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  1. Article ; Online: Identification of DNA Damage Repair-Associated Prognostic Biomarkers for Prostate Cancer Using Transcriptomic Data Analysis.

    Teng, Pai-Chi / Huang, Shu-Pin / Liu, Chia-Hsin / Lin, Ting-Yi / Cho, Yi-Chun / Lai, Yo-Liang / Wang, Shu-Chi / Yeh, Hsin-Chih / Chuu, Chih-Pin / Chen, Deng-Neng / Cheng, Wei-Chung / Li, Chia-Yang

    International journal of molecular sciences

    2021  Volume 22, Issue 21

    Abstract: In the recent decade, the importance of DNA damage repair (DDR) and its clinical application have been firmly recognized in prostate cancer (PC). For example, olaparib was just approved in May 2020 to treat metastatic castration-resistant PC with ... ...

    Abstract In the recent decade, the importance of DNA damage repair (DDR) and its clinical application have been firmly recognized in prostate cancer (PC). For example, olaparib was just approved in May 2020 to treat metastatic castration-resistant PC with homologous recombination repair-mutated genes; however, not all patients can benefit from olaparib, and the treatment response depends on patient-specific mutations. This highlights the need to understand the detailed DDR biology further and develop DDR-based biomarkers. In this study, we establish a four-gene panel of which the expression is significantly associated with overall survival (OS) and progression-free survival (PFS) in PC patients from the TCGA-PRAD database. This panel includes
    MeSH term(s) Biomarkers, Tumor/genetics ; DNA Damage ; DNA Repair ; Gene Expression Profiling ; Humans ; Male ; Mutation ; Prognosis ; Prostatic Neoplasms/diagnosis ; Prostatic Neoplasms/genetics ; Transcriptome
    Chemical Substances Biomarkers, Tumor
    Language English
    Publishing date 2021-10-29
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms222111771
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: LipidSig: a web-based tool for lipidomic data analysis.

    Lin, Wen-Jen / Shen, Pei-Chun / Liu, Hsiu-Cheng / Cho, Yi-Chun / Hsu, Min-Kung / Lin, I-Chen / Chen, Fang-Hsin / Yang, Juan-Cheng / Ma, Wen-Lung / Cheng, Wei-Chung

    Nucleic acids research

    2021  Volume 49, Issue W1, Page(s) W336–W345

    Abstract: With the continuing rise of lipidomic studies, there is an urgent need for a useful and comprehensive tool to facilitate lipidomic data analysis. The most important features making lipids different from general metabolites are their various ... ...

    Abstract With the continuing rise of lipidomic studies, there is an urgent need for a useful and comprehensive tool to facilitate lipidomic data analysis. The most important features making lipids different from general metabolites are their various characteristics, including their lipid classes, double bonds, chain lengths, etc. Based on these characteristics, lipid species can be classified into different categories and, more interestingly, exert specific biological functions in a group. In an effort to simplify lipidomic analysis workflows and enhance the exploration of lipid characteristics, we have developed a highly flexible and user-friendly web server called LipidSig. It consists of five sections, namely, Profiling, Differential Expression, Correlation, Network and Machine Learning, and evaluates lipid effects on cellular or disease phenotypes. One of the specialties of LipidSig is the conversion between lipid species and characteristics according to a user-defined characteristics table. This function allows for efficient data mining for both individual lipids and subgroups of characteristics. To expand the server's practical utility, we also provide analyses focusing on fatty acid properties and multiple characteristics. In summary, LipidSig is expected to help users identify significant lipid-related features and to advance the field of lipid biology. The LipidSig webserver is freely available at http://chenglab.cmu.edu.tw/lipidsig.
    MeSH term(s) Animals ; Biomarkers ; Data Mining ; Fatty Acids/chemistry ; Ferroptosis ; Internet ; Lipid Metabolism ; Lipidomics/methods ; Lipids/chemistry ; Machine Learning ; Mice ; Neoplasms/metabolism ; Software
    Chemical Substances Biomarkers ; Fatty Acids ; Lipids
    Language English
    Publishing date 2021-05-28
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab419
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  3. Article: Identification of a Steroid Hormone-Associated Gene Signature Predicting the Prognosis of Prostate Cancer through an Integrative Bioinformatics Analysis.

    Lai, Yo-Liang / Liu, Chia-Hsin / Wang, Shu-Chi / Huang, Shu-Pin / Cho, Yi-Chun / Bao, Bo-Ying / Su, Chia-Cheng / Yeh, Hsin-Chih / Lee, Cheng-Hsueh / Teng, Pai-Chi / Chuu, Chih-Pin / Chen, Deng-Neng / Li, Chia-Yang / Cheng, Wei-Chung

    Cancers

    2022  Volume 14, Issue 6

    Abstract: The importance of anti-androgen therapy for prostate cancer (PC) has been well recognized. However, the mechanisms underlying prostate cancer resistance to anti-androgens are not completely understood. Therefore, identifying pharmacological targets in ... ...

    Abstract The importance of anti-androgen therapy for prostate cancer (PC) has been well recognized. However, the mechanisms underlying prostate cancer resistance to anti-androgens are not completely understood. Therefore, identifying pharmacological targets in driving the development of castration-resistant PC is necessary. In the present study, we sought to identify core genes in regulating steroid hormone pathways and associating them with the disease progression of PC. The selection of steroid hormone-associated genes was identified from functional databases, including gene ontology, KEGG, and Reactome. The gene expression profiles and relevant clinical information of patients with PC were obtained from TCGA and used to examine the genes associated with steroid hormone. The machine-learning algorithm was performed for key feature selection and signature construction. With the integrative bioinformatics analysis, an eight-gene signature, including
    Language English
    Publishing date 2022-03-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers14061565
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Using bioinformatics approaches to identify survival-related oncomiRs as potential targets of miRNA-based treatments for lung adenocarcinoma.

    Liu, Chia-Hsin / Liu, Shu-Hsuan / Lai, Yo-Liang / Cho, Yi-Chun / Chen, Fang-Hsin / Lin, Li-Jie / Peng, Pei-Hua / Li, Chia-Yang / Wang, Shu-Chi / Chen, Ji-Lin / Wu, Heng-Hsiung / Wu, Min-Zu / Sher, Yuh-Pyng / Cheng, Wei-Chung / Hsu, Kai-Wen

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 4626–4635

    Abstract: Lung cancer is a major cause of cancer-associated deaths worldwide, and lung adenocarcinoma (LUAD) is the most common lung cancer subtype. Micro RNAs (miRNAs) regulate the pattern of gene expression in multiple cancer types and have been explored as ... ...

    Abstract Lung cancer is a major cause of cancer-associated deaths worldwide, and lung adenocarcinoma (LUAD) is the most common lung cancer subtype. Micro RNAs (miRNAs) regulate the pattern of gene expression in multiple cancer types and have been explored as potential drug development targets. To develop an oncomiR-based panel, we identified miRNA candidates that show differential expression patterns and are relevant to the worse 5-year overall survival outcomes in LUAD patient samples. We further evaluated various combinations of miRNA candidates for association with 5-year overall survival and identified a four-miRNA panel: miR-9-5p, miR-1246, miR-31-3p, and miR-3136-5p. The combination of these four miRNAs outperformed any single miRNA for predicting 5-year overall survival (hazard ratio [HR]: 3.47, log-rank p-value = 0.000271). Experiments were performed on lung cancer cell lines and animal models to validate the effects of these miRNAs. The results showed that singly transfected antagomiRs largely inhibited cell growth, migration, and invasion, and the combination of all four antagomiRs considerably reduced cell numbers, which is twice as effective as any single miRNA-targeted transfected. The
    Language English
    Publishing date 2022-08-22
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.08.042
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Using bioinformatics approaches to identify survival-related oncomiRs as potential targets of miRNA-based treatments for lung adenocarcinoma

    Liu, Chia-Hsin / Liu, Shu-Hsuan / Lai, Yo-Liang / Cho, Yi-Chun / Chen, Fang-Hsin / Lin, Li-Jie / Peng, Pei-Hua / Li, Chia-Yang / Wang, Shu-Chi / Chen, Ji-Lin / Wu, Heng-Hsiung / Wu, Min-Zu / Sher, Yuh-Pyng / Cheng, Wei-Chung / Hsu, Kai-Wen

    Computational and Structural Biotechnology Journal. 2022, v. 20

    2022  

    Abstract: Lung cancer is a major cause of cancer-associated deaths worldwide, and lung adenocarcinoma (LUAD) is the most common lung cancer subtype. Micro RNAs (miRNAs) regulate the pattern of gene expression in multiple cancer types and have been explored as ... ...

    Abstract Lung cancer is a major cause of cancer-associated deaths worldwide, and lung adenocarcinoma (LUAD) is the most common lung cancer subtype. Micro RNAs (miRNAs) regulate the pattern of gene expression in multiple cancer types and have been explored as potential drug development targets. To develop an oncomiR-based panel, we identified miRNA candidates that show differential expression patterns and are relevant to the worse 5-year overall survival outcomes in LUAD patient samples. We further evaluated various combinations of miRNA candidates for association with 5-year overall survival and identified a four-miRNA panel: miR-9-5p, miR-1246, miR-31-3p, and miR-3136-5p. The combination of these four miRNAs outperformed any single miRNA for predicting 5-year overall survival (hazard ratio [HR]: 3.47, log-rank p-value = 0.000271). Experiments were performed on lung cancer cell lines and animal models to validate the effects of these miRNAs. The results showed that singly transfected antagomiRs largely inhibited cell growth, migration, and invasion, and the combination of all four antagomiRs considerably reduced cell numbers, which is twice as effective as any single miRNA-targeted transfected. The in vivo studies revealed that antagomiR-mediated knockdown of all four miRNAs significantly reduced tumor growth and metastatic ability of lung cancer cells compared to the negative control group. The success of these in vivo and in vitro experiments suggested that these four identified oncomiRs may have therapeutic potential.
    Keywords adenocarcinoma ; animals ; bioinformatics ; biotechnology ; cell growth ; drug development ; gene expression ; gene expression regulation ; hazard ratio ; lung neoplasms ; lungs ; metastasis ; microRNA ; neoplasm cells ; patients ; therapeutics
    Language English
    Size p. 4626-4635.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.08.042
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: DriverDBv3: a multi-omics database for cancer driver gene research.

    Liu, Shu-Hsuan / Shen, Pei-Chun / Chen, Chen-Yang / Hsu, An-Ni / Cho, Yi-Chun / Lai, Yo-Liang / Chen, Fang-Hsin / Li, Chia-Yang / Wang, Shu-Chi / Chen, Ming / Chung, I-Fang / Cheng, Wei-Chung

    Nucleic acids research

    2019  Volume 48, Issue D1, Page(s) D863–D870

    Abstract: An integrative multi-omics database is needed urgently, because focusing only on analysis of one-dimensional data falls far short of providing an understanding of cancer. Previously, we presented DriverDB, a cancer driver gene database that applies ... ...

    Abstract An integrative multi-omics database is needed urgently, because focusing only on analysis of one-dimensional data falls far short of providing an understanding of cancer. Previously, we presented DriverDB, a cancer driver gene database that applies published bioinformatics algorithms to identify driver genes/mutations. The updated DriverDBv3 database (http://ngs.ym.edu.tw/driverdb) is designed to interpret cancer omics' sophisticated information with concise data visualization. To offer diverse insights into molecular dysregulation/dysfunction events, we incorporated computational tools to define CNV and methylation drivers. Further, four new features, CNV, Methylation, Survival, and miRNA, allow users to explore the relations from two perspectives in the 'Cancer' and 'Gene' sections. The 'Survival' panel offers not only significant survival genes, but gene pairs synergistic effects determine. A fresh function, 'Survival Analysis' in 'Customized-analysis,' allows users to investigate the co-occurring events in user-defined gene(s) by mutation status or by expression in a specific patient group. Moreover, we redesigned the web interface and provided interactive figures to interpret cancer omics' sophisticated information, and also constructed a Summary panel in the 'Cancer' and 'Gene' sections to visualize the features on multi-omics levels concisely. DriverDBv3 seeks to improve the study of integrative cancer omics data by identifying driver genes and contributes to cancer biology.
    MeSH term(s) DNA Copy Number Variations/genetics ; Databases, Genetic ; Epigenesis, Genetic/genetics ; Gene Expression Profiling ; Humans ; Internet ; Neoplasms/genetics ; Oncogenes/genetics ; Software
    Language English
    Publishing date 2019-11-07
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkz964
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  7. Article ; Online: Evading immune surveillance via tyrosine phosphorylation of nuclear PCNA.

    Wang, Yuan-Liang / Lee, Chuan-Chun / Shen, Yi-Chun / Lin, Pei-Le / Wu, Wan-Rong / Lin, You-Zhe / Cheng, Wei-Chung / Chang, Han / Hung, Yu / Cho, Yi-Chun / Liu, Liang-Chih / Xia, Wei-Ya / Ji, Jin-Huei / Liang, Ji-An / Chiang, Shu-Fen / Liu, Chang-Gong / Yao, Jun / Hung, Mien-Chie / Wang, Shao-Chun

    Cell reports

    2021  Volume 36, Issue 8, Page(s) 109537

    Abstract: Increased DNA replication and metastasis are hallmarks of cancer progression, while deregulated proliferation often triggers sustained replication stresses in cancer cells. How cancer cells overcome the growth stress and proceed to metastasis remains ... ...

    Abstract Increased DNA replication and metastasis are hallmarks of cancer progression, while deregulated proliferation often triggers sustained replication stresses in cancer cells. How cancer cells overcome the growth stress and proceed to metastasis remains largely elusive. Proliferating cell nuclear antigen (PCNA) is an indispensable component of the DNA replication machinery. Here, we show that phosphorylation of PCNA on tyrosine 211 (pY211-PCNA) regulates DNA metabolism and tumor microenvironment. Abrogation of pY211-PCNA blocks fork processivity, resulting in biogenesis of single-stranded DNA (ssDNA) through a MRE11-dependent mechanism. The cytosolic ssDNA subsequently induces inflammatory cytokines through a cyclic GMP-AMP synthetase (cGAS)-dependent cascade, triggering an anti-tumor immunity by natural killer (NK) cells to suppress distant metastasis. Expression of pY211-PCNA is inversely correlated with cytosolic ssDNA and associated with poor survival in patients with cancer. Our results pave the way to biomarkers and therapies exploiting immune responsiveness to target metastatic cancer.
    MeSH term(s) Animals ; Female ; Humans ; MCF-7 Cells ; Mice ; Mice, Transgenic ; Neoplasms, Experimental/genetics ; Neoplasms, Experimental/immunology ; Neoplasms, Experimental/mortality ; Phosphorylation ; Proliferating Cell Nuclear Antigen/genetics ; Proliferating Cell Nuclear Antigen/immunology ; Tumor Escape ; Tumor Microenvironment/genetics ; Tumor Microenvironment/immunology ; Tyrosine/genetics ; Tyrosine/immunology
    Chemical Substances PCNA protein, human ; Proliferating Cell Nuclear Antigen ; Tyrosine (42HK56048U)
    Language English
    Publishing date 2021-08-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2021.109537
    Database MEDical Literature Analysis and Retrieval System OnLINE

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