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Meng F, Ren S. Identification of hub genes and molecular pathways in keratoconus by integrating bioinformatics and literature mining at the RNA level. Int Ophthalmol 2024; 44:244. [PMID: 38904678 DOI: 10.1007/s10792-024-03071-3] [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: 07/11/2023] [Accepted: 02/16/2024] [Indexed: 06/22/2024]
Abstract
OBJECTIVE Keratoconus (KC) is a condition characterized by progressive corneal steepening and thinning. However, its pathophysiological mechanism remains vague. We mainly performed literature mining to extract bioinformatic and related data on KC at the RNA level. The objective of this study was to explore the potential pathological mechanisms of KC by identifying hub genes and key molecular pathways at the RNA level. METHODS We performed an exhaustive search of the PubMed database and identified studies that pertained to gene transcripts derived from diverse corneal layers in patients with KC. The identified differentially expressed genes were intersected, and overlapping genes were extracted for further analyses. Significantly enriched genes were screened using "Gene Ontology" (GO) and "Kyoto Encyclopedia of Genes and Genomes" (KEGG) analysis with the "Database for Annotation, Visualization, and Integrated Discovery" (DAVID) database. A protein-protein interaction (PPI) network was constructed for the significantly enriched genes using the STRING database. The PPI network was visualized using the Cytoscape software, and hub genes were screened via betweenness centrality values. Pathways that play a critical role in the pathophysiology of KC were discovered using the GO and KEGG analyses of the hub genes. RESULTS 68 overlapping genes were obtained. Fifty genes were significantly enriched in 67 biological processes, and 16 genes were identified in 7 KEGG pathways. Moreover, 14 nodes and 32 edges were identified via the PPI network constructed using the STRING database. Multiple analyses identified 4 hub genes, 12 enriched biological processes, and 6 KEGG pathways. GO enrichment analysis showed that the hub genes are mainly involved in the positive regulation of apoptotic process, and KEGG analysis showed that the hub genes are primarily associated with the interleukin-17 (IL-17) and tumor necrosis factor (TNF) pathways. Overall, the matrix metalloproteinase 9, IL-6, estrogen receptor 1, and prostaglandin-endoperoxide synthase 2 were the potential important genes associated with KC. CONCLUSION Four genes, matrix metalloproteinase 9, IL-6, estrogen receptor 1, and prostaglandin endoperoxide synthase 2, as well as IL-17 and TNF pathways, are critical in the development of KC. Inflammation and apoptosis may contribute to the pathogenesis of KC.
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Affiliation(s)
- Feiying Meng
- Henan Eye Hospital, Henan Provincial People's Hospital/People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, China
| | - Shengwei Ren
- Henan Eye Hospital, Henan Provincial People's Hospital/People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, China.
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Song T, Song J, Li J, Ben Hilal H, Li X, Feng P, Chen W. The candidate proteins associated with keratoconus: A meta-analysis and bioinformatic analysis. PLoS One 2024; 19:e0299739. [PMID: 38483957 PMCID: PMC10939257 DOI: 10.1371/journal.pone.0299739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
PURPOSE Keratoconus (KC) is a multifactorial disorder. This study aimed to conduct a systematic meta-analysis to exclusively explore the candidate proteins associated with KC pathogenesis. METHODS Relevant literature published in the last ten years in Pubmed, Web of Science, Cochrane, and Embase databases were searched. Protein expression data were presented as the standard mean difference (SMD) and 95% confidence intervals (CI). The meta-analysis is registered on PROSPERO, registration number CRD42022332442 and was conducted in accordance with the Preferred Reporting Items for Systematic reviews and Meta-Analyses statement (PRISMA). GO and KEGG enrichment analysis were performed, as well as the miRNAs and chemicals targeting the candidate proteins were predicted. PPI was analyzed to screen the hub proteins, and their expression was verified by RT-qPCR. RESULTS A total of 21 studies were included in the meta-analysis, involving 346 normal eyes and 493 KC eyes. 18 deregulated proteins with significant SMD values were subjected to further analysis. In which, 7 proteins were up-regulated in KC compared with normal controls, including IL6 (SMD 1.54, 95%CI [0.85, 2.24]), IL1B (SMD 2.07, 95%CI [0.98, 3.16]), TNF (SMD 2.1, 95%CI [0.24, 3.96]), and MMP9 (SMD 1.96, 95%CI [0.68, 3.24]). While 11 proteins were down-regulated in KC including LOX (SMD 2.54, 95%CI [-4.51, -0.57]). GO and KEGG analysis showed that the deregulated proteins were involved in inflammation, extracellular matrix (ECM) remodeling, and apoptosis. MMP9, IL6, LOX, TNF, and IL1B were regarded as hub proteins according to the PPI analysis, and their transcription changes in stromal fibroblasts of KC were consistent with the results of the meta-analysis. Moreover, 10 miRNAs and two natural polyphenols interacting with hub proteins were identified. CONCLUSION This study obtained 18 candidate proteins and demonstrated altered cytokine profiles, ECM remodeling, and apoptosis in KC patients through meta-analysis and bioinformatic analysis. It will provide biomarkers for further understanding of KC pathogenesis, and potential therapeutic targets for the drug treatment of KC.
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Affiliation(s)
- Ting Song
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Jie Song
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Jingyi Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Halima Ben Hilal
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Xiaona Li
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Pengfei Feng
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Weiyi Chen
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, China
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Rigi M, Son HS, Moon L, Matthaei M, Srikumaran D, Jun AS, Eberhart CG, Soiberman US. Collagen type XII is undetectable in keratoconus Bowman's layer. Br J Ophthalmol 2024; 108:343-348. [PMID: 36746614 PMCID: PMC10466210 DOI: 10.1136/bjo-2022-322180] [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: 07/06/2022] [Accepted: 01/21/2023] [Indexed: 02/08/2023]
Abstract
PURPOSE Corneal biomechanical failure is the hallmark of keratoconus (KC); however, the cause of this failure remains elusive. Collagen type XII (COL12A1), which localises to Bowman's layer (BL), is thought to function in stress-bearing areas, such as BL. Given the putative protective role of COL12A1 in biomechanical stability, this study aims to characterise COL12A1 expression in all corneal layers involved in KC. METHODS TaqMan quantitative PCR was performed on 31 corneal epithelium samples of progressive KC and myopic control eyes. Tissue microarrays were constructed using full-thickness corneas from 61 KC cases during keratoplasty and 18 non-KC autopsy eyes and stained with an antibody specific to COL12A1. Additionally, COL12A1 was knocked out in vitro in immortalised HEK293 cells. RESULTS COL12A1 expression was reduced at transcript levels in KC epithelium compared with controls (ratio: 0.58, p<0.03). Immunohistochemical studies demonstrated that COL12A1 protein expression in BL was undetectable, with reduced expression in KC epithelium, basement membrane and stroma. CONCLUSIONS The apparent absence of COL12A1 in KC BL, together with the functional importance that COL12A1 is thought to have in stress bearing areas, suggests that COL12A1 may play a role in the pathogenesis of KC. Further studies are necessary to investigate the mechanisms that lead to COL12A1 dysregulation in KC.
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Affiliation(s)
- Mohammed Rigi
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Hyeck-Soo Son
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
- Department of Ophthalmology, University Hospital Heidelberg, Heidelberg, Germany
| | - Loren Moon
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Mario Matthaei
- Department of Ophthalmology, University Hospital Cologne, Cologne, Germany
| | - Divya Srikumaran
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Albert S Jun
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Charles G Eberhart
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Uri S Soiberman
- Wilmer Eye Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
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Vaccaro S, Vivarelli C, Yu AC, Pecora N, Lionetti G, Gioia R, Scorcia V, Giannaccare G. Longitudinal Changes of Cornea Volume Measured by Means of Anterior Segment-Optical Coherence Tomography in Patients with Stable and Progressive Keratoconus. Life (Basel) 2024; 14:176. [PMID: 38398685 PMCID: PMC10890364 DOI: 10.3390/life14020176] [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: 12/10/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Keratoconus is a corneal disease which results in progressive thinning and protrusion of the cornea leading to irregular astigmatism. The purpose of this study was to evaluate longitudinal changes in corneal volume (CV) occurring over time in keratoconus eyes. Consecutive patients affected by keratoconus were evaluated by means of anterior segment-optical coherence tomography (AS-OCT) at two different time points: baseline (T0) and after 1 year (T1). Anterior and posterior refractive value; corneal thickness at the thinnest point (TP) and corneal volume (CV) calculated within discs of 3, 5 and 8 mm of diameter; anterior chamber depth (ACD); and anterior chamber volume (ACV) were obtained. Enrolled patients were divided into 3 groups (groups 1, 2, 3) according to the increasing disease severity and into 2 groups (groups A, B) according to the progression or stability of the disease. Overall, 116 eyes of 116 patients (76 males and 40 females, mean age 34.76 ± 13.99 years) were included. For the entire group of keratoconus patients, in comparison with T0, mean TP decreased at T1 from 458.7 ± 52.2 µm to 454.6 ± 51.6 µm (p = 0.0004); in parallel, mean value of CV calculated at 5 mm and 8 mm decreased significantly (from 10.78 ± 0.8 at T0 to 10.75 ± 0.79 at T1 (p = 0.02), and from 32.03 ± 2.01 mm3 at T0 to 31.95 ± 1.98 at T1 (p = 0.02), respectively). Conversely, there were no statistically significant differences in CV at 3 mm from T0 to T1 (p = 0.08), as well as for ACD and ACV. Regarding the course of the disease, patients belonging to group A showed statistically significant differences from T0 to T1 for TP, and for CV at 3 mm, 5 mm and 8 mm (p < 0.0001, p < 0.0001, p < 0.001 and p = 0.0058 respectively). There were no statistically significant differences for ACD (p = 0.6916) and ACV calculated at 3, 5 and 8 mm (p = 0.7709, p = 0.3765, p = 0.2475, respectively) in group A. At the same time, no statistically significant differences for ACD (p = 0.2897) and ACV calculated at 3, 5 and 8 mm (p = 0.9849, p = 0.6420, p = 0.8338, respectively) were found in group B. There were statistically significant positive correlations between changes of TP and CV at 3 mm (r = 0.6324, p < 0.0001), 5 mm (r = 0.7622, p < 0.0001) and 8 mm (r = 0.5987 p < 0.0001). In conclusion, given the strong correlation with TP, CV might be considered an additional AS-OCT parameter to be used in association with conventional parameters when detecting longitudinal changes in keratoconic eyes.
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Affiliation(s)
- Sabrina Vaccaro
- Department of Ophthalmology, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy; (S.V.); (N.P.); (G.L.); (R.G.); (V.S.)
| | - Chiara Vivarelli
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (C.V.); (A.C.Y.)
- Department of Ophthalmology, Ospedali Privati Forlì “Villa Igea”, 47122 Forlì, Italy
| | - Angeli Christy Yu
- Department of Translational Medicine, University of Ferrara, 44121 Ferrara, Italy; (C.V.); (A.C.Y.)
- Department of Ophthalmology, Ospedali Privati Forlì “Villa Igea”, 47122 Forlì, Italy
| | - Nicolò Pecora
- Department of Ophthalmology, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy; (S.V.); (N.P.); (G.L.); (R.G.); (V.S.)
| | - Giovanna Lionetti
- Department of Ophthalmology, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy; (S.V.); (N.P.); (G.L.); (R.G.); (V.S.)
| | - Raffaella Gioia
- Department of Ophthalmology, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy; (S.V.); (N.P.); (G.L.); (R.G.); (V.S.)
| | - Vincenzo Scorcia
- Department of Ophthalmology, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy; (S.V.); (N.P.); (G.L.); (R.G.); (V.S.)
| | - Giuseppe Giannaccare
- Eye Clinic, Department of Surgical Sciences, University of Cagliari, Via Università 40, 09124 Cagliari, Italy
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Jaskiewicz K, Maleszka-Kurpiel M, Kabza M, Karolak JA, Gajecka M. Sequence variants contributing to dysregulated inflammatory responses across keratoconic cone surface in adolescent patients with keratoconus. Front Immunol 2023; 14:1197054. [PMID: 37483635 PMCID: PMC10359427 DOI: 10.3389/fimmu.2023.1197054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
Background Keratoconus (KTCN) is the most common corneal ectasia resulting in a conical shape of the cornea. Here, genomic variation in the corneal epithelium (CE) across the keratoconic cone surface in patients with KTCN and its relevance in the functioning of the immune system were assessed. Methods Samples from four unrelated adolescent patients with KTCN and two control individuals were obtained during the CXL and PRK procedures, respectively. Three topographic regions, central, middle, and peripheral, were separated towards the whole-genome sequencing (WGS) study embracing a total of 18 experimental samples. The coding and non-coding sequence variation, including structural variation, was assessed and then evaluated together with the previously reported transcriptomic outcomes for the same CE samples and full-thickness corneas. Results First, pathway enrichment analysis of genes with identified coding variants pointed to "Antigen presentation" and "Interferon alpha/beta signaling" as the most overrepresented pathways, indicating the involvement of inflammatory responses in KTCN. Both coding and non-coding sequence variants were found in genes (or in their close proximity) linked to the previously revealed KTCN-specific cellular components, namely, "Actin cytoskeleton", "Extracellular matrix", "Collagen-containing extracellular matrix", "Focal adhesion", "Hippo signaling pathway", and "Wnt signaling" pathways. No genomic heterogeneity across the corneal surface was found comparing the assessed topographic regions. Thirty-five chromosomal regions enriched in both coding and non-coding KTCN-specific sequence variants were revealed, with a most representative 5q locus previously recognized as involved in KTCN. Conclusion The identified genomic features indicate the involvement of innate and adaptive immune system responses in KTCN pathogenesis.
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Affiliation(s)
| | - Magdalena Maleszka-Kurpiel
- Optegra Eye Health Care Clinic in Poznan, Poznan, Poland
- Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Michał Kabza
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marzena Gajecka
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
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Shah R, Amador C, Chun ST, Ghiam S, Saghizadeh M, Kramerov AA, Ljubimov AV. Non-canonical Wnt signaling in the eye. Prog Retin Eye Res 2023; 95:101149. [PMID: 36443219 PMCID: PMC10209355 DOI: 10.1016/j.preteyeres.2022.101149] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/12/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
Wnt signaling comprises a group of complex signal transduction pathways that play critical roles in cell proliferation, differentiation, and apoptosis during development, as well as in stem cell maintenance and adult tissue homeostasis. Wnt pathways are classified into two major groups, canonical (β-catenin-dependent) or non-canonical (β-catenin-independent). Most previous studies in the eye have focused on canonical Wnt signaling, and the role of non-canonical signaling remains poorly understood. Additionally, the crosstalk between canonical and non-canonical Wnt signaling in the eye has hardly been explored. In this review, we present an overview of available data on ocular non-canonical Wnt signaling, including developmental and functional aspects in different eye compartments. We also discuss important changes of this signaling in various ocular conditions, such as keratoconus, aniridia-related keratopathy, diabetes, age-related macular degeneration, optic nerve damage, pathological angiogenesis, and abnormalities in the trabecular meshwork and conjunctival cells, and limbal stem cell deficiency.
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Affiliation(s)
- Ruchi Shah
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cynthia Amador
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Steven T Chun
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; University of California Los Angeles, Los Angeles, CA, USA
| | - Sean Ghiam
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Sackler School of Medicine, New York State/American Program of Tel Aviv University, Tel Aviv, Israel
| | - Mehrnoosh Saghizadeh
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Andrei A Kramerov
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alexander V Ljubimov
- Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Regenerative Medicine Institute Eye Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA; David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA; Neurosurgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Ren S, Yang K, Fan Q, Wang Q, Zhu M, Yin S, Gu Y, Xu L. Bioinformatics analysis of key candidate genes and pathways in Chinese patients with keratoconus. Exp Eye Res 2023; 231:109488. [PMID: 37116607 DOI: 10.1016/j.exer.2023.109488] [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: 03/21/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023]
Abstract
Keratoconus (KC) is a multifactorial disease in which genetic factors played important roles in its pathogenesis. The purpose of the current study was to identify the key candidate genes and pathways in Chinese patients with KC through bioinformatics analysis. Totally, we identified 71 candidate genes by analyzing the results of whole exome sequencing on 51 Chinese patients with KC, combining with previous reports on differential expression at transcription and protein levels in KC. Gene enrichment analysis with GeneCodis demonstrated that two significantly enriched terms including 21 genes in biological process (BP) were detected, and six significantly enriched terms containing 14 genes in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were discovered. The STRING was utilized to construct the protein-protein interaction (PPI) network of identified genes. The result showed that a PPI network consisted of 14 nodes with 14 edges was constructed, and two gene modules were obtained. Eight hub genes (LAMB3, LAMA3, LAMA1, ITGA6, ITGA3, COL6A3, COL6A2, and COL6A1) were identified as key candidate genes for KC by cytoHubba in Cytoscape. Functional enrichment analysis with ClueGO and CluePedia indicated that the ECM-receptor interaction was the key pathway accounted for KC. The findings might provide novel insights on the genetic basis of KC.
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Affiliation(s)
- Shengwei Ren
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China; Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, 450003, China
| | - Kaili Yang
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Qi Fan
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Qing Wang
- Henan University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, 450003, China
| | - Meng Zhu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, 450003, China
| | - Shanshan Yin
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, 450003, China
| | - Yuwei Gu
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Liyan Xu
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
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Karamichos D, Nicholas SE, Khan A, Riaz KM. Collagen Crosslinking for Keratoconus: Cellular Signaling Mechanisms. Biomolecules 2023; 13:696. [PMID: 37189443 PMCID: PMC10135890 DOI: 10.3390/biom13040696] [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: 02/11/2023] [Revised: 04/07/2023] [Accepted: 04/15/2023] [Indexed: 05/17/2023] Open
Abstract
Collagen crosslinking (CXL) is a widely used treatment to halt the progression of keratoconus (KC). Unfortunately, a significant number of patients with progressive KC will not qualify for CXL, including those with corneas thinner than 400 µm. The present study aimed to investigate the molecular effects of CXL using in vitro models, mirroring the normal, as well as thinner corneal stroma seen in KCs. Primary human corneal stromal cells were isolated from healthy (HCFs) and keratoconus (HKCs) donors. Cells were cultured and stimulated with stable Vitamin C resulting in 3D self-assembled extracellular matrix (ECM), cell-embedded, constructs. CXL was performed on (a) thin ECM with CXL performed at week 2 and (b) normal ECM with CXL performed at week 4. Constructs without CXL served as controls. All constructs were processed for protein analysis. The results showed modulation of Wnt signaling, following CXL treatment, as measured by the protein levels of Wnt7b and Wnt10a, correlated to the expression of α-smooth muscle actin (SMA). Further, the expression of a recently identified KC biomarker candidate, prolactin-induced protein (PIP), was positively impacted by CXL in HKCs. CXL-driven upregulation of PGC-1 and the downregulation of SRC and Cyclin D1 in HKCs were also noted. Although the cellular/molecular impacts of CXL are largely understudied, our studies provide an approximation to the complex mechanisms of KC and CXL. Further studies are warranted to determine factors influencing CXL outcomes.
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Affiliation(s)
- Dimitrios Karamichos
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, IREB-505, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Sarah E. Nicholas
- North Texas Eye Research Institute, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, IREB-505, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, 3500 Camp Bowie Blvd, Fort Worth, TX 76107, USA
| | - Asher Khan
- Dean McGee Eye Institute, University of Oklahoma, 608 Stanton L Young Blvd, Oklahoma City, OK 73104, USA
- College of Medicine, University of Oklahoma, 800 Stanton L Young Blvd, Oklahoma City, OK 73117, USA
| | - Kamran M. Riaz
- Dean McGee Eye Institute, University of Oklahoma, 608 Stanton L Young Blvd, Oklahoma City, OK 73104, USA
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Akoto T, Cai J, Nicholas S, McCord H, Estes AJ, Xu H, Karamichos D, Liu Y. Unravelling the Impact of Cyclic Mechanical Stretch in Keratoconus-A Transcriptomic Profiling Study. Int J Mol Sci 2023; 24:7437. [PMID: 37108600 PMCID: PMC10139219 DOI: 10.3390/ijms24087437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/04/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
Biomechanical and molecular stresses may contribute to the pathogenesis of keratoconus (KC). We aimed to profile the transcriptomic changes in healthy primary human corneal (HCF) and KC-derived cells (HKC) combined with TGFβ1 treatment and cyclic mechanical stretch (CMS), mimicking the pathophysiological condition in KC. HCFs (n = 4) and HKCs (n = 4) were cultured in flexible-bottom collagen-coated 6-well plates treated with 0, 5, and 10 ng/mL of TGFβ1 with or without 15% CMS (1 cycle/s, 24 h) using a computer-controlled Flexcell FX-6000T Tension system. We used stranded total RNA-Seq to profile expression changes in 48 HCF/HKC samples (100 bp PE, 70-90 million reads per sample), followed by bioinformatics analysis using an established pipeline with Partek Flow software. A multi-factor ANOVA model, including KC, TGFβ1 treatment, and CMS, was used to identify differentially expressed genes (DEGs, |fold change| ≥ 1.5, FDR ≤ 0.1, CPM ≥ 10 in ≥1 sample) in HKCs (n = 24) vs. HCFs (n = 24) and those responsive to TGFβ1 and/or CMS. PANTHER classification system and the DAVID bioinformatics resources were used to identify significantly enriched pathways (FDR ≤ 0.05). Using multi-factorial ANOVA analyses, 479 DEGs were identified in HKCs vs. HCFs including TGFβ1 treatment and CMS as cofactors. Among these DEGs, 199 KC-altered genes were responsive to TGFβ1, thirteen were responsive to CMS, and six were responsive to TGFβ1 and CMS. Pathway analyses using PANTHER and DAVID indicated the enrichment of genes involved in numerous KC-relevant functions, including but not limited to degradation of extracellular matrix, inflammatory response, apoptotic processes, WNT signaling, collagen fibril organization, and cytoskeletal structure organization. TGFβ1-responsive KC DEGs were also enriched in these. CMS-responsive KC-altered genes such as OBSCN, CLU, HDAC5, AK4, ITGA10, and F2RL1 were identified. Some KC-altered genes, such as CLU and F2RL1, were identified to be responsive to both TGFβ1 and CMS. For the first time, our multi-factorial RNA-Seq study has identified many KC-relevant genes and pathways in HKCs with TGFβ1 treatment under CMS, suggesting a potential role of TGFβ1 and biomechanical stretch in KC development.
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Affiliation(s)
- Theresa Akoto
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jingwen Cai
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Sarah Nicholas
- North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Hayden McCord
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Amy J. Estes
- Department of Ophthalmology, Augusta University, Augusta, GA 30912, USA
- James & Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Hongyan Xu
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Dimitrios Karamichos
- North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Pharmaceutical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Yutao Liu
- Department of Cellular Biology & Anatomy, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- James & Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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10
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Lalgudi VG, Shetty R, Nischal KK, Ziai S, Koaik M, Sethu S. Biochemical and molecular alterations and potential clinical applications of biomarkers in keratoconus. Saudi J Ophthalmol 2022; 36:7-16. [PMID: 35971485 PMCID: PMC9375466 DOI: 10.4103/sjopt.sjopt_203_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/05/2021] [Accepted: 02/19/2022] [Indexed: 11/06/2022] Open
Abstract
Keratoconus (KC) is a complex multifactorial corneal ectatic disorder, with disease onset commonly in the second-third decades significantly affecting quantity, quality of vision, and quality of life. Several pathways and factors such as eye rubbing, inflammatory, oxidative, metabolic, genetic, and hormonal among others have been studied in the last two decades. However, the management of KC is still based on a few "one-size fits all" approaches and is predominantly guided by topo/tomographic parameters. Consideration of the several novel factors which have the potential to be biomarkers in addressing several unanswered questions in the disease process could help in the better predictive ability of progression or vision loss and customization of treatment options. This article delves into the understanding of these novel factors or biomarkers based on the pathogenesis of KC and features a special focus on their potential clinical applications and their future role in personalized medicine.
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Affiliation(s)
- Vaitheeswaran G. Lalgudi
- Department of Cornea, External Disease and Refractive Surgery, University of Ottawa Eye Institute, The Ottawa Hospital, Ottawa, ON, Canada,Address for correspondence: Dr. Vaitheeswaran G. Lalgudi, Department of Cornea, External Disease and Refractive Surgery, University of Ottawa Eye Institute, The Ottawa Hospital, 501, Smyth Road, Ottawa, ON, Canada. E-mail:
| | - Rohit Shetty
- Department of Cornea and Refractive Surgery, Narayana Nethralaya, Bengaluru, Karnataka, India
| | - Kanwal K. Nischal
- UPMC Eye Centre, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA,Department of Pediatric Ophthalmology and Strabismus, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Setareh Ziai
- Department of Cornea, External Disease and Refractive Surgery, University of Ottawa Eye Institute, The Ottawa Hospital, Ottawa, ON, Canada,Department of Ophthalmology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Mona Koaik
- Department of Cornea, External Disease and Refractive Surgery, University of Ottawa Eye Institute, The Ottawa Hospital, Ottawa, ON, Canada,Department of Ophthalmology, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Swaminathan Sethu
- Molecular and Genetic Research, GROW Laboratories, Narayana Nethralaya Foundation, Bengaluru, Karnataka, India
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de Barros MRM, Chakravarti S. Pathogenesis of keratoconus: NRF2-antioxidant, extracellular matrix and cellular dysfunctions. Exp Eye Res 2022; 219:109062. [PMID: 35385756 DOI: 10.1016/j.exer.2022.109062] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/19/2022] [Accepted: 03/30/2022] [Indexed: 11/04/2022]
Abstract
Keratoconus (KC) is a degenerative disease associated with cell and extracellular matrix (ECM) loss that causes gradual thinning and steepening of the cornea and loss of vision. Collagen cross linking with ultraviolet light treatment can strengthen the ECM and delay weakening of the cornea, but severe cases require corneal transplantation. KC is multifactorial and multigenic, but its pathophysiology is still an enigma. Multiple approaches are being pursued to elucidate the molecular changes that underlie the corneal phenotype to identify relevant genes for tailored candidate searches and to develop potential biomarkers and targets for therapeutic interventions. Recent proteomic and transcriptomic studies suggest dysregulations in oxidative stress, NRF2-regulated antioxidant programs, WNT-signaling, TGF-β, ECM and matrix metalloproteinases. This review aims to provide a broad update on the transcriptomic and proteomic studies of KC with a focus on findings that relate to oxidative stress, and dysregulations in cellular and extracellular matrix functions.
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Affiliation(s)
| | - Shukti Chakravarti
- Department of Ophthalmology, NYU Grossman School of Medicine, NY, 10016, USA; Department of Pathology, NYU Grossman School of Medicine, NY, 10016, USA.
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