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Pucchio A, Krance SH, Pur DR, Bhatti J, Bassi A, Manichavagan K, Brahmbhatt S, Aggarwal I, Singh P, Virani A, Stanley M, Miranda RN, Felfeli T. Applications of artificial intelligence and bioinformatics methodologies in the analysis of ocular biofluid markers: a scoping review. Graefes Arch Clin Exp Ophthalmol 2024; 262:1041-1091. [PMID: 37421481 DOI: 10.1007/s00417-023-06100-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/25/2023] [Accepted: 05/06/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE This scoping review summarizes the applications of artificial intelligence (AI) and bioinformatics methodologies in analysis of ocular biofluid markers. The secondary objective was to explore supervised and unsupervised AI techniques and their predictive accuracies. We also evaluate the integration of bioinformatics with AI tools. METHODS This scoping review was conducted across five electronic databases including EMBASE, Medline, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Web of Science from inception to July 14, 2021. Studies pertaining to biofluid marker analysis using AI or bioinformatics were included. RESULTS A total of 10,262 articles were retrieved from all databases and 177 studies met the inclusion criteria. The most commonly studied ocular diseases were diabetic eye diseases, with 50 papers (28%), while glaucoma was explored in 25 studies (14%), age-related macular degeneration in 20 (11%), dry eye disease in 10 (6%), and uveitis in 9 (5%). Supervised learning was used in 91 papers (51%), unsupervised AI in 83 (46%), and bioinformatics in 85 (48%). Ninety-eight papers (55%) used more than one class of AI (e.g. > 1 of supervised, unsupervised, bioinformatics, or statistical techniques), while 79 (45%) used only one. Supervised learning techniques were often used to predict disease status or prognosis, and demonstrated strong accuracy. Unsupervised AI algorithms were used to bolster the accuracy of other algorithms, identify molecularly distinct subgroups, or cluster cases into distinct subgroups that are useful for prediction of the disease course. Finally, bioinformatic tools were used to translate complex biomarker profiles or findings into interpretable data. CONCLUSION AI analysis of biofluid markers displayed diagnostic accuracy, provided insight into mechanisms of molecular etiologies, and had the ability to provide individualized targeted therapeutic treatment for patients. Given the progression of AI towards use in both research and the clinic, ophthalmologists should be broadly aware of the commonly used algorithms and their applications. Future research may be aimed at validating algorithms and integrating them in clinical practice.
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Affiliation(s)
- Aidan Pucchio
- Department of Ophthalmology, Queen's University, Kingston, ON, Canada
- Queens School of Medicine, Kingston, ON, Canada
| | - Saffire H Krance
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Daiana R Pur
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jasmine Bhatti
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Arshpreet Bassi
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Shaily Brahmbhatt
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Priyanka Singh
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Aleena Virani
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Rafael N Miranda
- The Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Tina Felfeli
- The Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, University of Toronto, 340 College Street, Suite 400, Toronto, ON, M5T 3A9, Canada.
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Wolf J, Franco JA, Yip R, Dabaja MZ, Velez G, Liu F, Bassuk AG, Mruthyunjaya P, Dufour A, Mahajan VB. Liquid Biopsy Proteomics in Ophthalmology. J Proteome Res 2024; 23:511-522. [PMID: 38171013 PMCID: PMC10845144 DOI: 10.1021/acs.jproteome.3c00756] [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: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Minimally invasive liquid biopsies from the eye capture locally enriched fluids that contain thousands of proteins from highly specialized ocular cell types, presenting a promising alternative to solid tissue biopsies. The advantages of liquid biopsies include sampling the eye without causing irreversible functional damage, potentially better reflecting tissue heterogeneity, collecting samples in an outpatient setting, monitoring therapeutic response with sequential sampling, and even allowing examination of disease mechanisms at the cell level in living humans, an approach that we refer to as TEMPO (Tracing Expression of Multiple Protein Origins). Liquid biopsy proteomics has the potential to transform molecular diagnostics and prognostics and to assess disease mechanisms and personalized therapeutic strategies in individual patients. This review addresses opportunities, challenges, and future directions of high-resolution liquid biopsy proteomics in ophthalmology, with particular emphasis on the large-scale collection of high-quality samples, cutting edge proteomics technology, and artificial intelligence-supported data analysis.
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Affiliation(s)
- Julian Wolf
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Joel A. Franco
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Rui Yip
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Mohamed Ziad Dabaja
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Gabriel Velez
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Fei Liu
- Department
of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Alexander G. Bassuk
- Department
of Pediatrics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Prithvi Mruthyunjaya
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Antoine Dufour
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Vinit B. Mahajan
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
- Veterans
Affairs Palo Alto Health Care System, Palo Alto, California 94304, United States
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Tabbaa T, Mehra AA, Kesav NP, Mahajan VB, Swanson RD, Zubricky R, Sobol WM. Autosomal dominant neovascular inflammatory vitreoretinopathy with CAPN5 c.731T > C gene mutation; clinical management of a family cohort and review of the literature. Ophthalmic Genet 2023; 44:559-567. [PMID: 37782277 DOI: 10.1080/13816810.2023.2255257] [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: 08/21/2022] [Accepted: 08/30/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND To report a cohort of patients with clinically and genetically diagnosed autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV) and showcase the spectrum of the disease utilizing multimodal imaging and genetic testing. Additionally, the utility of multimodal imaging in guiding treatment will also be illustrated. MATERIALS/METHODS Five patients from a single-family pedigree in Ohio with clinical signs of ADNIV were evaluated. Medical history, family history, and complete ocular examinations were obtained during regular clinic visits. Multimodal imaging including ocular coherence tomography, fluorescein angiography, wide-field fundus photographs, and Humphrey visual field testing was obtained for all five patients. Additionally, genetic testing for the Calpain-5 (CAPN5) gene was conducted on all patients. RESULTS All five patients were noted to have a CAPN5 c.731T > C (p.L244P) mutation on genetic testing. Using multimodal imaging to supplement the clinical examination, pathologic changes such as retinal vascular inflammation, macular edema, and tractional retinal membranes were well illustrated and monitored over time. This allowed for earlier intervention when appropriate such as with intraocular steroid or systemic anti-inflammatory treatments. CONCLUSION Phenotypic presentation varied among patients in this series, but is consistent with the spectrum of pathologic changes previously described in patients with other CAPN5 gene mutations. Monitoring of patients with ADNIV utilizing multimodal imaging can help better assess progression of this disease and guide treatment decisions. Additionally, increased genetic testing in patients with inherited retinal diseases may reveal novel gene mutations that could serve as potential targets for future genetic treatment regimens.
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Affiliation(s)
- Tarek Tabbaa
- Department of Ophthalmology, Vitreoretinal Surgery Case Western Reserve University-University Hospitals Cleveland, Cleveland, Ohio, USA
| | - Ankur A Mehra
- Department of Ophthalmology, Vitreoretinal Surgery Case Western Reserve University-University Hospitals Cleveland, Cleveland, Ohio, USA
| | - Natasha P Kesav
- Department of Ophthalmology, Vitreoretinal Surgery Case Western Reserve University-University Hospitals Cleveland, Cleveland, Ohio, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - Roy D Swanson
- Department of Ophthalmology, Vitreoretinal Surgery Case Western Reserve University-University Hospitals Cleveland, Cleveland, Ohio, USA
| | - Ryan Zubricky
- Department of Ophthalmology, Vitreoretinal Surgery Case Western Reserve University-University Hospitals Cleveland, Cleveland, Ohio, USA
| | - Warren M Sobol
- Department of Ophthalmology, Vitreoretinal Surgery Case Western Reserve University-University Hospitals Cleveland, Cleveland, Ohio, USA
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Nair GKG, Pollalis D, Wren JD, Georgescu C, Sjoelund V, Lee SY. Proteomic Insight into the Role of Exosomes in Proliferative Vitreoretinopathy Development. J Clin Med 2022; 11:jcm11102716. [PMID: 35628842 PMCID: PMC9143131 DOI: 10.3390/jcm11102716] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 12/13/2022] Open
Abstract
Purpose: To characterize vitreous humor (VH) exosomes and to explore their role in the development of proliferative vitreoretinopathy (PVR) using mass spectrometry-based proteome profiling. Methods: Exosomes were isolated from undiluted VH from patients with retinal detachment (RD) with various stages of PVR (n = 9), macular hole (MH; n = 5), or epiretinal membrane (ERM; n = 5) using differential ultracentrifugation. The exosomal size, morphology, and exosome markers were analyzed using a nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and an exosome detection antibody array. The tryptic fragment sequencing of exosome-contained proteins was performed using liquid chromatography–tandem mass spectrometry (LC-MS/MS) and a Thermo Lumos Fusion Tribrid Orbitrap mass spectrometer. The pathway analysis of the MS data was performed. Results: The number of exosome particles were significantly increased only in the RD with severe PVR group compared with the control groups and the RD without PVR or with mild PVR groups. Of 724 exosome proteins identified, 382 were differentially expressed (DE) and 176 were uniquely present in PVR. Both DE proteins and exosome proteins that were only present in PVR were enriched in proteins associated with previously known key pathways related to PVR development, including reactive retinal gliosis, pathologic cellular proliferation, inflammation, growth of connective tissues, and epithelial mesenchymal transition (EMT). The SPP1, CLU, VCAN, COL2A1, and SEMA7A that are significantly upregulated in PVR were related to the tissue remodeling. Conclusions: Exosomes may play a key role in mediating tissue remodeling along with a complex set of pathways involved in PVR development.
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Affiliation(s)
- Gopa Kumar Gopinadhan Nair
- Ophthalmology, Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Dimitrios Pollalis
- USC Roski Eye Institute, USC Ginsburg Institute for Biomedical Therapeutics and Department of Ophthalmology, Keck School of Medicine, University of Southern California, 1450 San Pablo, Los Angeles, CA 90033, USA;
| | - Jonathan D. Wren
- Genes & Human Diseases Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (J.D.W.); (C.G.)
| | - Constantin Georgescu
- Genes & Human Diseases Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (J.D.W.); (C.G.)
| | - Virginie Sjoelund
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Sun Young Lee
- Ophthalmology, Dean McGee Eye Institute, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- USC Roski Eye Institute, USC Ginsburg Institute for Biomedical Therapeutics and Department of Ophthalmology, Keck School of Medicine, University of Southern California, 1450 San Pablo, Los Angeles, CA 90033, USA;
- Department of Physiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
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BOYCE TIMOTHYM, WHITMORE SSCOTT, VARZAVAND KATAYOUN, RUSSELL STEPHENR, SOHN ELLIOTTH, FOLK JAMESC, STONE EDWINM, HAN IANC. Long-Term Outcomes and Risk Factors for Severe Vision Loss in Autosomal Dominant Neovascular Inflammatory Vitreoretinopathy (ADNIV). Am J Ophthalmol 2022; 233:144-152. [PMID: 34302771 PMCID: PMC9177238 DOI: 10.1016/j.ajo.2021.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 01/03/2023]
Abstract
Autosomal dominant neovascular inflammatory vitreoretinopathy (ADNIV) is a rare disorder characterized by uveitis, retinal neovascularization, and retinal degeneration. We sought to describe the course of treated and untreated ADNIV and to identify risk factors for severe vision loss. DESIGN Observational case series. METHODS Clinical data from ADNIV patients from 4 families seen from 1967 through 2019 at a single academic, tertiary referral center were reviewed. The main outcome measures were visual acuity at baseline and follow-up, as well as risk factors for vision loss. RESULTS A total of 130 eyes from 65 ADNIV patients (45 female, 20 male; mean age 40.8 years, range 6-77 years) were included. Mean best corrected visual acuity (BCVA) at presentation was LogMAR 0.59 (about Snellen 20/80). Longitudinal analysis included 84 eyes from 42 patients (31 female, 11 male), with mean follow-up of 17.3 years (range 2-43.6 years). Mean BCVA at last follow-up was LogMAR 1.48 (about Snellen 20/600). The disease accelerated in the fifth decade of life, during which the majority of eyes went from normal vision or mild vision loss to at least moderate vision loss (20/70 Snellen equivalent); 25 eyes from 16 patients (29.8%;) showed a steep trajectory of vision loss to no light perception. Tractional retinal detachment was the greatest risk factor for severe vision loss (BCVA <20/200) on multivariable analysis (P < .05). CONCLUSIONS Patients with ADNIV have a high lifetime risk of severe vision loss. Tractional retinal detachment is an important risk factor for poor vision.
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Li T, Yang Y, Wang X, Dai W, Zhang L, Piao C. Flavonoids derived from buckwheat hull can break advanced glycation end-products and improve diabetic nephropathy. Food Funct 2021; 12:7161-7170. [PMID: 34169956 DOI: 10.1039/d1fo01170g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diabetic nephropathy (DN) is the most important complication in patients with diabetes. The accumulation of advanced glycation end-products (AGEs) is the main reason for the development of DN. In this study, we investigated the mechanism of buckwheat hull flavonoids to break AGEs in vitro by measuring fluorescence analysis, three-dimensional fluorescence, protein molecular weight, free amino groups, and the sulfhydryl group content. Proteomics analysis was used to determine the effect of total buckwheat hull flavonoids (TBHF) intervention on protein differential expression in the kidney of db/db mice. The results showed that buckwheat hull flavonoids were potent in breaking AGEs in vitro, and they protected mice kidneys by regulating the renal AGE-RAGE pathway. This study lays a strong experimental and theoretical foundation for the development of new lysing agents to break AGEs. The findings should make an important contribution to the field of flavonoids in improving the application of diabetic nephropathy in the diet.
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Affiliation(s)
- Tianzhu Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, Jilin, China.
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7
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Cunningham ET, Pichi F, Mahajan VB, Rosenbaum JT, Zierhut M. Genetics of Uveitis. Ocul Immunol Inflamm 2021; 29:215-218. [PMID: 33950774 DOI: 10.1080/09273948.2021.1910430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Emmett T Cunningham
- The Department of Ophthalmology, California Pacific Medical Center, San Francisco, California, USA.,The Department of Ophthalmology, Stanford University School of Medicine, Stanford, California, USA.,The Francis I. Proctor Foundation, UCSF School of Medicine, San Francisco, California, USA
| | - Francesco Pichi
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Vinit B Mahajan
- Omics Laboratory, Stanford University, Palo Alto, California, USA.,The Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, California, USA.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - James T Rosenbaum
- The Department of Ophthalmology, Oregon Health and Science University, Portland, Oregon, USA.,The Department of Medicine, Oregon Health and Science University, Portland, Oregon, USA.,Legacy Devers Eye Institute, Portland, Oregon, USA
| | - Manfred Zierhut
- Centre for Ophthalmology, University Tuebingen, Tuebingen, Germany
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Velez G, Mahajan VB. Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of Blindness. iScience 2020; 23:101667. [PMID: 33134897 PMCID: PMC7586135 DOI: 10.1016/j.isci.2020.101667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Rare diseases are an emerging global health priority. Although individually rare, the prevalence of rare "orphan" diseases is high, affecting approximately 300 million people worldwide. Treatments for these conditions are often inadequate, leaving the disease to progress unabated. Here, we review the clinical features and pathophysiology of neovascular inflammatory vitreoretinopathy (NIV), a rare inflammatory retinal disease caused by mutations in the CAPN5 gene. Although the prevalence of NIV is low (1 in 1,000,000 people), the disease mimics more common causes of blindness (e.g. uveitis, retinitis pigmentosa, proliferative diabetic retinopathy, and proliferative vitreoretinopathy) at distinct clinical stages. There is no cure for NIV to date. We highlight how personalized proteomics helped identify potential stage-specific biomarkers and drug targets in liquid vitreous biopsies. The NIV vitreous proteome revealed enrichment of molecular pathways associated with common retinal pathologies and implicated superior targets for therapeutic drug repositioning. In addition, we review our pipeline for collecting, storing, and analyzing ophthalmic surgical samples. This approach can be adapted to treat a variety of rare genetic diseases.
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Affiliation(s)
- Gabriel Velez
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
- Medical Scientist Training Program, University of Iowa, Iowa City, IA, USA
| | - Vinit B. Mahajan
- Omics Laboratory, Stanford University, Palo Alto, CA, USA
- Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA 94304, USA
- Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA
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