PhD Scientific Days 2025

Poster Session II. - B: Molecular Medicine

Selection of Cadherin-11 Specific Aptamers

Name of the presenter

Tar Alexandra

Institute/workplace of the presenter

Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University

Authors

Alexandra Tar¹, Jessica Lange², Brigitta Kállai¹, Krisztina Percze¹, Thomas Karonitsch², Felix Kartnig², Hans Kiener², Daniel Aletaha², Ákos Harkai¹, Anna Tory¹, Leonhard Heinz², Peter Mandl², Tamás Mészáros¹

1: Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University
2: Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna

Text of the abstract

Introduction
Rheumatoid arthritis (RA) is an autoimmune disease characterised by structural joint damage and functional impairment. Fibroblast-like synoviocytes (FLSs) contribute to the healthy synovial membrane; however, under pathological conditions they become activated and play a crucial role in the development of synovitis, the chronic inflammation of the synovial membrane. FLSs express cadherin-11 (CDH11), a vital protein in cell-cell adhesion and a potential therapeutic target in RA.
Aims
Our aim is to generate CDH11-selective, modified nucleotide holding aptamers by toggle-SELEX and functionally characterise the enriched oligonucleotide candidates.
Method
CDH11-selective aptamer candidates were produced using toggle-SELEX. Subsequently, the enriched library was inserted into a cloning vector and examined by colony PCR, lab-on-a-chip nucleic acid electrophoresis, and Sanger sequencing. In addition, next-generation sequencing (NGS) was used to analyse the oligonucleotide pool after each selection step, including the initial library. The NGS data was analysed using AptaSUITE in our laboratory and by our collaborating, generative AI applying company (PentaBind). Wet-lab screening of the sequences was performed using AlphaScreen interaction analysis. MicroScale Thermophoresis (MST) was applied to further characterise the interaction of aptamer candidates with CDH11 and CDH13.
Results
The sequencing data analysis revealed the enrichment of specific oligonucleotides and various sequence-structure motifs. Generative AI analysis identified additional aptamer candidates using uniqueness rank score. AlphaScreen demonstrated that most studied candidates could interact with the in vitro translated CDH11. MST results showed that four candidates exhibited low micromolar binding affinity to CDH11. Besides, one candidate displayed clearly higher affinity to CDH11 than to CDH13, suggesting specificity. This candidate also performed well in artificial synovial fluid.
Conclusion
The top-performing aptamer candidate exhibited specific binding to CDH11 with low micromolar affinity and preserved its efficacy in artificial synovial fluid. Currently, we are modifying the nucleic acid sequence of this aptamer to further enhance its performance.
Funding
OTKA-ANN-139564
TKP2021-EGA-24
tar.alexandra@semmelweis.hu
Semmelweis University, Molecular Medicine Division
Tamás Mészáros