The early pregnancy placenta foreshadows DNA methylation alterations of solid tumors

References

• Ferretti C, Bruni L, Dangles-Marie V, Pecking AP, Bellet D. Molecular circuits shared by placental and cancer cells, and their implications in the proliferative, invasive and migratory capacities of trophoblasts. Hum Reprod Update 2007; 13:121-41; PMID:17068222; https://doi.org/10.1093/humupd/dml048
   PubMed Web of Science ®Google Scholar
• Holtan SG, Creedon DJ, Haluska P, Markovic SN. Cancer and Pregnancy: Parallels in growth, invasion, and immune modulation and implications for cancer therapeutic agents. Mayo Clin Proc 2009; 84:985-1000; PMID:19880689; https://doi.org/10.1016/S0025-6196(11)60669-1
   PubMed Web of Science ®Google Scholar
• Louwen F, Muschol-Steinmetz C, Reinhard J, Reitter A, Yuan J. A lesson for cancer research: placental microarray gene analysis in preeclampsia. Oncotarget 2012; 3:759-73; PMID:22929622; https://doi.org/10.18632/oncotarget.595
   PubMed Web of Science ®Google Scholar
• Nehar-Belaid D, Courau T, Dérian N, Florez L, Ruocco MG, Klatzmann D. Regulatory T Cells orchestrate similar immune evasion of fetuses and tumors in mice. J Immunol 2016; 196:678-90; PMID:26643476; https://doi.org/10.4049/jimmunol.1501834
   PubMed Web of Science ®Google Scholar
• Novakovic B, Saffery R. Placental pseudo-malignancy from a DNA methylation perspective: unanswered questions and future directions. Front Genet 2013; 4:285; PMID:24368911; https://doi.org/10.3389/fgene.2013.00285
   PubMedGoogle Scholar
• Allis CD, Jenuwein T. The molecular hallmarks of epigenetic control. Nat Rev Genet 2016; 17:487-500; PMID:27346641; https://doi.org/10.1038/nrg.2016.59
   PubMed Web of Science ®Google Scholar
• Rousseaux S, Debernardi A, Jacquiau B, Vitte A-L, Vesin A, Nagy-Mignotte H, Moro-Sibilot D, Brichon P-Y, Lantuejoul S, Hainaut P, et al. Ectopic activation of germline and placental genes identifies aggressive metastasis-prone lung cancers. Sci Transl Med 2013; 5:186ra66; PMID:23698379; https://doi.org/10.1126/scitranslmed.3005723
   PubMed Web of Science ®Google Scholar
• Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, Mcdonald OG, Wen B, Wu H, Liu Y, Diep D, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet 2011; 43:768-75; PMID:21706001; https://doi.org/10.1038/ng.865
   PubMed Web of Science ®Google Scholar
• Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med 2014; 6:61; PMID:25191524; https://doi.org/10.1186/s13073-014-0061-y
   PubMed Web of Science ®Google Scholar
• Blair JD, Langlois S, McFadden DE, Robinson WP. Overlapping DNA methylation profile between placentas with trisomy 16 and early-onset preeclampsia. Placenta 2014; 35:216-22; PMID:24462402; https://doi.org/10.1016/j.placenta.2014.01.001
   PubMed Web of Science ®Google Scholar
• Cocquebert M, Berndt S, Segond N, Guibourdenche J, Murthi P, Aldaz-Carroll L, Evain-Brion D, Fournier T. Comparative expression of hCG β-genes in human trophoblast from early and late first-trimester placentas. Am J Physiol Endocrinol Metab 2012; 303:E950-8; PMID:22811468; https://doi.org/10.1152/ajpendo.00087.2012
   PubMed Web of Science ®Google Scholar
• Sandoval J, Heyn HA, Moran S, Serra-Musach J, Pujana MA, Bibikova M, Esteller M. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics 2011; 6:692-702; PMID:21593595; https://doi.org/10.4161/epi.6.6.16196
   PubMed Web of Science ®Google Scholar
• Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods 2015; 12:115-21; PMID:25633503; https://doi.org/10.1038/nmeth.3252
   PubMed Web of Science ®Google Scholar
• Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics 2014; 30:1363-9; PMID:24478339; https://doi.org/10.1093/bioinformatics/btu049
   PubMed Web of Science ®Google Scholar
• Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL. Gene set enrichment analysis : A knowledge-based approach for interpreting genome-wide. Proc Natl Acad Sci U S A 2005; 102:15545-50; PMID:16199517; https://doi.org/10.1073/pnas.0506580102
   PubMed Web of Science ®Google Scholar
• Beard J. Embryological Aspects and Etiology of Carcinoma. Lancet 1902; 159:1758-61; https://doi.org/10.1016/S0140-6736(01)89936-0
   Google Scholar
• Beard J. The cancer problem. Lancet 1905; 90:283
   Google Scholar
• Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011; 144:646-74; PMID:21376230; https://doi.org/10.1016/j.cell.2011.02.013
   PubMed Web of Science ®Google Scholar
• Fuke C, Shimabukuro M, Petronis A, Sugimoto J, Oda T, Miura K, Miyazaki T, Ogura C, Okazaki Y, Jinno Y. Age related changes in 5-methylcytosine content in human peripheral leukocytes and placentas: An HPLC-based study. Ann Hum Genet 2004; 68:196-204; PMID:15180700; https://doi.org/10.1046/j.1529-8817.2004.00081.x
   PubMed Web of Science ®Google Scholar
• Novakovic B, Rakyan V, Ng HK, Manuelpillai U, Dewi C, Wong NC, Morley R, Down T, Beck S, Craig JM, et al. Specific tumour-associated methylation in normal human term placenta and first-trimester cytotrophoblasts. Mol Hum Reprod 2008; 14:547-54; PMID:18708652; https://doi.org/10.1093/molehr/gan046
   PubMed Web of Science ®Google Scholar
• Guilleret I, Osterheld M-C, Braunschweig R, Gastineau V, Taillens S, Benhattar J. Imprinting of tumor-suppressor genes in human placenta. Epigenetics 2009; 4:62-8; PMID:19106645; https://doi.org/10.4161/epi.4.1.7471
   PubMed Web of Science ®Google Scholar
• Chiu RWK, Chim SSC, Wong IHN, Wong CSC, Lee W-S, To KF, Tong JHM, Yuen RKC, Shum ASW, Chan JKC, et al. Hypermethylation of RASSF1A in human and rhesus placentas. Am J Pathol 2007; 170:941-50; PMID:17322379; https://doi.org/10.2353/ajpath.2007.060641
   PubMed Web of Science ®Google Scholar
• Schroeder DI, Blair JD, Lott P, Yu HOK, Hong D, Crary F, Ashwood P, Walker C, Korf I, Robinson WP, et al. The human placenta methylome. Proc Natl Acad Sci U S A 2013; 110:6037-42; PMID:23530188; https://doi.org/10.1073/pnas.1215145110
   PubMed Web of Science ®Google Scholar
• Feinberg AP, Vogelstein B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 1983; 301:89-92; PMID:6185846; https://doi.org/10.1038/301089a0
   PubMed Web of Science ®Google Scholar
• Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, McCune RA, Gehrke C. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 1982; 10:2709-21; PMID:7079182; https://doi.org/10.1093/nar/10.8.2709
   PubMed Web of Science ®Google Scholar
• Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CPE, van Dijk CM, Tollenaar RAEM, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet 2011; 44:40-6; PMID:22120008; https://doi.org/10.1038/ng.969
   PubMed Web of Science ®Google Scholar
• Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 2012; 22:246-58; PMID:22156296; https://doi.org/10.1101/gr.125872.111
   PubMed Web of Science ®Google Scholar
• Hovestadt V, Jones DTW, Picelli S, Wang W, Kool M, Northcott P a, Sultan M, Stachurski K, Ryzhova M, Warnatz HJ, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature 2014; 510:537-41; PMID:24847876; https://doi.org/10.1038/nature13268
   PubMed Web of Science ®Google Scholar
• Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Res 2014; 24:177-84; PMID:24068705; https://doi.org/10.1101/gr.157743.113
   PubMed Web of Science ®Google Scholar
• Genbacev O, Zhou Y, Ludlow JW, Fisher SJ. Regulation of human placental development by oxygen tension. Science 1997; 277:1669-72; PMID:9287221; https://doi.org/10.1126/science.277.5332.1669
   PubMed Web of Science ®Google Scholar
• Timp W, Feinberg AP. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 2013; 13:497-510; PMID:23760024; https://doi.org/10.1038/nrc3486
   PubMed Web of Science ®Google Scholar
• Baltimore D. NF-κB is 25. Nat Immunol 2011; 12:683-5; PMID:21772275; https://doi.org/10.1038/ni.2072
   PubMed Web of Science ®Google Scholar
• Mor G, Cardenas I, Abrahams V, Guller S. Inflammation and pregnancy: the role of the immune system at the implantation site. Ann N Y Acad Sci 2011; 1221:80-7; PMID:21401634; https://doi.org/10.1111/j.1749-6632.2010.05938.x
   PubMed Web of Science ®Google Scholar
• Shalapour S, Karin M. Immunity, inflammation, and cancer: an eternal fight between good and evil. J Clin Invest 2015; 125:3347-55; PMID:26325032; https://doi.org/10.1172/JCI80007
   PubMed Web of Science ®Google Scholar
• Kawamura K, Kawamura N, Sato W, Fukuda J, Kumagai J, Tanaka T. Brain-derived neurotrophic factor promotes implantation and subsequent placental development by stimulating trophoblast cell growth and survival. Endocrinology 2009; 150:3774-82.
   PubMed Web of Science ®Google Scholar
• Huang S-M, Lin C, Lin H-Y, Chiu C-M, Fang C-W, Liao K-F, Chen D-R, Yeh W-L. Brain-derived neurotrophic factor regulates cell motility in human colon cancer. Endocr Relat Cancer 2015; 22:455-64; PMID:25876647; https://doi.org/10.1530/ERC-15-0007
   PubMed Web of Science ®Google Scholar
• Kawano T, Morimoto K, Uemura Y. Partial purification and properties of urokinase inhibitor from human placenta. J Biochem 1970; 67:333-42; PMID:5424370; https://doi.org/10.1093/oxfordjournals.jbchem.a129257
   PubMed Web of Science ®Google Scholar
• Roes EM, Sweep CGF, Thomas CM, Zusterzeel PL, Geurts-Moespot A, Peters WH, Steegers EA. Levels of plasminogen activators and their inhibitors in maternal and umbilical cord plasma in severe preeclampsia. Am J Obstet Gynecol 2002; 187:1019-25; PMID:12388999; https://doi.org/10.1067/mob.2002.126280
   PubMed Web of Science ®Google Scholar
• Croucher DR, Saunders DN, Lobov S, Ranson M. Revisiting the biological roles of PAI2 (SERPINB2) in cancer. Nat Rev Cancer 2008; 8:535-45; PMID:18548086; https://doi.org/10.1038/nrc2400
   PubMed Web of Science ®Google Scholar
• Gui S, Ni S, Jia J, Gong Y, Gao L, Zhang L, Zhou R. Inconformity of CXCL3 plasma level and placenta expression in preeclampsia and its effect on trophoblast viability and invasion. PLoS One 2014; 9:e114408; PMID:25485631; https://doi.org/10.1371/journal.pone.0114408
   PubMed Web of Science ®Google Scholar
• Alvarez H, Opalinska J, Zhou L, Sohal D, Fazzari MJ, Yu Y, Montagna C, Montgomery EA, Canto M, Dunbar KB, et al. Widespread hypomethylation occurs early and synergizes with gene amplification during esophageal carcinogenesis. PLoS Genet 2011; 7:e1001356; PMID:21483804; https://doi.org/10.1371/journal.pgen.1001356
   PubMed Web of Science ®Google Scholar
• De Simone M, Arrigoni A, Rossetti G, Gruarin P, Ranzani V, Politano C, Bonnal RJP, Provasi E, Sarnicola ML, Panzeri I, et al. Transcriptional landscape of human tissue lymphocytes unveils uniqueness of tumor-infiltrating T regulatory cells. Immunity 2016; 45:1135-47; PMID:27851914; https://doi.org/10.1016/j.immuni.2016.10.021
   PubMed Web of Science ®Google Scholar
• Samstein RM, Josefowicz SZ, Arvey A, Treuting PM, Rudensky AY. Extrathymic generation of regulatory T cells in placental mammals mitigates maternal-fetal conflict. Cell 2012; 150:29-38; PMID:22770213; https://doi.org/10.1016/j.cell.2012.05.031
   PubMed Web of Science ®Google Scholar
• Kliman HJ, Nestlert JE, Sermasi E, Sanger JM, Strauss JF. Purification, characterization, and in vitro differentiation of cytotrophoblasts from human term placentae. Endocrinology 1986; 118:1567-82; PMID:3512258; https://doi.org/10.1210/endo-118-4-1567
   PubMed Web of Science ®Google Scholar
• Noble WS. How does multiple testing correction work? Nat Biotechnol 2009; 27:1135-7; PMID:20010596; https://doi.org/10.1038/nbt1209-1135
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y, Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 1995; 57:289-300
   Google Scholar
• Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol 2012; 41:200-9; PMID:22422453; https://doi.org/10.1093/ije/dyr238
   PubMed Web of Science ®Google Scholar
• Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. Software for computing and annotating genomic ranges. PLoS Comput Biol 2013; 9:e1003118; PMID:23950696; https://doi.org/10.1371/journal.pcbi.1003118
   PubMed Web of Science ®Google Scholar
• Law CW, Chen Y, Shi W, Smyth GK. voom: Precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol 2014; 15:R29; PMID:24485249; https://doi.org/10.1186/gb-2014-15-2-r29
   PubMed Web of Science ®Google Scholar