Posters and Guidelines

Thank you for considering to present your work as a poster at Oligo 2022 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.
• Naming your poster files: Name your poster files as follows: <your surname>-Oligo22-Poster.pdf | <your surname>-Oligo22-Poster.png | <your surname>-Oligo22-Poster.jpg, etc. For example, for David Jones, name your file as Jones-Oligo22-Poster.pdf. DO NOT name your poster files as, e.g.,  Oxford-poster, poster2021v, Oxford-oligo-poster. Such files will be automatically rejected.
• Poster submission: Submit your final poster as both PDF and JPG/PNG files via the link below no later than 28th March 2022. Late posters may not be included in the symposium 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.

Poster presentation: Posters will be made available via a secure page to the conference participants before the meeting. There will be two ways to interact with the poster presenters:

• the participants will be able to ask questions via the Zoom chatbox during the mid-conference breaks; and/or
• the participants can post their questions on Twitter at any time using the meeting hashtag #OligoOx22, 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.

Antisense oligonucleotide-mediated splice modulation of epidermal growth factor receptor to overcome therapy resistance in cancer cells

#ABalachandran #OligoOx22

Akilandeswari A Balachandran^{1, 2}, Rakesh N Veedu^{1, 2}

¹Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia

²Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia

Antisense oligonucleotides (AOs) are synthetic nucleic acid molecules that has the potential to bind specifically to mRNA by Watson-Crick base pairing, thereby regulating gene expression. AOs modulate gene expression by steric blocking, RNAse H mediated cleavage, or splice modulation. These AOs has a great potential in regulating oncogene expression. Epidermal growth factor receptor (EGFR) is a transmembrane receptor involved in oncogenesis. The longest isoform of EGFR has 28 exons and is over-expressed in cancers. The mutant EGFR isoform EGFR vIII has an in-frame deletion of exon 2-7 resulting in lack of ligand-binding domain and is constitutively active. Current therapies targeting EGFR include tyrosine kinase inhibitors and monoclonal antibodies. Despite the advances in EGFR targeted cancer therapies, acquired mutations leading to therapy resistance need to be addressed. To overcome this therapy resistance, we designed splice modulating antisense oligonucleotides that target specific exons that harbor activating mutations. Exon 3, exon 18 and exon 21 targeting AOs were designed and screened in different cancer cells to evaluate their exon skipping activity. We observed that PNAT524, PNAT525 (targets exon 3), PNAT576 (targets exon 18) and PNAT578 (targets exon 21) performed better in skipping respective exons in glioblastoma, liver cancer and breast cancer cell lines. In addition to this, PNAT578 also skipped partial exon 19, complete exon 20 and partial exon 21. Exon 3 skipping resulted in premature stop codon leading to reduced EGFR expression. Exon 18, exon 20 and exon 21 skipping is advantageous as these exons were reported to have mutations that lead to therapy resistance. Wound healing assay revealed that a combination of PNAT576 and PNAT578 treatment reduced the migratory potential of glioblastoma cells. We presume that these AOs, when administered in combination with conventional therapies, has the potential to reduce therapy resistance.

The Synthesis and Biodistribution of [³H]Cobomarsen (MRG-106)

#JBloom #OligoOx22

Jon Bloom¹, Claire. Henson², Darren Price¹, Jack Haffenden¹, Kathryn Webbley² and Stephen Harris²

¹Pharmaron UK Ltd, The Old Glassworks, Nettlefold Road, Cardiff, CF24 5JU, UK

²Pharmaron UK Ltd, Pegasus Way, Crown Business Park, Rushden, NN10 6ER, UK

Radiolabeling a molecule allows the absorption, distribution, metabolism and excretion of a molecule to be studied.  We have radiolabeled the 14-mer antisense oligonucleotide Cobomarsen (MRG-106) with 3H and carried out a biodistribution study. A phosphoramidite with a 3H label in the 5’ position was prepared by chemical synthesis. This was used to label the oligonucleotide using automated oligonucleotide synthesis. Thus 2.3 mCi at 3 Ci/mmol was obtained. This material was used to study biodistribution by autoradiography in rats. Images showing the biodistribution after 4 and 96 hours are presented in the poster. Maximum concentrations of radioactivity were observed for the majority of tissues between 4 and 24 hours post-dose. Highest concentrations were associated with the kidney cortex at all sampling times, indicating some retention of test item-related material in this tissue.

Development of an Antisense Oligonucleotide Therapeutic Targeting UBE3A for Dup15q Syndrome

James J Fink, Karthiayani Harikrishnan, Aishwarya Dhandapani, Vaibhav Joshi, Caitlin Lewarch, David Gerber, Owen McManus, Luis A Williams, Graham T Dempsey

#JFink #OligoOx22

Q-State Biosciences Inc, Cambridge MA 02139, USA

Chromosome 15q duplication syndrome (Dup15q) is a neurodevelopmental disorder in which patients present with language impairments, hypotonia, intellectual disability, and seizures, which lead to an increased risk of sudden unexpected death in epilepsy. Despite the substantial unmet medical need, there is currently no disease-specific treatment for Dup15q. Although >30 genes are located within the duplicated region, the maternal-specific duplication of 15q11-q13 underlying the disorder indicates that the UBE3A gene is a critical pathogenic factor. Antisense oligonucleotides (ASOs) have emerged as a powerful therapeutic modality that can directly target the CNS, and gapmer ASOs can be designed to engage endogenous RNase H, leading to specific degradation of the target transcript. Here, we focus on developing gapmer ASOs to knock down excess UBE3A as a therapeutic approach to Dup15q. The overall objective is to bring a much-needed, genetically-targeted therapy to Dup15q patients. We have developed UBE3A ASO candidates using our technology platform, which integrates ASO design, patient-derived neuronal models, deep functional characterization of neuronal activity with single cell resolution and machine-learning based analytics to uncover disease relevant cellular phenotypes and to quantitatively assess on and off-target ASO activity. We have identified ASOs achieving >80% UBE3A transcript and protein knockdown that are de-risked for potential off-target perturbation of neuronal physiology. ASO activity was assessed across diverse cell types covering both human models and relevant preclinical toxicology species. Based on this characterization, we selected optimal UBE3A ASO leads for assessment in vivo, demonstrating initial rodent tolerability and knockdown of Ube3a in different brain regions following intrathecal delivery. Efforts are underway to demonstrate functional rescue of disease-relevant phenotypes identified in Dup15q patient-derived neuronal models.

Photo-crosslinkable nucleosides provide an easy-to-use platform to rapidly construct chemically modified CRISPR/Cas9 guide RNA libraries

#BLargey #OligoOx22

Brendan Largey, Afaf El-Sagheer, Tom Brown

Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK

CRISPR/Cas9 is an RNA-guided DNA endonuclease capable of creating precise dsDNA breaks that provide a basis for gene editing.  Cas9 has been adapted for a number of applications owing to its ease of use and programmability, and has significant therapeutic potential to knockout or correct disease-associated genes.  A variety of chemical modifications can be made to the ribose and phosphate linkages of the Cas9 guide RNA (gRNA) to improve its therapeutic profile; these effects include greater stability and reduced off-target effects and inflammation response.  A significant challenge towards implementing these modifications in Cas9 and CRISPR nuclease therapies is the large size of gRNAs (typically >100nt), which makes them difficult to chemically synthesize in great amounts or purity.  Our group has been exploring the potential of 3-cyanovinyl carbazole nucleosides (^CNVKs) to overcome this limitation. ^CNVK residues are capable of reversibly crosslinking to pyrimidine bases in hybridized oligonucleotide strands when exposed to 366 nm light in a rapid and site-specific manner.  Using this property, we have constructed synthetic gRNAs by photocrosslinking two portions of the molecule which individually provide targeting and structural functions for Cas9.  In vitro assays were performed to confirm that the ^CNVK-gRNA functioned with Cas9, and it was determined to cause DNA cleavage at comparable rates to a full-length single gRNA (sgRNA).  In vivo gene editing has been performed in human cell lines by electroporation of Cas9-RNP, and preliminary results indicates that the ^CNVK-gRNA causes InDel formation at similar rates to sgRNAs.  NGS analysis is underway to determine with greater accuracy if ^CNVK-gRNAs are more effective at forming InDels than their non-crosslinked gRNA counterparts.  A standard ^CNVK gRNA scaffold will greatly simplify the synthesis and optimization of modified gRNA libraries and help leverage the advancements made in RNA chemistry into gene therapy.

An amide backbone flanked by LNA is a promising modification combination for splice-switching oligonucleotide therapy

#LilliLie #OligoOx22

Lillian Lie, Ysobel Baker, Aaron Jones, Afaf El-Sagheer, Tom Brown

Department of Chemistry, University of Oxford, South Parks Road, OX1 3QZ

Antisense oligonucleotides (ASOs) are a promising new therapeutic modality for the treatment of notoriously difficult-to-treat diseases. The development of structural modifications has been the foundational research which make ASOs “druggable”; many modified ASOs have already entered the market as first-of-their-kind therapeutics. Improved modifications are in high demand to advance the properties and effectiveness of ASO drugs even further. We present the design and synthesis of a novel modification system in which an artificial amide backbone is flanked by two locked-nucleic acid ribose modifications. The group has developed an efficient route for the synthesis of a 3’-carboxylic acid LNA monomer and a 5’-amino LNA monomer. We have investigated two methods for the incorporation of the amide modification: a monomer method (amide backbone is installed on the resin) and a dimer method (amide backbone is installed in a dimer phosphoramidite). X-ray crystallography studies reveal the amide backbone produces minimal structural deviation in a DNA:RNA hybrid. Preliminary biophysical studies have shown that the amide-LNA modification system improves the ASO’s target affinity and binding to RNA while preliminary cell and enzymatic studies reveal improved nuclease resistance and importantly, improved cellular uptake. The group is currently working on the synthesis of exon skipping sequences for application in Duchenne’s Muscular Dystrophy mdx mouse model. We plan to investigate the in vitro ability of our modification system to restore the synthesis of mRNA dystrophin transcripts and functional dystrophin protein. In tandem, we are working on large scale oligonucleotide synthesis for future in vivo work with the mdx mouse model. We see great promise in the ability of the LNA-amide modification to confer an ASO with druggable properties as well as improved splice-switching therapeutic activity.

Antisense oligonucleotides targeting Required for Meiotic Nuclear Division 1 Homolog (RMND1) towards tackling breast cancer

#PRaguraman #OligoOx22

Prithi Raguraman^1,2, Stacey L. Edwards³, Rakesh N. Veedu^1,2

¹Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Australia

²Perron Institute for Neurological and Translational Science, Australia

³QIMR Berghofer Medical Research Institute, Brisbane, Australia

Modification of RNA splicing using synthetic antisense oligonucleotides (AOs) has been established as a feasible therapeutic strategy for tackling various diseases. RNA targeting therapies using AOs have become an effective treatment strategy with new drugs approved for the treatment of Duchene muscular dystrophy, familial hypercholesterolemia, cytomegaloviral retinitis, hereditary transthyretin amyloidosis, spinal muscular atrophy, Batten disease and familial chylomicronemia syndrome. In this study, we have investigated the potential of exon skipping mechanism to inhibit the expression of a gene, required for meiotic nuclear division 1 homolog (RMND1). Variations in the expression level of this mitochondrial protein is associated with different pathologies. RMND1 is also listed as a pan-cancer molecular (methylation) signature. It is present in the breast cancer susceptibility locus 6q25.1 and has an increased expression in breast cancer. We hypothesised that the expression of RMND1 will be inhibited with the removal of one or more exons. In this direction, we designed and synthesised several AOs targeting different exons of RMND1 gene transcript and examined their efficacy in breast cancer cells. We observed that, our AO efficiently skipped exon-3 in MDA-MB 231 breast cancer cells. Further, protein analysis was performed using western blotting and we observed a reduction in the protein expression. Our results suggest that AO mediated targeted therapy against RMND1 could be effective in combination with the already available therapeutic strategies to combat breast cancer.

A Targeted Click Chemistry Approach to Developing Metallated-PNA Hybrids

Anna Ziemele,^a, Nicolò Zuin Fantoni,^b,c Joseph Hennessy,^a Afaf H. El-Sagheer,^b Tom Brown,^b,c Andrew Kellett ^a*

^aSchool of Chemical Sciences and National Institute of Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland

^bDepartment of Chemistry, University of Oxford, Oxford, United Kingdom

^cATDBio, Magdalen Centre, Oxford Science Park, Oxford, United Kingdom

The design of sequence-specific molecular probes that enable manipulation and relay structural information is of growing interest to diverse fields of biochemical research.¹ Recent discoveries in probe design have enabled the hybridisation of oligonucleotides to distinctive metal complexes, thereby enabling site-specific reactivity under the guidance of the recognition probe.^2-3 Similar to deoxyribose-based triplex forming oligonucleotides (TFOs),⁴ peptide nucleic acids (PNAs) can bind oligonucleotide targets in a sequence-specific manner via triplex formation and triplex invasion.⁵ In this work, we employ strain-promoted click chemistry to conjugate azide-functionalised Ru(II) complexes to alkyne-modified oncogene-targeting PNA sequences to generate Ru(II)-PNA constructs. The Ru(II)-PNA hybrids are useful theranostic tools where the intercalative and luminescent properties of Ru(II) probes provide diagnostic recognition toward the oncogene of interest.