Accelerated Placental Aging in Early Onset Preeclampsia Pregnancies Identified By DNA Methylation

References

• Sharp AJ , StathakiE , MigliavaccaEet al. DNA methylation profiles of human active and inactive X chromosomes . Genome Res.21 ( 10 ), 1592 – 1600 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Novak P , StampferMR , Munoz-RodriguezJLet al. Cell-type specific DNA methylation patterns define human breast cellular identity . PLoS ONE7 ( 12 ), e52299 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Paulsen M , Ferguson-SmithAC . DNA methylation in genomic imprinting, development, and disease . J. Pathol.195 ( 1 ), 97 – 110 ( 2001 ).
   PubMed Web of Science ®Google Scholar
• Robertson KD . DNA methylation and human disease . Nat. Rev. Genet.6 ( 8 ), 597 – 610 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Horvath S . DNA methylation age of human tissues and cell types . Genome Biol.14 ( 10 ), R115 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Simpkin AJ , HemaniG , SudermanMet al. Prenatal and early life influences on epigenetic age in children: a study of mother-offspring pairs from two cohort studies . Hum. Mol. Genet.25 ( 1 ), 191 – 201 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Hon GC , HawkinsRD , CaballeroOLet al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer . Genome Res.22 ( 2 ), 246 – 258 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Berman BP , WeisenbergerDJ , AmanJFet al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains . Nat. Genet.44 ( 1 ), 40 – 46 ( 2012 ).
   Web of Science ®Google Scholar
• Lister R , PelizzolaM , DowenRHet al. Human DNA methylomes at base resolution show widespread epigenomic differences . Nature462 ( 7271 ), 315 – 322 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Schroeder DI , BlairJD , LottPet al. The human placenta methylome . Proc. Natl Acad. Sci. USA110 ( 15 ), 6037 – 6042 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Schultz MD , HeY , WhitakerJWet al. Human body epigenome maps reveal noncanonical DNA methylation variation . Nature523 ( 7559 ), 212 – 216 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Novakovic B , YuenRK , GordonLet al. Evidence for widespread changes in promoter methylation profile in human placenta in response to increasing gestational age and environmental/stochastic factors . BMC Genomics12529 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Redman CW , SargentIL , StaffAC . IFPA Senior Award Lecture: making sense of pre-eclampsia – two placental causes of preeclampsia?Placenta35 ( Suppl. ) S20 – S25 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Williams D , CraftN . Pre-eclampsia . BMJ345 , e4437 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Monk C , SpicerJ , ChampagneFA . Linking prenatal maternal adversity to developmental outcomes in infants: the role of epigenetic pathways . Dev. Psychopathol.24 ( 4 ), 1361 – 1376 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Novakovic B , SafferyR . The ever growing complexity of placental epigenetics – role in adverse pregnancy outcomes and fetal programming . Placenta33 ( 12 ), 959 – 970 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Bianco-Miotto T , MayneB , BuckberryS , BreenJ , Rodriguez LopezC , RobertsC . Recent progress towards understanding the role of DNA methylation in human placental development . Reproduction152 ( 1 ), R23 – R30 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Liu L , ZhangX , RongCet al. Distinct DNA methylomes of human placentas between pre-eclampsia and gestational diabetes mellitus . Cell. Physiol. Biochem.34 ( 6 ), 1877 – 1889 ( 2014 ).
   PubMedGoogle Scholar
• Anton L , BrownAG , BartolomeiMS , ElovitzMA . Differential methylation of genes associated with cell adhesion in preeclamptic placentas . PLoS ONE9 ( 6 ), e100148 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Blair JD , YuenRK , LimBK , McfaddenDE , Von DadelszenP , RobinsonWP . Widespread DNA hypomethylation at gene enhancer regions in placentas associated with early-onset pre-eclampsia . Mol. Hum. Reprod.19 ( 10 ), 697 – 708 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Chu T , BunceK , ShawPet al. Comprehensive analysis of preeclampsia-associated DNA methylation in the placenta . PLoS ONE9 ( 9 ), e107318 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Finer S , MathewsC , LoweRet al. Maternal gestational diabetes is associated with genome-wide DNA methylation variation in placenta and cord blood of exposed offspring . Hum. Mol. Genet.24 ( 11 ), 3021 – 3029 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Ruchat SM , HoudeAA , VoisinGet al. Gestational diabetes mellitus epigenetically affects genes predominantly involved in metabolic diseases . Epigenetics8 ( 9 ), 935 – 943 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Hillman SL , FinerS , SmartMCet al. Novel DNA methylation profiles associated with key gene regulation and transcription pathways in blood and placenta of growth-restricted neonates . Epigenetics10 ( 1 ), 50 – 61 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Jacob KJ , RobinsonWP , LefebvreL . Beckwith–Wiedemann and Silver–Russell syndromes: opposite developmental imbalances in imprinted regulators of placental function and embryonic growth . Clin. Genet.84 ( 4 ), 326 – 334 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Fowden AL , SibleyC , ReikW , ConstanciaM . Imprinted genes, placental development and fetal growth . Horm. Res.65 ( Suppl. 3 ), 50 – 58 ( 2006 ).
   PubMedGoogle Scholar
• Yu L , ChenM , ZhaoDet al. The H19 gene imprinting in normal pregnancy and pre-eclampsia . Placenta30 ( 5 ), 443 – 447 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Guo L , TsaiSQ , HardisonNEet al. Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas . Placenta34 ( 7 ), 599 – 605 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Nishizawa H , Pryor-KoishiK , KatoT , KowaH , KurahashiH , UdagawaY . Microarray analysis of differentially expressed fetal genes in placental tissue derived from early and late onset severe pre-eclampsia . Placenta28 ( 5–6 ), 487 – 497 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Van Uitert M , MoerlandPD , EnquobahrieDAet al. Meta-analysis of placental transcriptome data identifies a novel molecular pathway related to preeclampsia . PLoS ONE10 ( 7 ), e0132468 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Sober S , ReimanM , KikasTet al. Extensive shift in placental transcriptome profile in preeclampsia and placental origin of adverse pregnancy outcomes . Sci. Rep.5 , 13336 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Kaartokallio T , CerveraA , KyllonenA , LaivuoriK . Gene expression profiling of pre-eclamptic placentae by RNA sequencing . Sci. Rep.5 , 14107 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Nishizawa H , OtaS , SuzukiMet al. Comparative gene expression profiling of placentas from patients with severe pre-eclampsia and unexplained fetal growth restriction . Reprod. Biol. Endocrinol.9 , 107 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Teschendorff AE , MarabitaF , LechnerMet al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data . Bioinformatics29 ( 2 ), 189 – 196 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Leek JT , JohnsonWE , ParkerHS , JaffeAE , StoreyJD . The SVA package for removing batch effects and other unwanted variation in high-throughput experiments . Bioinformatics28 ( 6 ), 882 – 883 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Morris TJ , ButcherLM , FeberAet al. ChAMP: 450k Chip Analysis Methylation Pipeline . Bioinformatics30 ( 3 ), 428 – 430 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Aryee MJ , JaffeAE , Corrada-BravoHet al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays . Bioinformatics30 ( 10 ), 1363 – 1369 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Ritchie ME , PhipsonB , WuDet al. limma powers differential expression analyses for RNA-sequencing and microarray studies . Nucleic Acids Res.43 ( 7 ), e47 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Jaffe AE , MurakamiP , LeeHet al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies . Int. J. Epidemiol.41 ( 1 ), 200 – 209 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Friedman J , HastieT , TibshiraniR . Regularization paths for generalized linear models via coordinate descent . J. Stat. Softw.33 ( 1 ), 1 – 22 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Davis S . IlluminaHumanMethylation27k.db: Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k) . R package version 1.4.8 ( 2014 ).
   Google Scholar
• Triche T and Jr . IlluminaHumanMethylation450k.db: Illumina Human Methylation 450k annotation data . R package version 2.0.9 ( 2014 ).
   Google Scholar
• Barrett T , WilhiteSE , LedouxPet al. NCBI GEO: archive for functional genomics data sets – update . Nucleic Acids Res.41 , D991 – D995 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Buckberry S , Bianco-MiottoT , BentSJ , DekkerGA , RobertsCT . Integrative transcriptome meta-analysis reveals widespread sex-biased gene expression at the human fetal–maternal interface . Mol. Hum. Reprod.20 ( 8 ), 810 – 819 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Augui S , NoraEP , HeardE . Regulation of X-chromosome inactivation by the X-inactivation centre . Nat. Rev. Genet.12 ( 6 ), 429 – 442 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Terry J , SaitoT , SubramanianSet al. TLE1 as a diagnostic immunohistochemical marker for synovial sarcoma emerging from gene expression profiling studies . Am. J. Surg. Pathol.31 ( 2 ), 240 – 246 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Sood R , ZehnderJL , DruzinML , BrownPO . Gene expression patterns in human placenta . Proc. Natl Acad. Sci. USA103 ( 14 ), 5478 – 5483 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Bai Y , XiangX , LiangC , ShiL . Regulating Rac in the nervous system: molecular function and disease implication of Rac GEFs and GAPs . Biomed. Res. Int.2015 , 632450 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Roberts CT . IFPA award in placentology lecture: complicated interactions between genes and the environment in placentation, pregnancy outcome and long term health . Placenta31 ( Suppl. ), S47 – S53 ( 2010 ).
   PubMedGoogle Scholar
• Clifton VL . Review: sex and the human placenta: mediating differential strategies of fetal growth and survival . Placenta31 ( Suppl. ), S33 – S39 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Vatten LJ , SkjaervenR . Offspring sex and pregnancy outcome by length of gestation . Early Hum. Dev.76 ( 1 ), 47 – 54 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Verburg PE , TuckerG , ScheilW , ErwichJJ , DekkerGA , RobertsCT . Sexual dimorphism in adverse pregnancy outcomes – a Retrospective Australian Population Study 1981–2011 . PLoS ONE11 ( 7 ), e0158807 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Gude NM , RobertsCT , KalionisB , KingRG . Growth and function of the normal human placenta . Thromb. Res.114 ( 5–6 ), 397 – 407 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Moarii M , BoevaV , VertJ-P , ReyalF . Changes in correlation between promoter methylation and gene expression in cancer . BMC Genomics16 , 873 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Guo JU , SuY , ShinJHet al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain . Nat. Neurosci.17 ( 2 ), 215 – 222 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Suter M , MaJ , HarrisAet al. Maternal tobacco use modestly alters correlated epigenome-wide placental DNA methylation and gene expression . Epigenetics6 ( 11 ), 1284 – 1294 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Maccani JZ , KoestlerDC , HousemanEA , MarsitCJ , KelseyKT . Placental DNA methylation alterations associated with maternal tobacco smoking at the RUNX3 gene are also associated with gestational age . Epigenomics5 ( 6 ), 619 – 630 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Horvath S , ErhartW , BroschMet al. Obesity accelerates epigenetic aging of human liver . Proc. Natl Acad. Sci. USA111 ( 43 ), 15538 – 15543 ( 2014 ).
   PubMed Web of Science ®Google Scholar