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  1. Article ; Online: Toll-interacting protein may affect doxorubicin resistance in hepatocellular carcinoma cell lines.

    Demir, Ayse Banu / Baris, Elif / Kaner, Umay Bengi / Alotaibi, Hani / Atabey, Nese / Koc, Ahmet

    Molecular biology reports

    2023  Volume 50, Issue 10, Page(s) 8551–8563

    Abstract: Background: Liver cancer is the third leading cause of cancer-related deaths worldwide, and hepatocellular carcinoma (HCC) is the most common type of liver cancer. Transarterial interventions are among the chemotherapeutic approaches used in hardly ... ...

    Abstract Background: Liver cancer is the third leading cause of cancer-related deaths worldwide, and hepatocellular carcinoma (HCC) is the most common type of liver cancer. Transarterial interventions are among the chemotherapeutic approaches used in hardly operable regions prior to transplantation, and in electrochemotherapy, where doxorubicin is used. However, the efficacy of treatment is affected by resistance mechanisms. Previously, we showed that overexpression of the CUE5 gene results in doxorubicin resistance in Saccharomyces cerevisiae (S. cerevisiae). In this study, the effect of Toll-interacting protein (TOLLIP), the human ortholog of CUE5, on doxorubicin resistance was evaluated in HCC cells to identify its possible role in increasing the efficacy of transarterial interventions.
    Methods and results: The NIH Gene Expression Omnibus (GEO) and Oncomine datasets were analyzed for HCC cell lines with relatively low and high TOLLIP expression, and SNU449 and Hep3B cell lines were chosen, respectively. TOLLIP expression was increased by plasmid transfection and decreased by TOLLIP-siRNA in both cell lines and evaluated by RT-PCR and ELISA. Cell proliferation and viability were examined using xCELLigence and MTT assays after doxorubicin treatment, and growth inhibitory 50 (GI 50) concentrations were evaluated. Doxorubicin GI 50 concentrations decreased approximately 2-folds in both cell lines upon silencing TOLLIP after 48 h of drug treatment.
    Conclusions: Our results showed for the first time that silencing TOLLIP in hepatocellular carcinoma cells may help sensitize these cells to doxorubicin and increase the efficacy of chemotherapeutic regimens where doxorubicin is used.
    MeSH term(s) Humans ; Apoptosis ; Carcinoma, Hepatocellular/drug therapy ; Carcinoma, Hepatocellular/genetics ; Carcinoma, Hepatocellular/metabolism ; Cell Line, Tumor ; Doxorubicin/pharmacology ; Doxorubicin/therapeutic use ; Drug Resistance, Neoplasm/genetics ; Liver Neoplasms/drug therapy ; Liver Neoplasms/genetics ; Liver Neoplasms/metabolism ; Saccharomyces cerevisiae ; Intracellular Signaling Peptides and Proteins/genetics
    Chemical Substances Doxorubicin (80168379AG) ; TOLLIP protein, human ; Intracellular Signaling Peptides and Proteins
    Language English
    Publishing date 2023-08-29
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 186544-4
    ISSN 1573-4978 ; 0301-4851
    ISSN (online) 1573-4978
    ISSN 0301-4851
    DOI 10.1007/s11033-023-08737-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Implications of Possible HBV-Driven Regulation of Gene Expression in Stem Cell-like Subpopulation of Huh-7 Hepatocellular Carcinoma Cell Line.

    Demir, Ayse Banu / Benvenuto, Domenico / Karacicek, Bilge / Erac, Yasemin / Spoto, Silvia / Angeletti, Silvia / Ciccozzi, Massimo / Tosun, Metiner

    Journal of personalized medicine

    2022  Volume 12, Issue 12

    Abstract: Elevated levels of STIM1, an endoplasmic reticulum ... ...

    Abstract Elevated levels of STIM1, an endoplasmic reticulum Ca
    Language English
    Publishing date 2022-12-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm12122065
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Liver Stiffness Is Markedly Decreased After Chronic Hepatitis C Treatment.

    Gulumsek, Erdinc / Sumbul, Hilmi Erdem / Buyuksimsek, Mahmut / Demir, Kubra / Koc, Ayse Selcan / Tas, Adnan / Bulut, Yurdaer / Kara, Banu

    Ultrasound quarterly

    2022  Volume 38, Issue 2, Page(s) 142–148

    Abstract: Aim: The aim of the study was to demonstrate the liver stiffness (LS) change in chronic hepatitis C (CHC) patients obtained by elastography point quantification technique in before and after antiviral treatment (AVT).: Material and methods: This ... ...

    Abstract Aim: The aim of the study was to demonstrate the liver stiffness (LS) change in chronic hepatitis C (CHC) patients obtained by elastography point quantification technique in before and after antiviral treatment (AVT).
    Material and methods: This prospective study included 84 patients diagnosed with CHC who had not previously received treatment for CHC and who had an indication for using direct-acting AVT. Necessary measurements were recorded with noninvasive liver fibrosis (LF) examinations. Posttreatment control of patients was carried out (ombitasvir + paritaprevir + ritonavir) + 3 months after the start of treatment for those treated with dasabuvir and 6 months after the start of treatment for patients treated with sofosbuvir + ribavirin. Liver stiffness changed after AVT is accepted as (Δ-LS), LS before AVT-LS after AVT.
    Results: Basal LS was found to decrease significantly after AVT (8.00 ± 2.56 kPa vs 6.95 ± 2.86 kPa, P < 0.05). Similar aspartate aminotransferase-to-platelet ratio index and platelet number fibrosis 4 indices were observed before and after AVT (P > 0.05). It was observed that Δ-LS value after AVT was lower in patients with Child-Pugh class A cirrhosis than patients without cirrhosis (P < 0.05). In the comparison between Δ-LS value after AVT and LF score determined by liver biopsy, it was seen that the greatest Δ-LS value was in patients with fibrosis score of 3. An independent relationship was found between Δ-LS after AVT and LF score determined by biopsy (P < 0.05).
    Conclusions: The LS value determined by the elastography point quantification technique is more effective than other noninvasive laboratory methods in demonstrating the CHC treatment response in clinical practice.
    MeSH term(s) Antiviral Agents/therapeutic use ; Elasticity Imaging Techniques/methods ; Hepatitis C, Chronic/complications ; Hepatitis C, Chronic/diagnostic imaging ; Hepatitis C, Chronic/drug therapy ; Humans ; Liver/diagnostic imaging ; Liver/pathology ; Liver Cirrhosis/diagnostic imaging ; Prospective Studies
    Chemical Substances Antiviral Agents
    Language English
    Publishing date 2022-06-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 645107-x
    ISSN 1536-0253 ; 0894-8771
    ISSN (online) 1536-0253
    ISSN 0894-8771
    DOI 10.1097/RUQ.0000000000000572
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Analysis of Three Mutations in Italian Strains of SARS-CoV-2: Implications for Pathogenesis.

    Benvenuto, Domenico / Benedetti, Francesca / Demir, Ayse Banu / Ciccozzi, Massimo / Zella, Davide

    Chemotherapy

    2021  Volume 66, Issue 1-2, Page(s) 33–37

    Abstract: Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus initially detected in Wuhan in December 2019, responsible for coronavirus disease 2019 (COVID-19), a respiratory syndrome currently affecting >220 countries ... ...

    Abstract Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus initially detected in Wuhan in December 2019, responsible for coronavirus disease 2019 (COVID-19), a respiratory syndrome currently affecting >220 countries around the world, with >80 million cases registered and >1.8 million deaths.
    Objective: As several vaccines are still being developed and 2 have been approved, it is particularly important to perform evolutionary surveillance to identify mutations potentially affecting vaccine efficacy.
    Methods: DynaMut server has been used to evaluate the impact of the mutation found on SARS-CoV-2 isolates available on GISAID.
    Results: In this article, we analyze whole genomes sequenced from Italian patients, and we report the characterization of 3 mutations, one of which presents in the spike protein.
    Conclusion: The mutations analyzed in this article can be useful to evaluate the evolution of SARS-CoV-2.
    MeSH term(s) COVID-19/diagnosis ; COVID-19/epidemiology ; COVID-19/virology ; Epidemiological Monitoring ; Humans ; Italy/epidemiology ; Mutation ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Spike Glycoprotein, Coronavirus/genetics ; Whole Genome Sequencing/methods
    Chemical Substances Spike Glycoprotein, Coronavirus
    Language English
    Publishing date 2021-03-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 6708-8
    ISSN 1421-9794 ; 0009-3157
    ISSN (online) 1421-9794
    ISSN 0009-3157
    DOI 10.1159/000515342
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Implications of Possible HBV-Driven Regulation of Gene Expression in Stem Cell-like Subpopulation of Huh-7 Hepatocellular Carcinoma Cell Line

    Ayse Banu Demir / Domenico Benvenuto / Bilge Karacicek / Yasemin Erac / Silvia Spoto / Silvia Angeletti / Massimo Ciccozzi / Metiner Tosun

    Journal of Personalized Medicine, Vol 12, Iss 2065, p

    2022  Volume 2065

    Abstract: Elevated levels of STIM1, an endoplasmic reticulum Ca 2+ sensor/buffering protein, appear to be correlated with poor cancer prognosis in which microRNAs are also known to play critical roles. The purpose of this study is to investigate possible HBV ... ...

    Abstract Elevated levels of STIM1, an endoplasmic reticulum Ca 2+ sensor/buffering protein, appear to be correlated with poor cancer prognosis in which microRNAs are also known to play critical roles. The purpose of this study is to investigate possible HBV origins of specific microRNAs we identified in a stem cell-like subpopulation of Huh-7 hepatocellular carcinoma (HCC) cell lines with enhanced STIM1 and/or Orai1 expression that mimicked poor cancer prognosis. Computational strategies including phylogenetic analyses were performed on miRNome data we obtained from an EpCAM- and CD133-expressing Huh-7 HCC stem cell-like subpopulation with enhanced STIM1 and/or Orai1 expression originally cultured in the present work. Results revealed two putative regions in the HBV genome based on the apparent clustering pattern of stem loop sequences of microRNAs, including miR3653. Reciprocal analysis of these regions identified critical human genes, of which their transcripts are among the predicted targets of miR3653, which was increased significantly by STIM1 or Orai1 enhancement. Briefly, this study provides phylogenetic evidence for a possible HBV-driven epigenetic remodeling that alters the expression pattern of Ca 2+ homeostasis-associated genes in STIM1 - or Orai1 overexpressing liver cancer stem-like cells for a possible mutual survival outcome. A novel region on HBV-X protein may affect liver carcinogenesis in a genotype-dependent manner. Therefore, detection of the viral genotype would have a clinical impact on prognosis of HBV-induced liver cancers.
    Keywords hepatocellular carcinoma ; HBx ; miR3653 ; epithelial–mesenchymal transition (EMT) ; molecular evolution ; Medicine ; R
    Subject code 570
    Language English
    Publishing date 2022-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: High-Copy Overexpression Screening Reveals PDR5 as the Main Doxorubicin Resistance Gene in Yeast.

    Ayse Banu Demir / Ahmet Koc

    PLoS ONE, Vol 10, Iss 12, p e

    2015  Volume 0145108

    Abstract: Doxorubicin is one of the most potent anticancer drugs used in the treatment of various cancer types. The efficacy of doxorubicin is influenced by the drug resistance mechanisms and its cytotoxicity. In this study, we performed a high-copy screening ... ...

    Abstract Doxorubicin is one of the most potent anticancer drugs used in the treatment of various cancer types. The efficacy of doxorubicin is influenced by the drug resistance mechanisms and its cytotoxicity. In this study, we performed a high-copy screening analysis to find genes that play a role in doxorubicin resistance and found several genes (CUE5, AKL1, CAN1, YHR177W and PDR5) that provide resistance. Among these genes, overexpression of PDR5 provided a remarkable resistance, and deletion of it significantly rendered the tolerance level for the drug. Q-PCR analyses suggested that transcriptional regulation of these genes was not dependent on doxorubicin treatment. Additionally, we profiled the global expression pattern of cells in response to doxorubicin treatment and highlighted the genes and pathways that are important in doxorubicin tolerance/toxicity. Our results suggest that many efflux pumps and DNA metabolism genes are upregulated by the drug and required for doxorubicin tolerance.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2015-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: High-Copy Overexpression Screening Reveals PDR5 as the Main Doxorubicin Resistance Gene in Yeast.

    Demir, Ayse Banu / Koc, Ahmet

    PloS one

    2015  Volume 10, Issue 12, Page(s) e0145108

    Abstract: Doxorubicin is one of the most potent anticancer drugs used in the treatment of various cancer types. The efficacy of doxorubicin is influenced by the drug resistance mechanisms and its cytotoxicity. In this study, we performed a high-copy screening ... ...

    Abstract Doxorubicin is one of the most potent anticancer drugs used in the treatment of various cancer types. The efficacy of doxorubicin is influenced by the drug resistance mechanisms and its cytotoxicity. In this study, we performed a high-copy screening analysis to find genes that play a role in doxorubicin resistance and found several genes (CUE5, AKL1, CAN1, YHR177W and PDR5) that provide resistance. Among these genes, overexpression of PDR5 provided a remarkable resistance, and deletion of it significantly rendered the tolerance level for the drug. Q-PCR analyses suggested that transcriptional regulation of these genes was not dependent on doxorubicin treatment. Additionally, we profiled the global expression pattern of cells in response to doxorubicin treatment and highlighted the genes and pathways that are important in doxorubicin tolerance/toxicity. Our results suggest that many efflux pumps and DNA metabolism genes are upregulated by the drug and required for doxorubicin tolerance.
    MeSH term(s) ATP-Binding Cassette Transporters/biosynthesis ; ATP-Binding Cassette Transporters/genetics ; Doxorubicin/pharmacology ; Drug Resistance, Fungal/physiology ; Gene Expression Regulation, Fungal/drug effects ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/biosynthesis ; Saccharomyces cerevisiae Proteins/genetics
    Chemical Substances PDR5 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Doxorubicin (80168379AG)
    Language English
    Publishing date 2015
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1932-6203
    ISSN (online) 1932-6203
    DOI 10.1371/journal.pone.0145108
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Linking Peroxiredoxin and Vacuolar-ATPase Functions in Calorie Restriction-Mediated Life Span Extension.

    Molin, Mikael / Demir, Ayse Banu

    International journal of cell biology

    2014  Volume 2014, Page(s) 913071

    Abstract: Calorie restriction (CR) is an intervention extending the life spans of many organisms. The mechanisms underlying CR-dependent retardation of aging are still poorly understood. Despite mechanisms involving conserved nutrient signaling pathways proposed, ... ...

    Abstract Calorie restriction (CR) is an intervention extending the life spans of many organisms. The mechanisms underlying CR-dependent retardation of aging are still poorly understood. Despite mechanisms involving conserved nutrient signaling pathways proposed, few target processes that can account for CR-mediated longevity have so far been identified. Recently, both peroxiredoxins and vacuolar-ATPases were reported to control CR-mediated retardation of aging downstream of conserved nutrient signaling pathways. In this review, we focus on peroxiredoxin-mediated stress-defence and vacuolar-ATPase regulated acidification and pinpoint common denominators between the two mechanisms proposed for how CR extends life span. Both the activities of peroxiredoxins and vacuolar-ATPases are stimulated upon CR through reduced activities in conserved nutrient signaling pathways and both seem to stimulate cellular resistance to peroxide-stress. However, whereas vacuolar-ATPases have recently been suggested to control both Ras-cAMP-PKA- and TORC1-mediated nutrient signaling, neither the physiological benefits of a proposed role for peroxiredoxins in H2O2-signaling nor downstream targets regulated are known. Both peroxiredoxins and vacuolar-ATPases do, however, impinge on mitochondrial iron-metabolism and further characterization of their impact on iron homeostasis and peroxide-resistance might therefore increase our understanding of the beneficial effects of CR on aging and age-related diseases.
    Language English
    Publishing date 2014-02-03
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2536742-0
    ISSN 1687-8884 ; 1687-8876
    ISSN (online) 1687-8884
    ISSN 1687-8876
    DOI 10.1155/2014/913071
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Evidence for mutations in SARS-CoV-2 Italian isolates potentially affecting virus transmission.

    Benvenuto, Domenico / Demir, Ayse Banu / Giovanetti, Marta / Bianchi, Martina / Angeletti, Silvia / Pascarella, Stefano / Cauda, Roberto / Ciccozzi, Massimo / Cassone, Antonio

    Journal of medical virology

    2020  Volume 92, Issue 10, Page(s) 2232–2237

    Abstract: Italy is the first western country suffering heavy severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and disease impact after coronavirus disease-2019 pandemia started in China. Even though the presence of mutations on spike ... ...

    Abstract Italy is the first western country suffering heavy severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and disease impact after coronavirus disease-2019 pandemia started in China. Even though the presence of mutations on spike glycoprotein and nucleocapsid in Italian isolates has been reported, the potential impact of these mutations on viral transmission has not been evaluated. We have compared SARS-CoV-2 genome sequences from Italian patients with virus sequences from Chinese patients. We focussed upon three nonsynonymous mutations of genes coding for S(one) and N (two) viral proteins present in Italian isolates and absent in Chinese ones, using various bioinformatics tools. Amino acid analysis and changes in three-dimensional protein structure suggests the mutations reduce protein stability and, particularly for S1 mutation, the enhanced torsional ability of the molecule could favor virus binding to cell receptor(s). This theoretical interpretation awaits experimental and clinical confirmation.
    MeSH term(s) Amino Acid Substitution ; COVID-19/epidemiology ; COVID-19/pathology ; COVID-19/transmission ; COVID-19/virology ; China/epidemiology ; Coronavirus Nucleocapsid Proteins/chemistry ; Coronavirus Nucleocapsid Proteins/genetics ; Evolution, Molecular ; Genome, Viral ; Humans ; Italy/epidemiology ; Models, Molecular ; Molecular Epidemiology ; Mutation ; Pandemics ; Phosphoproteins/chemistry ; Phosphoproteins/genetics ; Phylogeny ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; Severity of Illness Index ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Travel ; Virus Replication
    Chemical Substances Coronavirus Nucleocapsid Proteins ; Phosphoproteins ; Spike Glycoprotein, Coronavirus ; nucleocapsid phosphoprotein, SARS-CoV-2 ; spike protein, SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-06-19
    Publishing country United States
    Document type Journal Article
    ZDB-ID 752392-0
    ISSN 1096-9071 ; 0146-6615
    ISSN (online) 1096-9071
    ISSN 0146-6615
    DOI 10.1002/jmv.26104
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Evidence for Mutations in SARS-CoV-2 Italian Isolates Potentially Affecting Virus Transmission

    Benvenuto, Domenico / Demir, Ayse Banu / Giovanetti, Marta / Bianchi, Martina / Angeletti, Silvia / Pascarella, Stefano / Cauda, Roberto / Ciccozzi, Massimo / Cassone, Antonio

    SSRN Electronic Journal ; ISSN 1556-5068

    2020  

    Keywords covid19
    Language English
    Publisher Elsevier BV
    Publishing country us
    Document type Article ; Online
    DOI 10.2139/ssrn.3596454
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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