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Ye HF, Zhang X, Zhao ZN, Zheng C, Fei P, Xu Y, Lyu J, Chen JL, Guo XX, Zhu H, Zhao PQ. Characterization of N 6-methyladenosine long non-coding RNAs in sporadic congenital cataract and age-related cataract. Int J Ophthalmol 2024; 17:1973-1986. [PMID: 39559306 PMCID: PMC11528264 DOI: 10.18240/ijo.2024.11.02] [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: 11/15/2023] [Accepted: 07/09/2024] [Indexed: 11/20/2024] Open
Abstract
AIM To characterize the N6-methyladenosine (m6A) modification patterns in long non-coding RNAs (lncRNAs) in sporadic congenital cataract (CC) and age-related cataract (ARC). METHODS Anterior capsule of the lens were collected from patients with CC and ARC. Methylated RNA immunoprecipitation with next-generation sequencing and RNA sequencing were performed to identify m6A-tagged lncRNAs and lncRNAs expression. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and Gene Ontology annotation were used to predict potential functions of the m6A-lncRNAs. RESULTS Large amount of m6A peaks within lncRNA were identified for both CC and ARC, while the level was much higher in ARC (49 870 peaks) than that in CC (18 688 peaks), yet those difference between ARC in younger age group (ARC-1) and ARC in elder age group (ARC-2) was quite slight. A total of 1305 hypermethylated and 1178 hypomethylated lncRNAs, as well as 182 differential expressed lncRNAs were exhibited in ARC compared with CC. On the other hand, 5893 hypermethylated and 5213 hypomethylated lncRNAs, as well as 155 significantly altered lncRNA were identified in ARC-2 compared with ARC-1. Altered lncRNAs in ARC were mainly associated with the organization and biogenesis of intracellular organelles, as well as nucleotide excision repair. CONCLUSION Our results for the first time present an overview of the m6A methylomes of lncRNA in CC and ARC, providing a solid basis and uncovering a new insight to reveal the potential pathogenic mechanism of CC and ARC.
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Affiliation(s)
- Hong-Fei Ye
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xiang Zhang
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Zhen-Nan Zhao
- Department of Ophthalmology and Vision Science, Eye Ear Nose and Throat Hospital of Fudan University, Shanghai 200031, China
| | - Ce Zheng
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Ping Fei
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Yu Xu
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Jiao Lyu
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Ji-Li Chen
- Department of Ophthalmology, Shanghai Shibei Hospital of Jing'an District, Shanghai 200040, China
| | - Xun-Xiang Guo
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Huang Zhu
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Pei-Quan Zhao
- Department of Ophthalmology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
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Sood S, Tiwari A, Sangwan J, Vohra M, Sinha NR, Tripathi R, Sangwan VS, Mohan RR. Role of epigenetics in corneal health and disease. Prog Retin Eye Res 2024; 104:101318. [PMID: 39547455 DOI: 10.1016/j.preteyeres.2024.101318] [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: 09/03/2024] [Revised: 11/12/2024] [Accepted: 11/13/2024] [Indexed: 11/17/2024]
Abstract
Epigenetics plays a vital role in corneal health and diseases. Epigenetic changes regulate the expression of genes by altering the accessibility of chromatin via histone modifications, DNA methylation and miRNAs without altering DNA sequence. Ocular trauma and infections are common causes of corneal damage, vision impairment, and mono/bilateral blindness worldwide. Mounting literature shows that epigenetic modifications can modulate corneal clarity, function, and pathogenesis including inflammation, wound healing, fibrosis, and neovascularization. Additionally, epigenetic modifications can be targeted to reverse corneal pathologies and develop interventional therapies. However, current understanding on how epigenetic modifications lead to corneal abnormalities and diseases is limited. This review provides in-depth knowledge and mechanistic understanding of epigenetics alterations in corneal pathogenesis, and information on potential epigenetic targets for treatment of corneal diseases.
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Affiliation(s)
- Swati Sood
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA
| | - Anil Tiwari
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Jyoti Sangwan
- Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Mehak Vohra
- Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Nishant R Sinha
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, MO, USA
| | - Ratnakar Tripathi
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA
| | - Virender S Sangwan
- Eicher-Shroff Centre for Stem Cells Research (ESC-SCR), Dr. Shroff Charity Eye Hospital, Delhi, India
| | - Rajiv R Mohan
- Departments of Veterinary Medicine & Surgery, College of Veterinary Medicine University of Missouri, Columbia, MO, USA; Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Department of Ophthalmology, School of Medicine, University of Missouri, Columbia, MO, USA.
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Xia Y, Chen K, Yang Q, Chen Z, Jin L, Zhang L, Yu X, Wang L, Xie C, Zhao Y, Shen Y, Tong J. Methylation in cornea and corneal diseases: a systematic review. Cell Death Discov 2024; 10:169. [PMID: 38589350 PMCID: PMC11002037 DOI: 10.1038/s41420-024-01935-2] [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: 11/30/2023] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Corneal diseases are among the primary causes of blindness and vision loss worldwide. However, the pathogenesis of corneal diseases remains elusive, and diagnostic and therapeutic tools are limited. Thus, identifying new targets for the diagnosis and treatment of corneal diseases has gained great interest. Methylation, a type of epigenetic modification, modulates various cellular processes at both nucleic acid and protein levels. Growing evidence shows that methylation is a key regulator in the pathogenesis of corneal diseases, including inflammation, fibrosis, and neovascularization, making it an attractive potential therapeutic target. In this review, we discuss the major alterations of methylation and demethylation at the DNA, RNA, and protein levels in corneal diseases and how these dynamics contribute to the pathogenesis of corneal diseases. Also, we provide insights into identifying potential biomarkers of methylation that may improve the diagnosis and treatment of corneal diseases.
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Affiliation(s)
- Yutong Xia
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Kuangqi Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Qianjie Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Zhitong Chen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Le Jin
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyue Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Xin Yu
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Liyin Wang
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Chen Xie
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Yuan Zhao
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China
| | - Ye Shen
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
| | - Jianping Tong
- Department of Ophthalmology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003, China.
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Nidhi V, Sangwan J, Sood S, Mondal M, Sangwan B, Vohra M, Gour A, Mathur U, Sangwan VS, Acharya M, Tiwari A. Krupple-like factor 4 (KLF4) methylation signature in host cell in active viral keratitis with epithelial manifestation. Exp Eye Res 2024; 240:109771. [PMID: 38163580 DOI: 10.1016/j.exer.2023.109771] [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: 10/08/2023] [Revised: 12/11/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
HSV1 presents as epithelial or stromal keratitis or keratouveitis and can lead to sight-threatening complications. KLF4, a critical transcription factor, and regulator of cell growth and differentiation, is essential in corneal epithelium stratification and homeostasis. Here, we want to understand the epigenetic modification specifically the methylation status of KLF4 in epithelium samples of HSV1 keratitis patients. After obtaining consent, epithelial scrapes were collected from 7 patients with clinically diagnosed HSV1 keratitis and 7 control samples (patients undergoing photorefractive keratectomy). Genomic DNA was isolated from the collected samples using the Qiagen DNeasy Kit. Subsequently, bisulfite modification was performed. The bisulphite-modified DNA was then subjected to PCR amplification using specific primers designed to target the KLF4, ACTB gene region, allowing for the amplification of methylated and unmethylated DNA sequences. The amplified DNA products were separated and visualized on a 3% agarose gel. KLF4 hypermethylation was found in 6 out of 7 (85.71%) eyes with viral keratitis, while 1 eye showed hypomethylation compared to PRK samples. Out of these 6, there were 2 each of epithelial dendritic keratitis, epithelial geographical keratitis, and neurotrophic keratitis. The patient with hypomethylated KLF4 had a recurrent case of HSV1 keratitis with multiple dendrites and associated vesicular lesions of the lip along with a history of fever. KLF4 hypermethylation in most viral keratitis cases indicated the under functioning of KLF4 and could indicate a potential association between KLF4 hypermethylation and the development or progression of HSV1 keratitis.
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Affiliation(s)
- Vatsala Nidhi
- Cornea and Refractive Services, Dr Shroff's Charity Eye Hospital, New Delhi, India
| | - Jyoti Sangwan
- Eicher Shroff Center for Stem Cells Research (ES-CSCR), Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Swati Sood
- Eicher Shroff Center for Stem Cells Research (ES-CSCR), Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Moumita Mondal
- Eicher Shroff Center for Stem Cells Research (ES-CSCR), Dr. Shroff's Charity Eye Hospital, New Delhi, India
| | - Bharti Sangwan
- Shroff-Pandorum Centre for Ocular Regeneration (SP-CORE), Dr Shroff's Charity Eye Hospital, New Delhi, India
| | - Mehak Vohra
- Shroff-Pandorum Centre for Ocular Regeneration (SP-CORE), Dr Shroff's Charity Eye Hospital, New Delhi, India
| | - Abha Gour
- Cornea and Refractive Services, Dr Shroff's Charity Eye Hospital, New Delhi, India; Eicher Shroff Center for Stem Cells Research (ES-CSCR), Dr. Shroff's Charity Eye Hospital, New Delhi, India; Shroff-Pandorum Centre for Ocular Regeneration (SP-CORE), Dr Shroff's Charity Eye Hospital, New Delhi, India
| | - Umang Mathur
- Cornea and Refractive Services, Dr Shroff's Charity Eye Hospital, New Delhi, India; Eicher Shroff Center for Stem Cells Research (ES-CSCR), Dr. Shroff's Charity Eye Hospital, New Delhi, India; Shroff-Pandorum Centre for Ocular Regeneration (SP-CORE), Dr Shroff's Charity Eye Hospital, New Delhi, India
| | - Virender Singh Sangwan
- Cornea and Refractive Services, Dr Shroff's Charity Eye Hospital, New Delhi, India; Eicher Shroff Center for Stem Cells Research (ES-CSCR), Dr. Shroff's Charity Eye Hospital, New Delhi, India; Shroff-Pandorum Centre for Ocular Regeneration (SP-CORE), Dr Shroff's Charity Eye Hospital, New Delhi, India
| | - Manisha Acharya
- Cornea and Refractive Services, Dr Shroff's Charity Eye Hospital, New Delhi, India
| | - Anil Tiwari
- Eicher Shroff Center for Stem Cells Research (ES-CSCR), Dr. Shroff's Charity Eye Hospital, New Delhi, India; Shroff-Pandorum Centre for Ocular Regeneration (SP-CORE), Dr Shroff's Charity Eye Hospital, New Delhi, India.
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Lin Y, Su H, Zou B, Huang M. EZH2 Promotes Corneal Endothelial Cell Apoptosis by Mediating H3K27me3 and Inhibiting HO-1 Transcription. Curr Eye Res 2023; 48:1122-1132. [PMID: 37800319 DOI: 10.1080/02713683.2023.2257401] [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: 02/14/2023] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
PURPOSE This paper aims to explore the molecular mechanism of Enhancer of Zeste Homolog 2 (EZH2)-mediated H3K27me3 in human corneal endothelial cells (HCEC) apoptosis by inhibiting Heme oxygenase-1 (HO-1) transcription to provide a potential target for the treatment of corneal apoptosis. METHODS HCECs were cultured in vitro and transfected with si-EZH2, pcDNA3.1-EZH2, pcDNA3.1-HO-1, GSK-J4 (an effective H3K27me3 demethylase inhibitor), and corresponding controls. Western Blot assay was used to detect the levels of EZH2, HO-1, H3K27me3, and apoptosis-related proteins (Bcl-2, Bax, and Cleaved-caspase-3) in HCECs; CCK-8 assay was conducted to detect cell viability and flow cytometry to analyze the apoptosis. HO-1 mRNA levels were detected by RT-qPCR and changes in H3K27me3 levels on the HO-1 promoter were detected by chromatin immunoprecipitation. RESULTS HCECs transfected with si-EZH2 showed significantly lower EZH2 mRNA and protein levels, higher HCEC viability, lower apoptosis rates, higher antiapoptotic protein Bcl-2 expression, lower proapoptotic protein (Bax and Cleaved-caspase-3) levels, and significantly higher HO-1 expression. HCECs transfected with pcDNA3.1-EZH2 showed the opposite results. EZH2 repressed HO-1 transcription by mediating H3K27me3. H3K27me27 was enriched in the HO-1 promoter and overexpression of EZH2 increased H3K27me27 levels. Promotion of H3K27me3 partially reversed the mitigating effect of si-EZH2 on HCEC apoptosis. Overexpression of HO-1 partially reversed the apoptosis-promoting effects of EZH2 and H3K27me3 on HCECs. CONCLUSIONS EZH2 promotes HCE cell apoptosis by mediating H3K27me3 to inhibit HO-1 transcription.
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Affiliation(s)
- Ying Lin
- Department of Ophthalmology, Liuzhou Workers' Hospital, Liuzhou, Guangxi, China
| | - Huanjun Su
- Department of Ophthalmology, Liuzhou Workers' Hospital, Liuzhou, Guangxi, China
| | - Baoyi Zou
- Department of Optometry, Liuzhou Workers' Hospital, Liuzhou, Guangxi, China
| | - Minli Huang
- Department of Optometry, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Lamas M. Epigenetic mechanisms of non-retinal components of the aging eye and novel therapeutic strategies. Exp Eye Res 2023; 236:109673. [PMID: 37802281 DOI: 10.1016/j.exer.2023.109673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023]
Abstract
The eye is a complex organ composed of various cell types, each serving a unique purpose. However, aging brings about structural and functional changes in these cells, leading to discomfort and potential pathology. Alterations in gene expression, influenced by aging and environmental factors, significantly affect cell structure and function. Epigenetics, a field focused on understanding the correlation between changes in gene expression, cell function, and environmental factors, plays a crucial role in unraveling the molecular events responsible for age-related eye changes. This prompts the possibility of developing epigenetic strategies to intervene in these changes or reinstate proper molecular activities. Indeed, research has demonstrated that epigenetic modifications, including DNA methylation, histone modification, and non-coding RNAs, are closely associated with age-related alterations in gene expression and cell function. This review aims to compile and synthesize the most recent body of evidence supporting the role of epigenetics in age-related alterations observed in various components of the eye. Specifically, it focuses on the impact of epigenetic changes in the ocular surface, tear film, aqueous humor, vitreous humor, and lens. Furthermore, it highlights the significant advancements that have been made in the field of epigenetic-based experimental therapies, specifically focusing on their potential for treating pathological conditions in the aging eye.
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Affiliation(s)
- Monica Lamas
- Departamento de Farmacobiología, CINVESTAV-Sede Sur, Centro de Investigación sobre el Envejecimiento, CINVESTAV Sede Sur, Calzada de los Tenorios 235, CDMX, Mexico.
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Zhang X, Dou S, Huang Y. Comprehensive landscape of RNA N6-methyladenosine modification in lens epithelial cells from normal and diabetic cataract. Exp Eye Res 2023; 237:109702. [PMID: 39492543 DOI: 10.1016/j.exer.2023.109702] [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: 09/01/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/05/2024]
Abstract
To gain more insight into the mechanism of cataract formation from the perspective of epigenetics in the diabetic population, lens epithelium from diabetic cataract patients and health individuals were collected separately and analyzed for N6-methyladenosine (m6A)-modified RNA using methylated RNA immunoprecipitation sequencing (MeRIP-Seq). Subsequently, differential expression analysis was performed on m6A-regulated messenger RNA (mRNA), circular RNA (circRNA), and long non-coding RNA (lncRNA), followed by functional annotation using the Gene Ontology (GO) database. Furthermore, analysis of single-cell data of lens complemented the intrinsic association and cellular heterogeneity of cataract and m6A regulators. In this study, both the global expression levels and peak intensity of m6A-tagged RNAs were increased in patients with diabetic cataract. And we noted multiple core enzymes were upregulated in the diabetic cataract (DC) samples. Besides, single-cell RNA sequencing analysis of the lens revealed the heterogeneous expression of RNA m6A regulators across different cell types, and we noted that the early fiber cell cluster was also closely associated with the onset of cataract and m6A modification. The results comprehensively revealed the dynamic modification landscape of m6A on mRNA, circRNA, and lncRNA, which might provide valuable resources for future studies of the pathogenesis of DCs.
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Affiliation(s)
- Xiaowen Zhang
- Eye Institute of Shandong First Medical University, Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Qingdao, China; School of Ophthalmology, Shandong First Medical University, Jinan, China
| | - Shengqian Dou
- Eye Institute of Shandong First Medical University, Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Qingdao, China.
| | - Yusen Huang
- Eye Institute of Shandong First Medical University, Qingdao Eye Hospital of Shandong First Medical University, Qingdao, China; State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Qingdao, China.
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Dutta T, Sangwan J, Mondal M, Vohra M, Nidhi V, Gour A, Kapur N, Gupta N, Bhowmick T, Chandru A, Mathur U, Sangwan VS, Acharya M, Tiwari A. Prolonged Inflammation and Infectious Changes in the Corneal Epithelium Are Associated with Persistent Epithelial Defect (PED). Pathogens 2023; 12:pathogens12020261. [PMID: 36839533 PMCID: PMC9960897 DOI: 10.3390/pathogens12020261] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/07/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Purpose: Failure of rapid re-epithelialization within 10-14 days after corneal injury, even with standard supportive treatment, is referred to as persistent corneal epithelial (CE) defect (PED). Though an array of genes regulates reepithelization, their mechanisms are poorly understood. We sought to understand the network of genes driving the re-epithelialization in PED. Method: After obtaining informed consent, patients underwent an ophthalmic examination. Epithelial scrapes and tears samples of six PED patients and six individuals (control) undergoing photorefractive keratectomy (PRK) were collected. RNA isolation and quantification were performed using either the epithelial scrape taken from PED patients or from HCLE cells treated with control tears or tears of PED patients. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect the expression of a few important genes in CE homeostasis, inflammation, and cell-cell communication, viz., Kruppel-like factor 4 (KLF4), GPX4, IL6, TNFα, STING, IL8, desmoglein, and E-cadherin, among others. Their expressions were normalized with their respective housekeeping genes and fold changes were recorded. KLF4 localization and MMPs activity was carried out via immunofluorescence and zymography, respectively. Results: KLF4, a transcription factor important for CE homeostasis, was upregulated in tears-treated HCLE cells and downregulated in PED patients compared to the healthy PRK group. Cell-cell communication genes were also upregulated in tears-treated cells, whereas they were downregulated in the PED tissue group. Genes involved in proinflammation (IL6, 282-fold; TNFα, 43-fold; IL8, 4.2-fold) were highly upregulated in both conditions. MMP9 activity increased upon tears treatment. Conclusions: This study suggests that tears create an acute proinflammatory milieu driving the PED disease pathology, whereas the PED patients scrapes are an indicator of the chronic stage of the disease. Interferons, pro-inflammatory genes, and their pathways are involved in PED, which can be a potential target for inducing epithelialization of the cornea.
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Affiliation(s)
- Tanmoy Dutta
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
- Institute of Medicine, Sahlgrenska Academy, Gothenburg University, 41345 Gothenburg, Sweden
| | - Jyoti Sangwan
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Moumita Mondal
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Mehak Vohra
- Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Vatsala Nidhi
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Abha Gour
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Neha Kapur
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Nidhi Gupta
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Tuhin Bhowmick
- Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Arun Chandru
- Pandorum Technologies Pvt. Ltd., Bangalore 560065, India
| | - Umang Mathur
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | | | - Manisha Acharya
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
| | - Anil Tiwari
- Dr Shroff’s Charity Eye Hospital, Cornea and Stem Cells Department, Delhi 110002, India
- Correspondence: or
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Sasamoto Y, Wu S, Lee CAA, Jiang JY, Ksander BR, Frank MH, Frank NY. Epigenetic Regulation of Corneal Epithelial Differentiation by TET2. Int J Mol Sci 2023; 24:2841. [PMID: 36769164 PMCID: PMC9917645 DOI: 10.3390/ijms24032841] [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: 11/05/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 02/05/2023] Open
Abstract
Epigenetic DNA modification by 5-hydroxymethylcytosine (5hmC), generated by the Ten-eleven translocation (TET) dioxygenases, regulates diverse biological functions in many organ tissues, including the mammalian eye. For example, 5hmC has been shown to be involved in epigenetic regulation of retinal gene expression. However, a functional role of 5hmC in corneal differentiation has not been investigated to date. Here, we examined 5hmC and TET function in the human cornea. We found 5hmC highly expressed in MUC16-positive terminally differentiated cells that also co-expressed the 5hmC-generating enzyme TET2. TET2 knockdown (KD) in cultured corneal epithelial cells led to significant reductions of 5hmC peak distributions and resulted in transcriptional repression of molecular pathways involved in corneal differentiation, as evidenced by downregulation of MUC4, MUC16, and Keratin 12. Additionally, integrated TET2 KD RNA-seq and genome-wide Reduced Representation Hydroxymethylation Profiling revealed novel epigenetically regulated genes expressed by terminally differentiated cells, including KRT78, MYEOV, and MAL. In aggregate, our findings reveal a novel function of TET2 in the epigenetic regulation of corneal epithelial gene expression and identify novel TET2-controlled genes expressed in differentiated corneal epithelial cells. These results point to potential roles for TET2 induction strategies to enhance treatment of corneal diseases associated with abnormal epithelial maturation.
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Affiliation(s)
- Yuzuru Sasamoto
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Transplant Research Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Siyuan Wu
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Transplant Research Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | | | - Jason Y. Jiang
- Transplant Research Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Bruce R. Ksander
- Massachusetts Eye & Ear Infirmary, Schepens Eye Research Institute, Boston, MA 02114, USA
| | - Markus H. Frank
- Transplant Research Program, Boston Children’s Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Harvard Skin Disease Research Center, Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115, USA
- School of Medical and Health Sciences, Edith Cowan University, Perth 6027, WA, Australia
| | - Natasha Y. Frank
- Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Department of Medicine, VA Boston Healthcare System, Boston, MA 02132, USA
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10
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Bonini S, Leonardi A. The multifaceted aspects of ocular allergies: Phenotypes and endotypes. Ocul Surf 2022; 26:174-183. [PMID: 36067980 DOI: 10.1016/j.jtos.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 12/01/2022]
Abstract
Like the lung, skin, and nose, the external eye is a common target of allergic inflammation. Ocular allergy (OA) represents a collection of underestimated diseases of the eye observed in children and adults. The ocular manifestations are the expression of multifactorial immune mechanisms that generally have a good prognosis, but for a few patients, long term inflammation may remarkably reduce the visual function. Evidence suggests that other co-participant systems, including epigenetic, genetic, environmental, individual factors, sex hormones, and the central and autonomic nervous systems may influence the ocular response from distant sites. This is consistent with the concept that the eye is an organ fully integrated with the rest of the body and that the therapeutic approach should be holistic, dynamic, and personalized. For instance, androgens and estrogens binding to receptors on the ocular surface and the continuous cross-talking of neuromediators and growth factors with immune cells act to maintain the ocular surface homeostasis in response to environmental challenges. The immune system links and regulates the response of the ocular surface. Complex and incompletely understood mechanisms influence the innate and adaptive immune responses and generate different OA phenotypes and endotypes discussed in the present review.
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Affiliation(s)
- Stefano Bonini
- Ophthalmology Operative Complex Unit, Campus Bio-Medico University Hospital, 00128, Rome, Italy
| | - Andrea Leonardi
- Department of Neuroscience, Ophthalmology Unit, University of Padova, Padova, Italy.
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Zhang F, Zhou Y, Ding J. The current landscape of microRNAs (miRNAs) in bacterial pneumonia: opportunities and challenges. Cell Mol Biol Lett 2022; 27:70. [PMID: 35986232 PMCID: PMC9392286 DOI: 10.1186/s11658-022-00368-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/01/2022] [Indexed: 11/12/2022] Open
Abstract
MicroRNAs (miRNAs), which were initially discovered in Caenorhabditis elegans, can regulate gene expression by recognizing cognate sequences and interfering with the transcriptional or translational machinery. The application of bioinformatics tools for structural analysis and target prediction has largely driven the investigation of certain miRNAs. Notably, it has been found that certain miRNAs which are widely involved in the inflammatory response and immune regulation are closely associated with the occurrence, development, and outcome of bacterial pneumonia. It has been shown that certain miRNA techniques can be used to identify related targets and explore associated signal transduction pathways. This enhances the understanding of bacterial pneumonia, notably for "refractory" or drug-resistant bacterial pneumonia. Although these miRNA-based methods may provide a basis for the clinical diagnosis and treatment of this disease, they still face various challenges, such as low sensitivity, poor specificity, low silencing efficiency, off-target effects, and toxic reactions. The opportunities and challenges of these methods have been completely reviewed, notably in bacterial pneumonia. With the continuous improvement of the current technology, the miRNA-based methods may surmount the aforementioned limitations, providing promising support for the clinical diagnosis and treatment of "refractory" or drug-resistant bacterial pneumonia.
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Affiliation(s)
- Fan Zhang
- Beijing Key Laboratory of Basic Research With Traditional Chinese Medicine On Infectious Diseases, Beijing Institute of Chinese Medicine, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Yunxin Zhou
- Beijing Key Laboratory of Basic Research With Traditional Chinese Medicine On Infectious Diseases, Beijing Institute of Chinese Medicine, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China
| | - Junying Ding
- Beijing Key Laboratory of Basic Research With Traditional Chinese Medicine On Infectious Diseases, Beijing Institute of Chinese Medicine, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing, 100010, China.
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Zhang X, Jiang Y, Wang Q, An W, Zhang X, Xu M, Chen Y. Atypical U3 snoRNA Suppresses the Process of Pterygium Through Modulating 18S Ribosomal RNA Synthesis. Invest Ophthalmol Vis Sci 2022; 63:17. [PMID: 35472218 PMCID: PMC9055567 DOI: 10.1167/iovs.63.4.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background The progression and recurrence of pterygium mainly occur due to the abnormal proliferation and migration of stromal pterygium fibroblasts. This research explores the aberrant expression of small nucleolar RNA U3 (U3 snoRNA) in pterygium and elucidates the molecular mechanisms of U3 snoRNA in pterygium development. Methods Primary human conjunctival fibroblasts (HCFs) and human pterygium fibroblasts (HPFs) were separated and cultured from fresh conjunctiva grafts and pterygium tissues. The PLKO.1 lentiviral system and CRISPR/Cas9 recombinant construct were, respectively, used to overexpress and silence U3 snoRNA in HPFs and HCFs for further specific phenotype analysis. RNA-seq and TMT-labeled quantitative protein mass spectrometry were utilized to evaluate the effect of U3 snoRNA on mRNA transcripts and protein synthesis. Results Reduced U3 snoRNA in pterygium promotes HCF or HPF cells’ proliferation, migration, and cell cycle but has no significant effect on apoptosis. U3 snoRNA modulates 18S rRNA synthesis through shearing precursor ribosomal RNA 47S rRNA at the 5′ external transcribed spacer (5′ ETS). Moreover, the altered U3 snoRNA causes mRNA and protein differential expression in HCF or HPF cells. Conclusions The atypical U3 snoRNA regulates the translation of specific proteins to exert a suppressive function in pterygium through modulating the 18S rRNA synthesis. Here, we uncover a novel insight into U3 snoRNA biology in the development of pterygium.
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Affiliation(s)
- Xin Zhang
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yaping Jiang
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Qian Wang
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weishu An
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyan Zhang
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai, China
| | - Ming Xu
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yihui Chen
- Department of Ophthalmology, Yangpu Hospital, School of Medicine, Tongji University, Shanghai, China
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Grigoryan EN. Pigment Epithelia of the Eye: Cell-Type Conversion in Regeneration and Disease. Life (Basel) 2022; 12:life12030382. [PMID: 35330132 PMCID: PMC8955580 DOI: 10.3390/life12030382] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/17/2022] Open
Abstract
Pigment epithelial cells (PECs) of the retina (RPE), ciliary body, and iris (IPE) are capable of altering their phenotype. The main pathway of phenotypic switching of eye PECs in vertebrates and humans in vivo and/or in vitro is neural/retinal. Besides, cells of amphibian IPE give rise to the lens and its derivatives, while mammalian and human RPE can be converted along the mesenchymal pathway. The PECs’ capability of conversion in vivo underlies the lens and retinal regeneration in lower vertebrates and retinal diseases such as proliferative vitreoretinopathy and fibrosis in mammals and humans. The present review considers these processes studied in vitro and in vivo in animal models and in humans. The molecular basis of conversion strategies in PECs is elucidated. Being predetermined onto- and phylogenetically, it includes a species-specific molecular context, differential expression of transcription factors, signaling pathways, and epigenomic changes. The accumulated knowledge regarding the mechanisms of PECs phenotypic switching allows the development of approaches to specified conversion for many purposes: obtaining cells for transplantation, creating conditions to stimulate natural regeneration of the retina and the lens, blocking undesirable conversions associated with eye pathology, and finding molecular markers of pathology to be targets of therapy.
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Affiliation(s)
- Eleonora N Grigoryan
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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Gouveia RM, Connon CJ. Biomechanical Modulation Therapy-A Stem Cell Therapy Without Stem Cells for the Treatment of Severe Ocular Burns. Transl Vis Sci Technol 2020; 9:5. [PMID: 33240564 PMCID: PMC7671857 DOI: 10.1167/tvst.9.12.5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/07/2020] [Indexed: 12/16/2022] Open
Abstract
Ocular injuries caused by chemical and thermal burns are often unmanageable and frequently result in disfigurement, corneal haze/opacification, and vision loss. Currently, a considerable number of surgical and pharmacological approaches are available to treat such injuries at either an acute or a chronic stage. However, these existing interventions are mainly directed at (and limited to) suppressing corneal inflammation and neovascularization while promoting re-epithelialization. Reconstruction of the ocular surface represents a suitable but last-option recourse in cases where epithelial healing is severely impaired, such as due to limbal stem cell deficiency. In this concise review, we discuss how biomechanical modulation therapy (BMT) may represent a more effective approach to promoting the regeneration of ocular tissues affected by burn injuries via restoration of the limbal stem cell niche. Specifically, the scientific basis supporting this new therapeutic modality is described, along with our growing understanding of the role that tissue biomechanics plays in stem cell fate and function. The potential impact of BMT as a future treatment option for the management of injuries affecting tissue compliance is also further discussed.
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Affiliation(s)
- Ricardo M Gouveia
- Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Che J Connon
- Biosciences Institute, Faculty of Medical Sciences, The Medical School, Newcastle University, Newcastle upon Tyne, UK
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Cheng S, Xi Z, Chen G, Liu K, Ma R, Zhou C. Extracellular vesicle-carried microRNA-27b derived from mesenchymal stem cells accelerates cutaneous wound healing via E3 ubiquitin ligase ITCH. J Cell Mol Med 2020; 24:11254-11271. [PMID: 32845084 PMCID: PMC7576224 DOI: 10.1111/jcmm.15692] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 02/06/2023] Open
Abstract
Mesenchymal stem cells (MSCs) have been highlighted as promising candidate cells in relation to cutaneous wound healing. The current study aimed to investigate whether MSC-derived extracellular vesicles (EVs) could transfer microRNA-27b (miR-27b) to influence cutaneous wound healing. The miR-27b expression was examined in the established cutaneous wound mouse model, and its correlation with the wound healing rate was evaluated by Pearson's correlation analysis. The identified human umbilical cord MSC-derived EVs were co-cultured with human immortal keratinocyte line HaCaT and human skin fibroblasts (HSFs). The mice with cutaneous wound received injections of MSC-derived EVs. The effects of EVs or miR-27b loaded on wound healing and cellular functions were analysed via gain- and loss-of-function approaches in the co-culture system. Dual-luciferase reporter gene assay was employed to verify the relationship between miR-27b and Itchy E3 ubiquitin protein ligase (ITCH). Rescue experiments were conducted to investigate the underlying mechanisms associated with the ITCH/JUNB/inositol-requiring enzyme 1α (IRE1α) axis. miR-27b was down-regulated in the mouse model, with its expression found to be positively correlated with the wound healing rate. Abundant miR-27b was detected in the MSC-derived EVs, while EV-transferred miR-27b improved cutaneous wound healing in mice and improved proliferation and migration of HaCaT cells and HSFs in vitro. As a target of miR-27b, ITCH was found to repress cell proliferation and migration. ITCH enhanced the JUNB ubiquitination and degradation, ultimately inhibiting JUNB and IRE1α expressions and restraining wound healing. Collectively, MSC-derived EVs transferring miR-27b can promote cutaneous wound healing via ITCH/JUNB/IRE1α signalling, providing insight with clinical implications.
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Affiliation(s)
- Shihuan Cheng
- Department of Rehabilitation, the First Hospital of Jilin University, Changchun, China
| | - Zhiyu Xi
- Department of Vascular Surgery, the First Hospital of Jilin University (Eastern Division), Changchun, China
| | - Guang Chen
- Department of Vascular Surgery, the First Hospital of Jilin University (Eastern Division), Changchun, China
| | - Kai Liu
- Department of Vascular Surgery, the First Hospital of Jilin University (Eastern Division), Changchun, China
| | - Renshi Ma
- Department of Vascular Surgery, the First Hospital of Jilin University (Eastern Division), Changchun, China
| | - Chen Zhou
- Personnel Department, the First Hospital of Jilin University, Changchun, China
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