Genome-wide mapping of 5mC and 5hmC identified differentially modified genomic regions in late-onset severe preeclampsia: A pilot study

PLoS ONE

Volumn 10, Issue 7, 2015, Pages

  Zhu, Lisha ^a   Lv, Ruitu ^b   Kong, Lingchun ^b   Cheng, Haidong ^a   Lan, Fei ^b,c   Li, Xiaotian ^a  

^a OBSTETRICS AND GYNECOLOGY HOSPITAL OF FUDAN UNIVERSITY   (China)

^b FUDAN UNIVERSITY   (China)

^c CHILDREN S HOSPITAL OF FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; EPIDERMAL GROWTH FACTOR RECEPTOR; TRANSCRIPTION FACTOR GATA 4; 5-HYDROXYMETHYLCYTOSINE; CYTOSINE; EGFR PROTEIN, HUMAN; PTPRN2 PROTEIN, HUMAN; RECEPTOR LIKE PROTEIN TYROSINE PHOSPHATASE;

5HMC GENE; 5MC GENE; AADACL3 GENE; ACAP2 GENE; ADULT; ARTICLE; BIOINFORMATICS; CASE REPORT; CCDC149 GENE; CHINESE; CLIC6 GENE; CONTROLLED STUDY; CPG ISLAND; DIASTOLIC BLOOD PRESSURE; DIFFERENTIALLY METHYLATED REGION; DNA HYDROXYMETHYLATION; DNA METHYLATION; DNA SEQUENCE; FEMALE; GATA4 GENE; GENE; GENE FUNCTION; GENE LOCUS; GENE MAPPING; GENE ONTOLOGY; GENE STRUCTURE; GENETIC ASSOCIATION; HUMAN; HUMAN TISSUE; IMMUNOPRECIPITATION; KCNJ4 GENE; LATE ONSET PREECLAMPSIA; OTUD5 GENE; PCDH9 GENE; PILOT STUDY; PREECLAMPSIA; PROMOTER REGION; PROTEINURIA; PTPRN2 GENE; RAB41 GENE; RAB5B GENE; RBFOX1 GENE; SERPINB7 GENE; SIGNAL TRANSDUCTION; SLC35B4 GENE; SYSTOLIC BLOOD PRESSURE; ANALOGS AND DERIVATIVES; BIOSYNTHESIS; GENETIC EPIGENESIS; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HUMAN GENOME; METABOLISM; PREGNANCY;

5-METHYLCYTOSINE; ADULT; CYTOSINE; DNA METHYLATION; EPIGENESIS, GENETIC; FEMALE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; PILOT PROJECTS; PRE-ECLAMPSIA; PREGNANCY; RECEPTOR, EPIDERMAL GROWTH FACTOR; RECEPTOR-LIKE PROTEIN TYROSINE PHOSPHATASES, CLASS 8; SIGNAL TRANSDUCTION;

EID: 84941660937     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0134119     Document Type: Article

References (53)

1. Steegers EA, von Dadelszen P, Duvekot JJ, Pijnenborg R. Pre-eclampsia. Lancet. 2010; 376 (9741): 631-44. doi: 10.1016/S0140-6736(10)60279-6 PMID: 20598363
2. von Dadelszen P, Magee LA, Roberts JM. Subclassification of preeclampsia. Hypertension in pregnancy. 2003; 22(2): 143-8. PMID: 12908998
3. Kornacki J, Skrzypczak J. [Results of Doppler examinations in fetuses of mothers with early-And lateonset preeclampsia]. Ginekologia polska. 2014; 85(7): 504-8. PMID: 25118501
4. Yung HW, Atkinson D, Campion-Smith T, Olovsson M, Charnock-Jones DS, Burton GJ. Differential activation of placental unfolded protein response pathways implies heterogeneity in causation of earlyand late-onset pre-eclampsia. The Journal of pathology. 2014; 234(2): 262-76. doi: 10.1002/path.4394 PMID: 24931423
5. Choudhury M, Friedman JE. Epigenetics and microRNAs in preeclampsia. Clinical and experimental hypertension. 2012; 34(5): 334-41. doi: 10.3109/10641963.2011.649931 PMID: 22468840
6. van Dijk M, Oudejans C. (Epi)genetics of pregnancy-Associated diseases. Frontiers in genetics. 2013; 4: 180. doi: 10.3389/fgene.2013.00180 PMID: 24058367
7. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science. 2011; 333(6047): 1300-3. doi: 10.1126/science. 1210597 PMID: 21778364
8. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science. 2009; 324 (5929): 930-5. doi: 10.1126/science.1170116 PMID: 19372391
9. Globisch D, Munzel M, Muller M, Michalakis S, Wagner M, Koch S, et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PloS one. 2010; 5(12): E15367. doi: 10.1371/journal.pone.0015367 PMID: 21203455
10. Ruzov A, Tsenkina Y, Serio A, Dudnakova T, Fletcher J, Bai Y, et al. Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development. Cell research. 2011; 21 (9): 1332-42. doi: 10.1038/cr.2011.113 PMID: 21747414
11. Tan L, Shi YG. Tet family proteins and 5-hydroxymethylcytosine in development and disease. Development. 2012; 139(11): 1895-902. doi: 10.1242/dev.070771 PMID: 22569552
12. Branco MR, Ficz G, Reik W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nature reviews Genetics. 2012; 13(1): 7-13.
13. Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, et al. Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell. 2013; 152(5): 1146-59. doi: 10.1016/j.cell. 2013.02.004 PMID: 23434322
14. Chouliaras L, Mastroeni D, Delvaux E, Grover A, Kenis G, Hof PR, et al. Consistent decrease in global DNA methylation and hydroxymethylation in the hippocampus of Alzheimer's disease patients. Neurobiology of aging. 2013; 34(9): 2091-9. doi: 10.1016/j.neurobiolaging.2013.02.021 PMID: 23582657
15. Figueroa-Romero C, Hur J, Bender DE, Delaney CE, Cataldo MD, Smith AL, et al. Identification of epigenetically altered genes in sporadic amyotrophic lateral sclerosis. PloS one. 2012; 7(12): E52672. doi: 10.1371/journal.pone.0052672 PMID: 23300739
16. Yao B, Lin L, Street RC, Zalewski ZA, Galloway JN, Wu H, et al. Genome-wide alteration of 5-hydroxymethylcytosine in a mouse model of fragile X-Associated tremor/ataxia syndrome. Human molecular genetics. 2014; 23(4): 1095-107. doi: 10.1093/hmg/ddt504 PMID: 24108107
17. Liu Y, Liu P, Yang C, Cowley AW Jr., Liang M. Base-resolution maps of 5-methylcytosine and 5-hydroxymethylcytosine in Dahl S rats: Effect of salt and genomic sequence. Hypertension. 2014; 63(4): 827-38. doi: 10.1161/HYPERTENSIONAHA.113.02637 PMID: 24420542
18. Ching T, Song MA, Tiirikainen M, Molnar J, Berry M, Towner D, et al. Genome-wide hypermethylation coupled with promoter hypomethylation in the chorioamniotic membranes of early onset pre-eclampsia. Molecular human reproduction. 2014; 20(9): 885-904. doi: 10.1093/molehr/gau046 PMID: 24944161
19. Blair JD, Yuen RK, Lim BK, McFadden DE, von Dadelszen P, Robinson WP. Widespread DNA hypomethylation at gene enhancer regions in placentas associated with early-onset pre-eclampsia. Molecular human reproduction. 2013; 19(10): 697-708. doi: 10.1093/molehr/gat044 PMID: 23770704
20. Nestor CE, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome research. 2012; 22(3): 467-77. doi: 10.1101/gr.126417.111 PMID: 22106369
21. American College of O, Gynecologists, Task Force on Hypertension in P. Hypertension in pregnancy. Report of the American College of Obstetricians and Gynecologists' Task Force on Hypertension in Pregnancy. Obstetrics and gynecology. 2013; 122(5): 1122-31. doi: 10.1097/01.AOG.0000437382. 03963.88 PMID: 24150027
22. Tan L, Xiong L, Xu W, Wu F, Huang N, Xu Y, et al. Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic acids research. 2013; 41(7): E84. doi: 10.1093/nar/gkt091 PMID: 23408859
23. Xu Y, Wu F, Tan L, Kong L, Xiong L, Deng J, et al. Genome-wide regulation of 5hmC, 5mC, and gene expression by Tet1 hydroxylase in mouse embryonic stem cells. Molecular cell. 2011; 42(4): 451-64. doi: 10.1016/j.molcel.2011.04.005 PMID: 21514197
24. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome biology. 2009; 10(3): R25. doi: 10.1186/gb-2009-10-3-r25 PMID: 19261174
25. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature protocols. 2009; 4(1): 44-57. doi: 10.1038/nprot.2008.211 PMID: 19131956
26. Kroeze LI, van der Reijden BA, Jansen JH. 5-Hydroxymethylcytosine: An epigenetic mark frequently deregulated in cancer. Biochimica et biophysica acta. 2015; 1855(2): 144-54. doi: 10.1016/j.bbcan. 2015.01.001 PMID: 25579174
27. Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013; 341(6146): 1237905. doi: 10.1126/science.1237905 PMID: 23828890
28. Chen J, Meng Y, Zhou J, Zhuo M, Ling F, Zhang Y, et al. Identifying candidate genes for Type 2 Diabetes Mellitus and obesity through gene expression profiling in multiple tissues or cells. Journal of diabetes research. 2013; 2013: 970435. doi: 10.1155/2013/970435 PMID: 24455749
29. Yazbek SN, Buchner DA, Geisinger JM, Burrage LC, Spiezio SH, Zentner GE, et al. Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis. Genome research. 2011; 21(7): 1065-73. doi: 10.1101/gr.120741.111 PMID: 21507882
30. Mbah AK, Kornosky JL, Kristensen S, August EM, Alio AP, Marty PJ, et al. Super-obesity and risk for early and late pre-eclampsia. BJOG: An international journal of obstetrics and gynaecology. 2010; 117 (8): 997-1004.
31. Park SY, Choi HK, Choi Y, Kwak S, Choi KC, Yoon HG. Deubiquitinase OTUD5 mediates the sequential activation of PDCD5 and p53 in response to genotoxic stress. Cancer letters. 2015; 357(1): 419-27. doi: 10.1016/j.canlet.2014.12.005 PMID: 25499082
32. Sharp AN, Heazell AE, Baczyk D, Dunk CE, Lacey HA, Jones CJ, et al. Preeclampsia is associated with alterations in the p53-pathway in villous trophoblast. PloS one. 2014; 9(1): E87621. doi: 10.1371/journal.pone.0087621 PMID: 24498154
33. Chen B, Longtine MS, Sadovsky Y, Nelson DM. Hypoxia downregulates p53 but induces apoptosis and enhances expression of BAD in cultures of human syncytiotrophoblasts. American journal of physiology Cell physiology. 2010; 299(5): C968-76. doi: 10.1152/ajpcell.00154.2010 PMID: 20810912
34. Parry S, Zhang H, Biggio J, Bukowski R, Varner M, Xu Y, et al. Maternal serum serpin B7 is associated with early spontaneous preterm birth. American journal of obstetrics and gynecology. 2014; 211(6): 678 e1-12. doi: 10.1016/j.ajog.2014.06.035 PMID: 24954659
35. Mendola P, Mumford SL, Mannisto TI, Holston A, Reddy UM, Laughon SK. Controlled direct effects of preeclampsia on neonatal health after accounting for mediation by preterm birth. Epidemiology. 2015; 26(1): 17-26. doi: 10.1097/EDE.0000000000000213 PMID: 25437315
36. Yuen RK, Penaherrera MS, von Dadelszen P, McFadden DE, Robinson WP. DNA methylation profiling of human placentas reveals promoter hypomethylation of multiple genes in early-onset preeclampsia. European journal of human genetics: EJHG. 2010; 18(9): 1006-12. doi: 10.1038/ejhg.2010.63 PMID: 20442742
37. Johansson A, Curran JE, Johnson MP, Freed KA, Fenstad MH, Bjorge L, et al. Identification of ACOX2 as a shared genetic risk factor for preeclampsia and cardiovascular disease. European journal of human genetics: EJHG. 2011; 19(7): 796-800. doi: 10.1038/ejhg.2011.19 PMID: 21343950
38. Haram K, Mortensen JH, Nagy B. Genetic Aspects of Preeclampsia and the HELLP Syndrome. Journal of pregnancy. 2014; 2014: 910751. doi: 10.1155/2014/910751 PMID: 24991435
39. Loewendorf AI, Nguyen TA, Yesayan MN, Kahn DA. Normal human pregnancy results in maternal immune activation in the periphery and at the uteroplacental interface. PloS one. 2014; 9(5): E96723. doi: 10.1371/journal.pone.0096723 PMID: 24846312
40. Liao AH, Liu LP, Ding WP, Zhang L. Functional changes of human peripheral B-lymphocytes in preeclampsia. American journal of reproductive immunology. 2009; 61(5): 313-21. doi: 10.1111/j.1600-0897.2009.00697.x PMID: 19341382
41. Schanz A, Winn VD, Fisher SJ, Blumenstein M, Heiss C, Hess AP, et al. Pre-eclampsia is associated with elevated CXCL12 levels in placental syncytiotrophoblasts and maternal blood. European journal of obstetrics, gynecology, and reproductive biology. 2011; 157(1): 32-7. doi: 10.1016/j.ejogrb.2011.02. 023 PMID: 21450389
42. Hwang HS, Kwon HS, Sohn IS, Park YW, Kim YH. Increased CXCL12 expression in the placentae of women with pre-eclampsia. European journal of obstetrics, gynecology, and reproductive biology. 2012; 160(2): 137-41. doi: 10.1016/j.ejogrb.2011.10.007 PMID: 22071114
43. Tejera E, Bernardes J, Rebelo I. Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia. BMC medical genomics. 2013; 6: 51. doi: 10.1186/1755-8794-6-51 PMID: 24219996
44. Ishibashi O, Ohkuchi A, Ali MM, Kurashina R, Luo SS, Ishikawa T, et al. Hydroxysteroid (17-beta) dehydrogenase 1 is dysregulated by miR-210 and miR-518c that are aberrantly expressed in preeclamptic placentas: A novel marker for predicting preeclampsia. Hypertension. 2012; 59(2): 265-73. doi: 10.1161/HYPERTENSIONAHA.111.180232 PMID: 22203747
45. Johnson MP, Brennecke SP, East CE, Dyer TD, Roten LT, Proffitt JM, et al. Genetic dissection of the pre-eclampsia susceptibility locus on chromosome 2q22 reveals shared novel risk factors for cardiovascular disease. Molecular human reproduction. 2013; 19(7): 423-37. doi: 10.1093/molehr/gat011 PMID: 23420841
46. Goyal R, Yellon SM, Longo LD, Mata-Greenwood E. Placental gene expression in a rat 'model' of placental insufficiency. Placenta. 2010; 31(7): 568-75. doi: 10.1016/j.placenta.2010.05.004 PMID: 20621762
47. Zhao J, Gu Y, Fan R, Groome LJ, Wang Y. Factors derived from preeclamptic placentas perturb polarity protein PARD-3 expression and distribution in endothelial cells. Reproductive sciences. 2011; 18 (2): 164-71. doi: 10.1177/1933719110382920 PMID: 20959641
48. Zhao S, Gu Y, Coates G, Groome LJ, Saleem MA, Mathieson PW, et al. Altered nephrin and podoplanin distribution is associated with disturbed polarity protein PARD-3 and PARD-6 expressions in podocytes from preeclampsia. Reproductive sciences. 2011; 18(8): 772-80. doi: 10.1177/1933719111398145 PMID: 21422051
49. Gould PS, Gu M, Liao J, Ahmad S, Cudmore MJ, Ahmed A, et al. Upregulation of urotensin II receptor in preeclampsia causes in vitro placental release of soluble vascular endothelial growth factor receptor 1 in hypoxia. Hypertension. 2010; 56(1): 172-8. doi: 10.1161/HYPERTENSIONAHA.110.152074 PMID: 20479331
50. Yoshida T, Kato K, Yokoi K, Oguri M, Watanabe S, Metoki N, et al. Association of genetic variants with chronic kidney disease in Japanese individuals with or without hypertension or diabetes mellitus. Experimental and therapeutic medicine. 2010; 1(1): 137-45. PMID: 23136606
51. Smyth LJ, McKay GJ, Maxwell AP, McKnight AJ. DNA hypermethylation and DNA hypomethylation is present at different loci in chronic kidney disease. Epigenetics: Official journal of the DNA Methylation Society. 2014; 9(3): 366-76.
52. Matsukawa R, Hirooka Y, Ito K, Sunagawa K. Inhibition of neuregulin-1/ErbB signaling in the rostral ventrolateral medulla leads to hypertension through reduced nitric oxide synthesis. American journal of hypertension. 2013; 26(1): 51-7. doi: 10.1093/ajh/hps005 PMID: 23382327
53. Armant DR, Kilburn BA, Petkova A, Edwin SS, Duniec-Dmuchowski ZM, Edwards HJ, et al. Human trophoblast survival at low oxygen concentrations requires metalloproteinase-mediated shedding of heparin-binding EGF-like growth factor. Development. 2006; 133(4): 751-9. PMID: 16407398