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  1. Article ; Online: Identification of DNA methylation biomarkers for evaluating cardiovascular disease risk from epigenome profiles altered by low-dose ionizing radiation.

    Park, Jihye / Lee, Hae-June / Han, Yu Kyeong / Kang, Keunsoo / Yi, Joo Mi

    Clinical epigenetics

    2024  Volume 16, Issue 1, Page(s) 19

    Abstract: Background: Environmental exposure, medical diagnostic and therapeutic applications, and industrial utilization of radionuclides have prompted a growing focus on the risks associated with low-dose radiation (< 100 mGy). Current evidence suggests that ... ...

    Abstract Background: Environmental exposure, medical diagnostic and therapeutic applications, and industrial utilization of radionuclides have prompted a growing focus on the risks associated with low-dose radiation (< 100 mGy). Current evidence suggests that such radiation can induce epigenetic changes. Nevertheless, whether exposure to low-dose radiation can disrupt endothelial cell function at the molecular level is unclear. Because endothelial cells play crucial roles in cardiovascular health and disease, we aimed to investigate whether low-dose radiation could lead to differential DNA methylation patterns at the genomic level in endothelial cell (EC) lines.
    Methods: We screened for changes in DNA methylation patterns in primary human aortic (HAECs) and coronary artery endothelial cells following exposure to low-dose ionizing radiation. Using a subset of genes altered via DNA methylation by low-dose irradiation, we performed gene ontology (GO) analysis to predict the possible biological network mediating the effect of low-dose radiation. In addition, we performed comprehensive validation using methylation and gene expression analyses, and ChIP assay to identify useful biomarkers among candidate genes for use in detecting low-dose radiation exposure in human primary normal ECs.
    Results: Low-dose radiation is sufficient to induce global DNA methylation alterations in normal EC lines. GO analysis demonstrated that these hyper- or hypo-methylated genes were linked to diverse biological pathways. Our findings indicated a robust correlation between promoter hypermethylation and transcriptional downregulation of four genes (PGRMC1, UNC119B, RERE, and FNDC3B) in response to low-dose ionizing radiation in HAECs.
    Conclusions: Based on these findings, the identified genes can serve as potential DNA methylation biomarkers for the assessment of cardiovascular risk upon exposure to low-dose radiation.
    MeSH term(s) Humans ; DNA Methylation ; Epigenome ; Endothelial Cells ; Cardiovascular Diseases/genetics ; Biomarkers ; Radiation, Ionizing ; Membrane Proteins/genetics ; Receptors, Progesterone/genetics
    Chemical Substances Biomarkers ; PGRMC1 protein, human ; Membrane Proteins ; Receptors, Progesterone
    Language English
    Publishing date 2024-02-01
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553921-8
    ISSN 1868-7083 ; 1868-7075
    ISSN (online) 1868-7083
    ISSN 1868-7075
    DOI 10.1186/s13148-024-01630-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Activation of OSM-STAT3 Epigenetically Regulates Tumor-Promoting Transcriptional Programs in Cervical Cancer.

    Noh, Junho / You, Chaelin / Kang, Keunsoo / Kang, Kyuho

    Cancers

    2022  Volume 14, Issue 24

    Abstract: Despite improvements in preventative strategies, such as regular screenings with Pap tests and human papillomavirus (HPV) tests as well as HPV vaccinations, effective treatment for advanced cervical cancer remains poor. Deregulation of STAT3 is an ... ...

    Abstract Despite improvements in preventative strategies, such as regular screenings with Pap tests and human papillomavirus (HPV) tests as well as HPV vaccinations, effective treatment for advanced cervical cancer remains poor. Deregulation of STAT3 is an oncogenic factor that promotes tumorigenesis and epithelial-to-mesenchymal transition (EMT) in various cancers. Oncostatin M (OSM), a pleiotropic cytokine, induces STAT3 activation, exacerbating cervical cancer. However, the mechanism by which the OSM-STAT3 axis epigenetically regulates tumor-progression-related genes in cervical cancer is not well understood. Here, we show that OSM-mediated STAT3 activation promotes pro-tumorigenic gene expression programs, with chromatin remodeling in cervical cancer. Reanalysis of scRNA-seq data performed in cervical cancer uncovered an interaction between the oncostatin M receptor (OSMR) on tumor cells and OSM induced by tumor-associated macrophages (TAMs). Our gene expression profiling (bulk RNA-seq) shows that OSM-induced genes were involved in hypoxia, wound healing, and angiogenesis, which were significantly inhibited by SD-36, a STAT3-selective degrader. Additionally, ATAC-seq experiments revealed that STAT3 binding motifs were preferentially enriched in open chromatin regions of the OSM-STAT3-regulated genes. Among the 50 candidate genes that were regulated epigenetically through the OSM-STAT3 axis, we found that the expression levels of
    Language English
    Publishing date 2022-12-10
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers14246090
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Corrigendum to: RNA Editing Enzyme ADAR1 Suppresses the Mobility of Cancer Cells via ARPIN.

    Park, Min Ji / Jeong, Eunji / Lee, Eun Ji / Choi, Hyeon Ji / Moon, Bo Hyun / Kang, Keunsoo / Chang, Suhwan

    Molecules and cells

    2023  Volume 46, Issue 11, Page(s) 725

    Language English
    Publishing date 2023-11-03
    Publishing country United States
    Document type Corrected and Republished Article
    ZDB-ID 1148964-9
    ISSN 0219-1032 ; 1016-8478
    ISSN (online) 0219-1032
    ISSN 1016-8478
    DOI 10.14348/molcells.2023.2174.e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing.

    Lee, Joongho / Kim, Minsoo / Kang, Keunsoo / Yang, Chul-Su / Yoon, Seokhyun

    Briefings in bioinformatics

    2023  Volume 24, Issue 2

    Abstract: Single-cell RNA-seq enabled in-depth study on tissue micro-environment and immune-profiling, where a crucial step is to annotate cell identity. Immune cells play key roles in many diseases, whereas their activities are hard to track due to their diverse ... ...

    Abstract Single-cell RNA-seq enabled in-depth study on tissue micro-environment and immune-profiling, where a crucial step is to annotate cell identity. Immune cells play key roles in many diseases, whereas their activities are hard to track due to their diverse and highly variable nature. Existing cell-type identifiers had limited performance for this purpose. We present HiCAT, a hierarchical, marker-based cell-type identifier utilising gene set analysis for statistical scoring for given markers. It features successive identification of major-type, minor-type and subsets utilising subset markers structured in a three-level taxonomy tree. Comparison with manual annotation and pairwise match test showed HiCAT outperforms others in major- and minor-type identification. For subsets, we qualitatively evaluated the marker expression profile demonstrating that HiCAT provide the clearest immune-cell landscape. HiCAT was also used for immune-cell profiling in ulcerative colitis and discovered distinct features of the disease in macrophage and T-cell subsets that could not be identified previously.
    MeSH term(s) Gene Expression Profiling ; Macrophages ; RNA
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-01-18
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2068142-2
    ISSN 1477-4054 ; 1467-5463
    ISSN (online) 1477-4054
    ISSN 1467-5463
    DOI 10.1093/bib/bbad006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: MarkerCount: A stable, count-based cell type identifier for single-cell RNA-seq experiments.

    Kim, HanByeol / Lee, Joongho / Kang, Keunsoo / Yoon, Seokhyun

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 3120–3132

    Abstract: Cell type identification is a key step toward downstream analysis of single cell RNA-seq experiments. Although the primary objective is to identify known cell populations, good identifiers should also recognize unknown clusters which may represent a ... ...

    Abstract Cell type identification is a key step toward downstream analysis of single cell RNA-seq experiments. Although the primary objective is to identify known cell populations, good identifiers should also recognize unknown clusters which may represent a previously unidentified subpopulation of a known cell type or tumor cells of an unknown phenotype. Herein, we present MarkerCount, which utilizes the number of expressed markers, regardless of their expression level. MarkerCount works in both reference- and marker-based mode, where the latter utilizes existing lists of markers, while the former uses a pre-annotated dataset to find markers to be used for cell type identification. In both modes, MarkerCount first utilizes the "marker count" to identify cell populations and, after rejecting uncertain cells, reassigns cell type and/or makes corrections in cluster-basis. The performance of MarkerCount was evaluated and compared with existing identifiers, both marker- and reference-based, that can be customized using publicly available datasets and marker databases. The results show that MarkerCount performs better in the identification of known populations as well as of unknown ones, when compared to other reference- and marker-based cell type identifiers for most of the datasets analyzed.
    Language English
    Publishing date 2022-06-14
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.06.010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Developmental self-reactivity determines pathogenic Tc17 differentiation potential of naive CD8

    Lee, Gil-Woo / Kim, Young Ju / Lee, Sung-Woo / Kim, Hee-Ok / Kim, Daeun / Kim, Jiyoung / Kim, You-Me / Kang, Keunsoo / Rhee, Joon Haeng / Chung, Ik Joo / Bae, Woo Kyun / Oh, In-Jae / Yang, Deok Hwan / Cho, Jae-Ho

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2919

    Abstract: The differentiation of naive ... ...

    Abstract The differentiation of naive CD8
    MeSH term(s) Mice ; Animals ; CD8-Positive T-Lymphocytes ; Disease Models, Animal ; Cell Differentiation ; Inflammation/pathology ; Receptors, Antigen, T-Cell/metabolism
    Chemical Substances Receptors, Antigen, T-Cell
    Language English
    Publishing date 2024-04-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47144-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Integrative Transcriptome Profiling Reveals

    You, Chaelin / Piao, Xuan-Mei / Kang, Keunsoo / Kim, Yong-June / Kang, Kyuho

    Cancers

    2021  Volume 13, Issue 18

    Abstract: Approximately 80% of all new bladder cancer patients are diagnosed with non-muscle invasive bladder cancer (NMIBC). However, approximately 15% of them progress to muscle-invasive bladder cancer (MIBC), for which prognosis is poor. The current study aimed ...

    Abstract Approximately 80% of all new bladder cancer patients are diagnosed with non-muscle invasive bladder cancer (NMIBC). However, approximately 15% of them progress to muscle-invasive bladder cancer (MIBC), for which prognosis is poor. The current study aimed to improve diagnostic accuracy associated with clinical outcomes in NMIBC patients. Nevertheless, it has been challenging to identify molecular biomarkers that accurately predict MIBC progression because this disease is complex and heterogeneous. Through integrative transcriptome profiling, we showed that high
    Language English
    Publishing date 2021-09-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527080-1
    ISSN 2072-6694
    ISSN 2072-6694
    DOI 10.3390/cancers13184673
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Integrative mapping of the dog epigenome: Reference annotation for comparative intertissue and cross-species studies.

    Son, Keun Hong / Aldonza, Mark Borris D / Nam, A-Reum / Lee, Kang-Hoon / Lee, Jeong-Woon / Shin, Kyung-Ju / Kang, Keunsoo / Cho, Je-Yoel

    Science advances

    2023  Volume 9, Issue 27, Page(s) eade3399

    Abstract: Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. ...

    Abstract Dogs have become a valuable model in exploring multifaceted diseases and biology relevant to human health. Despite large-scale dog genome projects producing high-quality draft references, a comprehensive annotation of functional elements is still lacking. We addressed this through integrative next-generation sequencing of transcriptomes paired with five histone marks and DNA methylome profiling across 11 tissue types, deciphering the dog's epigenetic code by defining distinct chromatin states, super-enhancer, and methylome landscapes, and thus showed that these regions are associated with a wide range of biological functions and cell/tissue identity. In addition, we confirmed that the phenotype-associated variants are enriched in tissue-specific regulatory regions and, therefore, the tissue of origin of the variants can be traced. Ultimately, we delineated conserved and dynamic epigenomic changes at the tissue- and species-specific resolutions. Our study provides an epigenomic blueprint of the dog that can be used for comparative biology and medical research.
    MeSH term(s) Animals ; Dogs ; Chromatin/genetics ; Epigenesis, Genetic ; Epigenome ; Epigenomics ; Genome ; Histone Code ; Regulatory Sequences, Nucleic Acid
    Chemical Substances Chromatin
    Language English
    Publishing date 2023-07-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2810933-8
    ISSN 2375-2548 ; 2375-2548
    ISSN (online) 2375-2548
    ISSN 2375-2548
    DOI 10.1126/sciadv.ade3399
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A Brief Review of Machine Learning-Based Bioactive Compound Research

    Jihye Park / Bo Ram Beck / Hoo Hyun Kim / Sangbum Lee / Keunsoo Kang

    Applied Sciences, Vol 12, Iss 2906, p

    2022  Volume 2906

    Abstract: Bioactive compounds are often used as initial substances for many therapeutic agents. In recent years, both theoretical and practical innovations in hardware-assisted and fast-evolving machine learning (ML) have made it possible to identify desired ... ...

    Abstract Bioactive compounds are often used as initial substances for many therapeutic agents. In recent years, both theoretical and practical innovations in hardware-assisted and fast-evolving machine learning (ML) have made it possible to identify desired bioactive compounds in chemical spaces, such as those in natural products (NPs). This review introduces how machine learning approaches can be used for the identification and evaluation of bioactive compounds. It also provides an overview of recent research trends in machine learning-based prediction and the evaluation of bioactive compounds by listing real-world examples along with various input data. In addition, several ML-based approaches to identify specific bioactive compounds for cardiovascular and metabolic diseases are described. Overall, these approaches are important for the discovery of novel bioactive compounds and provide new insights into the machine learning basis for various traditional applications of bioactive compound-related research.
    Keywords bioactive compound ; natural product ; machine learning ; bioinformatics ; cheminformatics ; chemical space ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
    Subject code 006
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: RNA Editing Enzyme ADAR1 Suppresses the Mobility of Cancer Cells via ARPIN.

    Park, Min Ji / Jeong, Eunji / Lee, Eun Ji / Choi, Hyeon Ji / Moon, Bo Hyun / Kang, Keunsoo / Chang, Suhwan

    Molecules and cells

    2023  Volume 46, Issue 6, Page(s) 351–359

    Abstract: Deamination of adenine or cytosine in RNA, called RNA editing, is a constitutively active and common modification. The primary role of RNA editing is tagging RNA right after its synthesis so that the endogenous RNA is recognized as self and distinguished ...

    Abstract Deamination of adenine or cytosine in RNA, called RNA editing, is a constitutively active and common modification. The primary role of RNA editing is tagging RNA right after its synthesis so that the endogenous RNA is recognized as self and distinguished from exogenous RNA, such as viral RNA. In addition to this primary function, the direct or indirect effects on gene expression can be utilized in cancer where a high level of RNA editing activity persists. This report identified actin-related protein 2/3 complex inhibitor (ARPIN) as a target of ADAR1 in breast cancer cells. Our comparative RNA sequencing analysis in MCF7 cells revealed that the expression of ARPIN was decreased upon ADAR1 depletion with altered editing on its 3'UTR. However, the expression changes of ARPIN were not dependent on 3'UTR editing but relied on three microRNAs acting on ARPIN. As a result, we found that the migration and invasion of cancer cells were profoundly increased by ADAR1 depletion, and this cellular phenotype was reversed by the exogenous ARPIN expression. Altogether, our data suggest that ADAR1 suppresses breast cancer cell mobility via the upregulation of ARPIN.
    MeSH term(s) 3' Untranslated Regions ; Adenosine Deaminase/genetics ; Adenosine Deaminase/metabolism ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Neoplasms/genetics ; RNA Editing ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Humans ; Cell Line, Tumor ; Carrier Proteins/metabolism
    Chemical Substances 3' Untranslated Regions ; Adenosine Deaminase (EC 3.5.4.4) ; MicroRNAs ; RNA-Binding Proteins ; ADAR protein, human (EC 3.5.4.37) ; arpin protein, human ; Carrier Proteins
    Language English
    Publishing date 2023-03-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1148964-9
    ISSN 0219-1032 ; 1016-8478
    ISSN (online) 0219-1032
    ISSN 1016-8478
    DOI 10.14348/molcells.2023.2174
    Database MEDical Literature Analysis and Retrieval System OnLINE

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