title: Selection of Aptamers Against Whole Living Cells: From Cell-SELEX to Identification of Biomarkers.
abstract: Aptamer selection protocols, named cell-SELEX, have been developed to target trans-membrane proteins using whole living cells as target. This technique presents several advantages. (1) It does not necessitate the use of purified proteins. (2) Aptamers are selected against membrane proteins in their native conformation. (3) Cell-SELEX can be performed to identify aptamers against biomarkers differentially expressed between different cell lines without prior knowledge of the targets. (4) Aptamers identified by cell-SELEX can be further used to purify their targets and to identify new biomarkers. Here, we provide a protocol of cell-SELEX including the preparation of an oligonucleotide library, next-generation sequencing and radioactive binding assays. Furthermore, we also provide a protocol to purify and identify the target of these aptamers. These protocols could be useful for the discovery of lead therapeutic compounds and diagnostic cell-surface biomarkers.
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Center (MIRCen), CNRS UMR 9199, Neurodegenerative Diseases Laboratory (LMN), Université Paris-Sud, Université Paris-Saclay, Bât 61, Pièce 113, 18 route du Panorama, BP No. 6, F-92265, Fontenay-aux-Roses, France.
authors.forename: Nam Nguyen
authors.initials: NN
authors.lastname: Quang
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Center (MIRCen), CNRS UMR 9199, Neurodegenerative Diseases Laboratory (LMN), Université Paris-Sud, Université Paris-Saclay, Bât 61, Pièce 113, 18 route du Panorama, BP No. 6, F-92265, Fontenay-aux-Roses, France.
authors.forename: Anna
authors.initials: A
authors.lastname: Miodek
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Center (MIRCen), CNRS UMR 9199, Neurodegenerative Diseases Laboratory (LMN), Université Paris-Sud, Université Paris-Saclay, Bât 61, Pièce 113, 18 route du Panorama, BP No. 6, F-92265, Fontenay-aux-Roses, France.
authors.forename: Agnes
authors.initials: A
authors.lastname: Cibiel
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Département de la Recherche Fondamentale (DRF), Institut d'Imagerie Biomédicale (I2BM), Molecular Imaging Center (MIRCen), CNRS UMR 9199, Neurodegenerative Diseases Laboratory (LMN), Université Paris-Sud, Université Paris-Saclay, Bât 61, Pièce 113, 18 route du Panorama, BP No. 6, F-92265, Fontenay-aux-Roses, France. frederic.duconge@cea.fr.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Ducongé
mesh_terms: D000818:Animals; D052157:Aptamers, Nucleotide / Q000235:genetics / Q000302:isolation & purification*; D015415:Biomarkers / Q000032:analysis; D016466:CHO Cells; D003412:Cricetulus; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics*; D011487:Protein Conformation; D052156:SELEX Aptamer Technique; D017422:Sequence Analysis, DNA
chemical_list: D052157:Aptamers, Nucleotide; D015415:Biomarkers; D008565:Membrane Proteins
keywords: Aptamer; Biomarkers; Cell-SELEX; Oligonucleotides