1
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Kim MJ, Kulkarni V, Goode MA, Hernandez J, Graham S, Sivesind TE, Manchadi ML. Utilizing systems genetics to enhance understanding into molecular targets of skin cancer. Exp Dermatol 2024; 33:e15043. [PMID: 38459629 PMCID: PMC11018140 DOI: 10.1111/exd.15043] [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: 12/31/2023] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 03/10/2024]
Abstract
Despite progress made with immune checkpoint inhibitors and targeted therapies, skin cancer remains a significant public health concern in the United States. The intricacies of the disease, encompassing genetics, immune responses, and external factors, call for a comprehensive approach. Techniques in systems genetics, including transcriptional correlation analysis, functional pathway enrichment analysis, and protein-protein interaction network analysis, prove valuable in deciphering intricate molecular mechanisms and identifying potential diagnostic and therapeutic targets for skin cancer. Recent studies demonstrate the efficacy of these techniques in uncovering molecular processes and pinpointing diagnostic markers for various skin cancer types, highlighting the potential of systems genetics in advancing innovative therapies. While certain limitations exist, such as generalizability and contextualization of external factors, the ongoing progress in AI technologies provides hope in overcoming these challenges. By providing protocols and a practical example involving Braf, we aim to inspire early-career experimental dermatologists to adopt these tools and seamlessly integrate these techniques into their skin cancer research, positioning them at the forefront of innovative approaches in combating this devastating disease.
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Affiliation(s)
- Minjae J Kim
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | | | - Micah A Goode
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Jacob Hernandez
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Sean Graham
- University of Tennessee Health Science Center School of Medicine, Memphis, Tennessee, USA
| | - Torunn E Sivesind
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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2
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Riesmeijer SA, Kamali Z, Ng M, Drichel D, Piersma B, Becker K, Layton TB, Nanchahal J, Nothnagel M, Vaez A, Hennies HC, Werker PMN, Furniss D, Nolte IM. A genome-wide association meta-analysis implicates Hedgehog and Notch signaling in Dupuytren's disease. Nat Commun 2024; 15:199. [PMID: 38172110 PMCID: PMC10764787 DOI: 10.1038/s41467-023-44451-0] [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: 06/07/2022] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Dupuytren's disease (DD) is a highly heritable fibrotic disorder of the hand with incompletely understood etiology. A number of genetic loci, including Wnt signaling members, have been previously identified. Our overall aim was to identify novel genetic loci, to prioritize genes within the loci for functional studies, and to assess genetic correlation with associated disorders. We performed a meta-analysis of six DD genome-wide association studies from three European countries and extensive bioinformatic follow-up analyses. Leveraging 11,320 cases and 47,023 controls, we identified 85 genome-wide significant single nucleotide polymorphisms in 56 loci, of which 11 were novel, explaining 13.3-38.1% of disease variance. Gene prioritization implicated the Hedgehog and Notch signaling pathways. We also identified a significant genetic correlation with frozen shoulder. The pathways identified highlight the potential for new therapeutic targets and provide a basis for additional mechanistic studies for a common disorder that can severely impact hand function.
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Affiliation(s)
- Sophie A Riesmeijer
- University of Groningen, University Medical Center Groningen, Department of Plastic Surgery, Groningen, The Netherlands.
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands.
| | - Zoha Kamali
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
- Department of bioinformatics, School of Advanced Medical Technologies, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Michael Ng
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Faculty of Medicine and the Cologne University Hospital, Cologne, Germany
| | - Bram Piersma
- University of Groningen, Groningen, The Netherlands
| | - Kerstin Becker
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | | | | | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Faculty of Medicine and the Cologne University Hospital, Cologne, Germany
| | - Ahmad Vaez
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
- Department of bioinformatics, School of Advanced Medical Technologies, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hans Christian Hennies
- Faculty of Medicine and the Cologne University Hospital, Cologne, Germany
- Department of Biological Sciences, University of Huddersfield, Huddersfield, UK
| | - Paul M N Werker
- University of Groningen, University Medical Center Groningen, Department of Plastic Surgery, Groningen, The Netherlands
| | - Dominic Furniss
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, Botnar Research Centre, University of Oxford, Oxford, UK
| | - Ilja M Nolte
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
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3
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Sharif NA. Gene therapies and gene product-based drug candidates for normalizing and preserving tissue functions in animal models of ocular hypertension and glaucoma. Mol Aspects Med 2023; 94:101218. [PMID: 37976898 DOI: 10.1016/j.mam.2023.101218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/01/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
More than 76 million people worldwide are afflicted with the neurodegenerative eye diseases described and grouped together as glaucoma. A common feature amongst the many forms of glaucoma is chronically elevated intraocular pressure (IOP) within the anterior chamber of the eye that physically damages the retina, optic nerve and parts of the brain connected with visual perception. The mediators of the contusing raised IOP responsible for such damage and loss of vision include locally released inflammatory agents, tissue remodeling enzymes and infiltrating immune cells which damage the retinal ganglion cell (RGC) axons and eventually kill a significant number of the RGCs. Additional culprits include genetic defects of the patient that involve aberrations in receptors, enzymes and/or endogenous ligands and possible over- or under-production of the latter. Other genetic abnormalities may include issues with signal transduction machinery within key cells of critical tissues in the front (e.g. trabecular meshwork [TM] and Schlemm's canal [SC]) and back of the eye (e.g. retinal ganglion cells and their axons). Genome-wide associated studies (GWAS) coupled with next generation sequencing have provided powerful linkage of certain gene defects and polymorphic variants to the onset and progression of diseases of the tissues involved in fluid dynamics in the TM and SC, and many retinal elements (lamina cribosa, optic nerve head) at the back of the eye which cause ocular hypertension (OHT) and glaucomatous optic neuropathy (GON), respectively. Despite the availability of some drugs, fluid drainage microshunts and full surgical techniques to lower and control intraocular pressure, the major modifiable biomarker of open-angle and other forms of glaucoma, their side-effect profiles, less than optimum effectiveness and short duration of action present opportunities to clinically manage the glaucomas with next generation of treatments with high therapeutic indices, including gene therapies. Thus, identification, characterization and deployment of genetic data coupled with traditional drug discovery and novel gene replacement, gene editing and genetic engineering technologies may provide some solutions to the aforementioned problems. These aspects will be discussed in this article.
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Affiliation(s)
- Najam A Sharif
- Eye-APC Duke-NUS Medical School, Singapore, 169856, Singapore; Institute of Ophthalmology, University College London, London, W2 1PG, UK; Imperial College of Science and Technology, St. Mary's Campus, London, WC1E 6BT, UK; Department of Pharmacy Sciences, Creighton University, Omaha, NE, 68178, USA; Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX, 77004, USA; Department of Pharmacology and Neuroscience, University of North Texas Health Sciences Center, Fort Worth, TX, 76107, USA; Singapore Eye Research Institute, Singapore, 169856, Singapore; Global Research & Development, Nanoscope Therapeutics Inc., Dallas, TX 75207, USA.
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4
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Wang W, Wang H. Understanding the complex genetics and molecular mechanisms underlying glaucoma. Mol Aspects Med 2023; 94:101220. [PMID: 37856931 DOI: 10.1016/j.mam.2023.101220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/21/2023]
Abstract
Glaucoma is the leading cause of irreversible blindness worldwide. Currently the only effective treatment for glaucoma is to reduce the intraocular pressure, which can halt the progression of the disease. Highlighting the importance of identifying individuals at risk of developing glaucoma and those with early-stage glaucoma will help patients receive treatment before sight loss. However, some cases of glaucoma do not have raised intraocular pressure. In fact, glaucoma is caused by a variety of different mechanisms and has a wide range of different subtypes. Understanding other risk factors, the underlying mechanisms, and the pathology of glaucoma might lead to novel treatments and treatment of underlying diseases. In this review we present the latest research into glaucoma including the genetics and molecular basis of the disease.
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Affiliation(s)
- Weiwei Wang
- Shaanxi Eye Hospital, Xi'an People's Hospital (Xi'an Fourth Hospital), Affiliated People's Hospital, Northwest University, Xi'an, 710004, Shaanxi Province, China.
| | - Huaizhou Wang
- Department of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
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5
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Kim MJ, Martin CA, Kim J, Jablonski MM. Computational methods in glaucoma research: Current status and future outlook. Mol Aspects Med 2023; 94:101222. [PMID: 37925783 PMCID: PMC10842846 DOI: 10.1016/j.mam.2023.101222] [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: 08/01/2023] [Revised: 10/06/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Advancements in computational techniques have transformed glaucoma research, providing a deeper understanding of genetics, disease mechanisms, and potential therapeutic targets. Systems genetics integrates genomic and clinical data, aiding in identifying drug targets, comprehending disease mechanisms, and personalizing treatment strategies for glaucoma. Molecular dynamics simulations offer valuable molecular-level insights into glaucoma-related biomolecule behavior and drug interactions, guiding experimental studies and drug discovery efforts. Artificial intelligence (AI) technologies hold promise in revolutionizing glaucoma research, enhancing disease diagnosis, target identification, and drug candidate selection. The generalized protocols for systems genetics, MD simulations, and AI model development are included as a guide for glaucoma researchers. These computational methods, however, are not separate and work harmoniously together to discover novel ways to combat glaucoma. Ongoing research and progresses in genomics technologies, MD simulations, and AI methodologies project computational methods to become an integral part of glaucoma research in the future.
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Affiliation(s)
- Minjae J Kim
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Cole A Martin
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Jinhwa Kim
- Graduate School of Artificial Intelligence, Graduate School of Metaverse, Department of Management Information Systems, Sogang University, 1 Shinsoo-Dong, Mapo-Gu, Seoul, South Korea.
| | - Monica M Jablonski
- Department of Ophthalmology, The Hamilton Eye Institute, The University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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Keuthan CJ, Schaub JA, Wei M, Fang W, Quillen S, Kimball E, Johnson TV, Ji H, Zack DJ, Quigley HA. Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Optic Nerve Crush and Experimental Glaucoma. Int J Mol Sci 2023; 24:13719. [PMID: 37762022 PMCID: PMC10531004 DOI: 10.3390/ijms241813719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
A major risk factor for glaucomatous optic neuropathy is the level of intraocular pressure (IOP), which can lead to retinal ganglion cell axon injury and cell death. The optic nerve has a rostral unmyelinated portion at the optic nerve head followed by a caudal myelinated region. The unmyelinated region is differentially susceptible to IOP-induced damage in rodent models and human glaucoma. While several studies have analyzed gene expression changes in the mouse optic nerve following optic nerve injury, few were designed to consider the regional gene expression differences that exist between these distinct areas. We performed bulk RNA-sequencing on the retina and separately micro-dissected unmyelinated and myelinated optic nerve regions from naïve C57BL/6 mice, mice after optic nerve crush, and mice with microbead-induced experimental glaucoma (total = 36). Gene expression patterns in the naïve unmyelinated optic nerve showed significant enrichment of the Wnt, Hippo, PI3K-Akt, and transforming growth factor β pathways, as well as extracellular matrix-receptor and cell membrane signaling pathways, compared to the myelinated optic nerve and retina. Gene expression changes induced by both injuries were more extensive in the myelinated optic nerve than the unmyelinated region, and greater after nerve crush than glaucoma. Changes present three and fourteen days after injury largely subsided by six weeks. Gene markers of reactive astrocytes did not consistently differ between injury states. Overall, the transcriptomic phenotype of the mouse unmyelinated optic nerve was significantly different from immediately adjacent tissues, likely dominated by expression in astrocytes, whose junctional complexes are inherently important in responding to IOP elevation.
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Affiliation(s)
- Casey J. Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (C.J.K.)
| | - Julie A. Schaub
- Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (C.J.K.)
| | - Meihan Wei
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Weixiang Fang
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Sarah Quillen
- Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (C.J.K.)
| | - Elizabeth Kimball
- Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (C.J.K.)
| | - Thomas V. Johnson
- Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (C.J.K.)
| | - Hongkai Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Donald J. Zack
- Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (C.J.K.)
- Departments of Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Harry A. Quigley
- Department of Ophthalmology, Wilmer Eye Institute, School of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA; (C.J.K.)
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7
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de Leeuw C, Werme J, Savage JE, Peyrot WJ, Posthuma D. On the interpretation of transcriptome-wide association studies. PLoS Genet 2023; 19:e1010921. [PMID: 37676898 PMCID: PMC10508613 DOI: 10.1371/journal.pgen.1010921] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/19/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023] Open
Abstract
Transcriptome-wide association studies (TWAS) aim to detect relationships between gene expression and a phenotype, and are commonly used for secondary analysis of genome-wide association study (GWAS) results. Results from TWAS analyses are often interpreted as indicating a genetic relationship between gene expression and a phenotype, but this interpretation is not consistent with the null hypothesis that is evaluated in the traditional TWAS framework. In this study we provide a mathematical outline of this TWAS framework, and elucidate what interpretations are warranted given the null hypothesis it actually tests. We then use both simulations and real data analysis to assess the implications of misinterpreting TWAS results as indicative of a genetic relationship between gene expression and the phenotype. Our simulation results show considerably inflated type 1 error rates for TWAS when interpreted this way, with 41% of significant TWAS associations detected in the real data analysis found to have insufficient statistical evidence to infer such a relationship. This demonstrates that in current implementations, TWAS cannot reliably be used to investigate genetic relationships between gene expression and a phenotype, but that local genetic correlation analysis can serve as a potential alternative.
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Affiliation(s)
- Christiaan de Leeuw
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Josefin Werme
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Jeanne E. Savage
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Wouter J. Peyrot
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
- Department of Psychiatry, Amsterdam UMC, location VUmc, Amsterdam, the Netherlands
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Centre for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychology and Psychiatry, section Complex Trait Genetics, Amsterdam Neuroscience, VU University Medical Centre, Amsterdam, The Netherlands
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8
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Sharif NA. Elevated Intraocular Pressure and Glaucomatous Optic Neuropathy: Genes to Disease Mechanisms, Therapeutic Drugs, and Gene Therapies. Pharmaceuticals (Basel) 2023; 16:870. [PMID: 37375817 DOI: 10.3390/ph16060870] [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: 05/17/2023] [Revised: 06/01/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
This review article focuses on the pathogenesis of and genetic defects linked with chronic ocular hypertension (cOHT) and glaucoma. The latter ocular disease constitutes a group of ocular degenerative diseases whose hallmark features are damage to the optic nerve, apoptotic demise of retinal ganglion cells, disturbances within the brain regions involved in visual perception and considerable visual impairment that can lead to blindness. Even though a number of pharmaceuticals, surgical and device-based treatments already exist addressing cOHT associated with the most prevalent of the glaucoma types, primary open-angle glaucoma (POAG), they can be improved upon in terms of superior efficacy with reduced side-effects and with longer duration of activity. The linkage of disease pathology to certain genes via genome-wide associated studies are illuminating new approaches to finding novel treatment options for the aforementioned ocular disorders. Gene replacement, gene editing via CRISPR-Cas9, and the use of optogenetic technologies may replace traditional drug-based therapies and/or they may augment existing therapeutics for the treatment of cOHT and POAG in the future.
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Affiliation(s)
- Najam A Sharif
- Eye-APC Duke-NUS Medical School, Singapore 169857, Singapore
- Singapore Eye Research Institute, Singapore 169856, Singapore
- Department of Pharmacology and Neuroscience, University of North Texas Health Sciences Center, Fort Worth, TX 76107, USA
- Department of Pharmacy Sciences, Creighton University, Omaha, NE 68178, USA
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, Texas Southern University, Houston, TX 77004, USA
- Imperial College of Science and Technology, St. Mary's Campus, London W2 1PG, UK
- Institute of Ophthalmology, University College London, London WC1E 6BT, UK
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9
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Keuthan CJ, Schaub J, Wei M, Fang W, Quillen S, Kimball E, Johnson TV, Ji H, Zack DJ, Quigley HA. Regional Gene Expression in the Retina, Optic Nerve Head, and Optic Nerve of Mice with Experimental Glaucoma and Optic Nerve Crush. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529410. [PMID: 36993314 PMCID: PMC10054954 DOI: 10.1101/2023.02.21.529410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A major risk factor for glaucomatous optic neuropathy is the level of intraocular pressure (IOP), which can lead to retinal ganglion cell axon injury and cell death. The optic nerve has a rostral unmyelinated portion at the optic nerve head followed by a caudal myelinated region. The unmyelinated region is differentially susceptible to IOP-induced damage in rodent models and in human glaucoma. While several studies have analyzed gene expression changes in the mouse optic nerve following optic nerve injury, few were designed to consider the regional gene expression differences that exist between these distinct areas. We performed bulk RNA-sequencing on the retina and on separately micro-dissected unmyelinated and myelinated optic nerve regions from naïve C57BL/6 mice, mice after optic nerve crush, and mice with microbead-induced experimental glaucoma (total = 36). Gene expression patterns in the naïve unmyelinated optic nerve showed significant enrichment of the Wnt, Hippo, PI3K-Akt, and transforming growth factor β pathways, as well as extracellular matrix-receptor and cell membrane signaling pathways, compared to the myelinated optic nerve and retina. Gene expression changes induced by both injuries were more extensive in the myelinated optic nerve than the unmyelinated region, and greater after nerve crush than glaucoma. Changes three and fourteen days after injury largely subsided by six weeks. Gene markers of reactive astrocytes did not consistently differ between injury states. Overall, the transcriptomic phenotype of the mouse unmyelinated optic nerve was significantly different from immediately adjacent tissues, likely dominated by expression in astrocytes, whose junctional complexes are inherently important in responding to IOP elevation.
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Affiliation(s)
- Casey J. Keuthan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Julie Schaub
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Meihan Wei
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Weixiang Fang
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sarah Quillen
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Elizabeth Kimball
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Thomas V. Johnson
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Donald J. Zack
- Departments of Ophthalmology, Wilmer Eye Institute, Neuroscience, Molecular Biology and Genetics, and Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Harry A. Quigley
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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Watanabe M, Sato T, Tsugeno Y, Higashide M, Furuhashi M, Umetsu A, Suzuki S, Ida Y, Hikage F, Ohguro H. All-trans Retinoic Acids Synergistically and Beneficially Affect In Vitro Glaucomatous Trabecular Meshwork (TM) Models Using 2D and 3D Cell Cultures of Human TM Cells. Int J Mol Sci 2022; 23:ijms23179912. [PMID: 36077314 PMCID: PMC9456377 DOI: 10.3390/ijms23179912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/25/2022] Open
Abstract
We report herein on the effects of all-trans retinoic acid (ATRA) on two-dimensional (2D) and three-dimensional (3D) cultures of human trabecular meshwork (HTM) cells that were treated with transforming growth factor β2 (TGF-β2). In the presence of 5 ng/mL TGF-β2, the effects of ATRA on the following were observed: (1) the barrier function of the 2D HTM monolayers, as determined by trans-endothelial electrical resistance (TEER) and fluorescein isothiocyanate (FITC) dextran permeability measurements; (2) a Seahorse cellular bio-metabolism analysis; (3) physical properties, including the size and stiffness, of 3D spheroids; (4) the gene expression of extracellular matrix (ECM) molecules, ECM modulators including tissue inhibitor of metalloproteinases (TIMPs), matrix metalloproteinases (MMPs), tight junction (TJ)-related molecules, and endoplasmic reticulum (ER)-stress-related factors. ATRA significantly inhibited the TGF-β2-induced increase in the TEER values and FITC dextran permeability of the 2D monolayers, while an ATRA monotreatment induced similar effects as TGF-β2. A real-time metabolic analysis revealed that ATRA significantly inhibited the TGF-β2-induced shift in metabolic reserve from mitochondrial oxidative phosphorylation to glycolysis in 2D HTM cells, whereas ATRA alone did not induce significant metabolic changes. In contrast, ATRA induced the formation of substantially downsized and softer 3D spheroids in the absence and presence of TGF-β2. The different effects induced by ATRA toward 2D and 3D HTM cells were also supported by the qPCR analysis of several proteins as above. The findings reported here indicate that ATRA may induce synergistic and beneficial effects on TGF-β2-treated 2D- and 3D-cultured HTM cells; those effects varied significantly between the 2D and 3D cultures.
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Affiliation(s)
- Megumi Watanabe
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Tatsuya Sato
- Departments of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
- Departments of Cellular Physiology and Signal Transduction, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Yuri Tsugeno
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Megumi Higashide
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Masato Furuhashi
- Departments of Cardiovascular, Renal and Metabolic Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Araya Umetsu
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Soma Suzuki
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Yosuke Ida
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Fumihito Hikage
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Hiroshi Ohguro
- Departments of Ophthalmology, School of Medicine, Sapporo Medical University, Sapporo 060-8556, Japan
- Correspondence: ; Tel.: +81-611-2111
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Large-Scale Multi-Omics Studies Provide New Insights into Blood Pressure Regulation. Int J Mol Sci 2022; 23:ijms23147557. [PMID: 35886906 PMCID: PMC9323755 DOI: 10.3390/ijms23147557] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022] Open
Abstract
Recent genome-wide association studies uncovered part of blood pressure’s heritability. However, there is still a vast gap between genetics and biology that needs to be bridged. Here, we followed up blood pressure genome-wide summary statistics of over 750,000 individuals, leveraging comprehensive epigenomic and transcriptomic data from blood with a follow-up in cardiovascular tissues to prioritise likely causal genes and underlying blood pressure mechanisms. We first prioritised genes based on coding consequences, multilayer molecular associations, blood pressure-associated expression levels, and coregulation evidence. Next, we followed up the prioritised genes in multilayer studies of genomics, epigenomics, and transcriptomics, functional enrichment, and their potential suitability as drug targets. Our analyses yielded 1880 likely causal genes for blood pressure, tens of which are targets of the available licensed drugs. We identified 34 novel genes for blood pressure, supported by more than one source of biological evidence. Twenty-eight (82%) of these new genes were successfully replicated by transcriptome-wide association analyses in a large independent cohort (n = ~220,000). We also found a substantial mediating role for epigenetic regulation of the prioritised genes. Our results provide new insights into genetic regulation of blood pressure in terms of likely causal genes and involved biological pathways offering opportunities for future translation into clinical practice.
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