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15 pages, 5760 KiB  
Article
Retinal Dystrophy Associated with Homozygous Variants in NRL
by Jordi Maggi, James V. M. Hanson, Lisa Kurmann, Samuel Koller, Silke Feil, Christina Gerth-Kahlert and Wolfgang Berger
Genes 2024, 15(12), 1594; https://doi.org/10.3390/genes15121594 - 12 Dec 2024
Viewed by 775
Abstract
Background/Objectives: Neural retina leucine zipper (NRL) is a transcription factor involved in the differentiation of rod photoreceptors. Pathogenic variants in the gene encoding NRL have been associated with autosomal dominant retinitis pigmentosa and autosomal recessive clumped pigmentary retinal degeneration. Only a dozen [...] Read more.
Background/Objectives: Neural retina leucine zipper (NRL) is a transcription factor involved in the differentiation of rod photoreceptors. Pathogenic variants in the gene encoding NRL have been associated with autosomal dominant retinitis pigmentosa and autosomal recessive clumped pigmentary retinal degeneration. Only a dozen unrelated families affected by recessive NRL-related retinal dystrophy have been described. The purpose of this study was to expand the genotypic spectrum of this disease by reporting clinical and genetic findings of two unrelated families. Methods: Index patients affected by retinal dystrophy were genetically tested by whole-exome sequencing (WES) and whole-genome sequencing (WGS). Segregation analysis within the families was performed for candidate variants. A minigene assay was performed to functionally characterize a variant suspected to affect splicing. Results: Variant filtering revealed homozygous NRL variants in both families. The variant in patient A was a small deletion encompassing the donor splice site of exon 1 of transcript NM_006177.3. The minigene assay revealed that this variant led to two aberrant transcripts that used alternative cryptic donor splice sites located in intron 1. In patient B, a stop-gain variant was identified in the last exon of NRL in a homozygous state due to maternal uniparental disomy of chromosome 14. Conclusions: Our study expands the genotypic spectrum of autosomal recessive NRL-related retinal dystrophy. Moreover, it underscores the importance of actively maintaining bioinformatic pipelines for variant detection and the utility of minigene assays in functionally characterizing candidate splicing variants. Full article
(This article belongs to the Special Issue Study of Inherited Retinal Diseases—Volume II)
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<p>(<b>a</b>–<b>g</b>). Clinical and imaging data for Patient A. (<b>a</b>,<b>b</b>) At age 15, kinetic visual field testing revealed concentrically reduced isopters in left (<b>a</b>) and right (<b>b</b>) eyes. V4e, I4e, and I2e isopters and static points are displayed in dark blue, dark green, and purple, respectively. Open circles represent stimuli presented statically that were seen by the patient, whilst filled circles represent static stimuli that were not seen by the patient. I1e stimuli were also presented, but the isopter is constricted and not visible on the diagram. (<b>c</b>,<b>d</b>) Optical coherence tomography findings were unchanged in the right (<b>c</b>) and left (<b>d</b>) eyes between the ages of 8 and 13. (<b>e</b>,<b>f</b>) Optos wide-field imaging at age 16 revealed clumped hypopigmentation along the vascular arcades and peripheral retinal atrophy corresponding to the autofluorescence (AF) pattern, which demonstrated centrally preserved and increased AF in both the right (<b>e</b>) and left (<b>f</b>) eyes. (<b>g</b>) Electroretinography (ERG) at age 7 revealed, from left to right, the following: non-recordable rod responses; reduced and delayed rod–cone responses with electronegative ERG configuration; light-adapted flicker responses contaminated by artifacts and therefore not interpretable; and reduced cone single flash responses with delayed a-waves and electronegative ERG configuration. At age 11, the rod–cone and cone single flashes had worsened, with the electronegative configuration remaining. Black traces are from the right eye and red traces from the left eye.</p>
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<p>(<b>a</b>–<b>g</b>). Clinical and imaging data for Patient B. (<b>a</b>,<b>b</b>) Optical coherence tomography showed grade 1 foveal hypoplasia and schisis with cystoid changes temporal to the fovea in both the right (<b>a</b>) and left (<b>b</b>) eyes. More detailed scanning was not possible due to nystagmus. (<b>c</b>,<b>d</b>) Kinetic perimetry at age 13 revealed intact isopters to larger stimuli and constricted isopters to smaller stimuli in both left (<b>c</b>) and right (<b>d</b>) eyes. V4e, I4e, and I2e isopters and static points are displayed in dark blue, dark green, and purple, respectively. Open circles represent stimuli presented statically that were seen by the patient, whilst filled circles represent static stimuli that were not seen by the patient. (<b>e</b>,<b>f</b>) Optos wide-field imaging revealed patchy hypopigmentation along the temporal vascular arcades corresponding to the reduced autofluorescence pattern in both right (<b>e</b>) and left (<b>f</b>) eyes. (<b>g</b>) Electroretinography (ERG) at age 13, was challenging due to nystagmus. From left to right: the rod response was non-recordable; the rod–cone response was reduced and delayed, with negative ERG configuration; analysis of the flicker response was not possible due to artifact; the cone single-flash response was reduced and delayed, but due to artifact, a negative ERG configuration could not be conclusively confirmed. All traces are from the left eye only (it was not possible to analyze the responses from the right eye due to nystagmus-related artifacts).</p>
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<p>Family pedigree for patient A illustrating cosegregation of <span class="html-italic">NRL</span> variant NM_006177.3:c.-41_-28+23del. The arrow indicates patient A (index patient; V:5). The genotype of the family members tested (IV:5, IV:6, V:4, and V:5) is represented underneath their identifiers; plus symbols (+) refer to the variant allele, and minus symbols represent the major allele. The two alleles are separated by a slash symbol. Both parents carry the variant heterozygously, while the sibling does not carry the variant. Double lines indicate consanguinity. Created in BioRender. Maggi, J. (2024) <a href="https://BioRender.com/m01g165" target="_blank">https://BioRender.com/m01g165</a>.</p>
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<p>Family pedigree for patient B illustrating segregation of <span class="html-italic">NRL</span> variant NM_006177.3:c.544C&gt;T. The arrow indicates patient B (index patient; II:1). The genotype of the parents (I:1 and I:2) is represented underneath their identifiers; plus symbols (+) refer to the variant allele, and minus symbols represent the major allele. The two alleles are separated by a slash symbol. Only the mother carries the variant (heterozygously); maternal uniparental disomy of chromosome 14 had been previously diagnosed in the index patient. Created in BioRender. Maggi, J. (2024) <a href="https://BioRender.com/y07r686" target="_blank">https://BioRender.com/y07r686</a>.</p>
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<p>Functional characterization of the <span class="html-italic">NRL</span> variant NM_006177.3:c.-41_-28+23del using a minigene assay. The panel shows an IGV screenshot highlighting the construct’s characteristics (displayed in blue), followed by the coverage plots (grey) for the reference (WT) and variant (MT) minigenes. Mismatches between the sequence of the reads and the reference sequence are highlighted in the coverage plot by a color different than grey. An overview of each transcript (name T#) identified in the analysis can be seen underneath the coverage plots. The green transcript represents the expected major (WT) transcript.</p>
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23 pages, 3727 KiB  
Review
Three-Dimensional Bioprinting for Retinal Tissue Engineering
by Kevin Y. Wu, Rahma Osman, Natalie Kearn and Ananda Kalevar
Biomimetics 2024, 9(12), 733; https://doi.org/10.3390/biomimetics9120733 - 1 Dec 2024
Viewed by 1284
Abstract
Three-dimensional bioprinting (3DP) is transforming the field of regenerative medicine by enabling the precise fabrication of complex tissues, including the retina, a highly specialized and anatomically complex tissue. This review provides an overview of 3DP’s principles, its multi-step process, and various bioprinting techniques, [...] Read more.
Three-dimensional bioprinting (3DP) is transforming the field of regenerative medicine by enabling the precise fabrication of complex tissues, including the retina, a highly specialized and anatomically complex tissue. This review provides an overview of 3DP’s principles, its multi-step process, and various bioprinting techniques, such as extrusion-, droplet-, and laser-based methods. Within the scope of biomimicry and biomimetics, emphasis is placed on how 3DP potentially enables the recreation of the retina’s natural cellular environment, structural complexity, and biomechanical properties. Focusing on retinal tissue engineering, we discuss the unique challenges posed by the retina’s layered structure, vascularization needs, and the complex interplay between its numerous cell types. Emphasis is placed on recent advancements in bioink formulations, designed to emulate retinal characteristics and improve cell viability, printability, and mechanical stability. In-depth analyses of bioinks, scaffold materials, and emerging technologies, such as microfluidics and organ-on-a-chip, highlight the potential of bioprinted models to replicate retinal disease states, facilitating drug development and testing. While challenges remain in achieving clinical translation—particularly in immune compatibility and long-term integration—continued innovations in bioinks and scaffolding are paving the way toward functional retinal constructs. We conclude with insights into future research directions, aiming to refine 3DP for personalized therapies and transformative applications in vision restoration. Full article
(This article belongs to the Special Issue Biomimetic 3D/4D Printing)
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<p>Three-dimensional bioprinting process and types of bioprinting. Created in BioRender.</p>
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<p>Keeling et al. [<a href="#B26-biomimetics-09-00733" class="html-bibr">26</a>] created reconstructed images of mice RPE 3D architecture (lateral view) showing apical microvilli (green) and nuclei (blue) with transparent cytoplasm allowing visualization of the convoluted basolateral Bruch’s membrane (yellow) with sub-RPE spaces (purple) and photoreceptors (light blue). Created in BioRender.</p>
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<p>Deep to the outer pigmented aspect of the retina is the nine layers within the inner neural layer of the retina. The retina is located between the vitreous body and choroid [<a href="#B27-biomimetics-09-00733" class="html-bibr">27</a>]. Copyright certificate is CC by 3.0 license.</p>
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<p>Retina structures cartoonized. Note: not all retinal layers are depicted in this figure. Created in BioRender.</p>
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<p>Diagrammatic representation of the major requirements for a successful bioink. Created in BioRender.</p>
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<p>Cartoonized rendering of the decellularization process for the development of decellularized ECM (dECM) biomaterial. The progressive loss of colour in this figure represents the loss of intracellular components in the decellularization process. The native retina tissue for which the ECM is derived is rendered in red, emblematic of the complex protein structures and intracellular environment supporting the native ECM. The final dECM product is rendered in gray, stripped of the native supportive proteins and growth-promoting intracellular environment. Created in BioRender.</p>
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<p>Flow chart summarizing recent advancements of scaffold engineering in 3D retinal bioprinting. Many scaffolds are made with gellan gum (GG) as a base for its improved strength during the printing process. Created in Biorender.</p>
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<p>Schematic representation of the oBRB. CC = choriocapillaris; TJ = tight junction. Created in Biorender.</p>
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<p>Graphical representation of the drug-loaded combined bevacizumab/dexamethasone rod invention [<a href="#B94-biomimetics-09-00733" class="html-bibr">94</a>]. Created in Biorender.</p>
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7 pages, 1865 KiB  
Brief Report
Orbital Hematoma Treatment—A Retrospective Study
by Bartosz Bielecki-Kowalski, Natalia Bielecka-Kowalska, Marek Jaxa-Kwiatkowski, Krzysztof Osmola and Marcin Kozakiewicz
J. Clin. Med. 2024, 13(19), 5788; https://doi.org/10.3390/jcm13195788 - 28 Sep 2024
Viewed by 632
Abstract
Background: Bleeding within the orbit in the form of a subperiosteal or retrobulbar hematoma is a relatively common complication of trauma and surgery. It affects up to 30% of patients fractures involving the orbital bones. Most cases do not require surgical intervention because [...] Read more.
Background: Bleeding within the orbit in the form of a subperiosteal or retrobulbar hematoma is a relatively common complication of trauma and surgery. It affects up to 30% of patients fractures involving the orbital bones. Most cases do not require surgical intervention because they do not cause retinal ischemia or optic nerve neuropathy. The above symptoms occur in only 0.5–1% of patients developing Orbital Compartment Syndrome (OCS). Due to the short period (60–100 min) of time in which the optic nerve and retina can tolerate increased intraocular pressure, it seemed reasonable to evaluate and standardize the surgical management protocol for this rare complication. Objective: The aim of this retrospective study was to retrospectively analyze cases of inframammary haematomas with clinically relevant correlations. Methods: Eighteen patients treated at the Department of Maxillofacial Surgery due to OCS, in Lodz and Poznan, Poland, between 2009 and 2022, were included. APTT, INR, systemic diseases, cause, location and size of hematoma, presence and number of fractures, visual disturbances and pupillary response on the day after surgery and one month after, the type of intervention and time between admission to the hospital and surgery were evaluated. Results: Statistically significant correlations were obtained between the size of the hematoma and the patients’ age, the degree of visual disturbance and the weakening of pupillary constriction, severe initial symptoms and poor postoperative outcomes at both postoperative periods studied, immediate and distant poor outcome after decompression surgery and good postoperative outcome persisting one month after. Conclusions: The results obtained in the study and the surgical protocol proposed by the authors are in line with the current state of knowledge regarding orbital hematomas. Some of the correlations described in the literature (such as OCS and anticoagulant treatment) were not demonstrated, but this is probably due to the small study group. Maintaining the 100 min limit as a standard was possible only in early postoperative diagnoses (only 1 of the patients was operated on up to 100 min after the appearance of symptoms). In other cases, the specialized diagnosis took an average of 2785 ± 4020 min or 46 ± 67 h. Full article
(This article belongs to the Special Issue Current Trends in Oral and Maxillofacial Surgery)
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<p>Relationship between pupil response to light and visual impairment (<b>a</b>), and the relationship between the volume of the retrobulbar hematoma and the age of the patients (<b>b</b>).</p>
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<p>Relationship between severe visual impairment and hematoma localization.</p>
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<p>Relationship between severe visual impairment at the time of diagnosis (blindness, light perception only, impaired visual acuity, diplopia) and on the first day after surgery (blindness, light perception only, light perception, seeing shades, impaired visual acuity) (<b>a</b>) and between severe visual impairment at the time of diagnosis (blindness, light perception only, impaired visual acuity, diplopia) and one month after surgery (blindness, visual field deficit) (<b>b</b>).</p>
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<p>Relationship between severe visual impairment at the time of diagnosis (blindness, light perception only, impaired visual acuity, diplopia) and on the first day after surgery (blindness, light perception only, light perception, seeing shades, impaired visual acuity) (<b>a</b>) and between severe visual impairment at the time of diagnosis (blindness, light perception only, impaired visual acuity, diplopia) and one month after surgery (blindness, visual field deficit) (<b>b</b>).</p>
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22 pages, 1295 KiB  
Review
Macular Pigment Optical Density as a Measurable Modifiable Clinical Biomarker
by Abdul Masri, Mohammed Armanazi, Keiko Inouye, Dennis L. Geierhart, Pinakin Gunvant Davey and Balamurali Vasudevan
Nutrients 2024, 16(19), 3273; https://doi.org/10.3390/nu16193273 - 27 Sep 2024
Viewed by 1900
Abstract
Background: Carotenoids are present throughout retina and body its dense deposition leads to an identifiable yellow spot in the macula. Macular pigment optical density (MPOD) measured in the macula is vital to macular well-being and high-resolution visual acuity. MPOD has also been associated [...] Read more.
Background: Carotenoids are present throughout retina and body its dense deposition leads to an identifiable yellow spot in the macula. Macular pigment optical density (MPOD) measured in the macula is vital to macular well-being and high-resolution visual acuity. MPOD has also been associated with various health and disease states. We sought to review the literature on this topic and summarize MPODs role as a measurable modifiable clinical biomarker, particularly as a measure of the eye’s antioxidant capacity in the context of oxidative damage and retinal ischemia. Methods: A literature review collated the articles relevant to MPOD, carotenoid intake or supplementation, and their influence on various health and disease states. Results: Literature reveals that MPOD can serve as a reliable biomarker for assessing the retinal defense mechanisms against oxidative stress and the deleterious effects of excessive light exposure. Elevated MPOD levels offer robust protection against the onset and progression of age-related macular degeneration (AMD), a prevalent cause of vision impairment among the elderly population. MPOD’s implications in diverse ocular conditions, including diabetic retinopathy and glaucoma, have been explored, underscoring the real need for clinical measurement of MPOD. The integration of MPOD measurement into routine eye examinations presents an unparalleled opportunity for early disease detection, precise treatment planning, and longitudinal disease monitoring. Conclusions: Longitudinal investigations underscore the significance of MPOD in the context of age-related ocular diseases. These studies show promise and elucidate the dynamic nuances of MPOD’s status and importance as a measurable, modifiable clinical biomarker. Full article
(This article belongs to the Section Clinical Nutrition)
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<p>MPOD model of inflammation. This figure illustrates the hypothesized links between neovascular mechanisms in the eye and the onset of glaucoma. The dotted lines represent theoretical pathways, suggesting potential interactions between increased neovascular activity and intraocular pressure changes leading to glaucomatous damage.</p>
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14 pages, 7142 KiB  
Article
The Neuroprotective and Anxiolytic Effects of Magnesium Sulfate on Retinal Dopaminergic Neurons in 6-OHDA-Induced Parkinsonian Rats: A Pilot Study
by Leyi Huang, Renxi Lin, Chunying Zhang, Shaoqing Zheng, Yiyang Wang, Zeyu Wu, Sihao Chen, Yihan Shen, Guoheng Zhang, Yuanlin Qi and Ling Lin
Brain Sci. 2024, 14(9), 861; https://doi.org/10.3390/brainsci14090861 - 26 Aug 2024
Cited by 1 | Viewed by 1111
Abstract
This study investigates the protective effects of magnesium sulfate on dopamine neurons in the retinas of rats with 6-hydroxydopamine (6-OHDA)-induced Parkinson’s disease (PD). Rapidly progressing cognitive decline often precedes or coincides with the motor symptoms associated with PD. PD patients also frequently exhibit [...] Read more.
This study investigates the protective effects of magnesium sulfate on dopamine neurons in the retinas of rats with 6-hydroxydopamine (6-OHDA)-induced Parkinson’s disease (PD). Rapidly progressing cognitive decline often precedes or coincides with the motor symptoms associated with PD. PD patients also frequently exhibit visual function abnormalities. However, the specific mechanisms underlying visual dysfunction in PD patients are not yet fully understood. Therefore, this study aims to investigate whether magnesium homeostasis affects dopaminergic neurons in the retina of PD rats. Thirty-six rats were divided into four groups: (1) control, (2) control with magnesium sulfate (control/MgSO4), (3) Parkinson’s disease (PD), and (4) Parkinson’s disease with magnesium sulfate (PD/MgSO4). The apomorphine-induced (APO) rotation test assessed the success of the PD models. The open-field experiment measured the rats’ anxiety levels. Tyrosine hydroxylase (TH) and glutamate levels, indicators of dopamine neuron survival, were detected using immunofluorescence staining. Protein levels of solute carrier family 41 A1 (SCL41A1), magnesium transporter 1 (MagT1), and cyclin M2 (CNNM2) in the retina were analyzed using Western blot. Results showed that, compared to the PD group, rats in the PD/MgSO4 group had improved psychological states and motor performance at two and four weeks post-surgery. The PD/MgSO4 group also exhibited significantly higher TH fluorescence intensity in the left retinas and lower glutamate fluorescence intensity than the PD group. Additional experiments indicated that the protein levels of SLC41A1, MagT1, and CNNM2 were generally higher in the retinas of the PD/MgSO4 group, along with an increase in retinal magnesium ion content. This suggests that magnesium sulfate may reduce glutamate levels and protect dopamine neurons in the retina. Thus, magnesium sulfate might have therapeutic potential for visual functional impairments in PD patients. Full article
(This article belongs to the Section Neuromuscular and Movement Disorders)
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<p>The APO-induced rotation test was performed 14 days and 28 days after surgery. # indicates the PD group vs. the control group, <span class="html-italic">p</span> &lt; 0.01; ** indicates the PD/MgSO<sub>4</sub> group vs. the PD group at 28 days after surgery and the PD/MgSO<sub>4</sub> group at 28 days vs. the PD/MgSO<sub>4</sub> group at 14 days, <span class="html-italic">p</span> &lt; 0.01; N = 6.</p>
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<p>(<b>A</b>) Total distance traveled. (<b>B</b>) Distance traveled in the central zone. (<b>C</b>) Activity time in the central zone. (<b>D</b>) Activity traces. # indicates the Control/MgSO<sub>4</sub> group vs. the control group at 28 days after surgery, <span class="html-italic">p</span> &lt; 0.05; ** indicates the PD group vs. the control group at 28 days after surgery, <span class="html-italic">p</span> &lt; 0.01; * indicates the PD group vs. the control group and the PD/MgSO<sub>4</sub> group vs. the PD group at 28 days after surgery, <span class="html-italic">p</span> &lt; 0.05; N = 6.</p>
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<p>(<b>A</b>) TH fluorescence was observed under a laser confocal microscope (bar = 25 μm) (red: CY3, blue: DAPI). IPL: inner plexiform layer; INL: inner nuclear layer. (<b>B</b>) TH immunofluorescence staining intensity in rat retinal tissue. * indicates the PD group vs. the control group (left side) and the PD/MgSO<sub>4</sub> group vs. the PD group (right side) at 14 days after surgery and the PD group vs. the control group (left side) and the PD/MgSO<sub>4</sub> group vs. the PD group (left side) at 28 days after surgery, <span class="html-italic">p</span> &lt; 0.05, N = 6.</p>
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<p>(<b>A</b>) Glutamate fluorescence was observed under a laser confocal microscope (bar = 25 μm) (red: CY3, blue: DAPI). IPL: inner plexiform layer; INL: inner nuclear layer. (<b>B</b>) Glutamate immunofluorescence staining intensity in rat retinal tissue. * indicates the PD group vs. the control group (left side) and the PD/MgSO<sub>4</sub> group vs. the PD group (left side) at 14 days after surgery and the PD group vs. the control group (left side) at 28 days after surgery, <span class="html-italic">p</span> &lt; 0.05; N = 6.</p>
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<p>Correlation analysis of the TH fluorescence intensity with the glutamate fluorescence intensity in the rat retina at 14 days ((<b>A</b>), <span class="html-italic">p</span> &gt; 0.05, N = 8) and 28 days ((<b>B</b>), <span class="html-italic">p</span> &lt; 0.05, N = 8) after surgery.</p>
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<p>Magnesium ion content in rat retinal tissue at 14 and 28 days after surgery was determined with a magnesium ion kit. ** indicates the left side in the PD group vs. the left side in the control group at 14 days after surgery, <span class="html-italic">p</span> &lt; 0.01; * indicates the right side in the PD/MgSO<sub>4</sub> group vs. the right side in the PD group at 28 days after surgery, <span class="html-italic">p</span> &lt; 0.05; N = 6.</p>
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<p>(<b>A</b>) Protein expression of the magnesium ion transporters CNNM2, SLC41A1, and MagT1 in rat retina at 14 days after surgery. (<b>B</b>) Representative Western blot. The relative expression in the right retina of the control group was set as 100%, and the relative expression for each group was calculated as (the experimental group gray value/the internal reference gray value)/(the control group gray value/the internal reference gray value). * indicates <span class="html-italic">p</span> &lt; 0.05; ** indicates <span class="html-italic">p</span> &lt; 0.01; N = 6.</p>
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<p>(<b>A</b>) Protein expression of the magnesium ion transporters CNNM2, SLC41A1, and MagT1 in rat retina at 28 days after surgery. (<b>B</b>) Representative Western blot. The relative expression in the right retina of the control group was set as 100%, and the relative expression for each group was calculated as (the experimental group gray value/the internal reference gray value)/(the control group gray value/the internal reference gray value). ** indicates <span class="html-italic">p</span> &lt; 0.01; N = 6.</p>
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28 pages, 6209 KiB  
Article
Implementation and Evaluation of Spatial Attention Mechanism in Apricot Disease Detection Using Adaptive Sampling Latent Variable Network
by Bingyuan Han, Peiyan Duan, Chengcheng Zhou, Xiaotong Su, Ziyan Yang, Shutian Zhou, Mengxue Ji, Yucen Xie, Jianjun Chen and Chunli Lv
Plants 2024, 13(12), 1681; https://doi.org/10.3390/plants13121681 - 18 Jun 2024
Viewed by 930
Abstract
In this study, an advanced method for apricot tree disease detection is proposed that integrates deep learning technologies with various data augmentation strategies to significantly enhance the accuracy and efficiency of disease detection. A comprehensive framework based on the adaptive sampling latent variable [...] Read more.
In this study, an advanced method for apricot tree disease detection is proposed that integrates deep learning technologies with various data augmentation strategies to significantly enhance the accuracy and efficiency of disease detection. A comprehensive framework based on the adaptive sampling latent variable network (ASLVN) and the spatial state attention mechanism was developed with the aim of enhancing the model’s capability to capture characteristics of apricot tree diseases while ensuring its applicability on edge devices through model lightweighting techniques. Experimental results demonstrated significant improvements in precision, recall, accuracy, and mean average precision (mAP). Specifically, precision was 0.92, recall was 0.89, accuracy was 0.90, and mAP was 0.91, surpassing traditional models such as YOLOv5, YOLOv8, RetinaNet, EfficientDet, and DEtection TRansformer (DETR). Furthermore, through ablation studies, the critical roles of ASLVN and the spatial state attention mechanism in enhancing detection performance were validated. These experiments not only showcased the contributions of each component for improving model performance but also highlighted the method’s capability to address the challenges of apricot tree disease detection in complex environments. Eight types of apricot tree diseases were detected, including Powdery Mildew and Brown Rot, representing a technological breakthrough. The findings provide robust technical support for disease management in actual agricultural production and offer broad application prospects. Full article
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<p>Samples from the dataset used in this paper: (<b>a</b>) Powdery Mildew Disease, (<b>b</b>) Brown Rot Disease, (<b>c</b>) Scab Disease, (<b>d</b>) Bacterial Leaf Spot Disease, (<b>e</b>) Almond Bee Disease, (<b>f</b>) Apricot Sore Disease, (<b>g</b>) Scale Chosomiasis Disease, and (<b>h</b>) Apricot Moth Disease.</p>
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<p>Image dataset enhancement methods used in this paper: (<b>a</b>) Cutout, (<b>b</b>) Cutmix (During training, the labels of the target objects can be weighted according to the mixing ratio of the regions. For example, if the proportions of the original image and the mixed image are <math display="inline"><semantics> <mi>λ</mi> </semantics></math> and <math display="inline"><semantics> <mrow> <mn>1</mn> <mo>−</mo> <mi>λ</mi> </mrow> </semantics></math>, respectively, the label weights of the target objects can be adjusted accordingly to <math display="inline"><semantics> <mi>λ</mi> </semantics></math> and <math display="inline"><semantics> <mrow> <mn>1</mn> <mo>−</mo> <mi>λ</mi> </mrow> </semantics></math>), (<b>c</b>) Mosaic, (<b>d</b>) Replication Augmentation (The duplicated target objects should retain the same label information as the original objects. In the annotation file, all duplicated target objects should have labels consistent with the original objects to ensure that the model can correctly identify and classify these target objects during training).</p>
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<p>The illustration describes the architecture flow of the apricot disease detection model proposed in this paper. This process includes image input, feature extraction, classification, and the training and prediction processes. Initially, the input images are processed through a CNN for feature extraction, where the CNN layers capture the key features within the images; subsequently, the extracted feature vectors are passed to fully connected layers, which output the final probabilities of disease categories through the softmax function. During the training phase, the model optimizes parameters via the loss function, whereas in the prediction phase, the model uses these trained parameters to assess new images for disease detection. This flowchart clearly demonstrates the complete steps from image processing to disease diagnosis, effectively supporting the experimental part and theoretical analysis of the method described in this paper.</p>
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<p>The illustration shows the conceptual model of the ASLVN (adaptive sampling latent variable network) structure proposed in this paper. It details the entire process from the input layer to the output layer and all its components, including the input data <math display="inline"><semantics> <mrow> <msubsup> <mi>x</mi> <mn>1</mn> <mi>k</mi> </msubsup> <mo>,</mo> <msubsup> <mi>x</mi> <mn>2</mn> <mi>k</mi> </msubsup> <mo>,</mo> <mo>…</mo> <mo>,</mo> <msubsup> <mi>x</mi> <mi>m</mi> <mi>k</mi> </msubsup> </mrow> </semantics></math> and the resulting outputs <math display="inline"><semantics> <mrow> <msubsup> <mi>o</mi> <mn>1</mn> <mi>k</mi> </msubsup> <mo>,</mo> <msubsup> <mi>o</mi> <mn>2</mn> <mi>k</mi> </msubsup> <mo>,</mo> <mo>…</mo> <mo>,</mo> <msubsup> <mi>o</mi> <mi>n</mi> <mi>k</mi> </msubsup> </mrow> </semantics></math> processed through the network. The diagram also shows the connections and information flow between different layers, particularly highlighting the latent variables in the hidden layers and how they impact the output results. The ASLVN structure effectively integrates data features and optimizes the learning process of the network through an adaptive sampling mechanism, enhancing the model’s ability to handle complex data structures. This structure diagram clearly expresses the core mechanism and working principles of the ASLVN, providing an intuitive view for understanding and analyzing the network structure.</p>
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<p>The illustration shows the architectural details of the spatial state attention mechanism proposed in this paper. This includes both channel attention and spatial attention modules, showing how the integration of these two attention mechanisms enhances the model’s focus on features. The channel attention module learns the importance of different channels through global average pooling and fully connected layers, thereby weighting the features of each channel; the spatial attention module focuses on the importance of spatial locations, emphasizing key spatial areas through convolution operations. The collaborative function of these two modules forms the spatial state attention mechanism described in this paper, effectively enhancing the model’s ability to recognize key features in apricot disease detection.</p>
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<p>The illustration describes the basic principle of the knowledge distillation process. It shows the knowledge transfer mechanism from the “teacher model” to the “student model”. Typically, the teacher model is a large and complex pre-trained deep learning model that has already acquired extensive knowledge through training. During the knowledge distillation process, the output of the teacher model is used as guidance information (soft labels) to help train a smaller student model. The student model learns and extracts important knowledge by mimicking the output of the teacher model, achieving near-teacher-model performance while being smaller and more computationally efficient. This diagram clearly demonstrates the application framework of knowledge distillation technology, i.e., how to optimize the learning process of the student model through the teacher model.</p>
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<p>Confuse matrix of detection results: (a) Powdery Mildew Disease, (b) Brown Rot Disease, (c) Scab Disease, (d) Bacterial Leaf Spot Disease, (e) Almond Bee Disease, (f) Apricot Sore Disease, (g) Scale Chosomiasis Disease, and (h) Apricot Moth Disease.</p>
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36 pages, 2067 KiB  
Review
Immunogenetic and Environmental Factors in Age-Related Macular Disease
by Sylwia Brodzka, Jędrzej Baszyński, Katarzyna Rektor, Karolina Hołderna-Bona, Emilia Stanek, Natalia Kurhaluk, Halina Tkaczenko, Grażyna Malukiewicz, Alina Woźniak and Piotr Kamiński
Int. J. Mol. Sci. 2024, 25(12), 6567; https://doi.org/10.3390/ijms25126567 - 14 Jun 2024
Cited by 3 | Viewed by 1208
Abstract
Age-related macular degeneration (AMD) is a chronic disease, which often develops in older people, but this is not the rule. AMD pathogenesis changes include the anatomical and functional complex. As a result of damage, it occurs, in the retina and macula, among other [...] Read more.
Age-related macular degeneration (AMD) is a chronic disease, which often develops in older people, but this is not the rule. AMD pathogenesis changes include the anatomical and functional complex. As a result of damage, it occurs, in the retina and macula, among other areas. These changes may lead to partial or total loss of vision. This disease can occur in two clinical forms, i.e., dry (progression is slowly and gradually) and exudative (wet, progression is acute and severe), which usually started as dry form. A coexistence of both forms is possible. AMD etiology is not fully understood. Extensive genetic studies have shown that this disease is multifactorial and that genetic determinants, along with environmental and metabolic-functional factors, are important risk factors. This article reviews the impact of heavy metals, macro- and microelements, and genetic factors on the development of AMD. We present the current state of knowledge about the influence of environmental factors and genetic determinants on the progression of AMD in the confrontation with our own research conducted on the Polish population from Kuyavian-Pomeranian and Lubusz Regions. Our research is concentrated on showing how polluted environments of large agglomerations affects the development of AMD. In addition to confirming heavy metal accumulation, the growth of risk of acute phase factors and polymorphism in the genetic material in AMD development, it will also help in the detection of new markers of this disease. This will lead to a better understanding of the etiology of AMD and will help to establish prevention and early treatment. Full article
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<p>The formation of AMD during aging. Non-genetic mechanisms of AMD are induced by retinal pigment epithelium (RPE) cell senescence, oxidative stress, hemodynamics, and during aging (modified after Deng et al. (2022) [<a href="#B14-ijms-25-06567" class="html-bibr">14</a>].</p>
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<p>AMD development and protective mechanism of antioxidants (modified after Arslan et al., 2018 [<a href="#B17-ijms-25-06567" class="html-bibr">17</a>]. Arrows indicate mutual relations between parameters in rectangles.</p>
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16 pages, 2981 KiB  
Review
The Role of Glutathione in Age-Related Macular Degeneration (AMD)
by Sylwia Brodzka, Jędrzej Baszyński, Katarzyna Rektor, Karolina Hołderna-Bona, Emilia Stanek, Natalia Kurhaluk, Halina Tkaczenko, Grażyna Malukiewicz, Alina Woźniak and Piotr Kamiński
Int. J. Mol. Sci. 2024, 25(8), 4158; https://doi.org/10.3390/ijms25084158 - 9 Apr 2024
Cited by 6 | Viewed by 2091
Abstract
Age-related macular degeneration (AMD) is a chronic disease that usually develops in older people. Pathogenetic changes in this disease include anatomical and functional complexes. Harmful factors damage the retina and macula. These changes may lead to partial or total loss of vision. The [...] Read more.
Age-related macular degeneration (AMD) is a chronic disease that usually develops in older people. Pathogenetic changes in this disease include anatomical and functional complexes. Harmful factors damage the retina and macula. These changes may lead to partial or total loss of vision. The disease can occur in two clinical forms: dry (the progression is slow and gentle) and exudative (wet—progression is acute and severe), which usually starts in the dry form; however, the coexistence of both forms is possible. The etiology of AMD is not fully understood, and the precise mechanisms of the development of this illness are still unknown. Extensive genetic studies have shown that AMD is a multi-factorial disease and that genetic determinants, along with external and internal environmental and metabolic-functional factors, are important risk factors. This article reviews the role of glutathione (GSH) enzymes engaged in maintaining the reduced form and polymorphism in glutathione S-transferase theta-1 (GSTT1) and glutathione S-transferase mu-1 (GSTM1) in the development of AMD. We only chose papers that confirmed the influence of the parameters on the development of AMD. Because GSH is the most important antioxidant in the eye, it is important to know the influence of the enzymes and genetic background to ensure an optimal level of glutathione concentration. Numerous studies have been conducted on how the glutathione system works till today. This paper presents the current state of knowledge about the changes in GSH, GST, GR, and GPx in AMD. GST studies clearly show increased activity in ill people, but for GPx, the results relating to activity are not so clear. Depending on the research, the results also suggest higher and lower GPx activity in patients with AMD. The analysis of polymorphisms in GST genes confirmed that mutations lead to weaker antioxidant barriers and may contribute to the development of AMD; unfortunately, a meta-analysis and some research did not confirm that connection. Unspecific results of many of the parameters that make up the glutathione system show many unknowns. It is so important to conduct further research to understand the exact mechanism of defense functions of glutathione against oxidative stress in the human eye. Full article
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<p>The figure shows the two different clinical forms of macular degeneration (modified from the work of Nayyar et al. (2020) [<a href="#B7-ijms-25-04158" class="html-bibr">7</a>]).</p>
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<p>The figure shows the risk factors for age-related macular degeneration (AMD). CFH: complement H activity; ApoE: apolipoprotein E; ARMS2: age-related maculopathy susceptibility 2 (modified from the work of Hyttinen et al. (2023) [<a href="#B9-ijms-25-04158" class="html-bibr">9</a>]).</p>
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<p>The figure shows the enzymes involved during glutathione synthesis and metabolism in the retina. AC: amacrine cell; BPC: bipolar cell; GC: ganglion cell; GCL: ganglion cell layer; γGCL: γ-glutamate cysteine ligase; G6PD: glucose-6-phosphate dehydrogenase; 6PG: 6-phosphogluconate; GPx: glutathione peroxidase; GR: glutathione reductase; GS: glutathione synthase; GSH: glutathione; ROD: rhodopsin; HC: horizontal cell; INL: inner nuclear layer; IPL: inner plexiform layer; IOSP: inner and outer segments of photoreceptors; NF: nerve fiber; ONL: outer nuclear layer; OPL: outer plexiform layer; protein-S2: protein-S−S; protein (SH)2: protein-SH; RPE: retinal pigment epithelium; TR: thioredoxin reductase; TRX (SH)2: thioredoxin; TRX-S2: oxidized thioredoxin (modified from the work of McBean et al. (2015) [<a href="#B48-ijms-25-04158" class="html-bibr">48</a>]).</p>
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<p>The figure shows the genes and their associations with AMD pathogenesis. Cellular functions, e.g., apoptotic, tumorigenesis, homologous recombination, angiogenesis, and inflammation are regulated by genes that stimulate the cardinal features of AMD abnormalities. Question marks symbolize the expected role of factors in the processes involved in AMD’s development (modified from the work of Anand et al. (2016) [<a href="#B95-ijms-25-04158" class="html-bibr">95</a>]).</p>
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23 pages, 1300 KiB  
Review
Retinal Ciliopathies and Potential Gene Therapies: A Focus on Human iPSC-Derived Organoid Models
by Andrew McDonald and Jan Wijnholds
Int. J. Mol. Sci. 2024, 25(5), 2887; https://doi.org/10.3390/ijms25052887 - 1 Mar 2024
Cited by 3 | Viewed by 2780
Abstract
The human photoreceptor function is dependent on a highly specialised cilium. Perturbation of cilial function can often lead to death of the photoreceptor and loss of vision. Retinal ciliopathies are a genetically diverse range of inherited retinal disorders affecting aspects of the photoreceptor [...] Read more.
The human photoreceptor function is dependent on a highly specialised cilium. Perturbation of cilial function can often lead to death of the photoreceptor and loss of vision. Retinal ciliopathies are a genetically diverse range of inherited retinal disorders affecting aspects of the photoreceptor cilium. Despite advances in the understanding of retinal ciliopathies utilising animal disease models, they can often lack the ability to accurately mimic the observed patient phenotype, possibly due to structural and functional deviations from the human retina. Human-induced pluripotent stem cells (hiPSCs) can be utilised to generate an alternative disease model, the 3D retinal organoid, which contains all major retinal cell types including photoreceptors complete with cilial structures. These retinal organoids facilitate the study of disease mechanisms and potential therapies in a human-derived system. Three-dimensional retinal organoids are still a developing technology, and despite impressive progress, several limitations remain. This review will discuss the state of hiPSC-derived retinal organoid technology for accurately modelling prominent retinal ciliopathies related to genes, including RPGR, CEP290, MYO7A, and USH2A. Additionally, we will discuss the development of novel gene therapy approaches targeting retinal ciliopathies, including the delivery of large genes and gene-editing techniques. Full article
(This article belongs to the Special Issue Molecular Advances in Retinal Diseases)
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<p>The structure of human cone and rod photoreceptors and connecting cilium. Both cone and rod photoreceptors are divided into two distinct sections, the inner segment, and the disc containing outer segment. The region connecting these distinct compartments is known as the connecting cilium or transition zone (CC/TZ). The outer segment lacks the capacity for protein synthesis and is dependent on protein trafficking across the CC/TZ and subsequent transport along the distal axoneme. Numerous proteins are required for cilial function and maintenance, such as RPGR and CEP290 localized in the CC/TZ or usherin located in the periciliary membrane (PCM). Black arrows depict anterograde and retrograde cilial transport.</p>
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<p>Alternative approaches for the delivery for large cilial genes. (<b>A</b>) Dual AAV trans-splicing: Two independently delivered viral genomes containing either the 5′ or 3′ coding sequence (CDS) recombined via concatemerization or homologous recombination mediated by the homology recombination domains (HRDs). The inclusion of splice donor (SD) and splice acceptor (SA) sequences permits RNA splicing to produce a mature mRNA encoding for full-length protein. (<b>B</b>) Protein trans-splicing: The CDS is split across two independent viral vectors resulting in the expression of either N- or C-terminal polypeptides of the desired full-length protein. Adjoined to these peptides are either the N- or C-terminal of a split-intein; post-translationally, the split-intein spontaneously recombines and self-excises, resulting in full-length protein. (<b>C</b>) mRNA trans-splicing: dual AAVs result in the transcription of two independent mRNAs encoding each half of the desired sequence, and the inclusion of complementary binding domains (BDs) allows for recombination. Flanking SD and SA sites facilitate RNA splicing and the removal of the BD sequences, resulting in a mature, full-length mRNA. (<b>D</b>) High-capacity adenovirus has a large cargo capacity of up to 36 kb; this facilitates the delivery of large genes in their entirety with a single vector. Promoter (blue arrow); polyadenylation signal (pA) (created with BioRender.com).</p>
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24 pages, 2326 KiB  
Review
Health Benefits of Oily Fish: Illustrated with Blue Shark (Prionace glauca), Shortfin Mako Shark (Isurus oxyrinchus), and Swordfish (Xiphias gladius)
by Franklin Chamorro, Paz Otero, Maria Carpena, Maria Fraga-Corral, Javier Echave, Sepidar Seyyedi-Mansour, Lucia Cassani and Miguel A. Prieto
Nutrients 2023, 15(23), 4919; https://doi.org/10.3390/nu15234919 - 25 Nov 2023
Cited by 3 | Viewed by 3122
Abstract
Oily fish is a rich source of energy, proteins, essential amino acids, lipids, vitamins, and minerals. Among the macronutrients with the highest contribution are lipids, mainly long-chain omega 3 polyunsaturated fatty acids (ω-3 LC-PUFA), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Both [...] Read more.
Oily fish is a rich source of energy, proteins, essential amino acids, lipids, vitamins, and minerals. Among the macronutrients with the highest contribution are lipids, mainly long-chain omega 3 polyunsaturated fatty acids (ω-3 LC-PUFA), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Both EPA and DHA play a beneficial role in promoting health and preventing many diseases, including cardiovascular diseases, such as stroke and acute myocardial infarction. They also contribute to the prevention of neurological, metabolic, and immune-system-related diseases, as well as supporting body-weight control. Oily fish consumption is also important at different stages of human life, from conception to old age. For example, DHA plays an important role in brain and retina development during fetal development and in the first two years of life, as it positively influences neurodevelopment, such as visual acuity, and cognitive functions. In contrast with the possible health benefits of the intake of oily fish, the presence of certain chemical pollutants, for example, heavy metals, can be a risk for the health of consumers, mainly in sensitive population groups such as pregnant women and children under 2 years of age. The presence of these pollutants is influenced to a greater extent by fish species, their role in the trophic chain, and their size. However, various studies state that the benefits outweigh the risk of consuming certain species. This review will be focused on the health benefits of the intake of three oily fish species, namely blue shark (Prionace glauca), shortfin mako shark (Isurus oxyrinchus), and swordfish (Xiphias gladius). Full article
(This article belongs to the Special Issue Fish Intake and Human Health: Evaluating the Nutrients and Benefits)
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<p>Nutritional composition of the species <span class="html-italic">Xiphias gladius</span>, <span class="html-italic">Prionace glauca</span>, and <span class="html-italic">Isurus oxyrinchus</span> expressed in percentage (%). (<b>A</b>) Nutritional composition and lipid profile. (<b>B</b>) Mineral composition. (<b>C</b>) Vitamin composition. <span class="html-italic"><span class="underline">Note</span></span>: those pie charts that do not reach 100%, correspond to small percentages (0.1–0.2%) of (<b>B</b>) other minerals (Fe, I, Zn) and (<b>C</b>) vitamins (folates, vitamin D).</p>
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<p>Summary of oily fish characteristics, chemical pollutants, and potential health benefits from the consumption of oily fish.</p>
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12 pages, 2024 KiB  
Review
Immune System, Inflammation and Autoantigens in Wet Age-Related Macular Degeneration: Pathological Significance and Therapeutic Importance
by Sreeraj Kuruppilakath Manikandan, Ann Logan, Marc Cerrada-Gimenez, Laurence Fitzhenry, Lee Coffey, Simon Kaja and Sweta Rani
Life 2023, 13(12), 2236; https://doi.org/10.3390/life13122236 - 21 Nov 2023
Cited by 1 | Viewed by 2257
Abstract
Wet age-related macular degeneration (wAMD) is a chronic inflammation-associated neurodegenerative disease affecting the posterior part of the eye in the aging population. Aging results in the reduced functionality of cells and tissues, including the cells of the retina. Initiators of a chronic inflammatory [...] Read more.
Wet age-related macular degeneration (wAMD) is a chronic inflammation-associated neurodegenerative disease affecting the posterior part of the eye in the aging population. Aging results in the reduced functionality of cells and tissues, including the cells of the retina. Initiators of a chronic inflammatory and pathologic state in wAMD may be a result of the accumulation of inevitable metabolic injuries associated with the maintenance of tissue homeostasis from a young age to over 50. Apart from this, risk factors like smoking, genetic predisposition, and failure to repair the injuries that occur, alongside attempts to rescue the hypoxic outer retina may also contribute to the pathogenesis. Aging of the immune system (immunosenescence) and a compromised outer blood retinal barrier (BRB) result in the exposure of the privileged milieu of the retina to the systemic immune system, further increasing the severity of the disease. When immune-privileged sites like the retina are under pathological stress, certain age- and disease-related conditions may necessitate assistance from cells distant from the resident ones to help restore the functionality of the tissue. As a necessary part of tissue repair, inflammation is a major response to disease and recruits immune cells to the site of damage. We suspect that the specific reparative inflammatory responses are controlled by an autoantigen-T cell-mediated mechanism, a process that may be hindered in wAMD. Full article
(This article belongs to the Special Issue Retinal Disease: Diagnosis and Treatment)
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<p>Schematic representation of the retinal structure. Showing an enlarged view of the neurosensory retina, where the central area is called the macular region, which is mostly composed of cone photoreceptor (PR) cells. The loss of macula PR cells affects the central vision since the cones are responsible for activities dependent on visual acuity like reading, driving, writing, and color recognition. Image created in <a href="http://Biorender.com" target="_blank">Biorender.com</a>.</p>
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<p>Hypothetical diagrammatic representation of the effects of autoantigen when presented in the AMD eye <span class="html-italic">versus</span> peripheral tissues. (<b>A</b>) The local delivery of autoantigens in retina is not able to produce a beneficial response by recruiting immune cells to the site (numbers 1–6 explains the sequence of mechanisms when autoantigen is delivered in the AMD eye). (<b>B</b>) The peripheral tissue delivery of autoantigens evokes a local beneficial response resulting in recruitment of immune cells to the retina mediated by T cells (numbers 1–6 explains the sequence of mechanisms when autoantigen is delivered in the peripheral tissues) APCs: antigen presenting cells; MHC: major histocompatibility complex; Ap: antigen presentation; RPE: retinal pigment epithelium; LOP: loss of photoreceptors; CNV: choroidal neovascularization; arrow: blue represents the peripheral route, and red represents the local ocular route.</p>
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<p>Advantages of peripheral route over intravitreal injection for delivery of drugs. Image created in <a href="http://Biorender.com" target="_blank">Biorender.com</a> [<a href="#B71-life-13-02236" class="html-bibr">71</a>,<a href="#B72-life-13-02236" class="html-bibr">72</a>,<a href="#B73-life-13-02236" class="html-bibr">73</a>].</p>
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29 pages, 3943 KiB  
Article
Patterns of Gene Expression, Splicing, and Allele-Specific Expression Vary among Macular Tissues and Clinical Stages of Age-Related Macular Degeneration
by Treefa Shwani, Charles Zhang, Leah A. Owen, Akbar Shakoor, Albert T. Vitale, John H. Lillvis, Julie L. Barr, Parker Cromwell, Robert Finley, Nadine Husami, Elizabeth Au, Rylee A. Zavala, Elijah C. Graves, Sarah X. Zhang, Michael H. Farkas, David A. Ammar, Karen M. Allison, Amany Tawfik, Richard M. Sherva, Mingyao Li, Dwight Stambolian, Ivana K. Kim, Lindsay A. Farrer and Margaret M. DeAngelisadd Show full author list remove Hide full author list
Cells 2023, 12(23), 2668; https://doi.org/10.3390/cells12232668 - 21 Nov 2023
Cited by 3 | Viewed by 2802
Abstract
Age-related macular degeneration (AMD) is a leading cause of blindness, and elucidating its underlying disease mechanisms is vital to the development of appropriate therapeutics. We identified differentially expressed genes (DEGs) and differentially spliced genes (DSGs) across the clinical stages of AMD in disease-affected [...] Read more.
Age-related macular degeneration (AMD) is a leading cause of blindness, and elucidating its underlying disease mechanisms is vital to the development of appropriate therapeutics. We identified differentially expressed genes (DEGs) and differentially spliced genes (DSGs) across the clinical stages of AMD in disease-affected tissue, the macular retina pigment epithelium (RPE)/choroid and the macular neural retina within the same eye. We utilized 27 deeply phenotyped donor eyes (recovered within a 6 h postmortem interval time) from Caucasian donors (60–94 years) using a standardized published protocol. Significant findings were then validated in an independent set of well-characterized donor eyes (n = 85). There was limited overlap between DEGs and DSGs, suggesting distinct mechanisms at play in AMD pathophysiology. A greater number of previously reported AMD loci overlapped with DSGs compared to DEGs between disease states, and no DEG overlap with previously reported loci was found in the macular retina between disease states. Additionally, we explored allele-specific expression (ASE) in coding regions of previously reported AMD risk loci, uncovering a significant imbalance in C3 rs2230199 and CFH rs1061170 in the macular RPE/choroid for normal eyes and intermediate AMD (iAMD), and for CFH rs1061147 in the macular RPE/choroid for normal eyes and iAMD, and separately neovascular AMD (NEO). Only significant DEGs/DSGs from the macular RPE/choroid were found to overlap between disease states. STAT1, validated between the iAMD vs. normal comparison, and AGTPBP1, BBS5, CERKL, FGFBP2, KIFC3, RORα, and ZNF292, validated between the NEO vs. normal comparison, revealed an intricate regulatory network with transcription factors and miRNAs identifying potential upstream and downstream regulators. Findings regarding the complement genes C3 and CFH suggest that coding variants at these loci may influence AMD development via an imbalance of gene expression in a tissue-specific manner. Our study provides crucial insights into the multifaceted genomic underpinnings of AMD (i.e., tissue-specific gene expression changes, potential splice variation, and allelic imbalance), which may open new avenues for AMD diagnostics and therapies specific to iAMD and NEO. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Genetic Eye Diseases)
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<p>Violin plot of Log<sub>10</sub>-transformed FPKM counts from 27 donor eye samples with both the macular RPE/choroid and macular retina shown. Abbreviations: AMD, age-related macular degeneration, RPE, retinal pigment epithelium, FPKM, fragments per kilobase of transcript per million mapped reads.</p>
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<p>Volcano plots of differentially expressed genes across disease states. (<b>A</b>–<b>F</b>) Each dot represents one of the 26,650 genes expressed. Blue and red represent significant genes, with red indicating upregulation and blue indicating downregulation in each disease comparison. Grey dots represent genes that did not meet the significance threshold of <span class="html-italic">padj</span> &lt; 0.05 and a fold change ≥ |1.5|. The ten most significant genes in each disease comparison are labeled. Abbreviations: AMD, age-related macular degeneration, RPE, retinal pigment epithelium.</p>
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<p>Overlap of differentially expressed genes (DEGs) and differentially spliced genes (DSGs) between intermediate AMD (iAMD) vs. normal and neovascular AMD (NEO) vs. normal. (<b>A</b>–<b>D</b>) Each circle represents the number of significant DEGs or DSGs in macular RPE (retinal pigment epithelium)/choroid and macular retina. The overlap between these two circles shows the number of overlapping genes that were regulated in the same direction between each comparison. Abbreviations: AMD, age-related macular degeneration, RPE, retinal pigment epithelium.</p>
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<p>Volcano plots of differentially spliced genes across disease states. (<b>A</b>–<b>F</b>) Each dot represents one of the 26,650 genes expressed. Blue and red represent significant genes, with red representing upregulation and blue representing downregulation in each disease comparison. Grey dots represent genes that did not meet the significance threshold of <span class="html-italic">padj</span> &lt; 0.05 and a fold change ≥ |1.5|. The ten most significant genes in each disease comparison are labelled. Abbreviations: AMD, age-related macular degeneration, RPE, retinal pigment epithelium.</p>
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<p>Gene set enrichment analysis (GSEA) using our normalized expression dataset. Thresholds were set based on the nominal <span class="html-italic">p</span>-value &lt; 0.05 and FDR q-value ≤ 0.05 generated by the GSEA software, v.4.3.2. (<b>A</b><span class="html-italic">–</span><b>C</b>) show the significant hallmarks (<span class="html-italic">p</span>-value &lt; 0.05, FDR q-value ≤ 0.05) identified in the macular RPE/choroid across disease state. (<b>D</b>,<b>E</b>) show the significant hallmarks (<span class="html-italic">p</span>-value &lt; 0.05, FDR q-value ≤ 0.05) identified in the macular retina across disease state. Please note: no hallmark was identified to be significantly upregulated in neovascular AMD for the macular retina. Abbreviations: GSEA, gene set enrichment analysis, AMD, age-related macular degeneration, RPE, retinal pigment epithelium.</p>
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<p>Visualization of significant DEGs and DSGs (previously associated with AMD) found in normal macular RPE/choroid vs. normal macular retina to illustrate directionality in normal tissues. Abbreviations: AMD, age-related macular degeneration, RPE, retinal pigment epithelium, DEG, differentially expressed gene, DSG, differentially spliced gene.</p>
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<p>Ingenuity Pathway Analysis (IPA)-generated network of our validated genes (DEGs, DSGs, and confirmed in an independent bulk RNAseq dataset): (<b>A</b>,<b>B</b>) show the 7 identified genes from NEO vs. normal; (<b>C</b>,<b>D</b>) show our 7 identified genes from NEO vs. normal combined with <span class="html-italic">STAT1</span>, our validated gene from iAMD vs. normal. Each network is overlaid with expression values/fold changes from either our DEG or DSG dataset for that disease state comparison. Red or green indicates the gene was found in our dataset and associated with increased or decreased measurement, respectively. Orange or blue indicates the gene was not in our dataset but is predicted to be associated with activation or inhibition. Further clarification is provided in the legend. Abbreviations: DEG, differentially expressed gene, DSG, differentially spliced gene.</p>
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30 pages, 2383 KiB  
Review
Senescent Cells: Dual Implications on the Retinal Vascular System
by Mohammad Reza Habibi-Kavashkohie, Tatiana Scorza and Malika Oubaha
Cells 2023, 12(19), 2341; https://doi.org/10.3390/cells12192341 - 23 Sep 2023
Cited by 1 | Viewed by 2456
Abstract
Cellular senescence, a state of permanent cell cycle arrest in response to endogenous and exogenous stimuli, triggers a series of gradual alterations in structure, metabolism, and function, as well as inflammatory gene expression that nurtures a low-grade proinflammatory milieu in human tissue. A [...] Read more.
Cellular senescence, a state of permanent cell cycle arrest in response to endogenous and exogenous stimuli, triggers a series of gradual alterations in structure, metabolism, and function, as well as inflammatory gene expression that nurtures a low-grade proinflammatory milieu in human tissue. A growing body of evidence indicates an accumulation of senescent neurons and blood vessels in response to stress and aging in the retina. Prolonged accumulation of senescent cells and long-term activation of stress signaling responses may lead to multiple chronic diseases, tissue dysfunction, and age-related pathologies by exposing neighboring cells to the heightened pathological senescence-associated secretory phenotype (SASP). However, the ultimate impacts of cellular senescence on the retinal vasculopathies and retinal vascular development remain ill-defined. In this review, we first summarize the molecular players and fundamental mechanisms driving cellular senescence, as well as the beneficial implications of senescent cells in driving vital physiological processes such as embryogenesis, wound healing, and tissue regeneration. Then, the dual implications of senescent cells on the growth, hemostasis, and remodeling of retinal blood vessels are described to document how senescent cells contribute to both retinal vascular development and the severity of proliferative retinopathies. Finally, we discuss the two main senotherapeutic strategies—senolytics and senomorphics—that are being considered to safely interfere with the detrimental effects of cellular senescence. Full article
(This article belongs to the Special Issue Molecular Regulation in Ocular Physiology and Diseases)
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<p>Cardinal features of senescent cells. The morphology, metabolism, and biomarkers of senescent cells are illustrated.</p>
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<p>Senescence molecular pathways. Cell cycle arrest occurs in senescent cells via two independent pathways: p53-dependet senescence pathway and p53-independent senescence pathway. Senescence inducers and the main effective downstream molecules are illustrated.</p>
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<p>Beneficial effects of SCs. Just the three beneficial effects (embryogenesis, regeneration, and wound healing) that are more related to the context of this review were discussed in the main text.</p>
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<p>Detrimental effect: vascular degeneration. Senescence phenotype in pericyte and retinal endothelial cells is associated with pericyte detachment and vascular leakage.</p>
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<p>Detrimental effect: pathological angiogenesis. In the stressed retina, senescence neurons in the avascular area attract tip cells of the retinal blood vessel by releasing various proinflammatory and angiogenic factors and lead to dysregulated angiogenesis as a common feature of proliferative retinopathies.</p>
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<p>Beneficial effects of cellular senescence: vascular remodeling. Immune-mediated clearance of retinal SCs promotes the regression of pathological neovessels. Neutrophils recruit NETs (neutrophil extracellular traps) and prepare the retina for a reparative mechanism of regeneration by eliminating tuft-like neovessels.</p>
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17 pages, 15651 KiB  
Article
Discriminative-Region Multi-Label Classification of Ultra-Widefield Fundus Images
by Van-Nguyen Pham, Duc-Tai Le, Junghyun Bum, Seong Ho Kim, Su Jeong Song and Hyunseung Choo
Bioengineering 2023, 10(9), 1048; https://doi.org/10.3390/bioengineering10091048 - 6 Sep 2023
Viewed by 1590
Abstract
Ultra-widefield fundus image (UFI) has become a crucial tool for ophthalmologists in diagnosing ocular diseases because of its ability to capture a wide field of the retina. Nevertheless, detecting and classifying multiple diseases within this imaging modality continues to pose a significant challenge [...] Read more.
Ultra-widefield fundus image (UFI) has become a crucial tool for ophthalmologists in diagnosing ocular diseases because of its ability to capture a wide field of the retina. Nevertheless, detecting and classifying multiple diseases within this imaging modality continues to pose a significant challenge for ophthalmologists. An automated disease classification system for UFI can support ophthalmologists in making faster and more precise diagnoses. However, existing works for UFI classification often focus on a single disease or assume each image only contains one disease when tackling multi-disease issues. Furthermore, the distinctive characteristics of each disease are typically not utilized to improve the performance of the classification systems. To address these limitations, we propose a novel approach that leverages disease-specific regions of interest for the multi-label classification of UFI. Our method uses three regions, including the optic disc area, the macula area, and the entire UFI, which serve as the most informative regions for diagnosing one or multiple ocular diseases. Experimental results on a dataset comprising 5930 UFIs with six common ocular diseases showcase that our proposed approach attains exceptional performance, with the area under the receiver operating characteristic curve scores for each class spanning from 95.07% to 99.14%. These results not only surpass existing state-of-the-art methods but also exhibit significant enhancements, with improvements of up to 5.29%. These results demonstrate the potential of our method to provide ophthalmologists with valuable information for early and accurate diagnosis of ocular diseases, ultimately leading to improved patient outcomes. Full article
(This article belongs to the Special Issue Biomedical Imaging and Analysis of the Eye)
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Graphical abstract

Graphical abstract
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<p>Lesions’ distribution of each disease.</p>
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<p>Dataset statistics.</p>
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<p>Samples of images with one disease: (<b>a</b>–<b>f</b>), two diseases: (<b>g</b>,<b>h</b>), three diseases: (<b>i</b>–<b>k</b>), and normal: (<b>l</b>).</p>
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<p>Overall process of the proposed method. Each output from CNNs represents the probability of containing a specific disease. If this value is greater than the cut-off threshold, the image is predicted as containing disease, otherwise, non-disease.</p>
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<p>The process of detecting the optic disc and macula.</p>
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<p>Optic disc and macula areas.</p>
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<p>ROC curves for each disease. The curve closer to the top left corner indicates better performance. <span style="color: #FF0000">Red</span>: Proposed, <span style="color: #FF9900">Orange</span>: Lee et al. [<a href="#B30-bioengineering-10-01048" class="html-bibr">30</a>], <span style="color: #00FF00">Green</span>: Wang et al. [<a href="#B31-bioengineering-10-01048" class="html-bibr">31</a>], <span style="color: #0000FF">Blue</span>: Zhang et al. [<a href="#B12-bioengineering-10-01048" class="html-bibr">12</a>], Dashed line: random classifier.</p>
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<p>Confusion matrix for each class of our method. For each class, “positive” refers to the corresponding class, while “negative” refers to all other classes.</p>
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<p>Illustration of ROIs with different edge lengths, <span class="html-italic">d</span> is the diagonal length of the detected optic disc box. The first and second rows show macula and optic disc areas, respectively.</p>
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<p>Number of misclassified images in each class.</p>
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32 pages, 458 KiB  
Review
Gene Therapy in Hereditary Retinal Dystrophies: The Usefulness of Diagnostic Tools in Candidate Patient Selections
by Mariaelena Malvasi, Lorenzo Casillo, Filippo Avogaro, Alessandro Abbouda and Enzo Maria Vingolo
Int. J. Mol. Sci. 2023, 24(18), 13756; https://doi.org/10.3390/ijms241813756 - 6 Sep 2023
Cited by 4 | Viewed by 2592
Abstract
Purpose: Gene therapy actually seems to have promising results in the treatment of Leber Congenital Amaurosis and some different inherited retinal diseases (IRDs); the primary goal of this strategy is to change gene defects with a wild-type gene without defects in a DNA [...] Read more.
Purpose: Gene therapy actually seems to have promising results in the treatment of Leber Congenital Amaurosis and some different inherited retinal diseases (IRDs); the primary goal of this strategy is to change gene defects with a wild-type gene without defects in a DNA sequence to achieve partial recovery of the photoreceptor function and, consequently, partially restore lost retinal functions. This approach led to the introduction of a new drug (voretigene neparvovec-rzyl) for replacement of the RPE65 gene in patients affected by Leber Congenital Amaurosis (LCA); however, the treatment results are inconstant and with variable long-lasting effects due to a lack of correctly evaluating the anatomical and functional conditions of residual photoreceptors. These variabilities may also be related to host immunoreactive reactions towards the Adenovirus-associated vector. A broad spectrum of retinal dystrophies frequently generates doubt as to whether the disease or the patient is a good candidate for a successful gene treatment, because, very often, different diseases share similar genetic characteristics, causing an inconstant genotype/phenotype correlation between clinical characteristics also within the same family. For example, mutations on the RPE65 gene cause Leber Congenital Amaurosis (LCA) but also some forms of Retinitis Pigmentosa (RP), Bardet Biedl Syndrome (BBS), Congenital Stationary Night Blindness (CSNB) and Usher syndrome (USH), with a very wide spectrum of clinical manifestations. These confusing elements are due to the different pathways in which the product protein (retinoid isomer-hydrolase) is involved and, consequently, the overlapping metabolism in retinal function. Considering this point and the cost of the drug (over USD one hundred thousand), it would be mandatory to follow guidelines or algorithms to assess the best-fitting disease and candidate patients to maximize the output. Unfortunately, at the moment, there are no suggestions regarding who to treat with gene therapy. Moreover, gene therapy might be helpful in other forms of inherited retinal dystrophies, with more frequent incidence of the disease and better functional conditions (actually, gene therapy is proposed only for patients with poor vision, considering possible side effects due to the treatment procedures), in which this approach leads to better function and, hopefully, visual restoration. But, in this view, who might be a disease candidate or patient to undergo gene therapy, in relationship to the onset of clinical trials for several different forms of IRD? Further, what is the gold standard for tests able to correctly select the patient? Our work aims to evaluate clinical considerations on instrumental morphofunctional tests to assess candidate subjects for treatment and correlate them with clinical and genetic defect analysis that, often, is not correspondent. We try to define which parameters are an essential and indispensable part of the clinical rationale to select patients with IRDs for gene therapy. This review will describe a series of models used to characterize retinal morphology and function from tests, such as optical coherence tomography (OCT) and electrophysiological evaluation (ERG), and its evaluation as a primary outcome in clinical trials. A secondary aim is to propose an ancillary clinical classification of IRDs and their accessibility based on gene therapy’s current state of the art. Material and Methods: OCT, ERG, and visual field examinations were performed in different forms of IRDs, classified based on clinical and retinal conditions; compared to the gene defect classification, we utilized a diagnostic algorithm for the clinical classification based on morphofunctional information of the retina of patients, which could significantly improve diagnostic accuracy and, consequently, help the ophthalmologist to make a correct diagnosis to achieve optimal clinical results. These considerations are very helpful in selecting IRD patients who might respond to gene therapy with possible therapeutic success and filter out those in which treatment has a lower chance or no chance of positive results due to bad retinal conditions, avoiding time-consuming patient management with unsatisfactory results. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Retinal Degeneration and How to Avoid It)
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