Colorectal cancer DNA methylation marker panel validated with high performance in Non-Hodgkin lymphoma

References

• American Cancer Society. Cancer Facts & Figures 2013. American Cancer Society. 2013
   Google Scholar
• Seto M. Genetic and epigenetic factors involved in B-cell lymphomagenesis. Cancer Sci 2004; 95:704 - 10; http://dx.doi.org/10.1111/j.1349-7006.2004.tb03249.x; PMID: 15471554
   PubMed Web of Science ®Google Scholar
• Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011; 144:646 - 74; http://dx.doi.org/10.1016/j.cell.2011.02.013; PMID: 21376230
   PubMed Web of Science ®Google Scholar
• Shi H, Guo J, Duff DJ, Rahmatpanah F, Chitima-Matsiga R, Al-Kuhlani M, Taylor KH, Sjahputera O, Andreski M, Wooldridge JE, et al. Discovery of novel epigenetic markers in non-Hodgkin’s lymphoma. Carcinogenesis 2007; 28:60 - 70; http://dx.doi.org/10.1093/carcin/bgl092; PMID: 16774933
   PubMed Web of Science ®Google Scholar
• Esteller M. Profiling aberrant DNA methylation in hematologic neoplasms: a view from the tip of the iceberg. Clin Immunol 2003; 109:80 - 8; http://dx.doi.org/10.1016/S1521-6616(03)00208-0; PMID: 14585279
   PubMed Web of Science ®Google Scholar
• Harden SV, Sanderson H, Goodman SN, Partin AAW, Walsh PC, Epstein JI, Sidransky D. Quantitative GSTP1 methylation and the detection of prostate adenocarcinoma in sextant biopsies. J Natl Cancer Inst 2003; 95:1634 - 7; http://dx.doi.org/10.1093/jnci/djg082; PMID: 14600096
   PubMed Web of Science ®Google Scholar
• Agathanggelou A, Cooper WN, Latif F. Role of the Ras-association domain family 1 tumor suppressor gene in human cancers. Cancer Res 2005; 65:3497 - 508; http://dx.doi.org/10.1158/0008-5472.CAN-04-4088; PMID: 15867337
   PubMed Web of Science ®Google Scholar
• Hesson LB, Cooper WN, Latif F. The role of RASSF1A methylation in cancer. Dis Markers 2007; 23:73 - 87; http://dx.doi.org/10.1155/2007/291538; PMID: 17325427
   PubMed Web of Science ®Google Scholar
• Lind GE, Danielsen SA, Ahlquist T, Merok MA, Andresen K, Skotheim RI, Hektoen M, Rognum TO, Meling GI, Hoff G, et al. Identification of an epigenetic biomarker panel with high sensitivity and specificity for colorectal cancer and adenomas. Mol Cancer 2011; 10:85; http://dx.doi.org/10.1186/1476-4598-10-85; PMID: 21777459
   PubMed Web of Science ®Google Scholar
• Lind GE, Ahlquist T, Kolberg M, Berg M, Eknaes M, Alonso MA, Kallioniemi A, Meling GI, Skotheim RI, Rognum TO, et al. Hypermethylated MAL gene - a silent marker of early colon tumorigenesis. J Transl Med 2008; 6:13; http://dx.doi.org/10.1186/1479-5876-6-13; PMID: 18346269
   PubMed Web of Science ®Google Scholar
• Lind GE, Raiborg C, Danielsen SA, Rognum TO, Thiis-Evensen E, Hoff G, Nesbakken A, Stenmark H, Lothe RA. SPG20, a novel biomarker for early detection of colorectal cancer, encodes a regulator of cytokinesis. Oncogene 2011; 30:3967 - 78; http://dx.doi.org/10.1038/onc.2011.109; PMID: 21499309
   PubMed Web of Science ®Google Scholar
• Copie-Bergman C, Gaulard P, Maouche-Chrétien L, Brière J, Haioun C, Alonso MA, Roméo PH, Leroy K. The MAL gene is expressed in primary mediastinal large B-cell lymphoma. Blood 1999; 94:3567 - 75
   PubMed Web of Science ®Google Scholar
• Pike BL, Greiner TC, Wang X, Weisenburger DD, Hsu YH, Renaud G, Wolfsberg TG, Kim M, Weisenberger DJ, Siegmund KD, et al. DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status. Leukemia 2008; 22:1035 - 43; http://dx.doi.org/10.1038/leu.2008.18; PMID: 18288132
   PubMed Web of Science ®Google Scholar
• O’Riain C, O’Shea DM, Yang Y, Le Dieu R, Gribben JG, Summers K, Yeboah-Afari J, Bhaw-Rosun L, Fleischmann C, Mein CA, et al. Array-based DNA methylation profiling in follicular lymphoma. Leukemia 2009; 23:1858 - 66; http://dx.doi.org/10.1038/leu.2009.114; PMID: 19587707
   PubMed Web of Science ®Google Scholar
• Wang XM, Greiner TC, Bibikova M, Pike BL, Siegmund KD, Sinha UK, Müschen M, Jaeger EB, Weisenburger DD, Chan WC, et al. Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations. J Cell Biochem 2010; 109:818 - 27; PMID: 20069569
   PubMed Web of Science ®Google Scholar
• Taylor KH, Kramer RS, Davis JW, Guo J, Duff DJ, Xu D, Caldwell CW, Shi H. Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res 2007; 67:8511 - 8; http://dx.doi.org/10.1158/0008-5472.CAN-07-1016; PMID: 17875690
   PubMed Web of Science ®Google Scholar
• Daibata M, Nemoto Y, Bandobashi K, Kotani N, Kuroda M, Tsuchiya M, Okuda H, Takakuwa T, Imai S, Shuin T, et al. Promoter hypermethylation of the bone morphogenetic protein-6 gene in malignant lymphoma. Clin Cancer Res 2007; 13:3528 - 35; http://dx.doi.org/10.1158/1078-0432.CCR-06-2766; PMID: 17575215
   PubMed Web of Science ®Google Scholar
• Eberth S, Schneider B, Rosenwald A, Hartmann EM, Romani J, Zaborski M, Siebert R, Drexler HG, Quentmeier H. Epigenetic regulation of CD44 in Hodgkin and non-Hodgkin lymphoma. BMC Cancer 2010; 10:517; http://dx.doi.org/10.1186/1471-2407-10-517; PMID: 20920234
   PubMed Web of Science ®Google Scholar
• Grønbaek K, Ralfkiaer U, Dahl C, Hother C, Burns JS, Kassem M, Worm J, Ralfkiaer EM, Knudsen LM, Hokland P, et al. Frequent hypermethylation of DBC1 in malignant lymphoproliferative neoplasms. Mod Pathol 2008; 21:632 - 8; http://dx.doi.org/10.1038/modpathol.2008.27; PMID: 18264085
   PubMed Web of Science ®Google Scholar
• Hagiwara K, Nagai H, Li Y, Ohashi H, Hotta T, Saito H. Frequent DNA methylation but not mutation of the ID4 gene in malignant lymphoma. J Clin Exp Hematop 2007; 47:15 - 8; http://dx.doi.org/10.3960/jslrt.47.15; PMID: 17510533
   PubMedGoogle Scholar
• Amara K, Trimeche M, Ziadi S, Laatiri A, Hachana M, Korbi S. Prognostic significance of aberrant promoter hypermethylation of CpG islands in patients with diffuse large B-cell lymphomas. Ann Oncol 2008; 19:1774 - 86; http://dx.doi.org/10.1093/annonc/mdn374; PMID: 18539616
   PubMed Web of Science ®Google Scholar
• Bennett LB, Schnabel JL, Kelchen JM, Taylor KH, Guo J, Arthur GL, Papageorgio CN, Shi H, Caldwell CW. DNA hypermethylation accompanied by transcriptional repression in follicular lymphoma. Genes Chromosomes Cancer 2009; 48:828 - 41; http://dx.doi.org/10.1002/gcc.20687; PMID: 19530241
   PubMed Web of Science ®Google Scholar
• Choi JH, Li Y, Guo J, Pei L, Rauch TA, Kramer RS, Macmil SL, Wiley GB, Bennett LB, Schnabel JL, et al. Genome-wide DNA methylation maps in follicular lymphoma cells determined by methylation-enriched bisulfite sequencing. PLoS One 2010; 5:e13020; http://dx.doi.org/10.1371/journal.pone.0013020; PMID: 20927367
   PubMed Web of Science ®Google Scholar
• Shaknovich R, Geng H, Johnson NA, Tsikitas L, Cerchietti L, Greally JM, Gascoyne RD, Elemento O, Melnick A. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood 2010; 116:e81 - 9; http://dx.doi.org/10.1182/blood-2010-05-285320; PMID: 20610814
   PubMed Web of Science ®Google Scholar
• Lee SM, Lee EJ, Ko Y-H, Lee SH, Maeng L, Kim K-M. Prognostic significance of O6-methylguanine DNA methyltransferase and p57 methylation in patients with diffuse large B-cell lymphomas. APMIS 2009; 117:87 - 94; http://dx.doi.org/10.1111/j.1600-0463.2008.00017.x; PMID: 19239430
   PubMed Web of Science ®Google Scholar
• Ying J, Li H, Murray P, Gao Z, Chen YW, Wang Y, Lee KY, Chan AT, Ambinder RF, Srivastava G, et al. Tumor-specific methylation of the 8p22 tumor suppressor gene DLC1 is an epigenetic biomarker for Hodgkin, nasal NK/T-cell and other types of lymphomas. Epigenetics 2007; 2:15 - 21; http://dx.doi.org/10.4161/epi.2.1.3883; PMID: 17965626
   PubMed Web of Science ®Google Scholar
• Seng TJ, Low JSW, Li H, Cui Y, Goh HK, Wong MLY, Srivastava G, Sidransky D, Califano J, Steenbergen RD, et al. The major 8p22 tumor suppressor DLC1 is frequently silenced by methylation in both endemic and sporadic nasopharyngeal, esophageal, and cervical carcinomas, and inhibits tumor cell colony formation. Oncogene 2007; 26:934 - 44; http://dx.doi.org/10.1038/sj.onc.1209839; PMID: 16862168
   PubMed Web of Science ®Google Scholar
• Low JSW, Tao Q, Ng KM, Goh HK, Shu XS, Woo WL, Ambinder RF, Srivastava G, Shamay M, Chan AT, et al. A novel isoform of the 8p22 tumor suppressor gene DLC1 suppresses tumor growth and is frequently silenced in multiple common tumors. Oncogene 2011; 30:1923 - 35; http://dx.doi.org/10.1038/onc.2010.576; PMID: 21217778
   PubMed Web of Science ®Google Scholar
• Li Y, Nagai H, Ohno T, Yuge M, Hatano S, Ito E, Mori N, Saito H, Kinoshita T. Aberrant DNA methylation of p57(KIP2) gene in the promoter region in lymphoid malignancies of B-cell phenotype. Blood 2002; 100:2572 - 7; http://dx.doi.org/10.1182/blood-2001-11-0026; PMID: 12239171
   PubMed Web of Science ®Google Scholar
• Rosenwald A, Wright G, Leroy K, Yu X, Gaulard P, Gascoyne RD, Chan WC, Zhao T, Haioun C, Greiner TC, et al. Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma. J Exp Med 2003; 198:851 - 62; http://dx.doi.org/10.1084/jem.20031074; PMID: 12975453
   PubMed Web of Science ®Google Scholar
• Horne HN, Lee PS, Murphy SK, Alonso MA, Olson JA Jr., Marks JR. Inactivation of the MAL gene in breast cancer is a common event that predicts benefit from adjuvant chemotherapy. Mol Cancer Res 2009; 7:199 - 209; http://dx.doi.org/10.1158/1541-7786.MCR-08-0314; PMID: 19208741
   PubMed Web of Science ®Google Scholar
• Hayslip J, Montero A. Tumor suppressor gene methylation in follicular lymphoma: a comprehensive review. Mol Cancer 2006; 5:44; http://dx.doi.org/10.1186/1476-4598-5-44; PMID: 17026765
   PubMed Web of Science ®Google Scholar
• Tsai HC, Baylin SB. Cancer epigenetics: linking basic biology to clinical medicine. Cell Res 2011; 21:502 - 17; http://dx.doi.org/10.1038/cr.2011.24; PMID: 21321605
   PubMed Web of Science ®Google Scholar
• Guan H, Xie L, Leithäuser F, Flossbach L, Möller P, Wirth T, Ushmorov A. KLF4 is a tumor suppressor in B-cell non-Hodgkin lymphoma and in classic Hodgkin lymphoma. Blood 2010; 116:1469 - 78; http://dx.doi.org/10.1182/blood-2009-12-256446; PMID: 20519630
   PubMed Web of Science ®Google Scholar
• Yusuf I, Kharas MG, Chen J, Peralta RQ, Maruniak A, Sareen P, Yang VW, Kaestner KH, Fruman DA. KLF4 is a FOXO target gene that suppresses B cell proliferation. Int Immunol 2008; 20:671 - 81; http://dx.doi.org/10.1093/intimm/dxn024; PMID: 18375530
   PubMed Web of Science ®Google Scholar
• Kawano S, Miller CW, Gombart AF, Bartram CR, Matsuo Y, Asou H, Sakashita A, Said J, Tatsumi E, Koeffler HP. Loss of p73 gene expression in leukemias/lymphomas due to hypermethylation. Blood 1999; 94:1113 - 20; PMID: 10419905
   PubMed Web of Science ®Google Scholar
• Nistala H, Lee-Arteaga S, Smaldone S, Siciliano G, Carta L, Ono RN, Sengle G, Arteaga-Solis E, Levasseur R, Ducy P, et al. Fibrillin-1 and -2 differentially modulate endogenous TGF-β and BMP bioavailability during bone formation. J Cell Biol 2010; 190:1107 - 21; http://dx.doi.org/10.1083/jcb.201003089; PMID: 20855508
   PubMed Web of Science ®Google Scholar
• Wang Y, Yu Q, Cho AH, Rondeau G, Welsh J, Adamson E, Mercola D, McClelland M. Survey of differentially methylated promoters in prostate cancer cell lines. Neoplasia 2005; 7:748 - 60; http://dx.doi.org/10.1593/neo.05289; PMID: 16207477
   PubMed Web of Science ®Google Scholar
• Slater AA, Alokail M, Gentle D, Yao M, Kovacs G, Maher ER, Latif F. DNA methylation profiling distinguishes histological subtypes of renal cell carcinoma. Epigenetics 2013; 8:252 - 67; http://dx.doi.org/10.4161/epi.23817; PMID: 23428843
   PubMed Web of Science ®Google Scholar
• Yan PS, Venkataramu C, Ibrahim A, Liu JC, Shen RZ, Diaz NM, Centeno B, Weber F, Leu YW, Shapiro CL, et al. Mapping geographic zones of cancer risk with epigenetic biomarkers in normal breast tissue. Clin Cancer Res 2006; 12:6626 - 36; http://dx.doi.org/10.1158/1078-0432.CCR-06-0467; PMID: 17121881
   PubMed Web of Science ®Google Scholar
• Matsumoto L, Takuma H, Tamaoka A, Kurisaki H, Date H, Tsuji S, Iwata A. CpG demethylation enhances alpha-synuclein expression and affects the pathogenesis of Parkinson’s disease. PLoS One 2010; 5:e15522; http://dx.doi.org/10.1371/journal.pone.0015522; PMID: 21124796
   PubMed Web of Science ®Google Scholar
• Jowaed A, Schmitt I, Kaut O, Wüllner U. Methylation regulates alpha-synuclein expression and is decreased in Parkinson’s disease patients’ brains. J Neurosci 2010; 30:6355 - 9; http://dx.doi.org/10.1523/JNEUROSCI.6119-09.2010; PMID: 20445061
   PubMed Web of Science ®Google Scholar
• Sx A. Xu Q, Hu Yc, Song Cy, Guo Jf, Shen L et al. Hypomethylation of SNCA in blood of patients with sporadic Parkinson's disease. Journal of the Neurological Sciences 2013, ISSN 0022-510X.
   Google Scholar
• Schimmack S, Lawrence B, Svejda B, Alaimo D, Schmitz-Winnenthal H, Fischer L, Büchler MW, Kidd M, Modlin I. The clinical implications and biologic relevance of neurofilament expression in gastroenteropancreatic neuroendocrine neoplasms. Cancer 2012; 118:2763 - 75; http://dx.doi.org/10.1002/cncr.26592; PMID: 21990041
   PubMed Web of Science ®Google Scholar
• Duffy MJ, Napieralski R, Martens JWM, Span PN, Spyratos F, Sweep FCGJ, Brunner N, Foekens JA, Schmitt M, EORTC PathoBiology Group. Methylated genes as new cancer biomarkers. Eur J Cancer 2009; 45:335 - 46; http://dx.doi.org/10.1016/j.ejca.2008.12.008; PMID: 19138839
   PubMed Web of Science ®Google Scholar
• Chim CS, Liang R, Tam CYY, Kwong YL. Methylation of p15 and p16 genes in acute promyelocytic leukemia: potential diagnostic and prognostic significance. J Clin Oncol 2001; 19:2033 - 40; PMID: 11283136
   PubMed Web of Science ®Google Scholar
• Shiozawa E, Takimoto M, Makino R, Adachi D, Saito B, Yamochi-Onizuka T, Yamochi T, Shimozuma J, Maeda T, Kohno Y, et al. Hypermethylation of CpG islands in p16 as a prognostic factor for diffuse large B-cell lymphoma in a high-risk group. Leuk Res 2006; 30:859 - 67; http://dx.doi.org/10.1016/j.leukres.2005.11.004; PMID: 16406514
   PubMed Web of Science ®Google Scholar
• Villuendas R, Sánchez-Beato M, Martínez JC, Saez AI, Martinez-Delgado B, García JF, Mateo MS, Sanchez-Verde L, Benítez J, Martínez P, et al. Loss of p16/INK4A protein expression in non-Hodgkin’s lymphomas is a frequent finding associated with tumor progression. Am J Pathol 1998; 153:887 - 97; http://dx.doi.org/10.1016/S0002-9440(10)65630-1; PMID: 9736037
   PubMed Web of Science ®Google Scholar
• De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, et al. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet 2013; 9:e1003137; http://dx.doi.org/10.1371/journal.pgen.1003137; PMID: 23326238
   PubMedGoogle Scholar
• Lee GW, Kang JH, Kim IS, Kim HG, Ko GH, Lee JH, Kim DC, Song DH, Yang JW, Lee JS. Is inactivation of O6-methylguanine DNA methyltransferase still a favorable prognostic factor of patients with diffuse large B-cell lymphoma in the era of R-CHOP chemotherapy?. Leuk Lymphoma 2009; 50:1992 - 8; http://dx.doi.org/10.3109/10428190903312462; PMID: 19860620
   PubMed Web of Science ®Google Scholar
• Esteller M, Gaidano G, Goodman SN, Zagonel V, Capello D, Botto B, Rossi D, Gloghini A, Vitolo U, Carbone A, et al. Hypermethylation of the DNA repair gene O(6)-methylguanine DNA methyltransferase and survival of patients with diffuse large B-cell lymphoma. J Natl Cancer Inst 2002; 94:26 - 32; http://dx.doi.org/10.1093/jnci/94.1.26; PMID: 11773279
   PubMed Web of Science ®Google Scholar
• Uccella S, Cerutti R, Placidi C, Marchet S, Carnevali I, Bernasconi B, Proserpio I, Pinotti G, Tibiletti MG, Furlan D, et al. MGMT methylation in diffuse large B-cell lymphoma: validation of quantitative methylation-specific PCR and comparison with MGMT protein expression. J Clin Pathol 2009; 62:715 - 23; http://dx.doi.org/10.1136/jcp.2009.064741; PMID: 19638543
   PubMed Web of Science ®Google Scholar
• Sehn LH. Optimal use of prognostic factors in non-Hodgkin lymphoma. Hematology Am Soc Hematol Educ Program 2006; 295 - 302; http://dx.doi.org/10.1182/asheducation-2006.1.295; PMID: 17124075
   PubMedGoogle Scholar
• Kwong YL. Predicting the outcome in non-Hodgkin lymphoma with molecular markers. Br J Haematol 2007; 137:273 - 87; http://dx.doi.org/10.1111/j.1365-2141.2007.06571.x; PMID: 17408399
   PubMed Web of Science ®Google Scholar
• Lübbert M, Rüter BH, Claus R, Schmoor C, Schmid M, Germing U, Kuendgen A, Rethwisch V, Ganser A, Platzbecker U, et al. A multicenter phase II trial of decitabine as first-line treatment for older patients with acute myeloid leukemia judged unfit for induction chemotherapy. Haematologica 2012; 97:393 - 401; http://dx.doi.org/10.3324/haematol.2011.048231; PMID: 22058219
   PubMed Web of Science ®Google Scholar
• Fenaux P, Mufti GJ, Hellstrom-Lindberg E, Santini V, Finelli C, Giagounidis A, Schoch R, Gattermann N, Sanz G, List A, et al, International Vidaza High-Risk MDS Survival Study Group. Efficacy of azacitidine compared with that of conventional care regimens in the treatment of higher-risk myelodysplastic syndromes: a randomised, open-label, phase III study. Lancet Oncol 2009; 10:223 - 32; http://dx.doi.org/10.1016/S1470-2045(09)70003-8; PMID: 19230772
   PubMed Web of Science ®Google Scholar
• Schoofs T, Müller-Tidow C. DNA methylation as a pathogenic event and as a therapeutic target in AML. Cancer Treat Rev 2011; 37:Suppl 1 S13 - 8; http://dx.doi.org/10.1016/j.ctrv.2011.04.013; PMID: 21612874
   PubMedGoogle Scholar
• Weisenberger DJ, Campan M, Long TI, Kim M, Woods C, Fiala E, Ehrlich M, Laird PW. Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res 2005; 33:6823 - 36; http://dx.doi.org/10.1093/nar/gki987; PMID: 16326863
   PubMed Web of Science ®Google Scholar