The transcriptome of Japanese quail Neuroretinas cell line (QNR/D)
ABSTRACT: Our research focus is to study the genetic etiology and molecular mechanisms of glaucoma, a disease characterized by death of the retinal ganglion cell. The QNR/D cells, the only well validated retinal ganglion cell line, are derived from the neuroretina of quail (Coturnix coturnix japonica) embryos at 7 days gestation, and contain RGC (80%) and amacrine cell (20%) populations. With the aim of investigating the effect of candidate gene on glaucoma, the QNR/D cells were transfected in four different conditions. The RNA-Sequencing analysis on these transfected cell lines to identify the related proteins with differential expression profiles.
Project description:This study aimed to identify differential expressed genes before and after treatment with Sulforaphene, using the A549 lung cancer cell line as a model. There were a total of 4 samples examined. Two replicates have been included (2 control samples and 2 test samples).
Project description:This study aimed to identify differential expressed genes before and after treatment with the compound sulforaphene, using the MDA-MB-453 breast cancer cell line as a model. There were a total of 2 samples examined.
Project description:Dogs frequently develop glaucoma, a disease that leads to vision loss due to loss of retinal ganglion cells and degeneration of axons within the optic nerve. We used Affymetrix Gene chips to characterize transcriptional changes between healthy and glaucomatous retinas. Overall design: These data describe gene expression changes in the canine retina with glaucoma. RNA was isolated from the retinas of 5 dogs with advanced glaucoma and from 5 normal individuals.
Project description:Dogs frequently develop glaucoma, a disease that leads to vision loss due to loss of retinal ganglion cells and degeneration of axons within the optic nerve. We used Affymetrix Gene chips to characterize transcriptional changes between healthy and glaucomatous retinas. These data describe gene expression changes in the canine retina with glaucoma. RNA was isolated from the retinas of 5 dogs with advanced glaucoma and from 5 normal individuals.
Project description:Glaucoma is a neurodegenerative disease in which vision is lost as a result of the apoptosis of retinal ganglion cells. When the trabecular meshwork cells, that regulate aqueous humor outflow, are stressed as they are in some forms of glaucoma, they considerably up-regulated secretion of a protein called myocilin into the aqueous. The function of this protein is unclear; but since some aqueous humor flows to the posterior of the eye, the effects of myocilin will also be felt by the retinal cells. We have a transgenic mouse that secretes large amounts of myocilin into aqueous humor. In these mice, there is a deposition of myocilin on membranes of certain cells suggesting myocilin might have some signaling functions. This signaling function could explain why stresses that increase intraocular pressures can increase the likelihood for glaucoma, cause the myocilin to be secreted at very high levels by the trabecular meshwork. Myocilin may be important in treating glaucoma. This experiment will determine if myocilin is altering gene expression in the retina. The results should show variations in expression levels and will give us some indication of the pathways that are important to preserve retinal ganglion cells after a diagnosis of glaucoma. Our hypothesis is that myocilin is acting like a signaling protein in the eye. It acts not only in the anterior segment but also in retina as a result of the flow of some aqueous to the back of the eye. This signaling function is protective to certain ocular cells. This function of myocilin may influence cells in the retina and may counter the apoptotic signals in the retinal ganglion cells that occur during glaucoma. Retinas from transgenic mice and from mice of the same strain that do not have the transgene will be dissected. The mice will be three weeks of age. Because of the small size of the retina, samples will be pooled to obtain the RNA necessary to run the microarray. Three control and three transgenic samples will be run and compared with each other. We have data indicating that myocilin is at high levels in the aqueous humor of the transgenic animals.
Project description:We report the application of single nucleotide sequencing technology for high-throughput profiling of ppargc1a in mouse hepatome cells (Hepa1-6). By obtaining 1.2 billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide maps of ppargc1a sin mouse hepatoma cells. We identify novel non- coding sites of ppargc1a occupation in hepatic cells for Sirt5, Idh3b, Pfkl, and Hmox2 strongly corresponds with the enrichment of enhancer -associated RNAs. Examination of the genomic disttribution of the total pool of ppargc1a and the lysine methylated (K779me) enriched pool of ppargc1a in mouse Hepa1-6 hepatoma cells.
Project description:The pathogenesis of glaucoma is strongly associated with the occurrence of autoimmune-mediated loss of retinal ganglion cells (RGCs) and recently it was proven that specific antibody-derived signature peptides are significantly differentially expressed in sera of primary open angle glaucoma patients (POAG) compared to healthy controls. Synthetic antibody-derived peptides are known since several years to modulate various effector functions of the immune system and to act as antimicrobial or antiviral molecules. The present study shows for the first time that polyclonal-derived complementarity-determining regions (CDRs) significantly increased the survival rate of RGCs in an ex vivo glaucoma model (P=0.013) by using immunohistochemical staining techniques. Affinity capture experiments verified serine protease HTRA2 (mitochondrial) as high-confident retinal epitope target of CDR1 sequence motive ASGYTFTNYGLSWVR. Quantitative proteomic analysis of the CDR-treated retinal explants revealed increased expression of various anti-apoptotic and anti-oxidative proteins (e.g. VDAC2 and TXN) compared to untreated controls (P<0.05) and decreased expression levels of cellular stress response markers (e.g. HSPE1 and HSP90AA1) were observed. Mitochondrial dysfunction, protein ubiquitination pathway and oxidative phosphorylation were annotated as the most significantly affected signaling pathways and can possibly be traced back to the CDR-induced inhibition or modulation of the master regulator HTRA2. These findings emphasize the great potential of synthetic polyclonal-derived CDR peptides as therapeutic agents in future glaucoma therapy and provide an excellent basis for affinity-based biomarker discovery purposes.
Project description:RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells Overall design: Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls