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Chen X, Su D, Sun Z, Fu Y, Hu Y, Zhang Y, Zhang X, Wei Q, Zhu W, Ma X, Hu S. Preliminary study on whole genome methylation and transcriptomics in age-related cataracts. Gene 2024; 898:148096. [PMID: 38128790 DOI: 10.1016/j.gene.2023.148096] [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: 09/10/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
DNA methylation plays an important role in the occurrence and development of age-related cataracts (ARC). This study aims to reveal potential epigenetic biomarkers of ARC by detecting modifications to the DNA methylation patterns of genes shown to be related to ARC by transcriptomics. The MethylationEPIC BeadChip (850 K) was used to analyze the DNA methylation levels in ARC patients and unaffected controls, and the Pearson correlation test was used to perform genome-wide integration analysis of DNA methylation and transcriptome data. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were used to perform functional analysis of the whole genome, promoter regions (TSS1500/TSS200), and the associated differentially methylated genes (DMG). Pyrosequencing was used to verify the methylation levels of the selected genes. The results showed that, compared with the control group, a total of 52,705 differentially methylated sites were detected in the ARC group, of which 13,858 were hypermethylated and 38,847 were hypomethylated. GO and KEGG analyses identified functions related to the cell membrane, the calcium signaling pathway, and their possible molecular mechanisms. Then, 57 DMGs with negative promoter methylation correlations were screened by association analysis. Pyrosequencing verified that the ARC group had higher methylation levels of C3 and CCKAR and lower methylation levels of NLRP3, LEFTY1, and GPR35 compared with the control group. In summary, our study reveals the whole-genome DNA methylation patterns and gene expression profiles in ARC, and the molecular markers of methylation identified herein may aid in the prevention, diagnosis, treatment, and prognosis of ARC.
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Affiliation(s)
- Xiaoya Chen
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Dongmei Su
- Department of Genetics, NHC Key Laboratory of Reproductive Health Engineering Technology Research, National Research Institute for Family Planning, Health Department, Beijing 100081, China; Graduate School, Peking Union Medical College, Beijing 100081, China
| | - Zhaoyi Sun
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Yanjiang Fu
- Daqing Eye Hospital, Daqing 163000, Heilongjiang, China
| | - Yuzhu Hu
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Yue Zhang
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Xiao Zhang
- Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Qianqiu Wei
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Wenna Zhu
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China
| | - Xu Ma
- Department of Genetics, NHC Key Laboratory of Reproductive Health Engineering Technology Research, National Research Institute for Family Planning, Health Department, Beijing 100081, China; Graduate School, Peking Union Medical College, Beijing 100081, China.
| | - Shanshan Hu
- Hongqi Hospital of Mudanjiang Medical University, Mudanjiang 157011, Heilongjiang, China.
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Kaushik M, Tiwari P, Dada T, Dada R. Beyond the optic nerve: Genetics, diagnosis, and promising therapies for glaucoma. Gene 2024; 894:147983. [PMID: 37952746 DOI: 10.1016/j.gene.2023.147983] [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: 09/29/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/14/2023]
Abstract
Glaucoma stands as a leading global cause of blindness, affecting millions. It entails optic nerve damage and vision loss, categorized into open-angle and closed-angle glaucoma with subtypes like POAG, ACG, XFG, PCG, PDG, and developmental glaucoma. The pathophysiological and genetic factors behind glaucoma remain partially understood, with past studies linking intraocular pressure (IOP) levels to retinal ganglion cell death. Open-angle glaucoma involves elevated resistance to aqueous outflow via the trabecular meshwork, while angle-closure glaucoma typically sees drainage pathways obstructed by the iris. Genes have been identified for POAG, ACG, XFG, PCG, PDG, and developmental glaucoma, allowing for early-onset detection and the emergence of gene therapy as an effective treatment. Nevertheless, diagnostic and treatment options have their constraints, necessitating large-scale, well-designed studies to deepen our grasp of genetics' role in glaucoma's pathogenesis. This review delves into glaucoma's risk factors, pathophysiology, genetics, diagnosis, and available treatment options, including gene therapy. Additionally, it suggests alternative therapies like yoga and meditation as adjunct treatments for glaucoma prevention. Overall, this review advances our comprehension of the pathophysiology and genetic associations of glaucoma while highlighting the potential of gene therapy as a treatment avenue. Further research is imperative to fully elucidate the genetic mechanisms underpinning glaucoma and to devise effective treatments.
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Affiliation(s)
- Meenakshi Kaushik
- Lab for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Prabhakar Tiwari
- Lab for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India.
| | - Tanuj Dada
- Dr. Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, New Delhi, India
| | - Rima Dada
- Lab for Molecular Reproduction and Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India.
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