2,176
Views
32
CrossRef citations to date
0
Altmetric
Research Paper

Genome-wide DNA methylation associations with spontaneous preterm birth in US blacks: findings in maternal and cord blood samples

, , , , , , , , , , , , , , , & show all
Pages 163-172 | Received 17 Nov 2016, Accepted 20 Jan 2017, Published online: 06 Mar 2018

References

  • Callaghan WM, MacDorman MF, Rasmussen SA, et al. The contribution of preterm birth to infant mortality rates in the United States. Pediatrics. 2006;118:1566–1573. doi:10.1542/peds.2006-0860. PMID:17015548
  • Lopez-Serra P, Esteller M. DNA methylation-associated silencing of tumor-suppressor microRNAs in cancer. Oncogene. 2012;31:1609–1622. doi:10.1038/onc.2011.354. PMID:21860412
  • Laurent L, Wong E, Li G, et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20:320–331. doi:10.1101/gr.101907.109. PMID:20133333
  • Maunakea AK, Nagarajan RP, Bilenky M, et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010;466:253–257. doi:10.1038/nature09165. PMID:20613842
  • Heyn H, Esteller M. DNA methylation profiling in the clinic: applications and challenges. Nat Rev Gene. 2012;13:679–692. doi:10.1038/nrg3270. PMID:22945394
  • Parets SE, Conneely KN, Kilaru V, et al. Fetal DNA methylation associates with early spontaneous preterm birth and gestational age. PloS One. 2013;8:e67489. doi:10.1371/journal.pone.0067489. PMID:23826308
  • Parets SE, Conneely KN, Kilaru V, et al. DNA methylation provides insight into intergenerational risk for preterm birth in African Americans. Epigenetics. 2015;10:784–792. doi:10.1080/15592294.2015.1062964. PMID:26090903
  • Fernando F, Keijser R, Henneman P, et al. The idiopathic preterm delivery methylation profile in umbilical cord blood DNA. BMC Genomics. 2015;16:736. doi:10.1186/s12864-015-1915-4. PMID:26419829
  • Lee H, Jaffe AE, Feinberg JI, et al. DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth. Int J Epidemiol. 2012;41:188–199. doi:10.1093/ije/dyr237. PMID:22422452
  • Schroeder JW, Conneely KN, Cubells JC, et al. Neonatal DNA methylation patterns associate with gestational age. Epigenetics. 2011;6:1498–1504. doi:10.4161/epi.6.12.18296. PMID:22139580
  • Cruickshank MN, Oshlack A, Theda C, et al. Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy. Genome Med. 2013;5:96. doi:10.1186/gm500. PMID:24134860
  • Burris HH, Rifas-Shiman SL, Baccarelli A, et al. Associations of LINE-1 DNA Methylation with preterm birth in a prospective cohort study. J Dev Orig Health Dis. 2012;3:173–181. doi:10.1017/S2040174412000104. PMID:22720130
  • Bakulski KM, Feinberg JI, Andrews SV, et al. DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Epigenetics. 2016;11:354–362. doi:10.1080/15592294.2016.1161875. PMID:27019159
  • Fleischer T, Frigessi A, Johnson KC, et al. Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Genome Biol. 2014;15:435. doi:10.1186/s13059-014-0435-x, PMID:25146004
  • Tang P, Cheng TP, Agnello D, et al. Cybr, a cytokine-inducible protein that binds cytohesin-1 and regulates its activity. Proc Nat Acad Sci USA. 2002;99:2625–2629. doi:10.1073/pnas.052712999. PMID:11867758
  • Chen Q, Coffey A, Bourgoin SG, et al. Cytohesin binder and regulator augments T cell receptor-induced nuclear factor of activated T Cells.AP-1 activation through regulation of the JNK pathway. J Biol Chem. 2006;281:19985–19994. doi:10.1074/jbc.M601629200. PMID:16702224
  • Coppola V, Barrick CA, Bobisse S, et al. The scaffold protein Cybr is required for cytokine-modulated trafficking of leukocytes in vivo. Mol Cell Biol. 2006;26:5249–5258. doi:10.1128/MCB.02473-05. PMID:16809763
  • O'Brien M, Morrison JJ, Smith TJ. Upregulation of PSCDBP, TLR2, TWIST1, FLJ35382, EDNRB, and RGS12 gene expression in human myometrium at labor. Reproductive Sci. 2008;15:382–393. doi:10.1177/1933719108316179. PMID:18497345
  • Mosher AA, Rainey KJ, Bolstad SS, et al. Development and validation of primary human myometrial cell culture models to study pregnancy and labour. BMC Pregnancy Childbirth. 2013;13(Suppl 1):S7. doi:10.1186/1471-2393-13-S1-S7, PMID:23445904
  • Esteller M. Non-coding RNAs in human disease. Nat Rev Genet. 2011;12:861–874. doi:10.1038/nrg3074. PMID:22094949
  • Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 2009;23:1494–1504. doi:10.1101/gad.1800909. PMID:19571179
  • Okazaki Y, Furuno M, Kasukawa T, et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002;420:563–573. doi:10.1038/nature01266. PMID:12466851
  • Luo X, Shi Q, Gu Y, et al. LncRNA pathway involved in premature preterm rupture of membrane (PPROM): an epigenomic approach to study the pathogenesis of reproductive disorders. PloS One. 2013;8:e79897. doi:10.1371/journal.pone.0079897. PMID:24312190
  • Luo X, Pan J, Wang L, et al. Epigenetic regulation of lncRNA connects ubiquitin-proteasome system with infection-inflammation in preterm births and preterm premature rupture of membranes. BMC Pregnancy Childbirth. 2015;15:35. doi:10.1186/s12884-015-0460-0. PMID:25884766
  • Boyd HA, Poulsen G, Wohlfahrt J, et al. Maternal contributions to preterm delivery. Am J Epidemiol. 2009;170:1358–1364. doi:10.1093/aje/kwp324. PMID:19854807
  • Roessler J, Ammerpohl O, Gutwein J, et al. Quantitative cross-validation and content analysis of the 450k DNA methylation array from Illumina, Inc. BMC Res Notes. 2012;5:210. doi:10.1186/1756-0500-5-210. PMID:22546179
  • Nestor CE, Barrenas F, Wang H, et al. DNA methylation changes separate allergic patients from healthy controls and may reflect altered CD4+ T-cell population structure. PLoS Genet. 2014;10:e1004059. doi:10.1371/journal.pgen.1004059. PMID:24391521
  • Liang L, Willis-Owen SA, Laprise C, et al. An epigenome-wide association study of total serum immunoglobulin E concentration. Nature. 2015;520:670–674. doi:10.1038/nature14125. PMID:25707804
  • Murphy SK, Adigun A, Huang Z, et al. Gender-specific methylation differences in relation to prenatal exposure to cigarette smoke. Gene. 2012;494:36–43. doi:10.1016/j.gene.2011.11.062. PMID:22202639
  • Wang X, Zuckerman B, Pearson C, et al. Maternal cigarette smoking, metabolic gene polymorphism, and infant birth weight. Jama. 2002;287:195–202. doi:10.1001/jama.287.2.195. PMID:11779261
  • Wang G, Divall S, Radovick S, et al. Preterm birth and random plasma insulin levels at birth and in early childhood. JAMA. 2014;311:587–596. doi:10.1001/jama.2014.1. PMID:24519298
  • Gupta M, Mestan KK, Martin CR, et al. Impact of clinical and histologic correlates of maternal and fetal inflammatory response on gestational age in preterm births. J Matern Fetal Neonatal Med. 2007;20:39–46. doi:10.1080/14767050601156861. PMID:17437198
  • Laurie CC, Doheny KF, Mirel DB, et al. Quality control and quality assurance in genotypic data for genome-wide association studies. Genet Epidemiol. 2010;34:591–602. doi:10.1002/gepi.20516. PMID:20718045
  • Price AL, Patterson NJ, Plenge RM, et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet. 2006;38:904–909. doi:10.1038/ng1847. PMID:16862161
  • Aryee MJ, Jaffe AE, Corrada-Bravo H, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30:1363–1369. doi:10.1093/bioinformatics/btu049. PMID:24478339
  • Hong X, Hao K, Ladd-Acosta C, et al. Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. Nat Comm. 2015;6:6304. doi:10.1038/ncomms7304. PMID:25710614
  • Chen YA, Lemire M, Choufani S, et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray. Epigenetics. 2013;8:203–209. doi:10.4161/epi.23470. PMID:23314698
  • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8:118–127. doi:10.1093/biostatistics/kxj037. PMID:16632515
  • Leek JT, Johnson WE, Parker HS, et al. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics. 2012;28:882–883. doi:10.1093/bioinformatics/bts034. PMID:22257669
  • Du P, Zhang X, Huang CC, et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics. 2010;11:587. doi:10.1186/1471-2105-11-587. PMID:21118553
  • Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014;15:R31. doi:10.1186/gb-2014-15-2-r31. PMID:24495553
  • Houseman EA, Accomando WP, Koestler DC, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics. 2012;13:86. doi:10.1186/1471-2105-13-86. PMID:22568884
  • Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 2004;3:1–25, ISSN (Online) 1544–6115. doi:10.2202/1544-6115.1027. PMID:16646809

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.