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Riina N, Harris A, Siesky BA, Ritzer L, Pasquale LR, Tsai JC, Keller J, Wirostko B, Arciero J, Fry B, Eckert G, Verticchio Vercellin A, Antman G, Sidoti PA, Guidoboni G. Using Multi-Layer Perceptron Driven Diagnosis to Compare Biomarkers for Primary Open Angle Glaucoma. Invest Ophthalmol Vis Sci 2024; 65:16. [PMID: 39250119 PMCID: PMC11385878 DOI: 10.1167/iovs.65.11.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2024] Open
Abstract
Purpose To use neural network machine learning (ML) models to identify the most relevant ocular biomarkers for the diagnosis of primary open-angle glaucoma (POAG). Methods Neural network models, also known as multi-layer perceptrons (MLPs), were trained on a prospectively collected observational dataset comprised of 93 glaucoma patients confirmed by a glaucoma specialist and 113 control subjects. The base model used only intraocular pressure, blood pressure, heart rate, and visual field (VF) parameters to diagnose glaucoma. The following models were given the base parameters in addition to one of the following biomarkers: structural features (optic nerve parameters, retinal nerve fiber layer [RNFL], ganglion cell complex [GCC] and macular thickness), choroidal thickness, and RNFL and GCC thickness only, by optical coherence tomography (OCT); and vascular features by OCT angiography (OCTA). Results MLPs of three different structures were evaluated with tenfold cross validation. The testing area under the receiver operating characteristic curve (AUC) of the models were compared with independent samples t-tests. The vascular and structural models both had significantly higher accuracies than the base model, with the hemodynamic AUC (0.819) insignificantly outperforming the structural set AUC (0.816). The GCC + RNFL model and the model containing all structural and vascular features were also significantly more accurate than the base model. Conclusions Neural network models indicate that OCTA optic nerve head vascular biomarkers are equally useful for ML diagnosis of POAG when compared to OCT structural biomarker features alone.
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Affiliation(s)
- Nicholas Riina
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Alon Harris
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Brent A Siesky
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Lukas Ritzer
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
| | - James C Tsai
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
- New York Eye and Ear Infirmary of Mount Sinai, New York, New York, United States
| | - James Keller
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, United States
| | - Barbara Wirostko
- University of Utah Health John A Moran Eye Center, Salt Lake City, Utah, United States
| | - Julia Arciero
- Department of Mathematical Sciences, IUPUI School of Science, Indianapolis, Indiana, United States
| | - Brendan Fry
- Department of Mathematics and Statistics, Metropolitan State University of Denver, Denver, Colorado, United States
| | - George Eckert
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | | | - Gal Antman
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
- Department of Ophthalmology, Rabin Medical Center, Petah Tikva, Central, Israel
- Faculty of Medicine, Tel Aviv University, Israel
| | - Paul A Sidoti
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, United States
- New York Eye and Ear Infirmary of Mount Sinai, New York, New York, United States
| | - Giovanna Guidoboni
- Maine College of Engineering and Computing, The University of Maine, Orono, Maine, United States
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Jordan JA, Daniel E, Chen Y, Salowe RJ, Zhu Y, Miller-Ellis E, Addis V, Sankar PS, Zhu D, Smith EJ, Lee R, Ying GS, O’Brien JM. Features Associated with Visible Lamina Cribrosa Pores in Individuals of African Ancestry with Glaucoma: Primary Open-Angle African Ancestry Glaucoma Genetics (POAAGG) Study. Vision (Basel) 2024; 8:24. [PMID: 38651445 PMCID: PMC11036295 DOI: 10.3390/vision8020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024] Open
Abstract
There are scarce data regarding the rate of the occurrence of primary open-angle glaucoma (POAG) and visible lamina cribrosa pores (LCPs) in the eyes of individuals with African ancestry; the potential impact of these features on disease burden remains unknown. We recruited subjects with POAG to the Primary Open-Angle African American Glaucoma Genetics (POAAGG) study. Through regression models, we evaluated the association between the presence of LCPs and various phenotypic features. In a multivariable analysis of 1187 glaucomatous eyes, LCPs were found to be more likely to be present in eyes with cup-to-disc ratios (CDR) of ≥0.9 (adjusted risk ratio (aRR) 1.11, 95%CI: 1.04-1.19, p = 0.005), eyes with cylindrical-shaped (aRR 1.22, 95%CI: 1.11-1.33) and bean pot (aRR 1.24, 95%CI: 1.13-1.36) cups versus conical cups (p < 0.0001), moderate cup depth (aRR 1.24, 95%CI: 1.06-1.46) and deep cups (aRR 1.27, 95%CI: 1.07-1.50) compared to shallow cups (p = 0.01), and the nasalization of central retinal vessels (aRR 1.33, 95%CI: 1.23-1.44), p < 0.0001). Eyes with LCPs were more likely to have a higher degree of African ancestry (q0), determined by means of SNP analysis (aRR 0.96, 95%CI: 0.93-0.99, p = 0.005 for per 0.1 increase in q0). Our large cohort of POAG cases of people with African ancestry showed that LCPs may be an important risk factor in identifying severe disease, potentially warranting closer monitoring by physicians.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Joan M. O’Brien
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (J.A.J.); (E.D.); (Y.C.); (R.J.S.); (Y.Z.); (E.M.-E.); (V.A.); (P.S.S.); (D.Z.); (E.J.S.); (R.L.); (G.-S.Y.)
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Yun JS, Jung SH, Lee SN, Jung SM, Won HH, Kim D, Choi JA. Polygenic risk score-based phenome-wide association for glaucoma and its impact on disease susceptibility in two large biobanks. J Transl Med 2024; 22:355. [PMID: 38622600 PMCID: PMC11020996 DOI: 10.1186/s12967-024-05152-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Glaucoma is a leading cause of worldwide irreversible blindness. Considerable uncertainty remains regarding the association between a variety of phenotypes and the genetic risk of glaucoma, as well as the impact they exert on the glaucoma development. METHODS We investigated the associations of genetic liability for primary open angle glaucoma (POAG) with a wide range of potential risk factors and to assess its impact on the risk of incident glaucoma. The phenome-wide association study (PheWAS) approach was applied to determine the association of POAG polygenic risk score (PRS) with a wide range of phenotypes in 377, 852 participants from the UK Biobank study and 43,623 participants from the Penn Medicine Biobank study, all of European ancestry. Participants were stratified into four risk tiers: low, intermediate, high, and very high-risk. Cox proportional hazard models assessed the relationship of POAG PRS and ocular factors with new glaucoma events. RESULTS In both discovery and replication set in the PheWAS, a higher genetic predisposition to POAG was specifically correlated with ocular disease phenotypes. The POAG PRS exhibited correlations with low corneal hysteresis, refractive error, and ocular hypertension, demonstrating a strong association with the onset of glaucoma. Individuals carrying a high genetic burden exhibited a 9.20-fold, 11.88-fold, and 28.85-fold increase in glaucoma incidence when associated with low corneal hysteresis, high myopia, and elevated intraocular pressure, respectively. CONCLUSION Genetic susceptibility to POAG primarily influences ocular conditions, with limited systemic associations. Notably, the baseline polygenic risk for POAG robustly associates with new glaucoma events, revealing a large combined effect of genetic and ocular risk factors on glaucoma incidents.
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Affiliation(s)
- Jae-Seung Yun
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Su-Nam Lee
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seung Min Jung
- Department of Internal Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea.
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jin A Choi
- Department of Ophthalmology, College of Medicine, St. Vincent's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
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Qin P, He Y, Shao H, Jiang D. Genetic insights into gut microbiota and risk of prostatitis: a Mendelian randomization study. Front Microbiol 2024; 15:1389715. [PMID: 38680919 PMCID: PMC11045958 DOI: 10.3389/fmicb.2024.1389715] [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: 02/22/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024] Open
Abstract
Background The dysbiosis of gut microbiota (GM) is considered a contributing factor to prostatitis, yet the causality remains incompletely understood. Methods The genome-wide association study (GWAS) data for GM and prostatitis were sourced from MiBioGen and FinnGen R10, respectively. In the two-sample Mendelian randomization (MR) analysis, inverse variance weighting (IVW), MR-Egger, weighted median, simple mode, weighted mode, and maximum likelihood (ML) methods were utilized to investigate the causal relationship between GM and prostatitis. A series of sensitivity analysis were conducted to confirm the robustness of the main results obtained from the MR analysis. Results According to the IVW results, genus Sutterella (OR: 1.37, 95% CI: 1.09-1.71, p = 0.006) and genus Holdemania (OR: 1.21, 95% CI: 1.02-1.43, p = 0.028) were associated with an increased risk of prostatitis. The phylum Verrucomicrobia (OR: 0.76, 95% CI: 0.58-0.98, p = 0.033) and genus Parasutterella (OR: 0.84, 95% CI: 0.70-1.00, p = 0.045) exhibited a negative association with prostatitis, indicating a potential protective effect. Sensitivity analysis showed that these results were not affected by heterogeneity and horizontal pleiotropy. Furthermore, the majority of statistical methods yielded results consistent with those of the IVW analysis. Conclusions In this study, we identified two GM taxon that might be protective against prostatitis and two GM taxon that could increase the risk of developing prostatitis. These findings could potentially provide a valuable theoretical basis for the future development of preventive and therapeutic strategies for prostatitis.
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Affiliation(s)
| | | | | | - Dawei Jiang
- Department of Urology, Zhejiang Chinese Medical University Affiliated Jiaxing TCM Hospital, Jiaxing, China
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McDermott CE, Salowe RJ, Di Rosa I, O’Brien JM. Stress, Allostatic Load, and Neuroinflammation: Implications for Racial and Socioeconomic Health Disparities in Glaucoma. Int J Mol Sci 2024; 25:1653. [PMID: 38338933 PMCID: PMC10855412 DOI: 10.3390/ijms25031653] [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: 12/26/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Glaucoma is the leading cause of irreversible blindness, and its pathophysiology includes neuroinflammatory changes. The present therapies for glaucoma target pressure-lowering mechanisms with limited success, making neuroinflammation a target for future interventions. This review summarizes the neuroinflammatory pathways seen in glaucoma and their interplay with stress. Glucocorticoids have been shown to activate proinflammatory glial cells, contributing to the neuroinflammation in glaucoma. Glucocorticoids have also been shown to increase the IOP directly. Stress-associated autonomic dysfunction can affect the vascular homeostasis in the retina and create oxidative stress. Diabetes, hyperglycemic-mediated endothelial damage, and vascular inflammation also play important roles in the neuroinflammation in glaucoma and diabetic retinopathy. Psychosocial stress has been implicated in an increased IOP and glaucoma outcomes. People who experience maladaptive chronic stress suffer from a condition known as allostatic load, which describes pathologic neuroendocrine dysregulation. The effects of allostatic load and chronic stress have been studied in patients affected by a lower socioeconomic status (SES) and marginalized racial identities. A lower SES is associated with higher rates of glaucoma and also affects the access to care and screening. Additionally, people of African ancestry are disproportionately affected by glaucoma for reasons that are multifactorial. In conclusion, this review explores neuroinflammation in glaucoma, highlighting opportunities for future investigation.
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Affiliation(s)
- Colleen E. McDermott
- Department of Surgery, University of Utah, Salt Lake City, UT 84101, USA
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.J.S.); (I.D.R.)
| | - Rebecca J. Salowe
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.J.S.); (I.D.R.)
| | - Isabel Di Rosa
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.J.S.); (I.D.R.)
| | - Joan M. O’Brien
- Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (R.J.S.); (I.D.R.)
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Mackey DA, Staffieri SE. Making glaucoma genetic studies more diverse. Cell 2024; 187:273-275. [PMID: 38242084 DOI: 10.1016/j.cell.2023.12.023] [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: 11/27/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]
Abstract
Although the blinding eye disease glaucoma is more common in people of African ancestry, previous genetic studies predominantly involved European subjects. In this issue of Cell, O'Brien et al. report a genome-wide association study for glaucoma in individuals of African ancestry, showing overlap with European studies and refining an African polygenic risk score.
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Affiliation(s)
- David A Mackey
- Lions Eye Institute, University of Western Australia, Perth, WA, Australia; Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.
| | - Sandra E Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Ophthalmology, Department of Surgery, University of Melbourne, Parkville, VIC, Australia
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