Elucidation of the transcriptional programme of memory T cells by a systems approach

Lead Research Organisation: Imperial College London
Department Name: Life Sciences

Abstract

This project aims to reveal the fundamental molecular mechanisms of immunological memory at the gene level. Immunological memory is a unique attribute of the adaptive immune system and provides extremely efficient defense against pathogens. Because the immune system has this capacity, humans and animals (including mammals, birds, and fish) can efficiently eradicate life-threatening pathogens, especially viruses, that were once encountered in the past or for which they were immunised. Thus, immunological memory is essential for maintaining health and longevity, and the control of immunological memory will provide a mean for improving the prevention and treatment of infectious diseases, and for developing effective vaccines against pathogens such as HIV. It is, however, still unclear how immunological memory is determined and maintained in the immune system.

This study aims to reveal how immunological memory is provided by lymphocytes, especially in T cells. T cells coordinate the activities of other immune cells, and generate efficient and rapid responses to pathogens. Thus, not surprisingly, some viruses such as HIV target T cells, and thereby cause the major symptoms of acquired immune deficiency syndrome (AIDS). Memory T cells may play central roles both in immunity to pathogens and on vaccination. Research on memory T cells, however, has been difficult and will require multiple approaches, including immunology, molecular biology, and systems biology.

Thus, we will employ an integrated approach of immunology, molecular biology, genomics, and systems biology, and address how immunological memory is maintained in memory T cells at the gene level. Immunological and molecular approaches will identify which of already known molecules are involved in generation and function of memory T cells. Genomics will identify new molecular mechanisms for controlling memory T cells. The systems approach will identify the complex regulatory mechanisms between the molecules and thereby provide rigid frameworks to fully discover the mechanisms of the generation and function of memory T cells. These together will reveal the critical mechanisms that underlie T cell memory, which can then be exploited for the development of new immunosuppressive drugs and vaccine designs.

The project is designed to swiftly transfer knowledge and technology to industry, including the pharmaceutical industry. The understanding of the mechanism of T cell memory at the gene level is important not only for scientific progress but also for patency and for the development of new immunosuppressive drugs and vaccines. We also aim to use the findings of the project to improve the efficiency of the screening processes in the development of new drugs. The combined approach of experiments and mathematical modelling in this study can be directly used for screening processes for immunomodulative drugs, which can contribute to improve the cost performance of drug development at the preclinical stage.

This study is highly multidisciplinary. The applicant is an immunologist and molecular biologist, and has recently trained for genomics and systems biology. With this background, the applicant will coordinate collaborations with mathematical modellers, statisticians, and immunologists to provide the most efficient answers to this problem. The findings of this study will benefit broad scientific communities and contribute to health and well-being of humans and animals. In addition, this study will provide novel frameworks for systems biology, which can be used in many biological areas.

Technical Summary

The memory response is the key feature of immunological memory, where the immune system responds to antigens in a more rapid and efficient way than during the primary response. T cells are central to such adaptive responses, and memory T cells show a more rapid and efficient response upon antigenic stimulation. It is, however, still obscure how memory T cells are generated by encounter with pathogens, and how memory T cells efficiently respond to antigens and propagate activation through interacting with other T cells and antigen-presenting cells. In addition, currently memory T cells lack specific markers and can be identified only by the expression of a set of markers or their situation, which hampers the analysis of the dynamic response of memory T cells.
The major objectives of this study are to understand T cell memory as a network of proteins/genes or as a cell population, by a systems approach using time course analysis and mathematical modelling: (1) analysis of the gene regulatory mechanisms of T cell activation-related molecules in memory T cells during the memory response; (2) analysis of the propagation of the activation from memory T cells through the naive T cell pool. The dynamics of the activation of T cells will be analysed at single cell level. This will identify physiological memory T cell populations; (3) identification of the transcriptional regulations that are specific to memory T cells by time course analysis of these cells during the memory response using a novel framework of microarray analysis with a multidimensional technique. These three stand-alone approaches will elucidate the mechanisms at different levels of T cell memory, and together strengthen the biological relevance of this study. In addition, these will define memory T cells and thereby provide the basis for future studies and applications. In addition, the modelling and multidimensional frameworks to analyse memory T cells can be used in other areas of biology.

Planned Impact

The project will benefit the following groups and thereby contribute to human well-being and health, and enhance the economic competitiveness of the UK.

1) Pharmaceutical industry
The project will contribute to pharmaceutical industry by providing drug targets as well as screening methods for candidate compounds. First, the molecular mechanism of memory T cells will provide targets for immunoregulatory drugs. Second, the combined system of experiments and theories that will be established in the project can be used at the preclinical stage of development of immunosuppressive drugs. We plan to start collaborations with pharmaceutical industry and aim to realise these benefits within 2-10 years thereafter.

2) Biotechnological industry
The antibodies to key molecules in T cell memory will be widely used in immunology and related areas and their commercialisation will benefit the biotechnological industry. I will use my informal connections with biotechnological companies, starting collaborations with them in the lifetime of the project and aiming to realise these benefits within 1-3 years thereafter.

3) Immunisation practice and vaccine development
The monoclonal antibodies or molecular markers for memory T cells can be used for monitoring the effectiveness of immunisation, which will optimise immunisation plans. In addition, elucidation of the mechanisms of T cell memory will provide molecular targets for boosting the immune system, which can be exploited for vaccine development. These collectively will benefit public and global health and vaccine industry.

4) Governmental policy in public health regarding immunisation
The project will provide a modern understanding of the mechanisms of immunisation, which will make the governmental policy more effective in providing new plans for immunisation. We will liaise with the Research Council to transfer our knowledge to policy communities. This will be done within the lifetime of the project.

5) General Public
The project will benefit the health and the quality of life of the general public via three pathways: (a) improved healthcare service (see 6); (b) improved immunisation practice (see 3); and (c) in-depth understanding of immunisation. We will hold workshops to convey the frontline understanding of immunisation through educating pupils, which will improve their uptake of necessary vaccines at proper timings. We will publish the contents of these workshop to influence broad audience.

6) Health service
The project will contribute to improve health practice via three pathways. First, the findings of this project will promote studies in related clinical research areas to elucidate the molecular mechanism of immunity against pathogens. Second, the proposed project will identify drug target for controlling memory T cells to enhance immunity in aged people. The realisation of these benefits will be within 2- 10 years after the completion of the proposed project. Third, we will rapidly disseminate our findings to health and public health professionals by publishing our perspectives in medical journals for the successful development of the health service section.

7) Animal health
The project will contribute to improve health practice of animals, and thereby contribute to animal welfares, farming, and food production via three pathways: (i) effective development of vaccines (see 3); (ii) prevention and treatment of infectious disease including zoonosises. The realisation of these benefits will be within 2- 10 years after the completion of the proposed project.

8) Education and training of scientists
The project will nurture the involved post-doc and students to have a high quality research capacity by providing a wide range of skills and knowledge of experiments, modelling, and data analysis and their integration.

Publications

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Related Projects

Project Reference Relationship Related To Start End Award Value
BB/J013951/1 01/02/2013 30/04/2015 £1,335,113
BB/J013951/2 Transfer BB/J013951/1 01/05/2015 31/01/2019 £830,332
 
Description This project aimed to reveal the fundamental molecular mechanisms of immunological memory at the gene level. Specifically, it aimed to reveal how immunological memory is provided by lymphocytes, especially in T cells. To this end, we used an integrated approach of immunology, molecular biology, genomics, and systems biology, and developed new tools and thereby obtained new knowledge on the regulation of T cell memory responses.

During the lifetime of the project, we successfully developed a new experimental tool, Timer-of-Cell-Kinetics-and-Activity (Tocky), which allows analysis of time-dependent changes in T cells during immune responses (e.g. infection) or during development (i.e. when T cells are produced in the thymus) (Bending et al, J Cell Biol, 2018). Tocky uses a new reporter system using Fluorescent Timer protein, which spontaneously changes colour from blue to red, and computer algorithms to analyse Timer fluorescence data in individual cells. Thus Tocky analyses time-dependent changes in individual T cells and allows tracking of T cells at the single cell level.

In addition, using a systems biology approach, we established a new theoretical framework for understanding T cell memory and T cell regulation (which is currently understood as regulatory T cells) through analysing temporally-dynamic changes of T cell activities at single-cell level (Ono & Tanaka, Immunol Cell Biol, 2015).

The understanding of the mechanism of T cell memory at the gene level is important not only for scientific progress but also for patency and for the development of new immunosuppressive drugs and vaccines. To this end, we showed how Tocky can be used to analyse effects of immunotherapy on T cells and thus established a proof-of-concept for Tocky as a new method for strategic design of immunotherapy (Bending et al, EMBO J, 2018; Bending & Ono, Clin Exp Immunol, 2018). In addition, we have successfully identified new mechanisms for parasite infection (precisely, nematode, which is a major health problem for humans and animals in developing countries) using Tocky (manuscript in preparation), and this will have impacts on animal health and global health. Thus, the findings of this study will benefit broad scientific communities and contribute to health and well-being of humans and animals.

Furthermore, we developed new analysis methods for genomic data using a multidimensional analysis (Canonical Correspondence Analysis, CCA). Firstly, we developed a CCA based method for cross-analysis of biological functions and gene expression (Ono et al, BMC Genomics, 2014). Subsequently, we adapted this method to single cell data analysis, thereby analysed single cell RNA-seq data from tumour-infiltrating T cells, and showed the dynamic generation of effector memory T cells and regulatory T cells in tumours (Bradley et al, Front Immunol, 2018). Thus, the project provided novel frameworks for systems biology, which can be used in many biological areas.
Exploitation Route We have provided our new experimental tools to the research groups in the following areas on a collaboration basis:
(1) Groups working on investigating human viral infections
(2) Groups working on cancer immunology
(3) Groups working on autophagy and molecular biology
(4) Groups working on immunology

Studies by ourselves and these collaborations are considered to benefit the following groups:
(1) Groups working on developing vaccines (clinical, veterinary, and basic vaccinology).
(2) Groups working on drug development (research sections of the pharmaceutical industry).
(3) Groups working on cellular differentiation (genomicists, bioinformaticians, developmental biologists, stem cell research).
(4) Groups working on analysing complex biological data (biostatisticians, bioinformaticians, biomathematicians, systems biologists)
(5) Groups working on the activities of transcription factors (molecular biologists, biochemists, developmental biologists).
(6) Groups working on mammalian (including humans) and bird pathogens (medical and agricultural/veterinary infectionologists, bacteriologists, virologists)
Sectors Agriculture, Food and Drink,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Our research by the Tocky technology was communicated by several media: • Two news stories released by Imperial in 2018 - "Watching the immune system in action reveals what happens when things goes wrong", 25 June 2018, Imperial College website (news article for Bending et al, J Cell Biol, 2018) - Immune cells can switch from 'gang members' to 'police officers', 25 June 2018, Imperial College website (Bending et al, EMBO J, 2018 and Bradley et al, Front Immunol, 2018) • The online news, Multiple Sclerosis News Today, released two news stories: - "Overreactive T-cells Can Transition into T-cells That Control the Immune Response, Study Shows", 12th July 2018 - "New Fluorescent Imaging Tool Allows Researchers to Track Immune Cell Dynamics in MS Mouse Model", June 27, 2018 • My article about Tocky was published in Yahoo Japan News, and obtained 20k views to date.
First Year Of Impact 2018
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

 
Description BBSRC Impact Acceleration Account 2015-2016
Amount £14,909 (GBP)
Funding ID 4020012831 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2015 
End 06/2016
 
Description CRCE pump priming collaborative pilot project grant
Amount £29,913 (GBP)
Organisation Imperial College London 
Sector Academic/University
Country United Kingdom
Start 09/2017 
End 08/2018
 
Description Development of vaccine for gastrointestinal nematode parasite of livestock
Amount £40,257 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2016 
End 03/2017
 
Description Facility usage at the University of Tokushima, Japan
Amount ¥500,000 (JPY)
Organisation University of Tokushima 
Sector Academic/University
Country Japan
Start 09/2016 
End 03/2017
 
Description Investigating the molecular mechanisms downstream of T cell receptor signalling during T cell differentiation and response.
Amount £8,541,424 (GBP)
Funding ID 1814289 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2020
 
Description Investigation of the generation and functional maturation of regulatory T cells in vivo
Amount £492,938 (GBP)
Funding ID MR/S000208/1 
Organisation Imperial College London 
Sector Academic/University
Country United Kingdom
Start 02/2019 
End 01/2022
 
Description Repurposing computational tools to evaluate anti-cancer immunity for development of cancer immunotherapy
Amount £21,476 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 03/2017
 
Title Single cell RNA-seq analysis method 
Description Our multidimensional methods Canonical Correspondence Analysis (CCA) was adapted to single cell RNA-seq data analysis, and designated as Single Cell Combinatorial CCA (SC4A) (Bradley et al, Frontiers in Immunology, 2018) 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact The paper obtained a good online attention (Altemetric score 50), and this led to (1) an award of a JSPS grant from the Japanese government; and (2) a new collaboration with Prof Kinya Otsu, Kings College London. 
 
Title Timer of Cell Kinetics and Activity (Tocky) 
Description A novel transgenic reporter method, Timer of Cell Kinetics and Activity (Tocky) was established for analysing in vivo temporal dynamics of transcriptional activities and cellular differentiation in vivo. This system uses transgenic reporter mice using Fluorescent Timer protein and computational algorithms to analyse Timer fluorescence data. 
Type Of Material Model of mechanisms or symptoms - mammalian in vivo 
Year Produced 2018 
Provided To Others? No  
Impact Our tool paper (Bending et al, J Cell Biol, 2018) received a high online attention (Altmetric score >100; F1000 recommendation). • Seven new collaborations were established for sharing the Tocky tools. • Seminar invitations (including Oxford, Kings College London, UCL, University of Birmingham, Technical University of Munich, Kyoto University [by Prof Tasuku Honjo, the Nobel Laureate 2018]) • Invitations to conference key note talk (Japanese Biochemical Society) 
 
Title Canonical Correspondence Analysis 
Description We have adapted Canonical Correspondence Analysis to analyse immunological genomic data including microarray and RNA-sequencing data. 
Type Of Material Data analysis technique 
Year Produced 2014 
Provided To Others? Yes  
Impact The data analysis tool has been used by the following publications: Kenefeck et al, J Clin Inv, 2015; Sahni et al, Oncotarget, 2015; Sinclair et al, Immunol Cell Biol, 2015. 
URL http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-1028
 
Description Julie Josse 
Organisation Agrocampus Ouest
Department Laboratory of Applied Mathematics Agrocampus (LMA)
Country France 
Sector Academic/University 
PI Contribution To lead a collaborative project, providing experimental data and performing data analysis.
Collaborator Contribution To provide statistical knowledge.
Impact One publication (Fujii et al, J Immunol, 2016). We have applied for a BBSRC funding with Julie Josse in Agrocampus Ouest as a collaborator.
Start Year 2013
 
Description Reiko J Tanaka 
Organisation Imperial College London
Department Department of Bioengineering
Country United Kingdom 
Sector Academic/University 
PI Contribution To lead a collaborative project, provide experimental data and data anlaysis.
Collaborator Contribution To provide mathematical analysis.
Impact With Dr Reiko J Tanaka in the organisation as a co-PI, I have been awarded a BBSRC IAA. The collaboration is multi-disciplinary involving immunology, molecular biology, mathematical modelling, multidimensional data analysis.
Start Year 2013
 
Description Visiting Associate Professorship, University of Kumamoto 
Organisation University of Kumamoto
Department International Research Center for Medical Sciences
Country Japan 
Sector Academic/University 
PI Contribution Dr Yorifumi Satou is a collaborator at the institute of the University. I have provided my data analysis skills to their research.
Collaborator Contribution The institute has offered me a visiting associate professorship, so that the collaboration can be further deepened to enable research visits and also apply for funding.
Impact This is a multidisciplinary collaboration between immunology and haematology.
Start Year 2017
 
Description Immuno-dancing 
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 Immuno-dancing: I have established a novel way to convey immunology to primary school pupils by combining immunology with dancing (which I have named Immuno-dancing). The session is composed of two activities: (1) 14~15 pupils dance in a ring, and thereby become a big macrophage, which is a special immune cell dedicated for eating germs; (2) to learn Division of Labour of the immune system. We make 3 groups (dendritic cells, B cells, macrophages), and each of which has 5-6 pupils. The roles are given to each groups, to understand how immune cells coordinate an immune response. We have done the Immuno-dancing in a local primary school with a great success, and will continue developing the method.
Year(s) Of Engagement Activity 2016
 
Description Immunology workshop for primary school 2018 
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 We delivered a workshop for immunological memory and vaccination to a primary school (St Clemant Danes CoE primary school, London).
Year(s) Of Engagement Activity 2018
 
Description Powys Dance CELL Project 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact On behalf of Imperial's Outreach Department, I have been collaborating with a Welsh dance company (Powys Dance) for the production of the show CELL DANCE. We have given scientific inputs to the choreographer, dancers, music composer, and inflatable artist. The show will visualise (1) the research life and lab; (2) cells; (3) T cell response; and DNA and chromatin. The first show will be at Imperial in July 2019, and Powys Dance will do a tour in Wales. We will also produce a website (will be hosted by Imperial) to provide scientific backgrounds to children and teachers. Furthermore, we are preparing to produce a comic for the show.
The impact is so far ~10 artists involved (since the show is still being prepared) but after the release of website and the tour, we expect that we can reach more than 500 people.
Year(s) Of Engagement Activity 2018