Effect of NK-5962 on Gene Expression Profiling of Retina in a Rat Model of Retinitis Pigmentosa

Purpose: NK-5962 is a key component of photoelectric dye-coupled polyethylene film, designated Okayama University type-retinal prosthesis (OUReP™). Previously, we found that NK-5962 solution could reduce the number of apoptotic photoreceptors in the eyes of the Royal College of Surgeons (RCS) rats by intravitreal injection under a 12 h light/dark cycle. This study aimed to explore possible molecular mechanisms underlying the anti-apoptotic effect of NK-5962 in the retina of RCS rats. Methods: RCS rats received intravitreal injections of NK-5962 solution in the left eye at the age of 3 and 4 weeks, before the age of 5 weeks when the speed in the apoptotic degeneration of photoreceptors reaches its peak. The vehicle-treated right eyes served as controls. All rats were housed under a 12 h light/dark cycle, and the retinas were dissected out at the age of 5 weeks for RNA sequence (RNA-seq) analysis. For the functional annotation of differentially expressed genes (DEGs), the Metascape and DAVID databases were used. Results: In total, 55 up-regulated DEGs, and one down-regulated gene (LYVE1) were found to be common among samples treated with NK-5962. These DEGs were analyzed using Gene Ontology (GO) term enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Reactome pathway analyses. We focused on the up-regulated DEGs that were enriched in extracellular matrix organization, extracellular exosome, and PI3K–Akt signaling pathways. These terms and pathways may relate to mechanisms to protect photoreceptor cells. Moreover, our analyses suggest that SERPINF1, which encodes pigment epithelium-derived factor (PEDF), is one of the key regulatory genes involved in the anti-apoptotic effect of NK-5962 in RCS rat retinas. Conclusions: Our findings suggest that photoelectric dye NK-5962 may delay apoptotic death of photoreceptor cells in RCS rats by up-regulating genes related to extracellular matrix organization, extracellular exosome, and PI3K–Akt signaling pathways. Overall, our RNA-seq and bioinformatics analyses provide insights in the transcriptome responses in the dystrophic RCS rat retinas that were induced by NK-5962 intravitreal injection and offer potential target genes for developing new therapeutic strategies for patients with retinitis pigmentosa.

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Alterations in NMDA receptor expression during retinal degeneration in the RCS rat

Visual Neuroscience ◽

10.1017/s0952523801185111 ◽

2001 ◽

Vol 18 (5) ◽

pp. 781-787 ◽

Cited By ~ 19

Author(s):

TATIANA GRÜNDER ◽

KONRAD KOHLER ◽

ELKE GUENTHER

Keyword(s):

Ganglion Cells ◽

Plexiform Layer ◽

Amacrine Cells ◽

Photoreceptor Cells ◽

Receptor Expression ◽

Signal Pathways ◽

Inner Plexiform Layer ◽

Functional Changes ◽

Rcs Rat ◽

Rcs Rats

To determine how a progressive loss of photoreceptor cells and the concomitant loss of glutamatergic input to second-order neurons can affect inner-retinal signaling, glutamate receptor expression was analyzed in the Royal College of Surgeons (RCS) rat, an animal model of retinitis pigmentosa. Immunohistochemistry was performed on retinal sections of RCS rats and congenic controls between postnatal (P) day 3 and the aged adult (up to P350) using specific antibodies against N-methyl-D-aspartate (NMDA) subunits. All NMDA subunits (NR1, NR2A–2D) were expressed in control and dystrophic retinas at all ages, and distinct patterns of labeling were found in horizontal cells, subpopulations of amacrine cells and ganglion cells, as well as in the outer and inner plexiform layer (IPL). NR1 immunoreactivity in the inner plexiform layer of adult control retinas was concentrated in two distinct bands, indicating a synaptic localization of NMDA receptors in the OFF and ON signal pathways. In the RCS retina, these bands of NR1 immunoreactivity in the IPL were much weaker in animals older than P40. In parallel, NR2B immunoreactivity in the outer plexiform layer (OPL) of RCS rats was always reduced compared to controls and vanished between P40 and P120. The most striking alteration observed in the degenerating retina, however, was a strong expression of NR1 immunoreactivity in Müller cell processes in the inner retina which was not observed in control animals and which was present prior to any visible sign of photoreceptor degeneration. The results suggest functional changes in glutamatergic receptor signaling in the dystrophic retina and a possible involvement of Müller cells in early processes of this disease.

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An extracellular retinol-binding glycoprotein in the eyes of mutant rats with retinal dystrophy: development, localization, and biosynthesis.

The Journal of Cell Biology ◽

10.1083/jcb.99.6.2092 ◽

1984 ◽

Vol 99 (6) ◽

pp. 2092-2098 ◽

Cited By ~ 62

Author(s):

F Gonzalez-Fernandez ◽

R A Landers ◽

P A Glazebrook ◽

S L Fong ◽

G I Liou ◽

...

Keyword(s):

Pigment Epithelium ◽

Retinal Pigment ◽

Retinal Dystrophy ◽

Photoreceptor Cells ◽

Retinol Binding Protein ◽

Rcs Rat ◽

Rapid Fall ◽

Rcs Rats ◽

Extracellular Transport ◽

Interphotoreceptor Matrix

Interstitial retinol-binding protein (IRBP) is a soluble glycoprotein in the interphotoreceptor matrix of bovine, human, monkey, and rat eyes. It may transport retinol between the retinal pigment epithelium and the neural retina. In light-reared Royal College of Surgeons (RCS) and RCS retinal dystrophy gene (rdy)+ rats, the amount of IRBP in the interphotoreceptor matrix increased in corresponding proportion to the amount of total rhodopsin through postnatal day 22 (P22). In the RCS-rdy+ rats, the amount increased slightly after P23. However, in the RCS rats there was a rapid fall in the quantity of IRBP as the photoreceptors degenerated between P23 and P29. No IRBP was detected by immunocytochemistry in rats at P28. The amount of rhodopsin fell more slowly. Although retinas from young RCS and RCS-rdy+ rats were able to synthesize and secrete IRBP, this ability was lost in retinas from older RCS rats (P51, P88) but not their congenic controls. The photoreceptor cells have degenerated at these ages in the RCS animals, and may therefore be the retinal cells responsible for IRBP synthesis. The putative function of IRBP in the extracellular transport of retinoids during the visual cycle is consistent with a defect in retinol transport in the RCS rat reported by others.

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Photoelectric Dye, NK-5962, as a Potential Drug for Preventing Retinal Neurons from Apoptosis: Pharmacokinetic Studies Based on Review of the Evidence

Life ◽

10.3390/life11060591 ◽

2021 ◽

Vol 11 (6) ◽

pp. 591

Author(s):

Toshihiko Matsuo ◽

Shihui Liu ◽

Tetsuya Uchida ◽

Satomi Onoue ◽

Shinsaku Nakagawa ◽

...

Keyword(s):

Biological Evaluation ◽

Pharmacokinetic Studies ◽

Retinal Neurons ◽

Retinal Cells ◽

Intravitreous Injection ◽

Rcs Rats ◽

Photoelectric Dye ◽

Dark Conditions

NK-5962 is a key component of photoelectric dye-based retinal prosthesis (OUReP). In testing the safety and efficacy, NK-5962 was safe in all tests for the biological evaluation of medical devices (ISO 10993) and effective in preventing retinal cells from death even under dark conditions. The long-term implantation of the photoelectric dye-coupled polyethylene film in the subretinal space of hereditary retinal dystrophic (RCS) rats prevented neurons from apoptosis in the adjacent retinal tissue. The intravitreous injection of NK-5962 in the eyes of RCS rats, indeed, reduced the number of apoptotic cells in the retinal outer nuclear layer irrespective of light or dark conditions. In this study, we reviewed the in vitro and in vivo evidence of neuroprotective effect of NK-5962 and designed pharmacokinetic experiments. The in vitro IC50 of 1.7 μM, based on the protective effect on retinal cells in culture, could explain the in vivo EC50 of 3 μM that is calculated from concentrations of intravitreous injection to prevent retinal neurons from apoptosis. Pharmacokinetics of NK-5962 showed that intravenous administration, but not oral administration, led to the effective concentration in the eye of rats. NK-5962 would be a candidate drug for delaying the deterioration of retinal dystrophy, such as retinitis pigmentosa.

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Anti-apoptotic Effect of MiR-223-3p Suppressing PIK3C2A in Cardiomyocytes from Myocardial Infarction Rat Through Regulating PI3K/Akt Signaling Pathway

Cardiovascular Toxicology ◽

10.1007/s12012-021-09658-x ◽

2021 ◽

Author(s):

Liu Xiaoyu ◽

Zhang Wei ◽

Zhao Ming ◽

Jia Guowei

Keyword(s):

Myocardial Infarction ◽

Signaling Pathway ◽

Akt Signaling ◽

Akt Signaling Pathway ◽

Apoptotic Effect

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The Effect of Cyanine Dye NK-4 on Photoreceptor Degeneration in a Rat Model of Early-Stage Retinitis Pigmentosa

Pharmaceuticals ◽

10.3390/ph14070694 ◽

2021 ◽

Vol 14 (7) ◽

pp. 694

Author(s):

Shihui Liu ◽

Toshihiko Matsuo ◽

Mary Miyaji ◽

Osamu Hosoya

Keyword(s):

Retinitis Pigmentosa ◽

Rat Model ◽

Metal Ion ◽

Toxic Substance ◽

Cyanine Dye ◽

Pathway Enrichment Analysis ◽

Rna Seq ◽

Pathway Enrichment ◽

Metal Ion Homeostasis ◽

Rcs Rats

The present study aimed to evaluate the effects of NK-4 on the apoptosis of photoreceptors in a rat model of retinitis pigmentosa and explore the mechanism underlying anti-apoptosis activity. The Royal College of Surgeons (RCS) rats received an intravitreous injection of NK-4 solution in the left eye and vehicle control in the right eye. Apoptosis was detected by TUNEL method in frozen sections of the eyes. The retinal tissues of the rats were dissected for RNA-seq analysis. Functional and pathway enrichment analyses of differentially expressed genes (DEGs) were performed by using Metascape and DAVID software. The expression levels of DEGs were confirmed by real-time quantitative PCR (RT-qPCR). The number of apoptotic cells decreased in the outer nuclear layer (ONL) and the thickness of the ONL was significantly thicker in the retina of NK-4-injected eyes, compared with control eyes. Five DEGs were identified by RNA-seq analysis, and Hmox1, Mt1, Atf5, Slc7a11, and Bdh2 were confirmed to be up-regulated by RT-qPCR. Functional and pathway enrichment analysis of the up-regulated genes showed that anti-apoptosis effects of NK-4 in the retina of RCS rats may be related to the pathways of metal ion homeostasis, negative regulation of neuron death, response to toxic substance, and pigment metabolic process. We found a potential mechanism of NK-4, providing a new viewpoint for the development of more therapeutic uses of NK-4 in the future.

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Planar cell polarity proteins differentially regulate extracellular matrix organization and assembly during zebrafish gastrulation

Developmental Biology ◽

10.1016/j.ydbio.2013.08.027 ◽

2013 ◽

Vol 383 (1) ◽

pp. 39-51 ◽

Cited By ~ 27

Author(s):

Michael R. Dohn ◽

Nathan A. Mundell ◽

Leah M. Sawyer ◽

Julie A. Dunlap ◽

Jason R. Jessen

Keyword(s):

Extracellular Matrix ◽

Cell Polarity ◽

Planar Cell Polarity ◽

Matrix Organization ◽

Polarity Proteins

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Construction of Prognostic Prediction Model for Stomach Adenocarcinoma Based on the TCGA Database.

10.21203/rs.3.rs-114928/v1 ◽

2020 ◽

Author(s):

Zhengzhong Gu ◽

Xiaohan Cui ◽

Xudong Wang

Keyword(s):

Gastric Cancer ◽

Extracellular Matrix ◽

Protein Kinase ◽

Network Analysis ◽

Differentially Expressed Genes ◽

Differentially Expressed ◽

Stomach Adenocarcinoma ◽

Matrix Organization ◽

Prognostic Prediction ◽

New Biomarkers

Abstract Background: Prognostic prediction models have been developed to detect new biomarkers of gastric cancer (GC). The identification of new biomarkers could provide theoretical foundations for the application of molecular targeted therapy in advanced GC. The aim of this study was to construct a prognostic prediction model for stomach adenocarcinoma (STAD) based on The Cancer Genome Atlas (TCGA) database. Methods: First, we used the "limma" package to screen differentially expressed genes (DEGs) based on TCGA database. Gene ontology (GO) analysis was performed using the "ClusterProfiler" package. The interactions between proteins and the relationships between differentially expressed genes and clinical features were analyzed by protein-protein interaction (PPI) network analysis and weighted gene coexpression network analysis (WGCNA), respectively. Then, gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to identify differentially enriched pathways. The GenVisR package and CIBERSORT were used to identify mutations and assess immune infiltration. Finally, the expression of COL3A1 in STAD tissues was verified by reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blotting.Results: Six differentially expressed genes were screened out, namely, COL3A1, ADAMTS12, BGN, FNDC1, AEBP1 and HTRA3. The enrichment results showed that differentially expressed genes were involved in multiple pathways in STAD, such as those related to the extracellular matrix, extracellular structure organization, and extracellular matrix organization. The differentially expressed genes were related to immune infiltration via the mitogen-activated protein kinase (MAPK) and phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) pathways. The western blotting and RT-qPCR results suggested that COL3A1 was overexpressed in STAD tissues compared with normal tissues.Conclusion: COL3A1, ADAMTS12, BGN, FNDC1, AEBP1 and HTRA3 could play important roles in the tumorigenesis and progression of STAD via various pathways, including those involving the extracellular matrix, extracellular structure organization, and extracellular matrix organization. COL3A1, ADAMTS12, BGN, FNDC1, AEBP1, and HTRA3 act as oncogenes in most cancers and may be biomarkers. Additionally, the identification of COL3A1 as a candidate biomarker provides a direction for further research on the role of tumor immunity in gastric cancer.

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Mining Prognostic Significance Genes in Human Thyroid Cancer Using Bioinformatics Analysis

10.21203/rs.3.rs-137529/v1 ◽

2021 ◽

Author(s):

Hui Zhao ◽

Pengjie Li ◽

Junjian Li ◽

Lian Duan ◽

Yanzhu Jiao ◽

...

Keyword(s):

Gene Expression ◽

Extracellular Matrix ◽

Thyroid Cancer ◽

Function Analysis ◽

Akt Signaling ◽

Differentially Expressed ◽

Human Thyroid ◽

Marker Genes ◽

Clinical Prognosis ◽

Mesenchymal Transition

Abstract Background Thyroid carcinoma (THC) is very common, yet its pathogenesis and the key tumor marker genes remain unclear.Methods Gene expression datasets from the Gene Expression Omnibus (GEO) and the Cancer Genome Atlas Project (TCGA) were used for gene differential expression analysis. Functional annotation analysis, Clinical prognosis analysis and Differential DNA methylation analysis were conducted on the differentially expressed genes (DEGs). Results Compared with induced pluripotent stem cells (iPSCs), 237 differentially expressed THC intersection genes derived from GEO and TCGA were obtained, of which 153 genes were closely related to clinicopathological features and prognostic effects. Biological function analysis indicated that most of these DEGs were involved in the proteinaceous extracellular matrix, epithelial-to-mesenchymal transition (EMT), and PI3K-Akt signaling pathway, resulting in effects on tumor invasion and metastasis. Finally, the results of differential methylation levels demonstrated that the high expression of 4 genes (CHI3L1, NFE2L3, S100A2, and LAMB3) was strongly correlated with the development of thyroid cancer.Conclusions Proteinaceous extracellular matrix, EMT, and PI3K-Akt signaling pathways were of great significance in the metastasis and invasion of THC. Genes such as CHI3L1, NFE2L3, S100A2, and LAMB3 were susceptible to THC.

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