Integrative analysis of DNA methylation and gene expression data among preterm and/or small for gestational age infants during perinatal period [methylation]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE110828 | GEO | 2021/02/09
REPOSITORIES: GEO
Similar Datasets
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 | GSE110822 | GEO
Project description:BACKGROUND: Babies born at lower gestational ages or smaller birthweights have a greater risk of poorer health in later life. Both the causes of these sub-optimal birth outcomes and the mechanism by which the effects are transmitted over decades are the subject of extensive study. We investigated whether a transcriptomic signature of either birthweight or gestational age could be detected in umbilical cord RNA. METHODS: The gene expression patterns of 32 umbilical cords from Singaporean babies of Chinese ethnicity across a range of birthweights (BW, 1698-4151g) and gestational ages (GA, 35-41 weeks) were determined. We confirmed the differential expression pattern by gestational age for 12 genes in a series of 127 umbilical cords of Chinese, Malay and Indian ethnicity. RESULTS: We found that the transcriptome is substantially influenced by gestational age; but less so by birthweight. We show that some of the expression changes dependent on gestational age are enriched in signal transduction pathways, such as Hedgehog and in genes with roles in cytokine signalling and angiogenesis. We show that some of the gene expression changes we report are reflected in the epigenome. CONCLUSIONS: We studied the umbilical cord which is peripheral to disease susceptible tissues. The results suggest that soma-wide transcriptome changes, preserved at the epigenetic level, may be a mechanism whereby birth outcomes are linked to the risk of adult metabolic and arthritic disease and suggest that greater attention be given to the association between premature birth and later disease risk. 8 umbilical cords form low birth weight babies, 8 umbilical cords from high birth weight babies, 14 umbilical cords from normal birth weigth babies, 7 matching the gestational ages of the low birth weigth group (norm1) and 7 matching the getsational ages of the high birth weight group (norm2). Replicates for array, cRNA and slide spotting REPLICATES: biological replicate: LBW_1, LBW_2, LBW_3A, LBW_3B, LBW_3C, LBW_4, LBW_5, LBW_6, LBW_7, LBW_8A, LBW_8B biological replicate: HBW_1, HBW_2A, HBW_2B, HBW_2C, HBW3, HBW4, HBW5, HBW6, HBW7, HBW8 biological replicate: norm1_1, norm1_2, norm1_3, norm1_4, norm1_5, norm1_7A, norm1_7B, norm1_7C, norm1_7D biological replicate: norm2_1, norm2_2, norm2_3, norm2_4, norm2_5, norm2_6A, norm2_6B, norm2_7 technical replicate: HBW_2A, HBW_2B, HBW_2C technical replicate: LBW_3A, LBW_3B, LBW_3C technical replicate: LBW_8A, LBW_8B techical replicate: norm1_7A, norm1_7B, norm1_7C, norm1_7D technical repliacte: norm2_6A, norm2_6B
2012-09-24 | E-GEOD-37100 | biostudies-arrayexpress
Project description:A prospective study was conducted in the Neonatal Intensive Care Unit of the University Children's hospital between September 1, 2008 and November 30, 2010. The entry criteria were (1) preterm birth below 32 weeks gestational age, (2) birthweight<1500g (VLBW). During the follow-up period, bronchopulmonary dysplasia (BPD) was diagnosed in 68 (61%) infants, including 40 (36%) children with mild disease, 13 (12%) with moderate and 15 (13%) with severe BPD. Forty-three babies served as a control group (no BPD).
2011-11-01 | GSE32472 | GEO
Project description:BACKGROUND: Babies born at lower gestational ages or smaller birthweights have a greater risk of poorer health in later life. Both the causes of these sub-optimal birth outcomes and the mechanism by which the effects are transmitted over decades are the subject of extensive study. We investigated whether a transcriptomic signature of either birthweight or gestational age could be detected in umbilical cord RNA. METHODS: The gene expression patterns of 32 umbilical cords from Singaporean babies of Chinese ethnicity across a range of birthweights (BW, 1698-4151g) and gestational ages (GA, 35-41 weeks) were determined. We confirmed the differential expression pattern by gestational age for 12 genes in a series of 127 umbilical cords of Chinese, Malay and Indian ethnicity. RESULTS: We found that the transcriptome is substantially influenced by gestational age; but less so by birthweight. We show that some of the expression changes dependent on gestational age are enriched in signal transduction pathways, such as Hedgehog and in genes with roles in cytokine signalling and angiogenesis. We show that some of the gene expression changes we report are reflected in the epigenome. CONCLUSIONS: We studied the umbilical cord which is peripheral to disease susceptible tissues. The results suggest that soma-wide transcriptome changes, preserved at the epigenetic level, may be a mechanism whereby birth outcomes are linked to the risk of adult metabolic and arthritic disease and suggest that greater attention be given to the association between premature birth and later disease risk.
2012-09-24 | GSE37100 | GEO
Project description:A prospective study was conducted in the Neonatal Intensive Care Unit of the University Children's hospital between September 1, 2008 and November 30, 2010. The entry criteria were (1) preterm birth below 32 weeks gestational age, (2) birthweight<1500g (VLBW). During the follow-up period, bronchopulmonary dysplasia (BPD) was diagnosed in 68 (61%) infants, including 40 (36%) children with mild disease, 13 (12%) with moderate and 15 (13%) with severe BPD. Forty-three babies served as a control group (no BPD). One hundred twenty newborns were included at the start of the study. Three blood samples (0.3 ml) were drawn from all the study participants for microarray assessment of gene expression profiles around the 5th, 14th and 28th days of life. Note that microarrays were not taken for all patients at all time points (A,B,C).
2011-11-01 | E-GEOD-32472 | biostudies-arrayexpress
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
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. Peripheral blood DNA (at days 14 and 28) from preterm neonates that went on to develop BPD (n = 14) or not (nonBPD, n = 93) was applied to Illumina EPIC 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 at different time points.
2023-07-05 | GSE225313 | GEO
Project description:This study contrasts the expression profiles of peripheral blood leukocytes from third trimester pregnant mothers, with cord blood leukocytes from their newborn children. It is a companion to (GSE21311). After normalization for RNA integrity, major principal components of the variation were found to distinguish individuals. Transmission of gene expression profiles from mother to child was documented, along with differences between gestational diabetic, obese, and normal weight mothers and their children. 56 individulas (Brisbane, Australia) were sampled for the mother-newborn study, under informed consent. 19 mothers sample were collected in the last month of pregnancy (between 30th and 36th week of pregnancy) and 37 cord blood samples were obtained at birth from newborn babies. Mothers having BMI values over 30 before pregnancy were classified as obese. From the 37 newborn babies, 10 were born to obese mothers, 8 to gestational diabetic mothers (with a wide range of body mass indices), and 19 to normal-weight mothers. There were 16 mother-newborn pairs in the dataset. RNA from each was hybridized to an Illumina HT12 array.
2011-01-01 | E-GEOD-21342 | biostudies-arrayexpress
Project description:<p><strong>BACKGROUND:</strong> Birthweight reflects in utero exposures and later health evolution. Despite existing studies employing high-dimensional molecular measurements, the understanding of underlying mechanisms of birthweight remains limited.</p><p><strong>METHODS:</strong> To investigate the systems biology of birthweight, we cross-sectionally integrated the methylome, the transcriptome, the metabolome and a set of inflammatory proteins measured in cord blood samples, collected from four birth-cohorts (n=489). We focused on two sets of 68 metabolites and 903 CpGs previously related to birthweight and investigated the correlation structures existing between these two sets and all other omic features via bipartite Pearson correlations.</p><p><strong>RESULTS:</strong> This dataset revealed that the set of metabolome and methylome signatures of birthweight have seven signals in common, including three metabolites [PC(34:2), plasmalogen PC(36:4)/PC(O-36:5), and a compound with m/z of 781.0545], two CpGs (on the DHCR24 and SC4MOL gene), and two proteins (periostin and CCL22). CCL22, a macrophage-derived chemokine has not been previously identified in relation to birthweight. Since the results of the omics integration indicated the central role of cholesterol metabolism, we explored the association of cholesterol levels in cord blood with birthweight in the ENVIRONAGE cohort (n=1,097), finding that higher birthweight was associated with increased high-density lipoprotein cholesterol and that high-density lipoprotein cholesterol was lower in small versus large for gestational age newborns.</p><p><strong>CONCLUSIONS:</strong> Our data suggests that an integration of different omic-layers in addition to single omics studies is a useful approach to generate new hypotheses regarding biological mechanisms. CCL22 and cholesterol metabolism in cord blood play a mechanistic role in birthweight.</p>
2020-06-19 | MTBLS1684 | MetaboLights
Project description:Birthweight reflects in utero exposures and later health evolution. Despite existing studies employing high-dimensional molecular measurements, the understanding of underlying mechanisms of birthweight remains limited. To investigate the systems biology of birthweight, we cross-sectionally integrated the methylome, the transcriptome, the metabolome and a set of inflammatory proteins measured in cord blood samples, collected from four birth-cohorts (n=489). We focused on two sets of 68 metabolites and 903 CpGs previously related to birthweight and investigated the correlation structures existing between these two sets and all other omic features via bipartite Pearson correlations. This dataset revealed that the set of metabolome and methylome signatures of birthweight have seven signals in common, including three metabolites [PC(34:2), plasmalogen PC(36:4)/PC(O-36:5), and a compound with m/z of 781.0545], two CpGs (on the DHCR24 and SC4MOL gene), and two proteins (periostin and CCL22). CCL22, a macrophage-derived chemokine has not been previously identified in relation to birthweight. Since the results of the omics integration indicated the central role of cholesterol metabolism, we explored the association of cholesterol levels in cord blood with birthweight in the ENVIRONAGE cohort (n=1,097), finding that higher birthweight was associated with increased high-density lipoprotein cholesterol and that high-density lipoprotein cholesterol was lower in small versus large for gestational age newborns. Our data suggests that an integration of different omic-layers in addition to single omics studies is a useful approach to generate new hypotheses regarding biological mechanisms. CCL22 and cholesterol metabolism in cord blood play a mechanistic role in birthweight.
2020-06-19 | GSE151042 | GEO