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  1. Article ; Online: HIV-1 capsid stability and reverse transcription are finely balanced to minimize sensing of reverse transcription products

    Eschbach, Jenna E / Puray-Chavez, Maritza / Mohammed, Shawn / Wang, Qiankun / Xia, Ming / Huang, Lin-Chen / Shan, Liang / Kutluay, Sebla B

    mBio

    2024  , Page(s) e0034824

    Abstract: A critical determinant for early post-entry events, the HIV-1 capsid (CA) protein forms the conical core when it rearranges around the dimeric RNA genome and associated viral proteins. Although mutations in CA have been reported to alter innate immune ... ...

    Abstract A critical determinant for early post-entry events, the HIV-1 capsid (CA) protein forms the conical core when it rearranges around the dimeric RNA genome and associated viral proteins. Although mutations in CA have been reported to alter innate immune sensing of HIV-1, a direct link between core stability and sensing of HIV-1 nucleic acids has not been established. Herein, we assessed how manipulating the stability of the CA lattice through chemical and genetic approaches affects innate immune recognition of HIV-1. We found that destabilization of the CA lattice resulted in potent sensing of reverse transcription products when destabilization
    Importance: In HIV-1 particles, the dimeric RNA genome and associated viral proteins and enzymes are encased in a proteinaceous lattice composed of the viral capsid protein. Herein, we assessed how altering the stability of this capsid lattice through orthogonal genetic and chemical approaches impacts the induction of innate immune responses. Specifically, we found that decreasing capsid lattice stability results in more potent sensing of viral reverse transcription products, but not the genomic RNA, in a cGAS-STING-dependent manner. The recently developed capsid inhibitors lenacapavir and GS-CA1 enhanced the innate immune sensing of HIV-1. Unexpectedly, due to increased levels of reverse transcription and cytosolic accumulation of the resulting viral cDNA, capsid mutants with hyperstable cores also resulted in the potent induction of type I interferon-mediated innate immunity. Our findings suggest that HIV-1 capsid lattice stability and reverse transcription are finely balanced to minimize exposure of reverse transcription products in the cytosol of host cells.
    Language English
    Publishing date 2024-03-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.00348-24
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models.

    Puray-Chavez, Maritza / LaPak, Kyle M / Jasuja, Ria / Pan, Jiehong / Xu, Jian / Eschbach, Jenna E / Mohammed, Shawn / Lawson, Dana Q / Wang, Qibo / Brody, Steven L / Major, Michael B / Goldfarb, Dennis / Kutluay, Sebla B

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high ... ...

    Abstract Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high endogenous levels of ACE2 but surprisingly did not support SARS-CoV-2 replication. Here we report that this resistance is mediated by a basally active cGAS-STING pathway culminating in interferon (IFN)-mediated restriction of SARS-CoV-2 replication at a post-entry step. Pharmacological inhibition of JAK1/2, depletion of the IFN-α receptor and cGAS-STING pathway effectors substantially increased SARS-CoV-2 replication in these cell models. While depletion of cGAS or STING was sufficient to reduce the preexisting levels of IFN-stimulated genes (ISGs), SARS-CoV-2 infection in STING knockout cells independently induced ISG expression. Remarkably, SARS-CoV-2-induced ISG expression in STING knockout cell as well as in primary human airway cultures was limited to uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway, but not viral sensing or IFN production, in productively infected cells. Of note, SARS-CoV-2-infected primary human airway cells also displayed markedly lower levels of STING expression, raising the possibility that SARS-CoV-2 can target STING expression or preferentially infect cells that express low levels of STING. Finally, ectopic ACE2 overexpression overcame the IFN-mediated blocks, suggesting the ability of SARS-CoV-2 to overcome these possibly saturable blocks to infection. Our study highlights that in addition to viral receptors, basal activation of the cGAS-STING pathway and innate immune defenses may contribute to defining SARS-CoV-2 cellular tropism.
    Language English
    Publishing date 2024-01-08
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.07.574522
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Emergence of Compensatory Mutations Reveals the Importance of Electrostatic Interactions between HIV-1 Integrase and Genomic RNA.

    Shema Mugisha, Christian / Dinh, Tung / Kumar, Abhishek / Tenneti, Kasyap / Eschbach, Jenna E / Davis, Keanu / Gifford, Robert / Kvaratskhelia, Mamuka / Kutluay, Sebla B

    mBio

    2022  Volume 13, Issue 5, Page(s) e0043122

    Abstract: HIV-1 integrase (IN) has a noncatalytic function in virion maturation through its binding to the viral RNA genome (gRNA). Class II IN substitutions inhibit IN-gRNA binding and result in the formation of virions with aberrant morphologies marked by ... ...

    Abstract HIV-1 integrase (IN) has a noncatalytic function in virion maturation through its binding to the viral RNA genome (gRNA). Class II IN substitutions inhibit IN-gRNA binding and result in the formation of virions with aberrant morphologies marked by mislocalization of the gRNA between the capsid lattice and the lipid envelope. These viruses are noninfectious due to a block at an early reverse transcription stage in target cells. HIV-1 IN utilizes basic residues within its C-terminal domain (CTD) to bind to the gRNA; however, the molecular nature of how these residues mediate gRNA binding and whether other regions of IN are involved remain unknown. To address this, we have isolated compensatory substitutions in the background of a class II IN mutant virus bearing R269A/K273A substitutions within the IN-CTD. We found that the nearby D256N and D270N compensatory substitutions restored the ability of IN to bind gRNA and led to the formation of mature infectious virions. Reinstating the local positive charge of the IN-CTD through individual D256R, D256K, D278R, and D279R substitutions was sufficient to specifically restore IN-gRNA binding and reverse transcription for the IN R269A/K273A as well as the IN R262A/R263A class II mutants. Structural modeling suggested that compensatory substitutions in the D256 residue created an additional interaction interface for gRNA binding, whereas other substitutions acted locally within the unstructured C-terminal tail of IN. Taken together, our findings highlight the essential role of CTD in gRNA binding and reveal the importance of pliable electrostatic interactions between the IN-CTD and the gRNA.
    MeSH term(s) RNA, Viral/genetics ; RNA, Viral/metabolism ; Virus Assembly/genetics ; Static Electricity ; Aspartic Acid/metabolism ; HIV-1/physiology ; Virion/genetics ; Virion/metabolism ; Mutation ; Genomics ; Lipids
    Chemical Substances p31 integrase protein, Human immunodeficiency virus 1 (YY6481J2FF) ; RNA, Viral ; Aspartic Acid (30KYC7MIAI) ; Lipids
    Language English
    Publishing date 2022-08-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mbio.00431-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models

    Puray-Chavez, Maritza / LaPak, Kyle M. / Jasuja, Ria / Pan, Jiehong / Xu, Jian / Eschbach, Jenna E. / Mohammed, Shawn / Lawson, Dana Q. / Wang, Qibo / Brody, Steven L. / Major, Michael B. / Goldfarb, Dennis / Kutluay, Sebla B.

    bioRxiv

    Abstract: Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high ... ...

    Abstract Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high endogenous levels of ACE2 but surprisingly did not support SARS-CoV-2 replication. Here we report that this resistance is mediated by a basally active cGAS-STING pathway culminating in interferon (IFN)-mediated restriction of SARS-CoV-2 replication at a post-entry step. Pharmacological inhibition of JAK1/2, depletion of the IFN-alpha; receptor and cGAS-STING pathway effectors substantially increased SARS-CoV-2 replication in these cell models. While depletion of cGAS or STING was sufficient to reduce the preexisting levels of IFN-stimulated genes (ISGs), SARS-CoV-2 infection in STING knockout cells independently induced ISG expression. Remarkably, SARS-CoV-2-induced ISG expression in STING knockout cell as well as in primary human airway cultures was limited to uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway, but not viral sensing or IFN production, in productively infected cells. Of note, SARS-CoV-2-infected primary human airway cells also displayed markedly lower levels of STING expression, raising the possibility that SARS-CoV-2 can target STING expression or preferentially infect cells that express low levels of STING. Finally, ectopic ACE2 overexpression overcame the IFN-mediated blocks, suggesting the ability of SARS-CoV-2 to overcome these possibly saturable blocks to infection. Our study highlights that in addition to viral receptors, basal activation of the cGAS-STING pathway and innate immune defenses may contribute to defining SARS-CoV-2 cellular tropism.
    Keywords covid19
    Language English
    Publishing date 2024-01-08
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.01.07.574522
    Database COVID19

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  5. Article ; Online: Capsid Lattice Destabilization Leads to Premature Loss of the Viral Genome and Integrase Enzyme during HIV-1 Infection.

    Eschbach, Jenna E / Elliott, Jennifer L / Li, Wen / Zadrozny, Kaneil K / Davis, Keanu / Mohammed, Shawn J / Lawson, Dana Q / Pornillos, Owen / Engelman, Alan N / Kutluay, Sebla B

    Journal of virology

    2020  Volume 95, Issue 2

    Abstract: The human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral ribonucleoprotein complex (vRNP) consisting of a dimeric viral genome and associated proteins, together constituting the viral core. Upon entry ... ...

    Abstract The human immunodeficiency virus type 1 (HIV-1) capsid (CA) protein forms a conical lattice around the viral ribonucleoprotein complex (vRNP) consisting of a dimeric viral genome and associated proteins, together constituting the viral core. Upon entry into target cells, the viral core undergoes a process termed uncoating, during which CA molecules are shed from the lattice. Although the timing and degree of uncoating are important for reverse transcription and integration, the molecular basis of this phenomenon remains unclear. Using complementary approaches, we assessed the impact of core destabilization on the intrinsic stability of the CA lattice
    MeSH term(s) Animals ; Capsid/metabolism ; Capsid Proteins/genetics ; Capsid Proteins/metabolism ; Cell Line ; Cricetinae ; Genome, Viral ; HIV Integrase/metabolism ; HIV-1/physiology ; Humans ; Mutation ; RNA, Viral/metabolism ; Reverse Transcription ; Viral Core Proteins/metabolism ; Virion/genetics ; Virion/metabolism ; Virus Uncoating
    Chemical Substances Capsid Proteins ; RNA, Viral ; Viral Core Proteins ; HIV Integrase (EC 2.7.7.-)
    Language English
    Publishing date 2020-12-22
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80174-4
    ISSN 1098-5514 ; 0022-538X
    ISSN (online) 1098-5514
    ISSN 0022-538X
    DOI 10.1128/JVI.00984-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Integrase-RNA interactions underscore the critical role of integrase in HIV-1 virion morphogenesis.

    Elliott, Jennifer L / Eschbach, Jenna E / Koneru, Pratibha C / Li, Wen / Puray-Chavez, Maritza / Townsend, Dana / Lawson, Dana Q / Engelman, Alan N / Kvaratskhelia, Mamuka / Kutluay, Sebla B

    eLife

    2020  Volume 9

    Abstract: A large number of human immunodeficiency virus 1 (HIV-1) integrase (IN) alterations, referred to as class II substitutions, exhibit pleiotropic effects during virus replication. However, the underlying mechanism for the class II phenotype is not known. ... ...

    Abstract A large number of human immunodeficiency virus 1 (HIV-1) integrase (IN) alterations, referred to as class II substitutions, exhibit pleiotropic effects during virus replication. However, the underlying mechanism for the class II phenotype is not known. Here we demonstrate that all tested class II IN substitutions compromised IN-RNA binding in virions by one of the three distinct mechanisms: (i) markedly reducing IN levels thus precluding the formation of IN complexes with viral RNA; (ii) adversely affecting functional IN multimerization and consequently impairing IN binding to viral RNA; and (iii) directly compromising IN-RNA interactions without substantially affecting IN levels or functional IN multimerization. Inhibition of IN-RNA interactions resulted in the mislocalization of viral ribonucleoprotein complexes outside the capsid lattice, which led to premature degradation of the viral genome and IN in target cells. Collectively, our studies uncover causal mechanisms for the class II phenotype and highlight an essential role of IN-RNA interactions for accurate virion maturation.
    MeSH term(s) Capsid/metabolism ; Genome, Viral/genetics ; HEK293 Cells ; HIV Infections/virology ; HIV Integrase/genetics ; HIV Integrase/metabolism ; HIV-1/enzymology ; HIV-1/genetics ; HIV-1/growth & development ; HIV-1/physiology ; Humans ; Phenotype ; Protein Binding ; Protein Multimerization ; RNA, Viral/metabolism ; Ribonucleoproteins/metabolism ; Virion/enzymology ; Virion/genetics ; Virion/growth & development ; Virion/physiology ; Virus Integration ; Virus Replication
    Chemical Substances RNA, Viral ; Ribonucleoproteins ; HIV Integrase (EC 2.7.7.-) ; p31 integrase protein, Human immunodeficiency virus 1 (YY6481J2FF)
    Language English
    Publishing date 2020-09-22
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.54311
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell.

    Puray-Chavez, Maritza / LaPak, Kyle M / Schrank, Travis P / Elliott, Jennifer L / Bhatt, Dhaval P / Agajanian, Megan J / Jasuja, Ria / Lawson, Dana Q / Davis, Keanu / Rothlauf, Paul W / Liu, Zhuoming / Jo, Heejoon / Lee, Nakyung / Tenneti, Kasyap / Eschbach, Jenna E / Shema Mugisha, Christian / Cousins, Emily M / Cloer, Erica W / Vuong, Hung R /
    VanBlargan, Laura A / Bailey, Adam L / Gilchuk, Pavlo / Crowe, James E / Diamond, Michael S / Hayes, D Neil / Whelan, Sean P J / Horani, Amjad / Brody, Steven L / Goldfarb, Dennis / Major, M Ben / Kutluay, Sebla B

    Cell reports

    2021  Volume 36, Issue 2, Page(s) 109364

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) variants govern transmissibility, responsiveness to vaccination, and disease severity. In a screen for new models of SARS-CoV-2 infection, we identify human H522 lung adenocarcinoma ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) variants govern transmissibility, responsiveness to vaccination, and disease severity. In a screen for new models of SARS-CoV-2 infection, we identify human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of angiotensin-converting enzyme 2 (ACE2) expression. Remarkably, H522 infection requires the E484D S variant; viruses expressing wild-type S are not infectious. Anti-S monoclonal antibodies differentially neutralize SARS-CoV-2 E484D S in H522 cells as compared to ACE2-expressing cells. Sera from vaccinated individuals block this alternative entry mechanism, whereas convalescent sera are less effective. Although the H522 receptor remains unknown, depletion of surface heparan sulfates block H522 infection. Temporally resolved transcriptomic and proteomic profiling reveal alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type I interferon signaling. These findings establish an alternative SARS-CoV-2 host cell receptor for the E484D SARS-CoV-2 variant, which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.
    MeSH term(s) Amino Acid Substitution ; Angiotensin-Converting Enzyme 2 ; Animals ; Antibodies, Monoclonal/immunology ; Antibodies, Viral/immunology ; COVID-19/immunology ; COVID-19/metabolism ; Cell Cycle ; Cell Line, Tumor ; Chlorocebus aethiops ; Gene Expression Profiling ; Heparitin Sulfate/metabolism ; Humans ; Interferon Type I/metabolism ; Interferon-Induced Helicase, IFIH1/metabolism ; Models, Biological ; Protein Binding ; Protein Domains ; Proteomics ; Receptors, Virus/metabolism ; SARS-CoV-2 ; Serine Endopeptidases/metabolism ; Signal Transduction ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Vero Cells ; Virus Internalization ; Virus Replication
    Chemical Substances Antibodies, Monoclonal ; Antibodies, Viral ; Interferon Type I ; Receptors, Virus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Heparitin Sulfate (9050-30-0) ; 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.-) ; IFIH1 protein, human (EC 3.6.1.-) ; Interferon-Induced Helicase, IFIH1 (EC 3.6.4.13)
    Language English
    Publishing date 2021-06-23
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2021.109364
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article: Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell.

    Puray-Chavez, Maritza / LaPak, Kyle M / Schrank, Travis P / Elliott, Jennifer L / Bhatt, Dhaval P / Agajanian, Megan J / Jasuja, Ria / Lawson, Dana Q / Davis, Keanu / Rothlauf, Paul W / Jo, Heejoon / Lee, Nakyung / Tenneti, Kasyap / Eschbach, Jenna E / Mugisha, Christian Shema / Vuong, Hung R / Bailey, Adam L / Hayes, D Neil / Whelan, Sean P J /
    Horani, Amjad / Brody, Steven L / Goldfarb, Dennis / Major, M Ben / Kutluay, Sebla B

    bioRxiv : the preprint server for biology

    2021  

    Abstract: ... ...

    Abstract Established
    Language English
    Publishing date 2021-03-01
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2021.03.01.433431
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell

    Puray-Chavez, Maritza / Lapak, Kyle M / Schrank, Travis P. / Elliott, Jennifer L / Bhatt, Dhaval P / Agajanian, Megan J / Jasuja, Ria / Lawson, Dana Q / Davis, Keanu / Rothlauf, Paul W / Jo, Heejoon / Lee, Nakyung / Tenneti, Kasyap / Eschbach, Jenna E / Shema Mugisha, Christian / Vuong, Hung R / Bailey, Adam L / Hayes, D. Neil / Whelan, Sean P.J. /
    Horani, Amjad / Brody, Steven L / Goldfarb, Dennis / Major, M. Ben / Kutluay, Sebla B

    bioRxiv

    Abstract: Established in vitro models for SARS-CoV-2 infection are limited and include cell lines of non-human origin and those engineered to overexpress ACE2, the cognate host cell receptor. We identified human H522 lung adenocarcinoma cells as naturally ... ...

    Abstract Established in vitro models for SARS-CoV-2 infection are limited and include cell lines of non-human origin and those engineered to overexpress ACE2, the cognate host cell receptor. We identified human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of ACE2. Infection of H522 cells required the SARS-CoV-2 spike protein, though in contrast to ACE2-dependent models, spike alone was not sufficient for H522 infection. Temporally resolved transcriptomic and proteomic profiling revealed alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type-I interferon signaling. Focused chemical screens point to important roles for clathrin-mediated endocytosis and endosomal cathepsins in SARS-CoV-2 infection of H522 cells. These findings imply the utilization of an alternative SARS-CoV-2 host cell receptor which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.
    Keywords covid19
    Language English
    Publishing date 2021-03-01
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2021.03.01.433431
    Database COVID19

    Kategorien

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