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Updated: Nov 8, 2025
A Flow Cytometry-Based Cell Surface Protein Binding Assay for Assessing Selectivity and Specificity of an Anticancer Aptamer
Published on: September 13, 2022
Selection of aptamers against triple negative breast cancer cells using high throughput sequencing
Débora Ferreira1,2, Joaquim Barbosa1,2, Diana A Sousa1,2
1CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
Abstract:
Triple-negative breast cancer is the most aggressive subtype of invasive breast cancer with a poor prognosis and no approved targeted therapy. Hence, the identification of new and specific ligands is essential to develop novel targeted therapies. In this study, we aimed to identify new aptamers that bind to highly metastatic breast cancer MDA-MB-231 cells using the cell-SELEX technology aided by high throughput sequencing. After 8 cycles of selection, the aptamer pool was sequenced and the 25 most frequent sequences were aligned for homology within their variable core region, plotted according to their free energy and the key nucleotides possibly involved in the target binding site were analyzed. Two aptamer candidates, Apt1 and Apt2, binding specifically to the target cells with [Formula: see text] values of 44.3 ± 13.3 nM and 17.7 ± 2.7 nM, respectively, were further validated. The binding analysis clearly showed their specificity to MDA-MB-231 cells and suggested the targeting of cell surface receptors. Additionally, Apt2 revealed no toxicity in vitro and showed potential translational application due to its affinity to breast cancer tissue sections. Overall, the results suggest that Apt2 is a promising candidate to be used in triple-negative breast cancer treatment and/or diagnosis.
Insights
Researchers identified Apt2, a novel aptamer, as a promising candidate for treating and diagnosing aggressive triple-negative breast cancer. This DNA-based therapeutic shows high specificity and low toxicity for targeted cancer therapy.
Area of Science:
- Biotechnology
- Molecular Biology
- Oncology
Background:
- Triple-negative breast cancer (TNBC) is an aggressive subtype with poor prognosis.
- Lack of approved targeted therapies necessitates novel treatment strategies.
- Identifying specific ligands for TNBC cells is crucial for developing targeted treatments.
Purpose of the Study:
- To identify novel aptamers that specifically bind to highly metastatic breast cancer MDA-MB-231 cells.
- To develop targeted therapies for triple-negative breast cancer.
Main Methods:
- Cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) technology was employed.
- High-throughput sequencing was used to analyze aptamer pools after 8 selection cycles.
- Aptamer candidates were validated for binding affinity and specificity to MDA-MB-231 cells.
Main Results:
- Two aptamer candidates, Apt1 and Apt2, were identified with high binding affinity (Kd values of 44.3 ± 13.3 nM and 17.7 ± 2.7 nM, respectively).
- Aptamer Apt2 demonstrated high specificity for MDA-MB-231 cells, suggesting potential targeting of cell surface receptors.
- Apt2 showed no in vitro toxicity and exhibited affinity for breast cancer tissue sections, indicating translational potential.
Conclusions:
- Apt2 is a promising candidate for triple-negative breast cancer treatment and diagnosis.
- The study highlights the potential of aptamer technology in developing targeted therapies for aggressive cancers.
- Further research is warranted to explore the clinical application of Apt2 in TNBC management.
