Effect of DKK1 on embryo elongation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA522975 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8587120_1.fastq.gz | Fastqsanger.gz | |||
| SRR8587120_2.fastq.gz | Fastqsanger.gz | |||
| SRR8587130_1.fastq.gz | Fastqsanger.gz | |||
| SRR8587130_2.fastq.gz | Fastqsanger.gz | |||
| SRR8587121_1.fastq.gz | Fastqsanger.gz |
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Project description:We report the effect of DKK1 treatment during culture on the length and transcriptome of embryos on day 15 of development, supporting the notion that changes early in development affect later stages of development.
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Project description:Super Enhancers are a class of DNA Cis-regulatory elements that can regulate cell identity, cell fate, stem cell pluripotency, and even tumorigenesis.Increasing evidence shows that epigenetic modifications play an important role in the pathogenesis of various types of cancer. However, current research is far from sufficient to reveal the complex mechanisms behind epigenetic modifications.The aim of this study is to explore the function and mechanism of a new Super Enhancer in Pancreatic ductal adenocarcinoma (PDAC) tumors. By using epigenetic modification and chromatin interaction information, we found a new Super Enhancer enriched with abnormal active histone modifications in PDAC tumors and cells, called DKK1-super-enhancer (DKK1-SE).DKK1-SE was grouped according to the activity modification information, and the e1 component was identified as the main active unit by dual luciferase reporter gene system and dCas9-KRAB system.DNA motif analysis and core site deletion assay revealed that the e1 component possessed AP1 transcription factor family binding sites.Mechanically, AP1 activates DKK1 transcriptional activity by recruiting JUND and FOSL2 to induce enhancer chromatin remodeling.CRISPR/ Cas9-mediated deletion of DKK1-SE resulted in significant downregulation of its target gene DKK1.Analysis of TCGA data of PDAC tumors combined with immunohistochemical results of PDAC patients demonstrated that DKK1 was closely related to malignant clinical features of PDAC.Bioinformatics analysis of RNA-seq data showed that DKK1 was mainly related to tumor-related biological functions such as extracellular matrix, cell adhesion, angiogenesis, and cell proliferation.Cell malignant phenotype assay showed that deletion or interference of DKK1-SE significantly inhibited the proliferation, colony formation, migration and invasion of PANC-1, and these phenomena were partially alleviated after restoring DKK1 expression in DKK1-SE deficient cells.Experiments of Subcutaneous transplantation tumor in nude mice and Orthotopic transplantation tumor model showed that DKK1-SE deletion not only inhibited tumor proliferation, but also reduced the complexity of tumor microenvironment, resulting in less angiogenesis of tumor tissues and reduced fibrosis degree.In conclusion, DKK1-SE drives the expression of DKK1 by recruiting AP1 family transcription factors, which plays a carcinogenic role in PDAC tumors and enhances the complexity of the tumor microenvironment.
2023-12-12 | GSE248887 | GEO
Project description:Background: During the process of elongation, the embryo increases in size within the uterus while the extra-embryonic tissues (EET) develop and differentiate in preparation for implantation. As it grows, the ovoid embryo changes shape into first a tubular and then a filamentous form. This process is directed by numerous genes and pathways, the expression of which may be altered in the case of developmental irregularities such as when the conceptus is shorter than expected or when the embryo develops after splitting. In bovines, efforts to understand the molecular basis of elongation have employed trophoblastic vesicles (TVs)—short tubular EET pieces lacking an embryo—which also elongate in vivo. To date, however, we lack molecular analyses of TVs at the ovoid or filamentous stages that might shed light on the expression changes involved. Methods: Following in vivo development, we collected bovine conceptuses from the ovoid (D12) to filamentous stages (D18), sectioned them into small pieces with or without their embryonic disc (ED), and then transferred them to a receptive bovine uterus to assess their elongation abilities. We also grew spherical blastocysts in vitro up to D8, and subjected them to the same treatment. We then assessed differences in gene expression between the different samples and fully elongating controls at different stages of elongation using a bovine array (10K) and an extended qPCR array comprising 224 genes across 24 pathways. Results: In vivo, TVs elongated more or less depending on the stage at which they had been created and the time spent in utero. Their daily elongation rates differed from control EET, with the rates of TVs sometimes resembling those of earlier-stage EET. Overall, the molecular signatures of TVs followed a similar developmental trajectory as intact EET from D12–D18. However, within each stage, TVs and intact EET displayed distinct expression dynamics, some of which were shared with other short epithelial models. Conclusions: Differences between TVs and EET likely result from multiple factors, including a reduction in the length and signaling capabilities of TVs, delayed elongation from inadequate uterine signals, and modified crosstalk between the conceptus and the uterus. These findings confirm that close coordination between uterine, embryonic, and extraembryonic tissues is required to orchestrate proper elongation and, based on the partial differentiation observed, raise questions about the presence/absence of certain developmental cues or even their asynchronies.
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Project description:Understanding Bovine Embryo Elongation: A Transcriptomic Study of Trophoblastic Vesicles
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Project description:Assessed effect of DKK1 treatment on gene expression during the first four days of ES cell differentiation in serum containing medium.
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Project description:Dickkopf 1 (DKK1), which is expressed at high mRNA levels by fibroblasts in the dermis of human skin on the palms and soles, inhibits the function and proliferation of melanocytes in the epidermis of those areas via the suppression of beta-catenin and microphthalmia-associated transcriptor factor (MITF). In this study, we report that treatment of keratinocytes with DKK1 increases their proliferation and decreases their uptake of melanin, and that treatment of reconstructed skin with DKK1 induces a thicker and less pigmented epidermis. We investigated the effects of DKK1 on keratinocytes using DNA microarray technology. Keywords: compound treatment design
2007-12-31 | GSE9211 | GEO
Project description:DKK1 recruits osteoclast precursor cells in a concentration gradient-dependent manner. In order To clarify the transcriptome changes when osteoclast precursor cells are recruited by DKK1.We compared the expression profiles of osteoclast precursor cells with or without DKK1 stimulation.
2023-09-16 | GSE184248 | GEO
Project description:To systematically evaluate the effect of embryo lysates feeding, we conducted small RNA sequencing on day 7 N2 worms treated with either embryo or day 6 worm lysates. Our findings revealed that embryo lysates affected the 21ur-6059 expression.
2024-09-07 | GSE265889 | GEO
Project description:Successful embryonic development depends upon molecules secreted by the reproduc-tive tract. Among such molecules is dickkopf 1 (DKK1), an canonical WNT antagonist that can also activate the planar cell polarity (PCP) pathway. Objectives were to determine whether DKK1 regulates expression of genes that promote differentiation, possibly through the PCP pathway, and to determine if actions of DKK1 on the embryonic transcriptome were dependent on embryo sex. Bovine oocytes were fertilized with pools of X- or Y-sorted sperm. Embryos were treated with 100 ng/ml DKK1 or vehicle at Day 5 of development and harvested 24 h later for microarray analysis of global gene expression. A total of 9,931 transcripts were identified as being expressed. with124 being differentially expressed genes between females and males. A total of 68% of the genes upregulated in females were located on the X chromosome. DKK1 changed expression of 132 genes in females and 136 in males. Of these, 34 genes were regulated by DKK1 in both sexes - 14 in the same direction and 20 in opposite directions. Evidence for regulation of the PCP pathway by DKK1 was the finding that DKK1 regulated expression of genes involved in cell polarization and differentiation in both females and males. In both sexes, DKK1 regulated expression of many genes associated with HNF4A, a marker of hypoblast cells that promotes formation of cell junctions. In conclusion, DKK1 regulates cell differentiation and embryonic development in a sex-dependent manner and effects may be mediated, at least in part, by activation of the PCP pathway. Bovine embryos produced with X- or Y-sorted sperm were cultured in vitro and treated with vehicle or DKK1 at day 5 of development and harvested at day 6 for RNA isolation, amplification and hibridization to Affymetrix Bovine Gene 1.0 ST arrays. The study was done in 5 replicates using pools of 20 morulae for each treatment.
2014-08-06 | E-GEOD-60098 | biostudies-arrayexpress