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Gong N, Tuo Y, Liu P. Identification and Mendelian randomization validation of pathogenic gene biomarkers in obstructive sleep apnea. Front Neurol 2024; 15:1442835. [PMID: 39220737 PMCID: PMC11363542 DOI: 10.3389/fneur.2024.1442835] [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: 06/03/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Background By 2020, obstructive sleep apnea (OSA), a prevalent respiratory disorder, had affected 26.6-43.2% of males and 8.7-27.8% of females worldwide. OSA is associated with conditions such as hypertension, diabetes, and tumor progression; however, the precise underlying pathways remain elusive. This study aims to identify genetic markers and molecular mechanisms of OSA to improve understanding and treatment strategies. Methods The GSE135917 dataset related to OSA was obtained from the GEO database. Differentially expressed genes (DEGs) were subsequently identified. Weighted gene co-expression network analysis (WGCNA) was conducted to pinpoint disease-associated genes. The intersection of these data enabled the identification of potential diagnostic DEGs. Further analyses included Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment studies, exploration of protein-protein interactions based on these genes, and an examination of immune infiltration. Mendelian randomization was employed to validate core genes against the Genome-Wide Association Study database. Results A total of 194 DEGs were identified in this study. WGCNA network analysis highlighted 2,502 DEGs associated with OSA. By intersecting these datasets, 53 diagnostic DEGs primarily involved in metabolic pathways were identified. Significant alterations were observed in immune cell populations, including memory B cells, plasma cells, naive CD4 T cells, M0 macrophages, and activated dendritic cells. CETN3, EEF1E1, PMM2, GTF2A2, and RRM2 emerged as hub genes implicated in the pathogenesis. A line graph model provides diagnostic insights. Mendelian randomization analysis confirmed a causal link between CETN3 and GTF2A2 with OSA. Conclusion Through WGCNA, this analysis uncovered significant genetic foundations of OSA, identifying 2,502 DEGs and 194 genes associated with the disorder. Among these, CETN3 and GTF2A2 were found to have causal relationships with OSA.
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Affiliation(s)
- Nianjin Gong
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Yu Tuo
- Department of Oncology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Peijun Liu
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
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Park JA, Amri C, Kwon Y, Lee JH, Lee T. Recent Advances in DNA Nanotechnology for Plasmonic Biosensor Construction. BIOSENSORS 2022; 12:bios12060418. [PMID: 35735565 PMCID: PMC9220935 DOI: 10.3390/bios12060418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/16/2022]
Abstract
Since 2010, DNA nanotechnology has advanced rapidly, helping overcome limitations in the use of DNA solely as genetic material. DNA nanotechnology has thus helped develop a new method for the construction of biosensors. Among bioprobe materials for biosensors, nucleic acids have shown several advantages. First, it has a complementary sequence for hybridizing the target gene. Second, DNA has various functionalities, such as DNAzymes, DNA junctions or aptamers, because of its unique folded structures with specific sequences. Third, functional groups, such as thiols, amines, or other fluorophores, can easily be introduced into DNA at the 5′ or 3′ end. Finally, DNA can easily be tailored by making junctions or origami structures; these unique structures extend the DNA arm and create a multi-functional bioprobe. Meanwhile, nanomaterials have also been used to advance plasmonic biosensor technologies. Nanomaterials provide various biosensing platforms with high sensitivity and selectivity. Several plasmonic biosensor types have been fabricated, such as surface plasmons, and Raman-based or metal-enhanced biosensors. Introducing DNA nanotechnology to plasmonic biosensors has brought in sight new horizons in the fields of biosensors and nanobiotechnology. This review discusses the recent progress of DNA nanotechnology-based plasmonic biosensors.
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Affiliation(s)
- Jeong Ah Park
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Korea; (J.A.P.); (Y.K.)
| | - Chaima Amri
- Department of Convergence Medical Sciences, School of Medicine, Pusan National University, Yangsan 50612, Korea;
| | - Yein Kwon
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Korea; (J.A.P.); (Y.K.)
| | - Jin-Ho Lee
- Department of Convergence Medical Sciences, School of Medicine, Pusan National University, Yangsan 50612, Korea;
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan 50612, Korea
- Correspondence: (J.-H.L.); (T.L.); Tel.: +82-51-510-8547 (J.-H.L.); +82-2-940-5771 (T.L.)
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, Seoul 01897, Korea; (J.A.P.); (Y.K.)
- Correspondence: (J.-H.L.); (T.L.); Tel.: +82-51-510-8547 (J.-H.L.); +82-2-940-5771 (T.L.)
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Yu Y, Guo Q, Jiang W, Zhang H, Cai C. Dual-Aptamer-Assisted AND Logic Gate for Cyclic Enzymatic Signal Amplification Electrochemical Detection of Tumor-Derived Small Extracellular Vesicles. Anal Chem 2021; 93:11298-11304. [PMID: 34369142 DOI: 10.1021/acs.analchem.1c02489] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small extracellular vesicles (sEVs), often referred to as exosomes, are potential biomarkers for noninvasive cancer diagnosis. However, because of their phenotype heterogeneity, precise detection of tumor-derived sEVs is a great challenge. Herein, a dual-aptamer-assisted AND logic gate was fabricated for sensitive electrochemical detection of tumor-derived sEVs based on a cyclic enzymatic signal amplification strategy. Four different tumor-derived sEVs were used to verify the feasibility of the AND logic gate, and CCRF-CEM sEVs were successfully detected by this assay. The electrochemical assay shows a good linear response from 4 × 103 to 8 × 107 particles/μL, with a detection limit of 920 particles/μL, for CCRF-CEM sEVs, indicating potential application in accurate cancer diagnostics.
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Affiliation(s)
- Yongqi Yu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Qunqun Guo
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Wenli Jiang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
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Fang X, Gao W, Yang Z, Gao Z, Li H. Dual Anti-/Prooxidant Behaviors of Flavonoids Pertaining to Cu(II)-Catalyzed Tyrosine Nitration of the Insulin Receptor Kinase Domain in an Antidiabetic Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6202-6211. [PMID: 32395994 DOI: 10.1021/acs.jafc.0c01676] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Flavonoid, as a potent antioxidant, exerts many beneficial effects in type 2 diabetes, whereas the prooxidative property may be also important in vivo if copper is involved. Here, we chose an insulin receptor kinase domain fragment (KK-1, residues 1126-1165), containing the A-loop of the receptor as well as three key autophosphorylation sites (Tyr1158, Tyr1162, and Tyr1163) associated with receptor signal transduction to investigate the roles and the structure-activity relationship of three antidiabetic flavonoids (kaempferol, luteolin, and apigenin) and two others with a similar structure (diosmetin and genistein), on modulation of Cu(II)-mediated tyrosine nitration and the corresponding effect on its functional phosphorylation in the Cu2+/H2O2/NO2- system. We found that both properties of flavonoid played roles on inhibition of Cu(II)-mediated protein nitration in the H2O2/NO2- system: (1) on the one hand, flavonoid scavenged free radicals as antioxidants, inhibited tyrosine nitration, and thus inhibited the reduction of tyrosine phosphorylation caused by tyrosine nitration; and (2) on the other hand, flavonoid promoted •OH production as a prooxidant, which increased 3,3'-dityrosine formation. The formation of 3,3'-dityrosine decreased Cu2+-induced tyrosine nitration and thus interfered with its phosphorylation. This study confirms that the weight relationship between antioxidation and prooxidation of a flavonoid needs to be studied clearly before nutritional and medical applications.
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Affiliation(s)
- Xu Fang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science & Technology, Wuhan 430074, P. R. China
| | - Wanxia Gao
- School of Basic Medical Science, Hubei University of Science and Technology, Xianning 437000, P. R. China
| | - Zhen Yang
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77004, United States
| | - Zhonghong Gao
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science & Technology, Wuhan 430074, P. R. China
| | - Hailing Li
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science & Technology, Wuhan 430074, P. R. China
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Li M, Zhang W, Yang B. N‑(6‑Aminohexyl)‑5‑chloro‑1‑naphthalenesulfonamide, a centrin antagonist, inhibits Tb 3+/peptides-binding properties. J Inorg Biochem 2019; 193:15-24. [PMID: 30660047 DOI: 10.1016/j.jinorgbio.2019.01.002] [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: 08/21/2018] [Revised: 12/07/2018] [Accepted: 01/06/2019] [Indexed: 10/27/2022]
Abstract
N‑(6‑Aminohexyl)‑5‑chloro‑1‑naphthalenesulfonamide (W-7), a kind of adjuvant chemotherapy, can bind to calmodulin and inhibit Ca2+/calmodulin-regulated enzyme activities and cell proliferation. Similar to calmodulin, euplotes octocarinatus centrin (EoCen) belongs to EF-hand superfamily of calcium-binding proteins. It is associated with nucleotide excision repair (NER), cell division cycle and ciliogenesis. In the present study, the comparative interaction of W-7 with EoCen was first examined by using various spectroscopic, calorimetric methods and molecular docking. The obtain results recommend that only one W-7 molecule is identified binding to the C-terminal hydrophobic pocket of centrin that normally plays a role in anchoring targets. Methyl groups of Ala126, Met141, Ile161 and M162 of C-terminal may react with W-7 chloronaphthalene ring, other aliphatic or aromatic side-chains in a deep hydrophobic pocket of protein. Circular dichroism (CD) and fluorescence lifetime experiments reveal that W-7 triggers a conformational change of centrin. As a result, W-7 is identified to be an antagonist of centrin. It appears to inhibit the centrin-mediated activation of target proteins by blocking the hydrophobic pocket. Moreover, the complex formation leads to affinity decrease of Tb3+ binding to C-terminal of protein and self-assembly affected. Our present study provides the first view of centrin recognizing a naphthalene-sulfonamide derivative. It is proposed that W-7 and its analogues can serve as a useful tool for research on the participation of centrin in biological processes and cell biology-related studies.
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Affiliation(s)
- Min Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Taiyuan 030006, China; Department of Chemistry, Changzhi University, Changzhi 046011, China
| | - Wenlong Zhang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Taiyuan 030006, China
| | - Binsheng Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Taiyuan 030006, China.
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Kurowska A, Brzeczek-Szafran A, Zassowski P, Lapkowski M, Domagala W, Wagner P, Wagner K. Mono and di-substituted BODIPY with electron donating carbazole, thiophene, and 3,4-ethylenedioxythiophene units. Electrochim Acta 2018. [DOI: 10.1016/j.electacta.2018.03.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Zhang W, Shi E, Zhao Y, Yang B. Modulation effect of double strand DNA on the self-assembly of N-terminal domain of Euplotes octocarinatus centrin. J Inorg Biochem 2017; 180:15-25. [PMID: 29223826 DOI: 10.1016/j.jinorgbio.2017.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 11/24/2022]
Abstract
Centrin is a member of the EF-hand super family of calcium-binding proteins, which can behave as a part of damage detector initiated the initiation of nucleotide excision repair (NER). Its self-assembly plays a causative role in fiber contraction associated with the cell division cycle and ciliogenesis. To explore the possible role of DNA in the process of centrin self-assembly, the aggregation properties of N-terminal domain of Euplotes octocarinatus centrin (N-EoCen) in the presence of DNA with or without metal ions are investigated. It is verified that metal ions, such as Ca2+ and Tb3+, can bind to N-EoCen with 2:1 stoichiometry by isothermal titration calorimetry (ITC). Importantly, this study reports that double strand DNA (dsDNA) is capable of binding N-EoCen, changing conformation of protein and modulating centrin aggregation, as demonstrated by extensive biophysical assays. Interestingly, the open conformation of protein induced by metal ions may be favour of the interaction of protein with dsDNA. Nevertheless, the randomly coiled single strand DNA (ssDNA) is completely inefficient to the aggregation regulation. Furthermore, results reveal that hydrophobic site could play important role in the process. This finding may link to the potent roles of centrin in the NER process.
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Affiliation(s)
- Wenlong Zhang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Taiyuan 030006, China
| | - Enxian Shi
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Taiyuan 030006, China; Department of Pharmacy, Shanxi Medical University, Taiyuan 030006, China
| | - Yaqin Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Taiyuan 030006, China
| | - Binsheng Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Taiyuan 030006, China.
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Abstract
Centrin belongs to the calcium-binding super-family, and is essential for the microtubule-organizing center (MTOC).
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Affiliation(s)
- Yaqin Zhao
- Institute of Molecular Science
- Key Laboratory of Chemical Biology
- Molecular Engineering of Ministry of Education
- Shanxi University
- Taiyuan 030006
| | - Xiaofang Cui
- Institute of Molecular Science
- Key Laboratory of Chemical Biology
- Molecular Engineering of Ministry of Education
- Shanxi University
- Taiyuan 030006
| | - Binsheng Yang
- Institute of Molecular Science
- Key Laboratory of Chemical Biology
- Molecular Engineering of Ministry of Education
- Shanxi University
- Taiyuan 030006
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