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Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [RNA-seq]

ABSTRACT: Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [RNA-seq]

PROVIDER: PRJNA934960 | ENA |

REPOSITORIES: ENA

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Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [array]

Project description:Trophectoderm biopsy for preimplantation genetic testing (TEBx) impacts placental and embryonic health during early development, with some alterations resolving while others worsening later in development. We observed that at E12.5, IVF + TEBx had a worse outcome in terms of changes in DNA methylation and differential gene expression in placentas and whole embryos compared with IVF alone. These changes were reflected in alterations in placental morphology and blood vessel density. At E18.5, early changes in embryos were maintained or worsened, while molecular and morphological changes in the placenta were not different from the IVF group, except for changes in blood vessel density, which persisted. Of note is that most differences were sex specific. We conclude that TEBx has more detrimental effects in both mid-gestation placental and embryonic tissues, with changes in embryonic tissues persisting or worsening in later developmental stages compared to IVF alone. Additionally, consistent with previous work, we report sex differences in the observed effects. Finally, we identified that the addition of vitrification after TEBx has a more pronounced detrimental effect on placental and fetal health. Our findings provide additional support that more studies should be done to assess the impact of new procedures during ART to ensure healthy pregnancies and offspring outcomes.

2024-04-24 | GSE224844 | GEO

Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [RNA-seq]

2024-04-24 | GSE225317 | GEO

Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model

Project description:Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model

| PRJNA934952 | ENA

Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [array]

| PRJNA932777 | ENA

Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-04-24 | GSE225318 | GEO

Transcriptome analysis of human blastocysts with different levels of chromosomal mosaicism after preimplantation genetic testing.

Project description:An inner cell mass biopsy and the remaining trophectoderm were separately collected from 14 blastocysts with preimplantation genetic testing result into RNAse-free PCR tubes containing 2 µl of 10X reaction buffer (SMART-Seq v4 Ultra-Low Input RNA kit for Sequencing, Takara Bio, USA). cDNA was obtained from mRNA with 3′SMART-Seq CDS primer II (Takara Bio, USA) and PCR-amplified (17 cycles) from 10 pg of RNA. Amplified cDNA was purified using AMPure XP magnetic beads (Illumina, USA). After confirming cDNA integrity on a 2100 Bioanalyzer (Agilent Technologies, USA), 1 ng of cDNA per sample were fragmented, and libraries were constructed using NexteraXT DNA sample preparation (Illumina, USA). Samples were quantified using Qubit dsDNA Quantitation Assay (Thermo Fisher Scientific, USA), and 3 samples were excluded due to poor cDNA quality. An RNA pool was generated with 25 samples using equal concentration (5 nM) of RNA per sample. Sequencing was performed in duplicate in a single run using an Illumina NovaSeq 6000 S1 platform (Illumina, USA) with a 200-nucleotide read length in a paired-end design (100-bp fragments). FastQC was used for checking the quality of the raw sequence data. Fragments that did not meet quality requirements were trimmed using Trimmomatic. Alignment and quantification were performed using the Salmon algorithm (reference genome GRCh38). Raw counts were directly used for differential gene expression analysis.

2022-01-31 | GSE194306 | GEO

Preimplantation stage-specific effect of culture environment on the DNA methylome of bovine blastocysts

Project description:The culture conditions of the early preimplantation embryos affects the DNA methylation landscape of the resulting blastocysts.

2015-10-07 | GSE69173 | GEO

Transcriptome of in vitro fertilized 7-day-old bovine blastocysts

Project description:Blastocysts consist of cells that form the inner cell mass and the trophectoderm. The full transcriptome of bovine blastocyst embryos was examined in this study. Total RNA was isolated from three independent batches of blastocysts. Using Poly(A) capture mRNA was isolated and cDNA libraries prepared using Illumina TruSeq RNA sample Prep Kit. The libraries were sequenced using Illumina HiSeq 4000. This dataset should serve as a baseline for understanding bovine pluripotency and trophoblast stem cells providing a snapshot for functional interpretation of preimplantation embryo development.

2021-10-17 | GSE169674 | GEO

The Role and Mechanism of TEAD4 in Preimplantation Embryonic Development in Mice and Cattle

Project description:Tead4 is a critical transcription factor expressed during preimplantation development and is essential for the expression of trophectoderm-specific genes in mice. However, the mechanism of Tead4’s function in mouse preimplantation development and its conservation across mammals remains unclear. Here, we report that Tead4 is a crucial transcription factor necessary for blastocyst formation in mice. Disruption of TEAD4 through base editing results in developmental arrest at the morula stage. Additionally, RNA-seq analysis reveals dysregulation of 670 genes in Tead4 knockout embryos. As anticipated, Tead4 knockout leads to a decrease in trophectoderm genes CDX2 and GATA3. Intriguingly, we observed a reduction in KRT8, suggesting that Tead4 influences the integrity of the trophectoderm epithelium in mice. More importantly, we noted a decrease in nuclear YAP for Tead4-deficient embryos, indicating that Tead4 directly regulates Hippo signaling. In contrast, bovine embryos with TEAD4 depletion can still develop to blastocysts with normal expression of CDX2, GATA3, and SOX2, albeit with a decrease in total cell number and ICM cell number. In conclusion, we propose that Tead4 regulates mouse blastocyst formation via Krt8 and Yap, both of which are critical regulators of mouse preimplantation development.

2024-07-15 | GSE237418 | GEO

Comprehensive Analysis of Karyotypic Mosaicism between Trophectoderm and Inner Cell Mass

Project description:Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. In this study our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from seventeen couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e., one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of fifty-one (96.1%) inner cell mass (ICM) samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that trophectoderm karyotype is an excellent predictor of inner cell mass karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations.

2010-09-28 | GSE22864 | GEO

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