Thank you for considering presenting your work as a poster at this conference.
Thank you for considering to present your work as a poster at this conference.
Before uploading your poster, you must make sure that you follow ALL of the instructions above!
Please keep an eye on this page for any future updates.
Before uploading your poster, you must make sure that you follow ALL of the instructions above!
(Presenters in Bold)
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 AptamersOxford@gmail.com.
Synthetic small molecule-binding aptamers as versatile regulatory elements
Leon Boettger, Beatrix Suess
Synthetic RNA Biology, TU Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany One of the most exciting areas of synthetic biology is to control cellular behavior using engineered genetic circuits. To combine genes of interest in a building block-like manner and transfer them to organisms of interest in order to achieve desired biological functions. However, the expression levels of the corresponding genes need to be regulated and fine-tuned to avoid unbalanced gene expression and the accumulation of toxic intermediates. Synthetic RNA-based systems have increasingly been used for the regulation of gene expression. Due to their structural properties, riboswitches provide a convenient basis for the development of ligand-dependent controllable systems. Here, we present a set of five synthetic riboswitches for the control of gene expression using small molecules as a ligand. Our devices can be used for the control of translation initiation, pre-mRNA splicing, RNA self-cleavage as well as fluorogenic aptamers. Thereby, we offer modular investigative tools for the design and study of complex regulatory systems, metabolic pathways, and biosensors.
Aptamers for detection in novel assays and delivery of therapeutic payloads
George W Jackson
Base Pair Biotechnologies, Inc., 8619 Broadway St, Suite 100. Houston, TX, USA
Aptamers represent a highly promising modality for sensing targets across a broad size range, from small molecules to whole viral particles, in “self-reporting” (i.e., label-free) biosensors. This advantage arises from their ability to undergo significant conformational changes upon target binding, often exceeding those observed with antibody-based reagents. Beyond biosensing, aptamers are increasingly utilized as both standalone therapeutic agents and as targeted delivery vehicles for other therapeutic payloads, enhancing drug specificity and efficacy. Their versatility, high affinity, and ease of modification make them attractive for applications in diagnostics, targeted therapy, and drug delivery. This presentation highlights recent advancements in aptamer-based biosensing and therapeutic strategies, showcasing their expanding role in precision medicine and biotechnology.
Specific Targeting and Imaging of RNA G-Quadruplex (rG4) Structure using Non-G4-Containing L-RNA Aptamer and Fluorogenic L-Aptamer
Hill Lam Lau[‡], Haizhou Zhao[‡], Hengxin Feng1, and Chun Kit Kwok
[‡]These authors contribute equally to this work
Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 000000, China
2Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China RNA G-quadruplex structures (rG4s) play important roles in the regulation of biological processes. So far, all the L-RNA aptamers developed to target rG4 of interest contain G4 motif itself, raising the question of whether non-G4-containing L-RNA aptamer can be developed to target rG4. Furthermore, it is unclear whether an L-aptamer-based tool can be generated for G4 detection in vitro and imaging in cells. Herein, we design a new strategy using a low GC content template library to develop a novel non-G4-containing L-RNA aptamer with strong binding affinity and improved binding specificity to rG4 of interest. We identify the first non-G4-containing L-Aptamer, L-Apt.1-1 with nanomolar binding affinity to amyloid precursor protein (APP) D-rG4. We apply L-Apt.1-1 to control APP gene expression in cells via targeting APP D-rG4 structure. Moreover, we develop the first L-RNA-based fluorogenic bi-functional aptamer (FLAP) system, and engineer L-Apt.1-1_Pepper for in vitro detection and cellular imaging of APP D-rG4. Our work provides an original approach for developing non-G4-containing L-RNA aptamer for rG4 targeting, and the novel L-Apt.1-1 developed for APP gene regulation, as well as the L-Apt.1-1_Pepper generated for imaging of APP rG4 structure can be further used in other applications in vitro and in cells.
Development of multivalent aptamers targeting gastric cancer cells
Gorann Lepied1,2, Christine Varon2, Pierre Dubus2,3, Jeanne Leblond Chain1
1University Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, F-33000 Bordeaux, France
2University Bordeaux, INSERM, BRIC, U 1312, F-33000 Bordeaux, France
3CHU Bordeaux, Tumor Biology, F-33000 France
Multivalency refers to constructing molecular structures that incorporate two or more aptamers, either identical or distinct. This strategy has already demonstrated powerful outcomes in oncology where numerous different biomarkers are often used as entry points for targeted therapies, increasing both specificity and efficacy against cancer cells. In this project, we aim to develop a dual-aptamer-based approach targeting specific gastric cancer stem cells (GCSCs) biomarkers – EpCAM (CD326) and CD44(v9) – to enhance both diagnostic accuracy and chemotherapy precision. Here, we developed bi-specific aptamer assemblies to improve the selective recognition of GCSCs. A CD44v9-binding aptamer (Apt4) was hybridized with an EpCAM-binding aptamer (SYL3C) via a 15-nucleotide linker. Size-adjustable spacers such as hexaethylene glycol or poly-thymine strands were integrated into the sequence to evaluate length and flexibility contribution to the dual-recognition process. Assembly formation was assessed by native PAGE. The targeting ability of the aptamers was evaluated on four gastric cancer cell lines—AGS, NCI-N87, MKN74, and MKN45—via flow cytometry and compared to conventional antibodies targeting both CD44 and EpCAM receptors, allowing the selection of the most relevant model for EpCAM+/CD44(v9)+ GCSCs. Binding curves of both EpCAM- and CD44(v9)-specific single aptamers were generated via flow cytometry, demonstrating affinity values consistent with literature reports. Single aptamers were compared with different SYL3C-Apt4 assembly designs for their targeting capacity toward EpCAM+/CD44(v9)+ GCSCs. We finally demonstrated receptor specificity through flow cytometry competition assay between dual assemblies and their respective antibody, revealing distinct aptamer binding kinetics for the two receptors. The next steps of this study will focus on improving assembly specificity, diagnostic capabilities, and developing aptamer-drug conjugates for targeted delivery.
The UTexas Aptamer Database: Lessons Learned and an AI-Driven Future
Gwendolyn M Stovall, Dhruv Kumar, Shriya Swamy, Einez Wu, and Amrut Pennaka
Freshman Research Initiative, University of Texas, Austin, Texas, USA
The UTexas Aptamer Database (https://sites.utexas.edu/aptamerdatabase) is a publicly accessible repository of over 1,500 aptamer sequences designed to facilitate research by integrating sequence data, selection conditions, and target information. Despite rigorous efforts to extract aptamer sequences and selection data from the literature, our research found frequent, unexplained sequence alterations in the literature itself, highlighting the need for improved validation in future iterations. Additionally, despite peer review and researcher training, we identified discrepancies between our database and others. While cross-referencing helped resolve some inconsistencies, these challenges persist across databases and underscore the need for automated validation. As aptamer publications continue to grow rapidly, so does the need for efficient curation of sequence and selection data. To address these challenges, we are leveraging Large Language Models (LLMs) to automate aptamer data extraction, improving efficiency and scalability. Our work focuses on training OpenAI’s GPT-4o Mini using a curated subset of aptamer publications to ensure high-quality training data. We will evaluate model performance on an independent subset of analyzed papers, refining extraction accuracy through API integration, prompt engineering, dataset curation, and iterative training. Performance will be assessed using standard evaluation metrics (precision, recall, and F1 score) to optimize accuracy while reducing manual workload. This work will guide the development of a framework and toolkit for systematically aggregating aptamer selection experiments and sequence data. By enhancing the accessibility and interoperability of aptamer data, we aim to expand research opportunities and improve the visibility of aptamer information.
Development of an aptamer against the immune checkpoint protein B7-H4 using Cell-SELEX
Kien T Vien1,2, Derek Richard1, Laura Croft1
1School of Biomedical Science, Faculty of Health, Queensland University of Technology; 60 Musk Avenue, Kelvin Grove, Brisbane, 4059, Queensland, Australia
2Training Center, Pasteur Institute in Ho Chi Minh City; 167 Pasteur Street, District 3, Ho Chi Minh City, Viet Nam
The immune checkpoint protein B7-H4 plays a crucial role in regulating T-cell responses by inhibiting T-cell activity when expressed in cancer cells, making it a promising target for anticancer therapy. Recently, aptamers have emerged as potential candidates to target this checkpoint due to their specific binding capabilities and cost-effective production. This study utilized Cell-SELEX to develop an aptamer specific to the membrane protein B7-H4 in human breast cancer cell line SK-BR-3. Through 20 rounds of Cell-SELEX between SK-BR-3 and MCF-7 cells, aptamer candidates were enriched and selected. The top 17 candidates were analyzed, and the top 3 were validated via flow cytometry using both wild-type (WT) and B7-H4 knock-out (KO) SK-BR-3 cells. Two-way ANOVA analysis revealed statistically significant differences in binding rates between WT and KO cells across all 3 candidates. The aptamer with the strongest binding affinity, characterized by the lowest dissociation constant (KD) of 59.06 ± 60.69 nM to B7-H4, was selected for further development. Future work will involve aptamer modification and Electrophoretic mobility shift assay (EMSA) validation, but this candidate shows promise as a potential therapeutic agent to block B7-H4 and initiate an antitumor immune response.
Functional Selection of Molecular Aptamers Beacons
Anielle Villeronce, Jeanne Leblond Chain, Laurent Azéma
ARNA-Inserm U1212-UMR CNRS 5023-Université de Bordeaux
TAMS group-2, rue Dr. Hoffman Martinot 33000 Bordeaux
Designed for nucleic acid detection, Molecular Beacons (MB) are a powerful detection tool due to their ability to signal the target presence in real-time. To increase MB affinity and selectivity for their targets and extend their application to non-nucleic acid targets, Molecular Aptamers Beacons (MAB) were developed. Such systems gather the recognition properties of aptamers and the switching ability of MB triggering a fluorescence signal for imaging or drug release in a specific environment, with an improved signal/noise ratio. MAB designed from previous aptamers by trial-and-error or strand displacement can be tedious and do not ensure a successful candidate. Developing a SELEX method that can directly provide MAB without post-SELEX modification is valuable. In this project, we aim to develop a MAB SELEX method to detect Thrombospondin-1 (TSP1), a relevant biomarker of Glioblastoma, for theragnostic purposes. To reach that goal, we designed a library bearing FRET pair, and a two-step selection: first, 4 regular SELEX rounds were achieved using TSP1 immobilized on magnetic beads to reduce the diversity required for the next step. Then, 4 functional selection rounds were realized where monoclonal beads were produced by emulsion PCR and fluorophores grafted through NHS chemistry. The beads were incubated with TSP1; beads exhibiting fluorescence enhancement were sorted. A negative selection was used to discard sequences switching in absence of TSP1. After sequencing of all rounds, our method led to identification of Apta_1, which was synthesized and assessed by MST and fluorescence. Apta_1 exhibits moderate affinity (KD = 1.8 µM) and its fluorescence is enhanced in the presence of TSP1, compared to non-specific binding, demonstrating its structure-switching ability. Although this candidate confirmed our experimental approach, we aim to improve affinity and fluorescence switch, through some protocol optimization: further selection rounds and a Doped-SELEX library.
Re-selection using G4-SLSELEX-Seq uncovers G4-specific targeting L-RNA aptamers with unique structure features
Tianying Wu1, Chun Kit Kwok1,2,*
1Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR 999077, China
2Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
G-quadruplexes (G4s) are non-canonical nucleic acid structures that can adopt different folding topologies, including parallel, anti-parallel and hybrid conformations. G4-containing L-RNA aptamers have shown promise in binding various G4 targets and regulating G4-mediated gene expression. However, aptamers for selectively targeting specific G4 conformations are still limited. The binding motif structure of aptamers also needs to be broadened to enhance selectivity. To further investigate the structure diversity of L-RNA aptamer for enhanced selectivity toward specific G4 conformations, we carried out re-selection of the binding motif of existing G4-containing L-RNA aptamer. Here, we developed a new G-triplex L-RNA aptamer, L-Apt.G3, by using G4-stem-loop(SL)SELEX-Seq. We demonstrated that L-Apt.G3 exhibited strong binding affinity and selectivity to G4 targets with parallel and antiparallel conformations. Spectroscopic analysis, mutagenesis analysis and structure probing assays verified that L-Apt.G3 possessed a nonconical G-triplex structure folding from three guanine runs which is a vital motif for G4 binding. Furthermore, L-Apt.G3 could interfere the interaction between c-kit 1 dG4 and G4-binding protein DHX36. This study provides insight into the promising prospects of G4-triplex-containing L-RNA aptamers for specific G4 targeting.