Differential binding cell-SELEX method to identify cell-specific aptamers using high-throughput sequencing

Area of Science:

• Biotechnology
• Molecular Biology
• Bioinformatics

Background:

• Aptamers are increasingly used as alternatives to antibodies.
• High-throughput sequencing (HTS) has advanced aptamer research, but its full potential remains untapped in public databases.
• Current HTS applications in aptamer research often overlook critical selection biases.

Purpose of the Study:

• To develop a more informative and efficient cell-SELEX workflow for aptamer identification.
• To adapt existing bioinformatics tools for enhanced aptamer selection analysis.
• To improve the aptamer selection rate against live cells, particularly cancer cells.

Main Methods:

• Implemented a differential binding cell-SELEX workflow.
• Utilized the FASTAptamer toolbox and the edgeR bioinformatics tool.
• Performed aptamer selection against clear cell renal cell carcinoma (ccRCC) cells with negative selection using healthy kidney cells.

Main Results:

• Presented a practical high-throughput aptamer identification method.
• Demonstrated increased aptamer selection rate against live cells.
• Showcased the workflow's feasibility using a ccRCC cell line.

Conclusions:

• The proposed method offers a more informative approach to aptamer selection.
• This workflow enhances the efficiency and accuracy of aptamer discovery against specific cell targets.
• The differential binding cell-SELEX strategy provides valuable insights into the aptamer selection process.