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Qing KX, Lo ACY, Lu S, Zhou Y, Yang D, Yang D. Integrated bioinformatics analysis of retinal ischemia/reperfusion injury in rats with potential key genes. BMC Genomics 2024; 25:367. [PMID: 38622534 PMCID: PMC11017533 DOI: 10.1186/s12864-024-10288-0] [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: 12/29/2023] [Accepted: 04/07/2024] [Indexed: 04/17/2024] Open
Abstract
The tissue damage caused by transient ischemic injury is an essential component of the pathogenesis of retinal ischemia, which mainly hinges on the degree and duration of interruption of the blood supply and the subsequent damage caused by tissue reperfusion. Some research indicated that the retinal injury induced by ischemia-reperfusion (I/R) was related to reperfusion time.In this study, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model group and at different reperfusion time (24h, 72h, and 7d) with the aid of whole transcriptome sequencing technology, and the trend changes in time-varying mRNA, lncRNA, circRNA were obtained by chronological analysis. Then, candidate circRNAs, lncRNAs, and mRNAs were obtained as the intersection of differentially expression genes and trend change genes. Importance scores of the genes selected the key genes whose expression changed with the increase of reperfusion time. Also, the characteristic differentially expressed genes specific to the reperfusion time were analyzed, key genes specific to reperfusion time were selected to show the change in biological process with the increase of reperfusion time.As a result, 316 candidate mRNAs, 137 candidate lncRNAs, and 31 candidate circRNAs were obtained by the intersection of differentially expressed mRNAs, lncRNAs, and circRNAs with trend mRNAs, trend lncRNAs and trend circRNAs, 5 key genes (Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa) were selected by importance scores of the genes. The result of GSEA showed that key genes were found to play vital roles in antigen processing and presentation, regulation of the actin cytoskeleton, and the ribosome. A network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 34 miRNAs and 48 lncRNAs, and 81 regulatory relationship axes, and a network included 4 key genes (Cd74, RT1-Da, RT1-Bb, RT1-DOa), 9 miRNAs and 3 circRNAs (circRNA_10572, circRNA_03219, circRNA_11359) and 12 regulatory relationship axes were constructed, the subcellular location, transcription factors, signaling network, targeted drugs and relationship to eye diseases of key genes were predicted. 1370 characteristic differentially expressed mRNAs (spec_24h mRNA), 558 characteristic differentially expressed mRNAs (spec_72h mRNA), and 92 characteristic differentially expressed mRNAs (spec_7d mRNA) were found, and their key genes and regulation networks were analyzed.In summary, we screened the differentially expressed circRNAs, lncRNAs, and mRNAs between the control and model groups and at different reperfusion time (24h, 72h, and 7d). 5 key genes, Cd74, RT1-Da, RT1-CE5, RT1-Bb, RT1-DOa, were selected. Key genes specific to reperfusion time were selected to show the change in biological process with the increased reperfusion time. These results provided theoretical support and a reference basis for the clinical treatment.
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Affiliation(s)
- Kai-Xiong Qing
- Department of Cardiac & Vascular Surgery, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - Amy C Y Lo
- Department of Ophthalmology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Siduo Lu
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - You Zhou
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - Dan Yang
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China
| | - Di Yang
- Department of Ophthalmology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, Yunnan Province, China.
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Lee D, Tomita Y, Shinojima A, Ban N, Yamaguchi S, Nishioka K, Negishi K, Yoshino J, Kurihara T. Nicotinamide mononucleotide, a potential future treatment in ocular diseases. Graefes Arch Clin Exp Ophthalmol 2024; 262:689-700. [PMID: 37335334 DOI: 10.1007/s00417-023-06118-w] [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: 02/06/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 06/21/2023] Open
Abstract
PURPOSE The burden of ocular diseases has been gradually increasing worldwide. Various factors are suggested for the development and progression of ocular diseases, such as ocular inflammation, oxidative stress, and complex metabolic dysregulation. Thus, managing ocular diseases requires the modulation of pathologic signaling pathways through many mechanisms. Nicotinamide mononucleotide (NMN) is a bioactive molecule naturally found in life forms. NMN is a direct precursor of the important molecule nicotinamide adenine dinucleotide (NAD+), an essential co-enzyme required for enormous cellular functions in most life forms. While the recent experimental evidence of NMN treatment in various metabolic diseases has been well-reviewed, NMN treatment in ocular diseases has not been comprehensively summarized yet. In this regard, we aimed to focus on the therapeutic roles of NMN treatment in various ocular diseases with recent advances. METHODS How we came to our current opinion with a recent summary was described based on our own recent reports as well as a search of the related literature. RESULTS We found that NMN treatment might be available for the prevention of and protection from various experimental ocular diseases, as NMN treatment modulated ocular inflammation, oxidative stress, and complex metabolic dysregulation in murine models for eye diseases such as ischemic retinopathy, corneal defect, glaucoma, and age-related macular degeneration. CONCLUSION Our current review suggests and discusses new modes of actions of NMN for the prevention of and protection from various ocular diseases and can urge future research to obtain more solid evidence on a potential future NMN treatment in ocular diseases at the preclinical stages.
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Affiliation(s)
- Deokho Lee
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yohei Tomita
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Ari Shinojima
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Norimitsu Ban
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Shintaro Yamaguchi
- Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Ken Nishioka
- Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Kazuno Negishi
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Jun Yoshino
- Department of Internal Medicine, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Toshihide Kurihara
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo, 160-8582, Japan.
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, 160-8582, Japan.
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Zhang C, Li Y, Bai F, Talifu Z, Ke H, Xu X, Li Z, Liu W, Pan Y, Gao F, Yang D, Wang X, Du H, Guo S, Gong H, Du L, Yu Y, Li J. The identification of new roles for nicotinamide mononucleotide after spinal cord injury in mice: an RNA-seq and global gene expression study. Front Cell Neurosci 2023; 17:1323566. [PMID: 38155866 PMCID: PMC10752985 DOI: 10.3389/fncel.2023.1323566] [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: 10/18/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Background Nicotinamide mononucleotide (NMN), an important transforming precursor of nicotinamide adenine dinucleotide (NAD+). Numerous studies have confirmed the neuroprotective effects of NMN in nervous system diseases. However, its role in spinal cord injury (SCI) and the molecular mechanisms involved have yet to be fully elucidated. Methods We established a moderate-to-severe model of SCI by contusion (70 kdyn) using a spinal cord impactor. The drug was administered immediately after surgery, and mice were intraperitoneally injected with either NMN (500 mg NMN/kg body weight per day) or an equivalent volume of saline for seven days. The central area of the spinal cord was harvested seven days after injury for the systematic analysis of global gene expression by RNA Sequencing (RNA-seq) and finally validated using qRT-PCR. Results NMN supplementation restored NAD+ levels after SCI, promoted motor function recovery, and alleviated pain. This could potentially be associated with alterations in NAD+ dependent enzyme levels. RNA sequencing (RNA-seq) revealed that NMN can inhibit inflammation and potentially regulate signaling pathways, including interleukin-17 (IL-17), tumor necrosis factor (TNF), toll-like receptor, nod-like receptor, and chemokine signaling pathways. In addition, the construction of a protein-protein interaction (PPI) network and the screening of core genes showed that interleukin 1β (IL-1β), interferon regulatory factor 7 (IRF 7), C-X-C motif chemokine ligand 10 (Cxcl10), and other inflammationrelated factors, changed significantly after NMN treatment. qRT-PCR confirmed the inhibitory effect of NMN on inflammatory factors (IL-1β, TNF-α, IL-17A, IRF7) and chemokines (chemokine ligand 3, Cxcl10) in mice following SCI. Conclusion The reduction of NAD+ levels after SCI can be compensated by NMN supplementation, which can significantly restore motor function and relieve pain in a mouse model. RNA-seq and qRT-PCR systematically revealed that NMN affected inflammation-related signaling pathways, including the IL-17, TNF, Toll-like receptor, NOD-like receptor and chemokine signaling pathways, by down-regulating the expression of inflammatory factors and chemokines.
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Affiliation(s)
- Chunjia Zhang
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Yan Li
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Fan Bai
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Zuliyaer Talifu
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, Shandong, China
| | - Han Ke
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Orthopedics, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Xin Xu
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Zehui Li
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Wubo Liu
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Department of Orthopedics, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Yunzhu Pan
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
- School of Rehabilitation Sciences and Engineering, University of Health and Rehabilitation Sciences, Qingdao, Shandong, China
| | - Feng Gao
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Degang Yang
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xiaoxin Wang
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Huayong Du
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Shuang Guo
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Han Gong
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liangjie Du
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Yan Yu
- School of Rehabilitation, Capital Medical University, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jianjun Li
- School of Rehabilitation, Capital Medical University, Beijing, China
- Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center, Beijing, China
- China Rehabilitation Science Institute, Beijing, China
- Center of Neural Injury and Repair, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
- Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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9
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Lee D, Tomita Y, Miwa Y, Jeong H, Shinojima A, Ban N, Yamaguchi S, Nishioka K, Negishi K, Yoshino J, Kurihara T. Nicotinamide Mononucleotide Protects against Retinal Dysfunction in a Murine Model of Carotid Artery Occlusion. Int J Mol Sci 2022; 23:ijms232314711. [PMID: 36499037 PMCID: PMC9741448 DOI: 10.3390/ijms232314711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022] Open
Abstract
Cardiovascular abnormality-mediated retinal ischemia causes severe visual impairment. Retinal ischemia is involved in enormous pathological processes including oxidative stress, reactive gliosis, and retinal functional deficits. Thus, maintaining retinal function by modulating those pathological processes may prevent or protect against vision loss. Over the decades, nicotinamide mononucleotide (NMN), a crucial nicotinamide adenine dinucleotide (NAD+) intermediate, has been nominated as a promising therapeutic target in retinal diseases. Nonetheless, a protective effect of NMN has not been examined in cardiovascular diseases-induced retinal ischemia. In our study, we aimed to investigate its promising effect of NMN in the ischemic retina of a murine model of carotid artery occlusion. After surgical unilateral common carotid artery occlusion (UCCAO) in adult male C57BL/6 mice, NMN (500 mg/kg/day) was intraperitoneally injected to mice every day until the end of experiments. Electroretinography and biomolecular assays were utilized to measure ocular functional and further molecular alterations in the retina. We found that UCCAO-induced retinal dysfunction was suppressed, pathological gliosis was reduced, retinal NAD+ levels were preserved, and the expression of an antioxidant molecule (nuclear factor erythroid-2-related factor 2; Nrf2) was upregulated by consecutive administration of NMN. Our present outcomes first suggest a promising NMN therapy for the suppression of cardiovascular diseases-mediated retinal ischemic dysfunction.
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Affiliation(s)
- Deokho Lee
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yohei Tomita
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yukihiro Miwa
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Aichi Animal Eye Clinic, Nagoya 466-0827, Japan
| | - Heonuk Jeong
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ari Shinojima
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Norimitsu Ban
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Shintaro Yamaguchi
- Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ken Nishioka
- Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kazuno Negishi
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Jun Yoshino
- Department of Internal Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toshihide Kurihara
- Laboratory of Photobiology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan
- Correspondence:
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