Analysing antibacterial immunity from two sides: host versus pathogen
Lead Research Organisation:
Imperial College London
Department Name: Infectious Disease
Abstract
Bacterial infections represent a major problem to human health; often causing life-threatening diseases and persistent infections that can require extensive treatment with antibiotics. Salmonella causes a range of disease in humans, from gastro-enteritis to typhoid fever and is also prevalent in animals such as cattle, which can have serious economic consequences as well as public health implications.
Normally, upon infection, host cells respond to bacterial products, activating a cascade of events that culminate in the production of molecules that trigger a robust immune defence programme to inactivate the bacteria. Many bacteria, including Salmonella, manipulate these host responses by the action of so-called virulence factors, producing a complex interaction between the host immune response and the incoming pathogen. This project on the one hand aims to understand how bacterial virulence factors produced and transported into host cells alter the outcome of infection to the advantage of the pathogen. We have identified several virulence factors that modulate host cell responses and we will now characterise their mechanism of action in detail. Deciphering how these virulence factors influence immune signalling cascades during infection provides valuable insight into what makes the bacteria pathogenic, provides important information on host processes that are targeted by the pathogen and is likely to provide valuable information for vaccine design and novel therapeutics.
To complement this, research efforts are required to understand in molecular detail novel host mechanisms that restrict bacterial pathogens. Therefore, this project will also investigate the role of a family of host molecules (a group of proteins) that are called TRIMs. Research efforts have focused on TRIM function during viral infection but few have been studied in detail and the family remains poorly characterised during bacterial infection. Despite this, several lines of evidence suggest they have important functions upon host infection with bacteria. Therefore, I shall study how this group of proteins responds to bacterial infection and determine whether they can restrict the growth of bacteria within cells. These findings will reveal new functions for these proteins, many of which when mutated cause disease. Ultimately, with the improved understanding of host immune responses we are better informed on the best methods to combat bacterial infection. This is an important consideration given the rapidly developing rise in antibiotic resistant bacterial species.
Normally, upon infection, host cells respond to bacterial products, activating a cascade of events that culminate in the production of molecules that trigger a robust immune defence programme to inactivate the bacteria. Many bacteria, including Salmonella, manipulate these host responses by the action of so-called virulence factors, producing a complex interaction between the host immune response and the incoming pathogen. This project on the one hand aims to understand how bacterial virulence factors produced and transported into host cells alter the outcome of infection to the advantage of the pathogen. We have identified several virulence factors that modulate host cell responses and we will now characterise their mechanism of action in detail. Deciphering how these virulence factors influence immune signalling cascades during infection provides valuable insight into what makes the bacteria pathogenic, provides important information on host processes that are targeted by the pathogen and is likely to provide valuable information for vaccine design and novel therapeutics.
To complement this, research efforts are required to understand in molecular detail novel host mechanisms that restrict bacterial pathogens. Therefore, this project will also investigate the role of a family of host molecules (a group of proteins) that are called TRIMs. Research efforts have focused on TRIM function during viral infection but few have been studied in detail and the family remains poorly characterised during bacterial infection. Despite this, several lines of evidence suggest they have important functions upon host infection with bacteria. Therefore, I shall study how this group of proteins responds to bacterial infection and determine whether they can restrict the growth of bacteria within cells. These findings will reveal new functions for these proteins, many of which when mutated cause disease. Ultimately, with the improved understanding of host immune responses we are better informed on the best methods to combat bacterial infection. This is an important consideration given the rapidly developing rise in antibiotic resistant bacterial species.
Technical Summary
Innate immunity provides a first line of defence against pathogens and is essential for inducing the adaptive arm of immunity and ultimately, pathogen clearance. Numerous pathogens, including the intracellular bacterium Salmonella enterica, serovars of which cause gastroenteritis and typhoid fever, interfere with innate immune responses, contributing to pathogenicity. My overall goal is to investigate the complex host-pathogen interactions that mediate the outcome of infection. Using a multidisciplinary approach encompassing proteomics, cell biology and structural biology, I will elucidate the molecular mechanisms by which virulence "effector" proteins, delivered across host membranes via type-3-secretion systems, contribute to innate immune modulation and ultimately the pathology of infection.
To complement this, I will study the host family of TRIM E3 ligases, the majority of which transfer ubiquitin to substrates. TRIMs function in a variety of core host cell processes including; cell differentiation, inflammation and innate immune signalling and mutations in a number of TRIMs are associated with diverse diseases. However, their role in antibacterial immunity is poorly characterised. I will investigate their regulation, sub-cellular localisation and function during bacterial infection.
Together, this study on fundamental bioscience will provide valuable insight into the pathophysiology of bacterial infections and provide key information on innate immune signalling pathways as well as having potential clinical and/or therapeutic applications in the future. All of this is important with respect to the rising risk of antibiotic resistant pathogens, including Salmonella.
To complement this, I will study the host family of TRIM E3 ligases, the majority of which transfer ubiquitin to substrates. TRIMs function in a variety of core host cell processes including; cell differentiation, inflammation and innate immune signalling and mutations in a number of TRIMs are associated with diverse diseases. However, their role in antibacterial immunity is poorly characterised. I will investigate their regulation, sub-cellular localisation and function during bacterial infection.
Together, this study on fundamental bioscience will provide valuable insight into the pathophysiology of bacterial infections and provide key information on innate immune signalling pathways as well as having potential clinical and/or therapeutic applications in the future. All of this is important with respect to the rising risk of antibiotic resistant pathogens, including Salmonella.
Planned Impact
This research will have far-reaching impact beyond the Salmonella and TRIM academic fields.
1. General public- This proposal falls under the remit of the BBSRC's vision into improving the health and wellbeing of humans. Salmonella is one of the most common zoonotic diseases, spreading between animals and humans. It causes significant socioeconomic and health implications throughout the world, especially in Sub-Saharan Africa where non-typhoidal strains of Salmonella cause high rates of death in patients who are mal nourished, HIV positive or infected with malaria. Fundamental biomedical research that increases the understanding of Salmonella virulence mechanisms and host innate immune signalling pathways that attenuate bacterial infection will, in the long term, have impact on the general public, both with respect to health and economics. In addition I will add to this by partaking in specific programmes for public engagement such as the "Superbug Zone" which disseminates the CMBI research on bacterial pathogens and "Soapbox Science" which promotes women scientists and the research they conduct.
2. Junior Researchers- I will ensure that the staff and students I supervise will develop a wide range of technical expertise from protein affinity purification to mouse work, flow cytometry and confocal microscopy. In addition, lab members will develop critical skills for planning and executing experiments that are ethical and rigorous in design. Moreover, I will help them develop transferable skills that include written and oral communication both to expert and general audiences, organisation and literature investigation.
3. Young scientists- During the award I aim to engage the next generation on the importance of antimicrobial resistance and bacterial infections on human health. I will do this is by generating excitement about science through speaking to schoolchildren about my research, providing advice on studying science at school and university and hosting sixth form students for short laboratory experiences, which I've done before.
4. Biotechnology and pharmaceutical companies- One aim of my project is to understand at a molecular level the role of Salmonella virulence proteins in modulating host immune responses. In the longer term, this could attract R&D investment and inform research by companies that are interested in developing novel drugs for inhibiting bacteria, using bacteria to deliver therapeutics or in vaccine development. In addition, my research into TRIM E3 ligases may be of therapeutic interest. Abnormalities in numerous TRIMs are associated with human diseases, for example cancer, inflammatory diseases, neuronal function and infectious diseases. My research aims to catalogue the function of TRIMs in antibacterial immunity and uncover new functions, which will inform the biology of TRIM-associated diseases. In the longer term, this could impact clinicians, potentially producing diagnostic tools and will help identify which TRIMs are candidates for novel therapeutic manipulation for treating diseases that impact on the health and wellbeing of humans. In this respect, TRIM-edicine investigates TRIM72 among other proteins for therapeutic approaches to target cellular pathways altered in disease, highlighting that such ideas are not too far-reaching. Whilst it is not possible to predict with certainty whether intellectual property will emerge from the planned work, any potential commercialisation and exploitation of scientific knowledge will be protected properly by patents through Imperial College and its technology transfer company Innovations.
5. Academic beneficiaries- These are detailed in another section but in brief I will disseminate my research to broad audiences by attending both national and international conferences and workshops, partaking in various research networks (e.g. London Inflammation Network) and by forming new collaborations with scientists in diverse fields.
1. General public- This proposal falls under the remit of the BBSRC's vision into improving the health and wellbeing of humans. Salmonella is one of the most common zoonotic diseases, spreading between animals and humans. It causes significant socioeconomic and health implications throughout the world, especially in Sub-Saharan Africa where non-typhoidal strains of Salmonella cause high rates of death in patients who are mal nourished, HIV positive or infected with malaria. Fundamental biomedical research that increases the understanding of Salmonella virulence mechanisms and host innate immune signalling pathways that attenuate bacterial infection will, in the long term, have impact on the general public, both with respect to health and economics. In addition I will add to this by partaking in specific programmes for public engagement such as the "Superbug Zone" which disseminates the CMBI research on bacterial pathogens and "Soapbox Science" which promotes women scientists and the research they conduct.
2. Junior Researchers- I will ensure that the staff and students I supervise will develop a wide range of technical expertise from protein affinity purification to mouse work, flow cytometry and confocal microscopy. In addition, lab members will develop critical skills for planning and executing experiments that are ethical and rigorous in design. Moreover, I will help them develop transferable skills that include written and oral communication both to expert and general audiences, organisation and literature investigation.
3. Young scientists- During the award I aim to engage the next generation on the importance of antimicrobial resistance and bacterial infections on human health. I will do this is by generating excitement about science through speaking to schoolchildren about my research, providing advice on studying science at school and university and hosting sixth form students for short laboratory experiences, which I've done before.
4. Biotechnology and pharmaceutical companies- One aim of my project is to understand at a molecular level the role of Salmonella virulence proteins in modulating host immune responses. In the longer term, this could attract R&D investment and inform research by companies that are interested in developing novel drugs for inhibiting bacteria, using bacteria to deliver therapeutics or in vaccine development. In addition, my research into TRIM E3 ligases may be of therapeutic interest. Abnormalities in numerous TRIMs are associated with human diseases, for example cancer, inflammatory diseases, neuronal function and infectious diseases. My research aims to catalogue the function of TRIMs in antibacterial immunity and uncover new functions, which will inform the biology of TRIM-associated diseases. In the longer term, this could impact clinicians, potentially producing diagnostic tools and will help identify which TRIMs are candidates for novel therapeutic manipulation for treating diseases that impact on the health and wellbeing of humans. In this respect, TRIM-edicine investigates TRIM72 among other proteins for therapeutic approaches to target cellular pathways altered in disease, highlighting that such ideas are not too far-reaching. Whilst it is not possible to predict with certainty whether intellectual property will emerge from the planned work, any potential commercialisation and exploitation of scientific knowledge will be protected properly by patents through Imperial College and its technology transfer company Innovations.
5. Academic beneficiaries- These are detailed in another section but in brief I will disseminate my research to broad audiences by attending both national and international conferences and workshops, partaking in various research networks (e.g. London Inflammation Network) and by forming new collaborations with scientists in diverse fields.
Publications
Panagi I
(2020)
Salmonella Effector SteE Converts the Mammalian Serine/Threonine Kinase GSK3 into a Tyrosine Kinase to Direct Macrophage Polarization.
in Cell host & microbe
Pham THM
(2020)
Salmonella-Driven Polarization of Granuloma Macrophages Antagonizes TNF-Mediated Pathogen Restriction during Persistent Infection.
in Cell host & microbe
Panagi I
(2023)
Ready, STAT3, Go! Bacteria in the race for M2 macrophage polarisation.
in Current opinion in microbiology
Schroeder GN
(2021)
Editorial: Bacterial Effectors as Drivers of Human Disease: Models, Methods, Mechanisms.
in Frontiers in cellular and infection microbiology
Mak H
(2021)
Interesting Biochemistries in the Structure and Function of Bacterial Effectors.
in Frontiers in cellular and infection microbiology
Rajpoot S
(2021)
TIRAP in the Mechanism of Inflammation.
in Frontiers in immunology
Aleksandrowicz A
(2024)
Membrane properties modulation by SanA: implications for xenobiotic resistance in Salmonella Typhimurium
in Frontiers in Microbiology
Switzer A
(2022)
A Role for the RNA Polymerase Gene Specificity Factor s54 in the Uniform Colony Growth of Uropathogenic Escherichia coli.
in Journal of bacteriology
Thurston T
(2023)
The Salmonella Typhi SPI-2 injectisome enigma
in Microbiology
Pillay TD
(2023)
Speaking the host language: how Salmonella effector proteins manipulate the host.
in Microbiology (Reading, England)
Szczesna M
(2023)
Dedicated bacterial esterases reverse lipopolysaccharide ubiquitylation to block immune sensing.
in Research square
Jennings E
(2018)
Structure-function analyses of the bacterial zinc metalloprotease effector protein GtgA uncover key residues required for deactivating NF-?B.
in The Journal of biological chemistry
Aleksandrowicz A
(2024)
SanA is an inner membrane protein mediating the early stages of Salmonella infection
Description | Salmonella enterica is a bacterial pathogen that causes a range of diseases in humans, from gastro-enteritis to typhoid fever. It is also prevalent in animals such as cattle and chickens and can infect humans via contaminated food products. Our research has discovered how one of the Salmonella virulence factors (called SteE), which promotes the virulence of Salmonella, functions within side host cells. SteE is a small bacterial protein that interacts with a protein found in host cells. This interaction changes the activity of the host protein, so that it obtains a new function it wouldn't otherwise have. In this way, Salmonella manipulates the host cell that it lives in, creating a more favourable environment that is anti-inflammatory and beneficial to the long term survival of Salmonella within the host. |
Exploitation Route | These findings describe in molecular detail a new way in which Salmonella manipulates the host immune response to promote virulence. This could have long-term future implications for academic research in combatting Salmonella infection from humans and animals. Understanding how the pathogen and host interact is essential for longer-term research into the impact of Salmonella on human health and the food (eg chicken) industry. It also provides fundamental knowledge for future curiosity driven research. |
Sectors | Agriculture, Food and Drink,Healthcare |
Description | Deciphering the molecular mechanisms and physiological consequences of macrophage polarisation during Salmonella infection |
Amount | £808,297 (GBP) |
Funding ID | MR/V031058/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 11/2021 |
End | 10/2024 |
Description | Functional analysis of immune-modulatory Salmonella virulence proteins |
Amount | £75,000 (GBP) |
Funding ID | 2144804 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 10/2018 |
End | 03/2022 |
Description | Prof Denise Monack |
Organisation | Stanford University |
Country | United States |
Sector | Academic/University |
PI Contribution | We shared unpublished findings with the Monack lab so that we could form a collaboration on the in vivo analysis of the Salmonella effector SteE during granuloma formation |
Collaborator Contribution | The Monack lab provided in vivo data for macrophage polarisation during Salmonella infection of mice. This data was included in our publication (Panagi et al., 2020) In addition the Monack lab led an in vivo study (Pham et al., 2020) for which I became an author. |
Impact | Publications that include work from the collaboration are 1. Panagi I, Jennings E, Zeng Z, Günster RA, Stones CD, Mak H, Jin E, Stapels DAC, Subari NZ, Pham THM, Brewer SM, Ong SYQ, Monack DM, Helaine S, Thurston TLM. The Salmonella effector SteE converts the mammalian serine/threonine kinase GSK3 into a tyrosine kinase. Cell Host & Microbe. 2020 Jan 8;27(1):41-53.e6. The collaboration has a multi-disciplinary element where my laboratory carried out the biochemical and cell biological analysis and the Monack lab provided in vivo infection data. 2. Pham THM, Brewer SM, Thurston TLM, Massis L, Honeycutt J, Jacobson AR, Vilches-Moure JG, Lugo K, Helaine S, Monack DM. Salmonella-Driven Polarization of Granuloma Macrophages Counteracts TNF-Mediated Pathogen Restriction During Persistent Infection. Cell Host & Microbe. 2020 Jan 8;27(1):54-67.e5. |
Start Year | 2018 |
Description | Rittinger |
Organisation | Francis Crick Institute |
Department | Mill Hill Laboratory |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | I provided expertise in the area of host pathogen interaction, innate immune signalling and infection biology as well as the leading the research direction of the project and provided the lead training to the PhD student who worked on this collaboration. |
Collaborator Contribution | Our collaborators provided critical advice, support, reagents and access to equipment in the area of structural biology and x-ray crystallography. The collaborating group helped train my PhD student in the use of software and provided essential experimental guidance as well as data that was used in publication. |
Impact | Under this award, the collaboration resulted in one publication to date DOI 10.1074/jbc.RA118.004255 The collaboration was multi-disciplinary, bringing my expertise in host cell signaling, innate immunity and infection biology together with that of structural and biochemical experts from the Francis Crick Institute. |
Start Year | 2017 |
Description | Sophie Helaine |
Organisation | Imperial College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Sharing of knowledge and experimental data in relation to immune signalling and bacterial pathogenesis |
Collaborator Contribution | Sharing of knowledge and experimental data relating to macrophage polarisation |
Impact | PMID: 31862381 PMID: 31883922 |
Start Year | 2018 |
Description | Steven Ley |
Organisation | Imperial College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We supported work with bacterial pathogens in the study of innate immune signaling and phagosome biology. A student from the Ley lab spent some time in our lab learning techniques and gathering data. |
Collaborator Contribution | The collaborator is the lead of the project. |
Impact | A manuscript is under revision for publication. |
Start Year | 2019 |
Description | Ubiquitin-based collaboration with Pruneda |
Organisation | Oregon Health and Science University |
Country | United States |
Sector | Academic/University |
PI Contribution | We bring expertise in bacterial effector biology, microbiology, cell biology as well as structural biology. Intellectually the project arose in this laboratory. |
Collaborator Contribution | Our partner provided intellectual input in structural biology and has carried out some experiments in their laboratory based on our findings. |
Impact | It is a multi-disciplinary collaboration involving infection biology, cell biology, genetics and microbiology together with structural biology. A manuscript is in preparation. |
Start Year | 2022 |
Description | Career panel member |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Postgraduate students |
Results and Impact | Activity involved either short presentation about career progress followed by questions (2021; University of Birmingham) or panel career event with Q&A (2022; Imperial College London). |
Year(s) Of Engagement Activity | 2021,2022 |
Description | Hosting school students in the laboratory |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | A school pupil who is seeing a laboratory experience prior to applying to university is given the chance to spend up to one week shadowing and learning about microbiology in the laboratory. |
Year(s) Of Engagement Activity | 2021,2022 |
Description | Imperial Festival - The Superbug Zone |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Superbug zone runs as part of Imperial Science Festival over a weekend, on a yearly basis. My team helped run several different stalls and activities that represent the research we conduct at our Centre on bacteria. The purpose is to discuss with general public and especially children, that bacteria can be both good and bad, that they live in the body and that our immune system can fight bacteria. Games illustrate how bacteria fight back against the body's immune system and also antibiotics. Lots of questions arise from the public and these are discussed. |
Year(s) Of Engagement Activity | 2019 |