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  1. Article ; Online: Dose-Dependent Effects of Radiation on Mitochondrial Morphology and Clonogenic Cell Survival in Human Microvascular Endothelial Cells.

    Wang, Li / Rivas, Rafael / Wilson, Angelo / Park, Yu Min / Walls, Shannon / Yu, Tianzheng / Miller, Alexandra C

    Cells

    2023  Volume 13, Issue 1

    Abstract: To better understand radiation-induced organ dysfunction at both high and low doses, it is critical to understand how endothelial cells (ECs) respond to radiation. The impact of irradiation (IR) on ECs varies depending on the dose administered. High ... ...

    Abstract To better understand radiation-induced organ dysfunction at both high and low doses, it is critical to understand how endothelial cells (ECs) respond to radiation. The impact of irradiation (IR) on ECs varies depending on the dose administered. High doses can directly damage ECs, leading to EC impairment. In contrast, the effects of low doses on ECs are subtle but more complex. Low doses in this study refer to radiation exposure levels that are below those that cause immediate and necrotic damage. Mitochondria are the primary cellular components affected by IR, and this study explored their role in determining the effect of radiation on microvascular endothelial cells. Human dermal microvascular ECs (HMEC-1) were exposed to varying IR doses ranging from 0.1 Gy to 8 Gy (~0.4 Gy/min) in the AFRRI 60-Cobalt facility. Results indicated that high doses led to a dose-dependent reduction in cell survival, which can be attributed to factors such as DNA damage, oxidative stress, cell senescence, and mitochondrial dysfunction. However, low doses induced a small but significant increase in cell survival, and this was achieved without detectable DNA damage, oxidative stress, cell senescence, or mitochondrial dysfunction in HMEC-1. Moreover, the mitochondrial morphology was assessed, revealing that all doses increased the percentage of elongated mitochondria, with low doses (0.25 Gy and 0.5 Gy) having a greater effect than high doses. However, only high doses caused an increase in mitochondrial fragmentation/swelling. The study further revealed that low doses induced mitochondrial elongation, likely via an increase in mitochondrial fusion protein 1 (Mfn1), while high doses caused mitochondrial fragmentation via a decrease in optic atrophy protein 1 (Opa1). In conclusion, the study suggests, for the first time, that changes in mitochondrial morphology are likely involved in the mechanism for the radiation dose-dependent effect on the survival of microvascular endothelial cells. This research, by delineating the specific mechanisms through which radiation affects endothelial cells, offers invaluable insights into the potential impact of radiation exposure on cardiovascular health.
    MeSH term(s) Humans ; Endothelial Cells ; Cell Survival ; Mitochondria ; Cellular Senescence ; Mitochondrial Proteins ; Radiation Injuries ; Mitochondrial Diseases
    Chemical Substances Mitochondrial Proteins
    Language English
    Publishing date 2023-12-23
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells13010039
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Protein nanoparticle vaccines induce potent neutralizing antibody responses against MERS-CoV.

    Chao, Cara W / Sprouse, Kaitlin R / Miranda, Marcos C / Catanzaro, Nicholas J / Hubbard, Miranda L / Addetia, Amin / Stewart, Cameron / Brown, Jack T / Dosey, Annie / Valdez, Adian / Ravichandran, Rashmi / Hendricks, Grace G / Ahlrichs, Maggie / Dobbins, Craig / Hand, Alexis / Treichel, Catherine / Willoughby, Isabelle / Walls, Alexandra C / McGuire, Andrew T /
    Leaf, Elizabeth M / Baric, Ralph S / Schäfer, Alexandra / Veesler, David / King, Neil P

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral fusogen and the target of neutralizing antibodies, and ... ...

    Abstract Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic betacoronavirus that causes severe and often lethal respiratory illness in humans. The MERS-CoV spike (S) protein is the viral fusogen and the target of neutralizing antibodies, and has therefore been the focus of vaccine design efforts. Currently there are no licensed vaccines against MERS-CoV and only a few candidates have advanced to Phase I clinical trials. Here we developed MERS-CoV vaccines utilizing a computationally designed protein nanoparticle platform that has generated safe and immunogenic vaccines against various enveloped viruses, including a licensed vaccine for SARS-CoV-2. Two-component protein nanoparticles displaying MERS-CoV S-derived antigens induced robust neutralizing antibody responses and protected mice against challenge with mouse-adapted MERS-CoV. Electron microscopy polyclonal epitope mapping and serum competition assays revealed the specificities of the dominant antibody responses elicited by immunogens displaying the prefusion-stabilized S-2P trimer, receptor binding domain (RBD), or N-terminal domain (NTD). An RBD nanoparticle vaccine elicited antibodies targeting multiple non-overlapping epitopes in the RBD, whereas anti-NTD antibodies elicited by the S-2P- and NTD-based immunogens converged on a single antigenic site. Our findings demonstrate the potential of two-component nanoparticle vaccine candidates for MERS-CoV and suggest that this platform technology could be broadly applicable to betacoronavirus vaccine development.
    Language English
    Publishing date 2024-03-14
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.13.584735
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Closing coronavirus spike glycoproteins by structure-guided design.

    McCallum, Matthew / Walls, Alexandra C / Corti, Davide / Veesler, David

    bioRxiv : the preprint server for biology

    2020  

    Abstract: The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes ... ...

    Abstract The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface, determining host and tissue tropism, and fusion of the viral and host membranes. Although SARS-CoV-2 S is the main target of neutralizing antibodies and the focus of vaccine design, its stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a prefusion SARS-CoV-2 S ectodomain trimer construct covalently stabilized in the closed conformation. Structural and antigenicity analysis showed we successfully shut S in the closed state without otherwise altering its architecture. Finally, we show that this engineering strategy is applicable to other β-coronavirus S glycoproteins and might become an important tool for vaccine design, structural biology, serology and immunology studies.
    Keywords covid19
    Language English
    Publishing date 2020-06-03
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2020.06.03.129817
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: ACE2 binding is an ancestral and evolvable trait of sarbecoviruses.

    Starr, Tyler N / Zepeda, Samantha K / Walls, Alexandra C / Greaney, Allison J / Alkhovsky, Sergey / Veesler, David / Bloom, Jesse D

    Nature

    2022  Volume 603, Issue 7903, Page(s) 913–918

    Abstract: Two different sarbecoviruses have caused major human outbreaks in the past two ... ...

    Abstract Two different sarbecoviruses have caused major human outbreaks in the past two decades
    MeSH term(s) Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; Animals ; Binding Sites ; COVID-19/virology ; Chiroptera/virology ; Evolution, Molecular ; Humans ; Protein Binding ; SARS Virus/classification ; SARS Virus/genetics ; SARS Virus/metabolism ; SARS-CoV-2/chemistry ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
    Language English
    Publishing date 2022-02-03
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-022-04464-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Structural changes in the SARS-CoV-2 spike E406W mutant escaping a clinical monoclonal antibody cocktail.

    Addetia, Amin / Park, Young-Jun / Starr, Tyler / Greaney, Allison J / Sprouse, Kaitlin R / Bowen, John E / Tiles, Sasha W / Van Voorhis, Wesley C / Bloom, Jesse D / Corti, Davide / Walls, Alexandra C / Veesler, David

    Cell reports

    2023  Volume 42, Issue 6, Page(s) 112621

    Abstract: Continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is eroding antibody responses elicited by prior vaccination and infection. The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated ... ...

    Abstract Continued evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is eroding antibody responses elicited by prior vaccination and infection. The SARS-CoV-2 receptor-binding domain (RBD) E406W mutation abrogates neutralization mediated by the REGEN-COV therapeutic monoclonal antibody (mAb) COVID-19 cocktail and the AZD1061 (COV2-2130) mAb. Here, we show that this mutation remodels the receptor-binding site allosterically, thereby altering the epitopes recognized by these three mAbs and vaccine-elicited neutralizing antibodies while remaining functional. Our results demonstrate the spectacular structural and functional plasticity of the SARS-CoV-2 RBD, which is continuously evolving in emerging SARS-CoV-2 variants, including currently circulating strains that are accumulating mutations in the antigenic sites remodeled by the E406W substitution.
    MeSH term(s) Humans ; SARS-CoV-2 ; Combined Antibody Therapeutics ; COVID-19 ; Antibodies, Viral ; Antibodies, Neutralizing ; Antibodies, Monoclonal ; Spike Glycoprotein, Coronavirus ; Neutralization Tests
    Chemical Substances Combined Antibody Therapeutics ; Antibodies, Viral ; Antibodies, Neutralizing ; Antibodies, Monoclonal ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2023-05-26
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2023.112621
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains.

    Starr, Tyler N / Greaney, Allison J / Stewart, Cameron M / Walls, Alexandra C / Hannon, William W / Veesler, David / Bloom, Jesse D

    PLoS pathogens

    2022  Volume 18, Issue 11, Page(s) e1010951

    Abstract: SARS-CoV-2 continues to acquire mutations in the spike receptor-binding domain (RBD) that impact ACE2 receptor binding, folding stability, and antibody recognition. Deep mutational scanning prospectively characterizes the impacts of mutations on these ... ...

    Abstract SARS-CoV-2 continues to acquire mutations in the spike receptor-binding domain (RBD) that impact ACE2 receptor binding, folding stability, and antibody recognition. Deep mutational scanning prospectively characterizes the impacts of mutations on these biochemical properties, enabling rapid assessment of new mutations seen during viral surveillance. However, the effects of mutations can change as the virus evolves, requiring updated deep mutational scans. We determined the impacts of all single amino acid mutations in the Omicron BA.1 and BA.2 RBDs on ACE2-binding affinity, RBD folding, and escape from binding by the LY-CoV1404 (bebtelovimab) monoclonal antibody. The effects of some mutations in Omicron RBDs differ from those measured in the ancestral Wuhan-Hu-1 background. These epistatic shifts largely resemble those previously seen in the Alpha variant due to the convergent epistatically modifying N501Y substitution. However, Omicron variants show additional lineage-specific shifts, including examples of the epistatic phenomenon of entrenchment that causes the Q498R and N501Y substitutions present in Omicron to be more favorable in that background than in earlier viral strains. In contrast, the Omicron substitution Q493R exhibits no sign of entrenchment, with the derived state, R493, being as unfavorable for ACE2 binding in Omicron RBDs as in Wuhan-Hu-1. Likely for this reason, the R493Q reversion has occurred in Omicron sub-variants including BA.4/BA.5 and BA.2.75, where the affinity buffer from R493Q reversion may potentiate concurrent antigenic change. Consistent with prior studies, we find that Omicron RBDs have reduced expression, and identify candidate stabilizing mutations that ameliorate this deficit. Last, our maps highlight a broadening of the sites of escape from LY-CoV1404 antibody binding in BA.1 and BA.2 compared to the ancestral Wuhan-Hu-1 background. These BA.1 and BA.2 deep mutational scanning datasets identify shifts in the RBD mutational landscape and inform ongoing efforts in viral surveillance.
    MeSH term(s) Humans ; Angiotensin-Converting Enzyme 2/genetics ; Spike Glycoprotein, Coronavirus ; SARS-CoV-2/genetics ; COVID-19/genetics ; Antibodies, Neutralizing/chemistry ; Mutation
    Chemical Substances Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Spike Glycoprotein, Coronavirus ; Antibodies, Neutralizing ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-11-18
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
    ZDB-ID 2205412-1
    ISSN 1553-7374 ; 1553-7374
    ISSN (online) 1553-7374
    ISSN 1553-7374
    DOI 10.1371/journal.ppat.1010951
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.

    Walls, Alexandra C / Park, Young-Jun / Tortorici, M Alejandra / Wall, Abigail / McGuire, Andrew T / Veesler, David

    Cell

    2020  Volume 183, Issue 6, Page(s) 1735

    Language English
    Publishing date 2020-12-14
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2020.11.032
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Structure-guided covalent stabilization of coronavirus spike glycoprotein trimers in the closed conformation.

    McCallum, Matthew / Walls, Alexandra C / Bowen, John E / Corti, Davide / Veesler, David

    Nature structural & molecular biology

    2020  Volume 27, Issue 10, Page(s) 942–949

    Abstract: SARS-CoV-2 is the causative agent of the COVID-19 pandemic, with 10 million infections and more than 500,000 fatalities by June 2020. To initiate infection, the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface and fusion of ... ...

    Abstract SARS-CoV-2 is the causative agent of the COVID-19 pandemic, with 10 million infections and more than 500,000 fatalities by June 2020. To initiate infection, the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface and fusion of the viral and host membranes. Prefusion SARS-CoV-2 S is the main target of neutralizing antibodies and the focus of vaccine design. However, its limited stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a construct corresponding to the prefusion SARS-CoV-2 S ectodomain trimer, covalently stabilized by a disulfide bond in the closed conformation. Structural and antigenicity analyses show we successfully shut S in the closed state without otherwise altering its architecture. We demonstrate that this strategy is applicable to other β-coronaviruses, such as SARS-CoV and MERS-CoV, and might become an important tool for structural biology, serology, vaccine design and immunology studies.
    MeSH term(s) Antibodies, Monoclonal/metabolism ; Antibodies, Neutralizing/metabolism ; Betacoronavirus/chemistry ; Betacoronavirus/genetics ; Betacoronavirus/immunology ; Betacoronavirus/metabolism ; Cryoelectron Microscopy ; Disulfides/chemistry ; Electrophoresis, Polyacrylamide Gel ; Enzyme-Linked Immunosorbent Assay ; Humans ; Models, Molecular ; Mutation ; Protein Conformation ; Protein Domains ; Protein Engineering ; Protein Multimerization ; Protein Stability ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/immunology ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Antibodies, Monoclonal ; Antibodies, Neutralizing ; Disulfides ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-08-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-020-0483-8
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Structure, function and antigenicity of the SARS-CoV-2 spike glycoprotein

    Walls, Alexandra C. / Park, Young-Jun / Tortorici, M. Alexandra / Wall, Abigail / McGuire, Andrew T. / Veesler, David

    bioRxiv

    Keywords covid19
    Language English
    Publishing date 2020-02-20
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2020.02.19.956581
    Database COVID19

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  10. Article ; Online: Deep mutational scans for ACE2 binding, RBD expression, and antibody escape in the SARS-CoV-2 Omicron BA.1 and BA.2 receptor-binding domains.

    Tyler N Starr / Allison J Greaney / Cameron M Stewart / Alexandra C Walls / William W Hannon / David Veesler / Jesse D Bloom

    PLoS Pathogens, Vol 18, Iss 11, p e

    2022  Volume 1010951

    Abstract: SARS-CoV-2 continues to acquire mutations in the spike receptor-binding domain (RBD) that impact ACE2 receptor binding, folding stability, and antibody recognition. Deep mutational scanning prospectively characterizes the impacts of mutations on these ... ...

    Abstract SARS-CoV-2 continues to acquire mutations in the spike receptor-binding domain (RBD) that impact ACE2 receptor binding, folding stability, and antibody recognition. Deep mutational scanning prospectively characterizes the impacts of mutations on these biochemical properties, enabling rapid assessment of new mutations seen during viral surveillance. However, the effects of mutations can change as the virus evolves, requiring updated deep mutational scans. We determined the impacts of all single amino acid mutations in the Omicron BA.1 and BA.2 RBDs on ACE2-binding affinity, RBD folding, and escape from binding by the LY-CoV1404 (bebtelovimab) monoclonal antibody. The effects of some mutations in Omicron RBDs differ from those measured in the ancestral Wuhan-Hu-1 background. These epistatic shifts largely resemble those previously seen in the Alpha variant due to the convergent epistatically modifying N501Y substitution. However, Omicron variants show additional lineage-specific shifts, including examples of the epistatic phenomenon of entrenchment that causes the Q498R and N501Y substitutions present in Omicron to be more favorable in that background than in earlier viral strains. In contrast, the Omicron substitution Q493R exhibits no sign of entrenchment, with the derived state, R493, being as unfavorable for ACE2 binding in Omicron RBDs as in Wuhan-Hu-1. Likely for this reason, the R493Q reversion has occurred in Omicron sub-variants including BA.4/BA.5 and BA.2.75, where the affinity buffer from R493Q reversion may potentiate concurrent antigenic change. Consistent with prior studies, we find that Omicron RBDs have reduced expression, and identify candidate stabilizing mutations that ameliorate this deficit. Last, our maps highlight a broadening of the sites of escape from LY-CoV1404 antibody binding in BA.1 and BA.2 compared to the ancestral Wuhan-Hu-1 background. These BA.1 and BA.2 deep mutational scanning datasets identify shifts in the RBD mutational landscape and inform ongoing efforts in viral ...
    Keywords Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
    Subject code 570
    Language English
    Publishing date 2022-11-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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