Posters and Guidelines

Thank you for considering to present your work as a poster at Oligo 2024 Oxford. Please submit your poster abstract online within the advertised deadlines.

Poster preparation

• Page size: Prepare your poster as you would normally do for printing. You can prepare your poster in sizes A1 or A0, but the page size of your poster is not important as the posters will be presented digitally. However, if you are attending in-person and would like to bring along a physical poster, prepare your poster in A1 portrait format (59cm wide x 84cm long). Do not laminate your poster, or use heavy printing material.
• Naming your poster files: Name your poster files as follows: <your surname>-Oligo25-Poster.pdf, etc. For example, for David Jones, name your file as Jones-Oligo25-Poster.pdf. DO NOT name your poster files as, e.g.,  Oxford-poster, poster2025, Oxford-oligo-poster. Such files will be automatically rejected.
• Poster submission: Submit your final poster as PDF files via the link below no later than 11th April 2025 Late posters may not be included in the conference programme. Please DO NOT send your poster or abstract files by email. Please ensure you send us the very final version of your poster (as well as your poster abstract), as once published, it cannot be replaced.

Before uploading your poster, you must make sure that you follow ALL of the instructions above!

Upload your poster

Poster presentation:

• Poster PDF files (required): Whether the presenter is attending virtually or in-person, poster PDF files are required, which will be made available via the secure conference documents page to the conference participants. The participants will be able to ask questions via the Zoom chatbox during the conference. There is no specific time for presenting digital posters.
• Flash-talk videos (optional): We are pleased to offer poster presenters the opportunity to prepare a short video presentation about their poster and send it before the conference. The videos will be made available on the LPMHealthcare YouTube channel. Below is further information for sending your video presentation.
  • Give your presentation (no longer than 5 minutes) using Zoom or another platform of your choice.
  • Convert the video into a format compatible with YouTube (e.g., MP4).
  • Send your video to OligoOxford@gmail.com using a file transfer program, such as MailBigFile or WeTransfer.
• Hardcopy posters (optional): If attending in-person, you may bring along a printed copy of your poster (maximum A1 size) to be displayed during the conference. You may be assigned a specific day to display your poster.
• The participants can post their questions on X at any time using the meeting hashtag #OligoOx25, as well as the poster specific hashtag (given under each poster abstract) – do tag @LPMHealthcare in your tweets.
• Any further information about the poster presentations at this digital meeting will be available in the future.

Before uploading your poster, you must make sure that you follow ALL of the instructions above!

Upload your poster

(Presenters in Bold)

Accepted poster abstracts (Unedited) will be published below. If your abstract has been accepted for presentation but it does not appear in the list below, please let us know as soon as possible by emailing OligoOxford@gmail.com.

Bulge-loop forming peptidyl-oligonucleotide conjugates: Multiple cleavage of oncogenic miR-17 reinforced by RNAse H recruitment

Lina A Alaydi, Elena Bichenkova, David J Clarke

Faculty of Biology, Medicine and Health, School of Health Sciences, Division of Pharmacy and Optometry, University of Manchester, Oxford Rd, Manchester M13 9PT, UK

Therapeutic Oligonucleotides constitute the third platform alongside small drug molecules and protein therapy for cancers. Although small drug therapy have been used for decades, the tremendous side- effects and recurrent of cancer have been challenging the quality of patient life during and after therapy. In recent years, artificial antisense Peptidyl- oligonucleotides conjugates (aaPOC) has been investigated for suppression of pathogenic non-coding microRNA in many cancers. Common cancers such as breast cancer, and non-curable cancers including pancreatic and stomach cancers are being studied in efforts to re-program malignant cells to become healthy and therefore destroy their pathological activity. In this study, we aim to evaluate and further study the inactivation of emerging copies of over-expressed microRNA-17 found in pancreatic and stomach cancers. Our strategy is to allow complementary hybridization of designed site-selective POC to copies of microRNA-17 in order to cleave those targets in a multiple catalytic turnover manner. Artificial ribonucleases POC contains a sequence-specific recognition motifs that forms a bulge-loop in the central region of the targeted oncogenic miRNA, POC are covalently attached to catalytic peptides for subsequent cleavage of microRNA-17. Additional recruitment of naturally occurring RNAse H enzymes in the cells provides synergy for cleavage at multiple locations of microRNA, thus leading to multiple turnover of RNA substrates. As a result, we have successfully achieved about 90% cleavage of the target by POC in 1: 2 ratio of the target in vitro. Furthermore, the synergistic effect of RNAse H, has increased the multiple turn-over effect of POC cleavage up to 5 folds of targeted microRNA-17 in less than 72h. These promising outcomes open future studies in non-clinical and clinical studies.

SELEX of modified aptamers to study the catalytic mechanism underlying peptidoglycan polymerization by transpeptidase

Yan Badji^1,2, Mélanie Etheve-Quelquejeu¹, Laura Iannazzo¹, Marcel Hollenstein²

¹Team “Chemistry of RNAs, Nucleosides, Peptides and Heterocycles”, CNRS UMR8601, Université Paris cité, 45 Rue des Saints-Pères, 75006 Paris, France

²Team “Bioorganic chemistry of nucleic acids”, CNRS UMR 3523, Institut Pasteur, 75015 Paris, France

Antibiotics are known to treat serious bacterial infections, such as pneumonia, tuberculosis but also more benign infections such as angina. These compounds can do so kill or prevent bacterial growth. Nevertheless, bacteria can quickly mutate, and bacterial resistance against antibiotics can occur. Because of antibacterial resistance, the treatment of some infections becomes increasingly difficult. In a recent assessment, antibiotic resistance will soon become one of the main causes of death worldwide. To fight against this phenomenon, it is very important to understand the mechanism and mode of action of bacterial resistance. In this context our group is interested in Penicillin binding protein (PBP) transpeptidases which are involved in the biosynthesis of the peptidoglycan, the most important constituent of the bacteria cell wall. Our understanding of the cross-linking reaction catalysed by PBPs and the identification of inhibitors of these enzymes have been limited by the absence of a versatile assay. The SELEX approach will be applied to the identification of peptide-DNA aptamers that will act as soluble surrogates of the complex substrates of the transpeptidase. This is mandatory for (i) understanding the mechanism of the transpeptidation reaction, which is largely unknown due to limited access of chemically defined substrates, and (ii) developing assays to determine the efficacy of transpeptidase inhibitors. Our objective is to obtain peptide-nucleotides conjugates and raise aptamers via SELEX against transpeptidases. The peptidic substituent will mimic the amino acids of the natural substrate while the role of the glycan chain will be adopted by the aptamer. The bioconjugation between peptide and nucleic acid will be carried out by application of click chemistry. The synthetic pathway developed in the group to access to peptide-nucleotides conjugates will be presented here.

Evaluating Computational Methods for ssDNA Aptamer Structure Prediction

Selma Bengaouer, Bérangère Avalle, Irene Maffucci

Université de technologie de Compiègne, UPJV, CNRS, Enzyme and Cell Engineering, Centre de recherche Royallieu, CS 60 319 – 60 203, Compiègne Cedex, France

Aptamers’ inherent flexibility enables them to adopt specific 3D conformations, allowing high-affinity and selective binding to diverse target molecules, often with dissociation constants in the nM to pM range. Thus, high-resolution structural determination is crucial to understand their function, though the existing experimental methods are often costly and long. In this context, in silico 3D structure prediction is an efficient alternative to study aptamers function and design. Many algorithms have been developed for 3D structure prediction, with a focus on RNA. However, the growing interest in single stranded DNA (ssDNA), due to its greater stability and ease of synthesis, has highlighted the need to adapt these methods for DNA aptamers. To explore this potential, this study assessed three RNA 3D structure prediction methods (RNAComposer, SimRNA, and Vfold3D) based on their performance in the CASP15 challenge to evaluate their applicability to ssDNA. At this scope, a dataset of 93 experimentally determined ssDNA structures, including challenging motifs such as G-quadruplexes and pseudoknots, was built. Various metrics, such as RMSD, GDT_TS, INF, and TM-scores, were employed to benchmark the accuracy of the predictions. Vfold3D demonstrated the most proficiency in capturing global folds and interaction networks; however, it encountered challenges with smaller structures, faltering 15 out of the 93 cases. In contrast, SimRNA and RNAComposer successfully predicted all structures, with SimRNA slightly outperforming RNAComposer. However, all methods encountered difficulties with G-quadruplexes, and with structures containing multiple loops or long-distance interactions, which strongly increase the intrinsic flexibility of ssDNA. Therefore, these results indicate that much effort has still to be done for the modeling of ssDNA and that their structures need to be investigated considering their dynamics, e.g. by means of enhanced sampling molecular dynamics techniques.

Aptamer-based delivery of carbocyclic 5-Aza-2′-deoxycytidine (cAzadC) to cancer cells

Emmanuel A Bisong, Jahongir Nabiev, Ghofrane B Helal, Thomas Carell

Institute for Chemical Epigenetics, Department of Chemistry, Ludwig Maximilian University Munich, Würmtalstrasse 201, Munich, Germany

cAzadC is a carbocyclic analogue of 5-Aza-2′-deoxycytidine (AzadC, also known as Decitabine) – an epigenetic anti-cancer drug used in clinics as a cytostatic agent against myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML). Decitabine is integrated into DNA during replication due to its structural similarity to deoxycytidine and inhibits DNA methyltransferases such as DNMT1. This results in global hypomethylation which influences the epigenetic regulation of gene expression. The main disadvantage of this nucleoside drug is its strong side effects which limit the application in chemotherapy.  The pre-clinical studies show that the carbocyclic AzadC (cAzadC or Carbacitabine) has lower toxicity than the parent compound AzadC. To further decrease the off-target effects of the drug, selective delivery to the cells of interest is required. In this work, we present how aptamers could be used as carriers for selective delivery of nucleoside drugs such as cAzadC to cancer cells. One of the promising candidates is the aptamer Sgc8c which targets PTK7 receptors. These receptors are overexpressed in certain types of cancer cells such as lung cancer, leukaemia and neuroblastoma. In the course of this work, we demonstrate successful enzymatic incorporation of cAzadC into the aptamer chain, forming an aptamer-cAzadC-conjugate. Our results show promising features in oligonucleotides as drug delivery agents.

Custom Synthesis: unlocking the potential of modified oligonucleotides

Nicolas Chopin¹, Jean-Christophe Truffert¹, Sébastien Picard¹, Tirtsa Kleinmann²

¹Nucleosyn, 111 bd Duhamel de Monceau, 45160 Olivet, France

²Bio-Lab ltd, 22 Hayetzira Street, P.O. Box 34038, Jerusalem 91340, Israel

The synthesis of modified nucleic acids is a major breakthrough in the production of therapeutic oligonucleotides. These modifications enhance the stability, efficiency, and specificity of the ONs, allowing for better drug delivery to the target. This opens up new pathways for the treatment of various diseases, including genetic diseases, cancers, and infectious diseases. Moreover, this technology could revolutionize the field of personalized medicine. Nowadays, the main oligonucleotide-based therapies are characterized by first- and second-generation modifications such as 2-fluoro-RNA, 2-O-methyl RNA, phosphorothioates, 2-O-(2-methoxyethyl)-RNA (MOE) and morpholino phosphorodiamidates (PMO). However, developing new modifications of oligonucleotides is crucial for creating increasingly effective therapeutic compounds.In this context, the expertise in custom synthesis becomes paramount for the development of various analogues characterized by modifications of the sugar, phosphate backbone, nucleic bases, etc. The ability to precisely modify these components allows for the creation of oligonucleotides with specific properties.Here, we present the synthesis and properties of different analogues such as: Pyrazolo-triazine C-nucleosides that are compounds of interest as the C-C bond between sugar and base decreases sensitivity to acid hydrolysis; Sphingolipid-polyalkylamines (that modification of the corresponding oligonucleotide is useful to increase cellular uptake, enhance endosomal release, prolong circulation time, improve biodistribution or reduce off-target effects when compared to an unmodified nucleic acid molecule); 2’-O-Neopentyl modified oligonucleotides, useful for tuning the hybridization properties of ONs and finally Threose Nucleic acid Phosphoramidite (the TNA modification is known to enhanced nuclease resistance more than 2′-O-methyl or 2′-fluoro ribose modifications).

Lyme borreliosis diagnosis: characterization and enhancement of detection probes

Hugo Da Ponte, Mickaël GUERIN, Pauline TREZEL, Irene MAFFUCCI, Stéphane OCTAVE, Bérangère BIHAN-AVALLE, Séverine PADIOLLEAU-LEFÈVRE

Université de Technologie de Compiègne. Sorbonne Université. Rue Personne de Roberval – CS 60319 60 203 Compiègne Cedex, France…

Lyme borreliosis (LB) is the most commonly tick-borne disease in the world. Transmitted by ticks from the genus Ixodes, the etiological agent of LB is bacteria from the Borrelia burgdorferi sensu lato complex. With more than 700,000 new cases estimated each year in the United States and in Europe, the incidence of LB remains underestimated. Several factors contribute to this underestimation. These include: (i) the indirect serological detection of the infection, based on the detection of antibodies rather than the direct detection of pathogens; (ii) the challenge of clinical diagnosis due to the frequent absence of the pathognomonic erythema migrans rash; (iii) The occurrence of non-specific symptoms like arthritis, carditis, and neurological issues, especially in untreated cases.; and (iv) the concept of co-infections frequently associated with Lyme disease.This diagnostic challenge can delay or misguide treatment, highlighting the critical need for improve diagnostics approaches.  In this context, our project aims to select new molecular probes for the direct and rapid detection of CspZ, a surface protein of Borrelia. Building upon our previous work, where we selected promising aptamers, the current project aims to develop more effective novel probes by employing an optimized cross-over SELEX approach. We aim to select probes that display improved performance characteristics, including high affinity (low K_D), increased serum resistance, and reduced non-specific binding. Melting curve analysis and NGS analysis were used to monitor the SELEX process and identify new aptamer candidates. These candidates are currently being characterized for their binding affinity to the CspZ protein using various methods, including ELONA, dot blot, and SPR. The ultimate goal is to establish a foundation for (i) the development of a multiplexed biochemical assay and (ii) the application of artificial intelligence to design novel molecular probes tailored to specific requirements.

Novel Approaches to the Cytosolic Penetration of a Proprietary Antiviral Peptide (AVP)

Timothy Gomez¹, Natalie Youens¹, Joachim Bugert² and Simon C W Richardson¹

¹Exogenix Laboratory, University of Greenwich at Medway, Grenville Building, Central Avenue, Chatham, Kent, ME4 4TB, UK

²Bundeswehr Institute for Microbiology, Neuherbergstr. 11 80937 München Germany

There remain several rate limiting steps preventing the safe, efficient and reproducible delivery of large anti-viral molecules such as proteins (AVPs) to the cytosol. Previously protein architecture based upon attenuated anthrax toxin was characterised and found to be capable of delivering both antisense and siRNA molecules as well as custom peptides including LFn- diphtheria toxin a chain (DTA) into the cytosol where pharmacological activity was measured. Here a proprietary antiviral peptide (AVP) has been fused in frame with either an attenuated component of anthrax toxin (LFn) or attenuated Clostridium botulinum toxin A (aBoT) to target either somatic or neuronal viral diseases. Here we report our initial characterisations of two peptide delivery systems. After affinity enrichment the LFn fused AVP peptide was recorded at the predicted molecular weight after SDS-PAGE and Coomassie staining. It was predicted to be 42.4KDa and bands were observed at 40 and 80KDa presumably representing a dimer. The aBoT antiviral peptide was predicted to be expressed as a single hydrolysable chain of 115 KDa and bands were recorded at 75 and 37 KDa representing the aBoT heavy chain and the truncated (attenuated) light chain containing the AVP. These recombinant peptides displayed the immunological tags that would be predicted (LFn-AVP) displayed the predicted V5 and 6H epitopes and the aBoT variant only 6H. When incubated for 72h with HeLa cells, PA+LFn-AVP did not display any toxicity across all the parameters measured i.e., IC₅₀ > 250 µg/ml. Similarly, the aBoT-AVP did not display a measurable IC₅₀ below 250µg/ml when incubated for 72h with the human glioblastoma cell line U87-MG. In conclusion these two vehicles designed to deliver an AVP show promise and warrant further exploration.

Coupling Copper Sensitive DNAzyme to Enzyme-Free DNA Strand Displacement based Signal Amplifier for Cancer Diagnostic Solutions

Hyeyun Jung^1,2,3, Alexander Jackson³, Patricia Muller², Harold Fellermann^1,3

¹ICOS, School of Computing, Newcastle University, Newcastle upon Tyne, United Kingdom

²Department of Biosciences, Durham University, Durham, United Kingdom

³Nanovery, Newcastle upon Tyne, United Kingdom

Early cancer diagnosis increases the likelihood of successful treatment. Copper has recently emerged as an important biomarker for the onset and progression of several cancers, including breast, lung, and gastrointestinal cancers. However, current methods cannot reliably distinguish between bound and bioavailable copper in liquid samples. Given the growing interest in the effects of elevated bioavailable copper levels, there is a pressing need for a reliable method to detect, amplify, and report free copper in aqueous solutions. This poster outlines early-stage research aimed at developing such a method by integrating a previously reported copper-sensitive, DNA-cleaving DNAzyme with a DNA strand displacement-based signal amplifier known as Entropy-Driven Catalysis (EDC). Our approach involves optimising the DNAzyme buffer conditions using a design of experiments methodology and coupling the optimised DNAzyme with the EDC amplifier. Our results present a systematic workflow for enhancing the performance of the copper-specific DNAzyme, ultimately advancing the development of a mobilisation-free method to detect bioavailable copper in solution.

Reactivating the STING pathway in PTK7-positive acute leukemia cells using DNA-based theranostic nanodevices

Elisa Ottalagana^1,2, Andrea Marranci¹, Aldo Moscardini², Francesco Olimpico¹, Fabio Beltram^1,2, Stefano Luin^2,# & Andrea Ghelli Luserna di Rorà^1,#

¹Fondazione Pisana per la Scienza Onlus, San Giuliano Terme, Italy

²NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Pisa, Italy

^#Equal contributions

In eukaryotic cells, the STING pathway primarily responds to cytosolic DNA coming from viral/bacterial infection or damaged genomic DNA. Once activated, this pathway boosts the immune response by triggering the production of interferon type-I and other pro-inflammatory cytokines. In cancer cells, the STING pathways can be downregulated or silent because of the lack of cytosolic dsDNA, allowing them to evade the immune system and resist eradication. Thus, in oncology, reactivating the STING pathway is a promising innovative therapeutic strategy to enhance host immune response against cancer cells. For this reason, the aim of this project is to develop and test in vitro an aptamer-based nanodevice (hereafter StingApt) for activating the STING pathway selectively in cancer cells and, in particular, in acute lymphoblastic and myeloid leukemia (ALL and AML, respectively) models. StingApt is an oligomer comprehending a ssDNA aptamer targeting PTK7 receptor, and a 90-bases dsDNA sequence that activates the STING pathway; this version of StingApt should work therefore for PTK7⁺ cell lines. Firstly, we tested the basal protein/gene expression of several STING pathway components in a panel of cell lines. We then characterized in these cells, by immunoblotting and/or rtPCR, the effect of reactivating the STING pathway using a commercially available STING agonist (STING agonist-4, SA-4), the electroporated StingApt and 90-base dsDNA, finding similar results. Using confocal microscopy and flow cytometry analyses, we demonstrated that StingApt selectively binds to, and is internalized by, PTK7⁺ ALL cells more efficiently than the 90-base dsDNA. Finally, to increase the efficacy of our nanosystem in activating the STING pathway, we are currently developing an endosomal escape strategy based on nigericin conjugation to StingApt. Our preclinical data sustain the use of aptamer-based nanodevices for selectively delivering STING agonists against PTK7⁺ cells.