Cell-internalization SELEX: method for identifying cell- internalizing RNA aptamers for delivering siRNAs to target cells

Methods in Molecular Biology

Volumn 1218, Issue , 2015, Pages 187-199

  Thiel, William H ^a   Thiel, Kristina W ^a   Flenker, Katie S ^a   Bair, Tom ^a   Dupuy, Adam J ^a   Mc namara, James O ^a   Miller, Francis J ^a   H Giangrande, Paloma ^a  

^a NONE

Author keywords

Bioinformatics; Cell internalization SELEX; Cell targeted aptamers; Next generation sequencing (NGS); Quantitative PCR; RNA aptamers; Systematic evolution of ligands by exponential enrichment (SELEX)

Indexed keywords

APTAMER; RNA; SMALL INTERFERING RNA; BACTERIOPHAGE T7 RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; DRUG CARRIER; VIRUS PROTEIN;

ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; CELL CULTURE; CELL INTERNALIATION SELEX; CELL SPECIFICITY; CELLS BY BODY ANATOMY; CONJUGATION; CYTOPLASM; INTERNALIZATION; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; RNA INTERFERENCE; TARGET CELL; TECHNOLOGY; BIOLOGY; CELL ADHESION; CELL LINE; CHEMISTRY; CLINICAL TRIAL (TOPIC); COMBINATORIAL CHEMISTRY; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; TRANSPORT AT THE CELLULAR LEVEL;

APTAMERS, NUCLEOTIDE; BIOLOGICAL TRANSPORT; CELL ADHESION; CELL LINE; CLINICAL TRIALS AS TOPIC; COMPUTATIONAL BIOLOGY; DNA-DIRECTED RNA POLYMERASES; DRUG CARRIERS; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RNA INTERFERENCE; RNA, SMALL INTERFERING; SELEX APTAMER TECHNIQUE; VIRAL PROTEINS;

EID: 84955376343     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1538-5_11     Document Type: Article

References (31)

1. Keefe AD, Pai S, Ellington A (2010) Aptamers as therapeutics. Nat Rev Drug Discov 9: 537–550.
2. Thiel KW, Giangrande PH (2009) Therapeutic applications of DNA and RNA aptamers. Oligonucleotides 19:209–222.
3. Ng EW, Shima DT, Calias P, Cunningham ET Jr, Guyer DR, Adamis AP (2006) Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease. Nat Rev Drug Discov 5:123–132.
4. Apte RS (2008) Pegaptanib sodium for the treatment of age-related macular degeneration. Expert Opin Pharmacother 9:499–508.
5. Sundaram P, Kurniawan H, Byrne ME, Wower J (2013) Therapeutic RNA aptamers in clinical trials. Eur J Pharm Sci 48:259–271.
6. Thiel KW, Giangrande PH (2010) Intracellular delivery of rna-based therapeutics using aptamers. Ther Deliv 1:849–861.
7. Cerchia L, Giangrande PH, McNamara JO, de Franciscis V (2009) Cell-specifi c aptamers for targeted therapies. Methods Mol Biol 535:59–78.
8. Zhou J, Rossi JJ (2011) Cell-specifi c aptamermediated targeted drug delivery. Oligonucleotides 21:1–10
9. Zhou J, Bobbin ML, Burnett JC, Rossi JJ (2012) Current progress of RNA aptamerbased therapeutics. Front Genet 3:234.
10. Kanwar JR, Roy K, Kanwar RK (2011) Chimeric aptamers in cancer cell-targeted drug delivery. Crit Rev Biochem Mol Biol 46: 459–477.
11. Sundaram P, Wower J, Byrne ME (2012) A nanoscale drug delivery carrier using nucleic acid aptamers for extended release of therapeutic. Nanomedicine 8:1143–1151.
12. McNamara JO II, Andrechek ER, Wang Y, Viles KD, Rempel RE, Gilboa E, Sullenger BA, Giangrande PH (2006) Cell type-specifi c delivery of siRNAs with aptamer-siRNA chimeras. Nat Biotechnol 24:1005–1015.
13. Pastor F, Kolonias D, Giangrande PH, Gilboa E (2010) Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay. Nature 465:227–230.
14. Dassie JP, Liu XY, Thomas GS, Whitaker RM, Thiel KW, Stockdale KR, Meyerholz DK, McCaffrey AP, McNamara JO II, Giangrande PH (2009) Systemic administration of optimized aptamer-siRNA chimeras promotes regression of PSMA-expressing tumors. Nat Biotechnol 27:839–849.
15. Wheeler LA, Vrbanac V, Trifonova R, Brehm MA, Gilboa-Geffen A, Tanno S, Greiner DL, Luster AD, Tager AM, Lieberman J (2013) Durable knockdown and protection from hiv transmission in humanized mice treated with gel-formulated cd4 aptamer-siRNA chimeras. Mol Ther 21:1378–1389.
16. Neff CP, Zhou J, Remling L, Kuruvilla J, Zhang J, Li H, Smith DD, Swiderski P, Rossi JJ, Akkina R (2011) An aptamer-siRNA chimera suppresses hiv-1 viral loads and protects from helper cd4(+) t cell decline in humanized mice. Sci Transl Med 3:66ra66.
17. Ni X, Zhang Y, Ribas J, Chowdhury WH, Castanares M, Zhang Z, Laiho M, DeWeese TL, Lupold SE (2011) Prostate-targeted radiosensitization via aptamer-shRNA chimeras in human tumor xenografts. J Clin Invest 121: 2383–2390.
18. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specifi c ligands. Nature 346:818–822.
19. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: Rna ligands to bacteriophage t4 DNA polymerase. Science 249:505–510.
20. Thiel KW, Hernandez LI, Dassie JP, Thiel WH, Liu X, Stockdale KR, Rothman AM, Hernandez FJ, McNamara JO II, Giangrande PH (2012) Delivery of chemo-sensitizing siRNAs to her2+-breast cancer cells using RNA aptamers. Nucleic Acids Res 40:6319–6337.
21. Thiel WH, Bair T, Peek AS, Liu X, Dassie J, Stockdale KR, Behlke MA, Miller FJ Jr, Giangrande PH (2012) Rapid identifi cation of cell-specifi c, internalizing RNA aptamers with bioinformatics analyses of a cell-based aptamer selection. PLoS One 7:e43836.
22. Huang YZ, Hernandez FJ, Gu B, Stockdale KR, Nanapaneni K, Scheetz TE, Behlke MA, Peek AS, Bair T, Giangrande PH, McNamara JO II (2012) RNA aptamer-based functional ligands of the neurotrophin receptor, trkb. Mol Pharmacol 82:623–635.
23. Thiel WH, Bair T, Thiel WK, Dassie JP, Rockey WM, Howell CA, Liu XY, Dupuy AJ, Huang L, Owczarzy R, Behlke MA, McNamara JO, Giangrande PH (2011) Nucleotide bias observed with a short selex RNA aptamer library. Nucleic Acid Ther 21:253–263.
24. Meyer S, Maufort JP, Nie J, Stewart R, McIntosh BE, Conti LR, Ahmad KM, Soh HT, Thomson JA (2013) Development of an effi - cient targeted cell-selex procedure for DNA aptamer reagents. PLoS One 8:e71798.
25. Reiss DJ, Howard FM, Mobley HL (2012) A novel approach for transcription factor analysis using selex with high-throughput sequencing (tfast). PLoS One 7:e42761.
26. Zimmermann B, Gesell T, Chen D, Lorenz C, Schroeder R (2010) Monitoring genomic sequences during selex using high-throughput sequencing: neutral selex. PLoS One 5:e9169.
27. Jagannathan V, Roulet E, Delorenzi M, Bucher P (2006) Htpselex–a database of high-throughput selex libraries for transcription factor binding sites. Nucleic Acids Res 34:D90–D94.
28. Roulet E, Busso S, Camargo AA, Simpson AJ, Mermod N, Bucher P (2002) High-throughput selex sage method for quantitative modeling of transcription-factor binding sites. Nat Biotechnol 20:831–835.
29. McNamara JO, Kolonias D, Pastor F, Mittler RS, Chen L, Giangrande PH, Sullenger B, Gilboa E (2008) Multivalent 4-1bb binding aptamers costimulate cd8+ t cells and inhibit tumor growth in mice. J Clin Invest 118: 376–386.
30. Sousa R, Padilla R (1995) A mutant t7 RNA polymerase as a DNA polymerase. EMBO J 14:4609–4621.
31. Hernandez FJ, Stockdale KR, Huang L, Horswill AR, Behlke MA, McNamara JO II (2012) Degradation of nuclease-stabilized RNA oligonucleotides in mycoplasma-contaminated cell culture media. Nucleic Acid Ther 22:58–68