Female-biased embryonic death from genomic instability-induced inflammation
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE119710 | GEO | 2018/12/21
REPOSITORIES: GEO
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Project description:The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at the N-terminal tails of Mcm2, Mcm4 and Mcm6. At present, it remains poorly understood how DDK docks onto the helicase and how the kinase targets distal Mcm subunits for phosphorylation. By cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. Moreover, a rotation of DDK along its anchoring point allows phosphorylation of Mcm2 and Mcm6 on opposite hexamers. In summary, our work provides fundamental insights in the DDK structure, control and the selective activation of the MCM2-7 helicase during DNA replication, which can be exploited for development of novel DDK inhibitors.
2022-05-31 | PXD031315 | Pride
Project description:This submission contains 3 different datasets:
- series A: D. melanogaster female ? D. simulans male embryos vs internal standard of pooled D. simulans and D. melanogaster (1:1) embryos
- series B: D. simulans female ? D. melanogaster male embryos vs internal standard of pooled D. simulans and D. melanogaster (1:1) embryos
- series E: D. melanogaster female ? D. simulans male adult heads vs internal standard of pooled D. simulans and D. melanogaster (1:1) adult heads
Each dataset is in triplicates.
Quantitation was performed with isobaric isotopologues labelling.
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Project description:In this experiment we inhibited FGF signalling in E14.5 mouse lungs by using a dominant negative mouse model. We are interested in assessing the genetic regulation by FGF signalling at this stage of lung development. Specifically, we used a tetracycline controlled transcriptional activation model (Tet(o)) to manipulate FGF signalling. Genetically modified male mice that expressed a reverse tetracycline-controlled trans activator (rtTA) on the Rosa26 locus and a soluble FGFR2b on the Tet(o) promoter (Tet(o)sFgfr2b) (B6.Cg-Gt(ROSA)26Sortm1.1(rtTA,EGFP)NagyTg(tetO-Fgfr2b/Igh)1.3Jaw/sbel), were crossed with females lacking the Tet(o)sFgfr2b allele. Pregnant females were injected with doxycycline intraperitonally at E14.5. Doxycycline then induced the transcription soluble FGFR2b in the embryos, which inhibited FGF signalling by sequestering FGF ligands, preventing them from binding to the native FGFR2b receptor. We harvested embryonic lungs after 9 hrs of inhibition. We took the left lobe of each sample for RNA isolation. We set-up our matings so that 50% of the embryos in a litter were expected to contain the soluble FGFR2b. The remaining littermates will serve as the control group. We will compare the gene expression profiles of the experimental embryonic lungs with those of littermate controls.
2020-06-22 | GSE115876 | GEO
Project description:In this experiment we inhibited FGF signalling in E16.5 mouse lungs by using a dominant negative mouse model. We are interested in assessing the genetic regulation by FGF signalling at this stage of lung development. Specifically, we used a tetracycline controlled transcriptional activation model (Tet(o)) to manipulate FGF signalling. Genetically modified male mice that expressed a reverse tetracycline-controlled trans activator (rtTA) on the Rosa26 locus and a soluble FGFR2b on the Tet(o) promoter (Tet(o)sFgfr2b) (B6.Cg-Gt(ROSA)26Sortm1.1(rtTA,EGFP)NagyTg(tetO-Fgfr2b/Igh)1.3Jaw/sbel), were crossed with females lacking the Tet(o)sFgfr2b allele. Pregnant females were injected with doxycycline intraperitonally at E16.5. Doxycycline then induced the transcription soluble FGFR2b in the embryos, which inhibited FGF signalling by sequestering FGF ligands, preventing them from binding to the native FGFR2b receptor. We harvested embryonic lungs after 9 hrs of inhibition. We took the left lobe of each sample for RNA isolation. We set-up our matings so that 50% of the embryos in a litter were expected to contain the soluble FGFR2b. The remaining littermates will serve as the control group. We will compare the gene expression profiles of the experimental embryonic lungs with those of littermate controls.
2021-06-01 | GSE115877 | GEO
Project description:Background: Maternal iron deficiency (ID) is associated with poor pregnancy and fetal outcomes. The effect is thought to be mediated by the placenta but there is no comprehensive assessment of placental response to maternal ID. Additionally, whether the influence of maternal ID on the placenta differs by fetal sex is unknown. Objectives: Our primary aim was to identify gene and protein signatures of ID mouse placentas at mid-gestation. A secondary objective was to profile the expression of iron genes in mouse placentas across gestation. Methods: We used a real-time PCR based array to determine the mRNA expression of all known iron genes in mouse placentas at embryonic day (E) 12.5, E14.5, E16.5, and E19.5 (n=3 placentas/time point). To determine the effect of maternal ID, we performed RNA sequencing and proteomics in male and female placentas from ID and iron adequate mice at E12.5 (n=8 dams/diet). Results: In female placentas, six genes including transferrin receptor (Tfrc) and solute carrier family 11 member 2 were significantly changed by maternal ID. An additional 154 genes were altered in male ID placentas. Proteomic analysis quantified 7662 proteins in the placenta. Proteins translated from iron responsive element (IRE) containing mRNAs were altered in abundance; ferritin and ferroportin 1 decreased while TFRC increased in ID placenta. Less than 4% of the significantly altered genes in ID placentas occurred both at the transcriptional and translational levels. Conclusions: Our data demonstrate that the impact of maternal ID on placental gene expression in mice is limited in scope and magnitude at mid-gestation. We provide strong evidence for IRE-based transcriptional and translational coordination of iron gene expression in the mouse placenta. Finally, we discover sexually dimorphic effects of maternal ID on placental gene expression, with more genes and pathways altered in male compared with female mouse placentas.
2021-03-12 | PXD023454 | Pride
Project description:The RNA-seq experiment was designed to determine the effects of blastocyst transfer on the transcriptome of whole placentas at embryonic day (E) 10.5. C57Bl/6 blastocysts that were from natural matings without superovulation were transferred into the uteri of pseudopregnant B6D2F1 females (at gestational day 2.5 equivalent). RNA libraries were prepared from whole male placentas at E10.5 (N = 4 placentas) from the transfer group alongside RNA libraries from control placentas from C57Bl/6 conceptuses derived from natural matings and did not undergo the transfer process (N = 4 placentas). Libraries were muliplexed and pooled for sequencing on the Illumina NextSeq500 platform with 75-base-pair single-end reads. Sequencing was performed in duplicate to provide at least 18 million reads per sample, and 1% PhiX Control (Illumina) spike-in was used. Quality control of Fastq files was performed using FastQC and fastq_screen. Sequences were trimmed with Trim Galore!, and alinged to GRCm38 mouse genome using STAR aligner.Alignments were processed using custom ClusterFlow (v0.5dev) pipelines and assessed using MultiQC (0.9.dev0). Gene quantification was determined with HTSeq-Counts (v0.6.1p1). Additional quality control was performed with rRNA and mtRNA counts script, feature counts (v 1.5.0-p2) and qualimap (v2.2). Differential gene expression was performed with DESeq2 package (v1.16.1, R v3.4.0). Read counts were normalised on the estimated size factors.
2019-12-31 | E-MTAB-8036 | biostudies-arrayexpress
Project description:This study compared the gene expression of extraembryonic membranes (EEM) from in vitro produced (IVP) and in vivo (AI) derived embryos. Samples of EEM from AI and IVP pregnancies were collected on days 18 and 32. A piece of the conceptus (day 18) or chorioallantois (day 32) were used for DNA and RNA isolation and subsequent determination of the sex by amplification of a Y-linked region of the DNA. The male and female ratios were analyzed by Chi-square of SAS. A subset of three female and three male EEM samples from each group (AI and IVP, days 18 and 32) were used for transcriptome analysis. Differentially expressed genes (DEGs) between groups, sex, and days were determined using edgeR-robust. A false discovery rate (FDR) <0.05 was used for statistical significance, and Toppgene platform was used for biological processes analysis. Sex ratio was similar on day 18 for AI and IVP groups. On day 32, the IVP group had a greater number of females than males (75 vs 25%, P=0.004). On day 18 female embryos, out of 71 DEGs identified, 50 were upregulated in IVP, and 21 in AI. The trophectoderm marker, TKDP2, was upregulated in the AI group, whereas IGF2, which is involved in placenta development, and APOA2, APOB, and APOE, which are important for lipid metabolism, were upregulated in the IVP group. Male embryos on day 18 had 22 DEGs, being 15 upregulated in AI and 7 in IVP. Female embryos on day 32 had 74 DEGs, with 21 upregulated in AI and 53 in IVP embryos. Some of the genes with increased expression in the IVP group were PTGIS, APOB, and APOH, which are related to lipid synthesis and metabolism. Male embryos on day 32 presented 899 DEGs, 564 upregulated in AI and 335 in IVP. Embryos from IVP had increased expression of genes related to embryo development, morphogenesis, neurogenesis, and developmental growth. In addition, male IVP embryos had decreased expression of genes related to lipid and carbohydrate metabolism. Interestingly, PLAC8B, BRB, pregnancy-associated glycoproteins (PAG) 7, 9, 10, and 19, were also downregulated in IVP male EEM. When comparing IVP males and females, there were 6753 DEGs, with 3091 being upregulated in females, and 3662 in male conceptuses on day 18. Some of the genes upregulated in females were related to placental function such as TKDP4, PLAC8A and PAGs 6, 8, 10, 12, 17, 18 and 19. On males, IFNT-related genes were upregulated (IFNT, IFNT2 IFNT3 and IFN-T). On day d32, there were 6772 DEGs, with 3252 genes with increased expression in female, and 3520 in male placentas. Among the genes increased in female placentas are genes involved in placentation: PAGs 17, 19, 9 and PLAC8B. On the other hand, PAG1 was detected as highly expressed in male placentas. In conclusion, IVP-derived male embryos were more susceptible to alterations in gene expression and these effects extend to the peri-implantation period including genes associated with placental development and markers of placental function.
2023-12-15 | GSE192417 | GEO
Project description:STUDY QUESTION: Could clinically-relevant moderate and/or high dose maternal folic acid supplementation prevent aberrant developmental and epigenetic outcomes associated with assisted reproductive technologies (ART)? SUMMARY ANSWER: Our results demonstrate dose-dependent and sex-specific effects of folic acid supplementation in ART and provide evidence that moderate dose supplements may be optimal for both sexes. WHAT IS KNOWN ALREADY: Children conceived using ART are at an increased risk for growth and genomic imprinting disorders, often associated with DNA methylation defects. Folic acid supplementation is recommended during pregnancy to prevent adverse offspring outcomes; however, the effects of folic acid supplementation in ART remain unclear. STUDY DESIGN, SIZE, DURATION: Outbred female mice were fed 3 folic-acid supplemented diets, control (rodent daily recommended intake or DRI; CD), moderate (4-fold DRI; 4FASD) or high (10-fold DRI; 10FASD) dose, for six weeks prior to ART and throughout gestation. Mouse ART involved a combination of superovulation, in vitro fertilization, embryo culture and embryo transfer. PARTICIPANTS/MATERIALS, SETTING, METHODS: Upon collection of midgestation embryos and placentas (n=74-99 embryos/group), all embryos were assessed for developmental delay and gross morphological abnormalities. Embryos and placentas were also examined at the epigenetic level. We assessed methylation at four imprinted genes (Snrpn, Kcnq1ot1, Peg1, and H19) in matched midgestation embryos and placentas (n=31-32/group) using bisulfite pyrosequencing. In addition, we examined genome-wide DNA methylation patterns in midgestation placentas (n=6 normal placentas per sex/group) and embryos (n=6 normal female embryos/group; n=3 delayed female embryos/group) using reduced representation bisulfite sequencing. MAIN RESULTS AND THE ROLE OF CHANCE: Moderate, but not high dose supplementation, was associated with a decrease in the proportion of developmentally delayed embryos. Although moderate dose folic acid supplementation reduced DNA methylation variance at certain imprinted genes in embryonic and placental tissues, high dose supplementation exacerbated the negative effects of ART at imprinted loci. Furthermore, folic acid supplements resolved female-biased aberrant imprinted gene methylation. Supplementation was more effective at correcting ART-induced genome-wide methylation defects in male versus female placentas; however, folic acid supplementation also led to additional methylation perturbations which were far more pronounced in males. LIMITATIONS, REASONS FOR CAUTION: Although the combination of mouse ARTs utilized in this study consisted of techniques commonly used in human fertility clinics, there may be species differences. Therefore, human studies, designed to determine the optimal levels of folic acid supplementation for ART pregnancies, and taking into account fetal sex, are warranted. WIDER IMPLICATIONS OF THE FINDINGS: Taken together, our findings support moderation in the dose of folic acid supplements taken during ART.
2019-05-15 | GSE123143 | GEO
Project description:Transfer of frozen-thawed embryos leads to sex-specific DNA hypermethylation in both human and mouse placentas. : In humans, frozen ET led to placentas with significant alterations in DNA methylation with most genes demonstrating hypermethylation compared to placentas from fresh ET (4402 CpGs; 1600 genes; p-value < 0.05 in two–tailed unpaired t tests, and a mean methylation difference > 0.05). When compared to control samples, both frozen and fresh samples showed significant differences in methylation.(Frozen vs Control: 5600 CpGs, 2775 genes; Fresh vs Control: 4096 CpGS; 1914 genes; p-value < 0.05, mean methylation difference > 0.05). Paired analysis showed similar trends, despite controlling for maternal environment. Sex specific analysis revealed that these changes were primarily driven by male placentas, as seen by a larger number of CpGs that were differentially methylated, and a larger proportion of genes with at least 2 differentially methylated CpG sites in male placentas as compared to female placentas. (Males: 15572 CpGs, 4399 genes; Females: 7441 CpGs, 3070 genes; p-value < 0.05, mean methylation difference > 0.05). In order to isolate the effects of vitrification we utilized the mouse model, controlling for the effect of the maternal hormonal milieu. In the first genome-wide profiling of DNA methylation in a mouse IVF model, we found that trends in DNA methylation differences paralleled those seen in human placentas. Using similar significance cutoffs as for human samples, and BumpHunter analysis that identifies differentially methylated regions to compensate for a lower number of samples, placentas derived from frozen embryos were predominantly hypermethylated compared to placentas after fresh ET (589 DMRs, 445 genes). Both frozen and fresh embryo transfer samples demonstrated perturbations compared to control samples (Frozen vs Control: 1787 DMRs, 1319 genes; Fresh vs Control: 1119 DMRs, 808 genes). Consistent with the sex-specific trends we observed in human placentas, differences between samples derived from frozen compared to fresh embryo transfer were driven by changes in male placentas (Males: 1069 DMRs, 798 genes; Females:14 DMRs, 11 genes) . When considering the effect of IVF as a whole, murine placentas were predominantly hypomethylated, replicating existing human genome-wide methylation data. As seen previously, IVF led to changes in placental weight, placental morphology and microvessel density in mice, but no persistent changes were seen after embryo vitrification alone. Sexually dimorphic epigenetic changes could indicate differential susceptibility of male and female embryos to IVF-associated perturbations. This observation highlights the importance of sex-specific evaluation of the incidence of adverse outcomes. Similarities between changes seen in mouse and human samples underscore the suitability of the mouse model in evaluating the effect of ART on the epigenetic landscape. This convergence is especially valuable, given limited access to human tissues and the ability to isolate specific interventions in the mouse model.
2023-01-01 | GSE196547 | GEO
Project description:Simple Markov model.
There are 3 disease states: Healthy, Sick, and Dead, where the Dead state is terminal.
The yearly transition probabilities are:
Healthy to Dead: 0.01; Healthy to Sick: 0.2 for Male and 0.1 for Female; Sick to Healthy: 0.1; Sick to Dead: 0.3.
The transition probability now depends on the cohort (Male or Female) and can be expressed as a function of a Boolean covariate Male.
Initial conditions: Healthy = (50 Male, 50 Female), Sick = (0,0) and Dead = (0,0).
Output: Number of men and women in each disease state for years 1-10.
2019-01-30 | MODEL1803120004 | BioModels