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APLNR promotes the progression of osteosarcoma by stimulating cell proliferation and invasion: Retraction. Anticancer Drugs 2023; 34:970. [PMID: 37555813 DOI: 10.1097/cad.0000000000001534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
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Wang Z, Wang L, Dai L, Wang Y, Li E, An S, Wang F, Liu D, Pan W. Identification of candidate aberrant differentially methylated/expressed genes in asthma. Allergy Asthma Clin Immunol 2022; 18:108. [PMID: 36550577 PMCID: PMC9784293 DOI: 10.1186/s13223-022-00744-5] [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: 08/04/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Asthma is an important non-communicable disease worldwide. DNA methylation is associated with the occurrence and development of asthma. We are aimed at assuring differential expressed genes (DEGs) modified by aberrantly methylated genes (DMGs) and pathways related to asthma by integrating bioinformatics analysis. METHODS One mRNA dataset (GSE64913) and one gene methylation dataset (GSE137716) were selected from the Gene Expression Omnibus (GEO) database. Functional enrichment analysis was performed using GeneCodies 4.0 database. All gene expression matrices were analyzed by Gene set enrichment analysis (GSEA) software. STRING was applied to construct a protein-protein interaction (PPI) network to find the hub genes. Then, electronic validation was performed to verify the hub genes, followed by the evaluation of diagnostic value. Eventually, quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to detect the expression of hub genes. RESULTS In total, 14 hypomethylated/high-expression genes and 10 hypermethylated/low-expression genes were obtained in asthma. Among them, 10 hub genes were identified in the PPI network. Functional analysis demonstrated that the differentially methylated/expressed genes were primarily associated with the lung development, cytosol and protein binding. Notably, HLA-DOA was enriched in asthma. FKBP5, WNT5A, TM4SF1, PDK4, EPAS1 and GMPR had potential diagnostic value for asthma. CONCLUSION The project explored the pathogenesis of asthma, which may provide a research basis for the prediction and the drug development of asthma.
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Affiliation(s)
- Zongling Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Lizhi Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Lina Dai
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Yanan Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Erhong Li
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Shuyuan An
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Fengliang Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Dan Liu
- Clinical laboratory, Qingdao Fuwai Cardiovascular Hospital, Qingdao, China
| | - Wen Pan
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
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Akimniyazova AN, Niyazova TK, Yurikova OY, Pyrkova AY, Zhanuzakov MA, Ivashchenko AT. piRNAs may regulate expression of candidate genes of esophageal adenocarcinoma. Front Genet 2022; 13:1069637. [PMID: 36531220 PMCID: PMC9747755 DOI: 10.3389/fgene.2022.1069637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/18/2022] [Indexed: 07/29/2023] Open
Abstract
Elucidation of ways to regulate the expression of candidate cancer genes will contribute to the development of methods for cancer diagnosis and therapy. The aim of the present study was to show the role of piRNAs as efficient regulators of mRNA translation of esophageal adenocarcinoma (EAC) candidate genes. We used bioinformatic methods to study the interaction characteristics of up to 200 thousand piRNAs with mRNAs of 38 candidate EAC genes. The piRNAs capable of binding to mRNA of AR, BTG3, CD55, ERBB3, FKBP5, FOXP1, LEP, SEPP1, SMAD4, and TP53 genes with high free energy by the formation of hydrogen bonds between canonical (G-C, A-U) and noncanonical (G-U, A-C) piRNA and mRNA nucleotide pairs were revealed. The organization of piRNA binding sites (BSs) in the mRNA of candidate genes was found to overlap nucleotide sequences to form clusters. Clusters of piRNA BSs were detected in the 5'-untranslated region, coding domain sequence, and 3'-untranslated region of mRNA. Due to the formation of piRNA binding site clusters, compaction of BSs occurs and competition between piRNAs for binding to mRNA of candidate EAC genes occurs. Associations of piRNA and candidate genes were selected for use as markers for the diagnosis of EAC.
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Affiliation(s)
- A. N. Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - T. K. Niyazova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - O. Yu. Yurikova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - A. Yu. Pyrkova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty, Kazakhstan
| | - M. A. Zhanuzakov
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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Jo D, Kim HK, Kim YK, Song J. Transcriptome Profile of Thyroid Glands in Bile Duct Ligation Mouse Model. Int J Mol Sci 2022; 23:ijms23158244. [PMID: 35897811 PMCID: PMC9332885 DOI: 10.3390/ijms23158244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/18/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Thyroid hormone (TH) contributes to multiple cellular mechanisms in the liver, muscle cells, adipose tissue, and brain, etc. In particular, the liver is an important organ in TH metabolism for the conversion of thyronine (T4) into triiodothyronine (T3) by the deiodinase enzyme. TH levels were significantly decreased and thyroid-stimulating hormone (TSH) levels were significantly increased in patients with liver failure compared with normal subjects. Among liver failure diseases, hepatic encephalopathy (HE) deserves more attention because liver damage and neuropathologies occur simultaneously. Although there is numerous evidence of TH dysregulation in the HE model, specific mechanisms and genetic features of the thyroid glands in the HE model are not fully understood. Here, we investigated the significantly different genes in the thyroid glands of a bile duct ligation (BDL) mouse model as the HE model, compared to the thyroid glands of the control mouse using RNA sequencing. We also confirmed the alteration in mRNA levels of thyroid gland function-related genes in the BDL mouse model. Furthermore, we evaluated the increased level of free T4 and TSH in the BDL mouse blood. Thus, we emphasize the potential roles of TH in liver metabolism and suggest that thyroid dysfunction-related genes in the HE model should be highlighted for finding the appropriate solution for an impaired thyroid system in HE.
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Affiliation(s)
- Danbi Jo
- Department of Anatomy, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Korea;
- Biomedical Science Graduate Program (BMSGP), Chonnam National University, Seoyangro 264, Hwasun 58128, Korea
| | - Hee Kyung Kim
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Korea;
| | - Young-Kook Kim
- Department of Biochemistry, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Korea;
| | - Juhyun Song
- Department of Anatomy, Chonnam National University Medical School, Seoyangro 264, Hwasun 58128, Korea;
- Biomedical Science Graduate Program (BMSGP), Chonnam National University, Seoyangro 264, Hwasun 58128, Korea
- Correspondence: ; Tel.: +82-61-379-2706
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Park C, Noh JS, Jung Y, Leem SH, Hyun JW, Chang YC, Kwon TK, Kim GY, Lee H, Choi YH. Fisetin Attenuated Oxidative Stress-Induced Cellular Damage in ARPE-19 Human Retinal Pigment Epithelial Cells Through Nrf2-Mediated Activation of Heme Oxygenase-1. Front Pharmacol 2022; 13:927898. [PMID: 35784747 PMCID: PMC9243462 DOI: 10.3389/fphar.2022.927898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Fisetin is a kind of bioactive flavonol, widely present in various fruits such as strawberries and apples, and is known to act as a potent free radical scavenger. However, the mechanism of action related to the antioxidant activity of this compound in human retinal pigment epithelial (RPE) cells is not precisely known. In this study, we aimed to investigate whether fisetin could attenuate oxidative stress-induced cytotoxicity on human RPE ARPE-19 cells. To mimic oxidative stress, ARPE-19 cells were treated with hydrogen peroxide (H2O2), and fisetin significantly inhibited H2O2-induced loss of cell viability and increase of intracellular reactive oxygen species (ROS) production. Fisetin also markedly attenuated DNA damage and apoptosis in H2O2-treated ARPE-19 cells. Moreover, mitochondrial dysfunction in H2O2-treated cells was alleviated in the presence of fisetin as indicated by preservation of mitochondrial membrane potential, increase of Bcl-2/Bax expression ratio, and suppression of cytochrome c release into the cytoplasm. In addition, fisetin enhanced phosphorylation and nuclear translocation of nuclear factor erythroid 2 related factor 2 (Nrf2), which was associated with increased expression and activity of heme oxygenase-1 (HO-1). However, the HO-1 inhibitor, zinc protoporphyrin, significantly reversed the protective effect of fisetin against H2O2-mediated ARPE-19 cell injury. Therefore, our results suggest that Nrf2-mediated activation of antioxidant enzyme HO-1 may play an important role in the ROS scavenging activity of fisetin in RPE cells, contributing to the amelioration of oxidative stress-induced ocular disorders.
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Affiliation(s)
- Cheol Park
- Division of Basic Sciences, College of Liberal Studies, Dong-Eui University, Busan, South Korea
| | - Jeong Sook Noh
- Department of Food Science and Nutrition, Tongmyong University, Busan, South Korea
| | - Youngmi Jung
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
- Department of Biological Sciences, Pusan National University, Busan, South Korea
| | - Sun-Hee Leem
- Department of Biomedical Sciences, Dong-A University, Busan, South Korea
- Department of Health Sciences, Dong-A University, Busan, South Korea
| | - Jin Won Hyun
- Department of Biochemistry, College of Medicine, Jeju National University, Jeju, South Korea
| | - Young-Chae Chang
- Research Institute of Biomedical Engineering and Department of Medicine, Catholic University of Daegu School of Medicine, Daegu, South Korea
| | - Taeg Kyu Kwon
- Department of Immunology, School of Medicine, Keimyung University, Daegu, South Korea
| | - Gi-Young Kim
- Department of Marine Life Science, Jeju National University, Jeju, South Korea
| | - Hyesook Lee
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
- *Correspondence: Hyesook Lee, ; Yung Hyun Choi,
| | - Yung Hyun Choi
- Anti-Aging Research Center and Core-Facility Center for Tissue Regeneration, Dong-Eui University, Busan, South Korea
- Department of Biochemistry, Dong-Eui University College of Korean Medicine, Busan, South Korea
- *Correspondence: Hyesook Lee, ; Yung Hyun Choi,
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