Cross-platform detection of epigenetic modifications from extracted chromatin in leucocytes from blood

Analytical Chemistry Research

Volumn 4, Issue , 2015, Pages 39-44

  Zhou, Zhongwu ^a   Cho, II Hood ^a,c   Shan, Zhi ^b   Irudayaraj, Joseph ^a  

^a Purdue University   (United States)

^b SICHUAN AGRICULTURAL UNIVERSITY   (China)

^c Eulji University   (South Korea)

Author keywords

Chromatin extraction; Cross platform multiplex detection; Enzyme based immunosorbent assay; Epigenetic modifications; Magnetic nanoparticles

Indexed keywords

EID: 84937958539     PISSN: None     EISSN: 22141812     Source Type: Journal    
DOI: 10.1016/j.ancr.2015.04.002     Document Type: Article

References (40)

1. Sharma S., Kelly T.K., Jones P.A. Epigenetics in cancer. Carcinogenesis 2010, 31:27-36.
2. Conway O' Brien E., Prideaux S., Chevassut T. The epigenetic landscape of acute myeloid leukemia. Adv. Hematol. 2014, 2014:15.
3. Greenblatt S.M., Nimer S.D. Chromatin modifiers and the promise of epigenetic therapy in acute leukemia. Leukemia 2014, 28:1396-1406.
4. Gutierrez S., Romero-Oliva F. Epigenetic changes: a common theme in acute myelogenous leukemogenesis. J. Hematol. Oncol. 2013, 6:57.
5. Voso M.T., D'Alò F., Greco M., Fabiani E., Criscuolo M., Migliara G., Pagano L., Fianchi L., Guidi F., Hohaus S., Leone G. Epigenetic changes in therapy-related MDS/AML. Chem. Biol. Interact. 2010, 184:46-49.
6. Xie X., Nie X., Yu B., Zhang X. Rapid enrichment of leucocytes and genomic DNA from blood based on bifunctional core-shell magnetic nanoparticles. J. Magn. Magn. Mater. 2007, 311:416-420.
7. Chambers W.H., Taylor J.R., Klesius P.H. Isolation of bovine polymorphonuclear leukocytes by density gradient centrifugation. Vet. Immunol. Immunopathol. 1983, 5:197-202.
8. Bhorjee J.S., Pederson T. Chromatin. Its isolation from cultured mammalian cells with particular reference to contamination by nuclear ribonucleoprotein particles. Biochemistry 1973, 12:2766-2773.
9. Harlow R., Wells J. Preparation of membrane-free chromatin bodies from avian erythroid cells and analysis of chromatin acidic proteins. Biochemistry 1975, 14:2665-2674.
10. Monahan J.J., Hall R.H. Preparation of chromatin from tissue culture cells-A convenient method. Anal. Biochem. 1975, 65:187-203.
11. Woodcock C.L., Sweetman H.E., Frado L.L. Structural repeating units in chromatin. II. Their isolation and partial characterization. Exp. Cell Res. 1976, 97:111-119.
12. Pederson T. Isolation and characterization of chromatin from the cellular slime mold, Dictyostelium discoideum. Biochemistry 1977, 16:2771-2777.
13. Kornberg R.D., Lapointe J.W., Lorch Y. Preparation of nucleosomes and chromatin. Methods in Enzymology 1989, 3-14. Academic Press. M.W. Paul, D.K. Roger (Eds.).
14. Zhou Z., Irudayaraj J. A native chromatin extraction method based on salicylic acid coated magnetic nanoparticles and characterization of chromatin. Analyst 2015, 140:938-944.
15. Shan Z., Wu Q., Wang X., Zhou Z., Oakes K.D., Zhang X., Huang Q., Yang W. Bacteria capture, lysate clearance, and plasmid DNA extraction using pH-sensitive multifunctional magnetic nanoparticles. Anal. Biochem. 2010, 398:120-122.
16. Chowdhury B., Cho I.-H., Hahn N., Irudayaraj J. Quantification of 5-methylcytosine, 5-hydroxymethylcytosine and 5-carboxylcytosine from the blood of cancer patients by an enzyme-based immunoassay. Anal. Chim. Acta 2014, 852:212-217.
17. Lago-Cachón D., Rivas M., López-Larrea C., López-Vázquez A., Martínez-Paredes G., García J.A. HeLa cells separation using MICA antibody conjugated to magnetite nanoparticles. Phys. Status Solidi C 2014, 11:1043-1047.
18. Herr J.K., Smith J.E., Medley C.D., Shangguan D., Tan W. Aptamer-conjugated nanoparticles for selective collection and detection of cancer cells. Anal. Chem. 2006, 78:2918-2924.
19. Kouassi G.K., Irudayaraj J. Magnetic and gold-coated magnetic nanoparticles as a DNA sensor. Anal. Chem. 2006, 78:3234-3241.
20. Ravindranath S.P., Wang Y., Irudayaraj J. SERS driven cross-platform based multiplex pathogen detection. Sens. Actuators, B Chem. 2011, 152:183-190.
21. Huang Y.-F., Wang Y.-F., Yan X.-P. Amine-functionalized magnetic nanoparticles for rapid capture and removal of bacterial pathogens. Environ. Sci. Technol. 2010, 44:7908-7913.
22. Zhou Z., Kadam U.S., Irudayaraj J. One-stop genomic DNA extraction by salicylic acid-coated magnetic nanoparticles. Anal. Biochem. 2013, 442:249-252.
23. Shan Z., Zhou Z., Chen H., Zhang Z., Zhou Y., Wen A., Oakes K.D., Servos M.R. PCR-ready human DNA extraction from urine samples using magnetic nanoparticles. J. Chromatogr. B 2012, 881-882:63-68.
24. Xie X., Zhang X., Zhang H., Chen D., Fei W. Preparation and application of surface-coated superparamagnetic nanobeads in the isolation of genomic DNA. J. Magn. Magn. Mater. 2004, 277:16-23.
25. Xie X., Zhang X., Yu B., Gao H., Zhang H., Fei W. Rapid extraction of genomic DNA from saliva for HLA typing on microarray based on magnetic nanobeads. J. Magn. Magn. Mater. 2004, 280:164-168.
26. Shan Z., Jiang Y., Guo M., Bennett J.C., Li X., Tian H., Oakes K., Zhang X., Zhou Y., Huang Q., Chen H. Promoting DNA loading on magnetic nanoparticles using a DNA condensation strategy. Colloids Surf., B 2015, 247-254.
27. Whitehouse I., Smith D.J. Chromatin dynamics at the replication fork: there's more to life than histones. Curr. Opin. Genet. Dev. 2013, 23:140-146.
28. MacAlpine D.M., Almouzni G. Chromatin and DNA replication. Cold Spring Harb. Perspect. Biol. 2013, 5.
29. Chen J., Odenike O., Rowley J.D. Leukaemogenesis: more than mutant genes. Nat. Rev. Cancer 2010, 10:23-36.
30. Herceg Z., Hainaut P. Genetic and epigenetic alterations as biomarkers for cancer detection, diagnosis and prognosis. Mol. Oncol. 2007, 1:26-41.
31. Ge C., Yu L., Fang Z., Zeng L. An enhanced strip biosensor for rapid and sensitive detection of histone methylation. Anal. Chem. 2013, 85:9343-9349.
32. Shahal T., Gilat N., Michaeli Y., Redy-Keisar O., Shabat D., Ebenstein Y. Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA. Anal. Chem. 2014, 86:8231-8237.
33. Fraga M.F., Ballestar E., Villar-Garea A., Boix-Chornet M., Espada J., Schotta G., Bonaldi T., Haydon C., Ropero S., Petrie K., Iyer N.G., Perez-Rosado A., Calvo E., Lopez J.A., Cano A., Calasanz M.J., Colomer D., Piris M.A., Ahn N., Imhof A., Caldas C., Jenuwein T., Esteller M. Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer. Nat. Genet. 2005, 37:391-400.
34. Li J., Chen P., Sinogeeva N., Gorospe M., Wersto R.P., Chrest F.J., Barnes J., Liu Y. Arsenic trioxide promotes histone H3 phosphoacetylation at the chromatin of CASPASE-10 in acute promyelocytic leukemia cells. J. Biol. Chem. 2002, 277:49504-49510.
35. Krivtsov A.V., Armstrong S.A. MLL translocations, histone modifications and leukaemia stem-cell development. Nat. Rev. Cancer 2007, 7:823-833.
36. Krivtsov A.V., Feng Z., Lemieux M.E., Faber J., Vempati S., Sinha A.U., Xia X., Jesneck J., Bracken A.P., Silverman L.B., Kutok J.L., Kung A.L., Armstrong S.A. H3K79 methylation profiles define murine and human MLL-AF4 leukemias. Cancer Cell 2008, 14:355-368.
37. Okada Y., Feng Q., Lin Y., Jiang Q., Li Y., Coffield V.M., Su L., Xu G., Zhang Y. HDOT1L links histone methylation to leukemogenesis. Cell 2005, 121:167-178.
38. Guenther M.G., Lawton L.N., Rozovskaia T., Frampton G.M., Levine S.S., Volkert T.L., Croce C.M., Nakamura T., Canaani E., Young R.A. Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia. Genes Dev. 2008, 22:3403-3408.
39. Sun L., Yu C., Irudayaraj J. Surface-enhanced raman scattering based nonfluorescent probe for multiplex dna detection. Anal. Chem. 2007, 79:3981-3988.
40. Lee K., Drachev V.P., Irudayaraj J. DNA-gold nanoparticle reversible networks grown on cell surface marker sites: application in diagnostics. ACS Nano 2011, 5:2109-2117.