Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcriptional Profile Analysis of RPGRORF15 frameshift mutation

ABSTRACT: Purpose: To identify genes and molecular mechanisms associated with disease progression during (7 weeks of age) and after (16 weeks) the peak of photoreceptor death in dogs affected with XLPRA2, a canine model of early-onset XLRP caused by a microdeletion in RPGR exon ORF15. Methods: Expression profiles of diseased and normal dog retinas at both ages were compared using a canine retinal custom cDNA microarray. Data normalization and filtering were performed with GeneSpring, statistical analysis with Significance Analysis of Microarrays. Real-time PCR using Taqman probes, western blot and immunohistochemistry (IHC) were applied on selected genes to confirm and expand the microarray results. Results: At 7 and 16 weeks, respectively, 56 and 18 transcripts were down-regulated in mutant retinas compared to normals. None of the transcripts was differentially expressed (DE) at both ages, suggesting the involvement of temporally distinct molecular pathways. Down-regulated genes included PAX6, CHML, and RDH11 at 7 weeks and CRX and SAG at 16 weeks, which are necessary for visual system development and function. Genes directly or indirectly active in apoptotic processes were altered at 7 weeks (CAMK2G, NTRK2, PRKCB, RALA, RBBP6, RNF41, SEPT5, SMYD3, SPP1, and TUBB2C) and 16 weeks (SLC25A5 and NKAP). Furthermore, DE genes at 7 weeks (ELOVL6, GLOD4, NDUFS4, and REEP1) and 16 weeks (SLC25A5 and TARS2) are related to mitochondrial functions. Real-time PCR of 11 genes confirmed the microarray results and showed differential expression for additional genes not on the array, such as GFAP, RHO, OPN1SW, CNGB3 and the mutated RPGR. Western blotting and IHC analysis also confirmed the high reliability of the presented transcriptomic data. Conclusions: A list of mutated genes in RPGRORF15 diseased retinas, which are likely candidates to further study their role in age-related photoreceptor degeneration diseases, is reported at different crucial ages. The results indicate that at 7 weeks a combination of non-classical anti- and pro-apoptotic genes appears to be involved in photoreceptor degeneration, whereas at both 7 and 16 weeks expression of mitochondria related genes indicates they may play a relevant role in the disease process. 3 biological replicates each for normal and XLPRA2 affected retinas were analyzed at 7 and 16 weeks of age. Each individual sample was hybridized in a reference design using a custom-made retinal cDNA microarray against brain pool to enable cross comparison between groups. Retina was labeled with Cy5 in all samples but 5615 (GSM474350).

ORGANISM(S): Canis lupus familiaris

SUBMITTER: Gustavo Aguirre

PROVIDER: E-GEOD-19124 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional profile analysis of RPGRORF15 frameshift mutation identifies novel genes associated with retinal degeneration.

Genini Sem S Zangerl Barbara B Slavik Julianna J Acland Gregory M GM Beltran William A WA Aguirre Gustavo D GD

Investigative ophthalmology & visual science 20100623 11

<h4>Purpose</h4>To identify genes and molecular mechanisms associated with photoreceptor degeneration in a canine model of XLRP caused by an RPGR exon ORF15 microdeletion. Methods. Expression profiles of mutant and normal retinas were compared by using canine retinal custom cDNA microarrays. qRT-PCR, Western blot analysis, and immunohistochemistry (IHC) were applied to selected genes, to confirm and expand the microarray results.<h4>Results</h4>At 7 and 16 weeks, respectively, 56 and 18 transcri ...[more]

PMID: 20574030

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Project description:Purpose: To identify genes and molecular mechanisms associated with disease progression during (7 weeks of age) and after (16 weeks) the peak of photoreceptor death in dogs affected with XLPRA2, a canine model of early-onset XLRP caused by a microdeletion in RPGR exon ORF15. Methods: Expression profiles of diseased and normal dog retinas at both ages were compared using a canine retinal custom cDNA microarray. Data normalization and filtering were performed with GeneSpring, statistical analysis with Significance Analysis of Microarrays. Real-time PCR using Taqman probes, western blot and immunohistochemistry (IHC) were applied on selected genes to confirm and expand the microarray results. Results: At 7 and 16 weeks, respectively, 56 and 18 transcripts were down-regulated in mutant retinas compared to normals. None of the transcripts was differentially expressed (DE) at both ages, suggesting the involvement of temporally distinct molecular pathways. Down-regulated genes included PAX6, CHML, and RDH11 at 7 weeks and CRX and SAG at 16 weeks, which are necessary for visual system development and function. Genes directly or indirectly active in apoptotic processes were altered at 7 weeks (CAMK2G, NTRK2, PRKCB, RALA, RBBP6, RNF41, SEPT5, SMYD3, SPP1, and TUBB2C) and 16 weeks (SLC25A5 and NKAP). Furthermore, DE genes at 7 weeks (ELOVL6, GLOD4, NDUFS4, and REEP1) and 16 weeks (SLC25A5 and TARS2) are related to mitochondrial functions. Real-time PCR of 11 genes confirmed the microarray results and showed differential expression for additional genes not on the array, such as GFAP, RHO, OPN1SW, CNGB3 and the mutated RPGR. Western blotting and IHC analysis also confirmed the high reliability of the presented transcriptomic data. Conclusions: A list of mutated genes in RPGRORF15 diseased retinas, which are likely candidates to further study their role in age-related photoreceptor degeneration diseases, is reported at different crucial ages. The results indicate that at 7 weeks a combination of non-classical anti- and pro-apoptotic genes appears to be involved in photoreceptor degeneration, whereas at both 7 and 16 weeks expression of mitochondria related genes indicates they may play a relevant role in the disease process.

Project description:Photoreceptor disorders are collectively known as retinal degeneration (RD), and include retinitis pigmentosa (RP), cone-rod dystrophy and age related macular degeneration (AMD). These disorders are largely genetic in origin; individual mutations in any one of >200 genes cause RD, making mutation specific therapies prohibitively expensive. A better treatment plan, particularly for late stage disease, may involve stem cell transplants into the photoreceptor or ganglion cell layers of the retina. Stem cells from young mouse retinas can be transplanted, and can form photoreceptors in adult retinas. These cells can be grown in tissue culture, but can no longer form photoreceptors. We have used microarrays to investigate differences in gene expression between cultured retinal progenitor cells (RPCs) that have lost photoreceptor potential, postnatal day 1 (pn1) retinas and the postnatal day 5 (pn5) retinas that contain transplantable photoreceptors. We have also compared FACS sorted Rho-eGFP expressing rod photoreceptors from pn5 retinas with Rho-eGFP negative cells from the same retinas. We have identified over 300 genes upregulated in rod photoreceptor development in multiple comparisons, 37 of which have been previously identified as causative of retinal disease when mutated. It is anticipated that this research should bring us closer to growing photoreceptors in culture and therefore better treatments for RD. This dataset is also a resource for those seeking to identify novel retinopathy genes in RD patients. We extracted whole retinas from postnatal day 1 (Pn1) and postnatal day 5 (Pn5) mice, and compared them with cultured RPCs derived from pn5 retinas, using Affymetrix mouse 430A_2 arrays. We also extracted cells from Rho-eGFP Pn5 retinas and FACS sorted them. GFP+ve cells represent immature rod photoreceptors, as they express the Rho-eGFP fusion protein, which is only expressed in rods. GFP-ve cells represent all other retinal neurons. These samples were amplified and compared using Affymetrix mouse 430A_2arrays, by Source Biosciences GMBH, Berlin, Germany. Results from immature rods were then compared with those from other retinal neurons, while results from whole Pn5 retinas were compared with Pn1 retinas (which don't yet express rod specific genes), and RPCs, which are glial precursors. RPCs were also compared with Pn1 retinas. Genes which showed changed expression profiles in at least 3/4 of comparisons were prioritised for further investigation.

Project description:Purpose. XOPS-mCFP transgenic zebrafish experience a continual cycle of rod photoreceptor development and degeneration throughout life, making them a useful model to investigate the molecular determinants of rod photoreceptor regeneration. The purpose of this study was to compare the gene expression profiles of wild type and XOPS-mCFP retinas in order to identify genes that may contribute to the regeneration of the rods. Methods. Wild type and XOPS-mCFP retinal mRNA was subjected to microarray analysis using the Agilent platform. The Ingenuity Pathway Analysis program was used to identify biologically relevant processes that were significantly represented in the dataset. Expression changes were verified by RT-PCR. Selected genes were further examined during retinal development and in adult retinas by in situ hybridization, immunohistochemistry, and using a transgenic fluorescent reporter line. Results. Over 600 genes displayed significant expression changes in XOPS-mCFP retinas compared to wild type controls. Many of the downregulated genes were associated with phototransduction, whereas upregulated genes were associated with several biological functions, including cell cycle, DNA replication and repair, cell development and cell death. RT-PCR analysis of a subset of these genes confirmed the microarray results. Three transcription factors (sox11b, insm1a, and c-myb) displaying increased expression in XOPS-mCFP retinas were also expressed throughout retinal development and in the persistently neurogenic ciliary marginal zone. Conclusions. This study identified numerous gene expression changes in response to rod degeneration in zebrafish, and further suggests a role for the transcriptional regulators sox11b, insm1a, and c-myb in both retinal development and rod photoreceptor regeneration. Two-condition experiment: wild-type vs. XOPS-mCFP retinas. Four biological replicates for each condition. RNA was prepared from one retina for each sample. Each hybridization was accompanied by a dye-swap control, for a total of eight array hybridizations.

Dataset Information

Transcriptional Profile Analysis of RPGRORF15 frameshift mutation

Publications

Transcriptional profile analysis of RPGRORF15 frameshift mutation identifies novel genes associated with retinal degeneration.

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