The application of epiphenotyping approaches to DNA methylation array studies of the human placenta

Wilhelm-Benartzi CS, Houseman EA, Maccani MA, Poage GM, Koestler DC, Langevin SM, et al. In utero exposures, infant growth, and DNA methylation of repetitive elements and developmentally related genes in human placenta. Environ Health Perspect. 2012;120(2):296–302.

Article  CAS  PubMed  Google Scholar 

Maccani JZ, Maccani MA. Altered placental DNA methylation patterns associated with maternal smoking: current perspectives. Adv Genomics Genet. 2015;2015(5):205–14.

Article  PubMed  PubMed Central  Google Scholar 

Shrestha D, Ouidir M, Workalemahu T, Zeng X, Tekola-Ayele F. Placental DNA methylation changes associated with maternal prepregnancy BMI and gestational weight gain. Int J Obes. 2020;44(6):1406–16.

Article  CAS  Google Scholar 

Hivert MF, Cardenas A, Allard C, Doyon M, Powe CE, Catalano PM, et al. Interplay of placental DNA methylation and maternal insulin sensitivity in pregnancy. Diabetes. 2020;69(3):484–92.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ruchat SM, Houde AA, Voisin G, St-Pierre J, Perron P, Baillargeon JP, et al. Gestational diabetes mellitus epigenetically affects genes predominantly involved in metabolic diseases. Epigenetics. 2013;8(9):935–43.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Konwar C, Del Gobbo GF, Terry J, Robinson WP. Association of a placental Interleukin-6 genetic variant (rs1800796) with DNA methylation, gene expression and risk of acute chorioamnionitis. BMC Med Genet. 2019;20(1):36.

Article  PubMed  PubMed Central  Google Scholar 

Wilson SL, Leavey K, Cox BJ, Robinson WP. Mining DNA methylation alterations towards a classification of placental pathologies. Hum Mol Genet. 2018;27(1):135–46.

Article  CAS  PubMed  Google Scholar 

Leavey K, Wilson SL, Bainbridge SA, Robinson WP, Cox BJ. Epigenetic regulation of placental gene expression in transcriptional subtypes of preeclampsia. Clin Epigenetics. 2018;10:28.

Article  PubMed  PubMed Central  Google Scholar 

Banister CE, Koestler DC, Maccani MA, Padbury JF, Houseman EA, Marsit CJ. Infant growth restriction is associated with distinct patterns of DNA methylation in human placentas. Epigenetics. 2011;6(7):920–7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Xiao X, Zhao Y, Jin R, Chen J, Wang X, Baccarelli A, et al. Fetal growth restriction and methylation of growth-related genes in the placenta. Epigenomics. 2016;8(1):33–42.

Article  CAS  PubMed  Google Scholar 

Tekola-Ayele F, Zeng X, Ouidir M, Workalemahu T, Zhang C, Delahaye F, et al. DNA methylation loci in placenta associated with birthweight and expression of genes relevant for early development and adult diseases. Clin Epigenetics. 2020;12(1):78.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rogers JM. Smoking and pregnancy: Epigenetics and developmental origins of the metabolic syndrome. Birth Defects Res. 2019;111(17):1259–69.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Almomani SN, Alsaleh AA, Weeks RJ, Chatterjee A, Day RC, Honda I, et al. Identification and validation of DNA methylation changes in pre-eclampsia. Placenta. 2021;110:16–23.

Article  CAS  PubMed  Google Scholar 

Cirkovic A, Garovic V, Milin Lazovic J, Milicevic O, Savic M, Rajovic N, et al. Systematic review supports the role of DNA methylation in the pathophysiology of preeclampsia: a call for analytical and methodological standardization. Biol Sex Differ. 2020;11(1):36.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yuan V, Hui D, Yin Y, Peñaherrera MS, Beristain AG, Robinson WP. Cell-specific characterization of the placental methylome. BMC Genomics. 2021;22(1):6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Inkster AM, Yuan V, Konwar C, Mathews AM, Brown CJ, Robinson WP. A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta. Bio Sex Diff. 2021;12(1):38.

Article  CAS  Google Scholar 

Novakovic B, Yuen RK, Gordon L, Penaherrera MS, Sharkey A, Moffett A, et al. Evidence for widespread changes in promoter methylation profile in human placenta in response to increasing gestational age and environmental/stochastic factors. BMC Genomics. 2011;28(12):529.

Article  Google Scholar 

Lee Y, Choufani S, Weksberg R, Wilson SL, Yuan V, Burt A, et al. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging. 2019;11(12):4238–53.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rahmani E, Shenhav L, Schweiger R, Yousefi P, Huen K, Eskenazi B, et al. Genome-wide methylation data mirror ancestry information. Epigenetics Chromatin. 2017;10:1.

Article  PubMed  PubMed Central  Google Scholar 

Smith JA, Zhao W, Wang X, Ratliff SM, Mukherjee B, Kardia SLR, et al. Neighborhood characteristics influence DNA methylation of genes involved in stress response and inflammation: the multi-ethnic study of atherosclerosis. Epigenetics. 2017;12(8):662–73.

Article  PubMed  PubMed Central  Google Scholar 

Fraser HB, Lam LL, Neumann SM, Kobor MS. Population-specificity of human DNA methylation. Genome Biol. 2012;13(2):R8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Delahaye F, Do C, Kong Y, Ashkar R, Salas M, Tycko B, et al. Genetic variants influence on the placenta regulatory landscape. PLoS Genet. 2018;14(11): e1007785.

Article  PubMed  PubMed Central  Google Scholar 

Teh AL, Pan H, Chen L, Ong ML, Dogra S, Wong J, et al. The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes. Genome Res. 2014;24(7):1064–74.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Horvath S. DNA methylation age of human tissues and cell types. Genome Biol. 2013;14(10):R115.

Article  PubMed  PubMed Central  Google Scholar 

Lu AT, Quach A, Wilson JG, Reiner AP, Aviv A, Raj K, et al. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging. 2019;11(2):303–27.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang Y, Hannon E, Grant OA, Gorrie-Stone TJ, Kumari M, Mill J, et al. DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy. BMC Genomics. 2021;22(1):484.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, et al. DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformat. 2012;8(13):86.

Article  Google Scholar 

Titus AJ, Gallimore RM, Salas LA, Christensen BC. Cell-type deconvolution from DNA methylation: a review of recent applications. Hum Mol Genet. 2017;26(R2):R216–24.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Yuan V. Planet: Placental DNA methylation analysis tools. 2021. https://doi.org/https://victor.rbind.io/planet/

Campbell KA, Colacino JA, Park SK, Bakulski KM. Cell types in environmental epigenetic studies: biological and epidemiological frameworks. Curr Environ Health Rep. 2020;7(3):185–97.

Article  PubMed  PubMed Central  Google Scholar 

Qi L, Teschendorff AE. Cell-type heterogeneity: Why we should adjust for it in epigenome and biomarker studies. Clin Epigenetics. 2022;14(1):31.

Article  PubMed  PubMed Central  Google Scholar 

Greally JM. A user’s guide to the ambiguous word “epigenetics.” Nat Rev Mol Cell Biol. 2018;19(4):207–8.

Article  CAS  PubMed  Google Scholar 

Yuan V, Price EM, Del Gobbo G, Mostafavi S, Cox B, Binder AM, et al. Accurate ethnicity prediction from placental DNA methylation data. Epigenetics Chromatin. 2019;12(1):51.

Article  PubMed  PubMed Central  Google Scholar 

Barfield RT, Almli LM, Kilaru V, Smith AK, Mercer KB, Duncan R, et al. Accounting for population stratification in DNA methylation studies. Genet Epidemiol. 2014;38(3):231–41.

Article  PubMed  PubMed Central  Google Scholar 

Rahmani E, Shenhav L, Schweiger R, Yousefi P, Huen K, Eskenazi B, et al. Genome-wide methylation data mirror ancestry information. Epigenetics Chromatin. 2017;10(1):1.

Article  PubMed  PubMed Central  Google Scholar 

Price EM, Robinson WP. Adjusting for batch effects in DNA methylation microarray data, a lesson learned. Front Genet. 2018. https://doi.org/10.3389/fgene.2018.00083/full.

Article 

留言 (0)

沒有登入
gif