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  1. Article ; Online: Airway Basal Cells in Chronic Obstructive Pulmonary Disease: A Continuum or a Dead End?

    Shaykhiev, Renat

    American journal of respiratory cell and molecular biology

    2021  Volume 65, Issue 1, Page(s) 10–12

    MeSH term(s) Humans ; Lung ; Pulmonary Disease, Chronic Obstructive
    Language English
    Publishing date 2021-04-13
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 1025960-0
    ISSN 1535-4989 ; 1044-1549
    ISSN (online) 1535-4989
    ISSN 1044-1549
    DOI 10.1165/rcmb.2021-0150ED
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Basal-like Cells in the BAL Fluid: An Echo of Regenerative Crisis in Idiopathic Pulmonary Fibrosis Lungs.

    Shaykhiev, Renat

    American journal of respiratory and critical care medicine

    2018  Volume 199, Issue 5, Page(s) 555–557

    MeSH term(s) Humans ; Idiopathic Pulmonary Fibrosis ; Lung
    Language English
    Publishing date 2018-09-04
    Publishing country United States
    Document type Journal Article ; Comment
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201808-1557ED
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Emerging biology of persistent mucous cell hyperplasia in COPD.

    Shaykhiev, Renat

    Thorax

    2018  Volume 74, Issue 1, Page(s) 4–6

    MeSH term(s) Epithelial Cells ; Goblet Cells ; Humans ; Hyperplasia ; Pulmonary Disease, Chronic Obstructive ; Receptor, Notch3 ; Rhinovirus
    Chemical Substances NOTCH3 protein, human ; Receptor, Notch3
    Language English
    Publishing date 2018-09-28
    Publishing country England
    Document type Editorial ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 204353-1
    ISSN 1468-3296 ; 0040-6376
    ISSN (online) 1468-3296
    ISSN 0040-6376
    DOI 10.1136/thoraxjnl-2018-212271
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Airway Epithelial Progenitors and the Natural History of Chronic Obstructive Pulmonary Disease.

    Shaykhiev, Renat

    American journal of respiratory and critical care medicine

    2018  Volume 197, Issue 7, Page(s) 847–849

    MeSH term(s) Humans ; Pulmonary Disease, Chronic Obstructive ; Respiratory System ; Stem Cells
    Language English
    Publishing date 2018-01-22
    Publishing country United States
    Document type Editorial ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201711-2327ED
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Multitasking basal cells: combining stem cell and innate immune duties.

    Shaykhiev, Renat

    The European respiratory journal

    2015  Volume 46, Issue 4, Page(s) 894–897

    MeSH term(s) Bacteria/immunology ; Basement Membrane/physiology ; Bronchi/immunology ; Cell Differentiation ; Epithelial Cells/cytology ; Humans ; Immunity, Innate/immunology ; Lung/immunology ; Lung/microbiology ; Phenotype ; Receptor, Epidermal Growth Factor/metabolism ; Regeneration ; Signal Transduction ; Stem Cells/cytology ; Trachea/immunology
    Chemical Substances Receptor, Epidermal Growth Factor (EC 2.7.10.1)
    Language English
    Publishing date 2015-10
    Publishing country England
    Document type Editorial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 639359-7
    ISSN 1399-3003 ; 0903-1936
    ISSN (online) 1399-3003
    ISSN 0903-1936
    DOI 10.1183/13993003.00521-2015
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Reply: Epithelial-Mesenchymal Transition: A Necessary New Therapeutic Target in Chronic Obstructive Pulmonary Disease?

    Yang, Jing / Shaykhiev, Renat

    American journal of respiratory and critical care medicine

    2017  Volume 196, Issue 3, Page(s) 394–395

    MeSH term(s) Epithelial-Mesenchymal Transition ; Humans ; Pulmonary Disease, Chronic Obstructive
    Language English
    Publishing date 2017--01
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Comment
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.201705-0981LE
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Author Correction: Unsupervised discovery of tissue architecture in multiplexed imaging.

    Kim, Junbum / Rustam, Samir / Mosquera, Juan Miguel / Randell, Scott H / Shaykhiev, Renat / Rendeiro, André F / Elemento, Olivier

    Nature methods

    2022  Volume 19, Issue 12, Page(s) 1662

    Language English
    Publishing date 2022-11-22
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01717-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Unsupervised discovery of tissue architecture in multiplexed imaging.

    Kim, Junbum / Rustam, Samir / Mosquera, Juan Miguel / Randell, Scott H / Shaykhiev, Renat / Rendeiro, André F / Elemento, Olivier

    Nature methods

    2022  Volume 19, Issue 12, Page(s) 1653–1661

    Abstract: Multiplexed imaging and spatial transcriptomics enable highly resolved spatial characterization of cellular phenotypes, but still largely depend on laborious manual annotation to understand higher-order patterns of tissue organization. As a result, ... ...

    Abstract Multiplexed imaging and spatial transcriptomics enable highly resolved spatial characterization of cellular phenotypes, but still largely depend on laborious manual annotation to understand higher-order patterns of tissue organization. As a result, higher-order patterns of tissue organization are poorly understood and not systematically connected to disease pathology or clinical outcomes. To address this gap, we developed an approach called UTAG to identify and quantify microanatomical tissue structures in multiplexed images without human intervention. Our method combines information on cellular phenotypes with the physical proximity of cells to accurately identify organ-specific microanatomical domains in healthy and diseased tissue. We apply our method to various types of images across healthy and disease states to show that it can consistently detect higher-level architectures in human tissues, quantify structural differences between healthy and diseased tissue, and reveal tissue organization patterns at the organ scale.
    MeSH term(s) Humans ; Diagnostic Imaging ; Transcriptome
    Language English
    Publishing date 2022-10-31
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2169522-2
    ISSN 1548-7105 ; 1548-7091
    ISSN (online) 1548-7105
    ISSN 1548-7091
    DOI 10.1038/s41592-022-01657-2
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  9. Article ; Online: A Unique Cellular Organization of Human Distal Airways and Its Disarray in Chronic Obstructive Pulmonary Disease.

    Rustam, Samir / Hu, Yang / Mahjour, Seyed Babak / Rendeiro, Andre F / Ravichandran, Hiranmayi / Urso, Andreacarola / D'Ovidio, Frank / Martinez, Fernando J / Altorki, Nasser K / Richmond, Bradley / Polosukhin, Vasiliy / Kropski, Jonathan A / Blackwell, Timothy S / Randell, Scott H / Elemento, Olivier / Shaykhiev, Renat

    American journal of respiratory and critical care medicine

    2023  Volume 207, Issue 9, Page(s) 1171–1182

    Abstract: Rationale: ...

    Abstract Rationale:
    MeSH term(s) Humans ; CD8-Positive T-Lymphocytes ; Pulmonary Disease, Chronic Obstructive ; Lung ; Bronchioles ; Diagnostic Imaging
    Language English
    Publishing date 2023-01-25
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1180953-x
    ISSN 1535-4970 ; 0003-0805 ; 1073-449X
    ISSN (online) 1535-4970
    ISSN 0003-0805 ; 1073-449X
    DOI 10.1164/rccm.202207-1384OC
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  10. Article ; Online: Early events in the pathogenesis of chronic obstructive pulmonary disease. Smoking-induced reprogramming of airway epithelial basal progenitor cells.

    Shaykhiev, Renat / Crystal, Ronald G

    Annals of the American Thoracic Society

    2014  Volume 11 Suppl 5, Page(s) S252–8

    Abstract: The airway epithelium is the primary site of the earliest pathologic changes induced by smoking, contributing to the development of chronic obstructive pulmonary disease (COPD). The normal human airway epithelium is composed of several major cell types, ... ...

    Abstract The airway epithelium is the primary site of the earliest pathologic changes induced by smoking, contributing to the development of chronic obstructive pulmonary disease (COPD). The normal human airway epithelium is composed of several major cell types, including differentiated ciliated and secretory cells, intermediate undifferentiated cells, and basal cells (BC). BC contain the stem/progenitor cell population responsible for maintenance of the normally differentiated airway epithelium. Although inflammatory and immune processes play a significant role in the pathogenesis of COPD, the earliest lesions include hyperplasia of the BC population, suggesting that the disease may start with this cell type. Apart from BC hyperplasia, smoking induces a number of COPD-relevant airway epithelial remodeling phenotypes that are likely initiated in the BC population, including mucous cell hyperplasia, squamous cell metaplasia, epithelial-mesenchymal transition, altered ciliated and nonmucous secretory cell differentiation, and suppression of junctional barrier integrity. Significant progress has been recently made in understanding the biology of human airway BC, including gene expression features, stem/progenitor, and other functions, including interaction with other airway cell types. Accumulating evidence suggests that human airway BC function as both sensors and cellular sources of various cytokines and growth factors relevant to smoking-associated airway injury, as well as the origin of various molecular and histological phenotypes relevant to the pathogenesis of COPD. In the context of these considerations, we suggest that early BC-specific smoking-induced molecular changes are critical to the pathogenesis of COPD, and these represent a candidate target for novel therapeutic approaches to prevent COPD progression in susceptible individuals.
    MeSH term(s) Cell Differentiation ; Cytokines/biosynthesis ; Cytokines/genetics ; DNA/genetics ; Gene Expression Regulation ; Humans ; Phenotype ; Pulmonary Disease, Chronic Obstructive/genetics ; Pulmonary Disease, Chronic Obstructive/metabolism ; Pulmonary Disease, Chronic Obstructive/pathology ; Respiratory Mucosa ; Respiratory System/metabolism ; Respiratory System/pathology ; Smoking/adverse effects ; Stem Cells/physiology ; Time Factors
    Chemical Substances Cytokines ; DNA (9007-49-2)
    Language English
    Publishing date 2014-11-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2717461-X
    ISSN 2325-6621 ; 1943-5665 ; 2325-6621
    ISSN (online) 2325-6621 ; 1943-5665
    ISSN 2325-6621
    DOI 10.1513/AnnalsATS.201402-049AW
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