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  1. Article: Genome-scale identification of SARS-CoV-2 and pan-coronavirus host factor networks.

    Schneider, William M / Luna, Joseph M / Hoffmann, H-Heinrich / Sánchez-Rivera, Francisco J / Leal, Andrew A / Ashbrook, Alison W / Le Pen, Jérémie / Michailidis, Eleftherios / Ricardo-Lax, Inna / Peace, Avery / Stenzel, Ansgar F / Lowe, Scott W / MacDonald, Margaret R / Rice, Charles M / Poirier, John T

    bioRxiv : the preprint server for biology

    2020  

    Abstract: The COVID-19 pandemic has claimed the lives of more than one million people worldwide. The causative agent, SARS-CoV-2, is a member of the : Highlights: Genome-wide CRISPR screens for SARS-CoV-2, HCoV-OC43, HCoV-NL63, and HCoV-229E coronavirus host ... ...

    Abstract The COVID-19 pandemic has claimed the lives of more than one million people worldwide. The causative agent, SARS-CoV-2, is a member of the
    Highlights: Genome-wide CRISPR screens for SARS-CoV-2, HCoV-OC43, HCoV-NL63, and HCoV-229E coronavirus host factors.Parallel genome-wide CRISPR screening uncovered host factors and pathways with pan-coronavirus and virus-specific functional roles.Coronaviruses co-opt multiple biological pathways, including glycosaminoglycan biosynthesis, SREBP signaling, and glycosylphosphatidylinositol biosynthesis and anchoring, among others.TMEM41B - a poorly understood factor with roles in autophagy and lipid mobilization - is a critical pan-coronavirus host factor.
    Keywords covid19
    Language English
    Publishing date 2020-10-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.10.07.326462
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genome-Scale Identification of SARS-CoV-2 and Pan-coronavirus Host Factor Networks.

    Schneider, William M / Luna, Joseph M / Hoffmann, H-Heinrich / Sánchez-Rivera, Francisco J / Leal, Andrew A / Ashbrook, Alison W / Le Pen, Jérémie / Ricardo-Lax, Inna / Michailidis, Eleftherios / Peace, Avery / Stenzel, Ansgar F / Lowe, Scott W / MacDonald, Margaret R / Rice, Charles M / Poirier, John T

    Cell

    2020  Volume 184, Issue 1, Page(s) 120–132.e14

    Abstract: The coronavirus disease 2019 (COVID-19) pandemic has claimed the lives of over one million people worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a member of the Coronaviridae family of viruses that can ... ...

    Abstract The coronavirus disease 2019 (COVID-19) pandemic has claimed the lives of over one million people worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a member of the Coronaviridae family of viruses that can cause respiratory infections of varying severity. The cellular host factors and pathways co-opted during SARS-CoV-2 and related coronavirus life cycles remain ill defined. To address this gap, we performed genome-scale CRISPR knockout screens during infection by SARS-CoV-2 and three seasonal coronaviruses (HCoV-OC43, HCoV-NL63, and HCoV-229E). These screens uncovered host factors and pathways with pan-coronavirus and virus-specific functional roles, including major dependency on glycosaminoglycan biosynthesis, sterol regulatory element-binding protein (SREBP) signaling, bone morphogenetic protein (BMP) signaling, and glycosylphosphatidylinositol biosynthesis, as well as a requirement for several poorly characterized proteins. We identified an absolute requirement for the VMP1, TMEM41, and TMEM64 (VTT) domain-containing protein transmembrane protein 41B (TMEM41B) for infection by SARS-CoV-2 and three seasonal coronaviruses. This human coronavirus host factor compendium represents a rich resource to develop new therapeutic strategies for acute COVID-19 and potential future coronavirus pandemics.
    MeSH term(s) A549 Cells ; Cell Line ; Clustered Regularly Interspaced Short Palindromic Repeats ; Coronavirus 229E, Human/physiology ; Coronavirus Infections/genetics ; Coronavirus Infections/virology ; Coronavirus NL63, Human/physiology ; Coronavirus OC43, Human/physiology ; Gene Knockout Techniques ; Genome-Wide Association Study ; HEK293 Cells ; Host-Pathogen Interactions/drug effects ; Humans ; Membrane Proteins/metabolism ; Metabolic Networks and Pathways/drug effects ; Protein Interaction Mapping ; SARS-CoV-2/physiology
    Chemical Substances Membrane Proteins ; TMEM41B protein, human
    Language English
    Publishing date 2020-12-09
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2020.12.006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Human hepatocyte PNPLA3-148M exacerbates rapid non-alcoholic fatty liver disease development in chimeric mice.

    Kabbani, Mohammad / Michailidis, Eleftherios / Steensels, Sandra / Fulmer, Clifton G / Luna, Joseph M / Le Pen, Jérémie / Tardelli, Matteo / Razooky, Brandon / Ricardo-Lax, Inna / Zou, Chenhui / Zeck, Briana / Stenzel, Ansgar F / Quirk, Corrine / Foquet, Lander / Ashbrook, Alison W / Schneider, William M / Belkaya, Serkan / Lalazar, Gadi / Liang, Yupu /
    Pittman, Meredith / Devisscher, Lindsey / Suemizu, Hiroshi / Theise, Neil D / Chiriboga, Luis / Cohen, David E / Copenhaver, Robert / Grompe, Markus / Meuleman, Philip / Ersoy, Baran A / Rice, Charles M / de Jong, Ype P

    Cell reports

    2022  Volume 40, Issue 11, Page(s) 111321

    Abstract: Advanced non-alcoholic fatty liver disease (NAFLD) is a rapidly emerging global health problem associated with pre-disposing genetic polymorphisms, most strikingly an isoleucine to methionine substitution in patatin-like phospholipase domain-containing ... ...

    Abstract Advanced non-alcoholic fatty liver disease (NAFLD) is a rapidly emerging global health problem associated with pre-disposing genetic polymorphisms, most strikingly an isoleucine to methionine substitution in patatin-like phospholipase domain-containing protein 3 (PNPLA3-I148M). Here, we study how human hepatocytes with PNPLA3 148I and 148M variants engrafted in the livers of broadly immunodeficient chimeric mice respond to hypercaloric diets. As early as four weeks, mice developed dyslipidemia, impaired glucose tolerance, and steatosis with ballooning degeneration selectively in the human graft, followed by pericellular fibrosis after eight weeks of hypercaloric feeding. Hepatocytes with the PNPLA3-148M variant, either from a homozygous 148M donor or overexpressed in a 148I donor background, developed microvesicular and severe steatosis with frequent ballooning degeneration, resulting in more active steatohepatitis than 148I hepatocytes. We conclude that PNPLA3-148M in human hepatocytes exacerbates NAFLD. These models will facilitate mechanistic studies into human genetic variant contributions to advanced fatty liver diseases.
    MeSH term(s) Acyltransferases ; Animals ; Hepatocytes/metabolism ; Humans ; Lipase/genetics ; Lipase/metabolism ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Mice ; Non-alcoholic Fatty Liver Disease/genetics ; Phospholipases A2, Calcium-Independent
    Chemical Substances Membrane Proteins ; Acyltransferases (EC 2.3.-) ; Lipase (EC 3.1.1.3) ; PNPLA3 protein, mouse (EC 3.1.1.3) ; Phospholipases A2, Calcium-Independent (EC 3.1.1.4)
    Language English
    Publishing date 2022-10-13
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; 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.2022.111321
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors.

    Hoffmann, H-Heinrich / Schneider, William M / Sánchez-Rivera, Francisco J / Luna, Joseph M / Ashbrook, Alison W / Soto-Feliciano, Yadira M / Leal, Andrew A / Le Pen, Jérémie / Ricardo-Lax, Inna / Michailidis, Eleftherios / Hao, Yuan / Stenzel, Ansgar F / Peace, Avery / Allis, C David / Lowe, Scott W / MacDonald, Margaret R / Poirier, John T / Rice, Charles M

    bioRxiv : the preprint server for biology

    2020  

    Abstract: The ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed nearly one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a ... ...

    Abstract The ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed nearly one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen four related coronaviruses (HCoV-229E, HCoV-NL63, HCoV-OC43 and SARS-CoV-2) at two physiologically relevant temperatures (33 °C and 37 °C), allowing us to probe this interactome at a much higher resolution relative to genome scale studies. This approach yielded several new insights, including unexpected virus and temperature specific differences in Rab GTPase requirements and GPI anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating COVID-19, and help prepare for future coronavirus outbreaks.
    Highlights: Focused CRISPR screens targeting host factors in the SARS-CoV-2 interactome were performed for SARS-CoV-2, HCoV-229E, HCoV-NL63, and HCoV-OC43 coronaviruses.Focused interactome CRISPR screens achieve higher resolution compared to genome-wide screens, leading to the identification of critical factors missed by the latter.Parallel CRISPR screens against multiple coronaviruses uncover host factors and pathways with pan-coronavirus and virus-specific functional roles.The number of host proteins that interact with a viral bait protein is not proportional to the number of functional interactors.Novel SARS-CoV-2 host factors are expressed in relevant cell types in the human airway.
    Keywords covid19
    Language English
    Publishing date 2020-09-11
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.09.11.291716
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors.

    Hoffmann, H-Heinrich / Sánchez-Rivera, Francisco J / Schneider, William M / Luna, Joseph M / Soto-Feliciano, Yadira M / Ashbrook, Alison W / Le Pen, Jérémie / Leal, Andrew A / Ricardo-Lax, Inna / Michailidis, Eleftherios / Hao, Yuan / Stenzel, Ansgar F / Peace, Avery / Zuber, Johannes / Allis, C David / Lowe, Scott W / MacDonald, Margaret R / Poirier, John T / Rice, Charles M

    Cell host & microbe

    2020  Volume 29, Issue 2, Page(s) 267–280.e5

    Abstract: The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has devastated the global economy and claimed more than 1.7 million lives, presenting an urgent global health crisis. To identify host factors required for infection by ... ...

    Abstract The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has devastated the global economy and claimed more than 1.7 million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen SARS-CoV-2 at two physiologically relevant temperatures along with three related coronaviruses (human coronavirus 229E [HCoV-229E], HCoV-NL63, and HCoV-OC43), allowing us to probe this interactome at a much higher resolution than genome-scale studies. This approach yielded several insights, including potential virus-specific differences in Rab GTPase requirements and glycosylphosphatidylinositol (GPI) anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating coronavirus disease 2019 (COVID-19) and help prepare for future coronavirus outbreaks.
    MeSH term(s) COVID-19/virology ; CRISPR-Cas Systems ; Coronavirus 229E, Human/genetics ; Coronavirus 229E, Human/metabolism ; Coronavirus NL63, Human/genetics ; Coronavirus NL63, Human/metabolism ; Coronavirus OC43, Human ; Genes, Viral ; Host-Pathogen Interactions ; Humans ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Viral Proteins/genetics ; Viral Proteins/metabolism
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2020-12-16
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2278004-X
    ISSN 1934-6069 ; 1931-3128
    ISSN (online) 1934-6069
    ISSN 1931-3128
    DOI 10.1016/j.chom.2020.12.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A Genome-Wide Arrayed CRISPR Screen Reveals PLSCR1 as an Intrinsic Barrier to SARS-CoV-2 Entry

    Le Pen, Jérémie / Paniccia, Gabrielle / Bauer, Michael / Hoffmann, H.-Heinrich / Kinast, Volker / Moncada-Velez, Marcela / Pinharanda, Ana / Ricardo-Lax, Inna / Stenzel, Ansgar F. / Rosado-Olivieri, Edwin A. / Ashbrook, Alison W. / Dinnon, Kenneth H. / Doyle, William C. / Freije, Catherine A. / Hong, Seon-Hui / Lee, Danyel / Lewy, Tyler / Luna, Joseph M. / Peace, Avery /
    Schmidt, Carltin / Schneider, William M. / Winkler, Roni / Larson, Chloe / McGinn, Timothy / Menezes, Miriam-Rose / Ramos-Espiritu, Lavoisier / Banerjee, Priyam / Poirier, John T. / Sànchez-Rivera, Francisco J. / Zhang, Qian / Casanova, Jean-Laurent / Carroll, Thomas S. / Glickman, J. Fraser / Michailidis, Eleftherios / Razooky, Brandon / MacDonald, Margaret R. / Rice, Charles M.

    bioRxiv

    Abstract: Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence SARS-CoV-2 ... ...

    Abstract Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence SARS-CoV-2 infection. We then performed an integrated analysis of genes interacting with SARS-CoV-2, drawing from a selection of 67 large-scale studies, including our own. We identified 28 genes of high relevance in both human genetic studies of COVID-19 patients and functional genetic screens in cell culture, with many related to the IFN pathway. Among these was the IFN-stimulated gene PLSCR1. PLSCR1 did not require IFN induction to restrict SARS-CoV-2 and did not contribute to IFN signaling. Instead, PLSCR1 specifically restricted spike-mediated SARS-CoV-2 entry. The PLSCR1-mediated restriction was alleviated by TMPRSS2 over-expression, suggesting that PLSCR1 primarily restricts the endocytic entry route. In addition, recent SARS-CoV-2 variants have adapted to circumvent the PLSCR1 barrier via currently undetermined mechanisms. Finally, we discuss the association between PLSCR1 variants and severe COVID-19 cases reported in a recent GWAS.
    Keywords covid19
    Language English
    Publishing date 2024-02-20
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.02.16.580725
    Database COVID19

    Kategorien

  7. Article ; Online: A Genome-Wide Arrayed CRISPR Screen Reveals PLSCR1 as an Intrinsic Barrier to SARS-CoV-2 Entry

    Le Pen, Jeremie / Paniccia, Gabrielle / Bauer, Michael / Hoffmann, H.-Heinrich / Kinast, Volker / Moncada-Velez, Marcela / Pinharanda, Ana / Ricardo-Lax, Inna / Stenzel, Ansgar F / Rosado-Olivieri, Edwin A / Ashbrook, Alison W / Dinnon, Kenneth H / Doyle, William / Freije, Catherine / Hong, Seon-Hui / Lee, Danyel / Lewy, Tyler / Luna, Joseph M / Peace, Avery /
    Schmidt, Carltin / Schneider, William M / Winkler, Roni / Larson, Chloe / McGinn, Timothy / Menezes, Miriam-Rose / Ramos-Espiritu, Lavoisier / Banerjee, Priyam / Poirier, John T / Sanchez-Rivera, Francisco J / Zhang, Qian / Casanova, Jean-Laurent / Carroll, Thomas S / Glickman, J. Fraser / Michailidis, Eleftherios / Razooky, Brandon / MacDonald, Margaret R / Rice, Charles M

    bioRxiv

    Abstract: Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence SARS-CoV-2 ... ...

    Abstract Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence SARS-CoV-2 infection. We then performed an integrated analysis of genes interacting with SARS-CoV-2, drawing from a selection of 67 large-scale studies, including our own. We identified 28 genes of high relevance in both human genetic studies of COVID-19 patients and functional genetic screens in cell culture, with many related to the IFN pathway. Among these was the IFN-stimulated gene PLSCR1. PLSCR1 did not require IFN induction to restrict SARS-CoV-2 and did not contribute to IFN signaling. Instead, PLSCR1 specifically restricted spike-mediated SARS-CoV-2 entry. The PLSCR1-mediated restriction was alleviated by TMPRSS2 over-expression, suggesting that PLSCR1 primarily restricts the endocytic entry route. In addition, recent SARS-CoV-2 variants have adapted to circumvent the PLSCR1 barrier via currently undetermined mechanisms. Finally, we discuss the association between PLSCR1 variants and severe COVID-19 cases reported in a recent GWAS.
    Keywords covid19
    Language English
    Publishing date 2024-02-20
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.02.16.580725
    Database COVID19

    Kategorien

  8. Article ; Online: Genome-scale identification of SARS-CoV-2 and pan-coronavirus host factor networks

    Schneider, William M. / Luna, Joseph M. / Hoffmann, H.-Heinrich / Sánchez-Rivera, Francisco J. / Leal, Andrew A. / Ashbrook, Alison W. / Le Pen, Jérémie / Michailidis, Eleftherios / Ricardo-Lax, Inna / Peace, Avery / Stenzel, Ansgar F. / Lowe, Scott W. / MacDonald, Margaret R. / Rice, Charles M. / Poirier, John T.

    bioRxiv

    Abstract: The COVID-19 pandemic has claimed the lives of more than one million people worldwide. The causative agent, SARS-CoV-2, is a member of the Coronaviridae family, which are viruses that cause respiratory infections of varying severity. The cellular host ... ...

    Abstract The COVID-19 pandemic has claimed the lives of more than one million people worldwide. The causative agent, SARS-CoV-2, is a member of the Coronaviridae family, which are viruses that cause respiratory infections of varying severity. The cellular host factors and pathways co-opted by SARS-CoV-2 and other coronaviruses in the execution of their life cycles remain ill-defined. To develop an extensive compendium of host factors required for infection by SARS-CoV-2 and three seasonal coronaviruses (HCoV-OC43, HCoV-NL63, and HCoV-229E), we performed parallel genome-scale CRISPR knockout screens. These screens uncovered multiple host factors and pathways with pan-coronavirus and virus-specific functional roles, including major dependency on glycosaminoglycan biosynthesis, SREBP signaling, and glycosylphosphatidylinositol biosynthesis, as well as an unexpected requirement for several poorly characterized proteins. We identified an absolute requirement for the VTT-domain containing protein TMEM41B for infection by SARS-CoV-2 and all other coronaviruses. This human Coronaviridae host factor compendium represents a rich resource to develop new therapeutic strategies for acute COVID-19 and potential future coronavirus spillover events.
    Keywords covid19
    Language English
    Publishing date 2020-10-08
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.10.07.326462
    Database COVID19

    Kategorien

  9. Article ; Online: Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors

    Hoffmann, H.-Heinrich / Schneider, William M. / Sánchez-Rivera, Francisco J. / Luna, Joseph M. / Ashbrook, Alison W. / Soto-Feliciano, Yadira M. / Leal, Andrew A. / Le Pen, Jérémie / Ricardo-Lax, Inna / Michailidis, Eleftherios / Hao, Yuan / Stenzel, Ansgar F. / Peace, Avery / Allis, C. David / Lowe, Scott W. / MacDonald, Margaret R. / Poirier, John T. / Rice, Charles M.

    bioRxiv

    Abstract: The ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed nearly one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a ... ...

    Abstract The ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed nearly one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen four related coronaviruses (HCoV-229E, HCoV-NL63, HCoV-OC43 and SARS-CoV-2) at two physiologically relevant temperatures (33°C and 37°C), allowing us to probe this interactome at a much higher resolution relative to genome scale studies. This approach yielded several new insights, including unexpected virus and temperature specific differences in Rab GTPase requirements and GPI anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating COVID-19, and help prepare for future coronavirus outbreaks.
    Keywords covid19
    Language English
    Publishing date 2020-09-11
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.09.11.291716
    Database COVID19

    Kategorien

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