Project Title: ‘Automated human lung organoids for translational infectious disease research’

Studentship: The Pandemic Institute Dstl HPRU PhD cohort

Research themes: Emerging and zoonotic infections; respiratory pathogens; human microphysiological systems; medical countermeasures; translational infection biology; health protection and pandemic preparedness.

Primary Supervisor: Dr Shaun Pennington

Abstract

Emerging and zoonotic respiratory pathogens remain a major threat to UK and global health security. This project will develop automated human lung microphysiological systems (MPS) to enable rapid, human-relevant assessment of aerosol-transmitted emerging pathogens and candidate medical countermeasures. The work combines advanced lung tissue models, automation, imaging and computational analysis to establish a next-generation platform for studying host–pathogen interactions and evaluating interventions.

Translational Aspects

The project addresses a critical gap in health protection by providing rapid, human-relevant approaches for evaluating respiratory pathogens and interventions. Outcomes will support preparedness activities, accelerate assessment of therapeutics, vaccines and biologics, and contribute to evidence generation for public-health decision making.

The work has direct applications in national preparedness for emerging infectious diseases, with collaboration across LSTM, UK Health Security Agency (UKHSA) and Defence Science and Technology Laboratory (Dstl).

Aims of The Pandemic Institute Dstl HPRU PhD cohort

This PhD studentship is part of an Integrated Health Security Cohort. Building on The Pandemic Institute’s strategic partnerships with UK Health Security Agency (UKHSA), NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU EZI), and Defence Science and Technology Laboratory (Dstl), this PhD programme aims to develop a new generation of interdisciplinary researchers equipped to address emerging infectious disease threats and strengthen national health protection and biosecurity capabilities. Through joint supervision and access to specialist expertise and infrastructure, the programme is designed to create impactful PhD projects that contribute directly to the UK’s health protection and defence agenda. The programme seeks to:

• Foster collaborative research across academia, public health, and defence sectors;
• Advance research aligned with UK health security priorities, including emerging and zoonotic infections, surveillance, diagnostics, modelling, AI, and medical countermeasures;
• Generate research with both academic excellence and real-world operational or policy impact;
• Build long-term national capability in pandemic preparedness, resilience, and rapid response.

For more information on The Pandemic Institute please visit www.thepandemicinstitute.org.

Methodological Aspects

The project will utilise human lung microphysiological systems, advanced epithelial culture models, automated tissue handling, infection assays, microscopy, high-content imaging, multiplex molecular analyses and computational data integration.

Expected Outputs

Peer-reviewed publications; validated automated lung MPS workflows; datasets describing infection phenotypes and host responses; comparative assessments of medical countermeasures; conference presentations; and translational frameworks supporting preparedness and response activities.

Presentations (oral/poster) at national and international conferences on antimalarial drug discovery or medicinal chemistry.

Anticipated Impact

The project will strengthen national capability for evaluating emerging respiratory threats and support prioritisation of medical countermeasures through robust non-animal experimental systems.

Development Opportunities

Training in human lung MPS, respiratory infection biology, translational virology, automated laboratory workflows, microscopy and countermeasure evaluation.

This PhD opportunity is part-funded by the National Institute for Health and Care Research (NIHR) Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections (EZI). The successful candidate will therefore join the NIHR HPRU-EZI.

NIHR is the UK’s largest funder of health and care research and provides the people, facilities and technology that enables research to thrive.

NIHR HPRUs undertake high quality research that enhances the ability of the UK Health Security Agency (UKHSA) to protect the public’s health and minimise the health impact of emergencies. There are 13 HPRUs across England.

The HPRU-EZI is a partnership between the University of Liverpool, Liverpool School of Tropical Medicine, University of Oxford, London School of Hygiene & Tropical Medicine and UKHSA, in collaboration with University of Glasgow. HPRU-EZI has been running since 2014, and supports and strengthens UKHSA in its role protecting England from emerging infections and zoonoses (i.e. those which spread from animals to humans). HPRU-EZI has played significant roles in the past in the UK response to Ebola, Zika, COVID-19 and mpox. We will continue to address the major emerging threats; these are transmitted by mosquitoes and ticks (e.g. dengue and Lyme), the respiratory route (e.g. COVID-19 and influenza), or directly through contact (e.g. Lassa fever).

For further details please see our brochure and our website:
http://hpruezi.nihr.ac.uk/media/artlflhc/hpru-ezi-brochure.pdf
http://hpruezi.nihr.ac.uk/

Academic Career Development Program

All HPRU-funded PhD students are part of the NIHR academy, which gives access to a wide range of excellent career development opportunities (https://www.nihr.ac.uk/career-development/nihr-academy). The HPRU-EZI runs a bespoke academic career development program, which HPRU PhD students are expected to engage in. This program comprises a variety of training, development and mentorship opportunities beyond the individual research group in which the PhD student is based. All HPRU students will have co-supervision from UKHSA and at least one higher education institution. Attendance at the career development events is covered by HPRU career development funding and does not come from the individual PhD project funds. Attendance at these events is expected of HPRU PhD students.

Patient and Public Involvement, Engagement, and Participation (PPIEP) will be an integral element of this PhD project. The project will have an allocated PPIEP budget. The PhD student will be expected to develop and lead PPIEP activities throughout the PhD timeline, and will be supported by the PPIEP leads and public contributors on the PPIEP working group. More information on this area can be found at: https://www.nihr.ac.uk/ppi-patient-and-public-involvement-resources-applicants-nihr-research-programmes.

Relevant Publications

1. A Quantitative Method for the Study of HIV-1 and Mycobacterium tuberculosis Coinfection, Donnellan S, Pennington SH, et al. Journal of Infectious Diseases (2023) DOI: 10.1093/infdis/jiac491
2. Oral Typhoid Vaccination With Live-Attenuated Salmonella Typhi Strain Ty21a Generates Ty21a-Responsive and Heterologous Influenza Virus–Responsive CD4+ and CD8+ T Cells at the Human Intestinal Mucosa. Pennington SH, Thompson AL, Wright AKA, et al. Journal of Infectious Diseases (2016) DOI: 10.1093/infdis/jiw030

What we are looking for

Applicants should have a strong academic background in biomedical sciences, virology, immunology, cell biology, biotechnology, pharmacology, bioengineering, data science or a related discipline, with enthusiasm for translational research and emerging infectious diseases.

People from diverse backgrounds have historically been under-represented in the health and social care research talent pipeline. We are committed to addressing under-representation in research training awards and encourage applications from diverse groups. Dedicated mentoring can be arranged with a focus on supporting people from underrepresented groups under the career development programme (identifying mentors, career progression support etc. outside of thesis supervision).

Indicative Start Date: 1st October 2026

Funding Package: The funding includes fees, stipend at the UKRI national rates (see Support for UKRI-funded students – UKRI), consumables, travel, publications and computer budget. Funding originates from LSTM, the NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Defence Science and Technology Laboratory (Dstl). The duration of the funding package is 3 years.

Eligibility

Academic

Applicants must hold at least a first class or high upper second-class Honours degree, or a degree of comparable standard awarded from outside the UK.

A Masters degree (at merit or distinction preferable) is also a pre-requisite.

Where an applicant does not meet the Honours degree requirement (e.g. they hold a lower second-class Honours degree), they may be eligible to apply if they also hold a Master’s degree with an awarded distinction in an area relevant to the research theme of the project. To be considered for this exemption, the qualification must be awarded at time of application and candidates must provide an award certificate and transcript for both qualifications. Unfortunately, we are unable to consider Master’s qualifications that have not yet been awarded for this purpose.

Residence

THIS OPPORTUNITY IS ONLY AVAILABLE TO CANDIDATES HOLDING A ‘HOME’ FEE STATUS AND WITH VALID IMMIGRATION PERMISSION TO LIVE AND STUDY IN THE UK FOR THE FULL DURATION OF THE STUDENTSHIP AT THE POINT OF APPLICATION.

‘Home’ fee status typically applies to students who are ‘settled’ in the UK—meaning they have no immigration restriction on the length of stay—and who have been ordinarily resident in the UK, the Republic of Ireland, the Channel Islands, or the Isle of Man for the three years immediately before the first day of their course. Eligibility also extends to certain groups such as British or Irish nationals, those with Indefinite Leave to Remain or equivalent rights, refugees or individuals with humanitarian protection, and some family members of qualifying persons.

Applicants must hold valid immigration permission to live and study in the UK for the full duration of the studentship at the point of application. This includes ensuring that your current visa category permits postgraduate study and will remain valid throughout the funded period.

IF YOU ARE UNABLE TO PROVIDE EVIDENCE OF BOTH OF THE ABOVE REQUIREMENTS, YOUR APPLICATION WILL BE REJECTED.

How to Apply: Stage 1 – Complete the following online form

Candidates are eligible to apply as soon as possible.

In order to be considered for this opportunity, candidates must:

• Submit a copy of their Curriculum Vitae to pgr@lstmed.ac.uk
• Complete the following form: Automated human lung organoids for translational infectious disease research – Fill in form

This application form will ask you to:

• Provide your personal details
• Answer 6 questions related to your motivation for doctoral study (up to 1250 characters [approx 250 words] per question)
• Detail your qualifications, any relevant research experience and your English language proficiency
• List any contextual information that you feel is important for assessors to know (optional)
• Provide diversity monitoring information

Deadline for application is noon UK time Monday 31 July. Applications are only considered complete if LSTM has received a copy of your Curriculum Vitae and a completed form.

Successful Candidates

Candidates that are successful for interview shortlisting will be notified within two weeks of application.

Successful candidates will be invited to submit documentation in support of the information they provided in their initial application prior to interviews expected to take place mid August.