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Pundkar C, Thanapaul RJRS, Govindarajulu M, Phuyal G, Long JB, Arun P. Dysregulation of Retinal Melatonin Biosynthetic Pathway and Differential Expression of Retina-Specific Genes Following Blast-Induced Ocular Injury in Ferrets. Neurol Int 2025; 17:42. [PMID: 40137463 PMCID: PMC11944890 DOI: 10.3390/neurolint17030042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2025] [Revised: 03/07/2025] [Accepted: 03/10/2025] [Indexed: 03/29/2025] Open
Abstract
BACKGROUND/OBJECTIVES Blast-induced traumatic ocular injuries (bTOI) pose a significant risk to military and civilian populations, often leading to visual impairment or blindness. Retina, the innermost layer of ocular tissue consisting of photoreceptor and glial cells, is highly susceptible to blast injuries. Despite its prevalence, the molecular mechanisms underlying retinal damage following bTOI remain poorly understood, hindering the development of targeted therapies. Melatonin, a neuroprotective indoleamine with antioxidant, anti-inflammatory, and circadian regulatory properties, is synthesized in the retina and plays a crucial role in retinal health. Similarly, retina-specific genes, such as Rhodopsin, Melanopsin, and RPE65, are essential for photoreceptor function, visual signaling, and the visual cycle. However, their responses to blast exposure have not been thoroughly investigated. METHODS In this study, we utilized a ferret model of bTOI to evaluate the temporal expression of melatonin-synthesizing enzymes, such as tryptophan hydroxylase 1 and 2 (TPH1 and TPH2), Aralkylamine N-acetyltransferase (AANAT), and Acetylserotonin-O-methyltransferase (ASMT), and retina-specific genes (Rhodopsin, Melanopsin) and retinal pigment epithelium-specific 65 kDa protein (RPE65) at 4 h, 24 h, 7 days, and 28 days post-blast. Ferrets were exposed to tightly coupled blast overpressure waves using an advanced blast simulator, and retinal tissues were collected for quantitative polymerase chain reaction (qPCR) analysis. RESULTS The results revealed dynamic and multiphasic transcriptional responses. TPH1 and TPH2 exhibited significant upregulation at 24 h, followed by downregulation at 28 days, indicating blast-induced dysregulation of tryptophan metabolism, including melatonin synthesis. Similarly, AANAT and ASMT showed acute downregulation post-blast, with late-phase disruptions. Rhodopsin expression increased at 24 h but declined at 28 days, while Melanopsin and RPE65 demonstrated early upregulation followed by downregulation, reflecting potential disruptions in circadian regulation and the visual cycle. CONCLUSIONS These findings highlight the complex regulatory mechanisms underlying retinal responses to bTOI, involving neuroinflammation, oxidative stress, and disruptions in melatonin synthesis and photoreceptor cell functions. The results emphasize the therapeutic potential of melatonin in mitigating retinal damage and preserving visual function.
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Affiliation(s)
- Chetan Pundkar
- Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.P.); (R.J.R.S.T.); (M.G.); (G.P.); (J.B.L.)
| | - Rex Jeya Rajkumar Samdavid Thanapaul
- Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.P.); (R.J.R.S.T.); (M.G.); (G.P.); (J.B.L.)
- National Research Council (NRC) Research Associateship Programs, National Academies of Sciences, Engineering, and Medicine, Washington, DC 20001, USA
| | - Manoj Govindarajulu
- Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.P.); (R.J.R.S.T.); (M.G.); (G.P.); (J.B.L.)
| | - Gaurav Phuyal
- Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.P.); (R.J.R.S.T.); (M.G.); (G.P.); (J.B.L.)
| | - Joseph B. Long
- Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.P.); (R.J.R.S.T.); (M.G.); (G.P.); (J.B.L.)
| | - Peethambaran Arun
- Blast-Induced Neurotrauma Branch, Center for Military Psychiatry and Neuroscience, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (C.P.); (R.J.R.S.T.); (M.G.); (G.P.); (J.B.L.)
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Tian Y, Liu P, Kong D, Nie Y, Xu H, Han X, Sang W, Li W. Genome-wide association analysis and KASP markers development for protein quality traits in winter wheat. BMC PLANT BIOLOGY 2025; 25:149. [PMID: 39910434 PMCID: PMC11796262 DOI: 10.1186/s12870-025-06171-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 01/29/2025] [Indexed: 02/07/2025]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is a significant cereal crop that plays a vital role in global food production. To expedite the breeding of wheat cultivars with high protein quality, it is necessary to genetically analyze the traits related to quality. A genome-wide association study (GWAS) was conducted to identify the genomic regions responsible for protein quality traits in winter wheat. RESULTS Six protein quality traits were evaluated across two locations and two years for a total of 341 wheat accessions. Utilizing the wheat 40 K SNP array, GWAS identified 97 significantly stable SNPs at 43 loci for five out of six protein quality traits using a linear mixed model. The 43 loci distribution was four for grain protein content, two for flour protein content, one for wet gluten content, four for gluten index, and thirty-two for Zeleny sedimentation value. The most significant associations were identified on chromosomes 1 A, 1B, and 1D. Haplotype analysis of loci associated with the gluten index in the 412-416 Mb interval on chromosome 1D identified three blocks. Accessions with superior haplotypes showed a significantly higher gluten index than those with inferior haplotypes. Six KASP markers were successfully developed for the gluten index, while five KASP markers were developed for the Zeleny sedimentation value. Additionally, eight candidate genes were identified that may affect protein accumulation during grain development. CONCLUSIONS Our study identified 97 SNPs significantly associated with protein quality traits; developed 6 KASP markers for gluten index, and 5 KASP markers for Zeleny sedimentation values; screened 8 candidate genes that may be related to protein quality during grain development. Thise research will offer valuable insights for wheat breeding programs in China and globally.
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Affiliation(s)
- Yousheng Tian
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- The Key Laboratory of the Oasis Ecological Agriculture, College of Agriculture, Shihezi University, Shihezi, 832003, China
| | - Pengpeng Liu
- Institute of Crop Science, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- Key Laboratory of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Dezhen Kong
- Institute of Crop Science, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- Key Laboratory of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Yingbin Nie
- Institute of Crop Science, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- Key Laboratory of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Hongjun Xu
- Institute of Crop Science, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- Key Laboratory of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Xinnian Han
- Institute of Crop Science, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
- Key Laboratory of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China
| | - Wei Sang
- Institute of Crop Science, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
- Key Laboratory of Xinjiang Production and Construction Corps for Cereal Quality Research and Genetic Improvement, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, China.
| | - Weihua Li
- The Key Laboratory of the Oasis Ecological Agriculture, College of Agriculture, Shihezi University, Shihezi, 832003, China.
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Kurzawa-Akanbi M, Tzoumas N, Corral-Serrano JC, Guarascio R, Steel DH, Cheetham ME, Armstrong L, Lako M. Pluripotent stem cell-derived models of retinal disease: Elucidating pathogenesis, evaluating novel treatments, and estimating toxicity. Prog Retin Eye Res 2024; 100:101248. [PMID: 38369182 DOI: 10.1016/j.preteyeres.2024.101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Blindness poses a growing global challenge, with approximately 26% of cases attributed to degenerative retinal diseases. While gene therapy, optogenetic tools, photosensitive switches, and retinal prostheses offer hope for vision restoration, these high-cost therapies will benefit few patients. Understanding retinal diseases is therefore key to advance effective treatments, requiring in vitro models replicating pathology and allowing quantitative assessments for drug discovery. Pluripotent stem cells (PSCs) provide a unique solution given their limitless supply and ability to differentiate into light-responsive retinal tissues encompassing all cell types. This review focuses on the history and current state of photoreceptor and retinal pigment epithelium (RPE) cell generation from PSCs. We explore the applications of this technology in disease modelling, experimental therapy testing, biomarker identification, and toxicity studies. We consider challenges in scalability, standardisation, and reproducibility, and stress the importance of incorporating vasculature and immune cells into retinal organoids. We advocate for high-throughput automation in data acquisition and analyses and underscore the value of advanced micro-physiological systems that fully capture the interactions between the neural retina, RPE, and choriocapillaris.
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Yin Z, Ge L, Cha Z, Gao H, A L, Zeng Y, Huang X, Cheng X, Yao K, Tao Z, Xu H. Identifying Hmga2 preserving visual function by promoting a shift of Müller glia cell fate in mice with acute retinal injury. Stem Cell Res Ther 2024; 15:54. [PMID: 38414051 PMCID: PMC10900711 DOI: 10.1186/s13287-024-03657-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Unlike in lower vertebrates, Müller glia (MG) in adult mammalian retinas lack the ability to reprogram into neurons after retinal injury or degeneration and exhibit reactive gliosis instead. Whether a transition in MG cell fate from gliosis to reprogramming would help preserve photoreceptors is still under exploration. METHODS A mouse model of retinitis pigmentosa (RP) was established using MG cell lineage tracing mice by intraperitoneal injection of sodium iodate (SI). The critical time point for the fate determination of MG gliosis was determined through immunohistochemical staining methods. Then, bulk-RNA and single-cell RNA seq techniques were used to elucidate the changes in RNA transcription of the retina and MG at that time point, and new genes that may determine the fate transition of MG were screened. Finally, the selected gene was specifically overexpressed in MG cells through adeno-associated viruses (AAV) in the mouse RP model. Bulk-RNA seq technique, immunohistochemical staining methods, and visual function testing were used to elucidate and validate the mechanism of new genes function on MG cell fate transition and retinal function. RESULTS Here, we found the critical time point for MG gliosis fate determination was 3 days post SI injection. Hmga2 was screened out as a candidate regulator for the cell fate transition of MG. After retinal injury caused by SI, the Hmga2 protein is temporarily and lowly expressed in MG cells. Overexpression of Hmga2 in MG down-regulated glial cell related genes and up-regulated photoreceptor related genes. Besides, overexpressing Hmga2 exclusively to MG reduced MG gliosis, made MG obtain cone's marker, and retained visual function in mice with acute retinal injury. CONCLUSION Our results suggested the unique reprogramming properties of Hmga2 in regulating the fate transition of MG and neuroprotective effects on the retina with acute injury. This work uncovers the reprogramming ability of epigenetic factors in MG.
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Affiliation(s)
- Zhiyuan Yin
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
- Department of Physiology, College of Basic Medical Sciences, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Lingling Ge
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Zhe Cha
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
- Department of Physiology, College of Basic Medical Sciences, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Hui Gao
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Luodan A
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Yuxiao Zeng
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Xiaona Huang
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Xuan Cheng
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, 430065, China.
| | - Zui Tao
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China.
| | - Haiwei Xu
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China.
- Key Lab of Visual Damage and Regeneration and Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China.
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Nilén G, Larsson M, Hyötyläinen T, Keiter SH. A complex mixture of polycyclic aromatic compounds causes embryotoxic, behavioral, and molecular effects in zebrafish larvae (Danio rerio), and in vitro bioassays. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167307. [PMID: 37804991 DOI: 10.1016/j.scitotenv.2023.167307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/09/2023]
Abstract
Polycyclic aromatic compounds (PACs) are prevalent in the environment, typically found in complex mixtures and high concentrations. Our understanding of the effects of PACs, excluding the 16 priority polycyclic aromatic hydrocarbons (16 PAHs), remains limited. Zebrafish embryos and in vitro bioassays were utilized to investigate the embryotoxic, behavioral, and molecular effects of a soil sample from a former gasworks site in Sweden. Additionally, targeted chemical analysis was conducted to analyze 87 PACs in the soil, fish, water, and plate material. CALUX® assays were used to assess the activation of aryl hydrocarbon and estrogen receptors, as well as the inhibition of the androgen receptor. Larval behavior was measured by analyzing activity during light and darkness and in response to mechanical stimulation. Furthermore, qPCR analyses were performed on a subset of 36 genes associated with specific adverse outcomes, and the total lipid content in the larvae was measured. Exposure to the sample resulted in embryotoxic effects (LC50 = 0.480 mg dry matter soil/mL water). The mixture also induced hyperactivity in darkness and hypoactivity in light and in response to the mechanical stimulus. qPCR analysis revealed differential regulation of 15 genes, including downregulation of opn1sw1 (eye pigmentation) and upregulation of fpgs (heart failure). The sample caused significant responses in three bioassays (ERα-, DR-, and PAH-CALUX), and the exposed larvae exhibited elevated lipid levels. Chemical analysis identified benzo[a]pyrene as the predominant compound in the soil and approximately half of the total PAC concentration was attributed to the 16 PAHs. This study highlights the value of combining in vitro and in vivo methods with chemical analysis to assess toxic mechanisms at specific targets and to elucidate the possible interactions between various pathways in an organism. It also enhances our understanding of the risks associated with environmental mixtures of PACs and their distribution during toxicity testing.
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Affiliation(s)
- Greta Nilén
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden.
| | - Maria Larsson
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden
| | - Tuulia Hyötyläinen
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, S-701 82 Örebro, Sweden
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Donato L, Mordà D, Scimone C, Alibrandi S, D’Angelo R, Sidoti A. Bridging Retinal and Cerebral Neurodegeneration: A Focus on Crosslinks between Alzheimer-Perusini's Disease and Retinal Dystrophies. Biomedicines 2023; 11:3258. [PMID: 38137479 PMCID: PMC10741418 DOI: 10.3390/biomedicines11123258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/02/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In the early stages of Alzheimer-Perusini's disease (AD), individuals often experience vision-related issues such as color vision impairment, reduced contrast sensitivity, and visual acuity problems. As the disease progresses, there is a connection with glaucoma and age-related macular degeneration (AMD) leading to retinal cell death. The retina's involvement suggests a link with the hippocampus, where most AD forms start. A thinning of the retinal nerve fiber layer (RNFL) due to the loss of retinal ganglion cells (RGCs) is seen as a potential AD diagnostic marker using electroretinography (ERG) and optical coherence tomography (OCT). Amyloid beta fragments (Aβ), found in the eye's vitreous and aqueous humor, are also present in the cerebrospinal fluid (CSF) and accumulate in the retina. Aβ is known to cause tau hyperphosphorylation, leading to its buildup in various retinal layers. However, diseases like AD are now seen as mixed proteinopathies, with deposits of the prion protein (PrP) and α-synuclein found in affected brains and retinas. Glial cells, especially microglial cells, play a crucial role in these diseases, maintaining immunoproteostasis. Studies have shown similarities between retinal and brain microglia in terms of transcription factor expression and morphotypes. All these findings constitute a good start to achieving better comprehension of neurodegeneration in both the eye and the brain. New insights will be able to bring the scientific community closer to specific disease-modifying therapies.
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Affiliation(s)
- Luigi Donato
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98122 Messina, Italy; (L.D.); (C.S.); (R.D.); (A.S.)
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, Euro-Mediterranean Institute of Science and Technology (I.E.ME.S.T.), 90139 Palermo, Italy;
| | - Domenico Mordà
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, Euro-Mediterranean Institute of Science and Technology (I.E.ME.S.T.), 90139 Palermo, Italy;
- Department of Veterinary Sciences, University of Messina, 98122 Messina, Italy
| | - Concetta Scimone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98122 Messina, Italy; (L.D.); (C.S.); (R.D.); (A.S.)
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, Euro-Mediterranean Institute of Science and Technology (I.E.ME.S.T.), 90139 Palermo, Italy;
| | - Simona Alibrandi
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98122 Messina, Italy; (L.D.); (C.S.); (R.D.); (A.S.)
- Department of Biomolecular Strategies, Genetics, Cutting-Edge Therapies, Euro-Mediterranean Institute of Science and Technology (I.E.ME.S.T.), 90139 Palermo, Italy;
| | - Rosalia D’Angelo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98122 Messina, Italy; (L.D.); (C.S.); (R.D.); (A.S.)
| | - Antonina Sidoti
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Division of Medical Biotechnologies and Preventive Medicine, University of Messina, 98122 Messina, Italy; (L.D.); (C.S.); (R.D.); (A.S.)
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Shrestha AP, Stiles M, Grambergs RC, Boff JM, Madireddy S, Mondal K, Rajmanna R, Porter H, Sherry DM, Proia RL, Vaithianathan T, Mandal N. The Role of Sphingosine-1-Phosphate Receptor 2 in Mouse Retina Light Responses. Biomolecules 2023; 13:1691. [PMID: 38136563 PMCID: PMC10741782 DOI: 10.3390/biom13121691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/09/2023] [Accepted: 11/19/2023] [Indexed: 12/24/2023] Open
Abstract
The bioactive sphingolipid sphingosine-1-phosphate (S1P) acts as a ligand for a family of G protein-coupled S1P receptors (S1PR1-5) to participate in a variety of signaling pathways. However, their specific roles in the neural retina remain unclear. We previously showed that S1P receptor subtype 2 (S1PR2) is expressed in murine retinas, primarily in photoreceptors and bipolar cells, and its expression is altered by retinal stress. This study aims to elucidate the role of S1PR2 in the mouse retina. We examined light responses by electroretinography (ERG), structural differences by optical coherence tomography (OCT), and protein levels by immunohistochemistry (IHC) in wild-type (WT) and S1PR2 knockout (KO) mice at various ages between 3 and 6 months. We found that a- and b-wave responses significantly increased at flash intensities between 400~2000 and 4~2000 cd.s/m2, respectively, in S1PR2 KO mice relative to those of WT controls at baseline. S1PR2 KO mice also exhibited significantly increased retinal nerve fiber layer (RNFL) and outer plexiform layer (OPL) thickness by OCT relative to the WT. Finally, in S1PR2 KO mice, we observed differential labeling of synaptic markers by immunohistochemistry (IHC) and quantitative reverse transcription polymerase chain reaction (RT-qPCR). These results suggest a specific involvement of S1PR2 in the structure and synaptic organization of the retina and a potential role in light-mediated functioning of the retina.
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Affiliation(s)
- Abhishek P. Shrestha
- Department of Pharmacology, Addiction Science, and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Megan Stiles
- Departments of Cell Biology, Neurosurgery, and Pharmacological Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Richard C. Grambergs
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Johane M. Boff
- Department of Pharmacology, Addiction Science, and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Saivikram Madireddy
- College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Koushik Mondal
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Rhea Rajmanna
- Department of Pharmacology, Addiction Science, and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Hunter Porter
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - David M. Sherry
- Departments of Cell Biology, Neurosurgery, and Pharmacological Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Richard L. Proia
- Genetics of Development and Disease Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thirumalini Vaithianathan
- Department of Pharmacology, Addiction Science, and Toxicology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Nawajes Mandal
- Department of Ophthalmology, Hamilton Eye Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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Shrestha AP, Stiles M, Grambergs RC, Boff JM, Madireddy S, Mondal K, Rajmanna R, Porter H, Sherry D, Proia RL, Vaithianathan T, Mandal N. The role of sphingosine-1-phosphate receptor 2 in mouse retina light responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555709. [PMID: 37732206 PMCID: PMC10508730 DOI: 10.1101/2023.09.01.555709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The bioactive sphingolipid sphingosine-1-phosphate (S1P) acts as a ligand for a family of G protein-coupled S1P receptors (S1PR1-5) to participate in a variety of signaling pathways. However, their specific roles in the neural retina remain unclear. We previously showed that S1P receptor subtype 2 (S1PR2) is expressed in murine retinas, primarily in photoreceptors and bipolar cells, and its expression is altered by retinal stress. This study aims to elucidate the role of S1PR2 in the mouse retina. We examined light responses by electroretinography (ERG), structural differences by optical coherence tomography (OCT), and protein levels by immunohistochemistry (IHC) in wild-type (WT) and S1PR2 knockout (KO) mice at various ages between 3 and 6 months. We found that a- and b-wave responses significantly increased at flash intensities between 400∼2000 and 4∼2,000 cd.s/m 2 respectively, in S1PR2 KO mice relative to those of WT controls at baseline. S1PR2 KO mice also exhibited significantly increased retinal nerve fiber layer (RNFL) and outer plexiform layer (OPL) thickness by OCT relative to the WT. Finally, in S1PR2 KO mice, we observed differential labeling of synaptic markers by immunohistochemistry (IHC) and quantitative reverse transcription polymerase chain reaction (RT-qPCR). These results suggest a specific involvement of S1PR2 in the structure and synaptic organization of the retina and a potential role in light-mediated functioning of the retina.
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Móvio MI, de Lima-Vasconcellos TH, Dos Santos GB, Echeverry MB, Colombo E, Mattos LS, Resende RR, Kihara AH. Retinal organoids from human-induced pluripotent stem cells: From studying retinal dystrophies to early diagnosis of Alzheimer's and Parkinson's disease. Semin Cell Dev Biol 2023; 144:77-86. [PMID: 36210260 DOI: 10.1016/j.semcdb.2022.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 11/18/2022]
Abstract
Human-induced pluripotent stem cells (hiPSCs) have provided new methods to study neurodegenerative diseases. In addition to their wide application in neuronal disorders, hiPSCs technology can also encompass specific conditions, such as inherited retinal dystrophies. The possibility of evaluating alterations related to retinal disorders in 3D organoids increases the truthfulness of in vitro models. Moreover, both Alzheimer's (AD) and Parkinson's disease (PD) have been described as causing early retinal alterations, generating beta-amyloid protein accumulation, or affecting dopaminergic amacrine cells. This review addresses recent advances and future perspectives obtained from in vitro modeling of retinal diseases, focusing on retinitis pigmentosa (RP). Additionally, we depicted the possibility of evaluating changes related to AD and PD in retinal organoids obtained from potential patients long before the onset of the disease, constituting a valuable tool in early diagnosis. With this, we pointed out prospects in the study of retinal dystrophies and early diagnosis of AD and PD.
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Affiliation(s)
- Marília Inês Móvio
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | | | | | - Marcela Bermudez Echeverry
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Elisabetta Colombo
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy; IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Leonardo S Mattos
- Biomedical Robotics Laboratory, Department of Advanced Robotics, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Rodrigo Ribeiro Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alexandre Hiroaki Kihara
- Laboratório de Neurogenética, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil; Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil.
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10
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Beč A, Cindrić M, Persoons L, Banjanac M, Radovanović V, Daelemans D, Hranjec M. Novel Biologically Active N-Substituted Benzimidazole Derived Schiff Bases: Design, Synthesis, and Biological Evaluation. Molecules 2023; 28:molecules28093720. [PMID: 37175129 PMCID: PMC10180076 DOI: 10.3390/molecules28093720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/19/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Herein, we present the design and synthesis of novel N-substituted benzimidazole-derived Schiff bases, and the evaluation of their antiviral, antibacterial, and antiproliferative activity. The impact on the biological activity of substituents placed at the N atom of the benzimidazole nuclei and the type of substituents attached at the phenyl ring were examined. All of the synthesized Schiff bases were evaluated in vitro for their antiviral activity against different viruses, antibacterial activity against a panel of bacterial strains, and antiproliferative activity on several human cancer cell lines, thus enabling the study of the structure-activity relationships. Some mild antiviral effects were noted, although at higher concentrations in comparison with the included reference drugs. Additionally, some derivatives showed a moderate antibacterial activity, with precursor 23 being broadly active against most of the tested bacterial strains. Lastly, Schiff base 40, a 4-N,N-diethylamino-2-hydroxy-substituted derivative bearing a phenyl ring at the N atom on the benzimidazole nuclei, displayed a strong antiproliferative activity against several cancer cell lines (IC50 1.1-4.4 μM). The strongest antitumoral effect was observed towards acute myeloid leukemia (HL-60).
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Affiliation(s)
- Anja Beč
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia
| | - Maja Cindrić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia
| | - Leentje Persoons
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium
| | - Mihailo Banjanac
- Pharmacology In Vitro, Selvita Ltd., Prilaz baruna Filipovića 29, HR-10000 Zagreb, Croatia
| | - Vedrana Radovanović
- Pharmacology In Vitro, Selvita Ltd., Prilaz baruna Filipovića 29, HR-10000 Zagreb, Croatia
| | - Dirk Daelemans
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, 3000 Leuven, Belgium
| | - Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia
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11
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Wu KY, Kulbay M, Toameh D, Xu AQ, Kalevar A, Tran SD. Retinitis Pigmentosa: Novel Therapeutic Targets and Drug Development. Pharmaceutics 2023; 15:685. [PMID: 36840007 PMCID: PMC9963330 DOI: 10.3390/pharmaceutics15020685] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of hereditary diseases characterized by progressive degeneration of retinal photoreceptors leading to progressive visual decline. It is the most common type of inherited retinal dystrophy and has a high burden on both patients and society. This condition causes gradual loss of vision, with its typical manifestations including nyctalopia, concentric visual field loss, and ultimately bilateral central vision loss. It is one of the leading causes of visual disability and blindness in people under 60 years old and affects over 1.5 million people worldwide. There is currently no curative treatment for people with RP, and only a small group of patients with confirmed RPE65 mutations are eligible to receive the only gene therapy on the market: voretigene neparvovec. The current therapeutic armamentarium is limited to retinoids, vitamin A supplements, protection from sunlight, visual aids, and medical and surgical interventions to treat ophthalmic comorbidities, which only aim to slow down the progression of the disease. Considering such a limited therapeutic landscape, there is an urgent need for developing new and individualized therapeutic modalities targeting retinal degeneration. Although the heterogeneity of gene mutations involved in RP makes its target treatment development difficult, recent fundamental studies showed promising progress in elucidation of the photoreceptor degeneration mechanism. The discovery of novel molecule therapeutics that can selectively target specific receptors or specific pathways will serve as a solid foundation for advanced drug development. This article is a review of recent progress in novel treatment of RP focusing on preclinical stage fundamental research on molecular targets, which will serve as a starting point for advanced drug development. We will review the alterations in the molecular pathways involved in the development of RP, mainly those regarding endoplasmic reticulum (ER) stress and apoptotic pathways, maintenance of the redox balance, and genomic stability. We will then discuss the therapeutic approaches under development, such as gene and cell therapy, as well as the recent literature identifying novel potential drug targets for RP.
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Affiliation(s)
- Kevin Y. Wu
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Merve Kulbay
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Dana Toameh
- Faculty of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - An Qi Xu
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Ananda Kalevar
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Simon D. Tran
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3A 1G1, Canada
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12
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Pedraza-González L, Barneschi L, Marszałek M, Padula D, De Vico L, Olivucci M. Automated QM/MM Screening of Rhodopsin Variants with Enhanced Fluorescence. J Chem Theory Comput 2023; 19:293-310. [PMID: 36516450 DOI: 10.1021/acs.jctc.2c00928] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We present a computational protocol for the fast and automated screening of excited-state hybrid quantum mechanics/molecular mechanics (QM/MM) models of rhodopsins to be used as fluorescent probes based on the automatic rhodopsin modeling protocol (a-ARM). Such "a-ARM fluorescence screening protocol" is implemented through a general Python-based driver, PyARM, that is also proposed here. The implementation and performance of the protocol are benchmarked using different sets of rhodopsin variants whose absorption and, more relevantly, emission spectra have been experimentally measured. We show that, despite important limitations that make unsafe to use it as a black-box tool, the protocol reproduces the observed trends in fluorescence and it is capable of selecting novel potentially fluorescent rhodopsins. We also show that the protocol can be used in mechanistic investigations to discern fluorescence enhancement effects associated with a near degeneracy of the S1/S2 states or, alternatively, with a barrier generated via coupling of the S0/S1 wave functions.
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Affiliation(s)
- Laura Pedraza-González
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Leonardo Barneschi
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Michał Marszałek
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiaǹskiego 27, 50-370 Wrocław, Poland
| | - Daniele Padula
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Luca De Vico
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy
| | - Massimo Olivucci
- Department of Biotechnology, Chemistry and Pharmacy, Università degli Studi di Siena, Via A. Moro 2, I-53100 Siena, Italy.,Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
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13
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Sundaresan Y, Banin E, Sharon D. Exonic Variants that Affect Splicing - An Opportunity for "Hidden" Mutations Causing Inherited Retinal Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:183-187. [PMID: 37440032 DOI: 10.1007/978-3-031-27681-1_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Inherited retinal diseases (IRDs) are an extremely diverse group of ocular disorders characterized by progressive loss of photoreceptors leading to blindness. So far, pathogenic variants in over 300 genes are reported to structurally and functionally affect the retina resulting in visual impairment. Around 15% of all IRD mutations are known to affect an essential regulatory mechanism, pre-mRNA splicing, which contributes to the transcriptomic diversity. These variants disrupt potential donor and acceptor splice sites as well as other crucial cis-acting elements resulting in aberrant splicing. One group of these elements, the exonic splicing enhancers (ESEs), are involved in promoting exon definition and are likely to harbor "hidden" mutations since sequence-analyzing pipelines cannot identify them efficiently. The main focus of this review is to discuss the molecular mechanisms behind various exonic variants affecting splice sites and ESEs that lead to impaired splicing which in turn result in an IRD pathology.
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Affiliation(s)
- Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
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14
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Zheng J, Wang X, Feng T, Rehman SU, Yan X, Shan H, Ma X, Zhou W, Xu W, Lu L, Liu J, Luo X, Cui K, Qin C, Chen W, Yu J, Li Z, Ruan J, Liu Q. Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes. Gigascience 2022; 12:giad023. [PMID: 37039117 PMCID: PMC10087013 DOI: 10.1093/gigascience/giad023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/14/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Leeches have been used in traditional Chinese medicine since prehistoric times to treat a spectrum of ailments, but very little is known about their physiological, genetic, and evolutionary characteristics. FINDINGS We sequenced and assembled chromosome-level genomes of 3 leech species (bloodsucking Hirudo nipponia and Hirudinaria manillensis and nonbloodsucking Whitmania pigra). The dynamic population histories and genome-wide expression patterns of the 2 bloodsucking leech species were found to be similar. A combined analysis of the genomic and transcriptional data revealed that the bloodsucking leeches have a presumably enhanced auditory sense for prey location in relatively deep fresh water. The copy number of genes related to anticoagulation, analgesia, and anti-inflammation increased in the bloodsucking leeches, and their gene expressions responded dynamically to the bloodsucking process. Furthermore, the expanded FBN1 gene family may help in rapid body swelling of leeches after bloodsucking, and the expanded GLB3 gene family may be associated with long-term storage of prey blood in a leech's body. CONCLUSIONS The high-quality reference genomes and comprehensive datasets obtained in this study may facilitate innovations in the artificial culture and strain optimization of leeches.
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Affiliation(s)
- Jinghui Zheng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Huiquan Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Xiaocong Ma
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, China
| | - Weiguan Zhou
- Biological Institute of Guangxi Academy of Sciences, Nanning 530007, China
| | - Wenhua Xu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, China
| | - Liying Lu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, China
| | - Jiasheng Liu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning 530011, China
| | - Xier Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Chaobin Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Weihua Chen
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Jue Ruan
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China
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15
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Yefimova MG. Myelinosome organelles in pathological retinas: ubiquitous presence and dual role in ocular proteostasis maintenance. Neural Regen Res 2022; 18:1009-1016. [PMID: 36254982 PMCID: PMC9827766 DOI: 10.4103/1673-5374.355753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The timely and efficient elimination of aberrant proteins and damaged organelles, formed in response to various genetic and environmental stressors, is a vital need for all cells of the body. Recent lines of evidence point out several non-classical strategies employed by ocular tissues to cope with aberrant constituents generated in the retina and in the retinal pigmented epithelium cells exposed to various stressors. Along with conventional strategies relying upon the intracellular degradation of aberrant constituents through ubiquitin-proteasome and/or lysosome-dependent autophagy proteolysis, two non-conventional mechanisms also contribute to proteostasis maintenance in ocular tissues. An exosome-mediated clearing and a myelinosome-driven secretion mechanism do not require intracellular degradation but provide the export of aberrant constituents and "waste proteins" outside of the cells. The current review is centered on the non-degradative myelinosome-driven secretion mechanism, which operates in the retina of transgenic Huntington's disease R6/1 model mice. Myelinosome-driven secretion is supported by rare organelles myelinosomes that are detected not only in degenerative Huntington's disease R6/1 retina but also in various pathological states of the retina and of the retinal pigmented epithelium. The intra-retinal traffic and inter-cellular exchange of myelinosomes was discussed in the context of a dual role of the myelinosome-driven secretion mechanism for proteostasis maintenance in different ocular compartments. Special focus was made on the interplay between degradative and non-degradative strategies in ocular pathophysiology, to delineate potential therapeutic approaches to counteract several vision diseases.
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Affiliation(s)
- Marina G. Yefimova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St-Petersburg, Russia,Laboratoire STIM CNRS ERL 7003, Université de Poitiers, Poitiers, France,Correspondence to: Marina G. Yefimova, .
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16
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Lee C, Su BH, Tseng YJ. Comparative studies of AlphaFold, RoseTTAFold and Modeller: a case study involving the use of G-protein-coupled receptors. Brief Bioinform 2022; 23:6658852. [PMID: 35945035 PMCID: PMC9487610 DOI: 10.1093/bib/bbac308] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/22/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Neural network (NN)-based protein modeling methods have improved significantly in recent years. Although the overall accuracy of the two non-homology-based modeling methods, AlphaFold and RoseTTAFold, is outstanding, their performance for specific protein families has remained unexamined. G-protein-coupled receptor (GPCR) proteins are particularly interesting since they are involved in numerous pathways. This work directly compares the performance of these novel deep learning-based protein modeling methods for GPCRs with the most widely used template-based software—Modeller. We collected the experimentally determined structures of 73 GPCRs from the Protein Data Bank. The official AlphaFold repository and RoseTTAFold web service were used with default settings to predict five structures of each protein sequence. The predicted models were then aligned with the experimentally solved structures and evaluated by the root-mean-square deviation (RMSD) metric. If only looking at each program’s top-scored structure, Modeller had the smallest average modeling RMSD of 2.17 Å, which is better than AlphaFold’s 5.53 Å and RoseTTAFold’s 6.28 Å, probably since Modeller already included many known structures as templates. However, the NN-based methods (AlphaFold and RoseTTAFold) outperformed Modeller in 21 and 15 out of the 73 cases with the top-scored model, respectively, where no good templates were available for Modeller. The larger RMSD values generated by the NN-based methods were primarily due to the differences in loop prediction compared to the crystal structures.
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Affiliation(s)
- Chien Lee
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Bo-Han Su
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Yufeng Jane Tseng
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan
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17
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Pedraza-González L, Barneschi L, Padula D, De Vico L, Olivucci M. Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol. Top Curr Chem (Cham) 2022; 380:21. [PMID: 35291019 PMCID: PMC8924150 DOI: 10.1007/s41061-022-00374-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/29/2022] [Indexed: 10/27/2022]
Abstract
In recent years, photoactive proteins such as rhodopsins have become a common target for cutting-edge research in the field of optogenetics. Alongside wet-lab research, computational methods are also developing rapidly to provide the necessary tools to analyze and rationalize experimental results and, most of all, drive the design of novel systems. The Automatic Rhodopsin Modeling (ARM) protocol is focused on providing exactly the necessary computational tools to study rhodopsins, those being either natural or resulting from mutations. The code has evolved along the years to finally provide results that are reproducible by any user, accurate and reliable so as to replicate experimental trends. Furthermore, the code is efficient in terms of necessary computing resources and time, and scalable in terms of both number of concurrent calculations as well as features. In this review, we will show how the code underlying ARM achieved each of these properties.
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Affiliation(s)
- Laura Pedraza-González
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, 56124, Pisa, Italy.
| | - Leonardo Barneschi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Daniele Padula
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy
| | - Luca De Vico
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy.
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Aldo Moro 2, 53100, Siena, Italy. .,Department of Chemistry, Bowling Green State University, Bowling Green, OH, 43403, USA.
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18
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Deolankar SC, Najar MA, Raghu SV, Prasad TSK. Aβ42 Expressing Drosophila melanogaster Model for Alzheimer's Disease: Quantitative Proteomics Identifies Altered Protein Dynamics of Relevance to Neurodegeneration. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:51-63. [PMID: 35006003 DOI: 10.1089/omi.2021.0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Production and deposition of β-amyloid peptides (Aβ) are among the major hallmarks of the pathogenesis of Alzheimer's disease (AD). Mapping the altered protein dynamics associated with Aβ accumulation and neuronal damage may open up new avenues to innovation for drug target discovery in AD. Using quantitative proteomics, we report new findings from the amyloid beta-peptide with 42 amino acids (Aβ42) expressing Drosophila melanogaster model for AD compared to that of the wild-type flies. We identified 302,241 peptide-spectrum matches with 25,641 nonredundant peptides corresponding to 7959 D. melanogaster proteins. Furthermore, we unraveled 538 significantly altered proteins in Aβ42 expressing flies. These differentially expressed proteins were enriched for biological processes associated with neuronal damage leading to AD progression. We also identified 463 unique post-translational modification events mapping to 202 proteins from the same dataset. Among these, 303 modified peptides corresponding to 246 proteins were also altered in the AD model. These modified proteins are known to be involved in the disruption of molecular functions maintaining neuronal plasticity. This study provides new molecular leads on altered protein dynamics relevant to neurodegeneration, neuroplasticity, and AD progression induced by Aβ42 toxicity. These proteins may prove useful to discover new drugs in an AD model of D. melanogaster and evaluate their efficacy and mode of molecular action in the future.
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Affiliation(s)
- Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Mohammad Altaf Najar
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Shamprasad Varija Raghu
- Neurogenetics Laboratory, Department of Applied Zoology, Mangalore University, Mangalore, India
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19
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Saçaki CS, Mogharbel BF, Stricker PEF, Dziedzic DSM, Irioda AC, Perussolo MC, Somma AT, Montiani-Ferreira F, Moreno JCD, Dornbusch P, Sato M, Shiokawa N, de Noronha L, Nagashima S, Bacelar-Galdino M, Franco CRC, Abdelwahid E, Carvalho KAT. Potential of Human Neural Precursor Cells in Diabetic Retinopathy Therapeutics - Preclinical Model. Curr Eye Res 2021; 47:450-460. [PMID: 34749546 DOI: 10.1080/02713683.2021.2002909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Purpose: This study aimed to evaluate a cell therapy strategy with human neural precursor cells (hNPCs) to treat diabetic retinopathy (DR) in Wistar rats induced to diabetes by injecting streptozotocin. Material and methods: Wharton's Jelly Mesenchymal stem cells (WJ-MSCs) were isolated, expanded, and seeded onto a biopolymer substrate to develop neurospheres and obtain the hNPCs. The animals were divided into three groups; non-diabetic (ND) n = four; diabetic without treatment (DM) n = nine; and diabetic with cell therapy (DM + hNPCs) n = nine. After eight weeks of diabetes induction and DR characteristics installed, intravitreal injection of hNPCs (1 x 106 cel/µL) was performed in the DM + hNPCs group. Optical Coherence Tomography (OCT) and Electroretinography (ERG) evaluations were before and during diabetes and after cell therapy. Four weeks post-treatment, histopathological and immunohistochemistry analyses were performed. Results: The repair of the retinal structures in the treated group (DM + hNPCs) was observed by increased thickness of neuroretinal layers, especially in the ganglion cell and photoreceptor layers, higher ERG oscillatory potentials (OPs) amplitudes, and transplanted hNPCs integration into the Retinal Pigment Epithelium. Conclusions: The results indicate that hNPCs reduced DR progression by a neuroprotective effect and promoted retinal repair, making them potential candidates for regenerating the neuroretinal tissue.
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Affiliation(s)
- Claudia Sayuri Saçaki
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, The Pelé Pequeno Príncipe Research Institute, Child and Adolescent Health Research & Pequeno Príncipe Faculties, Curitiba, Brazil
| | - Bassam Felipe Mogharbel
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, The Pelé Pequeno Príncipe Research Institute, Child and Adolescent Health Research & Pequeno Príncipe Faculties, Curitiba, Brazil
| | - Priscila Elias Ferreira Stricker
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, The Pelé Pequeno Príncipe Research Institute, Child and Adolescent Health Research & Pequeno Príncipe Faculties, Curitiba, Brazil
| | - Dilcele Silva Moreira Dziedzic
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, The Pelé Pequeno Príncipe Research Institute, Child and Adolescent Health Research & Pequeno Príncipe Faculties, Curitiba, Brazil
| | - Ana Carolina Irioda
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, The Pelé Pequeno Príncipe Research Institute, Child and Adolescent Health Research & Pequeno Príncipe Faculties, Curitiba, Brazil
| | - Maiara Carolina Perussolo
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, The Pelé Pequeno Príncipe Research Institute, Child and Adolescent Health Research & Pequeno Príncipe Faculties, Curitiba, Brazil
| | - André Tavares Somma
- Veterinary Medicine Department, Federal University of Paraná, Curitiba, Brazil
| | | | | | - Peterson Dornbusch
- Veterinary Medicine Department, Federal University of Paraná, Curitiba, Brazil
| | - Mário Sato
- Ophthalmology Department, Federal University of Paraná, Curitiba, Brazil
| | - Naoye Shiokawa
- Ophthalmology Department, Federal University of Paraná, Curitiba, Brazil
| | - Lúcia de Noronha
- Pathology Laboratory of Institute of Biological and Health Sciences of Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | - Seigo Nagashima
- Pathology Laboratory of Institute of Biological and Health Sciences of Pontifical Catholic University of Paraná (PUCPR), Curitiba, Brazil
| | | | | | - Eltyeb Abdelwahid
- Feinberg School of Medicine, Feinberg Cardiovascular Research Institute,Chicago, USA
| | - Katherine Athayde Teixeirade Carvalho
- Advanced Therapy and Cellular Biotechnology in Regenerative Medicine Department, The Pelé Pequeno Príncipe Research Institute, Child and Adolescent Health Research & Pequeno Príncipe Faculties, Curitiba, Brazil
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20
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Wiemann S, Yousf A, Joachim SC, Peters C, Mueller-Buehl AM, Wagner N, Reinhard J. Knock-Out of Tenascin-C Ameliorates Ischemia-Induced Rod-Photoreceptor Degeneration and Retinal Dysfunction. Front Neurosci 2021; 15:642176. [PMID: 34093110 PMCID: PMC8172977 DOI: 10.3389/fnins.2021.642176] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/14/2021] [Indexed: 12/19/2022] Open
Abstract
Retinal ischemia is a common pathomechanism in various eye diseases. Recently, evidence accumulated suggesting that the extracellular matrix (ECM) glycoprotein tenascin-C (Tnc) plays a key role in ischemic degeneration. However, the possible functional role of Tnc in retinal ischemia is not yet known. The aim of our study was to explore retinal function and rod-bipolar/photoreceptor cell degeneration in wild type (WT) and Tnc knock-out (KO) mice after ischemia/reperfusion (I/R) injury. Therefore, I/R was induced by increasing intraocular pressure in the right eye of wild type (WT I/R) and Tnc KO (KO I/R) mice. The left eye served as untreated control (WT CO and KO CO). Scotopic electroretinogram (ERG) recordings were performed to examine rod-bipolar and rod-photoreceptor cell function. Changes of Tnc, rod-bipolar cells, photoreceptors, retinal structure and apoptotic and synaptic alterations were analyzed by immunohistochemistry, Hematoxylin and Eosin staining, Western blot, and quantitative real time PCR. We found increased Tnc protein levels 3 days after ischemia, while Tnc immunoreactivity decreased after 7 days. Tnc mRNA expression was comparable in the ischemic retina. ERG measurements after 7 days showed lower a-/b-wave amplitudes in both ischemic groups. Nevertheless, the amplitudes in the KO I/R group were higher than in the WT I/R group. We observed retinal thinning in WT I/R mice after 3 and 7 days. Although compared to the KO CO group, retinal thinning was not observed in the KO I/R group until 7 days. The number of PKCα+ rod-bipolar cells, recoverin+ photoreceptor staining and Prkca and Rcvrn expression were comparable in all groups. However, reduced rhodopsin protein as well as Rho and Gnat1 mRNA expression levels of rod-photoreceptors were found in the WT I/R, but not in the KO I/R retina. Additionally, a lower number of activated caspase 3+ cells was observed in the KO I/R group. Finally, both ischemic groups displayed enhanced vesicular glutamate transporter 1 (vGlut1) levels. Collectively, KO mice showed diminished rod-photoreceptor degeneration and retinal dysfunction after I/R. Elevated vGlut1 levels after ischemia could be related to an impaired glutamatergic photoreceptor-bipolar cell signaling and excitotoxicity. Our study provides novel evidence that Tnc reinforces ischemic retinal degeneration, possibly by synaptic remodeling.
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Affiliation(s)
- Susanne Wiemann
- Department of Cell Morphology and Molecular Neurobiology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Aisha Yousf
- Department of Cell Morphology and Molecular Neurobiology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Stephanie C Joachim
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Carolin Peters
- Department of Cell Morphology and Molecular Neurobiology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Ana M Mueller-Buehl
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Natalie Wagner
- Experimental Eye Research Institute, University Eye Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Jacqueline Reinhard
- Department of Cell Morphology and Molecular Neurobiology, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
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21
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Sarmah T, Bhattacharyya DK. A study of tools for differential co-expression analysis for RNA-Seq data. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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22
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Kircheva N, Dobrev S, Nikolova V, Angelova S, Dudev T. Zinc and Its Critical Role in Retinitis pigmentosa: Insights from DFT/SMD Calculations. Inorg Chem 2020; 59:17347-17355. [DOI: 10.1021/acs.inorgchem.0c02664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nikoleta Kircheva
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Stefan Dobrev
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Valya Nikolova
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria
| | - Silvia Angelova
- Institute of Optical Materials and Technologies “Acad. J. Malinowski”, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University “St. Kl. Ohridski”, 1164 Sofia, Bulgaria
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