Development is a complex and well-defined process characterized by rapid cell proliferation and apoptosis. At this stage in life, a developmentally young organism is more sensitive to toxicants and other stressors when compared to an adult. In response to pro-oxidant exposure, members of the Cap’n’Collar (CNC) basic leucine zipper (b-ZIP) transcription factor family (including the Nfe2-related factors, Nrfs) activate the expression of genes that contribute to reduced toxicity. Here, we studied the role of the Nrf protein, Nfe2, in the developmental response to pro-oxidant exposure in the zebrafish. Following acute waterborne exposures to diquat or tert-buytlhydroperoxide (tBOOH) at three developmental stages, wildtype (WT) and nfe2 knockout (KO) embryos and larvae were morphologically scored and their transcriptomes sequenced. Overall design: Wildtype animals were on the AB background and an additional germline nfe2 knockout strain were created by disruption of the nfe2 reading frame. Waterborne exposures to either diquat or tBOOH were carried out at three different developmental stages: 2 hours post fertilization (hpf), 48hpf, and 96hpf in 3 pools of 30 embryos per condition. Animals were exposed to no treatment, 20µM diquat or 1mM tBOOH for a 4-hour dosing period. Total RNA was isolated from pooled animals and 50 bp, paired end, libraries were sequenced using the Illumina HiSeq 2000 platform, with approximately 25 million reads per sample. Reads were then aligned to the Ensembl GRCz10 zebrafish reference genome using Tophat2 and raw counts data normalized using DESeq2. Gene annotation was from Ensemble for GRCz10.
The transcription factor, Nuclear factor, erythroid 2 (Nfe2), is a regulator of the oxidative stress response during Danio rerio development.
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View SamplesThe level of trypsin-2 has been shown to correlate with the malignancy and metastatic potential of many cancer.
Trypsin-2 enhances carcinoma invasion by processing tight junctions and activating ProMT1-MMP.
Specimen part, Cell line
View SamplesIn this study, zebrafish ZF4 and PAC2 cells were seeded in 0.5% or 1% FCS, respectively, and grown to 85% confluence and subsequently cultured for 24 hours without serum. Then they were treated with either medium without serum or medium with serum (ZF4 in 10% FCS and PAC2 in 15% FCS).After 6 hours, RNA was extracted from the cells and analyzed using the Affymetrix GeneChip Zebrafish Genome Array (GeneChip 430). There are 15502 oligonucleotide sets on each Affymetrix chip, 14895 of which can be linked to a UniGene assignment (Unigene data set 06-12-2005).
Genetic and transcriptome characterization of model zebrafish cell lines.
Cell line, Compound
View SamplesTHO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here we show that human THO interacts with MFAP1, a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing ?H2AX foci and DNA breaks. This phenotype is not dependent either on transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381, also confer a similar transcription-independent genome instability supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses, that affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a novel functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role. Overall design: Analysis of gene expression in the Saccharomyces cerevisiae mutant spp381-ts under 1h of restrictive temperature.
Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability.
Cell line, Subject
View SamplesImmune responses in hemophilia A patients to replacement factor VIII can be either tolerogenic or immunogenic, the latter resulting in induction of non-neutralizing anti-factor VIII antibodies or neutralizing antibodies called inhibitors. Since these inhibitors render replacement FVIII treatment essentially ineffective, preventing or eliminating them are of top priority in disease management. The extended half-life recombinant factor VIII Fc fusion protein (rFVIIIFc) is an approved therapy for hemophilia A patients. In addition, it has been reported that rFVIIIFc can induce tolerance to FVIII in hemophilia A patients that have developed inhibitors. Given that the IgG1 Fc region has the potential to interact with immune cells expressing Fc receptors and thereby affect the immune response to rFVIII, we investigated how human macrophages, expressing both Fc receptors and receptors reported to bind FVIII, respond to rFVIIIFc. We show herein that rFVIIIFc, but not rFVIII, uniquely skews macrophages towards an alternatively activated regulatory phenotype. rFVIIIFc initiates signaling events that result in morphological changes, as well as a specific gene expression and metabolic profile that is characteristic of the regulatory type Mox/M2-like macrophages. Further, these changes are dependent on rFVIIIFc-Fc receptor interactions. Our findings elucidate mechanisms of potential immunomodulatory properties of rFVIIIFc. Overall design: Human monocyte-derived macrophages (n=3) were treated with hIgG1, rFVIII or rFVIIIFc for 6h
Recombinant factor VIII Fc fusion protein drives regulatory macrophage polarization.
Specimen part, Treatment, Subject
View SamplesSpinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Stem cell transplantation could represent a therapeutic approach for motor neuron diseases such as SMA. We examined the theraputics effects of a spinal cord neural stem cell population and their ability to modify SMA phenotype.
Neural stem cell transplantation can ameliorate the phenotype of a mouse model of spinal muscular atrophy.
No sample metadata fields
View SamplesUlcerative colitis (UC) is a chronic inflammatory disease of the colon with preiods of active disease followed by remission.
Transcriptional analysis of the intestinal mucosa of patients with ulcerative colitis in remission reveals lasting epithelial cell alterations.
Sex, Age, Treatment
View SamplesCrohn's Disease (CD) is a chronic inflammatory disease of the intestinal tract.
Identification of inflammatory mediators in patients with Crohn's disease unresponsive to anti-TNFα therapy.
Sex, Age, Specimen part, Subject
View SamplesTumor growth and metastasis is controlled by paracrine signaling between cells of the tumor microenvironment and malignant cells. Cancer-associated fibroblasts (CAFs), are functionally important components of the tumor microenvironment. Although some steps involved in the cross-talk between these cells are known, there is still a lot that is not clear. Thus, the addition of, the consideration of microenvironment in the development of the disease, to the clinical and pathological procedures (currently admitted as the consistent value cancer treatments) could lay the foundations for the development of new treatment strategies to control the disease.
Functional heterogeneity of cancer-associated fibroblasts from human colon tumors shows specific prognostic gene expression signature.
Specimen part
View SamplesThe vascular lining cells in the human spleens include littoral cells (LCs) and other splenic vascular endothelial cells (SVECs). LCs that comprise about 30 percent of the splenic red pulp are specialzed endothelial cells distinct from SVECs. They line the splenic sinusoids and function as the filters and scavengers for senescent or altered red blood cells. Patients with advanced forms of myelofibrosis (MF) often develope extramedullary hematopoiesis in the spleen.Vascular lining cells within MF spleens are thought to serve as a supportive microenvironment for MF hematopoietic cells. In this study we isolated MF and normal LCs and SVECs from human spleens using immunostaining and flow cytometric sorting and used microarrays to analyze the underling mechanism of LCs' unique functions that distinguish them from SVECs, and the properties of MF LCs and SVECs and their contributions to the microenvironment of MF spleens.
The characteristics of vessel lining cells in normal spleens and their role in the pathobiology of myelofibrosis.
Specimen part, Disease stage
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