Studentship: Ribosome profiling of cattle NK cells: insights into the development of phenotypic variation and the impact on viral infection
Lead Research Organisation:
The Pirbright Institute
Department Name: UNLISTED
Abstract
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Technical Summary
NK cell functions span both the innate and adaptive arms of the immune system and are essential in controlling viral infections. However, before an NK cell becomes functional it has to be 'licensed' to ensure it does not kill healthy host cells. Licensing and subsequent immune functions are all mediated by a diverse array of cell surface receptors many of which recognise equally diverse MHC class I ligands. This natural genetic diversity creates individuals that differ in their response to particular pathogens. We have established that cattle possess the most diverse receptor and ligand gene repertoire studied to date. The transcription of these receptors varies between animals and between individual NK cells within the same animal. Strikingly the transcription of particular receptors is dictated by the MHC genotype of the individual animal, an entirely novel finding. Consequently NK cell mediated immune responses between individual cattle are likely to be highly variable, and a pool of natural genetic variation exists that could be exploited to improve disease resistance. Our hypothesis is that the NK cell response to viral infection is determined by an animal's NK cell receptor and MHC genotype. Aim 1: characterise and compare NK cell receptor translation patterns in vivo. Aim 2: characterise and compare NK cell responses to viral exposure in vitro.
Planned Impact
unavailable
| Description | A new method has been developed to enable confident mapping of short RNA-seq reads onto immune gene complexes in cattle for the first time. RNA-seq of natural killer cells from Holstein cattle has shown the transcriptional profile of their receptors. This has now been extended to the development of an RNA-Seq pipeline to accurately identify transcription of gene loci containing highly duplicated and complex gene families. We have also pushed this protocol to help assemble genomic data over the same regions as well as identify the alleles that are present in any one individual. We have now completed the first accurate analysis of transcription of the leukocyte receptor complex (LRC) and the natural killer complex (NKC) in both Bos taurus and Capra hircus. We have then used publicly available data to look at gene transcription within different cell types as well as the global gene expression atlas looking at tissue types across the whole animal. This has led to the identification of gene subsets that have starkly different transcription profiles than expected and would appear to have very specialised roles outside the immune system. It is also allowing us to understand the likely functions of novel gene families that are only present in ruminants. The final piece of work was examining RNAseq data from goat PBMCs from a vaccination and infection study using peste-de- petis ruminants virus. We were able to combine our pipelines with publicly available methods to study global transcription as well as the immune genes of interest. This revealed a clear signature of differential transcription in animals that were vaccinated and protected, with overall less of a response. This will be followed up in the future when a larger sample set is available. This work has ended up with a unique bioinformatic pipeline that takes variation of the genome into account when looking at gene transcription. This is now being used to underpin several new lines of work studying more genomes and different gene complexes. |
| Exploitation Route | New methods for the analysis of transcription of complex gene clusters in species with high quality genome assemblies. |
| Sectors | Agriculture Food and Drink |
| Title | UniMMap- a pipeline for mapping RNAseq data over repetitive immune complexes. |
| Description | To exploit the abundance of available short read sequencing data we have developed a pipeline that uses mappability to accurately measure transcription over repetitive gene complexes. This methods uses known haplotypes to examine regions of uniqueness, and then the RNAseq data from the individual to train the method to be species or individual specific. This is particularly important over gene complexes that contain genes involved in the immune system, that are often highly similar in sequence but can have profoundly different functions. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | the immediate impact will be adding fine resolution data to livestock gene expression atlas projects lead by the FAANG consortium. Further impact will be arising as this method is published and we apply it to numerous existing datasets the are publically avaialable as well as generated at Pirbright and by our collaborators. |
| Description | RB - Sharing of cattle PBMC dataset from Azad at the University of Guelph |
| Organisation | University of Guelph |
| Department | Department of Molecular and Cellular Biology |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Use of pipeline to analyse transcription of genes of interest in the data. |
| Collaborator Contribution | Provided multiple cattle PBMC RNA-Seq data sets. |
| Impact | No outputs as yet. |
| Start Year | 2017 |
| Description | Richard Borne - received data from sequencing project by Azad K. Kaushik's group (University of Guelph, Ontario, Canada) in November 2016 |
| Organisation | University of Guelph |
| Country | Canada |
| Sector | Academic/University |
| PI Contribution | Received data from sequencing project by Azad K. Kaushik's group (University of Guelph, Ontario, Canada) on 14/11/16. Data was sent to us by Thomas Nalpathamkalam (The Hospital for Sick Children, University of Toronto). Collaboration still ongoing for the purpose of analysis of transcription of bovine immune cell receptors. |
| Collaborator Contribution | Received data from sequencing project by Azad K. Kaushik's group (University of Guelph, Ontario, Canada) on 14/11/16. Data was sent to us by Thomas Nalpathamkalam (The Hospital for Sick Children, University of Toronto). Collaboration still ongoing for the purpose of analysis of transcription of bovine immune cell receptors. |
| Impact | n/a |
| Start Year | 2016 |
| Description | Festival of Genomics |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I participated as an expert on a panel to discuss the new and emerging technologies in high throughput sequencing, the cost implications and how these will impact upon the market/science. GF |
| Year(s) Of Engagement Activity | 2023 |
| URL | http://www.FLAV.org.uk |
| Description | KIR Workshop 2018 - Richard Borne |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Share work from PhD with researchers in the same field and to get feedback on the work. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://eventi.dynamicom.it/events/kir-workshop-2018/ |
| Description | Pirbright Internal Seminar - Richard Borne |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Share work from PhD with researchers in similar fields and to get feedback on the work. Made analysis pipeline known to other people who may have utility for it. |
| Year(s) Of Engagement Activity | 2018 |
| Description | RB - Research presentation at KIR Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Present research to scientists in the field to share information and get feedback on work. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Richard Borne - Improved mapping of RNA-seq data to immune gene complexes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Presented overview of work on "Improved mapping of RNA-seq data to immune gene complexes" to staff/students at the Pirbright Institute |
| Year(s) Of Engagement Activity | 2016 |
| Description | Richard Borne - Improved mapping of RNA-seq data to immune gene complexes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Present work to fellow students on improved mapping of RNA-seq data to immune gene complexes |
| Year(s) Of Engagement Activity | 2017 |
| Description | Richard Borne - Ribosome profiling of cattle NK cells: insights into the development of phenotypic variation and the impact on viral infection |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | Talk given at TGAC Signalling 2016 training course Main purpose to Introduce work and raise awareness |
| Year(s) Of Engagement Activity | 2016 |
| Description | Sir John Kingman (UKRI) visit |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Visit to highlight Pirbright science to UKRI |
| Year(s) Of Engagement Activity | 2019 |