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CRISPR-Mediated Isogenic Cell-SELEX Approach for Generating Highly Specific Aptamers Against Native Membrane Proteins


Rosch JCJonah C , Neal EHEmma H , Balikov DADaniel A , Rahim MMohsin , Lippmann ESEthan S . Cellular and molecular bioengineering. 2020 9 11; 13(5). 559-574


INTRODUCTION: The generation of affinity reagents that bind native membrane proteins with high specificity remains challenging. Most selection paradigms utilize different cell types for positive and negative rounds of selection (where the positive selection is against a cell that expresses the desired membrane protein and the negative selection is against a cell that lacks the protein). However, this strategy can yield affinity reagents that bind unintended membrane proteins on the target cells. To address this issue, we developed a systematic evolution of ligands by exponential enrichment (SELEX) scheme that utilizes isogenic pairs of cells generated CRISPR techniques.

METHODS: Using a Caco-2 epithelial cell line with constitutive Cas9 expression, we knocked out the gene (encoding the GLUT1 glucose transporter) lipofection with synthetic gRNAs. Cell-SELEX rounds were carried out against wild-type and GLUT1-null cells using a single-strand DNA (ssDNA) library. Next-generation sequencing (NGS) was used to quantify enrichment of prospective binders to the wild-type cells.

RESULTS: 10 rounds of cell-SELEX were conducted simultaneous exposure of ssDNA pools to wild-type and GLUT1-null Caco-2 cells under continuous perfusion. The top binders identified from NGS were validated by flow cytometry and immunostaining for their specificity to the GLUT1 receptor.

CONCLUSIONS: Our data indicate that highly specific aptamers can be isolated with a SELEX strategy that utilizes isogenic cell lines. This approach may be broadly useful for generating affinity reagents that selectively bind to membrane proteins in their native conformations on the cell surface.