title: Rapid identification of cell-specific, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection.
abstract: BACKGROUND
  The broad applicability of RNA aptamers as cell-specific delivery tools for therapeutic reagents depends on the ability to identify aptamer sequences that selectively access the cytoplasm of distinct cell types. Towards this end, we have developed a novel approach that combines a cell-based selection method (cell-internalization SELEX) with high-throughput sequencing (HTS) and bioinformatics analyses to rapidly identify cell-specific, internalization-competent RNA aptamers.
  
  
  RESULTS
  We demonstrate the utility of this approach by enriching for RNA aptamers capable of selective internalization into vascular smooth muscle cells (VSMCs). Several rounds of positive (VSMCs) and negative (endothelial cells; ECs) selection were performed to enrich for aptamer sequences that preferentially internalize into VSMCs. To identify candidate RNA aptamer sequences, HTS data from each round of selection were analyzed using bioinformatics methods: (1) metrics of selection enrichment; and (2) pairwise comparisons of sequence and structural similarity, termed edit and tree distance, respectively. Correlation analyses of experimentally validated aptamers or rounds revealed that the best cell-specific, internalizing aptamers are enriched as a result of the negative selection step performed against ECs.
  
  
  CONCLUSIONS
  We describe a novel approach that combines cell-internalization SELEX with HTS and bioinformatics analysis to identify cell-specific, cell-internalizing RNA aptamers. Our data highlight the importance of performing a pre-clear step against a non-target cell in order to select for cell-specific aptamers. We expect the extended use of this approach to enable the identification of aptamers to a multitude of different cell types, thereby facilitating the broad development of targeted cell therapies.
authors.affiliation: Department of Internal Medicine, University of Iowa, Iowa City, Iowa, United States of America.
authors.forename: William H
authors.initials: WH
authors.lastname: Thiel
authors.forename: Thomas
authors.initials: T
authors.lastname: Bair
authors.forename: Andrew S
authors.initials: AS
authors.lastname: Peek
authors.forename: Xiuying
authors.initials: X
authors.lastname: Liu
authors.forename: Justin
authors.initials: J
authors.lastname: Dassie
authors.forename: Katie R
authors.initials: KR
authors.lastname: Stockdale
authors.forename: Mark A
authors.initials: MA
authors.lastname: Behlke
authors.forename: Francis J
authors.initials: FJ
authors.lastname: Miller
authors.forename: Paloma H
authors.initials: PH
authors.lastname: Giangrande
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D001692:Biological Transport; D019295:Computational Biology; D016503:Drug Delivery Systems; D042783:Endothelial Cells / Q000166:cytology / Q000378:metabolism; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009131:Muscle, Smooth, Vascular / Q000166:cytology / Q000378:metabolism*; D032389:Myocytes, Smooth Muscle / Q000166:cytology / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D052156:SELEX Aptamer Technique
chemical_list: D052157:Aptamers, Nucleotide; D012313:RNA