Resources
Publications
Publication
mRNA vaccine quality analysis using RNA sequencing. Gunter et. al., Nature Communications (2023)
mRNA vaccine quality analysis using RNA sequencing
Gunter, H.M., Idrisoglu, S., Singh, S., Han, D.J., Ariens, E., Peters, J.R., Wong, T., Cheetham, S.W., Xu, J., Rai, S.K., Feldman, R., Herbert, A., Marcellin, E., Tropee, R., Munro, T., Mercer, T.R.
Nature Communications (2023) Sep 21;14(1):5663.
The success of mRNA vaccines has been realised, in part, by advances in manufacturing that enabled billions of doses to be produced at sufficient quality and safety. However, mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants that reduce their effectiveness and induce side-effects. Currently, mRNA vaccines and therapies are analysed using a range of time-consuming and costly methods. Here we describe a streamlined method to analyse mRNA vaccines and therapies using long-read nanopore sequencing. Compared to other industry-standard techniques, VAX-seq can comprehensively measure key mRNA vaccine quality attributes, including sequence, length, integrity, and purity. We also show how direct RNA sequencing can analyse mRNA chemistry, including the detection of nucleoside modifications. To support this approach, we provide supporting software to automatically report on mRNA and plasmid template quality and integrity. Given these advantages, we anticipate that RNA sequencing methods, such as VAX-seq, will become central to the development and manufacture of mRNA drugs.
Publication
A universal molecular control for DNA, mRNA and protein expression. Gunter et. al., Nature Communications (2024)
A universal molecular control for DNA, mRNA and protein expression
Gunter, H.M., Youlten, S.E., Reis, A.L.M., McCubbin, T., Madala, B.S., Wong, T., Stevanovski, I., Cipponi, A., Deveson, I.W., Santini, N.S., Kummerfeld, S., Croucher, P.I., Marcellin, E., Mercer, T.R.
Nature Communications. 2024 Mar 20;15(1):2480.
The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.
Publication
Targeted mRNA delivery with bispecific antibodies that tether LNPs to cell surface markers. Dietmair et. al., Molecular Therapies Nucleic Acids (2025)
Targeted mRNA delivery with bispecific antibodies that tether LNPs to cell surface markers
Dietmair, B., Humphries, J., Mercer, T.R., Thurecht, K.J., Howard, C.B., Cheetham, S.W.
Molecular Therapies Nucleic Acids. 2025 Mar 19;36(2):102520.
Efficient delivery of mRNA-lipid nanoparticles (LNPs) to specific cell types remains a major challenge for mRNA therapeutics. Conventional targeting approaches involve modifying the lipid composition or functionalizing the surface of LNPs, which complicates manufacturing and alters nanoparticle size, charge, and stealth, impacting their delivery and immunogenicity. Here, we present a generalizable method for targeted mRNA-LNP delivery that uses bispecific antibodies (BsAbs) to form a bridge between LNPs and cell surface markers. BsAbs can be combined with LNPs or administered first, binding to surface proteins on target cells and later retaining unmodified LNPs in affected tissues. We demonstrate the efficient and cell-type-specific delivery of mRNA-LNPs beyond the liver, targeting epidermal growth factor receptor (EGFR)- and folate hydrolase 1 (PSMA)-positive cells in vitro and in vivo. The flexibility of this technology, achieved by substituting the cell-targeting region of the BsAbs, enables the rapid development of next-generation targeted mRNA drugs.
Publication
Mind the cap: Detecting degradation impurities in synthetic mRNAs. Nielsen et. al., Molecular Therapies Nucleic Acids (2025)
Mind the cap: Detecting degradation impurities in synthetic mRNAs
Nielsen, D., Victorova, M., Mercer, T.R., Cheetham, S.W.
Molecular Therapies Nucleic Acids. 2025 Sep 17;36(4):102701.
The 5′-cap on messenger RNA (mRNA) is essential for translation, stability, and innate immune avoidance. Methods to accurately quantify 5′-cap integrity are essential to ensuring the quality of mRNA medicines. A recent Molecular Therapy Nucleic Acids article comprehensively characterized mRNA 5′-cap integrity and its degraded products. The impact of 5′-cap degradation products on mRNA translation and the cellular immune response was also evaluated, with implications for the manufacture and quality control of mRNA medicines.
Publication
The design, manufacture and LNP formulation of mRNA for research use. Leighton et. al., Nature Protocols (2025)
The design, manufacture and LNP formulation of mRNA for research use
Leighton LJ, Chaudhary N, Tompkins HT, Kulkarni A, Carrodus NL, Budzinska MA, Lakshman Das S, Cheetham SW, Mercer TR.
Nature Protocols (2025) 20, 3552–3581
The delivery of mRNA provides a versatile platform to achieve rapid and robust protein expression within cells. mRNA delivery has therefore been widely adopted in research, and mRNA medicines are now being developed to treat a range of diseases. However, high-quality mRNA must be produced to ensure the safety, performance and effectiveness of these medicines. Here, we provide a validated, end-to-end protocol describing the production of mRNA for research and preclinical use. This protocol includes primary sequence design, DNA template production, mRNA synthesis by in vitro transcription, formulation into lipid nanoparticles and transfection into cultured cells. Each step is supported by a range of quality control tests to analyze mRNA integrity and purity and is illustrated with example results to provide information about expected performance. The protocol prioritizes simple production steps that are suitable for small-scale mRNA manufacture, such as PCR preparation of the DNA template, and that can be performed within a laboratory and avoid specialized equipment. The protocol produces high-quality mRNA that can be used for in vitro and in vivo preclinical studies, including for vaccine, protein and gene- and cell-therapy applications. Together, this provides a fast and reliable protocol to produce high-quality mRNA suitable for laboratory research and preclinical development.
Publication
Rapid expression of therapeutic antibodies in mammalian cells via mRNA transfection. Chavalparit et. al., MAbs (2026)
Rapid expression of therapeutic antibodies in mammalian cells via mRNA transfection.
Chavalparit, T., Barry, C., Gunter, H., Gillard, M., Mercer, T., & Marcellin, E.
MAbs. 2026 Dec;18(1):2599584.
Messenger RNA (mRNA) has emerged as a powerful tool for protein expression in clinical settings, yet its potential as a platform for biologics manufacturing remains underexplored. Here, we evaluate transient mRNA transfection in Chinese hamster ovary (CHO) cells as a rapid and versatile system for protein production. Using reporter mRNAs, we optimize transfection efficiency and benchmark performance against industry-standard plasmid transfection and stable cell line methods. We demonstrate that co-transfection of heavy and light chain mRNAs enables the efficient synthesis, assembly and secretion of the monoclonal antibody bevacizumab with high fidelity. Compared to conventional approaches, mRNA transfection drives rapid and predictable protein expression, reducing cell incubation times and enabling sequential or conditional expression. These features highlight mRNA as a flexible and efficient platform for transient expression, providing a foundation for accelerating the development and manufacturing of biologics.
Posters
Posters
mRNA Cancer Vaccines; Design, Delivery and Performance. O’Brien et. al., (2025)
Webinars
Webinars
Using nanopore sequencing to understand the manufacture, delivery, and action of mRNA vaccines. Dr Helen Gunter. London Calling. Jun 2023.
Webinars
Using nanopore sequencing for mRNA vaccine quality control a journey from R&D to GMP. Dr Helen Gunter. Oxford Nanopore Technologies. Sep 2024.
Webinars
The future of mRNA cancer, vaccines and health. Dr Seth Cheetham. AIBN. Jul 2026.
Webinars
PCR preparation of DNA templates. Dr Seth Cheetham. IDT webinar. Jan 2024.
Webinars
Closing the loop between in silico mRNA design and in-cell performance.Helen Gunter. University Of Queensland. Feb 2026.
Documents
Application Note
Experimental validation of reporter mRNAs
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Software & Data
Software & Data
Guide to design an mRNA medicine.
Software & Data
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Software & Data
mRNArchitect – Terms of Use
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