Transformation of Advanced Medicines Manufacture (TRANS-AM)

About the Project

Transformation of Advanced Medicines Manufacture (TRANS‑AM)

Gene therapies are a type of advanced medicine that represent exciting possibilities to treat and potentially cure many life‑altering and life‑threatening diseases. They also represent a major growth area, with several hundred therapies currently in development. Many of these products rely on recombinant adeno‑associated virus (rAAV) as a delivery vector. If even a small proportion of these therapies reach the market, current manufacturing and characterisation technologies across the sector will struggle to deliver them economically, reproducibly, and safely for patients.

This research programme aims to develop innovative solutions to address the manufacturing challenges associated with rAAV production. It brings together experts from two leading Irish institutions, the National Institute for Bioprocessing Research and Training (NIBRT) and University College Dublin (UCD), alongside APC‑VLE Ltd. (https://approcess.com/services/cell-and-gene-therapies), a leading Irish industrial partner. The programme is delivered as an ambitious five‑year collaborative initiative that integrates academic excellence with strong industrial relevance.

We are currently seeking applicants for three funded PhD projects described below. Successful candidates will be based in either NIBRT or UCD and will also undertake placements with the industrial partner. We welcome applications from ambitious, inquisitive, and innovative individuals seeking to join a multidisciplinary research team. As part of a dynamic environment, students will contribute to breakthrough research enabling scalable, efficient, and high‑quality viral vector manufacture, supporting the next generation of gene therapies. Candidates motivated by biotechnology, process development, and therapeutic innovation are strongly encouraged to apply.

NIBRT is a global centre of excellence headquartered in Dublin, providing training and research solutions to the international biopharmaceutical manufacturing sector. It arose from a collaboration between University College Dublin, Trinity College Dublin, Dublin City University, and the Institute of Technology, Sligo, supported by the Government of Ireland through IDA Ireland. NIBRT’s 8,300 m² facility employs over 100 staff and contains fully functional pilot plants for biologics manufacturing training, multiple research laboratories focused on biopharmaceutical manufacturing, and a dedicated facility for early‑stage biologics and advanced therapy development. The institute provides world‑leading infrastructure and a vibrant environment supporting scientific excellence, translational research, and career development.

University College Dublin (UCD) is one of Europe’s leading research‑intensive universities, where education, research, innovation, and engagement form a dynamic continuum. Established in 1854 by John Henry Newman, UCD is now Ireland’s largest university, with almost 25,000 students. It is the most popular destination for Irish school‑leavers and promotes academic and personal discovery through its innovative curricula. UCD is Ireland’s leader in postgraduate education, with almost 7,000 postgraduate students, including approximately 2,000 PhD researchers. Over fifty per cent of undergraduates progress to postgraduate study.

Project 1: CRISPR Library Screening to Identify Endogenous HEK293 Genes Impacting AAV Production

Supervisors: Prof. Niall Barron and Assoc. Prof. Colin Clarke

CRISPR library screening has proven powerful for identifying genetic determinants of cellular phenotypes, including cancer mechanisms, bioreactor behaviour, and viral restriction. This unbiased approach allows genome‑wide interrogation through gene knockout or activation. This project will apply CRISPR screening to a suspension‑adapted HEK293 cell line to identify genes that enhance or inhibit AAV production. A human CRISPR guide RNA library will generate a knock‑out population. Cells producing high and low AAV levels will be isolated, sequenced, and analysed to identify enriched guide RNAs and target genes. Key genes will be validated via targeted knockouts and assessed for AAV yield following triple transfection.

Applicants should hold or expect a high 2.1 or 1.1 degree in a relevant discipline, ideally cell or molecular biology. Training will be provided in advanced techniques. Strong teamwork, motivation, applied research interest, and effective communication skills are essential.

How to apply:

Project 1 applicants should email: a cover letter (including your motivation statement outlining why you wish to do a PhD and why you are suited to this project), a CV, and contact details for your academic referees to careers@nibrt.ie

Informal enquiries to niall.barron@nibrt.ie. Funding includes a €25,000 annual stipend plus fees for four years.

Project 2: Improving rAAV Safety through Glycoengineering

Supervisor: Dr Ioscani Jiménez del Val

Recombinant AAVs are the leading gene therapy vectors, with eight approved therapies and more than 250 in clinical trials. However, doses required for efficacy can trigger immune responses that reduce effectiveness and, in rare cases, cause severe adverse outcomes. rAAV capsids contain complex glycans, with high‑mannose structures known to stimulate immune recognition. Recent studies show most rAAV glycans are high‑mannose.

This project aims to convert pathogenic glycans into non‑immunogenic structures. Initial work will focus on in vitro enzymatic glycan remodelling. Following demonstration of immunological benefit, HEK293 cells will be genetically engineered to directly produce glycoengineered rAAV. The project combines enzyme catalysis, molecular biology, cell culture, assay development, and data analytics.

Applicants should hold or expect a high 2.1 or 1.1 degree in biochemistry, biotechnology, cell biology, or biochemical engineering. Experience in mammalian cell culture and molecular biology is advantageous. Training will be provided.

Applicants should submit a cover letter, CV, and motivation letter via https://forms.gle/ZTjUWotqvodkr9nK7 by 31/05/2026. Informal enquiries to ioscani.jimenezdelval@ucd.ie. Funding includes a €25,000 annual stipend plus fees for four years.

Project 3: Process Analytical Technology Applications for Monitoring AAV Production

Supervisor: Dr Jonathan Bones

This project focuses on developing process analytical technologies (PAT) for monitoring AAV production during cell culture. While PAT is widely used for chemical synthesis and protein biologics, its use for AAV is limited by viral complexity and low expression. The project will explore inline, online, and at‑line analytical methods supported by automated sampling in small‑scale bioreactors. Students will operate bioreactors, deploy spectroscopic and integrated analytical tools, generate large datasets, and apply multivariate and statistical approaches to enable advanced process control.

Applicants should hold or expect a high 2.1 or 1.1 degree in analytical science, biotechnology, or engineering. Experience with multivariate statistics or data modelling is beneficial. Training will be provided.

Applicants should email a covering letter, motivation statement (outlining why you would like to do a PhD), CV, and referee details to careers@nibrt.ie. Informal enquiries to jonathan.bones@nibrt.ie. Funding includes a €25,000 annual stipend plus fees for four years

Funding Notes

Research Ireland 23/SP/12173