
Provided To Others? No  
Impact Once we have the protocols optimised we will make our methods publicly available. This work will have a great impact on our research and on those trying to identify in an unbiased way direct targets of kinases. ***UPDATE 2023*** This work will be presented at the International C. elegans meeting in June 
 
Title PAR protein tracking method 
Description Our particle selection and tracking tools are currently based on the Kilfoil method (Pelletier et al., 2009) and developed in MATLAB in collaboration with Sundar Naganathan and Adam Wollman. We are exploring a particle detection algorithm that considers local intensity thresholds, reducing human bias in particle selection. Our tracking method has been tested with real super-resolution TIRF imaging data from embryos expressing PAR-6::GFP. In addition, we have increased the analysis capability of the Kilfoil package by adding scripts for example to plot diffusion coefficients or to visualise tracks within the embryo. We have tried to make our scripts more user-friendly and accessible. We have tested their accessibility by training undergraduate students, which have successfully used our analysis pipeline. ****UPDATE 2022**** Protein tracking method considering local intensity thresholds We have upgraded the Maria Kilfoil particle tracking package (Pelletier et al., 2009) with a particle detection algorithm that considers local intensity thresholds (signal vs. noise ratios), reducing human bias in particle selection and allowing the estimation of molecules per cluster (protein aggregates). We are currently trying to implement this method to the detection and tracking of two different population of PAR proteins in order to extract comparative data between the two populations. We are testing our methods on TIRF super-resolution imaging of PAR-3::GFP and PAR-6::HaloTag strain. ***UPDATE 2023*** We have upgraded the Maria Kilfoil particle tracking package (Pelletier et al., 2009) with a particle detection algorithm that considers local intensity thresholds (signal vs. noise ratios), not only for the analyses of PAR particle dynamics but also for actomyosin dynamics. 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? Yes  
Impact These computational tools will allow the automatic analysis of our data, extracting the nano-scale dynamics of PAR proteins at the membrane. In addition, these tools will be made available through GitHub making particle-tracking accessible to other researchers. 
 
Title Phosphoproteomics approach to identify targets of aPKC during early embryo developmental stages 
Description We have established a protocol to obtain phosphoproteomics data comparing early C. elegans embryos from wildtype and aPKC kinase-dead mutants. Optimisation steps performed: 1. Population expansion and egg collection to enrich for early-stage embryos 2. Determine the temperature and time window required to inactivate two alleles of aPKC temperature-sensitive mutants 3. Protein extraction buffer and sonication conditions 4. Comparision between unlabelled and TMT-labelled samples 
Type Of Material Technology assay or reagent 
Year Produced 2021 
Provided To Others? Yes  
Impact We will test our method and once confirmed we will make it available to our research community here at Newcastle University and to our C. elegans collaborators. This method will lead to publishing phosphoproteomics data, available to the international research community. ****UPDATE 2022**** We have already started sharing our method. The PhD student (Iolo Squires) has presented our work in the International C. elegans meeting 2021 
 
Title Phosphoproteomics data for wildtype and aPKC mutant embryos 
Description We have identified a collection of phosphopeptides in wild-type embryos and in aPKC kinase dead mutants, which can be used to obtain potential aPKC targets. Briefly, we have developed a protocol to extract proteins from very early C. elegans embryos. From these protein extracts, phosphopetides were enriched using TiO2 columns followed by TMT peptide labelling. Peptides were analysed by nanoflow-LC-MS/MS using a Orbitrap Q-Exactive-HF Mass Spectrometer (Thermo Scientific TM) coupled to a Dionex™ Ultimate™ 3000. Peptide Identification was carried out with MaxQuant (version 1.6.10.43). ***UPDATE 2023*** Our comprehensive phosphoproteomic comparison between aPKC-inhibited and control embryos to determine aPKC substrates, revealed 159 targets that contained potential aPKC phosphosites. Through bioinformatic scoring of these genes according to: their GO term, aPKC motif match and fold change in phosphorylation, the 159 genes were narrowed down to 60 genes. To identify which of these selected putative substrates have roles in the one-cell embryo, an RNAi phenotypic screen was undertaken which has identified 22 genes with early embryo phenotypes. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? No  
Impact This dataset has greatly increased our knowledge of aPKC dependent pathways and regulations in the early C. elegans embryo. We are currently trying to develop a pipeline to use this source to identify aPKC substrates. Given that key aspects of the development of an organism (cell division, epithelia organisation, cell migration) are dependent on aPKC and that misregulation of aPKC is involved in several developmental disorders (cardiac dysfunction, cancer, neural disorders), we expect this dataset to have a broad research impact. 
 
Title Tracking actomyosin pulsatility 
Description We have upgraded the Maria Kilfoil particle tracking package (Pelletier et al., 2009) with a particle detection algorithm that considers local intensity thresholds (signal vs. noise ratios) and adapted them for the analysis of actomyosin dynamics, in particular actomyosin pulsatility. 
Type Of Material Data analysis technique 
Year Produced 2023 
Provided To Others? No  
Impact This tool will help us understand the origin and regulation of actomyosin pulsatility, which is a biophysical property that could provide robustness to actomyosin networks. The most immediate impact will be on our research, where this tool is helping us understand the role of CDC42 in actomyosin pulsatility (manuscript in preparation). Furthermore, we have proposed the use of this tool in future projects/grant applications. 
 
Title Unbiased single particle tracking 
Description We have upgraded the Maria Kilfoil particle tracking package (Pelletier et al., 2009) with a particle detection algorithm that considers local intensity thresholds (signal vs. noise ratios), reducing human bias in particle selection and allowing the estimation of molecules per cluster (protein aggregates). We are currently trying to implement this method to the detection and tracking of two different population of PAR proteins in order to extract comparative data between the two populations. We are testing our methods on TIRF super-resolution imaging of PAR-3::GFP and PAR-6::HaloTag strain. 
Type Of Material Data analysis technique 
Year Produced 2022 
Provided To Others? Yes  
Impact These computational tools will allow the automatic analysis of our data, extracting the nano-scale dynamics of PAR proteins at the membrane. In addition, these tools will be deposited in GitHub to make particle-tracking accessible to other researchers. Moreover, we are currently training students in the use of our methods. ***UPDATE 2023*** We are preparing a manuscript for submission with all the PAR tracking data 
 
Title aPKC candidate targets with a role in the early embryo 
Description Our comprehensive phosphoproteomic comparison between aPKC-inhibited and control embryos to determine aPKC substrates, revealed 159 targets that contained potential. aPKC phosphosites. Through bioinformatic scoring of these genes according to: their GO term, aPKC motif match and fold change in phosphorylation, the 159 genes were narrowed down to 60 genes. To identify which of these selected putative substrates have roles in the one-cell embryo, an RNAi phenotypic screen was undertaken which has identified 22 genes with early embryo phenotypes. We are generating phosphomimetic and non-phosphorylatable forms of these putative substrates of aPKC and will generate GFP reporter lines of those which phospho-mutants show an early embryo phenotype. 
Type Of Material Data analysis technique 
Year Produced 2023 
Provided To Others? No  
Impact The methods and dataset from this work will be made available in the coming International C. elegans meeting (June, Glasgow) and will be published by the end of this year or beginning of next year. Given the importance of aPKC in embryo development, we expect this dataset to be of great interest to researchers in several fields, e.g morphogenesis, neuronal development, cell polarity and cancer. 
 
Description Developing cortical PAR protein tracking methods 
Organisation Newcastle University
Country United Kingdom 
Sector Academic/University 
PI Contribution The post-doc, John Packer, recruited with this BBSRC grant has optimized and compared different particle tracking methods to determine which one suits best our needs. He will also provide live sample material to help our collaborator develop a super-resolution TIRF microscope. UPDATE 2021 From the different particle detection and tracking methods tested we have settled with the Maria Kilfoil research group package (Pelletier et al., 2009). Currently, we are exploring the possibility to upgrade this package with a particle detection algorithm that considers local intensity thresholds (signal vs. noise ratios), reducing human bias in particle selection. The super-resolution TIRF microscope for one channel acquisition has been developed by our collaborator and we have acquired PAR-6 GFP movies from wild-type and aPKC kinase-dead mutant zygotes. John Packer (RA funded by this grant) has developed MATLAB scripts to analyse the outputs of PAR-6 particle tracking using the "Kilfoil method" and will be presenting his initial results at the Dynamic Cell IV conference (Biochemical Society and BSCB).
Collaborator Contribution Adam Wollman, recently recruited by Newcastle University, has provided John Packer with scripts and guidance to adapt different tracking methods to our needs. He will also ensure that the super-resoution TIRF microscope he is developing will be suitable to track simultaneously two different populations of cortical PARs in C. elegans zygote. UPDATE 2021 Adam Wollman has developed a super-resolution TIRF microscope for fast acquisition in one channel. He is currently expanding this microscope to enable two-channel simultaneous detection. Adam is also helping John Packer develop the scripts for particle detection and analysis of tracking data. ***UPDATE 2022-2023*** The team has focused in the in the incorporation of automatic intensity analyses to tracking data (Pelletier et al., 2009 upgraded with detection of local intensity thresholds) and in dual-color tracking analyses
Impact User-friendly Matlab script that can run three-particle tracking methods allowing comparison between them. This multi-disciplinary collaboration takes advantage of the engineering background from Adam Wollman and the molecular biology expertise in our lab. UPDATE 2021 Adam Wollman has used our samples to develop the TIRF microscope. John Packer has obtained data that might solve how aPKC controls PAR-6 asymmetry. In absence of aPKC activity, he observes that PAR-6 mobility at the membrane increases, but its directed transport towards the anterior half of the embryo decreases. Both of these events could explain why in absence of aPKC activity PAR-6 loses its asymmetric localisation. John Packer will be presenting this work at the upcoming Dynamic Cell IV conference. In addition, undergraduates have benefited from our particle tracking tools in their training on computational methods. UPDATE 2022 We have upgraded the Maria Kilfoil particle tracking package (Pelletier et al., 2009) with a particle detection algorithm that considers local intensity thresholds (signal vs. noise ratios), reducing human bias in particle selection and allowing the estimation of molecules per cluster (protein aggregates). Using this tool John Packer is generating publication quality data on PAR-6 particle organisation and dynamics at the membrane (cluster size and diffusion coefficients) which he has found are regulated by aPKC activity and the presence of each of the PAR members, PAR-3 and CDC-42. Our data supports a dynamic interchange of PAR-6 molecules between PAR-3 clusters and CDC-42 (which we had proposed in our previous publication, Rodriguez et. al. 2017). PAR-6 random mobility at the membrane decreases with PAR-3 promoting PAR-6 active transport to the anterior of the zygote. On the contrary PAR-6 mobility increases with CDC-42 and furthermore CDC-42 seems to limit PAR-3 clusters, which are required for PAR asymmetry. Our results are hinting at a tug of war between PAR-3 and CDC-42 in the generation of PAR asymmetry. We are putting these results into a manuscript and gathering preliminary data to support further grant applications. ***UPDATE 2023*** Intensity analyses of tracking data (Pelletier et al., 2009 upgraded with detection of local intensity thresholds) are allowing us to study the clustering state of PAR-6 (number of molecules per cluster), which is critical for the asymmetric localisation of aPAR proteins in the zygote. We are gaining a more detailed understanding of how PAR-3, CDC-42 and aPKC activity are regulating PAR-6 clusters, and hence PAR asymmetry. This is completing our results from the previous year showing a tug of war between PAR-3 and CDC-42 in the generation of PAR asymmetry and these results are being added into our manuscript. Moreover, we have already proposed to use the developed technique in future projects for which we are applying for grants.
Start Year 2019
 
Description Modelling PAR protein dynamics 
Organisation University of Liverpool
Country United Kingdom 
Sector Academic/University 
PI Contribution Meetings to update collaborator with recent findings that will help develop a model of PAR dynamics.
Collaborator Contribution A mathematical model in working progress on PAR protein complex formation and dissociation at the membrane.
Impact This collaboration is still in its early days. A skeleton of a mathematical model that can encompass our biological observations has been built. ****UPDATE 2022**** Collated data on PAR-6, PAR-3 and CDC-42 protein dynamics at the membrane (diffusion coefficients) that can be fed into the model. Determined PAR protein dynamics upon depletion of PAR members to try to model their dependency upon each other. Start to develop dual single molecule imaging to determine PAR co-localisation and dynamics, which can further inform the model.
Start Year 2020
 
Description Tracking actomyosin flow 
Organisation Swiss Federal Institute of Technology in Lausanne (EPFL)
Country Switzerland 
Sector Public 
PI Contribution We have provided confocal movies of non-muscular myosin and TIRF (super-resolution) movies of PAR-6 particles. ***UPDATE 2023*** John Packer, with the support of Sundar, has adapted tracking scripts to detect actomyosin flow. Iolo Squires, with the support of Sundar, has adapted PIVLab analysis tools (Particle image velocimetry, https://pivlab.blogspot.com/ ) for the tracking of actin organisation in the zygote
Collaborator Contribution Sundar Naganathan (EPFL Lausanne) has adapted the PIVLab analysis tools (Particle image velocimetry, https://pivlab.blogspot.com/ ) to the tracking of NMY-2 foci dynamics of C. elegans zygotes. He is currently determining if similar analyses can be done to analyse bulk movements of PAR-6 particles.
Impact This is a recently established collaboration. However, we have started to generate data on the tracking of NMY-2 foci on wild-type embryos and on embryos depleted of aPKC activity. Currently, we are trying to develop a computational tool that can subtract the bulk movement of PAR particles, subjected to actomyosin flow, from their diffusive mobility. This tool could be widely-applied when trying to understand protein dynamics subjected to active transport. UPDATE 2022 Using Sundar's scripts we have generated publication quality data on NMY-2 dynamics and NMY-2 foci organisation upon depletion of aPKC kinase, CDC-42 and inactivation of aPKC. We are still determining if similar analyses can be done on PAR protein dynamics and organisation. ***UPDATE 2023*** John Packer, with the support of Sundar, has adapted tracking scripts to detect actomyosin flow. They have shown that it performs as well as PIV analyses tools (Particle image velocimetry, https://pivlab.blogspot.com/ ) with the advantage that it can also track variations in intensity and hence report information regarding the actomyosin network's pulsatility (changes in intensity), which has been recently suggested to provide robustness to the network. This analysis tool is helping us extract data for our manuscript on how CDC42 regulates actomyosin pulsatility. Iolo squires has adapted PIV tools for the analyses of actin dynamics upon depletion of candidate targets of aPKC found in his phosphoproteomics screen.
Start Year 2021
 
Description School Visit (Newcastle) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact I visited the school as part of STEAM week. I gave a talk, organised discussions and the children had the chance to use a stereomicroscope to visualise different C. elegans strains.
Year(s) Of Engagement Activity 2023
 
Description Seminar series between asymmetric cell division researchers in the UK 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact These seminars are intended to be informal and aimed at increasing the participation of postdoctoral researchers, post-graduates, and master students in research discussions related to their work. In addition, we would like these seminars to promote scientific support, the interchange of reagents, and protocols. Currently, we have participation from five research groups in the UK.

****UPDATE 2022****
These seminars are still taking place. Student and post-docs in our labs have greatly benefited from these informal interactions, enhancing the development of their projects through shared methods, reagents and collaborations.
Year(s) Of Engagement Activity 2020,2021,2022
 
Description Undergraduate training on single-particle tracking 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact We have trained undergraduate students on single-particle tracking. The course required no initial programming skills and was built on ten formal, plus ten support sessions and scripting exercises to develop at their own pace. At the end of the course, the students were able to track and analyse single-particle data, using a pipeline of MATLAB scripts. The students reported to be very satisfied with their achievements and to have gain programming skills that will definitively impact their future careers. This course has also helped us improve our scripts and we have developed supporting documentation that we hope will increase the accessibility of the computer tools we are developing in our lab.

****UPDATE 2022****
Undergraduates that have join our research in 2022 are currently enjoying this training course. Previous students have greatly benefited from this course, using their learnt computer skills in research academic jobs. Moreover, a student has joined our research group and is applying her computer skills to one of our projects.
Year(s) Of Engagement Activity 2021,2022