Systematic evaluation of cell-SELEX enriched aptamers binding to breast cancer cells

• Published in: Biochimie 2018-02, Vol.145, p.53-62
• Main Authors: Civit, Laia, Taghdisi, Seyed Mohammad, Jonczyk, Anna, Haßel, Silvana K., Gröber, Carsten, Blank, Michael, Stunden, H. James, Beyer, Marc, Schultze, Joachim, Latz, Eicke, Mayer, Günter
• Format: Article
• Language: English
• Subjects: A549 Cells; Antineoplastic Agents - chemical synthesis; Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacokinetics; Antineoplastic Agents - pharmacology; Aptamers, Nucleotide - chemical synthesis; Aptamers, Nucleotide - chemistry; Aptamers, Nucleotide - pharmacokinetics; Aptamers, Nucleotide - pharmacology; Breast Neoplasms - drug therapy; Breast Neoplasms - metabolism; Breast Neoplasms - pathology; Broad-spectrum aptamers; Cell-SELEX; DNA aptamers; Drug Screening Assays, Antitumor - methods; Female; High-throughput sequencing; Humans; MCF-7 Cells; Screening methods; SELEX Aptamer Technique - methods
• ISSN: 0300-9084; 1638-6183
• DOI: 10.1016/j.biochi.2017.10.007

The sensitive and specific detection of pathogenic cells is essential in clinical diagnostics. To achieve this, molecular tools are required that unequivocally recognise appropriate cell surface molecules, such as biomarkers that come along with disease onset and progression. Aptamers are short single-stranded oligonucleotides that interact with cognate target molecules with high affinity and specificity. Within the last years they have gained an increased attention as cell-recognition tools. Here, we report a systematic analysis of a cell-SELEX procedure, for the identification of aptamers that recognise breast cancer cells. Besides a comparison of conventional (Sanger) with high-throughput sequencing techniques (next-generation sequencing), three different screening techniques have been applied to characterise the binding properties of selected aptamer candidates. This method has been found to be beneficial in finding DNA aptamers, rarely enriched in the libraries. Finally, four DNA aptamers were identified that exhibit broad-spectrum interaction patterns to different cancer cell lines derived from solid tumours. •We report a systematic analysis of a cell-SELEX procedure.•NGS analysis is a powerful tool for the identification of aptamer candidates.•High variability between analytical techniques for individual aptamers was observed.•Four DNA aptamers exhibited broad-spectrum interaction to several cancer cell lines.