Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer

Clinical Epigenetics

Volumn 7, Issue 1, 2015, Pages

  Legendre, Christophe ^a   Gooden, Gerald C ^a   Johnson, Kyle ^a   Martinez, Rae Anne ^a   Liang, Winnie S ^a   Salhia, Bodour ^a  

^a TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; DNA;

ADULT; ARTICLE; BREAST METASTASIS; CLINICAL ARTICLE; CONTROLLED STUDY; CPG ISLAND; DISEASE FREE SURVIVAL; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; GENE LOCUS; GENE ONTOLOGY; GENETIC ASSOCIATION; HUMAN; PATIENT IDENTIFICATION; PREDICTION; PRIORITY JOURNAL; RECURRENCE RISK;

EID: 84941631359     PISSN: 18687075     EISSN: 18687083     Source Type: Journal    
DOI: 10.1186/s13148-015-0135-8     Document Type: Article

References (29)

1. Weigelt B, Peterse JL. Breast cancer metastasis: markers and models. Nature reviews Cancer. 2005;5(8):591–602. doi:10.1038/nrc1670.
2. Blanco MA, Kang Y. Signaling pathways in breast cancer metastasis—novel insights from functional genomics. Breast cancer research: BCR. 2011;13(2):206. doi:10.1186/bcr2831.
3. Chaffer CL, Weinberg RA. A perspective on cancer cell metastasis. Science. 2011;331(6024):1559–64. doi:10.1126/science.1203543.
4. Melnikov AA, Scholtens D, Talamonti MS, Bentrem DJ, Levenson VV. Methylation profile of circulating plasma DNA in patients with pancreatic cancer. Journal of surgical oncology. 2009;99(2):119–22. doi:10.1002/jso.21208.
5. Nakayama G, Hibi K, Nakayama H, Kodera Y, Ito K, Akiyama S, et al. A highly sensitive method for the detection of p16 methylation in the serum of colorectal cancer patients. Anticancer Res. 2007;27(3B):1459–63.
6. Bastian PJ, Palapattu GS, Yegnasubramanian S, Rogers CG, Lin X, Mangold LA, et al. CpG island hypermethylation profile in the serum of men with clinically localized and hormone refractory metastatic prostate cancer. J Urol. 2008;179(2):529–34. doi:10.1016/j.juro.2007.09.038. discussion 34–5.
7. Fackler MJ, Lopez Bujanda Z, Umbricht C, Teo WW, Cho S, Zhang Z, et al. Novel methylated biomarkers and a robust assay to detect circulating tumor DNA in metastatic breast cancer. Cancer research. 2014;74(8):2160–70. doi:10.1158/0008-5472.CAN-13-3392.
8. Korshunova Y, Maloney RK, Lakey N, Citek RW, Bacher B, Budiman A, et al. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome research. 2008;18(1):19–29. doi:10.1101/gr.6883307.
9. Müller HMWA, Fiegl H, Ivarsson L, Goebel G, Perkmann E, Marth C, et al. DNA methylation in serum of breast cancer patients: an independent prognostic marker. Cancer research. 2003;63(22):7641–5.
10. Chan KC, Jiang P, Chan CW, Sun K, Wong J, Hui EP, et al. Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(47):18761–8. doi:10.1073/pnas.1313995110.
11. Lau QC, Raja E, Salto-Tellez M, Liu Q, Ito K, Inoue M, et al. RUNX3 is frequently inactivated by dual mechanisms of protein mislocalization and promoter hypermethylation in breast cancer. Cancer research. 2006;66(13):6512–20. doi:10.1158/0008-5472.CAN-06-0369.
12. Miyamoto K, Fukutomi T, Akashi-Tanaka S, Hasegawa T, Asahara T, Sugimura T, et al. Identification of 20 genes aberrantly methylated in human breast cancers. International journal of cancer Journal international du cancer. 2005;116(3):407–14. doi:10.1002/ijc.21054.
13. Kornegoor R, Moelans CB, Verschuur-Maes AH, Hogenes M, de Bruin PC, Oudejans JJ, et al. Promoter hypermethylation in male breast cancer: analysis by multiplex ligation-dependent probe amplification. Breast cancer research: BCR. 2012;14(4):R101. doi:10.1186/bcr3220.
14. Salhia B, Kiefer J, Ross JT, Metapally R, Martinez RA, Johnson KN, et al. Integrated genomic and epigenomic analysis of breast cancer brain metastasis. PloS one. 2014;9(1):e85448. doi:10.1371/journal.pone.0085448.
15. Appolloni I, Barilari M, Caviglia S, Gambini E, Reisoli E, Malatesta P. A cadherin switch underlies malignancy in high-grade gliomas. Oncogene. 2014. doi:10.1038/onc.2014.122.
16. Chung JH, Lee HJ, Kim BH, Cho NY, Kang GH. DNA methylation profile during multistage progression of pulmonary adenocarcinomas. Virchows Archiv: an international journal of pathology. 2011;459(2):201–11. doi:10.1007/s00428-011-1079-9.
17. Xue TC, Ge NL, Zhang L, Cui JF, Chen RX, You Y, et al. Goosecoid promotes the metastasis of hepatocellular carcinoma by modulating the epithelial-mesenchymal transition. PloS one. 2014;9(10):e109695. doi:10.1371/journal.pone.0109695.
18. Zhou L, Zhao X, Han Y, Lu Y, Shang Y, Liu C, et al. Regulation of UHRF1 by miR-146a/b modulates gastric cancer invasion and metastasis. FASEB journal: official publication of the Federation of American Societies for Experimental Biology. 2013;27(12):4929–39. doi:10.1096/fj.13-233387.
19. Jao TM, Tsai MH, Lio HY, Weng WT, Chen CC, Tzeng ST, et al. Protocadherin 10 suppresses tumorigenesis and metastasis in colorectal cancer and its genetic loss predicts adverse prognosis. International journal of cancer Journal international du cancer. 2014;135(11):2593–603. doi:10.1002/ijc.28899.
20. Fackler MJ, Umbricht CB, Williams D, Argani P, Cruz LA, Merino VF, et al. Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer research. 2011;71(19):6195–207. doi:10.1158/0008-5472.CAN-11-1630.
21. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013;368(13):1199–209. doi:10.1056/NEJMoa1213261.
22. Docherty SJ, Davis OS, Haworth CM, Plomin R, Mill J. Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation. Epigenetics & chromatin. 2009;2(1):3. doi:10.1186/1756-8935-2-3.
23. Kaplow IM, MacIsaac JL, Mah SM, McEwen LM, Kobor MS, Fraser HB. A pooling-based approach to mapping genetic variants associated with DNA methylation. Genome research. 2015;25(6):907–17. doi:10.1101/gr.183749.114.
24. Gormally E, Caboux E, Vineis P, Hainaut P. Circulating free DNA in plasma or serum as biomarker of carcinogenesis: practical aspects and biological significance. Mutat Res. 2007;635(2–3):105–17. doi:10.1016/j.mrrev.2006.11.002.
25. Gormally E, Hainaut P, Caboux E, Airoldi L, Autrup H, Malaveille C, et al. Amount of DNA in plasma and cancer risk: a prospective study. International journal of cancer Journal international du cancer. 2004;111(5):746–9. doi:10.1002/ijc.20327.
26. Bryzgunova OL P, Skvortsova T, Bondar A, Morozkin E, Lebedeva A, Krause H, et al. Efficacy of bisulfite modification and recovery of human genomic and circulating DNA using commercial kits. European Journal of Molecular Biology. 2013;1(1):1–8. doi:10.11648/j.ejmb.20130101.11.
27. Byun HM, Nordio F, Coull BA, Tarantini L, Hou L, Bonzini M, et al. Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations. PloS one. 2012;7(6):e39220. doi:10.1371/journal.pone.0039220.
28. Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011;27(11):1571–2. doi:10.1093/bioinformatics/btr167.
29. Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, et al. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012;13(10):R87. doi:10.1186/gb-2012-13-10-r87.