DNA aptamers as molecular probes for colorectal cancer study

PLoS ONE

Volumn 5, Issue 12, 2010, Pages 1-14

  Sefah, Kwame ^a   Meng, Ling ^a   Lopez Colon, Dalia ^a   Jimenez, Elizabeth ^a   Liu, Chen ^b   Tan, Weihong ^a,c  

^a UNIVERSITY OF FLORIDA   (United States)

^b UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^c H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; TUMOR MARKER; LIGAND;

ADENOCARCINOMA; ARTICLE; BINDING AFFINITY; CANCER CELL CULTURE; COLORECTAL CANCER; COMBINATORIAL CHEMISTRY; CONFOCAL MICROSCOPY; CONTROLLED STUDY; FLOW CYTOMETRY; HUMAN; HUMAN CELL; MOLECULAR PROBE; PROTEIN ANALYSIS; CHROMOSOME MAP; COLORECTAL TUMOR; GENETICS; KINETICS; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; TUMOR CELL LINE;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CELL LINE, TUMOR; CHROMOSOME MAPPING; COLORECTAL NEOPLASMS; FLOW CYTOMETRY; HUMANS; KINETICS; LIGANDS; MICROSCOPY, CONFOCAL; MOLECULAR PROBES; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; SELEX APTAMER TECHNIQUE; TUMOR MARKERS, BIOLOGICAL;

EID: 78650737100     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014269     Document Type: Article

References (48)

1. Ogino S, Goel A (2008) Molecular Classification and Correlates in Colorectal Cancer. Journal of Molecular Diagnostics 10: 13-27.
2. Bagg A, Kallakury BV (1999) Molecular pathology of leukemia and lymphoma. Am J Clin Pathol 112: S76-S92.
3. Arber DA (2000) Molecular diagnostic approach to non-Hodgkin's lymphoma. J Mol Diagn 2: 178-190.
4. Ventura RA, Martin-Subero JI, Jones M, McParland J, Gesk S, et al. (2006) FISH analysis for the detection of lymphomaassociated chromosomal abnormalities in routine paraffin-embedded tissue. J Mol Diagn 8: 141-151.
5. Casado E, De Castro J, Belda-Iniesta C, Cejas P, Feliu J, et al. (2007) Molecular markers in colorectal cancer: genetic bases for a customized treatment. Clin Transl Oncol 9: 549-554.
6. Kinzler KW, Vogelstein B (1998) Landscaping the cancer terrain. Science 280: 1036-1037.
7. Umar A, Srivastava S (2004) The promise of biomarkers in colorectal cancer detection. Disease Markers 20: 87-96.
8. Lindblom A (2001) Different mechanisms in the tumorigenesis of proximal and distal colon cancers. Curr Opin Oncol 13: 63-69.
9. Liu B, Nicolaides NC, Markowitz S, Willson JK, Parsons RE, et al. (1995) Mismatch repair gene defects in sporadic colorectal cancers with microsatellite instability. Nat Genet 9: 48-55.
10. Andre T, Tournigand C, Mineur L, Fellague-Chebra R, Flesch M, et al. (2007) Phase II study of an optimized 5-fluorouraciloxaliplatin strategy (OPTIMOX2) with celecoxib in metastatic colorectal cancer: a GERCOR study. Ann Oncol 18: 77-81.
11. Hurwitz H, Fehrenbacher L, Novotny W, Cartwright T, Hainsworth J, et al. (2004) Bevacizumab plus irinotecan, fluorouracil, and leucovorin for metastatic colorectal cancer. N Engl J Med 350: 2335-2342.
12. Hardcastle JD, Chamberlain JO, Robinson MH, Moss SM, Amar SS, et al. (1996) Randomised controlled trial of faecal-occult-blood screening for colorectal cancer. Lancet 348: 1472-1477.
13. Kronborg O, Fenger C, Olsen J, Jorgensen OD, Sondergaard O (1996) Randomised study of screening for colorectal cancer with faecal-occult-blood test. Lancet 348: 1467-1471.
14. Kim SY, Hahn WC (2007) Cancer genomics: integrating form and function. Carcinogenesis 28: 1387-1392.
15. Faca V, Krasnoselsky A, Hanash S (2007) Innovative proteomic approaches for cancer biomarker discovery. BioTechniques 43: 279-283.
16. Kim H-J, Yu M-H, Kim H, Byun J, Lee C (2008) Noninvasive molecular biomarkers for the detection of colorectal cancer. BMB reports. pp 685-692.
17. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249: 505-510.
18. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822.
19. Morris KN, Jensen KB, Julin CM, Weil M, Gold L (1998) High affinity ligands from in vitro selection: Complex targets. ProcNatl Acad Sci (U S A) 95: 2902-2907.
20. Hicke BJ, Marion C, Chang Y-F, Gould T, Lynott CK, et al. (2001) Tenascin-C Aptamers Are Generated Using Tumor Cells and Purified Protein. J Biol Chem 276: 48644-48654.
21. Wang C, Zhang M, Yang G, Zhang D, Ding H, et al. (2003) Single-stranded DNA aptamers that bind differentiated but not parental cells: subtractive systematic evolution of ligands by exponential enrichment. Journal of Biotechnology 102: 15-22.
22. Cerchia L, Ducongé F, Pestourie C, Boulay J, Aissouni Y, et al. (2005) Neutralizing aptamers from whole-cell SELEX inhibit the RET receptor tyrosine kinase. PLoS Biol 3: 0697-0704.
23. Shangguan D, Li Y, Tang Z, Cao ZC, Chen HW, et al. (2006) Aptamers evolved from live cells as effective molecular probes for cancer study. Proc Natl Acad Sci (U S A) 103: 11838-11843.
24. Tang Z, Shangguan D, Wang K, Shi H, Sefah K, et al. (2007) Selection of Aptamers for Molecular Recognition and Characterization of Cancer Cells. Anal Chem 79: 4900-4907.
25. Chen HW, Medley CD, Sefah K, Shangguan D, Tang Z, et al. (2008) Molecular Recognition of Small-Cell Lung Cancer Cells Using Aptamers. Chem Med Chem 3: 991-1001.
26. Sefah K, Tang ZW, Shangguan DH, Chen H, Lopez-Colon D, et al. (2009) Molecular recognition of acute myeloid leukemia using aptamers. Leukemia 23: 235-244.
27. Hofmann HP, Limmer S, Hornung V, Sprinzl M (1997) Ni2+ -binding RNA motifs with an asymmetric purine-rich internal loop and a G-A base pair. RNA 3: 1289-1300.
28. Rajendran M, Ellington AD (2008) Selection of fluorescent aptamer beacons that light up in the presence of zinc. Anal Bioanal Chem 390: 1067-1075.
29. Geiger A, Burgstaller P, von der Eltz H, Roeder A, Famulok M (1996) RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res 24: 1029-1036.
30. Wallace ST, Schroeder R (1998) In vitro selection and characterization of streptomycin-binding RNAs: recognition discrimination between antibiotics RNA 4: 112-123.
31. Williams KP, Liu X-H, Schumacher TNM, Lin HY, Ausiello DA, et al. (1997) Bioactive and nuclease-resistant l-DNA ligand of vasopressin. Proc Natl Acad Sci (U S A) 94: 11285-11290.
32. Tuerk C, MacDougal S, Gold L (1992) RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci (U S A) 89: 6988-6992.
33. Kubik MF, Stephens AW, Schneider D, Marlar RA, Tasset D (1994) Highaffinity RNA ligands to human a-thrombin. Nucl Acids Res 22: 2619-2626.
34. Jellinek D, Green LS, Bell C, Lynott CK, Gill N, et al. (1995) Potent 29-Amino- 29-deoxypyrimidine RNA Inhibitors of Basic Fibroblast Growth Factor. Biochemistry 34: 11363-11372.
35. Davis KA, Lin Y, Abrams B, Jayasena SD (1998) Staining of cell surface human CD4 with 29-F-pyrimidine-containing RNA aptamers for flow cytometry. Nucleic Acids Res 26: 3915-3924.
36. Mallikaratchy P, Stahelin RV, Cao Z, Chob W, Tan W (2006) Selection of DNA ligands for protein kinase C-d. Chem Commun. pp 3229-3231.
37. Pan W, Craven RC, Qiu Q, Wilson CB, Wills JW, Golovine S, et al. (1995) Isolation of virus-neutralizing RNAs from a large pool of random sequences. Proc Natl Acad Sci (U S A) 92: 11509-11513.
38. Kumar PKR, Machida K, Urvil PT, Kakiuchi N, Vishnuvardhan D, et al. (1997) Isolation of RNA aptamers specific to the NS3 protein of hepatitis C virus from a pool of completely random RNA. Virology 237: 270-282.
39. Misono TS, Kumar PKR (2005) Selection of RNA aptamers against human influenza virus hemagglutinin using surface Plasmon resonance. Anal Biochem 342: 312-317.
40. Gopinath SC B, Misono TS, Kawasaki K, Mizuno T, Imai M, et al. (2006) An RNA aptamer that distinguishes between closely related human influenza viruses and inhibits haemagglutinin-mediated membrane fusion. Journal of General Virology 87: 479-487.
41. Tang Z, Parekh P, Turner P, Moyer RW, Tan W (2009) Generating aptamers for recognition of virus-infected cells. Clinical Chemistry 55: 813-822.
42. Bruno JG, Kiel JL (1999) In vitro selection of DNA aptamers to anthrax spores with electrochemiluminescence detection. Biosens Bioelectron 14: 457-464.
43. Hamula CLA, Zhang H, Guan LL, Li X-F, Le C (2008) Selection of Aptamers against Live Bacterial Cells. Anal Chem 80: 7812-7819.
44. Shangguan D, Cao Z, Meng L, Mallikaratchy P, Sefah K, et al. (2008) Cell- Specific Aptamer Probes for Membrane Protein Elucidation in Cancer Cells. J Proteome Res 7: 2133-2139.
45. Mallikaratchy P, Tang Z, Sefah K, Meng L, Shangguan D, et al. (2007) Aptamer directly evolved from live cells recognizes membrane bound immunoglobin heavy mu chain in Burkitt's lymphoma cells. Mol Cell Proteomics 6: 2230-2238.
46. Hector S, Prehn JHM (2009) Apoptosis signaling proteins as prognostic biomarkers in colorectal cancer: A review. Biochimica et Biophysica Acta 1795: 117-129.
47. Petricoin III EF, Ardekani AM, Hitt BA, Levine PJ, Fusaro VA, et al. (2002) Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359: 572-577.
48. Diederichsen AC, Hansen TP, Nielsen O, Fenger C, Jensenius JC, et al. (1998) A comparison of flow cytometry and immunohistochemistry in human colorectal cancers. APMIS 106: 562-570.