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Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period

ABSTRACT: Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period

PROVIDER: PRJNA434671 | ENA |

REPOSITORIES: ENA

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Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]

Project description:Preterm or small for gestational age (SGA) infants are to be at high risk of noncommunicable diseases in adolescence, because they are exposed to hypoxia and malnutrition in and ex utero during perinatal period. Epigenetics could be one of the most important mechanisms of DOHaD.In the field of premature babies, previous studies investigated the methylation alterations related to gestational age and birthweight by using cord blood samples. In the field of preterm or SGA babies, there were few EWAS studies that examine whether methylation changes relate to RNA expression using cord blood samples, and the interpretation of postnatal blood methylation were different by studies.The objective is to investigate the epigenetic alterations associated with preterm birth and SGA by using methylation and expression microarray, and to explore the epigenetic changes which may persist after birth.

2021-02-09 | GSE110828 | GEO

Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [expression]

2021-02-09 | GSE110822 | GEO

Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [expression]

Project description:Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [expression]

| PRJNA434653 | ENA

Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]

Project description:Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]

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RNA-seq of peripheral whole blood from ten healthy preterm infants and ten preterm infants with bronchopulmonary dysplasia

Project description:We procured peripheral whole blood from ten healthy preterm infants and ten preterm infants with bronchopulmonary dysplasia

2024-10-27 | E-MTAB-14506 | biostudies-arrayexpress

Whole blood transcriptional responses of very preterm infants during late-onset sepsis

Project description:Host immune responses during late-onset sepsis (LOS) in very preterm infants are poorly characterised due to a complex and dynamic pathophysiology and challenges in working with small available blood volumes. We present here an unbiased transcriptomic analysis of whole peripheral blood from very preterm infants at the time of LOS. RNA-Seq was performed on peripheral blood samples (6 – 29 days postnatal age) taken at the time of suspected LOS from very preterm infants <30 weeks gestational age. Infants were classified based on blood culture positivity and elevated C-reactive protein concentrations as having confirmed LOS (n=5), possible LOS (n=4) or no LOS (n=9). Bioinformatics and statistical analyses performed included pathway over-representation and protein-protein interaction network analyses. Plasma cytokine immunoassays were performed to validate differentially expressed cytokine pathways.The blood leukocyte transcriptional responses of infants with confirmed LOS differed significantly from infants without LOS (1,317 differentially expressed genes). However, infants with possible LOS could not be distinguished from infants with no LOS or confirmed LOS. Transcriptional alterations associated with LOS included genes involved in pathogen recognition (mainly TLR pathways), cytokine signalling (both pro-inflammatory and inhibitory responses), immune and haematological regulation (including cell death pathways), and metabolism (altered cholesterol biosynthesis). At the transcriptional-level cytokine responses during LOS were characterised by over-representation of IFN-α/β, IFN-γ, IL-1 and IL-6 signalling pathways and up-regulation of genes for inflammatory responses. Infants with confirmed LOS had significantly higher levels of IL-1α and IL-6 in their plasma. Blood responses in very preterm infants with LOS are characterised by altered host immune responses that appear to reflect unbalanced immuno-metabolic homeostasis.

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Genomics of the ovine heart ontogeny during the perinatal period

Project description:The period of development from the last two weeks of gestation through the first two weeks of life spans a period of great functional and metabolic challenge to the fetal and neonatal lamb heart. Important changes in gene expression occur to meet these challenges. On this study, septa from sheep hearts at 130 days gestation (n=6), term (n=8, gestational lenght is around 145 days) and 14-days-old lambs (n=8) were used to model the changes in gene expression patterns during the perinatal period using Agilent 15k ovine microarrays. Weighted gene co-expression network analysis (WGCNA) determined five major patterns of co-expressed and functionally related genes during this critical period of cardiac transition. Septum samples from the heart were collected from non-treated fetuses at 130 days of gestational age (GA130d, n=6) and term (n=8); and from naturally born 14-days-old lambs (Lamb, n=8). None of the ewes suffered gestational diseases or showed signs of impending labor.

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Single-cell RNA sequencing of PBMCs from five healthy (HC) preterm infants and ten preterm infants with bronchopulmonary dysplasia(BPD)

Project description:We procured PBMCs whole blood from five HC preterm infants and five preterm infants with BPD. PBMCs were extracted using a density gradient centrifugation method. Initially, 10ml of peripheral blood was mixed with an equal volume of physiological saline, then carefully layered onto Ficoll solution (T10124, from Shangbao Biotech Co., Ltd., Shanghai). After centrifugation at 2,000 rpm for 20 minutes, the cells stratified due to differences in density, with PBMCs positioned between the red blood cells and plasma. Subsequently, the intermediate layer containing PBMCs was gently collected, washed several times with physiological saline to remove residual medium and red blood cells, and finally, PBMCs were isolated and collected through centrifugation.

2024-10-20 | E-MTAB-14507 | biostudies-arrayexpress

Cord blood methylation profiles of bronchopulmonary dysplasia in preterm infants

Project description:Bronchopulmonary dysplasia (BPD) is a lung disease in premature infants characterized by impaired pulmonary development which persists into later life. While advances in neonatal care have improved survival rates of premature infants, cases of BPD haves been increased. Therapeutic options are limited for prevention and treatment. This study was designed to explore the relationship between gestational age (GA), birth weight and estímate blood cell-type composition in premature infants and to elucidate early epigenetic biomarkers associated with BPD. Cord blood DNA from preterm neonates that went on to develop BPD (n = 14) or not (nonBPD, n = 93) was applied to Illumina 450K methylation arrays. Using DNA methylation analysis of cord blood DNA, we investigated association of GA and birth weight with the estimated distribution of cord blood cell types, particularly the nucleated red blood cell (NRBC) in a pilot-size cohort of preterm infants with or without BPD. We describe changes in methylation-based estimates of blood cell-type composition in relation to GA and birth weight. After adjusting for covariates (GA, birth weight, cell type proportions, etc.) we identify differentially methylated CpGs and genes associated with BPD.

2022-05-05 | GSE188949 | GEO

Airway Exosomal miRNA predicts Bronchopulmonary Dysplasis in Extremely Preterm Infants

Project description:We conducted a prospective cohort study with independent Discovery and Validation cohorts, to formulate predictive biomarkers for Bronchopulmonary Dysplasia in extremely preterm infants. Tracheal aspirate samples were collected at birth from extremely preterm infants. Exosomes were extracted from tracheal aspirates and total RNA was extracted from these exosomes from individual samples. miRNA profiling for all ~ 800 miRNAs was conducted on each sample by nanostring platform. This study found that a distinct airway exosomal miRNA sigrature at birth (decreased miR 876-3p) predicts future development of severe Bronchopulmonary Dysplasia in extremely preterm infants.

2017-12-29 | GSE108604 | GEO

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