An integrated model of host-parasite interactions in Coccidian parasites

Lead Research Organisation: Royal Veterinary College
Department Name: Pathology and Pathogen Biology

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Planned Impact

This proposal will contribute to a new understanding of the biology of three economically important parasitic diseases of commercial livestock. Our research will result in the discovery of novel biological candidates that will be exploited in collaboration with an industry partner through an Industrial Partnership Award (IPA) to develop improved methods of control for coccidian diseases in poultry, sheep, cattle and pigs. Outcomes will assist in increasing UK competitiveness in the global animal health market, improving animal welfare and helping to guarantee safe,healthy food for the public.

The following (a) beneficiaries have been identified; (b) methods of how they will benefit; and (c) what will be done to ensure that they have the opportunity to benefit from this research.

BENEFICIARY ONE
(a) Animal health pharmaceutical industries concerned with the development of new therapies for commercially important poultry and livestock; and/or, pharmaceutical industries with an interest in human health in the area of zoonotic protozoan disease.
(b) Outcomes will benefit the commercial sector (i) by identifying a range of clearly defined candidate molecules involved in the early stages of colonisation of the gut by coccidian parasites. Candidates will be from 3 of the most important coccidian infection of poultry and livestock, Eimeria, Cryptosporidium and Toxoplasma; (ii) by revealing a deeper understanding of the mechanisms of invasion, host response and colonisation of epithelial cells by these parasites and the generation of large datasets of transcriptional, proteomic and functional information available for data mining and additional target discovery.

(c) This proposal encourages commercial investment by (i) focussing, where possible, on core mechanisms/targets that are shared across all 3 species, thus making commercial investment as attractive as possible by maximising potential returns on product development; (ii) by providing functional information downstream from the systems analysis to enable IP to be sought for candidate targets. This boosts prospects of obtaining the investment required to move the R&D into the industry sector. IP will therefore be protected throughout to enhance value and maximise opportunities for collaborative research or licensing.

BENEFICIARY TWO
(a) The UK animal health sector; poultry and livestock producers and animal health professionals. Coccidian parasites cause ten of millions of pounds in lost production and there is a need for alternative/new vaccines and improved therapeutics in this area.
(b) By working with industry utilising their strengths in product development and experimental and field trials.
(c) By sharing the costs of the development of new control methods with the commercial sector we aim to make the route to new innovations becoming available in the field as rapid as possible.

BENEFICIARY THREE
(a) Skills, training and knowledge economy
(b) The PDRAs and any undergraduate, postgraduate or intern students that contribute to the project will develop key interdisciplinary skills that will be extremely valuable for UK industry and contribute to the knowledge economy and increase the economic competitiveness of the UK.
(c) The PDRAs will have the opportunity to spend time in placements with our industry partner.

BENEFICIARY FOUR
(a) International Development
(b) Coccidian parasites are a major source of lost animal production in developing counties and zoonotic Coccidia, such as Cryptosporidium are a major cause of human diarrhoeal disease.
(c) Improved methods of control, especially the wider availability of suitably priced vaccines, would provide a boost to the farming sector in developing countries. Both academic institutions have strong links with developing countries and it is likely that PGR students from these countries will become associated with the research programme resulting in training and knowledge exchange.
 
Description In this project, we have integrated host transcriptome and secretome data to guide the analysis of proteomics data. This multi-omics approach allowed us to reveal the key proteins involved in the host protein-protein interaction networks that are modulated during Toxoplasma gondii and Eimeria tenella sporozoite infections. The effect on parasite development of down-regulating some of these hub proteins in Eimeria infected cells was evaluated by RNA interference and quantitative PCR, providing one candidate with potential future applications in the control of infection. Several new parasite proteins related to invasion and development processes have been identified, including some derived from the secretome analysis of Eimeria, Toxoplasma and Cryptosporidium. The results obtained along the award have been communicated to various national/international conferences (ApiCOWplexa 2015&2017, Toxo-UK 2018). In addition to advancing understanding of coccidian parasite biology, the project has provided good training opportunities for the PDRAs involved, two of whom have now secured permanent academic positions. PDRAs were also involved in a collaboration on Neospora in a comparative omics study using the pipelines developed in this project, which led to a publication (Horcajo et al., 2018 J Proteomics 30;180:108-119). A manuscript describing the network model generated by the research funded under this award is in preparation and will be submitted for publication in 2020.
Exploitation Route We deposit the 'omics datasets to open access online repositories and share the expression datasets on EuPathDB, for the use of the international research communities. A final paper has been under preparation for some time and is now expected to be submitted towards the end of 2020
Proteomics analysis has confirmed the expression and regulation of potential dense granule proteins in Eimeria. These findings are being taken forward by Dr. Marugan-Hernandez (PDRA in the award, now an independent research fellow at the RVC) through a PhD studentship she has been awarded started in October 2019. In this PhD project the student will characterise the Eimeria dense granule proteins in more detail and evaluate their potential as immunoprotective vaccine antigens against chicken coccidiosis.

The bioinformatics analysis identified serious deficiencies in current genome annotations of Eimeria tenella and the availability of information on protein-protein interactions. A funded PhD project supervised by Dr. Xia (PDRA in the award) started in October 2018 and is now using the multi-omics data integration generated in the project to improve parasite functional annotation. Dr Xia submitted a BBSRC new investigator award on mapping parasite protein-protein interactions, take the work generated in this project forward, however that was not funded.
Sectors Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology

 
Description The cell culture models developed and improved during the course of this grant are now sought after by several academic and non-academic research groups. Investigators and a contracted researcher (now an independent research fellow) have been approached by ~ 6 private companies and now have contractual arrangements with two of these. The first is a nutritional feed additive company to whom we provide advice on a consultancy basis, and supply with parasites by contract under an MTA. The second is a small research translation company investigating potential novel parasite inhibitors with whom we have developed a contract research arrangement by which we test compounds in our cell culture system. We remain in discussion with additional companies who are interested to use the cell culture system for their own bespoke screening assays
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology
Impact Types Economic

 
Description Development of a poultry vaccine platform based on transgenic coccidia parasites and evaluation of immunoprotection against necrotic enteritis
Amount £318,876 (GBP)
Funding ID BSA21 
Organisation United Kingdom Research and Innovation 
Department The Bloomsbury SET
Sector Public
Country United Kingdom
Start 04/2019 
End 03/2021
 
Description Houghton Trust Small Grant Award (2016/2017)
Amount £8,000 (GBP)
Organisation The Houghton Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 10/2016 
End 10/2017
 
Description Novel vaccine candidate discovery through host-pathogen interaction network
Amount £10,000 (GBP)
Funding ID HT/SPRG/21/03 
Organisation The Houghton Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2022 
End 12/2022
 
Description Transfer of an in vitro model for the evaluation of anticoccidial compounds
Amount £73,136 (GBP)
Funding ID NC/W000881/1 
Organisation National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) 
Sector Public
Country United Kingdom
Start 09/2021 
End 03/2023
 
Description A multi-omics approach to improve Eimeria functional genome annotation 
Organisation University of Cambridge
Department Department of Biochemistry
Country United Kingdom 
Sector Academic/University 
PI Contribution We have contributed our domain knowledge on Eimeria parasite, expression profiles based on BB/L00299X/1 and raw biological materials for functional genome annotation.
Collaborator Contribution Professor Ross Waller's group has contributed their knowledge on LOPIT analysis and access to mass spectrometry instruments.
Impact Conference presentation: 2021 ToxoUK21: Subcellular Localisation of Eimeria tenella proteins by hyper-LOPIT analysis. Elizabeth Attree*, Konstantin Barylyuk*, Elin Einarsson, Ozan Gundogdu, Damer Blake, Fiona Tomley, Ross F Waller, Dong Xia.
Start Year 2020
 
Description Vaccine development through graph-based machine learning generated host-pathogen interactome 
Organisation University College London
Department Department of Electronic and Electrical Engineering
Country United Kingdom 
Sector Academic/University 
PI Contribution Our team at RVC contributes to the domain knowledge on Eimeria biology, vaccine development and gene expression datasets from BB/L00299X/1.
Collaborator Contribution Dr Laura Toni brought in expetise on graph-based machine learning and access to UCL training courses and GPU workstations to this project.
Impact Conference presentation: 2021 EMBL Conference: Visualizing Biological Data. "Eimeria vaccine development through graph-based machine learning"
Start Year 2020
 
Description Conference presentation on graph-based machine learning generated host-pathogen interactome 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact It is a presentation at an international conference VIZBI where the graph-based machine learning network model is presented and discussed with international researchers.
Year(s) Of Engagement Activity 2021
 
Description Conference talk on Subcellular Localisation of Eimeria tenella proteins by hyper-LOPIT analysis 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Conference talk at ToxoUK21. "Subcellular Localisation of Eimeria tenella proteins by hyper-LOPIT analysis"

This talk at ToxoUK21 has sparked many helpful discussions and has won best turbo talk award.
Year(s) Of Engagement Activity 2021
 
Description Engagement with MSc students at UCL on applications of computational techniques to improve understanding of biological interactions 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Interview with MSc student editor for in-class Science journalism magazine for the Science and Technology Studies department, UCL
Year(s) Of Engagement Activity 2020
 
Description PhD project on graph-based machine learning generated host-pathogen interactome (new collaboration with Institute of communications and Connected Systems, UCL) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact This was a presentation day for the UCL LiDO DTP rotation students in whcih the RNASeq dataset was used for a graph-based machine learning network project and presented to the student cohort.
Year(s) Of Engagement Activity 2020