Analysis of two birth tissues provides new insights into the epigenetic landscape of neonates born preterm.

Abstract:

BACKGROUND:Preterm birth (PTB), defined as child birth before completion of 37 weeks of gestation, is a major challenge in perinatal health care and can bear long-term medical and financial burden. Over a million children die each year due to PTB complications, and those who survive can face developmental delays. Unfortunately, our understanding of the molecular pathways associated with PTB remains limited. There is a growing body of evidence suggesting the role of DNA methylation (DNAm) in mediating the effects of PTB on future health outcomes. Thus, epigenome-wide association studies (EWAS), where DNAm sites are examined for associations with PTB, can help shed light on the biological mechanisms linking the two. RESULTS:In an Asian cohort of 1019 infants (68 preterm, 951 full term), we examined and compared the associations between PTB and genome-wide DNAm profiles using both cord tissue (n = 1019) and cord blood (n = 332) samples on Infinium HumanMethylation450 arrays. PTB was significantly associated (P < 5.8e-7) with DNAm at 296 CpGs (209 genes) in the cord blood. Over 95% of these CpGs were replicated in other PTB/gestational age EWAS conducted in (cord) blood. This replication was apparent even across populations of different ethnic origin (Asians, Caucasians, and African Americans). More than a third of these 296 CpGs were replicated in at least 4 independent studies, thereby identifying a robust set of PTB-linked epigenetic signatures in cord blood. Interrogation of cord tissue in addition to cord blood provided novel insights into the epigenetic status of the neonates born preterm. Overall, 994 CpGs (608 genes, P < 3.7e-7) associated with PTB in cord tissue, of which only 10 of these CpGs were identified in the analysis using cord blood. Genes from cord tissue showed enrichment of molecular pathways related to fetal growth and development, while those from cord blood showed enrichment of immune response pathways. A substantial number of PTB-associated CpGs from both the birth tissues were also associated with gestational age. CONCLUSIONS:Our findings provide insights into the epigenetic landscape of neonates born preterm, and that its status is captured more comprehensively by interrogation of more than one neonatal tissue in tandem. Both these neonatal tissues are clinically relevant in their unique ways and require careful consideration in identification of biomarkers related to PTB and gestational age. TRIAL REGISTRATION:This birth cohort is a prospective observational study designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875 .

journal_name

Clin Epigenetics

journal_title

Clinical epigenetics

authors

Wu Y,Lin X,Lim IY,Chen L,Teh AL,MacIsaac JL,Tan KH,Kobor MS,Chong YS,Gluckman PD,Karnani N

doi

10.1186/s13148-018-0599-4

subject

Has Abstract

pub_date

2019-02-11 00:00:00

pages

26

issue

1

eissn

1868-7075

issn

1868-7083

pii

10.1186/s13148-018-0599-4

journal_volume

11

pub_type

杂志文章
  • Single-molecule quantification of 5-hydroxymethylcytosine for diagnosis of blood and colon cancers.

    abstract:BACKGROUND:The DNA modification 5-hydroxymethylcytosine (5hmC) is now referred to as the sixth base of DNA with evidence of tissue-specific patterns and correlation with gene regulation and expression. This epigenetic mark was recently reported as a potential biomarker for multiple types of cancer, but its application ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-017-0368-9

    authors: Gilat N,Tabachnik T,Shwartz A,Shahal T,Torchinsky D,Michaeli Y,Nifker G,Zirkin S,Ebenstein Y

    更新日期:2017-07-14 00:00:00

  • Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients.

    abstract:BACKGROUND:Splicing is more efficient when coupled with transcription and it has been proposed that nucleosomes enriched in exons are important for splice site recognition. Lynch syndrome is a familial cancer syndrome that can be caused by the autosomal dominant inheritance of splice site mutations in the MutL homolog ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-014-0032-6

    authors: Sloane MA,Hesson LB,Nunez AC,Thompson BA,Ward RL

    更新日期:2014-12-13 00:00:00

  • Early detection of colorectal cancer based on presence of methylated syndecan-2 (SDC2) in stool DNA.

    abstract:BACKGROUND:Colorectal cancer (CRC) screening can effectively reduce disease-related mortality by detecting CRC at earlier stages. We have previously demonstrated that the presence of SDC2 methylation in stool DNA is significantly associated with the occurrence of CRC regardless of clinical stage. The aim of this study ...

    journal_title:Clinical epigenetics

    pub_type: 临床试验,杂志文章

    doi:10.1186/s13148-019-0642-0

    authors: Han YD,Oh TJ,Chung TH,Jang HW,Kim YN,An S,Kim NK

    更新日期:2019-03-15 00:00:00

  • Combined inhibition of BET proteins and class I HDACs synergistically induces apoptosis in urothelial carcinoma cell lines.

    abstract:Background:New efficient therapies for urothelial carcinoma (UC) are urgently required. Small-molecule drugs targeting chromatin regulators are reasonable candidates because these regulators are frequently mutated or deregulated in UC. Indeed, in previous work, Romidepsin, which targets class I histone deacetylases (HD...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-017-0434-3

    authors: Hölscher AS,Schulz WA,Pinkerneil M,Niegisch G,Hoffmann MJ

    更新日期:2018-01-04 00:00:00

  • Longitudinal epigenome-wide association studies of three male military cohorts reveal multiple CpG sites associated with post-traumatic stress disorder.

    abstract:BACKGROUND:Epigenetic mechanisms have been suggested to play a role in the development of post-traumatic stress disorder (PTSD). Here, blood-derived DNA methylation data (HumanMethylation450 BeadChip) collected prior to and following combat exposure in three cohorts of male military members were analyzed to assess whet...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-019-0798-7

    authors: Snijders C,Maihofer AX,Ratanatharathorn A,Baker DG,Boks MP,Geuze E,Jain S,Kessler RC,Pishva E,Risbrough VB,Stein MB,Ursano RJ,Vermetten E,Vinkers CH,PGC PTSD EWAS Consortium.,Smith AK,Uddin M,Rutten BPF,Nievergelt CM

    更新日期:2020-01-13 00:00:00

  • Overall and sex-specific associations between methylation of the ABCG1 and APOE genes and ischemic stroke or other atherosclerosis-related traits in a sibling study of Chinese population.

    abstract:BACKGROUND:Identifying subjects with a high risk of ischemic stroke is fundamental for prevention of the disease. Both genetic and environmental risk factors contribute to ischemic stroke, but the underlying epigenetic mechanisms which mediate genetic and environmental risk effects are not fully understood. The aim of ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-019-0784-0

    authors: Qin X,Li J,Wu T,Wu Y,Tang X,Gao P,Li L,Wang M,Wu Y,Wang X,Chen D,Hu Y

    更新日期:2019-12-10 00:00:00

  • Dietary intakes and biomarker patterns of folate, vitamin B6, and vitamin B12 can be associated with cognitive impairment by hypermethylation of redox-related genes NUDT15 and TXNRD1.

    abstract:BACKGROUND:B vitamins in the one-carbon metabolism pathway (folate, vitamin B6, and vitamin B12) have been implicated in DNA methylation, and their deficiency may contribute to cognitive decline through increased homocysteine (Hcy) levels and subsequent oxidative damage. The aim of this study was to investigate whether...

    journal_title:Clinical epigenetics

    pub_type: 临床试验,杂志文章

    doi:10.1186/s13148-019-0741-y

    authors: An Y,Feng L,Zhang X,Wang Y,Wang Y,Tao L,Qin Z,Xiao R

    更新日期:2019-10-11 00:00:00

  • The hyper-activation of transcriptional enhancers in breast cancer.

    abstract:BACKGROUND:Activation of transcription enhancers, especially super-enhancers, is one of the critical epigenetic features of tumorigenesis. However, very few studies have systematically identified the enhancers specific in cancer tissues. METHODS:Here, we studied the change of histone modifications in MMTV-PyVT breast ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-019-0645-x

    authors: Li QL,Wang DY,Ju LG,Yao J,Gao C,Lei PJ,Li LY,Zhao XL,Wu M

    更新日期:2019-03-12 00:00:00

  • Genome-wide methylomic analysis in individuals with HNF1B intragenic mutation and 17q12 microdeletion.

    abstract::Heterozygous mutation of the transcription factor HNF1B is the most common cause of monogenetic developmental renal disease. Disease-associated mutations fall into two categories: HNF1B intragenic mutations and a 1.3 Mb deletion at chromosome 17q12. An increase in neurodevelopmental disorders has been observed in indi...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-018-0530-z

    authors: Clissold RL,Ashfield B,Burrage J,Hannon E,Bingham C,Mill J,Hattersley A,Dempster EL

    更新日期:2018-07-18 00:00:00

  • Altered DNA methylation is associated with aberrant gene expression in parenchymal but not airway fibroblasts isolated from individuals with COPD.

    abstract:Background:Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease of the lungs that is currently the fourth leading cause of death worldwide. Genetic factors account for only a small amount of COPD risk, but epigenetic mechanisms, including DNA methylation, have the potential to mediate the interaction...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-018-0464-5

    authors: Clifford RL,Fishbane N,Patel J,MacIsaac JL,McEwen LM,Fisher AJ,Brandsma CA,Nair P,Kobor MS,Hackett TL,Knox AJ

    更新日期:2018-03-05 00:00:00

  • Comprehensive evaluation of targeted multiplex bisulphite PCR sequencing for validation of DNA methylation biomarker panels.

    abstract:BACKGROUND:DNA methylation is a well-studied epigenetic mark that is frequently altered in diseases such as cancer, where specific changes are known to reflect the type and severity of the disease. Therefore, there is a growing interest in assessing the clinical utility of DNA methylation as a biomarker for diagnosing ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-020-00880-y

    authors: Lam D,Luu PL,Song JZ,Qu W,Risbridger GP,Lawrence MG,Lu J,Trau M,Korbie D,Clark SJ,Pidsley R,Stirzaker C

    更新日期:2020-06-22 00:00:00

  • Aberrant DNA methylation and expression of SPDEF and FOXA2 in airway epithelium of patients with COPD.

    abstract:BACKGROUND:Goblet cell metaplasia, a common feature of chronic obstructive pulmonary disease (COPD), is associated with mucus hypersecretion which contributes to the morbidity and mortality among patients. Transcription factors SAM-pointed domain-containing Ets-like factor (SPDEF) and forkhead box protein A2 (FOXA2) re...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-017-0341-7

    authors: Song J,Heijink IH,Kistemaker LEM,Reinders-Luinge M,Kooistra W,Noordhoek JA,Gosens R,Brandsma CA,Timens W,Hiemstra PS,Rots MG,Hylkema MN

    更新日期:2017-04-24 00:00:00

  • Premature aging of leukocyte DNA methylation is associated with type 2 diabetes prevalence.

    abstract:BACKGROUND:Type 2 diabetes mellitus (T2D) is highly prevalent in Middle-Eastern and North African Arab populations, but the molecular basis for this susceptibility is unknown. Altered DNA methylation levels were reported in insulin-secreting and responding tissues, but whether methylation in accessible tissues such as ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-015-0069-1

    authors: Toperoff G,Kark JD,Aran D,Nassar H,Ahmad WA,Sinnreich R,Azaiza D,Glaser B,Hellman A

    更新日期:2015-03-28 00:00:00

  • Comparative DNA methylomic analyses reveal potential origins of novel epigenetic biomarkers of insulin resistance in monocytes from virally suppressed HIV-infected adults.

    abstract:BACKGROUND:Compared to healthy individuals, those with stably repressed HIV experience a higher risk of developing insulin resistance, a hallmark of pre-diabetes and a major determinant for cardiometabolic diseases. Although epigenetic processes, including in particular DNA methylation, appear to be dysregulated in ind...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-019-0694-1

    authors: Dye CK,Corley MJ,Li D,Khadka VS,Mitchell BI,Sultana R,Lum-Jones A,Shikuma CM,Ndhlovu LC,Maunakea AK

    更新日期:2019-06-28 00:00:00

  • Integrative DNA methylome analysis of pan-cancer biomarkers in cancer discordant monozygotic twin-pairs.

    abstract:BACKGROUND:A key focus in cancer research is the discovery of biomarkers that accurately diagnose early lesions in non-invasive tissues. Several studies have identified malignancy-associated DNA methylation changes in blood, yet no general cancer biomarker has been identified to date. Here, we explore the potential of ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-016-0172-y

    authors: Roos L,van Dongen J,Bell CG,Burri A,Deloukas P,Boomsma DI,Spector TD,Bell JT

    更新日期:2016-01-20 00:00:00

  • Bronchial biopsy specimen as a surrogate for DNA methylation analysis in inoperable lung cancer.

    abstract:Background:This study was aimed at understanding whether bronchial biopsy specimen can be used as a surrogate for DNA methylation analysis in surgically resected lung cancer. Methods:A genome-wide methylation was analyzed in 42 surgically resected tumor tissues, 136 bronchial washing, 12 sputum, and 8 bronchial biopsy...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-017-0432-5

    authors: Um SW,Kim HK,Kim Y,Lee BB,Kim D,Han J,Kim H,Shim YM,Kim DH

    更新日期:2017-12-20 00:00:00

  • T cell epigenetic remodeling and accelerated epigenetic aging are linked to long-term immune alterations in childhood cancer survivors.

    abstract:BACKGROUND:Cancer treatments have substantially improved childhood cancer survival but are accompanied by long-term complications, notably chronic inflammatory diseases. We hypothesize that cancer treatments could lead to long-term epigenetic changes in immune cells, resulting in increased prevalence of inflammatory di...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-018-0561-5

    authors: Daniel S,Nylander V,Ingerslev LR,Zhong L,Fabre O,Clifford B,Johnston K,Cohn RJ,Barres R,Simar D

    更新日期:2018-11-06 00:00:00

  • Epigenomic profiling of prostate cancer identifies differentially methylated genes in TMPRSS2:ERG fusion-positive versus fusion-negative tumors.

    abstract:BACKGROUND:About half of all prostate cancers harbor the TMPRSS2:ERG (T2E) gene fusion. While T2E-positive and T2E-negative tumors represent specific molecular subtypes of prostate cancer (PCa), previous studies have not yet comprehensively investigated how these tumor subtypes differ at the epigenetic level. We theref...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-015-0161-6

    authors: Geybels MS,Alumkal JJ,Luedeke M,Rinckleb A,Zhao S,Shui IM,Bibikova M,Klotzle B,van den Brandt PA,Ostrander EA,Fan JB,Feng Z,Maier C,Stanford JL

    更新日期:2015-12-12 00:00:00

  • Genome-wide blood DNA methylation alterations at regulatory elements and heterochromatic regions in monozygotic twins discordant for obesity and liver fat.

    abstract:BACKGROUND:The current epidemic of obesity and associated diseases calls for swift actions to better understand the mechanisms by which genetics and environmental factors affect metabolic health in humans. Monozygotic (MZ) twin pairs showing discordance for obesity suggest that epigenetic influences represent one such ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-015-0073-5

    authors: Ollikainen M,Ismail K,Gervin K,Kyllönen A,Hakkarainen A,Lundbom J,Järvinen EA,Harris JR,Lundbom N,Rissanen A,Lyle R,Pietiläinen KH,Kaprio J

    更新日期:2015-04-02 00:00:00

  • SLCO4C1 promoter methylation is a potential biomarker for prognosis associated with biochemical recurrence-free survival after radical prostatectomy.

    abstract:BACKGROUND:Prostate cancer (PC) is a commonly diagnosed malignancy in males, especially in the western hemisphere. The extensive use of multiple biomarkers plays an important role in the diagnosis and prognosis of PC. However, the accuracy of biomarkers for PC prognosis needs to be urgently improved. This study aimed t...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-019-0693-2

    authors: Li X,Zhang W,Song J,Zhang X,Ran L,He Y

    更新日期:2019-07-09 00:00:00

  • Individual epigenetic status of the pathogenic D4Z4 macrosatellite correlates with disease in facioscapulohumeral muscular dystrophy.

    abstract:BACKGROUND:Both forms of facioscapulohumeral muscular dystrophy (FSHD) are associated with aberrant epigenetic regulation of the chromosome 4q35 D4Z4 macrosatellite. Chromatin changes due to large deletions of heterochromatin (FSHD1) or mutations in chromatin regulatory proteins (FSHD2) lead to relaxation of epigenetic...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-015-0072-6

    authors: Jones TI,King OD,Himeda CL,Homma S,Chen JC,Beermann ML,Yan C,Emerson CP Jr,Miller JB,Wagner KR,Jones PL

    更新日期:2015-03-29 00:00:00

  • Is Friedreich ataxia an epigenetic disorder?

    abstract:: Friedreich ataxia (FRDA) is a debilitating and frequently fatal neurological disorder that is recessively inherited. It belongs to the group of genetic disorders known as the Repeat Expansion Diseases, in which pathology arises from the deleterious consequences of the inheritance of a tandem repeat array whose repeat...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/1868-7083-4-2

    authors: Kumari D,Usdin K

    更新日期:2012-01-30 00:00:00

  • Changes in DNA methylation at the aryl hydrocarbon receptor repressor may be a new biomarker for smoking.

    abstract:BACKGROUND:Smoking is the largest preventable cause of morbidity and mortality in the United States. In previous work, we demonstrated that altered DNA methylation at the aryl hydrocarbon receptor repressor (AHRR) is correlated with self-reported smoking in 19-year-old African Americans with relatively low levels of sm...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/1868-7083-5-19

    authors: Philibert RA,Beach SR,Lei MK,Brody GH

    更新日期:2013-10-11 00:00:00

  • Epigenetic regulation of AXL and risk of childhood asthma symptoms.

    abstract:Background:AXL is one of the TAM (TYRO3, AXL and MERTK) receptor tyrosine kinases and may affect numerous immune-related health conditions. However, the role for AXL in asthma, including its epigenetic regulation, has not been extensively studied. Methods:We investigated the association between AXL DNA methylation at ...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-017-0421-8

    authors: Gao L,Millstein J,Siegmund KD,Dubeau L,Maguire R,Gilliland FD,Murphy SK,Hoyo C,Breton CV

    更新日期:2017-11-07 00:00:00

  • Genome-wide assessment of DNA methylation in mouse oocytes reveals effects associated with in vitro growth, superovulation, and sexual maturity.

    abstract:BACKGROUND:In vitro follicle culture (IFC), as applied in the mouse system, allows the growth and maturation of a large number of immature preantral follicles to become mature and competent oocytes. In the human oncofertility clinic, there is increasing interest in developing this technique as an alternative to ovarian...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-019-0794-y

    authors: Saenz-de-Juano MD,Ivanova E,Billooye K,Herta AC,Smitz J,Kelsey G,Anckaert E

    更新日期:2019-12-19 00:00:00

  • Maternal B vitamins: effects on offspring weight and DNA methylation at genomically imprinted domains.

    abstract:BACKGROUND:Inadequate maternal nutrition during early fetal development can create permanent alterations in the offspring, leading to poor health outcomes. While nutrients involved in one-carbon cycle metabolism are important to fetal growth, associations with specific nutrients remain inconsistent. This study estimate...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-016-0174-9

    authors: McCullough LE,Miller EE,Mendez MA,Murtha AP,Murphy SK,Hoyo C

    更新日期:2016-01-22 00:00:00

  • Association between variation of circulating 25-OH vitamin D and methylation of secreted frizzled-related protein 2 in colorectal cancer.

    abstract:BACKGROUNDS:Colorectal cancer (CRC) results from the accumulation of epigenetic and genetic changes in colon cells during neoplasic transformation, which the activation of Wingless (Wnt) signaling pathway is a common mechanism for CRC initiation. The Wnt pathway is mainly regulated by Wnt antagonists, as secreted frizz...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-020-00875-9

    authors: Boughanem H,Cabrera-Mulero A,Hernández-Alonso P,Clemente-Postigo M,Casanueva FF,Tinahones FJ,Morcillo S,Crujeiras AB,Macias-Gonzalez M

    更新日期:2020-06-09 00:00:00

  • Association of DNA methylation with age, gender, and smoking in an Arab population.

    abstract:BACKGROUND:Modification of DNA by methylation of cytosines at CpG dinucleotides is a widespread phenomenon that leads to changes in gene expression, thereby influencing and regulating many biological processes. Recent technical advances in the genome-wide determination of single-base DNA-methylation enabled epigenome-w...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-014-0040-6

    authors: Zaghlool SB,Al-Shafai M,Al Muftah WA,Kumar P,Falchi M,Suhre K

    更新日期:2015-01-22 00:00:00

  • Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis.

    abstract:BACKGROUND:Despite the significant global loss of DNA hydroxymethylation marks in prostate cancer tissues, the locus-specific role of hydroxymethylation in prostate tumorigenesis is unknown. We characterized hydroxymethylation and methylation marks by performing whole-genome next-generation sequencing in representative...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-016-0195-4

    authors: Kamdar SN,Ho LT,Kron KJ,Isserlin R,van der Kwast T,Zlotta AR,Fleshner NE,Bader G,Bapat B

    更新日期:2016-03-15 00:00:00

  • Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration.

    abstract:BACKGROUND:Kawasaki disease (KD) is a prevalent pediatric disease worldwide and can cause coronary artery aneurysm as a severe complication. Typically, DNA methylation is thought to repress the expression of nearby genes. However, the cases in which DNA methylation promotes gene expression have been reported. In additi...

    journal_title:Clinical epigenetics

    pub_type: 杂志文章

    doi:10.1186/s13148-018-0557-1

    authors: Huang LH,Kuo HC,Pan CT,Lin YS,Huang YH,Li SC

    更新日期:2018-11-01 00:00:00