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Computational Inferring of Risk Subpathways Mediated by Dysfunctional Non-coding RNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1094:87-95. [DOI: 10.1007/978-981-13-0719-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Feng L, Xu Y, Zhang Y, Sun Z, Han J, Zhang C, Yang H, Shang D, Su F, Shi X, Li S, Li C, Li X. Subpathway-GMir: identifying miRNA-mediated metabolic subpathways by integrating condition-specific genes, microRNAs, and pathway topologies. Oncotarget 2016; 6:39151-64. [PMID: 26472186 PMCID: PMC4770763 DOI: 10.18632/oncotarget.5341] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/02/2015] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) regulate disease-relevant metabolic pathways. However, most current pathway identification methods fail to consider miRNAs in addition to genes when analyzing pathways. We developed a powerful method called Subpathway-GMir to construct miRNA-regulated metabolic pathways and to identify miRNA-mediated subpathways by considering condition-specific genes, miRNAs, and pathway topologies. We used Subpathway-GMir to analyze two liver hepatocellular carcinomas (LIHC), one stomach adenocarcinoma (STAD), and one type 2 diabetes (T2D) data sets. Results indicate that Subpathway-GMir is more effective in identifying phenotype-associated metabolic pathways than other methods and our results are reproducible and robust. Subpathway-GMir provides a flexible platform for identifying abnormal metabolic subpathways mediated by miRNAs, and may help to clarify the roles that miRNAs play in a variety of diseases. The Subpathway-GMir method has been implemented as a freely available R package.
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Affiliation(s)
- Li Feng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Zeguo Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Haixiu Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Fei Su
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xinrui Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Shang Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chunquan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.,Department of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, 163319, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
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Syed M, Skonberg C, Hansen SH. Mitochondrial toxicity of selective COX-2 inhibitors via inhibition of oxidative phosphorylation (ATP synthesis) in rat liver mitochondria. Toxicol In Vitro 2015; 32:26-40. [PMID: 26689325 DOI: 10.1016/j.tiv.2015.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/14/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
Abstract
Cyclooxygenase-2 (COX-2) inhibitors (coxibs) are non-steroidal anti-inflammatory drugs (NSAIDs) designed to selectively inhibit COX-2. However, drugs of this therapeutic class are associated with drug induced liver injury (DILI) and mitochondrial injury is likely to play a role. The effects of selective COX-2 inhibitors on inhibition of oxidative phosphorylation (ATP synthesis) in rat liver mitochondria were investigated. The order of potency of inhibition of ATP synthesis was: lumiracoxib (IC50: 6.48 ± 2.74 μM)>celecoxib (IC50: 14.92 ± 6.40 μM)>valdecoxib (IC50: 161.4 ± 28.6 μM)>rofecoxib (IC50: 238.4 ± 79.2 μM)>etoricoxib (IC50: 405.1 ± 116.3 μM). Mechanism based inhibition of ATP synthesis (Kinact 0.078 min(-1) and KI 21.46 μM and Kinact/KI ratio 0.0036 min(-1)μM(-1)) was shown by lumiracoxib and data suggest that the opening of the MPT pore may not be the mechanism of toxicity. A positive correlation (with r(2)=0.921) was observed between the potency of inhibition of ATP synthesis and the log P values. The in vitro metabolism of coxibs in rat liver mitochondria yielded for each drug substance a major single metabolite and identified a hydroxy metabolite with each of the coxibs and these metabolites did not alter the inhibition profile of ATP synthesis of the parent compound. The results suggest that coxibs themselves could be involved in the hepatotoxic action through inhibition of ATP synthesis.
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Affiliation(s)
- Muzeeb Syed
- Section of Analytical Biosciences, Department of Pharmacy, School of Pharmaceutical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Christian Skonberg
- Discovery ADME Department, Diabetes Pharmacology and Bioanalysis, Novo Nordisk A/S, Måløv, Copenhagen, Denmark
| | - Steen Honoré Hansen
- Section of Analytical Biosciences, Department of Pharmacy, School of Pharmaceutical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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SHAO DAN, KAN MUJIE, QIAO PING, PAN YUE, WANG ZHENG, XIAO XUANANG, LI JING, CHEN LI. Celecoxib induces apoptosis via a mitochondria-dependent pathway in the H22 mouse hepatoma cell line. Mol Med Rep 2014; 10:2093-8. [DOI: 10.3892/mmr.2014.2461] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 06/05/2014] [Indexed: 11/06/2022] Open
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Cheng HH, Chou CT, Lu YC, Lu T, Chi CC, Tseng LL, Liu SI, Cheng JS, Kuo CC, Liang WZ, Jan CR. Celecoxib-induced increase in cytosolic Ca(2+) levels and apoptosis in HA59T human hepatoma cells. Hum Exp Toxicol 2014; 33:1089-98. [PMID: 24972620 DOI: 10.1177/0960327112472996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Celecoxib has been shown to have antitumor effect in previous studies but the mechanisms are unclear. The effect of celecoxib on cytosolic Ca(2+) concentrations ([Ca(2+)]i) and viability in HA59T human hepatoma cells was explored. The Ca(2+)-sensitive fluorescent dye fura-2 was applied to measure [Ca(2+)]i. Celecoxib at concentrations of 10-50 μM induced a [Ca(2+)]i rise in a concentration-dependent manner. The response was reduced by 80% by removing Ca(2+). Celecoxib induced Mn(2+) influx, leading to quenching of fura-2 fluorescence. Celecoxib-evoked Ca(2+) entry was suppressed by nifedipine, econazole, SK&F96365, and protein kinase C modulators. In the absence of extracellular Ca(2+), incubation with the endoplasmic reticulum Ca(2+) pump inhibitor thapsigargin nearly abolished celecoxib-induced [Ca(2+)]i rise. Incubation with celecoxib abolished thapsigargin-induced [Ca(2+)]i rise. Inhibition of phospholipase C with U73122 abolished celecoxib-induced [Ca(2+)]i rise. At 1-50 μM, celecoxib inhibited cell viability by less than 20%, which was not reversed by chelating cytosolic Ca(2+) with 1,2-bis(2-aminophenoxy)ethane-N, N, N', N'-tetraacetic acid/acetoxy methyl (BAPTA/AM). Celecoxib (10-50 μM) also induced apoptosis. In sum, in HA59T hepatoma cells, celecoxib induced a [Ca(2+)]i rise by evoking phospholipase C-dependent Ca(2+) release from the endoplasmic reticulum and Ca(2+) entry via protein kinase C-sensitive store-operated Ca(2+) channels. Celecoxib also caused cell death via apoptosis.
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Affiliation(s)
- H-H Cheng
- Department of Medicine, Chang Bing Show Chwan Memorial Hospital, Changhua County, Taiwan
| | - C-T Chou
- Department of Nursing, Division of Basic Medical Sciences, Chang Gung University of Science and Technology, Chia-Yi, Taiwan Chronic Diseases and Health Promotion Research Center, Chang Gung University of Science and Technology, Chia-Yi, Taiwan
| | - Y-C Lu
- Department of Orthopedics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - T Lu
- Department of Psychiatry, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - C-C Chi
- Department of Otolaryngology, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - L-L Tseng
- Department of Dentistry, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - S-I Liu
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - J-S Cheng
- Department of Medicine, Yongkang Veterans Hospital, Tainan, Taiwan
| | - C-C Kuo
- Institute of Nursing and Department of Nursing, Chang Gung Institute of Technology Chiayi Campus, Taiwan
| | - W-Z Liang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - C-R Jan
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
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Xia J, Giovannozzi AM, Sadeghi SJ, Gilardi G, Rossi AM. Laser-written nanoporous silicon diffraction gratings for biosensors. APPLIED OPTICS 2013; 52:8802-8808. [PMID: 24513946 DOI: 10.1364/ao.52.008802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
Surface-relief diffraction gratings and planar diffraction gratings directly written on nanoporous silicon layers using 514 nm continuous-wave lasers at very low power (less than 20 mW) were demonstrated. Diffraction-based biosensing application to detect arachidonic acid was experimentally demonstrated at incident light wavelength of 632.8 nm. A comparison in sensing applications was made between the two types of gratings to show the distinct advantage of the planar grating with selective functionalization. Laser-written planar gratings enable directly immobilizing biomolecules in the laser oxidized area of nanoporous silicon, resulting in a new patterned functionalization technique for biosensing applications. The functionalization technique can not only simplify the functionalization procedure in biosensing but also it has potential to increase the sensitivity of sensors by accurately defining grating patterns using the laser direct writing technique.
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Ramer R, Walther U, Borchert P, Laufer S, Linnebacher M, Hinz B. Induction but not inhibition of COX-2 confers human lung cancer cell apoptosis by celecoxib. J Lipid Res 2013; 54:3116-29. [PMID: 23943857 DOI: 10.1194/jlr.m042283] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The antitumorigenic mechanism of the selective cyclooxygenase-2 (COX-2) inhibitor celecoxib is still a matter of debate. Among different structurally related COX-2 inhibitors, only celecoxib was found to cause apoptosis and cell death of human lung cancer cells (IC₅₀ values of 19.96 µM [A549], 12.48 µM [H460], and 41.39 µM [H358]) that was paralleled by a time- and concentration-dependent upregulation of COX-2 and peroxisome proliferator-activated receptor γ (PPARγ) at mRNA and protein levels. Apoptotic death of celecoxib-treated cancer cells was suppressed by the PPARγ antagonist GW9662 and by siRNA targeting PPARγ and, surprisingly, also by the selective COX-2 inhibitor NS-398 and siRNA targeting COX-2. NS-398 (1 µM) was shown to suppress celecoxib-induced COX-2 activity. Among the COX-2-dependent prostaglandins (PG) induced upon celecoxib treatment, PGD₂ and 15-deoxy-Δ¹²,¹⁴-PGJ₂ were found to induce a cytosol-to-nucleus translocation of PPARγ as well as a PPARγ-dependent apoptosis. Celecoxib-elicited PPARγ translocation was inhibited by NS-398. Finally, a COX-2- and PPARγ-dependent cytotoxic action of celecoxib was proven for primary human lung tumor cells. Together, our data demonstrate a proapoptotic mechanism of celecoxib involving initial upregulation of COX-2 and PPARγ and a subsequent nuclear translocation of PPARγ by COX-2-dependent PGs.
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Affiliation(s)
- Robert Ramer
- Institute of Toxicology and Pharmacology, University of Rostock, Schillingallee 70, D-18057 Rostock, Germany
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Yen HH, Shih KL, Lin TT, Su WW, Soon MS, Liu CS. Decreased mitochondrial deoxyribonucleic acid and increased oxidative damage in chronic hepatitis C. World J Gastroenterol 2012; 18:5084-9. [PMID: 23049218 PMCID: PMC3460336 DOI: 10.3748/wjg.v18.i36.5084] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 05/09/2012] [Accepted: 05/13/2012] [Indexed: 02/06/2023] Open
Abstract
AIM: To determine whether alteration of the mitochondria DNA (mtDNA) copy number and its oxidative damage index (mtDNA∆CT) can be detected by analysis of peripheral blood cells in hepatitis C virus (HCV)-infected patients.
METHODS: This study enrolled two groups of patients aged 40-60 years: a control group and an HCV-infected group in Department of Gastroenterology and Hepatology in Changhua Christian Hospital. Patients with co-infection with hepatitis B virus or human immunodeficiency virus, autoimmune disease, malignant neoplasia, pregnancy, thyroid disease, or alcohol consumption > 40 g/d were excluded. HCV-infected patients who met the following criteria were included: (1) positive HCV antibodies for > 6 mo; (2) alanine aminotransferase (ALT) levels more than twice the upper limit of normal on at least two occasions during the past 6 mo; and (3) histological fibrosis stage higher than F1. The mtDNA copy number and oxidative damage index of HCV mtDNA (mtDNA∆CT) were measured in peripheral blood leukocytes. The association between mtDNA copy number and mtDNA∆CT was further analyzed using clinical data.
RESULTS: Forty-seven normal controls (male/female: 26/21, mean age 50.51 ± 6.15 years) and 132 HCV-infected patients (male/female: 76/61, mean age 51.65 ± 5.50 years) were included in the study. The genotypes of HCV-infected patients include type 1a (n = 3), type 1b (n = 83), type 2a (n = 32), and type 2b (n = 14). Liver fibrosis stages were distributed as follows: F1/F2/F3/F4 = 1/61/45/25 and activity scores were A0/A1/A2/A3 = 7/45/55/25. There were no age or gender differences between the two groups. HCV-infected patients had higher hepatitis activity (aspartate transaminase levels 108.77 ± 60.73 vs 23.19 ± 5.47, P < 0.01; ALT levels 168.69 ± 93.12 vs 23.15 ± 9.45, P < 0.01) and lower platelet count (170.40 ± 58.00 vs 251.24 ± 63.42, P < 0.01) than controls. The mtDNA copy number was lower in HCV-infected patients than in controls (173.49 vs 247.93, P < 0.05). The mtDNA∆CT was higher in HCV-infected patients than in controls (2.92 vs 0.64, P < 0.05). To clarify the clinical significance of these results in HCV-infected patients, their association with different clinical parameters among HCV-infected patients was analyzed. A negative association was found between mtDNA copy number and elevated aspartate transaminase levels (r = -0.17, P < 0.05). Changes in mtDNA copy number were not associated with HCV RNA levels, HCV genotypes, liver fibrosis severity, or inflammatory activity in the liver biopsy specimen. However, a correlation was observed between mtDNA∆CT and platelet count (r = -0.22, P < 0.01), HCV RNA level (r = 0.36, P < 0.01), and hepatitis activity (r = 0.20, P = 0.02). However, no difference in the change in mtDNA∆CT was observed between different fibrosis stages or HCV genotypes.
CONCLUSION: Oxidative stress and mtDNA damage are detectable in patient’s peripheral leukocytes. Increased leukocyte mtDNA∆CT correlates with higher HCV viremia, increased hepatitis activity, and lower platelet count.
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P450-based porous silicon biosensor for arachidonic acid detection. Biosens Bioelectron 2011; 28:320-5. [DOI: 10.1016/j.bios.2011.07.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 07/17/2011] [Indexed: 12/19/2022]
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Cui RH, Chen JQ, Sun M, Sun ZZ. Celecoxib inhibits cell growth and up-regulates KAI1/CD82 protein expression in human hepatocellular carcinoma cell line HepG2. Shijie Huaren Xiaohua Zazhi 2011; 19:1336-1341. [DOI: 10.11569/wcjd.v19.i13.1336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the effect of celecoxib on cell proliferation, apoptosis and KAI1/CD82 expression in human hepatocellular carcinoma cell line HepG2.
METHODS: After HepG2 cells were treated with different concentrations of celecoxib (12.5, 25.0, 50.0, 100.0, 200.0 μmol/L), cell proliferation was measured by CCK-8 assay, cell apoptosis was detected by flow cytometry, and the expression of KAI1/CD82 protein was detected by Western blot.
RESULTS: Treatment with celecoxib significantly inhibited the proliferation of HepG2 cells (P < 0.05) in a dose- and time-dependent manner, and the reduced rate of growth of HepG2 cells treated with 200.0 μmol/L celecoxib for 72 h was 69.23%. Treatment with celecoxib induced apoptosis of HepG2 cells in a dose-dependent manner. The apoptosis rates of cells treated with 12.5, 50.0, or 200.0 μmol/L celecoxib for 48 h were significantly higher than that of control cells (18.79% ± 2.37%, 46.94% ± 0.78%, 69.48% ± 0.63% vs 16.72% ± 1.54%, all P < 0.05). Treatment with celecoxib significantly up-regulated the expression of KAI1/CD82 protein in a dose-dependent manner (48 h: 0.394 ± 0.007, 0.886 ± 0.057, 1.099 ± 0.079 vs 0.321 ± 0.020, all P < 0.05).
CONCLUSION: Celecoxib inhibits cell proliferation and induces apoptosis possibly by up-regulating KAI1/CD82 protein expression in human hepatocellular carcinoma cell line HepG2.
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