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Storås AM, Fineide F, Magnø M, Thiede B, Chen X, Strümke I, Halvorsen P, Galtung H, Jensen JL, Utheim TP, Riegler MA. Using machine learning model explanations to identify proteins related to severity of meibomian gland dysfunction. Sci Rep 2023; 13:22946. [PMID: 38135766 PMCID: PMC10746717 DOI: 10.1038/s41598-023-50342-7] [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: 07/14/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
Meibomian gland dysfunction is the most common cause of dry eye disease and leads to significantly reduced quality of life and social burdens. Because meibomian gland dysfunction results in impaired function of the tear film lipid layer, studying the expression of tear proteins might increase the understanding of the etiology of the condition. Machine learning is able to detect patterns in complex data. This study applied machine learning to classify levels of meibomian gland dysfunction from tear proteins. The aim was to investigate proteomic changes between groups with different severity levels of meibomian gland dysfunction, as opposed to only separating patients with and without this condition. An established feature importance method was used to identify the most important proteins for the resulting models. Moreover, a new method that can take the uncertainty of the models into account when creating explanations was proposed. By examining the identified proteins, potential biomarkers for meibomian gland dysfunction were discovered. The overall findings are largely confirmatory, indicating that the presented machine learning approaches are promising for detecting clinically relevant proteins. While this study provides valuable insights into proteomic changes associated with varying severity levels of meibomian gland dysfunction, it should be noted that it was conducted without a healthy control group. Future research could benefit from including such a comparison to further validate and extend the findings presented here.
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Affiliation(s)
- Andrea M Storås
- Department of Holistic Systems, Simula Metropolitan Center for Digital Engineering, Oslo, Norway.
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway.
| | - Fredrik Fineide
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
- The Norwegian Dry Eye Clinic, Oslo, Bergen, Norway
| | - Morten Magnø
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Oslo, Norway
| | - Bernd Thiede
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Xiangjun Chen
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Vestre Viken Hospital Trust, Drammen, Norway
| | - Inga Strümke
- Department of Computer Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Pål Halvorsen
- Department of Holistic Systems, Simula Metropolitan Center for Digital Engineering, Oslo, Norway
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
| | - Hilde Galtung
- Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Janicke L Jensen
- Department of Oral Surgery and Oral Medicine, University of Oslo, Oslo, Norway
| | - Tor P Utheim
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
- The Norwegian Dry Eye Clinic, Oslo, Bergen, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, Arendal, Norway
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, Oslo, Norway
| | - Michael A Riegler
- Department of Holistic Systems, Simula Metropolitan Center for Digital Engineering, Oslo, Norway
- Department of Computer Science, OsloMet - Oslo Metropolitan University, Oslo, Norway
- Department of Computer Science, UiT The Arctic University of Norway, Tromsø, Norway
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Oie Y, Yamaguchi T, Nishida N, Okumura N, Maeno S, Kawasaki R, Jhanji V, Shimazaki J, Nishida K. Systematic Review of the Diagnostic Criteria and Severity Classification for Fuchs Endothelial Corneal Dystrophy. Cornea 2023; 42:1590-1600. [PMID: 37603692 DOI: 10.1097/ico.0000000000003343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/28/2023] [Indexed: 08/23/2023]
Abstract
PURPOSE There are no defined diagnostic criteria and severity classification for Fuchs endothelial corneal dystrophy (FECD), which are required for objective standardized assessments. Therefore, we performed a systematic literature review of the current diagnosis and severity classification of FECD. METHODS We searched the Ovid MEDLINE and Web of Science databases for studies published until January 13, 2021. We excluded review articles, conference abstracts, editorials, case reports with <5 patients, and letters. RESULTS Among 468 articles identified, we excluded 173 and 165 articles in the first and second screenings, respectively. Among the 130 included articles, 61 (47%) and 99 (76%) mentioned the diagnostic criteria for FECD and described its severity classification, respectively. Regarding diagnosis, slitlamp microscope alone was the most frequently used device in 31 (51%) of 61 articles. Regarding diagnostic findings, corneal guttae alone was the most common parameter [adopted in 23 articles (38%)]. Regarding severity classification, slitlamp microscopes were used in 88 articles (89%). The original or modified Krachmer grading scale was used in 77 articles (78%), followed by Adami's classification in six (6%). Specular microscopes or Scheimpflug tomography were used in four articles (4%) and anterior segment optical coherence tomography in one (1%). CONCLUSIONS FECD is globally diagnosed by the corneal guttae using slitlamp examination, and its severity is predominantly determined by the original or modified Krachmer grading scale. Objective severity grading using Scheimpflug or anterior segment optical coherence tomography can be applied in the future innovative therapies such as cell injection therapy or novel small molecules.
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Affiliation(s)
- Yoshinori Oie
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takefumi Yamaguchi
- Department of Ophthalmology, Tokyo Dental College Ichikawa General Hospital, Ichikawa, Japan
| | - Nozomi Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Naoki Okumura
- Department of Biomedical Engineering, Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan; and
| | - Sayo Maeno
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryo Kawasaki
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Vishal Jhanji
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jun Shimazaki
- Department of Ophthalmology, Tokyo Dental College Ichikawa General Hospital, Ichikawa, Japan
| | - Kohji Nishida
- Department of Ophthalmology, Osaka University Graduate School of Medicine, Suita, Japan
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Transcriptomic analysis revealed increased expression of genes involved in keratinization in the tears of COVID-19 patients. Sci Rep 2021; 11:19817. [PMID: 34615949 PMCID: PMC8494911 DOI: 10.1038/s41598-021-99344-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 09/23/2021] [Indexed: 01/08/2023] Open
Abstract
Recent studies have focused their attention on conjunctivitis as one of the symptoms of coronavirus disease 2019 (COVID-19). Therefore, tear samples were taken from COVID-19 patients and the presence of SARS-CoV-2 was evidenced using Real Time reverse transcription polymerase chain reaction. The main aim of this study was to analyze mRNA expression in the tears of patients with COVID-19 compared with healthy subjects using Next Generation Sequencing (NGS). The functional evaluation of the transcriptome highlighted 25 genes that differ statistically between healthy individuals and patients affected by COVID-19. In particular, the NGS analysis identified the presence of several genes involved in B cell signaling and keratinization. In particular, the genes involved in B cell signaling were downregulated in the tears of COVID-19 patients, while those involved in keratinization were upregulated. The results indicated that SARS-CoV-2 may induce a process of ocular keratinization and a defective B cell response.
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Kuot A, Corbett MA, Mills RA, Snibson G, Wiffen S, Loh R, Burdon KP, Craig JE, Sharma S. Differential gene expression analysis of corneal endothelium indicates involvement of phagocytic activity in Fuchs' endothelial corneal dystrophy. Exp Eye Res 2021; 210:108692. [PMID: 34228965 DOI: 10.1016/j.exer.2021.108692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/31/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022]
Abstract
Fuchs' endothelial corneal dystrophy (FECD) is a progressive vision impairing disease caused by thickening of Descemet's membrane and gradual degeneration and loss of corneal endothelial cells. The aim of this study was to identify differentially expressed genes between FECD-affected and unaffected corneal endothelium to gain insight into the pathophysiological mechanisms underlying this disease. Microarray gene expression analysis was performed on total RNA from FECD-affected and unaffected corneal endothelium-Descemet's membrane (CE-DM) specimens using the Illumina HumanHT-12 v4.0 expression array. RNA from pools of FECD-affected (n = 3 per pool) and individual unaffected (n = 3) specimens was used for comparison. Altered expression of a sub-set of differentially expressed genes was validated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) in independent specimens. Bioinformatics analysis was performed using InnateDB to reveal functional relationships among the differentially expressed genes and molecular pathways involved in the disease. A total of 16,513 genes were found expressed in the corneal endothelium of which 142 genes were differentially expressed between FECD-affected and unaffected endothelium (log2 fold-change ≥1.5, corrected p-value ≤0.05). Most of the genes were up-regulated (126) and a small proportion down-regulated (16) in affected corneal endothelium. Of the twelve genes prioritised for validation, differential expression of 10 genes, including those ranked 57th and 81st by significance validated by qRT-PCR (8 up-regulated and 2 downregulated, corrected p ≤ 0.05), one gene showed a trend for up-regulation in affected endothelium, consistent with the microarray analysis and another was up-regulated in an independent study indicating robustness of the differential expression dataset. Bioinformatic analysis revealed significant over-representation of differentially expressed genes in extracellular matrix reorganisation, cellular remodelling, immune response, and inflammation. Network analysis showed functional inter-relatedness of the majority of the dysregulated genes and revealed known direct functional relationships between 20 of the genes; many of these genes have roles in macrophage differentiation, phagocytosis and inflammation. This is the second report of microarray gene expression analysis in FECD. This study revealed a set of highly dysregulated genes in the corneal endothelium in FECD. More than a third of the dysregulated genes in the disease have been discovered for the first time and thus are novel. The dysregulated genes strongly suggest the presence of phagocytic cells, most likely immune cells, and inflammation in corneal endothelium in the disease. This study provides a molecular framework for delineating the mechanisms underlying these cellular processes in FECD.
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Affiliation(s)
- Abraham Kuot
- Department of Ophthalmology, Flinders University, Bedford Park, SA, 5042, Australia
| | - Mark A Corbett
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA, 5042, Australia
| | - Richard A Mills
- Department of Ophthalmology, Flinders University, Bedford Park, SA, 5042, Australia
| | - Grant Snibson
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, 3002, Australia
| | - Steven Wiffen
- The Lions Eye Bank of Western Australia, Lions Eye Institute, Nedlands, WA, 6009, Australia
| | - Raymond Loh
- Department of Ophthalmology, Flinders University, Bedford Park, SA, 5042, Australia
| | - Kathryn P Burdon
- Department of Ophthalmology, Flinders University, Bedford Park, SA, 5042, Australia; Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Jamie E Craig
- Department of Ophthalmology, Flinders University, Bedford Park, SA, 5042, Australia
| | - Shiwani Sharma
- Department of Ophthalmology, Flinders University, Bedford Park, SA, 5042, Australia.
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Aghamollaei H, Parvin S, Shahriary A. Review of proteomics approach to eye diseases affecting the anterior segment. J Proteomics 2020; 225:103881. [PMID: 32565161 DOI: 10.1016/j.jprot.2020.103881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/08/2020] [Accepted: 06/16/2020] [Indexed: 01/12/2023]
Abstract
Visual impairment and blindness is a major health burden worldwide, and major ocular diseases causing visual impairment pertain to the anterior segment of the eye. Anterior segment ocular diseases are common, yet complex entities. Although many treatment options and surgical techniques are available for these ailments, the underlying cause and pathogenesis is still unclear. Finding ways to fundamentally treat these patients and rectify the underlying dysregulations leading to the disease may help cure patients completely without major complications. Proteomics approaches are a novel way to distinguish dysregulated proteins in a variety of biological tissues in a hypothesis-free manner, thus helping to find the responsible pathways leading to a certain disease. The aim of the current study is to review the available knowledge in scientific literature regarding the proteomics studies done on anterior segment eye diseases and suggest potential clinical implications to exploit the results of these studies. SIGNIFICANCE: Anterior segment ocular diseases are responsible for a major proportion of visual impairment and blindness worldwide. Although ophthalmologists have several treatment options that can alleviate or control the progression of these diseases, no definite cure is available for most of them. Moreover, because these diseases are progressive, prompt diagnosis is of utmost important. Proteomics studies enable us to identify and quantify the dysregulated proteins in a biological specimen in a hypothesis-free manner. Understanding the dysregulated protein pathways shines a light on the pathogenesis of the disease. Moreover, these dysregulated proteins may act as biomarkers to help in diagnosis and treatment follow-up. Hence, in this article we sought out to review the available scientific literature regarding the proteomics studies of anterior segment ocular diseases and to identify potential applications of proteomic studies in clinic.
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Affiliation(s)
- Hossein Aghamollaei
- Chemical Injuries Research Center, Systems biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Shahram Parvin
- Chemical Injuries Research Center, Systems biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Alireza Shahriary
- Chemical Injuries Research Center, Systems biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Mnatsakanyan N, Jonas EA. The new role of F 1F o ATP synthase in mitochondria-mediated neurodegeneration and neuroprotection. Exp Neurol 2020; 332:113400. [PMID: 32653453 DOI: 10.1016/j.expneurol.2020.113400] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/23/2020] [Accepted: 07/07/2020] [Indexed: 02/08/2023]
Abstract
The mitochondrial F1Fo ATP synthase is one of the most abundant proteins of the mitochondrial inner membrane, which catalyzes the final step of oxidative phosphorylation to synthesize ATP from ADP and Pi. ATP synthase uses the electrochemical gradient of protons (ΔμH+) across the mitochondrial inner membrane to synthesize ATP. Under certain pathophysiological conditions, ATP synthase can run in reverse to hydrolyze ATP and build the necessary ΔμH+ across the mitochondrial inner membrane. Tight coupling between these two processes, proton translocation and ATP synthesis, is achieved by the unique rotational mechanism of ATP synthase and is necessary for efficient cellular metabolism and cell survival. The uncoupling of these processes, dissipation of mitochondrial inner membrane potential, elevated levels of ROS, low matrix content of ATP in combination with other cellular malfunction trigger the opening of the mitochondrial permeability transition pore in the mitochondrial inner membrane. In this review we will discuss the new role of ATP synthase beyond oxidative phosphorylation. We will highlight its function as a unique regulator of cell life and death and as a key target in mitochondria-mediated neurodegeneration and neuroprotection.
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Affiliation(s)
- Nelli Mnatsakanyan
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT, USA.
| | - Elizabeth Ann Jonas
- Section of Endocrinology, Department of Internal Medicine, Yale University, New Haven, CT, USA
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