Epigenetic biomarkers: A new perspective in laboratory diagnostics

Clinica Chimica Acta

Volumn 413, Issue 19-20, 2012, Pages 1576-1582

  Garcia Gimenez J L ^a,b,c   Sanchis Gomar, F ^b,c   Lippi, G ^d   Mena, S ^e   Ivars, D ^f   Gomez Cabrera, M C ^b,c   Vina J ^b,c   Pallardo F V ^a,b,c  

^a CENTRO DE INVESTIGACIÓN BIOMÉDICA EN RED DE ENFERMEDADES RARAS CIBERER   (Spain)

^b UNIVERSITY OF VALENCIA   (Spain)

^c Instituto Universitario IVI INCLIVA   (Spain)

^d ACADEMIC HOSPITAL OF PARMA   (Italy)

^e Centro Nacional de Investigaciones Oncológicas   (Spain)

^f CDB University General Hospital of Valencia   (Spain)

Author keywords

Cancer; DNA methylation; Histone; MiRNAs; Rare disease

Indexed keywords

BIOLOGICAL MARKER; HISTONE; MICRORNA;

ANIMAL EXPERIMENT; AUTOANALYZER; BIOLOGICAL MONITORING; DNA METHYLATION; EPIGENETICS; GENE TECHNOLOGY; GENETIC EPIGENESIS; HISTONE MODIFICATION; HUMAN; LABORATORY DIAGNOSIS; MOUSE; NONHUMAN; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; PROGNOSIS; PROTEIN ANALYSIS; PROTEIN PROCESSING; PROTEIN PURIFICATION; REVIEW;

BIOLOGICAL MARKERS; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; HISTONES; HUMANS; MICRORNAS; PATHOLOGY, MOLECULAR; PROTEIN PROCESSING, POST-TRANSLATIONAL; SEQUENCE ANALYSIS, DNA;

EID: 84864395212     PISSN: 00098981     EISSN: 18733492     Source Type: Journal    
DOI: 10.1016/j.cca.2012.05.021     Document Type: Review

References (72)

1. Venter J.C., Adams M.D., Myers E.W., et al. The sequence of the human genome. Science 2001, 291:1304-1351.
2. Lander E.S., Linton L.M., Birren B., et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921.
3. Eccleston A., DeWitt N., Gunter C., Marte B., Nath D. Epigenetics. Nature 2007, 447:395.
4. Feinberg A.P. Phenotypic plasticity and the epigenetics of human disease. Nature 2007, 447:433-440.
5. Jenuwein T., Allis C.D. Translating the histone code. Science 2001, 293:1074-1080.
6. Hake S.B., Allis C.D. Histone H3 variants and their potential role in indexing mammalian genomes: the "H3 barcode hypothesis". Proc Natl Acad Sci U S A 2006, 103:6428-6435.
7. Grewal S.I., Elgin S.C. Transcription and RNA interference in the formation of heterochromatin. Nature 2007, 447:399-406.
8. Fraser P., Bickmore W. Nuclear organization of the genome and the potential for gene regulation. Nature 2007, 447:413-417.
9. Jaenisch R., Bird A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 2003, 33(Suppl.):245-254.
10. Craig J.M., Wong N.C. Epigenetics: a reference manual 2011, Caister Academic Press.
11. Sandoval J., Esteller M. Cancer epigenomics: beyond genomics. Curr Opin Genet Dev 2012, 22:50-55.
12. Zhang Y.J., Wu H.C., Shen J., et al. Predicting hepatocellular carcinoma by detection of aberrant promoter methylation in serum DNA. Clin Cancer Res 2007, 13:2378-2384.
13. Wong I.H., Lo Y.M., Yeo W., Lau W.Y., Johnson P.J. Frequent p15 promoter methylation in tumor and peripheral blood from hepatocellular carcinoma patients. Clin Cancer Res 2000, 6:3516-3521.
14. Tong Y.K., Lo Y.M. Plasma epigenetic markers for cancer detection and prenatal diagnosis. Front Biosci 2006, 11:2647-2656.
15. Tong Y.K., Ding C., Chiu R.W., et al. Noninvasive prenatal detection of fetal trisomy 18 by epigenetic allelic ratio analysis in maternal plasma: theoretical and empirical considerations. Clin Chem 2006, 52:2194-2202.
16. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
17. Wightman B., Ha I., Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993, 75:855-862.
18. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
19. Pallante P., Visone R., Croce C.M., Fusco A. Deregulation of microRNA expression in follicular-cell-derived human thyroid carcinomas. Endocr Relat Cancer 2010, 17:F91-F104.
20. Mack G.S. MicroRNA gets down to business. Nat Biotechnol 2007, 25:631-638.
21. Bibikova M., Talantov D., Chudin E., et al. Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am J Pathol 2004, 165:1799-1807.
22. Packer A.N., Xing Y., Harper S.Q., Jones L., Davidson B.L. The bifunctional microRNA miR-9/miR-9* regulates REST and CoREST and is downregulated in Huntington's disease. J Neurosci 2008, 28:14341-14346.
23. Keller A., Leidinger P., Lange J., et al. Multiple sclerosis: microRNA expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls. PLoS One 2009, 4:e7440.
24. Esquela-Kerscher A. MicroRNAs Function as Tumor Suppressor Genes and Oncogenes. MicroRNAs in Development and Cancer 2010, Imperial College Press. F. Slack (Ed.).
25. Esquela-Kerscher A., Slack F.J. Oncomirs-microRNAs with a role in cancer. Nat Rev Cancer 2006, 6:259-269.
26. Tavazoie S.F., Alarcon C., Oskarsson T., et al. Endogenous human microRNAs that suppress breast cancer metastasis. Nature 2008, 451:147-152.
27. Ma L., Teruya-Feldstein J., Weinberg R.A. Tumour invasion and metastasis initiated by microRNA-10b in breast cancer. Nature 2007, 449:682-688.
28. Png K.J., Yoshida M., Zhang X.H., et al. MicroRNA-335 inhibits tumor reinitiation and is silenced through genetic and epigenetic mechanisms in human breast cancer. Genes Dev 2011, 25:226-231.
29. Song G., Zhang Y., Wang L. MicroRNA-206 targets notch3, activates apoptosis, and inhibits tumor cell migration and focus formation. J Biol Chem 2009, 284:31921-31927.
30. Zampetaki A., Kiechl S., Drozdov I., et al. Plasma microRNA profiling reveals loss of endothelial miR-126 and other microRNAs in type 2 diabetes. Circ Res 2010, 107:810-817.
31. Zen K., Zhang C.Y. Circulating MicroRNAs: a novel class of biomarkers to diagnose and monitor human cancers. Med Res Rev 2012, 32:326-348.
32. Strahl B.D., Allis C.D. The language of covalent histone modifications. Nature 2000, 403:41-45.
33. Peserico A., Simone C. Physical and functional HAT/HDAC interplay regulates protein acetylation balance. J Biomed Biotechnol 2011, 2011:371832.
34. McDevitt M.A. Clinical applications of epigenetic markers and epigenetic profiling in myeloid malignancies. Semin Oncol 2012, 39:109-122.
35. Ammollo C.T., Semeraro F., Xu J., Esmon N.L., Esmon C.T. Extracellular histones increase plasma thrombin generation by impairing thrombomodulin-dependent protein C activation. J Thromb Haemost 2011, 9:1795-1803.
36. Xu J., Zhang X., Pelayo R., et al. Extracellular histones are major mediators of death in sepsis. Nat Med 2009, 15:1318-1321.
37. Lopez-Atalaya J.P., Gervasini C., Mottadelli F., et al. Histone acetylation deficits in lymphoblastoid cell lines from patients with Rubinstein-Taybi syndrome. J Med Genet 2012, 49:66-74.
38. Miller R.W., Rubinstein J.H. Tumors in Rubinstein-Taybi syndrome. Am J Med Genet 1995, 56:112-115.
39. Masuno M., Imaizumi K., Ishii T., Kuroki Y., Baba N., Tanaka Y. Pilomatrixomas in Rubinstein-Taybi syndrome. Am J Med Genet 1998, 77:81-82.
40. Iizuka M., Smith M.M. Functional consequences of histone modifications. Curr Opin Genet Dev 2003, 13:154-160.
41. Wiedemann S.M., Mildner S.N., Bonisch C., et al. Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. J Cell Biol 2010, 190:777-791.
42. Schwartzentruber J., Korshunov A., Liu X.Y., et al. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012, 482:226-231.
43. Huang H., Maertens A.M., Hyland E.M., et al. HistoneHits: a database for histone mutations and their phenotypes. Genome Res 2009, 19:674-681.
44. Shechter D., Dormann H.L., Allis C.D., Hake S.B. Extraction, purification and analysis of histones. Nat Protoc 2007, 2:1445-1457.
45. Rodriguez-Collazo P., Leuba S.H., Zlatanova J. Robust methods for purification of histones from cultured mammalian cells with the preservation of their native modifications. Nucleic Acids Res 2009, 37:e81.
46. Garcia-Gimenez J.L., Ledesma A.M., Esmoris I., et al. Histone carbonylation occurs in proliferating cells. Free Radic Biol Med 2012, 52:1453-1464.
47. Kim D.J., Linnstaedt S., Palma J., et al. Plasma components affect accuracy of circulating cancer-related microRNA quantitation. J Mol Diagn 2012, 14:71-80.
48. Rainen L., Oelmueller U., Jurgensen S., et al. Stabilization of mRNA expression in whole blood samples. Clin Chem 2002, 48:1883-1890.
49. Jung M., Klotzek S., Lewandowski M., Fleischhacker M., Jung K. Changes in concentration of DNA in serum and plasma during storage of blood samples. Clin Chem 2003, 49:1028-1029.
50. Umetani N., Hiramatsu S., Hoon D.S. Higher amount of free circulating DNA in serum than in plasma is not mainly caused by contaminated extraneous DNA during separation. Ann N Y Acad Sci 2006, 1075:299-307.
51. Hart C., Lipson D., Ozsolak F., et al. Single-molecule sequencing: sequence methods to enable accurate quantitation. Methods Enzymol 2010, 472:407-430.
52. Goren A., Ozsolak F., Shoresh N., et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods 2010, 7:47-49.
53. Kapranov P., Ozsolak F., Milos P.M. Profiling of short RNAs using Helicos single-molecule sequencing. Methods Mol Biol 2012, 822:219-232.
54. Taylor K.H., Kramer R.S., Davis J.W., et al. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res 2007, 67:8511-8518.
55. Choi J.H., Li Y., Guo J., et al. Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One 2010, 5.
56. Sandoval J., Heyn H., Moran S., et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 2011, 6:692-702.
57. Houshdaran S., Hawley S., Palmer C., et al. DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. PLoS One 2010, 5:e9359.
58. Down T.A., Rakyan V.K., Turner D.J., et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 2008, 26:779-785.
59. Butcher L.M., Beck S. Future impact of integrated high-throughput methylome analyses on human health and disease. J Genet Genomics 2008, 35:391-401.
60. Robertson G., Hirst M., Bainbridge M., et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4:651-657.
61. Luo S. MicroRNA expression analysis using the Illumina microRNA-Seq Platform. Methods Mol Biol 2012, 822:183-188.
62. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-D157.
63. Rao P.K., Toyama Y., Chiang H.R., et al. Loss of cardiac microRNA-mediated regulation leads to dilated cardiomyopathy and heart failure. Circ Res 2009, 105:585-594.
64. Kuchenbauer F., Morin R.D., Argiropoulos B., et al. In-depth characterization of the microRNA transcriptome in a leukemia progression model. Genome Res 2008, 18:1787-1797.
65. Radpour R., Haghighi M.M., Fan A.X., et al. High-throughput hacking of the methylation patterns in breast cancer by in vitro transcription and thymidine-specific cleavage mass array on MALDI-TOF silico-chip. Mol Cancer Res 2008, 6:1702-1709.
66. Gloss B.S., Patterson K.I., Barton C.A., et al. Integrative genome-wide expression and promoter DNA methylation profiling identifies a potential novel panel of ovarian cancer epigenetic biomarkers. Cancer Lett 2011, 318:76-85.
67. Mandel P., Metais P. Les acides nucleiques du plasma sanghin chez l'Homme. CR Acad Sci Paris 1948, 142:241-243.
68. Hu X.C., Wong I.H., Chow L.W. Tumor-derived aberrant methylation in plasma of invasive ductal breast cancer patients: clinical implications. Oncol Rep 2003, 10:1811-1815.
69. Papadopoulou E., Davilas E., Sotiriou V., et al. Cell-free DNA and RNA in plasma as a new molecular marker for prostate and breast cancer. Ann N Y Acad Sci 2006, 1075:235-243.
70. Rykova E.Y., Laktionov P.P., Skvortsova T.E., Starikov A.V., Kuznetsova N.P., Vlassov V.V. Extracellular DNA in breast cancer: Cell-surface-bound, tumor-derived extracellular DNA in blood of patients with breast cancer and nonmalignant tumors. Ann N Y Acad Sci 2004, 1022:217-220.
71. Skvortsova T.E., Rykova E.Y., Tamkovich S.N., et al. Cell-free and cell-bound circulating DNA in breast tumours: DNA quantification and analysis of tumour-related gene methylation. Br J Cancer 2006, 94:1492-1495.
72. Grunau C., Clark S.J., Rosenthal A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 2001, 29:e65.