scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2020 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Adam Bouras ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Background Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6c (pde6c) mutant. Results The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]), and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Conclusions Our data strongly indicate that, among these genes, the above-mentioned pathways’ genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2019 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Adam Bouras ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6C (pde6c) mutant. The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]) and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Our data strongly indicate that, among these genes, the abovementioned pathways’ genes—as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins—are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2020 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Adam Bouras ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Background: Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6c (pde6c) mutant. Results: The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]), and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Conclusions: Our data strongly indicate that, among these genes, the above-mentioned pathways’ genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2019 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov(Former Corresponding Author) ◽  
Adam Bouras ◽  
Hu Huang(New Corresponding Author)
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Tca Cycle ◽  
Kegg Pathways

Abstract Background Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6C (pde6c) mutant. Results The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the false discovery rate (FDR) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]) and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3,527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were downregulated, while fewer were upregulated in the retina of mutant zebrafish. Conclusions Our data strongly indicate that, among these genes, the above-mentioned pathways’ genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.

scholarly journals RNA-Seq reveals differential expression profile and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio

2019 ◽  
Author(s):  
Madhu Sudhana Saddala ◽  
Anton Lennikov ◽  
Hu Huang
Keyword(s):  
Gene Expression ◽  
Retinal Degeneration ◽  
Expression Profile ◽  
Calcium Binding ◽  
Vision Loss ◽  
Gene Annotation ◽  
Insulin Signalling ◽  
Tca Cycle ◽  
Kegg Pathways ◽  
Insulin Signalling Pathway

Abstract Retinal degenerative diseases affect millions of people and are the leading cause of vision loss. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes that are involved in phototransduction, biosynthesis, folding of the rhodopsin molecule and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear. The molecular basis of the retinal pathologies defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we have analyzed the differential gene expression profile of retina from a wild-type zebrafish and pde6c mutant. The datasets were downloaded from the Sequence Read Archive (SRA), removed adaptors and unbiased bases and checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish and calculated gene expression. The differentially expressed genes (DEGs) were filtered based on the FDR (±4) and p-values (p<0.001). We performed gene annotation (Molecular function, biological process, cellular component), and functional pathways (KEGG pathway) for the DEGs. Our result showed that 216 up-regulated and 3527 down-regulated between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways like Phototransduction (12 genes), mRNA surveillance pathway (17 genes), Phagosome (25 genes), Glycolysis / Gluconeogenesis (15 genes), Adrenergic signalling in cardiomyocytes (29 genes), Ribosome (20 genes), Citrate cycle (TCA cycle) (8 genes), Insulin signalling pathway (24 genes), Oxidative phosphorylation (20 genes) and RNA transport (22 genes) pathways respectively. Much more of all the pathways genes were down-regulated, but fewer genes were up-regulated in retina mutant of zebrafish. Our data strongly indicate that the among these genes, above mentioned pathways genes as well as calcium-binding proteins, neural damage proteins, peptidase proteins, immunological proteins, and apoptosis proteins are mostly involved in retinal and neural degeneration that cause abnormalities in photoreceptors or RPE cells.

Transduction of mouse retina by insect cell packaged recombinant adeno-associated virusess and their mutants via intravitreal injection

2021 ◽  
Author(s):  
Zheng Wei ◽  
Xiaomei Liu ◽  
Taiming Li ◽  
Xiaofang Li ◽  
Qungang Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Gene Expression Profiles ◽  
Mouse Retina ◽  
Transduction Efficiency ◽  
Egfp Expression ◽  
Wild Type ◽  
Gene Therapy Vector

Aim: Adeno-associated virus (AAV) is the most preferred gene therapy vector. The purpose of our research is to compare the infection tropism and gene expression efficiency of vitreous injection of recombinant AAVs (rAAVs) and their capsid mutants in mouse retina. Materials & methods: We packaged wild-type rAAV2/2,6,8,9 and their capsid mutants carrying EGFP expression cassette using insect cells. The gene expression profiles of rAAVs and their mutants in mouse retina were evaluated by optical imaging of retinal tissue flat mount and cryosections. Results & conclusion: The results showed that rAAV2 and rAAV2-Y444F mainly targeted retinal ganglion cell; rAAV8, rAAV8-Y733F, rAAV9 and mutants had obvious EGFP expression in retinal pigment epithelium cells. Compared with the wild-type rAAVs, capsid mutants have an improved transduction efficiency in mouse retina cells.

scholarly journals Potential therapy for progressive vision loss due to PCDH15-associated Usher syndrome developed in an orthologous Usher mouse

2021 ◽  
Author(s):  
Saumil Sethna ◽  
Wadih M Zein ◽  
Sehar Riaz ◽  
Arnaud P.J. Giese ◽  
Julie M Schultz ◽  
...  
Keyword(s):  
Retinal Degeneration ◽  
Vision Loss ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Usher Syndrome ◽  
Visual Field Loss ◽  
Type I ◽  
Ashkenazi Jews ◽  
Visual Deficits ◽  
Protocadherin 15

Usher syndrome type I (USH1) is characterized by congenital deafness, vestibular areflexia, and progressive retinal degeneration with age. The protein-truncating p.Arg245* founder variant of PCDH15 has an ~2% carrier frequency among Ashkenazi Jews, accounting for nearly 60% of their USH1 cases. Here, longitudinal ocular phenotyping in thirteen USH1F individuals harboring the p.Arg245* variant revealed progressive retinal degeneration, leading to severe loss of vision with macular atrophy by the sixth decade. Half of the affected individuals met either the visual acuity or visual field loss definition for legal blindness by the middle of their fifth decade of life. Mice homozygous for p.Arg250* (Pcdh15R250X; equivalent to human p.Arg245*) also have early visual deficits evaluated using electroretinography. Light-dependent translocation of phototransduction cascade proteins, arrestin and transducin, was found to be impaired in Pcdh15R250X mice. Retinal pigment epithelium- (RPE) specific visual retinoid cycle proteins, RPE65 which converts all-trans retinoids to 11-cis retinoids and CRALBP that transports retinoids, and key retinoid levels were also reduced in Pcdh15R250X mice, suggesting a dual role for protocadherin-15 in photoreceptors and RPE. Administration of exogenous 9-cis retinal, an analog of the naturally occurring 11-cis retinal, improved ERG amplitudes in these mutant mice, suggesting a basis for a clinical trial of exogenous FDA approved retinoids to preserve vision in USH1F patients.

scholarly journals Proposed therapy, developed in a Pcdh15-deficient mouse, for progressive loss of vision in human Usher Syndrome

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Saumil Sethna ◽  
Wadih M Zein ◽  
Sehar Riaz ◽  
Arnaud PJ Giese ◽  
Julie M Schultz ◽  
...  
Keyword(s):  
Retinal Degeneration ◽  
Vision Loss ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Usher Syndrome ◽  
Type I ◽  
Ashkenazi Jews ◽  
Visual Deficits ◽  
Severe Vision Loss ◽  
Protocadherin 15

Usher syndrome type I (USH1) is characterized by deafness, vestibular areflexia and progressive retinal degeneration. The protein-truncating p.Arg245* founder variant of PCDH15 (USH1F) has an ~2% carrier frequency amongst Ashkenazi Jews accountings for ~60% of their USH1 cases. Here, longitudinal phenotyping in thirteen USH1F individuals revealed progressive retinal degeneration, leading to severe vision loss with macular atrophy by the sixth decade. Half of the affected individuals were legally blind by their mid-fifties. The mouse Pcdh15R250X variant is equivalent to human p.Arg245*. Homozygous Pcdh15R250X mice also have visual deficits and aberrant light-dependent translocation of the phototransduction cascade proteins, arrestin and transducin. Retinal pigment epithelium- (RPE) specific retinoid cycle proteins, RPE65 and CRALBP, were also reduced in Pcdh15R250X mice, indicating a dual role for protocadherin-15 in photoreceptors and RPE. Exogenous 9-cis retinal improved ERG amplitudes in Pcdh15R250X mice, suggesting a basis for a clinical trial of FDA approved retinoids to preserve vision in USH1F patients.

scholarly journals Wide-field fundus autofluorescence imaging in patients with hereditary retinal degeneration: a literature review

2019 ◽  
Vol 5 (S1) ◽  
Author(s):  
Akio Oishi ◽  
Manabu Miyata ◽  
Shogo Numa ◽  
Yuki Otsuka ◽  
Maho Oishi ◽  
...  
Keyword(s):  
Retinal Degeneration ◽  
Vision Loss ◽  
Pigment Epithelium ◽  
Fundus Autofluorescence ◽  
Retinal Pigment ◽  
Peripheral Retina ◽  
Wide Field ◽  
Characteristic Appearance ◽  
Field Imaging ◽  
Wide Field Imaging

Abstract Background Inherited retinal degeneration (IRD) refers to a heterogenous group of progressive diseases that cause death of photoreceptor cells and subsequent vision loss. These diseases often affect the peripheral retina, objective evaluation of which has been difficult until recently. Fundus autofluorescence (FAF) is a non-invasive retinal imaging technique that depicts the distribution of intrinsic fluorophores in the retina. The primary source of retinal autofluorescence is lipofuscin, which is contained in the retinal pigment epithelium (RPE). Excessive accumulation of lipofuscin and a window defect attributable to loss of photoreceptor pigment result in increased FAF whereas loss of the RPE results in decreased FAF. These changes can be seen during the course of IRD. Mainbody While conventional modalities are limited in their angle of view, recent technologic advances, known as wide-field and ultra-widefield FAF imaging, have enabled visualization of the far peripheral retina. Although clinical application of this technique in patients with IRD is still in its infancy, some studies have already indicated its usefulness. For example, an area with decreased FAF correlates well with a visual field defect in an eye with retinitis pigmentosa (RP) or cone-rod dystrophy. An abnormal FAF pattern may help in the diagnosis of IRD and associated diseases. In addition, female carriers of X-linked RP and female choroideremia show characteristic appearance. Conversely, absence of abnormal FAF despite severe retinal degeneration helps differentiation of cancer-associated retinopathy. Conclusion This paper reviews the principles of FAF, wide-field imaging, and findings in specific diseases. Wide-field imaging, particularly wide-field FAF, will provide further information for the characteristics, prognosis, and pathogenesis of IRD.

scholarly journals Spaceflight influences gene expression, photoreceptor integrity, and oxidative stress-related damage in the murine retina

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Eliah G. Overbey ◽  
Willian Abraham da Silveira ◽  
Seta Stanbouly ◽  
Nina C. Nishiyama ◽  
Gina D. Roque-Torres ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Expression Profiles ◽  
Pigment Epithelium ◽  
Retinal Pigment ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Photoreceptor Layer ◽  
Rods And Cones ◽  
Old Adult

Abstract Extended spaceflight has been shown to adversely affect astronaut visual acuity. The purpose of this study was to determine whether spaceflight alters gene expression profiles and induces oxidative damage in the retina. Ten week old adult C57BL/6 male mice were flown aboard the ISS for 35 days and returned to Earth alive. Ground control mice were maintained on Earth under identical environmental conditions. Within 38 (+/−4) hours after splashdown, mice ocular tissues were collected for analysis. RNA sequencing detected 600 differentially expressed genes (DEGs) in murine spaceflight retinas, which were enriched for genes related to visual perception, the phototransduction pathway, and numerous retina and photoreceptor phenotype categories. Twelve DEGs were associated with retinitis pigmentosa, characterized by dystrophy of the photoreceptor layer rods and cones. Differentially expressed transcription factors indicated changes in chromatin structure, offering clues to the observed phenotypic changes. Immunofluorescence assays showed degradation of cone photoreceptors and increased retinal oxidative stress. Total retinal, retinal pigment epithelium, and choroid layer thickness were significantly lower after spaceflight. These results indicate that retinal performance may decrease over extended periods of spaceflight and cause visual impairment.

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