A 3-D perspective on neutrophil migration
Lead Research Organisation:
University of Warwick
Department Name: Warwick Systems Biology Centre
Abstract
Chemotaxis is the process by which cells can navigate towards sources of chemoattractant. It is crucial for development, immune function and the spread of cancer cells. It is based on the ability of cells to detect chemoattractants via highly specific receptors on their surface. Remarkably, when placed near to a source of chemottractant the cell can determine the direction towards its source. It achieves this by using both the fact that the attractant becomes more concentrated nearer the source and its ability to detect tiny differences in the concentration of chemoattractant around it. The cell then migrates in the direction of increasing concentration of chemottractant. Despite its importance our understanding of how chemotaxis works is very limited. It is clear that chemotaxis is made up of many component, or sub, responses. The ability to detect the chemottractant, the ability to sense changes in its concentration across very small distances and the ability to move in response to the chemoattractant (chemokinesis), which is in turn dependent on the ability of the cells to form reversible contacts with neighbouring cells or surfaces. A full understanding of chemotaxis will only emerge from an understanding of these elemental component responses. In this project we focus on the mechanisms underpinning chemokinesis (chemoattractant stimulated movement, in our assays the chemottractants are often uniform in concentration and the resulting migration is random and not directed as in chemotaxis) as a key event in chemotaxis. We aim to understand the chemical nature (the molecules that are acting as the signals) and spatial organisation of the processes inside cells that allow them to perform these responses. Neutrophils are a specialised form of white cell found in the blood. Their primary function is to ingest and kill bacterial and fungal pathogens. Neutrophils use the process of chemotaxis to migrate out of the blood stream towards areas of inflammation and also to home-in on pathogens. Thus chemotaxis is essential for neutrophils to perform their normal healthy function fighting disease. However, many long term inflammatory diseases are known to caused by neutrophils over-reacting. Too many neutrophils accumulate at the site of disease and actually contribute to host tissue damage, which in-turn leads to further accumulation of neutrophils. Hence a major objective in treating inflammatory disease such as arthritis is to reduce neutrophil migration into sites of inflammation. At the moment we have very few drugs that are able to effectively reduce neutrophil influx to sites of chronic inflammation with unwanted side effects because we do not know which steps in chemotaxis to best target. We aim to study neutrophil chemokinesis and chemotaxis. Recently there has been huge progress in understanding the events inside neutrophils that are involved in coordinating chemotaxis. This has been possible through the development of microscopes capable of seeing inside living neutrophils as they move and the use of genetic engineering techniques to make specific proteins we want to study inside cells fluorescent and hence possible to see with special illumination and detection systems in the microscopes. However, despite these advances our views of the inside of cells during chemotaxis has thus far been very 2-dimensional, that is as if we were looking down on them from above, and could not reveal any depth (the 'sides' of the cell). By using new imaging techniques we are able to begin to take many photos and combine them to give a sense of depth. What we have seen so far entirely changes our interpretation of the 2-D images and understanding of the spatial coordination of chemotaxis. In this project we hope to use mathematics and computers to improve our ability to create and interprete 3-D images of migrating neutrophils and to use this to find out the nature of the intracellular signals that regulate chemokinesis and chemotaxis.
Technical Summary
INTRO The capacity of neutrophils to fight bacterial and fungal infections is dependent on their ability to chemotax into zones of inflammation. Neutrophil's, like other cells, chemotaxis is built upon both their abilities to polarize and move in response to uniform stimulation (chemokinesis) and to sense, and navigate in accord with the sense of, gradients of chemottractants. Our, and others, work has shown that PIP3 signals induced by chemottractants are thought to become polarized, high at the 'leading edge', and important for polarization and chemokinesis. SUPPORTING DATA We argue, and show preliminary data indicating, that the dominant features of this polarization, both in terms of PIP3 and F-actin accumulation, are created by a combination of chemoattractant AND adhesion-generated signals. This creates a situation where, in contrast to the '2-D, leading edge dogma', the PIP3 is highest in the zone of attachment UNDER new protusions and is low under the uropod and the F-actin, although initially in a crescent at the front of the cell, becomes associated with substrate-fixed focal complexes in the centre of the cell. HYPOTHESIS The above is due to cycle started by GPCR/PI3Kgamma/PIP3-mediated activation of integrin adhesion. This leads to integrin activation of Class IA PI3Ks, further PIP3 accumulation, the evolution of focal complexes and ultimately the recruitment of suppressors such as SHIPI, creating a gradient of both PIP3 and adhesion/de-adhesion. QUESTIONS & AIMS What are the key regulators that govern the 3-D distribution of PIP3 signals during chemokinesis? Within this we consider how PIP3 signals can both direct, and get shaped by, the cycle of integrin and focal complex-dependent adhesion and de-adhesion. To answer these questions convincingly will require the development of analytical tools capable of interrogating and assimilating data from movies capturing the 3-D distribution of signalling molecules, we also aim to create such tools.
Planned Impact
A) Who will benefit (outside of our immediate academic community, see beneficiaries)? 1) The pharmaceutical sector, specifically, those interested in targetting inflammatory disease. The work is directly relevant to an understanding of the intracellular signalling underpinning neutrophil migration. This process is a key step in the development of inflammatory disease. Furthermor, our owrk focuses on PI3Ks, which are already accepted to be validated anti-inflammatory targets with a number of international pharmaceutical organisations taking PI3K inhibitors through clinical trials as anti-inflammatories. We have collaborations with a number of companies in this domain including Karus pharmaceuticals and in the recent past PIraMed (now Genentech). 2) Researchers within the NHS. We have substantial, long term collaborations with NHS, clinical researchers who are interested in human neutrophil migration. These clinicians co-supervise some students in our lab and attend our lab meetings. This helps us ensure our work is therapeutically and commercially relevant. 3) The medical charities. Aspects of our work on neutrophil signalling have been and are funded by the medical charities, specifically, the Wellcome trust, The Arthritis research council and the British Lung Foundation. We have a number of long term contacts in all of these organisations and attend some of their meetings. 4) PDRAs employed on the grant. B) How will they benefit? 1) In the context of the benefits to the pharmaceutical sector the benefits will be improved target selection for focused medicinal chemistry, better understanding of the mechanism of action of PI3K-selective drugs. These effects will be in both the short and medium term in the context of the fact PI3K-selective drugs are already in trials. Through any longer term successes in these trials there are potential benefits to health and, in the setting that our commercial collaborators are based in the UK, the competitiveness of the UK economy and jobs. The PDRAs will gain skills and experience that are directly relevant to the pharmaceutical sector. 2) Clinical colleagues in the NHS will gain from our work with mouse genetic models (that cannot be usedin human studies) and apply its conclusions to their work with clinical or human material. 3) The medical charities that have funded out work have gained through delivery of their strategic objectives. C) What will we do to ensure we engage our users and maximise the impact of this work? 1) We are already regularly invited to present our work in the commercial and NHS sectors, this would continue during this project. We already take time at internaional meetings to discuss our work with commercial colleagues that would continue. Clinicians already attend our lab meetings on a regular basis, that would continue. We would continue to seek out opportunties to obtain funding in this area from the commercial sector by listening and finding out their priorities. The Babraham Institute organises forums with pharmaceuticalc companies, we always try to attend and present our work at these events. 2) We will continue to collaborate with commercial and clinical colleagues as described above. We currently have active collaborations with Horizon Discovery, AstraZeneca and Karus pharmaceuticals, this is evidence of the effectiveness of our approach in this area. 3) If we obtain date with clear commercial implications we will discuss potential ways ahead with the commercial arm of BI, BB. However, in this project it unlikely this will be in the form of a patentable chemical entity. We have experience in translating our research into potentially valuable patents both in our lab (eg, we are named on patents with Onyx pharmaceuticals protecting the principle of targetting PI3Kgamma for anti-inflammatories) and in BBT. We also have a track record of transferring knowledge to the commercial sector through consultancies and other routes described above.
Organisations
Publications
Baniukiewicz P
(2019)
Generative Adversarial Networks for Augmenting Training Data of Microscopic Cell Images
in Frontiers in Computer Science
Baniukiewicz P
(2018)
QuimP: analyzing transmembrane signalling in highly deformable cells.
in Bioinformatics (Oxford, England)
Bond M
(2013)
Quantitative analysis of human ras localization and function in the fission yeast Schizosaccharomyces pombe.
in Yeast (Chichester, England)
Bretschneider T
(2011)
Cartography of spatio-temporal cellular dynamics
Bretschneider T
(2016)
Progress and perspectives in signal transduction, actin dynamics, and movement at the cell and tissue level: lessons from Dictyostelium.
in Interface focus
Collier S
(2017)
Image based modeling of bleb site selection.
in Scientific reports
Du CJ
(2013)
3D time series analysis of cell shape using Laplacian approaches.
in BMC bioinformatics
Description | We have developed new software tools to quantify cellular shape changes in 2D and 3D. This has resulted in a number of research publications and software that is being made available to others, enabling high quality research on cell motility and other cell biological processes involving deformations of the cell membrane such as macropinocytosis. |
Exploitation Route | The software we have developed in this project is used by researchers studying cell motility and transmembrane signalling. It is used by scientists to assay whether certain compounds have pharmacologically relevant activity. The recent availability of rapid 3D lattice light sheet microscopy which creates huge volumes of high quality data greatly increases demand for our tools for efficient 3D cell segmentation and shape analysis. |
Sectors | Chemicals,Digital/Communication/Information Technologies (including Software),Environment,Pharmaceuticals and Medical Biotechnology |
Description | Software tools we have developed have been used in 3Rs models for pharmacogenetics research. This has helped to identify novel human receptors in bitter tastant detection. |
First Year Of Impact | 2013 |
Sector | Pharmaceuticals and Medical Biotechnology |
Impact Types | Societal,Economic |
Description | "Software tools for studying 3D cell shape dynamics" |
Amount | £8,742 (GBP) |
Funding ID | RLFAA3002BRE |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 12/2013 |
End | 05/2014 |
Description | A Computational Framework for Cell Motility |
Amount | £20,416 (GBP) |
Organisation | University of Warwick |
Sector | Academic/University |
Country | United Kingdom |
Start | 01/2012 |
End | 01/2013 |
Description | Reconstructing cell surface dynamics from lightsheet microscopy data |
Amount | £426,000 (GBP) |
Funding ID | BB/R004579/1 |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 10/2017 |
End | 09/2020 |
Description | A framework for neutrophil cell shape analysis in 3D |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Seminar talk given by Chengjin Du. no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | A unified Laplace approach for neutrophil cell segmentation, topology fixing, spherical parameterization, and shape representation in 3D |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Seminar talk given by Chengjin Du. no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | BioImage Informatics conference, MPI-CBG, Dresden |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited talk byTB no actual impacts realised to date |
Year(s) Of Engagement Activity | 2012 |
URL | http://mosaic.mpi-cbg.de/web_conf/bioimageinformatics2012/Welcome.html |
Description | Cellular shape analysis in 3D using spherical harmonics |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | poster presentation |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Poster presented by Chengjin Du. Poster no actual impacts realised to date |
Year(s) Of Engagement Activity | 2011 |
Description | Conference "Nano and Bio-Imaging - latest developments in biophotonics" at Photonex 2013 |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Participants in your research or patient groups |
Results and Impact | Invited talk by TB no actual impacts realised to date |
Year(s) Of Engagement Activity | 2013 |
Description | Conference Cyto 2012 |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Plenary talk by Till Bretschneider. Proceedings abstract. no actual impacts realised to date |
Year(s) Of Engagement Activity | 2012 |
URL | http://cytoconference.org |
Description | EMBL Master Course on Bioimage Data Analysis |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | talk resulted in a number of people downloading our QuimP image analysis software a notable impact was increased downloads of our imaging software products |
Year(s) Of Engagement Activity | 2013 |
URL | http://www.embl.de/training/events/2013/IMA13-01/index.html |
Description | Fast random walker for neutrophil cell segmentation in 3D |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | poster presentation |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Poster presented by Chengjin Du. Poster no actual impacts realised to date |
Year(s) Of Engagement Activity | 2012 |
URL | http://www.ieee.org/conferences_events/conferences/conferencedetails/index.html?Conf_ID=17944 |
Description | Invited talk (Newton Institute Cambridge): How the Geometry of the Cell Boundary Couples Cellular Blebbing and Actin Based Protrusions |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Participants in your research and patient groups |
Results and Impact | talk resulted in an extensive discussion afterwards talk resulted in invitations to different other meetings and a request to organise a workshop on a related topic at the Newton Institute next year |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.turing-gateway.cam.ac.uk/frb_jun2014-programme.shtml |
Description | Invited talk: Gliwice Scientific Meetings |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Participants in your research and patient groups |
Results and Impact | will be entered after the meeting has finished |
Year(s) Of Engagement Activity | 2014 |
URL | http://gsn.io.gliwice.pl |
Description | Local shape representation in 3D: from weighted spherical harmonics to spherical wavelet |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | poster presentation |
Geographic Reach | International |
Primary Audience | Other academic audiences (collaborators, peers etc.) |
Results and Impact | Poster presented by Chengjin Du. Poster no actual impacts realised to date |
Year(s) Of Engagement Activity | 2012 |
URL | http://bmvc2012.surrey.ac.uk |
Description | Multi-scale non-local means with shape prior for enhancement of cell membrane images |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Poster presented by Till Bretschneider. Poster no actual impacts realised to date |
Year(s) Of Engagement Activity | 2014 |
Description | Society of Experimental Biology annual conference |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Participants in your research or patient groups |
Results and Impact | Invited talk by TB no actual impacts realised to date |
Year(s) Of Engagement Activity | 2012 |
Description | Workshop "Dynamic Organization and Motility of Single Cells", MPI-PKS, Dresden |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Participants in your research or patient groups |
Results and Impact | Invited talk by Till Bretschneider. no actual impacts realised to date |
Year(s) Of Engagement Activity | 2011 |
Description | Workshop Image based Systems Biology, Jena |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Participants in your research and patient groups |
Results and Impact | Invited talk by Till Bretschneider. A journal article will be submitted to a special issue of Cytometry A. no actual impacts realised to date |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.image-based-systems-biology.com |
Description | invited talk: InnoMol BioImaging workshop, Zagreb, Croatia |
Form Of Engagement Activity | Scientific meeting (conference/symposium etc.) |
Part Of Official Scheme? | No |
Type Of Presentation | keynote/invited speaker |
Geographic Reach | International |
Primary Audience | Participants in your research and patient groups |
Results and Impact | talk resulted in invitations to further conferences and extended discussions with a number of researchers at the Ruder Boskovich Institute during the course of the workshop I was interviewed by the Croatian national radio. |
Year(s) Of Engagement Activity | 2014 |
URL | http://www.innomol.eu/Project/Workshops/Bioimaging |