Development of Cell-Specific Aptamers: Recent Advances and Insight into the Selection Procedures

Systematic evolution of ligands by exponential enrichment (SELEX) is an established procedure for developing short single-stranded nucleic acid ligands called aptamers against a target of choice. This approach has also been used for developing aptamers specific to whole cells named Cell-SELEX. Aptamers selected by Cell-SELEX have the potential to act as cell specific therapeutics, cell specific markers or cell specific drug delivery and imaging agents. However, aptamer development is a laborious and time-consuming process which is often challenging due to the requirement of frequent optimization of various steps involved in Cell-SELEX procedures. This review provides an insight into various procedures for selection, aptamer enrichment, regeneration and aptamer-binding analysis, in addition to a very recent update on all aptamers selected by Cell-SELEX procedures.

[1]  F. Ducongé,et al.  Selection of Aptamers Against Whole Living Cells: From Cell-SELEX to Identification of Biomarkers. , 2017, Methods in molecular biology.

[2]  Subash C. B. Gopinath,et al.  Asymmetric PCR for good quality ssDNA generation towards DNA aptamer production , 2012 .

[3]  Lau Sie Yon,et al.  SELEX Modifications and Bioanalytical Techniques for Aptamer–Target Binding Characterization , 2016, Critical reviews in analytical chemistry.

[4]  Kemin Wang,et al.  Selection of aptamers for molecular recognition and characterization of cancer cells. , 2007, Analytical chemistry.

[5]  Arunima Sharma,et al.  Selective identification of specific aptamers for the detection of non-typhoidal salmonellosis in an apta-impedimetric sensing format , 2017, Microchimica Acta.

[6]  S. Jayasena Aptamers: an emerging class of molecules that rival antibodies in diagnostics. , 1999, Clinical chemistry.

[7]  Yi Xiao,et al.  Improving aptamer selection efficiency through volume dilution, magnetic concentration, and continuous washing in microfluidic channels. , 2011, Analytical chemistry.

[8]  R. Pei,et al.  In vitro selection of DNA aptamers against renal cell carcinoma using living cell-SELEX. , 2017, Talanta.

[9]  Chun-Wei Peng,et al.  Identification of an aptamer through whole cell-SELEX for targeting high metastatic liver cancers , 2016, Oncotarget.

[10]  F. Ducongé,et al.  From Ugly Duckling to Swan: Unexpected Identification from Cell-SELEX of an Anti-Annexin A2 Aptamer Targeting Tumors , 2014, PloS one.

[11]  H A Erlich,et al.  Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Fang Wang,et al.  DNA aptamers that target human glioblastoma multiforme cells overexpressing epidermal growth factor receptor variant III in vitro , 2013, Acta Pharmacologica Sinica.

[13]  Abhishek Parashar,et al.  Aptamers in Therapeutics. , 2016, Journal of clinical and diagnostic research : JCDR.

[14]  S. Gopinath Methods developed for SELEX , 2006, Analytical and bioanalytical chemistry.

[15]  Xiaohong Fang,et al.  Aptamers generated from cell-SELEX for molecular medicine: a chemical biology approach. , 2010, Accounts of chemical research.

[16]  L. Gold,et al.  A tenascin-C aptamer identified by tumor cell SELEX: Systematic evolution of ligands by exponential enrichment , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Jing Wang,et al.  Aptamers against cell surface receptors: selection, modification and application. , 2011, Current medicinal chemistry.

[18]  Gwo-Bin Lee,et al.  Screening of aptamers specific to colorectal cancer cells and stem cells by utilizing On-chip Cell-SELEX , 2015, Scientific Reports.

[19]  Laurence Choulier,et al.  Selection of Nucleic Acid Aptamers Targeting Tumor Cell-Surface Protein Biomarkers , 2017, Cancers.

[20]  J. McNamara,et al.  Multivalent 4-1BB binding aptamers costimulate CD8+ T cells and inhibit tumor growth in mice. , 2008, The Journal of clinical investigation.

[21]  Andrea Rentmeister,et al.  Cell-Specific Aptamers as Emerging Therapeutics , 2011, Journal of nucleic acids.

[22]  Nan Zhang,et al.  DNA Aptamer Evolved by Cell-SELEX for Recognition of Prostate Cancer , 2014, PloS one.

[23]  Lei Zheng,et al.  Aptamer-Based Technologies in Foodborne Pathogen Detection , 2016, Front. Microbiol..

[24]  R. Veedu,et al.  In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies , 2016, RNA biology.

[25]  Ji Won Kim,et al.  Selection of Aptamers for Mature White Adipocytes by Cell SELEX Using Flow Cytometry , 2014, PloS one.

[26]  James O McNamara,et al.  Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells. , 2015, Methods in molecular biology.

[27]  A. R. Ruslinda,et al.  Cell-targeting aptamers act as intracellular delivery vehicles , 2016, Applied Microbiology and Biotechnology.

[28]  S K Poddar,et al.  Symmetric vs asymmetric PCR and molecular beacon probe in the detection of a target gene of adenovirus. , 2000, Molecular and cellular probes.

[29]  Use of PCR primers containing a 3'-terminal ribose residue to prevent cross-contamination of amplified sequences. , 1993, Nucleic acids research.

[30]  R. Veedu Aptamers : Tools for Nanotherapy and Molecular Imaging , 2016 .

[31]  Kemin Wang,et al.  Metastatic cancer cell and tissue-specific fluorescence imaging using a new DNA aptamer developed by Cell-SELEX. , 2017, Talanta.

[32]  H. Lee,et al.  The DNA aptamer binds stemness‐enriched cancer cells in pancreatic cancer , 2017, Journal of molecular recognition : JMR.

[33]  R. Stoltenburg,et al.  SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands. , 2007, Biomolecular engineering.

[34]  Cuichen Wu,et al.  Molecular Recognition of Human Liver Cancer Cells Using DNA Aptamers Generated via Cell-SELEX , 2015, PloS one.

[35]  B. Shen,et al.  Single-stranded DNA aptamers that bind differentiated but not parental cells: subtractive systematic evolution of ligands by exponential enrichment. , 2003, Journal of biotechnology.

[36]  P. Dröge,et al.  Denaturing urea polyacrylamide gel electrophoresis (Urea PAGE). , 2009, Journal of visualized experiments : JoVE.

[37]  Tao Wang,et al.  RNA aptamers targeting cancer stem cell marker CD133. , 2013, Cancer letters.

[38]  H. Zarbl,et al.  Use of Cell-SELEX to Generate DNA Aptamers as Molecular Probes of HPV-Associated Cervical Cancer Cells , 2012, PloS one.

[39]  Chao Liang,et al.  Development of Cell-SELEX Technology and Its Application in Cancer Diagnosis and Therapy , 2016, International journal of molecular sciences.

[40]  M. Wood,et al.  Delivery of siRNA to the mouse brain by systemic injection of targeted exosomes , 2011, Nature Biotechnology.

[41]  J. Wengel,et al.  By-Product Formation in Repetitive PCR Amplification of DNA Libraries during SELEX , 2014, PloS one.

[42]  M. J. Silva,et al.  3D Cell-SELEX: Development of RNA aptamers as molecular probes for PC-3 tumor cell line. , 2016, Experimental cell research.

[43]  R. Derike Smiley,et al.  Selection and characterization of DNA aptamers with binding selectivity to Campylobacter jejuni using whole-cell SELEX , 2010, Applied Microbiology and Biotechnology.

[44]  K. Pierce,et al.  Linear-After-The-Exponential (LATE)–PCR: An advanced method of asymmetric PCR and its uses in quantitative real-time analysis , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[45]  S. Edwards,et al.  Rapid One-Step Selection Method for Generating Nucleic Acid Aptamers: Development of a DNA Aptamer against α-Bungarotoxin , 2012, PloS one.

[46]  Xin-guo Jiang,et al.  Precise glioma targeting of and penetration by aptamer and peptide dual-functioned nanoparticles. , 2012, Biomaterials.

[47]  W. Duan,et al.  RNA aptamer against a cancer stem cell marker epithelial cell adhesion molecule , 2011, Cancer science.

[48]  Hui Chen,et al.  Molecular recognition of acute myeloid leukemia using aptamers , 2008, Leukemia.

[49]  D. Shangguan,et al.  Aptamers evolved from live cells as effective molecular probes for cancer study , 2006, Proceedings of the National Academy of Sciences.

[50]  R. Wilson,et al.  Detection of glucose-6-phosphate dehydrogenase in malarial parasites. , 1981, Molecular and biochemical parasitology.

[51]  Qin Pan,et al.  Aptamers That Preferentially Bind Type IVB Pili and Inhibit Human Monocytic-Cell Invasion by Salmonella enterica Serovar Typhi , 2005, Antimicrobial Agents and Chemotherapy.

[52]  Gerhard Ziemer,et al.  Streptavidin-coated magnetic beads for DNA strand separation implicate a multitude of problems during cell-SELEX. , 2009, Oligonucleotides.

[53]  J. McNamara,et al.  RNA Aptamer-Based Functional Ligands of the Neurotrophin Receptor, TrkB , 2012, Molecular Pharmacology.

[54]  S. Gopinath,et al.  Conditions optimized for the preparation of single-stranded DNA (ssDNA) employing lambda exonuclease digestion in generating DNA aptamer , 2011 .

[55]  B. Kazemi,et al.  Challenges to Design and Develop of DNA Aptamers for Protein Targets. I. Optimization of Asymmetric PCR for Generation of a Single Stranded DNA Library , 2014, Iranian journal of pharmaceutical research : IJPR.

[56]  Yong-Min Huh,et al.  Isolation of RNA Aptamers Targeting HER -2-overexpressing Breast Cancer Cells Using Cell-SELEX , 2009 .

[57]  Gwo-Bin Lee,et al.  An on-chip Cell-SELEX process for automatic selection of high-affinity aptamers specific to different histologically classified ovarian cancer cells. , 2014, Lab on a chip.

[58]  Cell-SELEX-based selection of aptamers that recognize distinct targets on metastatic colorectal cancer cells. , 2014, Biomaterials.

[59]  Xiaobing Zhang,et al.  CD109 is identified as a potential nasopharyngeal carcinoma biomarker using aptamer selected by cell-SELEX , 2016, Oncotarget.

[60]  Xingmei Zhang,et al.  Cell-SELEX Aptamer for Highly Specific Radionuclide Molecular Imaging of Glioblastoma In Vivo , 2014, PloS one.

[61]  D. Shangguan,et al.  Development of DNA aptamers using Cell-SELEX , 2010, Nature Protocols.

[62]  Shun-ichiro Ogura,et al.  Selection of DNA aptamers recognizing small cell lung cancer using living cell-SELEX. , 2011, The Analyst.

[63]  Lim Wei Yap,et al.  Tumor cell-specific photothermal killing by SELEX-derived DNA aptamer-targeted gold nanorods. , 2016, Nanoscale.

[64]  M. Avci-Adali,et al.  Upgrading SELEX Technology by Using Lambda Exonuclease Digestion for Single-Stranded DNA Generation , 2009, Molecules.

[65]  H. U. Göringer,et al.  Post-SELEX chemical optimization of a trypanosome-specific RNA aptamer. , 2008, Combinatorial chemistry & high throughput screening.

[66]  Yan Deng,et al.  The aptamers generated from HepG2 cells , 2017, Science China Chemistry.

[67]  D. Drolet,et al.  An enzyme-linked oligonucleotide assay , 1996, Nature Biotechnology.

[68]  Jeffrey DeGrasse,et al.  A Single-Stranded DNA Aptamer That Selectively Binds to Staphylococcus aureus Enterotoxin B , 2012, PloS one.

[69]  K. Ninomiya,et al.  Cell-SELEX based selection and characterization of DNA aptamer recognizing human hepatocarcinoma. , 2013, Bioorganic & medicinal chemistry letters.

[70]  Michael Famulok,et al.  Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting. , 2008, Angewandte Chemie.

[71]  R. Kunert,et al.  Advances in recombinant antibody manufacturing , 2016, Applied Microbiology and Biotechnology.

[72]  J. Gariépy,et al.  Delivering cargoes into cancer cells using DNA aptamers targeting internalized surface portals. , 2010, Biochimica et biophysica acta.

[73]  A. Debrabant,et al.  Aptamer Based, Non-PCR, Non-Serological Detection of Chagas Disease Biomarkers in Trypanosoma cruzi Infected Mice , 2014, PLoS neglected tropical diseases.