Dataset Information

Bulk RNA-seq of eyes isolated from wildtype and Stra6 knockout mice maintained on either a vitamin A sufficient or deficient diet

ABSTRACT: Vitamin A deficiency is detrimental to the visual system throughout the lifecycle. Abundant expression of the retinoid transporter STRA6 in the retinal pigment epithelium (RPE) and homeostatic blood levels of retinol binding protein ensure the eyes are adequately supplied with the nutrient. STRA6 deficiency interrupts the supply pathway, but vitamin A in chylomicrons compensates for its failure. However, dependency on the chylomicron delivery pathway makes the eyes of STRA6-deficient mice vulnerable to dietary vitamin A deprivation. How the eyes adapt to vitamin A status has not been studied in molecular detail, and therefore we used RNA-seq to focus on diet-induced changes. We observed that mild ocular vitamin A deficiency was linked to an increase in transcript abundance levels of genes coding for proteins of stress pathways and a decrease in levels of transcripts coding for proteins of pathways of visual sensitivity and perception. These changes correlate with a loss of visual sensitivity and accumulation of fluorescent debris in the retina. Additionally, severe vitamin A deficiency decreased the transcript levels of genes involved in cell adhesion, cell differentiation, and transport of small molecules pathways. This response correlated with alterations in epithelial cell morphology and a “leaky” RPE barrier. Together, our analyses of STRA6-deficient mice define adaptive responses associated with ocular vitamin A status and reveal a previously unknown role of STRA6 in the maintenance and functioning of the outer blood-retina barrier.

ORGANISM(S): Mus musculus

PROVIDER: GSE219252 | GEO | 2023/06/07

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. While much is known about the distribution of cell types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue. Datasets such as these can be used to prioritize candidate genes for possible involvement in retinal diseases with regional phenotypes. Reprinted from <a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=25446321">Whitmore, S.S., Wagner, A.H., DeLuca, A.P., Drack, A.V., Stone, E.M., Tucker, B.A., Zeng, S., Braun, T.A., Mullins, R.F., Scheetz, T.E., 2014. Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. Experimental Eye Research</a>. Used under <a href="http://creativecommons.org/licenses/by-nc-sa/3.0/">Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported </a>license. Additional RNA sequencing was performed on temporal, macular, nasal, inferior, and superior retina from a fifth subject and is included in this dataset. See original publication for details.

Project description:Mutations in the membrane frizzled-related gene (Mfrp) are linked to posterior microphthalmia, retinitis pigmentosa and nanophthalmia in humans. In homozygous Mfrprd6 mice, a splice site mutation causes a slow photoreceptor degeneration characterized by shortening and disorganization of outer segments with eventual photoreceptor loss. To better understand the function of MFRP in the retina, microarray analysis was carried out in mutant and control mice at postnatal day14 (P14), prior to the loss of photoreceptors. Analysis of the data revealed differentially expressed RPE and neuroretina transcripts. Although the analysis of the microarray data from Mfrprd6 mutant mice compared to age-matched wild-type controls identified some transcripts with relative fold change > 5.0, most of the differentially expressed genes showed a relative fold change between1.5 - 2.0. Global gene expression analysis using Ingenuity Pathway Analysis software identified decreased levels of transcripts in phototransduction and visual pathways in Mfrprd6 mutants. Select candidate transcripts were validated by quantitative real-time PCR analyses. The expression of RPE-specific visual transduction protein, RPE65, was significantly decreased in Mfrprd6 mutants. As an indirect consequence of the primary RPE cell defect due to the Mfrprd6 mutation, retinal specific transcripts Rgr, Pde6a, GuCa1b, and Rgs9 were also significantly decreased. We also confirmed the significantly elevated levels of Prss56, a gene previously associated with myopia and open angle glaucoma. In the Mfrprd6 mutant, a progressive increase in Prss56 mRNA levels from 14- to 70-fold was observed from P7 to P21, respectively. In situ hybridization and glutamine synthetase staining of mutant eyes indirectly identified MM-CM-<ller glia in the inner nuclear layer of retina as the cell type expressing the Prss56 transcript. This experiment had one model term, a combination of strain and time, which consisted of four levels (B6_P0, B6_P14, Rd6_P0 and Rd6_P14). Three biological replicates were used per term level. A total of 12 Affymetrix Mouse 430v2 Arrays were used in gene expression analysis.

Dataset Information

Bulk RNA-seq of eyes isolated from wildtype and Stra6 knockout mice maintained on either a vitamin A sufficient or deficient diet

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets