2024-25 Project (Harrison & Wasserman & Jarvis & Lai)

Characterising immune pathways and pharmacokinetics in HIV-associated pneumocystis pneumonia



Professor Thomas Harrison at SGUL
Email: tharriso@sgul.ac.uk


Dr Sean Wasserman at SGUL
Email: swasserm@sgul.ac.uk


Professor Joseph Jarvis at LSHTM
Email: joseph.jarvis@lshtm.ac.uk


Dr Rachel Lai at Imperial College London
Email: rachel.lai@imperial.ac.uk


Project Summary

P. jirovecii is an opportunistic pathogen causing pneumocystis pneumonia (PCP) in immunocompromised individuals, a severe illness frequently leading to life-threatening respiratory failure. PCP contributes substantial burden of disease in high HIV-prevalence settings, but there are important knowledge gaps on disease mechanisms and treatment in this population.    

A cohort study conducted among patients with HIV-associated PCP in South Africa will generate clinical material for translational laboratory studies of host immune responses that drive immunopathogenesis and disease severity. In addition, drug concentration data will be available to investigate sources of pharmacokinetic (PK) variability and explore relationship with treatment response.   

For this project, the successful candidate will perform multi-omics (transcriptomic, proteomic and metabolomic) analyses to comprehensively investigate molecular mechanisms that underlie PCP pathologies and use PK data to inform treatment optimisation.

Project Key Words

Pneumocystis pneumonia, HIV, multi-omics, immunopathogenesis, pathway analysis, pharmacokinetics

MRC LID Themes

  • Global Health = Yes
  • Health Data Science = No
  • Infectious Disease = Yes
  • Translational and Implementation Research = Yes


MRC Core Skills

  • Quantitative skills = Yes
  • Interdisciplinary skills = Yes
  • Whole organism physiology = Yes

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

The successful student will acquire skills in RNA-sequencing and liquid chromatography mass spectrometry (LC-MS), analysis and interpretation of multi-omics and PK data, manuscript and grant writing, and ability to interact within a multidisciplinary scientific environment.


Which route/s is this project available for?

  • 1+4 = Yes
  • +4 = Yes

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

  • LSHTM – MSc Immunology of Infectious Diseases
  • LSHTM – MSc Medical Statistics
  • SGUL – MRes Biomedical Science – Infection and Immunity
  • SGUL – MSc Genomic Medicine
  • SGUL – MRes/MSc Translational Medicine

Full-time/Part-time Study

Is this project available for full-time study? Yes
Is this project available for part-time study? No


Particular prior educational requirements for a student undertaking this project

  • SGUL’s standard institutional eligibility criteria for doctoral study.
  • The successful student should have analytical skills and research experience, either from a BSc or MSc research project, or work experience, in at least one of the following areas:  infection immunity, biochemistry or analytical chemistry, or bioinformatics

Other useful information

  • Potential CASE conversion? = No
  • Change of primary supervisor following transfer: Professor Harrison will be the Primary Supervisor for this project until upgrading. After that the team envisages that Dr Wasserman will take over as Primary Supervisor (pending RD Committee approval).


Scientific description of this research project

1. Rationale and objectives 
P. jirovecii is an opportunistic pathogen causing pneumocystis pneumonia (PCP) in immunocompromised individuals, a severe illness frequently leading to life-threatening respiratory failure. PCP contributes substantial burden of disease in high HIV-prevalence settings, with important challenges and knowledge gaps in diagnosis and treatment.    

Disease severity is thought to be driven by host inflammatory response, evidenced by correlation with crude markers of lung inflammation (neutrophils and lactate dehydrogenase) and clinical response to glucocorticoids. However, knowledge of PCP pathophysiology is derived almost exclusively from murine P. carinii infection models, and there are limited data on disease mechanisms in patients with HIV-associated PCP. Immune pathways for fungal clearance are not completely understood but there appears to be complex interplay between fungal burden and host immune responses that drive immunopathogenesis and disease severity.    

Additionally, the optimal dose and duration of first-line PCP treatment, trimethoprim-sulfamethoxazole (TMP-SMX), is not established. Sources of variability in TMP-SMX pharmacokinetics (PK), which could influence treatment response, have not been described in patients with HIV-associated PCP but are needed to inform dose optimisation.    

Research priorities in PCP include
(1) identification of potentially modifiable outcome predictors for risk stratification and to design interventions for improved care;
(2) identification of biomarkers of treatment response, which do not currently exist for PCP, for future trial design and treatment optimisation;
(3) understanding host immune pathways to identify targets for development of novel therapeutic strategies; and
(4) dose optimisation of TMP-SMX to reduce toxicity and improve outcomes.   

We are undertaking an NIHR-funded cohort study (part of the IMPRINT NIHR Global Health Group, including LSHTM and SGUL; https://witsmycology.co.za/projects/IMPRINT/index.html) among inpatients with suspected HIV-associated PCP in Cape Town, South Africa, to characterise clinical phenotype and medium-term functional outcomes. Participants will undergo bronchoscopy, longitudinal blood sampling, including rich PK sampling, and detailed clinical metadata collection during hospital admission. Clinical data and materials generated from this study will enable PK and laboratory-based translational studies.     

For this Studentship, the successful candidate will undergo training to perform conventional immunoassays, microscopy and multi-omics (transcriptomic, proteomic and metabolomic) analyses to comprehensively investigate molecular mechanisms that underlie PCP pathologies and identify potential diagnostic and treatment targets. The student will also perform non-compartmental analysis of drug concentration data to describe the PK of TMP-SMX in patients with HIV-associated PCP.   

Specific scientific objectives include: 
1.       Delineate the global host cellular and immunological responses to PCP infection. 
2.       Identify biomarker(s) that can differentiate confirmed PCP infection in suspected cases. 
3.       Characterise the plasma and bronchoalveolar fluid PK of TMP-SMX    

2. Techniques to be used and lab environment 
During the MPhil year, the student will undertake training courses in RNA sequencing, metabolomics, and analytical methods. They will also perform initial laboratory-based work in the Lai Lab (Imperial College London) which has an established laboratory and bioinformatic pipeline for multi-omics analyses. The student will learn to extract RNA, prepare sequencing libraries and start to analyse RNA-Sequencing data from patient BALf samples. In parallel, the student will also learn to extract metabolites, perform LC-MS to generate metabolomic data from the same BALf samples. These preliminary analyses will form the basis of the MPhil dissertation.    

After transferring to the PhD the student will learn bioinformatic pipelines for RNA-Seq and metabolomic data analysis to investigate if there are systemic transcriptional and/or metabolic differences between clinical phenotypes and treatment outcomes. Proteomics data will also be generated externally using the commercial SOMAscan platform where its current multiplex assay can detect up to 10,000 protein analytes. Together with a computational scientist at LSHTM, the student will learn to perform multivariate analysis, pathway-based overrepresentation analysis, and different modelling approaches to integrate multi-omics data and clinical data to help unravel disease mechanisms and to provide novel insights for future investigation. RNA-sequencing and metabolomics will also be performed on whole blood to examine if the signatures found in BALf are reflected in whole blood.    

In the final year of the PhD, the student will work at SGUL (Sean Wasserman and collaborator) to analyse drug concentration data obtained from plasma and bronchoalveolar lavage fluid. They will apply non-compartmental analysis to summarise the PK of TMP-SMX, describe site of disease exposure, and explore relationships with clinical covariates to identify sources of PK variability.   

3. Availability of materials and data 
Clinical metadata and materials will be available from at least 80 patients, representing a heterogenous population of PCP severity and diagnostic certainty. Rich plasma PK sampling will be performed for 15 participants. All study procedures, sample storage, and shipment are funded. Funding is requested from this Studentship for drug assay costs, to be performed at the University of Cape Town PK lab. A material transfer agreement and export permit are in place for shipment of samples to the UK for analysis. The cohort study is currently enrolling patients at a rate of ~10/month and is expected to achieve the enrolment target before the start of this Studentship, ensuring sample availability.   

4. Risks and mitigation strategies 
The supervisors are spread across three UK institutions, with a risk of gaps in supervision. This is mitigated by a track record of close research collaboration and plans for regular in person meetings of the supervisory team. Involvement of multidisciplinary supervisors from different backgrounds enhances learning opportunities. Bulk RNA-Sequencing and bulk metabolomics protocol are well-established and we do not anticipate any technical difficulties. BALf samples are known to have low protein abundance and hence, the ultra-sensitive, aptamer-based SOMAscan platform will be used. The student will first determine total protein concentration and sample concentration will be performed if the protein level is too low in neat sample.

Further reading

(Relevant preprints and/or open access articles)

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.
    Harrison-Wasserman-Jarvis-Lai Recording


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