This PhD opportunity is being offered as part of the LSTM and Lancaster University Doctoral Training Partnership. Find out more about the studentships and how to apply.
| Abstract | The cell surface glycocalyx is a complex and dynamic structure formed by proteins and lipids bound to the plasma membrane. These are usually glycosylated (glycoproteins and glycolipids), playing important roles in cell physiology but also in infection biology as receptors for pathogens and defence molecules. In 2021, a new type of cell surface molecule was discovered, formed by a main RNA body modified by the addition of a glycan, and hence named glycoRNA. To date, the biological functions of glycoRNA remain largely unknown. This project aims at elucidating the role of glycoRNAs in infection using multiple viral (e.g., SARS-CoV-2, dengue, Zika virus, HIV-1) and parasitic (Leishmania, Plasmodium, nematodes) infection systems. The project will identify roles of glycoRNA in pathogen-host interactions, attachment and/or invasion of host cells, as well as changes in glycoRNA composition and abundance induced by infection. Our previous research has shown that viruses may use surface glycoRNA for attachment and invasion, so we aim to identify which specific glycoRNAs are essential for these interactions, with the ultimate goal of developing new disruptive strategies to tackle infections. This highly interdisciplinary project requires advanced cell and molecular biology methods to edit and knock out host glycoRNA genes using CRISPR-Cas9/13, as well as virus/parasite genome editing, and bioorthogonal (Click) chemistry to label glycoRNA for its detection using blotting-based methods. It also involves state-of-the-art confocal and high-content microscopy to analyse changes in glycoRNA at single-cell level using immunostaining, aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA), and in situ visualisation by hierarchical coding (HieCo). The project will involve using a combination of transcriptomics and glycomics to fully characterise changes in glycoRNAs due to infection. In summary, the study of glycoRNA presents us with huge potential for basic and translational discoveries in infection biology. |
| Where does this project lie in the translational pathway? | T1 - Basic Research |
| Expected outputs | The project is expected to deliver high-impact peer-reviewed publications (one for general findings, other individual ones for specific diseases/pathogens). It is also expected to generate data to support multiple follow up grant applications and fellowships. This project has the potential for huge impact in basic and translational science due to the novelty of glycoRNA as an unknown type of surface molecule. Patents may also arise on the disruption of glycoRNA-virus interactions as therapeutics. |
| Training opportunities | The student will learn a broad range of advanced methods in molecular biology (cloning and mutagenesis), biochemistry (bioorthogonal click chemistry), imaging (confocal and high content imaging), and cell biology (several viral and parasitic infection systems). The candidate will attend several courses to perfect or train on new methods required, and international conferences to present their results. The student will also have the opportunity of a placement in a collaborator lab. |
| Skills required | Not many skills and experience are essential, although experience in any standard molecular biology, biochemistry and imaging methods is desirable. The PhD candidate will be taught and learn all methods required, as well as develop and optimise new ones. More important and desirables are aptitudes like motivation, resilience, and critical thinking. |
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Key Publications associated with this project |
Flynn RA, Pedram K, Malaker SA, Batista PJ, Smith BAH, Johnson AG, George BM, Majzoub K, Villalta PW, Carette JE, Bertozzi CR. Small RNAs are modified with N-glycans and displayed on the surface of living cells. Cell. 2021 Jun 10;184(12):3109-3124.e22. doi: 10.1016/j.cell.2021.04.023. Epub 2021 May 17. PMID: 34004145; PMCID: PMC9097497. |
| Ma Y, Guo W, Mou Q, Shao X, Lyu M, Garcia V, Kong L, Lewis W, Ward C, Yang Z, Pan X, Yi SS, Lu Y. Spatial imaging of glycoRNA in single cells with ARPLA. Nat Biotechnol. 2023 May 22. doi: 10.1038/s41587-023-01801-z. Epub ahead of print. PMID: 37217750. | |
| Chai P, Lebedenko CG, Flynn RA. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet. 2023 Aug 25;24:85-107. doi: 10.1146/annurev-genom-101722-101224. Epub 2023 Apr 17. PMID: 37068783. |