Placental DNA methylation difference in spontaneous preterm delivery
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE49504 | GEO | 2016/07/25
SECONDARY ACCESSION(S): PRJNA214055
REPOSITORIES: GEO
Similar Datasets
Project description:Genome wide placental DNA methylation profiling of full term and preterm deliveries sampled from 5 full term deliveries and 4 preterm deliveries. The Illumina HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 485,577 CpGs in formalin fixed samples. Samples included 4 placental tissues from 4 women with preterm delivery and 5 placental tissues from 5 women with full term delivery. 9 women's placental DNA (4 women had perterm deliveries and 5 women had full term deliveries) were hybridised to the Illumina HumanMethylation450 Beadchip
2016-07-25 | E-GEOD-49504 | biostudies-arrayexpress
Project description:The amniotic fluid (AF) cell-free (cf) RNA was shown to reflect physiological and pathological processes in pregnancy, but its value in prediction of spontaneous preterm delivery is unknown. Here we profiled cfRNA in AF samples collected from women who underwent transabdominal amniocentesis after an episode of spontaneous preterm labor and subsequently delivered within 24h (n=10) or later (n=28) in gestation. Expression of known placental single cell (sc) RNA-Seq signatures were quantified in AF cfRNA and compared between groups. Random forest models were applied to predict time to delivery after amniocentesis. There were 2385 genes differentially expressed in AF samples of women who delivered within 24 hours of amniocentesis compared to gestational age-matched samples from women who delivered after 24 hours of amniocentesis.Genes with cfRNA changes were associated with immune and inflammatory processes related to the onset of labor, and expression of placental scRNA-Seq signatures of immune cells were increased with imminent delivery. AF transcriptomic prediction models captured these effects and predicted delivery within 24 hours of amniocentesis (AUROC =0.81). These results may inform development of biomarkers for spontaneous preterm birth.
2021-10-01 | GSE166956 | GEO
Project description:We compared fetal membrane tissue from preterm labor deliveries to fetal tissue from preterm labor with preterm prelabor rupture of membranes (PPROM) deliveries to further explore the concept that spontaneous preterm birth can result from the initializing of two separate but overlapping pathological events. Chorioamnion, separated into amnion and chorion, was collected from gestationally age-matched cases and controls within 15 minutes of birth, and analyzed using RNA sequencing. In our study, transcriptome analysis of preterm fetal membranes revealed distinct differentially expressed genes for PPROM, separate from preterm labor. This study is the first to report transcriptome data that reflects the individual pathophysiology of amnion and chorion tissue from PPROM deliveries.
2024-03-13 | GSE243831 | GEO
Project description:Comparing miRNAs expression levels in chorioamniotic membranes from women at term in labor (TL), women at term not in labor (TNL) and women who deliverd preterm (PTLC). The goal was to see if miRNA levels are indicators of preterm delivery or spontaneous labor at term. A two-channel technology was used in this experiment in which a pooled reference RNA was used for competitive hybridization. The pooled reference was generated at Exiqon in Denmark from a mixture of several human tissues (placenta, thyroid, brain, adipose, spleen, liver, colon, skeletal muscle, ovary, kidney, heart, cervix, testes, esophagus, small intestine, prostate, trachea, thymus, bladder, lung).
2008-10-01 | E-TABM-469 | biostudies-arrayexpress
Project description:Here we propose a pilot project to examine the contribution of lipid mediators and lipidomics to preterm delivery among obese women. Preterm delivery is one of the top causes of infant morbidity and mortality. Our specific interests are in understanding risks of preterm delivery among obese women, and in particular the contribution of the inflammatory response to early preterm delivery (<32 weeks) among obese women. The inflammatory response is a known contributor to preterm delivery, and obesity is associated with inflammation and an increased risk of early preterm delivery, but the distinct contribution of aberrations in the inflammatory response to preterm delivery among obese women has not been examined previously. Most previous studies of preterm delivery and the inflammatory response have examined one or only a few of its components at once, primarily cytokines, and a few studies have examined dyslipidemia. We propose to extend these types of investigations by examining lipid mediators and conducting global lipid profiling. Lipid mediators are key regulators of inflammation and include fatty acids and their oxygenated bioactive metabolites such as oxylipins (e.g., prostaglandins, HETEs or hydroxyeicosatetraenoic acids, and other eicosanoids), ceramides and sphingoid bases including sphingosine-1-phosphate. Examination of lipid mediators and lipid profiling is particularly relevant to understanding distinct risks among obese women, given the known inter-relatedness of obesity, dyslipidemia, and inflammation. Our overarching hypothesis is that the inflammatory response impacts risk of preterm delivery and that its impact is distinct among obese versus non-obese women. Here we propose a pilot project that compares mid-pregnancy measurements of lipid mediators and lipid profiling among obese pregnant women. Findings from this pilot will provide critical preliminary data to inform larger-scope grant proposals that will comprehensively address our overarching hypothesis. Specifically, we will examine mid-pregnancy lipid mediators in obese women who deliver preterm compared to those who deliver at term. In addition, we will use untargeted global profiling of complex lipids to determine whether obese women who deliver preterm have a distinct lipidomic signature, relative to obese women who deliver at term. We propose a nested case-control study that utilizes maternal mid-pregnancy (15-20 weeks gestation) serum samples from a biobank that represents over one million deliveries in California from 2007-2012. We propose to examine 50 obese women who delivered preterm and 50 who delivered at term. This will provide adequate preliminary data for a larger-scale grant proposal.
2017-07-20 | ST000811 | MetabolomicsWorkbench
Project description:Here we propose a pilot project to examine the contribution of lipid mediators and lipidomics to preterm delivery among obese women. Preterm delivery is one of the top causes of infant morbidity and mortality. Our specific interests are in understanding risks of preterm delivery among obese women, and in particular the contribution of the inflammatory response to early preterm delivery (<32 weeks) among obese women. The inflammatory response is a known contributor to preterm delivery, and obesity is associated with inflammation and an increased risk of early preterm delivery, but the distinct contribution of aberrations in the inflammatory response to preterm delivery among obese women has not been examined previously. Most previous studies of preterm delivery and the inflammatory response have examined one or only a few of its components at once, primarily cytokines, and a few studies have examined dyslipidemia. We propose to extend these types of investigations by examining lipid mediators and conducting global lipid profiling. Lipid mediators are key regulators of inflammation and include fatty acids and their oxygenated bioactive metabolites such as oxylipins (e.g., prostaglandins, HETEs or hydroxyeicosatetraenoic acids, and other eicosanoids), ceramides and sphingoid bases including sphingosine-1-phosphate. Examination of lipid mediators and lipid profiling is particularly relevant to understanding distinct risks among obese women, given the known inter-relatedness of obesity, dyslipidemia, and inflammation. Our overarching hypothesis is that the inflammatory response impacts risk of preterm delivery and that its impact is distinct among obese versus non-obese women. Here we propose a pilot project that compares mid-pregnancy measurements of lipid mediators and lipid profiling among obese pregnant women. Findings from this pilot will provide critical preliminary data to inform larger-scope grant proposals that will comprehensively address our overarching hypothesis. Specifically, we will examine mid-pregnancy lipid mediators in obese women who deliver preterm compared to those who deliver at term. In addition, we will use untargeted global profiling of complex lipids to determine whether obese women who deliver preterm have a distinct lipidomic signature, relative to obese women who deliver at term. We propose a nested case-control study that utilizes maternal mid-pregnancy (15-20 weeks gestation) serum samples from a biobank that represents over one million deliveries in California from 2007-2012. We propose to examine 50 obese women who delivered preterm and 50 who delivered at term. This will provide adequate preliminary data for a larger-scale grant proposal.
2017-07-20 | ST000809 | MetabolomicsWorkbench
Project description:Here we propose a pilot project to examine the contribution of lipid mediators and lipidomics to preterm delivery among obese women. Preterm delivery is one of the top causes of infant morbidity and mortality. Our specific interests are in understanding risks of preterm delivery among obese women, and in particular the contribution of the inflammatory response to early preterm delivery (<32 weeks) among obese women. The inflammatory response is a known contributor to preterm delivery, and obesity is associated with inflammation and an increased risk of early preterm delivery, but the distinct contribution of aberrations in the inflammatory response to preterm delivery among obese women has not been examined previously. Most previous studies of preterm delivery and the inflammatory response have examined one or only a few of its components at once, primarily cytokines, and a few studies have examined dyslipidemia. We propose to extend these types of investigations by examining lipid mediators and conducting global lipid profiling. Lipid mediators are key regulators of inflammation and include fatty acids and their oxygenated bioactive metabolites such as oxylipins (e.g., prostaglandins, HETEs or hydroxyeicosatetraenoic acids, and other eicosanoids), ceramides and sphingoid bases including sphingosine-1-phosphate. Examination of lipid mediators and lipid profiling is particularly relevant to understanding distinct risks among obese women, given the known inter-relatedness of obesity, dyslipidemia, and inflammation. Our overarching hypothesis is that the inflammatory response impacts risk of preterm delivery and that its impact is distinct among obese versus non-obese women. Here we propose a pilot project that compares mid-pregnancy measurements of lipid mediators and lipid profiling among obese pregnant women. Findings from this pilot will provide critical preliminary data to inform larger-scope grant proposals that will comprehensively address our overarching hypothesis. Specifically, we will examine mid-pregnancy lipid mediators in obese women who deliver preterm compared to those who deliver at term. In addition, we will use untargeted global profiling of complex lipids to determine whether obese women who deliver preterm have a distinct lipidomic signature, relative to obese women who deliver at term. We propose a nested case-control study that utilizes maternal mid-pregnancy (15-20 weeks gestation) serum samples from a biobank that represents over one million deliveries in California from 2007-2012. We propose to examine 50 obese women who delivered preterm and 50 who delivered at term. This will provide adequate preliminary data for a larger-scale grant proposal.
2017-07-20 | ST000810 | MetabolomicsWorkbench
Project description:Threatened preterm labour (TPTL) is the most common condition that requires hospitalisation during pregnancy. Most of these symptomatic women continue their pregnancies to term while only an estimated 5% will deliver a premature baby within ten days. Peripheral blood leukocytes are exposed to “activating signals” from reproductive tissues and may indicate the impending onset of labour. Objectives: 1) To investigate differential leukocyte gene expression in women with TPTL; and 2) to develop a gene signature to predict preterm birth (PTB) within 48 hours in symptomatic women. Design, Setting and Participants: Women clinically diagnosed with TPTL were recruited. Peripheral blood was obtained at point of admission prior to medical treatments. mRNA was extracted and microarrays (Affymetrix U133 Plus 2.0) were utilised to determine differential gene expressions between women who did (n=48) and did not (n=106) have a preterm delivery within 48 hours of hospital admission. Results: There were 394 significantly differentially expressed genes (FDR<0.05, Limma); 22 out of 30 genes chosen for qRT-PCR validation were differentially expressed (p<0.05). Total 154; 48 delivered within 48 hours of hospital admission; 106 did not deliver within 48 hours
2014-05-15 | E-GEOD-46510 | biostudies-arrayexpress
Project description:Preterm birth is a main determinant of neonatal mortality and morbidity and a major contributor to the overall mortality and burden of disease. However, precise phenotyping of the preterm birth is hampered by the imprecise definition of the clinical phenotype and complexity of the molecular phenotype due to multiple pregnancy tissue types and molecular processes that may contribute to the preterm birth. The studyâ??s aim was to comprehensively evaluate the mRNA transcriptome that characterizes preterm and term labor using precisely phenotyped samples. Expression profiles of 73 genes and non-coding RNA sequences uniquely identified the four groups of patients: delivering preterm with (PL) and without labor (PNL), term with (TL) and without labor (TNL). The largest differences in gene expression among the four groups occurred in decidua, chorion and amnion. The gene expression profiles showed suppression of chemokines expression in TNL, withdrawal of this suppression in TL, activation of multiple pathways of inflammation in PL, and an immune rejection profile in PNL. The genes constituting expression signatures showed over-representation of three putative regulatory elements in their 5â?? and 3â??UTR regions. The results suggest that pregnancy is maintained by downregulation of chemokines at the maternal-fetal interface. Withdrawal of this downregulation results in the term birth and its overriding by the activation of multiple pathways of the immune system in the preterm birth. Complications of the pregnancy associated with impairment of placental function, which necessitated premature delivery of the fetus in the absence of labor, show gene expression patterns associated with immune rejection. 183 total RNA samples from 8 tissue types collected from 35 women grouped into six categories of pregnancy outcome. One microarray replicate per sample. Other Contributors: Radek Bukowski, Sam Parry and the NICHD Genomic and Proteomic Network for Preterm Birth Research
2016-06-30 | E-GEOD-73685 | biostudies-arrayexpress
Project description:We hypothesized that preterm spontaneous labor involves aberrant changes in mRNA expression in the placenta. To test this hypothesis, we interrogated the mRNA levels of >50,000 genes and transcript variants using gene expression microarray (Human Genome U133 Plus 2.0 Array, Affymetrix) on 5 placentas collected from preterm spontaneous delivery (<34 weeks of gestation) and another 5 placentas collected from term spontaneous delivery (38-39 weeks). We have identified 229 and 162 genes that were up- or down-regulated, respectively, for more than 3-fold in the preterm placentas compared to the term placentas (Mann-Whitney Rank Sum Test, with multiple testing correction by the Benjamini-Hochberg method, adjusted p-value <= 0.05). Placentas collected from (i) preterm spontaneous delivery (<34 weeks of gestation) and (ii) term spontaneous delivery (38-39 weeks of gestation) were subjected to RNA extraction and hybridization on Affymetrix microarrays. To identify gene expression patterns that are commonly involved in preterm spontaneous labour, we analyzed 5 placentas from each of these 2 groups and tested for any differentially expressed genes by Mann-Whitney Rank Sum Test.
2009-10-31 | E-GEOD-18809 | biostudies-arrayexpress