2025-26 Project (Osborn & Chong)

Developing a novel model of mycobacterial infection to study human granulomatous disease.

SUPERVISORY TEAM

Supervisor

Dr Dan Osborn at City St George’s
Email: dosborn@sgul.ac.uk

Co-Supervisor

Dr Deborah Chong at City St George’s
Email: dchong@sgul.ac.uk

PROJECT SUMMARY

Project Summary

Mycobacterial infections are a complex set of human diseases that are a global health problem. The host response to mycobacterial infections is important in driving inflammation and tissue remodelling but this process is ill-defined. Furthermore, better models of mycobacterial infection that mirror human disease are needed, so we can better understand early host-mycobacterial interactions that cause immunopathology.    

This PhD project will involve the development of a new model of Mycobacterium marinum infection using zebrafish to study innate immune and tissue remodelling responses that cause tissue damage. Alongside mastering zebrafish husbandry and microbiological skills, the student will use a range of molecular and cellular techniques including qPCR, CRISPR-cas9 and live confocal microscopy. Overall, this exciting project will provide the student with an excellent foundation in immunology to greatly increase our understanding of mycobacterial infection to improve human health.

Project Key Words

Mycobacterial infection, innate immunity, inflammation, zebrafish

MRC LID Themes

  1. Infectious Disease
  2. Global Health
  3. Translational and Implementation Research
  4. Health Data Science

Skills

MRC Core Skills

  1. Whole organism physiology
  2. Quantitative skills
  3. Interdisciplinary skills

Skills we expect a student to develop/acquire whilst pursuing this project

The student will be trained in various techniques to define host-mycobacterial interactions in zebrafish. This will include: 

(i) zebrafish husbandry 
(ii) microbiology techniques involving M.marinum  
(iii) RNA-Seq transcriptomic analysis of mycobacterial and host genes 
(iv) molecular and cellular biology techniques, including qPCR and in vivo confocal microscopy. 
(v) gene editing techniques, including CRISPR-Cas9

Routes

Which route/s are available with this project?

  • 1+4 = Yes
  • +4 = Yes

Possible Master’s programme options identified by supervisory team for 1+4 applicants:

  • City St George’s – MRes Biomedical Science – Infection and Immunity

Full-time/Part-time Study

Is this project available for full-time study? Yes
Is this project available for part-time study? Yes

Location & Travel

Students funded through MRC LID are expected to work on site at their primary institution, meeting – at the minimum – the institutional research degree regulations and expectations. Students may also be required to travel for conferences (up to 3 over the duration of the studentship), and for any required training (for research degree study). Other travel expectations and opportunities highlighted by the supervisory team are noted below.

Primary location for duration of this research degree: City St George’s, London

Travel requirements for this project: None

Eligibility/Requirements

Particular prior educational requirements for a student undertaking this project

  • Minimum City St George’s institutional eligibility criteria for doctoral study.
  • BSc at 2.1 or above or MSc in an appropriate related subject area

Other useful information

  • Potential Industrial CASE (iCASE) conversion? = No

PROJECT IN MORE DETAIL

Scientific description of this research project

Scientific rationale:
Mycobacterial infections, including Tuberculosis (TB) and non-tuberculous mycobacteria (NTM) represent a global health problem. Innate immune responses (e.g. neutrophils and macrophages) are key drivers of granuloma formation during mycobacterial infection. However, the precise cellular networks leading to tissue remodelling are poorly understood and there are no host-directed therapies available to prevent tissue damage.   

To dissect the host response to TB, animal models are required. However, often mammalian models do not fully recapitulate human pathology. Mycobacterium marinum, a NTM that infects zebrafish, can cause human skin infection and granulomatous disease. As M.marinum is genetically closely related to TB, host responses and pathogenesis elicited by both mycobacterial species are assumed to be similar. Lastly, as zebrafish also have innate immunity, they would represent a powerful tool to investigate early host-mycobacterial interactions driving immunopathology, similar to those in humans.    

Project aim:
To develop a novel zebrafish model of mycobacterial infection and define mycobacterial-host responses driving immunopathology.   

Project objectives: 
1.) Develop a new zebrafish embryo model of M.marium infection. 
2.) Investigate inflammatory and tissue remodelling responses to M.marinum infection in zebrafish. 
3.) Identify gene expression changes in M.marium and infected zebrafish. 
4.) Dissect cellular networks driving tissue remodelling using transgenics lacking or labelling identified key immune or tissue remodelling mediators.   

Techniques to be used:
Wild-type, Tg(mpx:EGFP, neutrophil-labelled) or Tg(MPEG1:mCherry, macrophage-labelled) zebrafish embryos (1 day post-fertilisation) will be injected with 10^4-10^7 M.marinum in the caudal vein and maintained at 28’C for 5 days. Immune cell recruitment and tissue remodelling events will be observed by in vivo confocal microscopy and cell lysates collected to determine bacterial burden. To further dissect mycobacterial-host responses, RNA will be collected for RNA-Seq transcriptomic analysis of M.marinum and zebrafish (host) genes. Identified host candidate genes will be validated by qPCR and in situ hybridisation. Lastly, CRISPR mutant zebrafish will be created to investigate the role of identified host candidate genes in mediating inflammatory and tissue remodelling responses to M.marinum infection.   

Confirmed availability of required materials:
At CSGUL, we have a modern zebrafish facility and Dr Osborn has ethical approval to work with zebrafish and create new transgenics lines as necessary. Approval to work with M.marinum within a designated microbiology lab at CSGUL is being established and training will be provided to the student.    

Additional outcomes:
By developing a new animal model of mycobacterial infection, the student may be able to identify and test novel therapeutic targets to prevent mycobacterial immunopathology. This project has the potential for publication in high impact factor journals and data presentation at national and international conferences.    

Potential risk & mitigation plans:
By using a dual RNA-Seq approach, we will be able to define gene expression changes in both M.marinum and infected zebrafish (host). If we are unable to identify any key host mediators driving immunopathology, we will focus on mycobacterial genes responsible for infection and survival. 

Further reading

Relevant preprints and/or open access articles
(DOI = Digital Object Identifier)

  • Varela M & Meijer AH. A fresh look at mycobacterial pathogenicity with the zebrafish host model. Mol Microbiol. 2021. 117(3):661. doi: 10.1111/mmi.14838
  • Ramakrishnan L. Revisiting the role of the granuloma in tuberculosis. Nat Rev Immunol. 2012. 12(5):352-66. doi: 10.1038/nri3211

Additional information from the supervisory team

The supervisory team has provided a recording for prospective applicants who are interested in their project. This recording should be watched before any discussions begin with the supervisory team.

Osborn-Chong recording

MRC LID LINKS

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