2025-26 Project (Bull & Kipkorir & Saldaña)

Defining chronic intracellular mechanisms of persistence driving mycobacterial disease

SUPERVISORY TEAM

Supervisor

Professor Tim Bull at City St George’s
Email: tim.bull@sgul.ac.uk

Co-Supervisor

Dr Terry Kipkorir at LSHTM
Email: terry.kipkorir@lshtm.ac.uk

Co-Supervisor

Dr José Saldaña at City St George’s
Email: jsaldana@sgul.ac.uk

PROJECT SUMMARY

Project Summary

Mycobacterium tuberculosis is the world’s most successful pathogen. It can sense host environments and switch phenotypes to either grow and establish acute infection, inflammation and tissue destruction or await more suitable conditions by entering a persistent intracellular latent state, avoiding clearance and triggering chronic dysregulatory control able to weaken critical host immune capacity. Understanding how, why and when mycobacterial pathogens establish tolerance, long-term intracellular persistence and control of immune cell populations is important to improve interventions and diagnostics. In this project you will validate our newly developed macrophage/mycobacterial long-term infection model to generate persistent, intracellular mycobacterial phenotypes, then use the model to investigate and define critical host-pathogen interactions involved during development of latency. The work offers experience in cell/bacterial culture in a high containment setting, RNA-seq based genomics, flow cytometry and in-depth large data bioinformatic comparative analysis of expression and functional pathways relating to mechanisms of mycobacterial pathogenesis in humans.

Project Key Words

Mycobacteria, molecular, pathogenomics, chronic infectious disease

MRC LID Themes

  1. Infectious Disease
  2. Global Health

Skills

MRC Core Skills

  1. Quantitative skills
  2. Interdisciplinary skills

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

* Microbiological techniques for the handling and manipulation of both eukaryotic and pathogenic prokaryotic cells
* Storage, processing and handling of samples, with particular emphasis on RNA and DNA 
* Genomic sequencing
* Bioinformatic and statistical analysis with interpretation including study of differential relatedness to biological pathways and host-pathogen interactions   
* Immunological techniques including ELISA and flow cytometry
* Generic skills including lierature searching, scientific writing, oral presentation and general skills in scientific presentation

Routes

Which route/s are available with this project?

  • 1+4 = No
  • +4 = Yes

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

  • Not applicable

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: The student will have the opportunity to attend in person at least one related scientific colloquium per year including at least one international conference.

Eligibility/Requirements

Particular prior educational requirements for a student undertaking this project

  • Minimum City St George’s institutional eligibility criteria for doctoral study.
  • Master in Science or Research in a biomedical/medical field  (1st or 2i). A good knowledge of cell biology is required and a  keen interest in infectious diseases.
  • Previous experience in a laboratory setting would be advantageous

Other useful information

  • Potential Industrial CASE (iCASE) conversion? = No

PROJECT IN MORE DETAIL

Scientific description of this research project

Aim:
Describe the critical mechanisms, used by pathogenic mycobacteria to establish tolerance and long-term intracellular persistence in immune cell populations, which influence long term disease progression.

Rationale:
In only a minority of instances mycobacterial infection manifests acutely, marked by bacterial cell division, inflammation and tissue destruction. In the most part, mycobacterial pathogens sense their host environment and switch to a viable non-dividing phenotype. This allows them to  persist intracellularly without being cleared and provides opportunity to await more suitable environmental conditions for growth and to encourage/trigger this by eliciting chronic dysregulatory control and weakening of critical host immune capacity. The success of this strategy is exemplified by the huge pool of humankind (1/3 of the world population) known to already be latently infected by Mycobacterium tuberculosis (MTB) and latent Mycobacterium paratuberculosis (MAP) infection in over 50% of the world’s domestic animals. Understanding how, why and when these pathogens are able to control hosts in this manner is important to better devise interventions and develop accurate diagnostics. Studying viable non-culturable organisms in long term chronic infection animal models is expensive, difficult to maintain and can generate highly variable outcomes. In vitro macrophage infection models are more consistent but their requirement for activation limits their longevity to only a few days, thus only being able to model initial infection stages. In order to address this issue, our laboratory has recently developed a macrophage cell line that overcomes problems of host cell apoptosis/necroptosis. This advance provides novel opportunity to investigate in molecular detail, the progression and consequences of intracellular mycobacterial persistence over timescales at least ten-fold longer than previous studies.

Specific objectives:
a) Validate an intracellular mycobacterial infection model in macrophage cell lines with sufficient longevity to permit conversion to dormant, persistent, intracellular mycobacterial phenotypes consistent with latent sub-clinical infection.
b) Define the critical host-pathogen interactions and the molecular mechanisms involved during development of mycobacterial latency in a long-term infection model.  

In previous studies we have shown lipid, cholesterol and cobalamin usage to be important pathways used by mycobacteria, in the long term, to control host cell metabolism, abrogate apoptosis, deliver immunomodulatory control and maintain dormancy. Building on this work, our chronic infection model will be investigated to provide temporal in-depth RNA-seq based expression profiling of both pathogen and host transcriptomes to follow, decipher and synchronise the stages of host-pathogen interaction during entry, control and persistence. This will be achieved by functional profiling of cellular pathways using established pathway and blocking analysis that will be linked to differential host cell phenotypes and their immune reactivities via cytokine/chemokine profiling.

Methodology:
Manipulation of cell and bacterial culture including handling at Containment level 3, molecular sample processing, RNA-seq, flow cytometry and in depth Large-data bioinformatic comparative analysis of expression and functional (eukaryotic and prokaryotic) pathways.

Risk:
We do not foresee any significant risk in delivering the project as planned, as all cell lines, culture strains and suitable pathogen category handling & containment, sequencing and bioinformatic facilities are readily available or present on-site. Relevant specialised technical and academic expertise from the supervisory team will also be readily available to the student to ensure project feasibility.

Further reading

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

Additional pre-application materials:

  • doi: 10.4049/jimmunol.2300885
  • doi: 10.1186/s12890-024-03207-2 

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.

Bull-Kipkorir-Saldana recording

MRC LID LINKS

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