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  1. Article ; Online: SARS-CoV-2 cellular tropism and direct multiorgan failure in COVID-19 patients: Bioinformatic predictions, experimental observations, and open questions.

    Valyaeva, Anna A / Zharikova, Anastasia A / Sheval, Eugene V

    Cell biology international

    2022  Volume 47, Issue 2, Page(s) 308–326

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has led to an unprecedented public health emergency worldwide. While common cold symptoms are observed in mild cases, COVID-19 is ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has led to an unprecedented public health emergency worldwide. While common cold symptoms are observed in mild cases, COVID-19 is accompanied by multiorgan failure in severe patients. Organ damage in COVID-19 patients is partially associated with the indirect effects of SARS-CoV-2 infection (e.g., systemic inflammation, hypoxic-ischemic damage, coagulopathy), but early processes in COVID-19 patients that trigger a chain of indirect effects are connected with the direct infection of cells by the virus. To understand the virus transmission routes and the reasons for the wide-spectrum of complications and severe outcomes of COVID-19, it is important to identify the cells targeted by SARS-CoV-2. This review summarizes the major steps of investigation and the most recent findings regarding SARS-CoV-2 cellular tropism and the possible connection between the early stages of infection and multiorgan failure in COVID-19. The SARS-CoV-2 pandemic is the first epidemic in which data extracted from single-cell RNA-seq (scRNA-seq) gene expression data sets have been widely used to predict cellular tropism. The analysis presented here indicates that the SARS-CoV-2 cellular tropism predictions are accurate enough for estimating the potential susceptibility of different cells to SARS-CoV-2 infection; however, it appears that not all susceptible cells may be infected in patients with COVID-19.
    MeSH term(s) Humans ; COVID-19 ; SARS-CoV-2 ; Inflammation ; Tropism
    Language English
    Publishing date 2022-10-13
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1143453-3
    ISSN 1095-8355 ; 1065-6995
    ISSN (online) 1095-8355
    ISSN 1065-6995
    DOI 10.1002/cbin.11928
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19.

    Valyaeva, Anna A / Zharikova, Anastasia A / Kasianov, Artem S / Vassetzky, Yegor S / Sheval, Eugene V

    Scientific reports

    2020  Volume 10, Issue 1, Page(s) 17772

    Abstract: SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, ... ...

    Abstract SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.
    MeSH term(s) Angiotensin-Converting Enzyme 2 ; Betacoronavirus/isolation & purification ; Betacoronavirus/physiology ; COVID-19 ; Cell Differentiation ; Cell Line ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Humans ; Lung/cytology ; Pandemics ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Serine Endopeptidases/metabolism ; Stem Cells/cytology ; Stem Cells/metabolism ; Stem Cells/virology ; Viral Proteins/genetics ; Viral Proteins/metabolism ; Virus Internalization
    Chemical Substances Viral Proteins ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Serine Endopeptidases (EC 3.4.21.-) ; TMPRSS2 protein, human (EC 3.4.21.-)
    Keywords covid19
    Language English
    Publishing date 2020-10-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-020-74598-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Lung inflammation is associated with lipid deposition.

    Potashnikova, Daria M / Tvorogova, Anna V / Saidova, Aleena A / Sotnikova, Tatiana N / Arifulin, Eugene A / Lipina, Tatiana V / Shirokova, Olesya M / Melnikov, Eugene S / Rodina, Tatiana A / Valyaeva, Anna A / Zharikova, Anastasia A / Zayratyants, George O / Zayratyants, Oleg V / Sheval, Eugene V / Vasilieva, Elena J

    bioRxiv : the preprint server for biology

    2023  

    Abstract: Lung inflammation, pneumonia, is an acute respiratory disease of varying etiology that has recently drawn much attention during the COVID-19 pandemic as lungs are among the main targets for SARS-CoV-2. Multiple other etiological agents are associated ... ...

    Abstract Lung inflammation, pneumonia, is an acute respiratory disease of varying etiology that has recently drawn much attention during the COVID-19 pandemic as lungs are among the main targets for SARS-CoV-2. Multiple other etiological agents are associated with pneumonias. Here, we describe a newly-recognized pathology, namely abnormal lipid depositions in the lungs of patients who died from COVID-19 as well as from non-COVID-19 pneumonias. Our analysis of both semi-thin and Sudan III-stained lung specimens revealed extracellular and intracellular lipid depositions irrespective of the pneumonia etiology. Most notably, lipid depositions were located within vessels adjacent to inflamed regions, where they apparently interfere with the blood flow. Structurally, the lipid droplets in the inflamed lung tissue were homogeneous and lacked outer membranes as assessed by electron microscopy. Morphometric analysis of lipid droplet deposition area allowed us to distinguish the non-pneumonia control lung specimens from the macroscopically intact area of the pneumonia lung and from the inflamed area of the pneumonia lung. Our measurements revealed a gradient of lipid deposition towards the inflamed region. The pattern of lipid distribution proved universal for all pneumonias. Finally, lipid metabolism in the lung tissue was assessed by the fatty acid analysis and by expression of genes involved in lipid turnover. Chromato-mass spectrometry revealed that unsaturated fatty acid content was elevated at inflammation sites compared to that in control non-inflamed lung tissue from the same individual. The expression of genes involved in lipid metabolism was altered in pneumonia, as shown by qPCR and in silico RNA-seq analysis. Thus, pneumonias of various etiologies are associated with specific lipid abnormalities; therefore, lipid metabolism can be considered to be a target for new therapeutic strategies.
    Language English
    Publishing date 2023-11-20
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2022.12.30.522299
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Complex Analysis of Single-Cell RNA Sequencing Data.

    Khozyainova, Anna A / Valyaeva, Anna A / Arbatsky, Mikhail S / Isaev, Sergey V / Iamshchikov, Pavel S / Volchkov, Egor V / Sabirov, Marat S / Zainullina, Viktoria R / Chechekhin, Vadim I / Vorobev, Rostislav S / Menyailo, Maxim E / Tyurin-Kuzmin, Pyotr A / Denisov, Evgeny V

    Biochemistry. Biokhimiia

    2023  Volume 88, Issue 2, Page(s) 231–252

    Abstract: Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool for studying the physiology of normal and pathologically altered tissues. This approach provides information about molecular features (gene expression, mutations, chromatin accessibility, etc. ...

    Abstract Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool for studying the physiology of normal and pathologically altered tissues. This approach provides information about molecular features (gene expression, mutations, chromatin accessibility, etc.) of cells, opens up the possibility to analyze the trajectories/phylogeny of cell differentiation and cell-cell interactions, and helps in discovery of new cell types and previously unexplored processes. From a clinical point of view, scRNA-seq facilitates deeper and more detailed analysis of molecular mechanisms of diseases and serves as a basis for the development of new preventive, diagnostic, and therapeutic strategies. The review describes different approaches to the analysis of scRNA-seq data, discusses the advantages and disadvantages of bioinformatics tools, provides recommendations and examples of their successful use, and suggests potential directions for improvement. We also emphasize the need for creating new protocols, including multiomics ones, for the preparation of DNA/RNA libraries of single cells with the purpose of more complete understanding of individual cells.
    MeSH term(s) Gene Expression Profiling/methods ; RNA/genetics ; Cell Differentiation ; Gene Library ; Sequence Analysis, RNA/methods
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2023-04-18
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 1109-5
    ISSN 1608-3040 ; 0006-2979 ; 0320-9717
    ISSN (online) 1608-3040
    ISSN 0006-2979 ; 0320-9717
    DOI 10.1134/S0006297923020074
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19

    Valyaeva, Anna / Zharikova, Anastasia / Kasianov, Artem / Vassetzky, Yegor / Sheval, Eugene

    ISSN: 2045-2322 ; EISSN: 2045-2322 ; Scientific Reports ; https://hal.archives-ouvertes.fr/hal-02988626 ; Scientific Reports, Nature Publishing Group, 2020, 10 (1), ⟨10.1038/s41598-020-74598-5⟩

    2020  

    Abstract: International ... ...

    Abstract International audience
    Keywords [SDV]Life Sciences [q-bio] ; covid19
    Language English
    Publisher HAL CCSD
    Publishing country fr
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19

    Valyaeva, Anna / Zharikova, Anastasia / Kasianov, Artem / Vassetzky, Yegor / Sheval, Eugene

    ISSN: 2045-2322 ; EISSN: 2045-2322 ; Scientific Reports ; https://hal.archives-ouvertes.fr/hal-02988626 ; Scientific Reports, Nature Publishing Group, 2020, 10 (1), ⟨10.1038/s41598-020-74598-5⟩

    2020  

    Abstract: International ... ...

    Abstract International audience
    Keywords [SDV]Life Sciences [q-bio] ; covid19
    Language English
    Publisher HAL CCSD
    Publishing country fr
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19

    Valyaeva, Anna / Zharikova, Anastasia / Kasianov, Artem / Vassetzky, Yegor / Sheval, Eugene

    ISSN: 2045-2322 ; EISSN: 2045-2322 ; Scientific Reports ; https://hal.archives-ouvertes.fr/hal-02988626 ; Scientific Reports, Nature Publishing Group, 2020, 10 (1), ⟨10.1038/s41598-020-74598-5⟩

    2020  

    Abstract: International ... ...

    Abstract International audience
    Keywords [SDV]Life Sciences [q-bio] ; covid19
    Language English
    Publisher HAL CCSD
    Publishing country fr
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Article ; Online: Lung epithelial stem cells express SARS-CoV-2 entry factors

    Valyaeva, Anna / Zharikova, Anastasia / Kasianov, Artem / Vassetzky, Yegor / Sheval, Eugene

    https://hal.archives-ouvertes.fr/hal-02988684 ; 2020

    implications for COVID-19

    2020  

    Abstract: SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, ... ...

    Abstract SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2 . Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.

    SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be infected by SARS-CoV-2, which can lead to defects in regeneration capacity and account for the severity of SARS-CoV-2 infection and its consequences.
    Keywords [SDV]Life Sciences [q-bio] ; covid19
    Subject code 610 ; 571
    Language English
    Publishing date 2020-11-06
    Publisher HAL CCSD
    Publishing country fr
    Document type Book ; Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Book ; Article ; Online: Lung epithelial stem cells express SARS-CoV-2 entry factors

    Valyaeva, Anna / Zharikova, Anastasia / Kasianov, Artem / Vassetzky, Yegor / Sheval, Eugene

    https://hal.archives-ouvertes.fr/hal-02988684 ; 2020

    implications for COVID-19

    2020  

    Abstract: SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, ... ...

    Abstract SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2 . Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.

    SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be infected by SARS-CoV-2, which can lead to defects in regeneration capacity and account for the severity of SARS-CoV-2 infection and its consequences.
    Keywords [SDV]Life Sciences [q-bio] ; covid19
    Subject code 610 ; 571
    Language English
    Publishing date 2020-11-06
    Publisher HAL CCSD
    Publishing country fr
    Document type Book ; Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Book ; Article ; Online: Lung epithelial stem cells express SARS-CoV-2 entry factors

    Valyaeva, Anna / Zharikova, Anastasia / Kasianov, Artem / Vassetzky, Yegor / Sheval, Eugene

    https://hal.archives-ouvertes.fr/hal-02988684 ; 2020

    implications for COVID-19

    2020  

    Abstract: SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, ... ...

    Abstract SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2 . Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.

    SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be infected by SARS-CoV-2, which can lead to defects in regeneration capacity and account for the severity of SARS-CoV-2 infection and its consequences.
    Keywords [SDV]Life Sciences [q-bio] ; covid19
    Subject code 610 ; 571
    Language English
    Publishing date 2020-11-06
    Publisher HAL CCSD
    Publishing country fr
    Document type Book ; Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    More links

    Kategorien

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