Biology subjects

Johnston, A. P. R.

Publications and source records attributed to Johnston, A. P. R..

6 recordsLinked to original sources

bioRxiv2026

Long-read sequencing quantifies synthetic mRNA abundance, integrity and host response in vivo

Synthetic mRNA can be used to reprogram biological systems and is increasingly used in vaccines, gene therapies and other advanced therapeutics. However, measuring mRNA abundance, molecular integrity and biological effects in complex samples remains challenging. Existing assays typically quantify short transcript regions or infer delivery from lipid or protein readouts. Here we present a long-read nanopore sequencing method that directly quantifies synthetic mRNA in complex cell and tissue samples. The approach enables absolute quantification of full-length synthetic mRNA, maps degradation at nucleotide resolution and simultaneously profiles associated host transcriptional responses. Applied to lipid nanoparticle (LNP) delivered mRNA in mice, the method revealed tissue-specific delivery and degradation patterns and uncovered a critical disconnect between mRNA accumulation and protein expression across organs. This approach enables integrated measurement of mRNA fate, integrity and biological responses, and will enable mechanistic studies of RNA delivery, stability, translation and innate immune recognition.

pharmacology and toxicology↗

bioRxiv2024

A modular encapsulation system for precision delivery of proteins, nucleic acids and therapeutics

Targeted nanoparticles have the potential to revolutionize therapeutics for medical applications. Here, we demonstrate the utility of a flexible precision nanovesicle delivery system for functional delivery of DNA, RNA, proteins and drugs into target cells. Nanovesicles generated by the membrane sculpting protein caveolin, termed caveospheres, can be loaded with RNA, DNA, proteins or drugs post-synthesis or incorporate genetically-encoded cargo proteins during production without the need for protein purification. Functionalized fluorescently-labeled caveospheres form a modular system that shows high stability in biological fluids, specific uptake by target-positive cells, and can deliver proteins, drugs, DNA, and mRNA directly to the cytoplasm and nuclei of only the target cells. The negligible level of off-target transduction and uniform levels of targeted expression demonstrates advantages of the system over lipid-mediated gene delivery. Caveospheres can also be engineered to mimic viral particles by displaying the SARS-CoV-2-RBD protein, enabling targeted delivery to human bronchial epithelial cells. We demonstrate their application as a targeted transfection system for cells in culture, and critically, their efficacy in precision tumor killing in vivo.

bioengineering↗

bioRxiv2024

A Versatile Antibody Capture System that Drives Precise In Vivo Delivery of mRNA loaded Lipid Nanoparticles and Enhances Gene Expression

Efficient and precise delivery of mRNA is critical to advance mRNA therapies beyond their current use as vaccines. Lipid nanoparticles (LNP) efficiently encapsulate and protect mRNA, but non-specific cellular uptake may lead to off-target delivery and minimal delivery to target cells. Functionalizing LNPs with antibodies enables targeted mRNA delivery, but traditional modification techniques require complex conjugation and purification, which often reduces antibody affinity. Here, we present a simple method for capturing antibodies in their optimal orientation on LNPs, without antibody modification or complex purification. This strategy uses an optimally oriented anti-Fc nanobody on the LNP surface to capture antibodies, resulting in protein expression levels >1000 times higher than non-targeted LNPs and >8 times higher than conventional antibody functionalization techniques. These precisely targeted LNPs showed highly efficient in vivo targeting to T cells, with minimal delivery to other immune cells. This approach enables the rapid development of targeted LNPs and has the potential to broaden the use of mRNA therapies.

bioengineering↗

bioRxiv2022

Resolving subcellular pH with a quantitative fluorescent lifetime biosensor

Changes in sub-cellular pH play a key role in metabolism, cell growth, membrane transport, and can also be exploited to control cargo release from therapeutic delivery systems. Most methods to measure pH rely on intensity changes of pH sensitive fluorophores, however these measurements are hampered by high uncertainty in the inferred pH and the need for multiple fluorophores. To address this, we have developed a method to accurately quantify sub-cellular pH in individual vesicles using fluorescent lifetime imaging microscopy (pHLIM). pHLIM exploits the linear pH dependant lifetime of the fluorescent protein mApple and uses deep learning models to automatically identify and measure the pH of subcellular compartments. We have engineered mApple fusion proteins to measure the pH of the cytosol, endosomes, lysosomes and demonstrated the utility of pHLIM by measuring pH changes induced by drugs (bafilomycin A1) and polyethylenimine (a common transfection reagent). pHLIM is a simple and quantitative method to measure sub-cellular pH that has the potential to help with the design of the next generation of controlled drug release systems and to understand drug action and disease progression.

cell biology↗

bioRxiv2020

Unravelling cytosolic delivery of endosomal escape peptides with a quantitative endosomal escape assay (SLEEQ)

Endosomal escape is an essential requirement but a major obstacle to efficient delivery of therapeutic peptides, proteins and nucleic acids. Current understanding of endosomal escape mechanisms remains limited due to significant number of conflicting reports, which are compounded by low sensitivity and indirect assays. To resolve this, we developed a highly sensitive Split Luciferase Endosomal Escape Quantification (SLEEQ) assay to probe mechanisms of cytosolic delivery. We applied SLEEQ to evaluate the endosomal escape of a range of widely studied putative endosomal escape peptides (EEPs). We demonstrated that positively-charged EEPs enhanced cytosolic delivery as a result of increased non-specific cell membrane association, rather than increased endosomal escape efficiency. These findings transform our current understanding of how EEPs increase cytosolic delivery. SLEEQ is a powerful tool that addresses fundamental questions in intracellular drug delivery and will significantly improve the way materials are engineered to increase therapeutic delivery to the cytosol.

cell biology↗

bioRxiv2019

SNAPSwitch: A Molecular Sensor to Quantify the Localization of Proteins, DNA and Nanoparticles in Cells

Intracellular trafficking governs receptor signalling, pathogenesis, immune responses and the cellular fate of nanomedicines. These processes are typically tracked by confocal microscopy, where colocalization of fluorescent markers implies an interaction or co-compartmentalization. However, this type of analysis is inherently low-throughput, is limited by the resolution of microscopy, and can miss fleeting interactions. To address this, we have developed a localization sensor composed of a quenched and attachable SNAP-tag substrate (SNAPSwitch). SNAPSwitch enables quantitative detection of protein, nucleic acid and nanoparticle trafficking to locations of interest within live cells using flow cytometry. Using this approach, we followed the trafficking of DNA complexes travelling from endosomes into the cytosol and to the nucleus. We also show that antibody targeted to the transferrin (CD71) or hyaluronan (CD44) receptor is initially sorted into different compartments following endocytosis. These results demonstrate SNAPSwitch is a high-throughput and broadly applicable tool to quantitatively track the localization of materials in cells.

cell biology↗