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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Effect of DJ-1 on early development in porcine nuclear transfer embryos

ABSTRACT: We aimed to identify a reprogramming factor in mammalian oocytes. DJ-1 is one candidate gene of the factor. Inhibition of DJ-1 function in nuclear transfer embryos affected developmental abilities. The downstream effect of this DJ-1 inhibition was examined using microarrays. Nuclear transfer (NT) embryos (23-26 embryos per each sample) were collected at 28 h after nuclear transfer when many of the embryos had just reached the 2-cell stage. Total RNA was extracted and hybridized on the Affymetrix GeneChip Porcine Genome Array. Global transcripts were compared among NT embryos injected with anti-DJ1 antibody (αDJ1-NT_1), NT embryos injected with IgG (IgG-NT_1), non-injected NT embryos (NT_1) and donor cells (DonorCell_1). Biologically different samples of αDJ1-NT (αDJ1-NT_2) and IgG-NT (IgG-NT_2) were prepared and the microarray analysis was repeated. In both trials, NT embryos injected with IgG (IgG-NT_1 or IgG-NT_2) were used as controls.

ORGANISM(S): Sus scrofa

SUBMITTER: Kei Miyamoto

PROVIDER: E-GEOD-18104 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Effect of DJ-1 on early development in porcine nuclear transfer embryos

Project description:We aimed to identify a reprogramming factor in mammalian oocytes. DJ-1 is one candidate gene of the factor. Inhibition of DJ-1 function in nuclear transfer embryos affected developmental abilities. The downstream effect of this DJ-1 inhibition was examined using microarrays.

2011-04-07 | GSE18104 | GEO

Transcriptional reprogramming of somatic cells after nuclear transfer to mouse 4-cell embryos

Project description:We have developed a nuclear transfer (NT) system in which somatic nuclei are transplanted into mouse embryos arrested at the 4-cell stage. The transplanted somatic nuclei show swelling and epigenetic reprogramming towards 4-cell-like nuclei. To assess genome-wide transcriptional reprogramming of the injected nuclei, the newly transcribed genes in NT embryos were examined by RNA-seq analyses. As a control, NT was also performed using mouse embryos at the 2-cell stage.

2021-11-03 | GSE162345 | GEO

Genome-wide comparison of EpiSC lines derived from fertilized (FT) and somatic cell nuclear transfer (NT) embryos

Project description:Genome wide comparison of gene expression between EpiSC lines derived from fertilized (FT) embryos and somatic cell nuclear transfer (NT) embryos. EpiSC lines were derived from fertilized and somatic cell nuclear transfer embryos and cultured until 15 to 20 passages. RNA was then extracted in order to compare transcriptomic profiles.

2010-02-05 | GSE17402 | GEO

Sus scrofa

Project description:Effect of DJ-1 on early development in porcine nuclear transfer embryos

| PRJNA119395 | ENA

Global gene expression profiles of NT, AI and IVF bovine blastocysts, examination of nuclear reprogramming

Project description:Nuclear transfer (NT) has potential applications in agriculture and biomedicine, but the technology is hindered by low efficiency. Global gene expression analysis of clones is important for the comprehensive study of nuclear reprogramming. Here, we compared global gene expression profiles of individual bovine NT blastocysts with their somatic donor cells and fertilized control embryos utilizing cDNA microarray technology. The NT embryos’ gene expression profiles were drastically different from those of their donor cells and closely resembled those of the naturally fertilized embryos. Our findings demonstrate that the NT embryos have undergone significant nuclear reprogramming by the blastocyst stage; however, problems may occur during re-differentiation for tissue- and organogenesis, and small reprogramming errors may be magnified downstream in development. Keywords: cDNA microarray

2005-11-30 | GSE3568 | GEO

DJ-1 is dispensable for human stem cell homeostasis

Project description:our data showed that the absence of DJ-1 had no adverse effects on proliferation, differentiation, and oxidative stress responses of human stem cells such as hNSCs and hMSCs as well as hVECs, suggesting that loss of DJ-1 function alone is insufficient to disrupt the homeostasis of these human cells. In addition, we found that CHCHD2 was upregulated upon DJ-1 deficiency, which may account for the absence of severe phenotypes in various types of DJ-1-deficient cells. For the first time, our study revealed the 'see-saw' expression pattern of two Parkinson’s disease-associated genes, providing potential clues for understanding the mechanisms of DJ-1- and CHCHD2-associated Parkinson’s disease.

2019-09-05 | GSE136834 | GEO

DJ-1 depletion prevents immunoaging in T-cell compartments

Project description:Decline in immune function during aging increases susceptibility to different aging related diseases. However, the underlying molecular mechanisms, especially the genetic factors contributing to imbalance of naïve/memory T-cell subpopulations, still remain largely elusive. Here we show that loss of DJ-1 encoded by PARK7/DJ-1, causing early-onset familial Parkinson’s disease (PD), unexpectedly diminished signs of immunoaging in T-cell compartments of both human and mice. Compared with two gender-matched unaffected siblings of similar ages, the index PD patient with DJ-1 deficiency showed a decline in many critical immunoaging features, including almost doubled non-senescent T cells. The observation was further consolidated by the results in 45-week-old DJ-1 knockout mice. Our data demonstrated that DJ-1 regulates several immunoaging features via hematopoietic-intrinsic and naïve-CD8-intrinsic mechanisms. Mechanistically, DJ-1 depletion reduced oxidative phosphorylation (OXPHOS) and impaired TCR sensitivity in naïve CD8 T cells at a young age, accumulatively leading to a reduced aging process in T-cell compartments in older mice. Our finding suggests an unrecognized critical role of DJ-1 in regulating immunoaging, discovering a potent target to interfere with immunoaging- and aging-associated diseases.

2022-01-17 | GSE173904 | GEO

DJ-1 governs airway progenitor cell/eosinophil interactions to promote allergic inflammation

Project description:Background DJ-1 is an antioxidant protein known to regulate mast cell mediated allergic response, but its role in airway eosinophilic interactions and allergic inflammation is not known. Objective The aim of this study was to investigate the role of DJ-1 in airway eosinophilic inflammation in vitro and in vivo. Methods Ovalbumin-induced airway allergic inflammation was established in mice. ELISA was adopted to analyze DJ-1 and cytokine levels in mouse bronchoalveolar lavage fluid. Transcriptional profiling of mouse lung tissues was conducted by single-cell RNA sequencing technology. The role of DJ-1 in the differentiation of airway progenitor cells into goblet cells was examined by organoid cultures, immunofluorescence staining, quantitative PCR, and cell transplantation in normal, DJ-1 knockout (KO), or conditional DJ-1 KO mice. Results We observed that DJ-1 was increased in the lung tissues of ovalbumin-sensitized and challenged mice. DJ-1 KO mice exhibited reduced airway eosinophil infiltration and goblet cell differentiation. Mechanistically, we discovered that eosinophil-club cell interactions are reduced in the absence of DJ-1. Organoid cultures indicated that eosinophils impair the proliferative potential of club cells. Intratracheal transplantation of DJ-1-deficient eosinophils suppresses airway goblet cell differentiation. Loss of DJ-1 inhibits the metabolism of arachidonic acid into cysteinyl leukotrienes in eosinophils while these secreted metabolites promote airway goblet cell fate in organoid cultures and in vivo. Conclusion DJ-1-mediated interactions between airway epithelial progenitor cells and immune cells are essential in controlling airway goblet cell metaplasia and eosinophilia. Blockade of the DJ-1 pathway is protective against airway allergic inflammation.

2022-12-21 | GSE203079 | GEO

Transcriptional defects and reprogramming barriers in somatic cell nuclear reprogramming as revealed by single-embryo RNA sequencing

Project description:Nuclear reprogramming reinstates totipotency or pluripotency in somatic cells by changing their genetic transcription. This technology is widely used in medicine, animal husbandry and other industries. However, certain deficiencies, such as the poor developmental ability of reprogrammed nuclear transfer (NT) embryos and the low birth rate (less than 5%) of cloned animals, severely restrict the promotion of this technology. Multiple nuclear reprogramming barriers likely exist in the process of somatic nuclear reprogramming. Furthermore, the NT embryos obtained via this technology have transcriptional defects in embryonic development. To address these problems, in this study, two types of NT embryos were constructed using the same genetic background in mice. We detected the full transcriptome of all stages of NT embryos using single-cell RNA-seq and obtained the following results: 1) NT embryos have translation initiation defects during the minor zygotic genome activation (ZGA) period; NT embryos display RNA processing and RNA modification defects during the major ZGA period, and their protein kinase activity in protein phosphorylation exhibits defects during blastocyst formation; and 2) 2003 constant genes cannot be reprogrammed in cumulus cells (CCs) and mouse embryo fibroblast cells (MEFs); of these constant genes, 399/583 reprogramming barrier genes (RBGs) continue to mis-transcribe from the pronuclear stage to the blastula stage, and the same 136 RBGs are found in both the CCs and MEFs. The main functions of these RBGs is to positively regulate certain factors. In conclusion, our study offers full transcriptome blueprints of all stages of CC donor NT embryos, MEF donor NT embryos and in vivo embryos and reveals new transcriptional defects and reprogramming barriers in nuclear reprogramming. These findings provide insight for further mechanism studies investigating somatic nuclear reprogramming.

2018-08-11 | GSE113164 | GEO

Transcriptomic analysis of DJ-1 knockout rat brains using RNA-Seq

Project description:Mutations in the DJ-1 gene cause rare forms of autosomal recessive Parkinson's disease in humans. Recently, DJ-1 knockout rats have been generated and they have been reported to have subtle motor defects and neurodegeneration. We hypothesized that measuring the differences in mRNA expression in the brains of wildtype and DJ-1 knockout rats would provide insight into the mechanisms underlying these phenotypes. Using RNA-Seq, we were able to measure differential expression of over 2,000 genes in the DJ-1 knockout rat brains.

2017-09-11 | GSE71968 | GEO

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