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  1. Article: Aberrant Bodies: An Alternative Metabolic Homeostasis Allowing Survivability?

    Kozusnik, Thomas / Adams, Simone E / Greub, Gilbert

    Microorganisms

    2024  Volume 12, Issue 3

    Abstract: ... ...

    Abstract The
    Language English
    Publishing date 2024-02-29
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms12030495
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Generation and characterization of interferon-beta-resistant H1N1 influenza A virus.

    Hickerson, Brady T / Adams, Simone E / Bovin, Nicolai V / Donnelly, Raymond P / Ilyushina, Natalia A

    Acta virologica

    2022  Volume 66, Issue 3, Page(s) 263–274

    Abstract: Interferons (IFNs) mediate innate antiviral activity against many types of viruses, including influenza viruses. In light of their potential use as anti-influenza agents, we examined whether resistance to these host antiviral proteins can develop. We ... ...

    Abstract Interferons (IFNs) mediate innate antiviral activity against many types of viruses, including influenza viruses. In light of their potential use as anti-influenza agents, we examined whether resistance to these host antiviral proteins can develop. We generated IFN-β-resistant variants of the A/California/04/09 (H1N1) virus by serial passage in a human airway epithelial cell line, Calu-3, under IFN-β selective pressure. The combination of specific mutations (i.e., L373I in PB1, K154E1, D222G1, I56V2, and V122I2 in HA, and M269I in NA) correlated with decreased ability of the virus to induce expression of IFN (IFNB1, IFNL1, and IFNL2/3) and IFN-stimulated genes (IFIT1, IFIT3, OAS1, IRF7, and MX1) by target respiratory epithelial cells. In addition, the IFN-induced mutations were associated with decreased HA binding affinity to α2,6 sialyl receptors, reduced NA enzyme catalytic activity, and decreased polymerase transcription activity. Our findings demonstrate that the mutations in the influenza HA, NA, and PB1 proteins induced by IFN-b selective pressure significantly increase viral ability to productively infect and replicate in host cells. Keywords: influenza A virus; interferon-β; lung epithelial cells; interferon response.
    MeSH term(s) Antiviral Agents/pharmacology ; Cytokines ; Humans ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A virus ; Influenza, Human/genetics ; Interferon-beta/genetics ; Interferons/genetics ; Interferons/pharmacology ; Virus Replication
    Chemical Substances Antiviral Agents ; Cytokines ; Interferon-beta (77238-31-4) ; Interferons (9008-11-1)
    Language English
    Publishing date 2022-08-26
    Publishing country Slovakia
    Document type Journal Article
    ZDB-ID 210452-0
    ISSN 1336-2305 ; 0001-723X
    ISSN (online) 1336-2305
    ISSN 0001-723X
    DOI 10.4149/av_2022_311
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Effect of influenza H1N1 neuraminidase V116A and I117V mutations on NA activity and sensitivity to NA inhibitors.

    Adams, Simone E / Lee, Nicolette / Lugovtsev, Vladimir Y / Kan, Anastasia / Donnelly, Raymond P / Ilyushina, Natalia A

    Antiviral research

    2019  Volume 169, Page(s) 104539

    Abstract: Neuraminidase inhibitors (NAIs) play a key role in the management of influenza. Given the limited number of FDA-approved anti-influenza drugs, evaluation of potential drug-resistant variants is of high priority. Two NA mutations, V116A and I117V, are ... ...

    Abstract Neuraminidase inhibitors (NAIs) play a key role in the management of influenza. Given the limited number of FDA-approved anti-influenza drugs, evaluation of potential drug-resistant variants is of high priority. Two NA mutations, V116A and I117V, are found in ∼0.6% of human, avian, and swine N1 isolates. Using the A/California/04/09-like (CA/04, H1N1) background, we examined the impact of V116A and I117V NA mutations on NAI susceptibility, substrate specificity, and replicative capacity in normal human bronchial (NHBE) cells and a human respiratory epithelial cell line (Calu-3). We compared the impact of V116A and I117V on the functional properties of NA and compared these mutations with that of previously reported NAI-resistant mutations, E119A, H275Y, and N295S. All NA mutations were genetically stable. None of the viruses carrying NA mutations grew to significantly lower titers than CA/04 in Calu-3 cells. In contrast, V116A, I117V, E119A, and N295S substitutions resulted in significantly lower viral titers (1.2 logs) than the parental CA/04 virus in NHBE cells. V116A conferred reduced sensitivity to oseltamivir and zanamivir (13.7-fold). When MUNANA, 3'SL, and 6'SL substrates were applied, we observed that V116A reduced binding ability for all substrates (13.9-fold) and I117V led to the significantly decreased affinity for MUNANA and 6'SL (4.2-fold). Neither mutation altered the catalytic efficiency (k
    MeSH term(s) Animals ; Antiviral Agents/pharmacology ; Cell Line ; Drug Resistance, Viral/drug effects ; Drug Resistance, Viral/genetics ; Enzyme Inhibitors/pharmacology ; Humans ; Hymecromone/analogs & derivatives ; Hymecromone/pharmacology ; Influenza A Virus, H1N1 Subtype/drug effects ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza, Human/virology ; Kinetics ; Mutation ; Neuraminidase/antagonists & inhibitors ; Neuraminidase/genetics ; Oseltamivir/pharmacology ; Sequence Analysis ; Swine ; Zanamivir/pharmacology
    Chemical Substances Antiviral Agents ; Enzyme Inhibitors ; Oseltamivir (20O93L6F9H) ; Hymecromone (3T5NG4Q468) ; 2'-(4-methylumbelliferyl)-alpha-D-N-acetylneuraminic acid (59322-44-0) ; Neuraminidase (EC 3.2.1.18) ; Zanamivir (L6O3XI777I)
    Language English
    Publishing date 2019-06-19
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 306628-9
    ISSN 1872-9096 ; 0166-3542
    ISSN (online) 1872-9096
    ISSN 0166-3542
    DOI 10.1016/j.antiviral.2019.104539
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Antigenic Architecture of the H7N2 Influenza Virus Hemagglutinin Belonging to the North American Lineage.

    Lyashko, Aleksandr V / Timofeeva, Tatiana A / Rudneva, Irina A / Lomakina, Natalia F / Treshchalina, Anastasia A / Gambaryan, Alexandra S / Sorokin, Evgenii V / Tsareva, Tatiana R / Adams, Simone E / Prilipov, Alexey G / Sadykova, Galina K / Timofeev, Boris I / Logunov, Denis Y / Gintsburg, Alexander L

    International journal of molecular sciences

    2023  Volume 25, Issue 1

    Abstract: The North American low pathogenic H7N2 avian influenza A viruses, which lack the 220-loop in the hemagglutinin (HA), possess dual receptor specificity for avian- and human-like receptors. The purpose of this work was to determine which amino acid ... ...

    Abstract The North American low pathogenic H7N2 avian influenza A viruses, which lack the 220-loop in the hemagglutinin (HA), possess dual receptor specificity for avian- and human-like receptors. The purpose of this work was to determine which amino acid substitutions in HA affect viral antigenic and phenotypic properties that may be important for virus evolution. By obtaining escape mutants under the immune pressure of treatment with monoclonal antibodies, antigenically important amino acids were determined to be at positions 125, 135, 157, 160, 198, 200, and 275 (H3 numbering). These positions, except 125 and 275, surround the receptor binding site. The substitutions A135S and A135T led to the appearance of an N-glycosylation site at 133N, which reduced affinity for the avian-like receptor analog and weakened binding with tested monoclonal antibodies. Additionally, the A135S substitution is associated with the adaptation of avian viruses to mammals (cat, human, or mouse). The mutation A160V decreased virulence in mice and increased affinity for the human-type receptor analog. Conversely, substitution G198E, in combination with 157N or 160E, displayed reduced affinity for the human-type receptor analog.
    MeSH term(s) Humans ; Animals ; Mice ; Hemagglutinins ; Influenza A Virus, H7N2 Subtype ; Influenza, Human ; Antibodies, Monoclonal ; North America ; Mammals
    Chemical Substances Hemagglutinins ; Antibodies, Monoclonal
    Language English
    Publishing date 2023-12-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms25010212
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Pleiotropic Effects of Influenza H1, H3, and B Baloxavir-Resistant Substitutions on Replication, Sensitivity to Baloxavir, and Interferon Expression.

    Hickerson, Brady T / Adams, Simone E / Barman, Subrata / Miller, Lance / Lugovtsev, Vladimir Y / Webby, Richard J / Ince, William L / Donnelly, Raymond P / Ilyushina, Natalia A

    Antimicrobial agents and chemotherapy

    2022  Volume 66, Issue 4, Page(s) e0000922

    Abstract: Baloxavir is an anti-influenza endonuclease inhibitor that targets the polymerase acidic (PA) protein of influenza A and B viruses. Our knowledge regarding the pleiotropic effects of baloxavir resistance-associated substitutions is limited. We generated ... ...

    Abstract Baloxavir is an anti-influenza endonuclease inhibitor that targets the polymerase acidic (PA) protein of influenza A and B viruses. Our knowledge regarding the pleiotropic effects of baloxavir resistance-associated substitutions is limited. We generated recombinant A/California/04/09 (H1N1)-, A/Hong Kong/218849/2006 (H3N2)-, and B/Victoria/504/2000-like viruses that contained PA substitutions identified in baloxavir clinical trials and surveillance that could potentially be associated with baloxavir resistance. We characterized their susceptibility to baloxavir, impact on polymerase activity, viral growth, and ability to induce interferon (IFN) and IFN-stimulated genes expression
    MeSH term(s) Amino Acid Substitution ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use ; Dibenzothiepins ; Drug Resistance, Viral/genetics ; Humans ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A Virus, H3N2 Subtype/genetics ; Influenza, Human/drug therapy ; Interferons/therapeutic use ; Morpholines ; Pyridones/pharmacology ; Pyridones/therapeutic use ; Triazines/pharmacology ; Triazines/therapeutic use
    Chemical Substances Antiviral Agents ; Dibenzothiepins ; Morpholines ; Pyridones ; Triazines ; baloxavir (4G86Y4JT3F) ; Interferons (9008-11-1)
    Language English
    Publishing date 2022-03-09
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, P.H.S. ; Research Support, N.I.H., Extramural
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/aac.00009-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Laninamivir-Interferon Lambda 1 Combination Treatment Promotes Resistance by Influenza A Virus More Rapidly than Laninamivir Alone.

    Adams, Simone E / Lugovtsev, Vladimir Y / Kan, Anastasia / Bovin, Nicolai V / Donnelly, Raymond P / Ilyushina, Natalia A

    Antimicrobial agents and chemotherapy

    2020  Volume 64, Issue 7

    Abstract: Each year, 5% to 20% of the population of the United States becomes infected with influenza A virus. Combination therapy with two or more antiviral agents has been considered a potential treatment option for influenza virus infection. However, the ... ...

    Abstract Each year, 5% to 20% of the population of the United States becomes infected with influenza A virus. Combination therapy with two or more antiviral agents has been considered a potential treatment option for influenza virus infection. However, the clinical results derived from combination treatment with two or more antiviral drugs have been variable. We examined the effectiveness of cotreatment with two distinct classes of anti-influenza drugs, i.e., neuraminidase (NA) inhibitor, laninamivir, and interferon lambda 1 (IFN-λ1), against the emergence of drug-resistant virus variants
    MeSH term(s) Antiviral Agents/pharmacology ; Drug Resistance, Viral/genetics ; Enzyme Inhibitors/pharmacology ; Guanidines/pharmacology ; Humans ; Influenza A Virus, H1N1 Subtype/drug effects ; Influenza, Human/drug therapy ; Interferons/pharmacology ; Neuraminidase/genetics ; Pyrans ; Sialic Acids ; Zanamivir/pharmacology
    Chemical Substances Antiviral Agents ; Enzyme Inhibitors ; Guanidines ; Pyrans ; Sialic Acids ; Interferons (9008-11-1) ; laninamivir (B408IW3GL5) ; Neuraminidase (EC 3.2.1.18) ; Zanamivir (L6O3XI777I)
    Language English
    Publishing date 2020-06-23
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
    ZDB-ID 217602-6
    ISSN 1098-6596 ; 0066-4804
    ISSN (online) 1098-6596
    ISSN 0066-4804
    DOI 10.1128/AAC.00301-20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Regional Differences in Human Biliary Tissues and Corresponding In Vitro-Derived Organoids.

    Rimland, Casey A / Tilson, Samantha G / Morell, Carola M / Tomaz, Rute A / Lu, Wei-Yu / Adams, Simone E / Georgakopoulos, Nikitas / Otaizo-Carrasquero, Francisco / Myers, Timothy G / Ferdinand, John R / Gieseck, Richard L / Sampaziotis, Fotios / Tysoe, Olivia C / Ross, Alexander / Kraiczy, Judith M / Wesley, Brandon / Muraro, Daniele / Zilbauer, Matthias / Oniscu, Gabriel C /
    Hannan, Nicholas R F / Forbes, Stuart J / Saeb-Parsy, Kourosh / Wynn, Thomas A / Vallier, Ludovic

    Hepatology (Baltimore, Md.)

    2020  Volume 73, Issue 1, Page(s) 247–267

    Abstract: Background and aims: Organoids provide a powerful system to study epithelia in vitro. Recently, this approach was applied successfully to the biliary tree, a series of ductular tissues responsible for the drainage of bile and pancreatic secretions. More ...

    Abstract Background and aims: Organoids provide a powerful system to study epithelia in vitro. Recently, this approach was applied successfully to the biliary tree, a series of ductular tissues responsible for the drainage of bile and pancreatic secretions. More precisely, organoids have been derived from ductal tissue located outside (extrahepatic bile ducts; EHBDs) or inside the liver (intrahepatic bile ducts; IHBDs). These organoids share many characteristics, including expression of cholangiocyte markers such as keratin (KRT) 19. However, the relationship between these organoids and their tissues of origin, and to each other, is largely unknown.
    Approach and results: Organoids were derived from human gallbladder, common bile duct, pancreatic duct, and IHBDs using culture conditions promoting WNT signaling. The resulting IHBD and EHBD organoids expressed stem/progenitor markers leucine-rich repeat-containing G-protein-coupled receptor 5/prominin 1 and ductal markers KRT19/KRT7. However, RNA sequencing revealed that organoids conserve only a limited number of regional-specific markers corresponding to their location of origin. Of particular interest, down-regulation of biliary markers and up-regulation of cell-cycle genes were observed in organoids. IHBD and EHBD organoids diverged in their response to WNT signaling, and only IHBDs were able to express a low level of hepatocyte markers under differentiation conditions.
    Conclusions: Taken together, our results demonstrate that differences exist not only between extrahepatic biliary organoids and their tissue of origin, but also between IHBD and EHBD organoids. This information may help to understand the tissue specificity of cholangiopathies and also to identify targets for therapeutic development.
    MeSH term(s) Animals ; Bile ; Bile Ducts, Extrahepatic/cytology ; Bile Ducts, Extrahepatic/physiology ; Bile Ducts, Intrahepatic/cytology ; Bile Ducts, Intrahepatic/physiology ; Cell Differentiation ; Common Bile Duct/cytology ; Epithelial Cells/cytology ; Epithelial Cells/physiology ; Gallbladder/cytology ; Gene Expression Regulation ; Humans ; Keratin-19/analysis ; Liver/physiology ; Mice ; Organoids/physiology ; RNA-Seq ; Tissue and Organ Procurement
    Chemical Substances Keratin-19
    Language English
    Publishing date 2020-05-04
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 604603-4
    ISSN 1527-3350 ; 0270-9139
    ISSN (online) 1527-3350
    ISSN 0270-9139
    DOI 10.1002/hep.31252
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