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  1. Article ; Online: Evidence for a Hepatitis B Virus Short RNA Fragment Directly Targeting the Cellular RRM2 Gene.

    Broennimann, Karin / Ricardo-Lax, Inna / Adler, Julia / Shaul, Yosef

    Cells

    2022  Volume 11, Issue 14

    Abstract: The hepatitis B virus (HBV) is one of the smallest but most highly infectious human pathogens. With a DNA genome of only 3.2 kb and only four genes, HBV successfully completes its life cycle by using intricate processes to hijack the host machinery. HBV ... ...

    Abstract The hepatitis B virus (HBV) is one of the smallest but most highly infectious human pathogens. With a DNA genome of only 3.2 kb and only four genes, HBV successfully completes its life cycle by using intricate processes to hijack the host machinery. HBV infects non-dividing liver cells in which dNTPs are limited. As a DNA virus, HBV requires dNTPs for its replication. HBV induces the ATR-mediated cellular DNA damage response pathway to overcome this constraint. This pathway upregulates R2 (RRM2) expression in generating an active RNR holoenzyme catalyzing de novo dNTP synthesis. Previously we reported that ERE, a small RNA fragment within the HBx ORF, is sufficient to induce R2 upregulation. Interestingly, there is high sequence similarity between ERE and a region within the R2 5'UTR that we named R2-box. Here, we established a mutant cell line in the R2-box region of the R2 gene using CRISPR-Cas9 technology to investigate the R2 regulation by ERE. This cell line expresses a much lower R2 level than the parental cell line. Interestingly, the HBV infection and life cycle were severely impaired. These cells became permissive to HBV infection upon ectopically R2 expression. These results validate the requirement of the R2 gene expression for HBV replication. Remarkably, the R2-box mutated cells became ERE refractory, suggesting that the homology region between ERE and R2 gene is critical for ERE-mediated R2 upregulation. Thus, along with the induction of the ATR pathway of the DNA damage response, ERE might also directly target the R2 gene via the R2-box.
    MeSH term(s) Hep G2 Cells ; Hepatitis B ; Hepatitis B virus/genetics ; Humans ; RNA ; Virus Replication/genetics
    Chemical Substances RNA (63231-63-0)
    Language English
    Publishing date 2022-07-20
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells11142248
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A general method for quantitative fractionation of mammalian cells.

    Udi, Yael / Zhang, Wenzhu / Stein, Milana E / Ricardo-Lax, Inna / Pasolli, Hilda A / Chait, Brian T / Rout, Michael P

    The Journal of cell biology

    2023  Volume 222, Issue 6

    Abstract: Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such ... ...

    Abstract Subcellular fractionation in combination with mass spectrometry-based proteomics is a powerful tool to study localization of key proteins in health and disease. Here we offered a reliable and rapid method for mammalian cell fractionation, tuned for such proteomic analyses. This method proves readily applicable to different cell lines in which all the cellular contents are accounted for, while maintaining nuclear and nuclear envelope integrity. We demonstrated the method's utility by quantifying the effects of a nuclear export inhibitor on nucleoplasmic and cytoplasmic proteomes.
    MeSH term(s) Animals ; Cell Fractionation/methods ; Cell Line ; Cell Nucleus/chemistry ; Mammals ; Proteome/analysis ; Proteomics/methods ; Cytoplasm/chemistry
    Chemical Substances Proteome
    Language English
    Publishing date 2023-03-15
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 218154-x
    ISSN 1540-8140 ; 0021-9525
    ISSN (online) 1540-8140
    ISSN 0021-9525
    DOI 10.1083/jcb.202209062
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: RNR-R2 Upregulation by a Short Non-Coding Viral Transcript.

    Broennimann, Karin / Ricardo-Lax, Inna / Adler, Julia / Michailidis, Eleftherios / de Jong, Ype P / Reuven, Nina / Shaul, Yosef

    Biomolecules

    2021  Volume 11, Issue 12

    Abstract: DNA viruses require dNTPs for replication and have developed different strategies to increase intracellular dNTP pools. Hepatitis B virus (HBV) infects non-dividing cells in which dNTPs are scarce and the question is how viral replication takes place. ... ...

    Abstract DNA viruses require dNTPs for replication and have developed different strategies to increase intracellular dNTP pools. Hepatitis B virus (HBV) infects non-dividing cells in which dNTPs are scarce and the question is how viral replication takes place. Previously we reported that the virus induces the DNA damage response (DDR) pathway culminating in RNR-R2 expression and the generation of an active RNR holoenzyme, the key regulator of dNTP levels, leading to an increase in dNTPs. How the virus induces DDR and RNR-R2 upregulation is not completely known. The viral HBx open reading frame (ORF) was believed to trigger this pathway. Unexpectedly, however, we report here that the production of HBx protein is dispensable. We found that a small conserved region of 125 bases within the HBx ORF is sufficient to upregulate RNR-R2 expression in growth-arrested HepG2 cells and primary human hepatocytes. The observed HBV mRNA embedded regulatory element is named ERE. ERE in isolation is sufficient to activate the ATR-Chk1-E2F1-RNR-R2 DDR pathway. These findings demonstrate a non-coding function of HBV transcripts to support its propagation in non-cycling cells.
    MeSH term(s) Cells, Cultured ; HEK293 Cells ; Hep G2 Cells ; Hepatitis B virus/physiology ; Hepatocytes/cytology ; Hepatocytes/metabolism ; Hepatocytes/virology ; Humans ; Open Reading Frames ; Primary Cell Culture ; RNA, Untranslated/genetics ; RNA, Viral/genetics ; Ribonucleoside Diphosphate Reductase/genetics ; Trans-Activators/genetics ; Trans-Activators/metabolism ; Up-Regulation ; Viral Regulatory and Accessory Proteins/genetics ; Viral Regulatory and Accessory Proteins/metabolism ; Virus Replication
    Chemical Substances RNA, Untranslated ; RNA, Viral ; Trans-Activators ; Viral Regulatory and Accessory Proteins ; hepatitis B virus X protein ; ribonucleotide reductase M2 (EC 1.17.4.-) ; Ribonucleoside Diphosphate Reductase (EC 1.17.4.1)
    Language English
    Publishing date 2021-12-03
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom11121822
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The nonreceptor tyrosine kinase c-Src attenuates SCF(β-TrCP) E3-ligase activity abrogating Taz proteasomal degradation.

    Shanzer, Matan / Adler, Julia / Ricardo-Lax, Inna / Reuven, Nina / Shaul, Yosef

    Proceedings of the National Academy of Sciences of the United States of America

    2017  Volume 114, Issue 7, Page(s) 1678–1683

    Abstract: The polyomavirus middle T antigen (PyMT) oncogene activates the cellular nonreceptor tyrosine kinase c-Src and recruits the Hippo pathway effectors, Yap (yes-associated protein) and Taz (transcriptional coactivator with PDZ-binding motif), as key steps ... ...

    Abstract The polyomavirus middle T antigen (PyMT) oncogene activates the cellular nonreceptor tyrosine kinase c-Src and recruits the Hippo pathway effectors, Yap (yes-associated protein) and Taz (transcriptional coactivator with PDZ-binding motif), as key steps in oncogenesis. Yap and Taz are transcription coactivators shuttling from the cytoplasm to the nucleus. The Hippo pathway kinase Lats1/2 (large tumor suppressor homolog) reduces Yap/Taz nuclear localization and minimizes their cytoplasmic levels by facilitating their ubiquitination by the E3 ligase SCF(β-TrCP). In contrast, PyMT increases the cytoplasmic Taz level. Here we show that this unique PyMT behavior is mediated by Src. We demonstrate that PyMT-induced Src activation inhibits degradation of both wild-type and tyrosine-less Taz, ruling out Taz modification as a mechanism of escaping degradation. Instead, we found that Src attenuates the SCF(β-TrCP) E3-ligase activity in blunting Taz proteasomal degradation. The role of Src in rescuing Taz from TrCP-mediated degradation gives rise to higher cell proliferation under dense cell culture. Finally, IkB (NF-kappa-B inhibitor), a known substrate of β-TrCP, was rescued by Src, suggesting a wider effect of Src on β-TrCP substrates. These findings introduce the Src tyrosine kinase as a regulator of SCF(β-TrCP).
    MeSH term(s) Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Antigens, Polyomavirus Transforming/genetics ; Antigens, Polyomavirus Transforming/metabolism ; CSK Tyrosine-Protein Kinase ; Cell Line ; Cell Line, Tumor ; Cell Transformation, Neoplastic/genetics ; HCT116 Cells ; HEK293 Cells ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Mice ; NIH 3T3 Cells ; Phosphoproteins/genetics ; Phosphoproteins/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Protein-Serine-Threonine Kinases/genetics ; Protein-Serine-Threonine Kinases/metabolism ; Proteolysis ; Trans-Activators ; Transcription Factors ; Tumor Suppressor Proteins/genetics ; Tumor Suppressor Proteins/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; beta-Transducin Repeat-Containing Proteins/genetics ; beta-Transducin Repeat-Containing Proteins/metabolism ; src-Family Kinases/genetics ; src-Family Kinases/metabolism
    Chemical Substances Adaptor Proteins, Signal Transducing ; Antigens, Polyomavirus Transforming ; Intracellular Signaling Peptides and Proteins ; Phosphoproteins ; Trans-Activators ; Transcription Factors ; Tumor Suppressor Proteins ; WWTR1 protein, human ; YAP1 protein, human ; beta-Transducin Repeat-Containing Proteins ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; LATS1 protein, human (EC 2.7.1.-) ; LATS2 protein, human (EC 2.7.1.11) ; CSK Tyrosine-Protein Kinase (EC 2.7.10.2) ; src-Family Kinases (EC 2.7.10.2) ; CSK protein, human (EC 2.7.10.23) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2017-02-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.1610223114
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. 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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  6. 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
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  7. 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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  8. Article ; Online: Hepatitis B virus induces RNR-R2 expression via DNA damage response activation.

    Ricardo-Lax, Inna / Ramanan, Vyas / Michailidis, Eleftherios / Shamia, Tal / Reuven, Nina / Rice, Charles M / Shlomai, Amir / Shaul, Yosef

    Journal of hepatology

    2015  Volume 63, Issue 4, Page(s) 789–796

    Abstract: Background & aims: Hepatitis B virus (HBV) infects and replicates in quiescent hepatocytes, which are deficient in dNTPs, the critical precursors of HBV replication. Most tumor viruses promote dNTP production in host cells by inducing cell proliferation. ...

    Abstract Background & aims: Hepatitis B virus (HBV) infects and replicates in quiescent hepatocytes, which are deficient in dNTPs, the critical precursors of HBV replication. Most tumor viruses promote dNTP production in host cells by inducing cell proliferation. Although HBV is known as a major cause of hepatocellular carcinoma, it does not lead to cellular proliferation. Instead, HBV acquires dNTPs by activating the expression of the R2 subunit of the Ribonucleotide Reductase (RNR) holoenzyme, the cell cycle gene that is rate-limiting for generation of dNTPs, without inducing the cell cycle. We wished to elucidate the molecular basis of HBV-dependent R2 expression in quiescent cells.
    Methods: Quiescent HepG2 cells were transduced with an HBV-containing lentiviral vector, and primary human hepatocytes were infected with HBV. DNA damage response and RNR-R2 gene expression were monitored under this condition.
    Results: We report here that HBV-induced R2 expression is mediated by the E2F1 transcription factor, and that HBV induces E2F1 accumulation, modification and binding to the R2 promoter. We found that Chk1, a known E2F1 kinase that functions in response to DNA damage, was activated by HBV. In cells where Chk1 was pharmacologically inhibited, or depleted by shRNA-mediated knockdown, HBV-mediated R2 expression was severely attenuated. Furthermore, we found that HBV attenuates DNA repair, thus reducing cellular dNTP consumption.
    Conclusions: Our findings demonstrate that HBV exploits the Chk1-E2F1 axis of the DNA damage response pathway to induce R2 expression in a cell cycle-independent manner. This suggests that inhibition of this pathway may have a therapeutic value for HBV carriers.
    MeSH term(s) Apoptosis ; Blotting, Southern ; Blotting, Western ; Cell Cycle ; Cell Division ; Cell Proliferation ; DNA Damage/genetics ; Electrophoresis, Gel, Pulsed-Field ; Gene Expression Regulation, Viral ; Hepatitis B virus/genetics ; Hepatitis B virus/metabolism ; Hepatitis C/metabolism ; Hepatitis C/pathology ; Hepatitis C/virology ; Hepatocytes/metabolism ; Hepatocytes/pathology ; Humans ; Immunoprecipitation ; Polymerase Chain Reaction ; RNA, Viral/genetics ; Ribonucleotide Reductases/biosynthesis ; Ribonucleotide Reductases/genetics ; Virus Activation/genetics
    Chemical Substances RNA, Viral ; Ribonucleotide Reductases (EC 1.17.4.-) ; ribonucleotide reductase R2 subunit (EC 1.17.4.-)
    Language English
    Publishing date 2015-10
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 605953-3
    ISSN 1600-0641 ; 0168-8278
    ISSN (online) 1600-0641
    ISSN 0168-8278
    DOI 10.1016/j.jhep.2015.05.017
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  9. 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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  10. 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
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