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The DNA Methylation patterns of ART and naturally conceived pregnancies

ABSTRACT: The DNA Methylation patterns of ART and naturally conceived pregnancies

PROVIDER: PRJNA597363 | ENA |

REPOSITORIES: ENA

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The DNA Methylation patterns of ART and naturally conceived pregnancies

Project description:Genome wide DNA methylation profiling of normal and ART newborn. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples included 6 normal newborn heelblood, 6 ART newborn heelblood.

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Impact of Assisted Reproduction, Infertility, Sex, and Paternal Factors on the Placental DNA Methylome

Project description:Children conceived using Assisted Reproductive Technologies (ART) have a higher incidence of growth and birth defects, attributable in part to epigenetic perturbations. Both ART and germline defects associated with parental infertility could interfere with epigenetic reprogramming events in germ cells or early embryos. Mouse models indicate that the placenta is more susceptible to the induction of epigenetic abnormalities than the embryo, and thus the placental methylome may provide a sensitive indicator of ‘at risk’ conceptuses. Our goal was to use genome-wide profiling to examine the extent of epigenetic abnormalities in matched placentas from an ART/infertility group and control singleton pregnancies (n=44/group) from a human prospective longitudinal birth cohort, the 3D Study. Principal component analysis revealed a group of ART outliers. The ART outlier group was enriched for females and a subset of placentas showing loss of methylation of several imprinted genes including GNAS, SGCE, KCNQT1OT1 and BLCAP/NNAT. Within the ART group, placentas from pregnancies conceived with IVF/ICSI showed distinct epigenetic profiles as compared to those conceived with less invasive procedures (ovulation induction, intrauterine insemination). Male factor infertility and paternal age further differentiated the IVF/ICSI group, suggesting an interaction of infertility and techniques in perturbing the placental epigenome. Together, the results suggest that the human placenta is sensitive to the induction of epigenetic defects by ART and/or infertility, and we stress the importance of considering both sex and paternal factors and that some but not all ART conceptuses will be susceptible.

2018-10-01 | GSE120250 | GEO

Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies.

Project description: Not available

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Differential gene expression during placentation in pregnancies conceived with different fertility treatments compared with spontaneous pregnancies

Project description:This SMAART cohort study uses bulk total RNA-sequencing to assses the impact of mode of conception on first trimester human placenta gene expression [PMID: 30611556]. Pregnancies were singleton, gestational age 10-14 weeks, normal karyotype, fetal race Caucasian or biracial Caucasian/Asian, and conceived either with fertility treatments (IVF=in vitro fertilization, NIFT=non-IVF fertility treatment) or without fertility treatments (spontaneous, also called unassisted). Pregnancies were balanced for fetal sex. Chorionic villi tissue leftover after clinical genetic testing was collected for research with informed consent and stored in RNAlater RNA Stabilization Reagent (QIAGEN) at -80C until RNA isolation with the AllPrep DNA/RNA Mini Kit (QIAGEN). RNA-seq libraries of >200 nt were constructed with Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold sample prep kits (Illumina) and depleted of cytoplasmic and mitochondrial ribosomal RNAs. After quality check with FastQC, transcript abundances were quantified against the human reference genome (Ensembl build GRCh38) using Kallisto. Differential expression analysis with DESeq2 was performed to compare mode of conception, adjusted for fetal sex and RNA-seq dataset. The dataset adjustment corrected for batch effects from RNA isolation and/or sequencing runs. There were N=141 subjects total, including 74 spontaneous, 33 non-IVF (NIFT), and 34 IVF pregnancies. The subject columns at the end of the DESeq2 files are counts normalized for sequencing depth.

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Differential Gene Expression in HIV-Infected Individuals Following ART.

Project description:A paired analysis of peripheral blood mononuclear cells (PBMCs) isolated before and after antiretroviral therapy (ART) from a robust number of HIV-infected patients (N=36). Results identify a total of 4,157 DEGs following ART in HIV-infected participants and the transition from a period of active virus replication before ART to one of viral suppression This study evaluated PBMC gene expression in cells from 36 (4 dropped from analysis) recently HIV-infected individuals to identify differentially expressed genes following 48 weeks of ART

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Expression profile for overproduction of ArT

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Integrated Analysis of Hub Genes and MicroRNAs in Human Placental Tissues from In Vitro Fertilization-Embryo Transfer [RNA-seq]

Project description:Next generation sequencing was perfomed to identify differentially expressed gene in Placental tissue samples from IVF-ET assisted or natural conceived pregnancies

2021-10-21 | GSE186147 | GEO

siRNA profiling of human steroid-deprived LNCaP cells were transfected with control or ART-27 siRNA to investigate the genome-wide impact of ART-27 loss on androgen-regulated transcription

Project description:The androgen receptor (AR) directs diverse biological processes through interaction with coregulators such as androgen receptor trapped clone-27 (ART-27). The impact of ART-27 on genome-wide transcription was examined. The studies indicate that loss of ART-27 enhances expression of many androgen-regulated genes, suggesting that ART-27 inhibits gene expression. Surprisingly, classes of genes that are upregulated upon ART-27 depletion include regulators of DNA damage checkpoint and cell cycle progression, suggesting that ART-27 functions to keep expression levels of these genes low. Experiment Overall Design: Steroid-deprived LNCaP cells were transfected with control or ART-27 siRNA and stimulated with ethanol vehicle or 10 nM R1881 for 18 hrs. 8 samples, 4 conditions, 2 replicates per condition.

2009-06-08 | E-GEOD-14043 | biostudies-arrayexpress

Integrated Analysis of Hub Genes and MicroRNAs in Human Placental Tissues from In Vitro Fertilization-Embryo Transfer [miRNA-seq]

Project description:Next generation sequencing was perfomed to identify differentially expressed micro-RNA in Placental tissue samples from IVF-ET assisted or natural conceived pregnancies

2021-10-21 | GSE186148 | GEO

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