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Yuan W, Li J, Gao S, Sun W, Zhao F. Novel therapeutic targets for primary open-angle glaucoma identified through multicenter proteome-wide mendelian randomization. Front Pharmacol 2024; 15:1428472. [PMID: 39221148 PMCID: PMC11362091 DOI: 10.3389/fphar.2024.1428472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 08/09/2024] [Indexed: 09/04/2024] Open
Abstract
Background This study aimed to identify novel therapeutic targets for primary open-angle glaucoma (POAG). Methods The summary-data-based Mendelian randomization (SMR) method was used to evaluate the genetic association between plasma proteins and POAG. Two sets of plasma protein quantitative trait loci (pQTLs) data considered exposures were obtained from the Icelandic Decoding Genetics Study and UK Biobank Pharma Proteomics Project. The summary-level genome-wide association studies data for POAG were extracted from the latest Round 10 release of the FinnGen consortium (8,530 cases and 391,275 controls) and the UK Biobank (4,737 cases and 458,196 controls). Colocalization analysis was used to screen out pQTLs that share the same variant with POAG as drug targets identified. The two-sample Mendelian randomization, reverse causality testing and phenotype scanning were performed to further validate the main findings. Protein-protein interaction, pathway enrichment analysis and druggability assessment were conducted to determine whether the identified plasma proteins have potential as drug targets. Results After systematic analysis, this study identified eight circulating proteins as potential therapeutic targets for POAG. Three causal proteins with strong evidence of colocalization, ROBO1 (OR = 1.38, p = 1.48 × 10-4, PPH4 = 0.865), FOXO3 (OR = 0.35, p = 4.34 × 10-3, PPH4 = 0.796), ITIH3 (OR = 0.89, p = 2.76 × 10-4, PPH4 = 0.767), were considered tier one targets. Five proteins with medium support evidence of colocalization, NCR1 (OR = 1.25, p = 4.18 × 10-4, PPH4 = 0.682), NID1 (OR = 1.38, p = 1.54 × 10-3, PPH4 = 0.664), TIMP3 (OR = 0.91, p = 4.01 × 10-5, PPH4 = 0.659), SERPINF1 (OR = 0.81, p = 2.77 × 10-4, PPH4 = 0.59), OXT (OR = 1.17, p = 9.51 × 10-4, PPH4 = 0.526), were classified as tier two targets. Additional sensitivity analyses further validated the robustness and directionality of these findings. According to druggability assessment, Pimagedine, Resveratrol, Syringaresinol and Clozapine may potentially be important in the development of new anti-glaucoma agents. Conclusion Our integrated study identified eight potential associated proteins for POAG. These proteins play important roles in neuroprotection, extracellular matrix regulation and oxidative stress. Therefore, they have promising potential as therapeutic targets to combat POAG.
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Affiliation(s)
- Weichen Yuan
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Jun Li
- Department of Ultrasonography, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shang Gao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Wei Sun
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Fangkun Zhao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
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Fang Z, Peltz G. An automated multi-modal graph-based pipeline for mouse genetic discovery. Bioinformatics 2022; 38:3385-3394. [PMID: 35608290 PMCID: PMC9992076 DOI: 10.1093/bioinformatics/btac356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Our ability to identify causative genetic factors for mouse genetic models of human diseases and biomedical traits has been limited by the difficulties associated with identifying true causative factors, which are often obscured by the many false positive genetic associations produced by a GWAS. RESULTS To accelerate the pace of genetic discovery, we developed a graph neural network (GNN)-based automated pipeline (GNNHap) that could rapidly analyze mouse genetic model data and identify high probability causal genetic factors for analyzed traits. After assessing the strength of allelic associations with the strain response pattern; this pipeline analyzes 29M published papers to assess candidate gene-phenotype relationships; and incorporates the information obtained from a protein-protein interaction network and protein sequence features into the analysis. The GNN model produces markedly improved results relative to that of a simple linear neural network. We demonstrate that GNNHap can identify novel causative genetic factors for murine models of diabetes/obesity and for cataract formation, which were validated by the phenotypes appearing in previously analyzed gene knockout mice. The diabetes/obesity results indicate how characterization of the underlying genetic architecture enables new therapies to be discovered and tested by applying 'precision medicine' principles to murine models. AVAILABILITY AND IMPLEMENTATION The GNNHap source code is freely available at https://github.com/zqfang/gnnhap, and the new version of the HBCGM program is available at https://github.com/zqfang/haplomap. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhuoqing Fang
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gary Peltz
- Department of Anesthesia, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Nguyen B, Bix G, Yao Y. Basal lamina changes in neurodegenerative disorders. Mol Neurodegener 2021; 16:81. [PMID: 34876200 PMCID: PMC8650282 DOI: 10.1186/s13024-021-00502-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Neurodegenerative disorders are a group of age-associated diseases characterized by progressive degeneration of the structure and function of the CNS. Two key pathological features of these disorders are blood-brain barrier (BBB) breakdown and protein aggregation. MAIN BODY The BBB is composed of various cell types and a non-cellular component---the basal lamina (BL). Although how different cells affect the BBB is well studied, the roles of the BL in BBB maintenance and function remain largely unknown. In addition, located in the perivascular space, the BL is also speculated to regulate protein clearance via the meningeal lymphatic/glymphatic system. Recent studies from our laboratory and others have shown that the BL actively regulates BBB integrity and meningeal lymphatic/glymphatic function in both physiological and pathological conditions, suggesting that it may play an important role in the pathogenesis and/or progression of neurodegenerative disorders. In this review, we focus on changes of the BL and its major components during aging and in neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS). First, we introduce the vascular and lymphatic systems in the CNS. Next, we discuss the BL and its major components under homeostatic conditions, and summarize their changes during aging and in AD, PD, and ALS in both rodents and humans. The functional significance of these alterations and potential therapeutic targets are also reviewed. Finally, key challenges in the field and future directions are discussed. CONCLUSIONS Understanding BL changes and the functional significance of these changes in neurodegenerative disorders will fill the gap of knowledge in the field. Our goal is to provide a clear and concise review of the complex relationship between the BL and neurodegenerative disorders to stimulate new hypotheses and further research in this field.
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Affiliation(s)
- Benjamin Nguyen
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Gregory Bix
- Clinical Neuroscience Research Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
- Departments of Neurosurgery and Neurology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Yao Yao
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA.
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, MDC 8, Tampa, Florida, 33612, USA.
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Preclinical challenges for developing long acting intravitreal medicines. Eur J Pharm Biopharm 2020; 153:130-149. [DOI: 10.1016/j.ejpb.2020.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/01/2020] [Accepted: 05/08/2020] [Indexed: 02/07/2023]
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Abstract
Located at the interface of the circulation system and the CNS, the basement membrane (BM) is well positioned to regulate blood-brain barrier (BBB) integrity. Given the important roles of BBB in the development and progression of various neurological disorders, the BM has been hypothesized to contribute to the pathogenesis of these diseases. After stroke, a cerebrovascular disease caused by rupture (hemorrhagic) or occlusion (ischemic) of cerebral blood vessels, the BM undergoes constant remodeling to modulate disease progression. Although an association between BM dissolution and stroke is observed, how each individual BM component changes after stroke and how these components contribute to stroke pathogenesis are mostly unclear. In this review, I first briefly introduce the composition of the BM in the brain. Next, the functions of the BM and its major components in BBB maintenance under homeostatic conditions are summarized. Furthermore, the roles of the BM and its major components in the pathogenesis of hemorrhagic and ischemic stroke are discussed. Last, unsolved questions and potential future directions are described. This review aims to provide a comprehensive reference for future studies, stimulate the formation of new ideas, and promote the generation of new genetic tools in the field of BM/stroke research.
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Affiliation(s)
- Yao Yao
- Yao Yao, Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 340 Pharmacy South Building, 250 West Green Street, Athens, GA 30602, USA.
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Basement membranes in the cornea and other organs that commonly develop fibrosis. Cell Tissue Res 2018; 374:439-453. [PMID: 30284084 DOI: 10.1007/s00441-018-2934-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 09/20/2018] [Indexed: 12/19/2022]
Abstract
Basement membranes are thin connective tissue structures composed of organ-specific assemblages of collagens, laminins, proteoglycan-like perlecan, nidogens, and other components. Traditionally, basement membranes are thought of as structures which primarily function to anchor epithelial, endothelial, or parenchymal cells to underlying connective tissues. While this role is important, other functions such as the modulation of growth factors and cytokines that regulate cell proliferation, migration, differentiation, and fibrosis are equally important. An example of this is the critical role of both the epithelial basement membrane and Descemet's basement membrane in the cornea in modulating myofibroblast development and fibrosis, as well as myofibroblast apoptosis and the resolution of fibrosis. This article compares the ultrastructure and functions of key basement membranes in several organs to illustrate the variability and importance of these structures in organs that commonly develop fibrosis.
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Hunt NC, Hallam D, Karimi A, Mellough CB, Chen J, Steel DHW, Lako M. 3D culture of human pluripotent stem cells in RGD-alginate hydrogel improves retinal tissue development. Acta Biomater 2017; 49:329-343. [PMID: 27826002 DOI: 10.1016/j.actbio.2016.11.016] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 12/22/2022]
Abstract
No treatments exist to effectively treat many retinal diseases. Retinal pigmented epithelium (RPE) and neural retina can be generated from human embryonic stem cells/induced pluripotent stem cells (hESCs/hiPSCs). The efficacy of current protocols is, however, limited. It was hypothesised that generation of laminated neural retina and/or RPE from hiPSCs/hESCs could be enhanced by three dimensional (3D) culture in hydrogels. hiPSC- and hESC-derived embryoid bodies (EBs) were encapsulated in 0.5% RGD-alginate; 1% RGD-alginate; hyaluronic acid (HA) or HA/gelatin hydrogels and maintained until day 45. Compared with controls (no gel), 0.5% RGD-alginate increased: the percentage of EBs with pigmented RPE foci; the percentage EBs with optic vesicles (OVs) and pigmented RPE simultaneously; the area covered by RPE; frequency of RPE cells (CRALBP+); expression of RPE markers (TYR and RPE65) and the retinal ganglion cell marker, MATH5. Furthermore, 0.5% RGD-alginate hydrogel encapsulation did not adversely affect the expression of other neural retina markers (PROX1, CRX, RCVRN, AP2α or VSX2) as determined by qRT-PCR, or the percentage of VSX2 positive cells as determined by flow cytometry. 1% RGD-alginate increased the percentage of EBs with OVs and/or RPE, but did not significantly influence any other measures of retinal differentiation. HA-based hydrogels had no significant effect on retinal tissue development. The results indicated that derivation of retinal tissue from hESCs/hiPSCs can be enhanced by culture in 0.5% RGD-alginate hydrogel. This RGD-alginate scaffold may be useful for derivation, transport and transplantation of neural retina and RPE, and may also enhance formation of other pigmented, neural or epithelial tissue. STATEMENT OF SIGNIFICANCE The burden of retinal disease is ever growing with the increasing age of the world-wide population. Transplantation of retinal tissue derived from human pluripotent stem cells (PSCs) is considered a promising treatment. However, derivation of retinal tissue from PSCs using defined media is a lengthy process and often variable between different cell lines. This study indicated that alginate hydrogels enhanced retinal tissue development from PSCs, whereas hyaluronic acid-based hydrogels did not. This is the first study to show that 3D culture with a biomaterial scaffold can improve retinal tissue derivation from PSCs. These findings indicate potential for the clinical application of alginate hydrogels for the derivation and subsequent transplantation retinal tissue. This work may also have implications for the derivation of other pigmented, neural or epithelial tissue.
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Affiliation(s)
- Nicola C Hunt
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle NE1 3BZ, UK.
| | - Dean Hallam
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle NE1 3BZ, UK.
| | - Ayesha Karimi
- Cumberland Infirmary, North Cumbria University Hospitals NHS Trust, Carlisle CA2 7HY, UK
| | - Carla B Mellough
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle NE1 3BZ, UK.
| | - Jinju Chen
- School of Mechanical & Systems Engineering, Stephenson Building, Newcastle University, Newcastle upon Tyne, UK.
| | - David H W Steel
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle NE1 3BZ, UK; Sunderland Eye Infirmary, Queen Alexandra Road, Sunderland SR2 9HP, UK.
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Central Parkway, Newcastle NE1 3BZ, UK.
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Murgiano L, Jagannathan V, Calderoni V, Joechler M, Gentile A, Drögemüller C. Looking the cow in the eye: deletion in the NID1 gene is associated with recessive inherited cataract in Romagnola cattle. PLoS One 2014; 9:e110628. [PMID: 25347398 PMCID: PMC4210201 DOI: 10.1371/journal.pone.0110628] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/16/2014] [Indexed: 12/15/2022] Open
Abstract
Cataract is a known condition leading to opacification of the eye lens causing partial or total blindness. Mutations are known to cause autosomal dominant or recessive inherited forms of cataracts in humans, mice, rats, guinea pigs and dogs. The use of large-sized animal models instead of those using mice for the study of this condition has been discussed due to the small size of rodent lenses. Four juvenile-onset cases of bilateral incomplete immature nuclear cataract were recently observed in Romagnola cattle. Pedigree analysis suggested a monogenic autosomal recessive inheritance. In addition to the cataract, one of the cases displayed abnormal head movements. Genome-wide association and homozygosity mapping and subsequent whole genome sequencing of a single case identified two perfectly associated sequence variants in a critical interval of 7.2 Mb on cattle chromosome 28: a missense point mutation located in an uncharacterized locus and an 855 bp deletion across the exon 19/intron 19 border of the bovine nidogen 1 (NID1) gene (c.3579_3604+829del). RT-PCR showed that NID1 is expressed in bovine lenses while the transcript of the second locus was absent. The NID1 deletion leads to the skipping of exon 19 during transcription and is therefore predicted to cause a frameshift and premature stop codon (p.1164fs27X). The truncated protein lacks a C-terminal domain essential for binding with matrix assembly complexes. Nidogen 1 deficient mice show neurological abnormalities and highly irregular crystal lens alterations. This study adds NID1 to the list of candidate genes for inherited cataract in humans and is the first report of a naturally occurring mutation leading to non-syndromic catarct in cattle provides a potential large animal model for human cataract.
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Affiliation(s)
- Leonardo Murgiano
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | | | - Monika Joechler
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy
| | - Arcangelo Gentile
- Department of Veterinary Medical Sciences, University of Bologna, Ozzano dell'Emilia, Italy
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- * E-mail:
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