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  1. Article ; Online: Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences.

    Saputri, Dianita S / Ismanto, Hendra S / Nugraha, Dendi K / Xu, Zichang / Horiguchi, Yasuhiko / Sakakibara, Shuhei / Standley, Daron M

    mSystems

    2023  Volume 8, Issue 6, Page(s) e0072223

    Abstract: Importance: Determining antigen and epitope specificity is an essential step in the discovery of therapeutic antibodies as well as in the analysis adaptive immune responses to disease or vaccination. Despite extensive efforts, deciphering antigen ... ...

    Abstract Importance: Determining antigen and epitope specificity is an essential step in the discovery of therapeutic antibodies as well as in the analysis adaptive immune responses to disease or vaccination. Despite extensive efforts, deciphering antigen specificity solely from BCR amino acid sequence remains a challenging task, requiring a combination of experimental and computational approaches. Here, we describe and experimentally validate a simple and straightforward approach for grouping antibodies that share antigen and epitope specificities based on their CDR sequence similarity. This approach allows us to identify the specificities of a large number of antibodies whose antigen targets are unknown, using a small fraction of antibodies with well-annotated binding specificities.
    MeSH term(s) Complementarity Determining Regions/genetics ; Antibodies/chemistry ; Antigens/chemistry ; Epitopes/chemistry ; Immunity ; Cluster Analysis
    Chemical Substances Complementarity Determining Regions ; Antibodies ; Antigens ; Epitopes
    Language English
    Publishing date 2023-11-17
    Publishing country United States
    Document type Journal Article
    ISSN 2379-5077
    ISSN (online) 2379-5077
    DOI 10.1128/msystems.00722-23
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Advances in antibody discovery from human BCR repertoires.

    Xu, Zichang / Ismanto, Hendra S / Zhou, Hao / Saputri, Dianita S / Sugihara, Fuminori / Standley, Daron M

    Frontiers in bioinformatics

    2022  Volume 2, Page(s) 1044975

    Abstract: Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it ... ...

    Abstract Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.
    Language English
    Publishing date 2022-10-20
    Publishing country Switzerland
    Document type Journal Article ; Review
    ISSN 2673-7647
    ISSN (online) 2673-7647
    DOI 10.3389/fbinf.2022.1044975
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Structural Modeling of Adaptive Immune Responses to Infection.

    Lusiany, Tina / Xu, Zichang / Saputri, Dianita S / Ismanto, Hendra S / Nazlica, Sedat Aybars / Standley, Daron M

    Methods in molecular biology (Clifton, N.J.)

    2022  Volume 2552, Page(s) 283–294

    Abstract: Antibody and TCR modeling are becoming important as more and more sequence data becomes available to the public. One of the pressing questions now is how to use such data to understand adaptive immune responses to disease. Infectious disease is of ... ...

    Abstract Antibody and TCR modeling are becoming important as more and more sequence data becomes available to the public. One of the pressing questions now is how to use such data to understand adaptive immune responses to disease. Infectious disease is of particular interest because the antigens driving such responses are often known to some extent. Here, we describe tips for gathering data and cleaning it for use in downstream analysis. We present a method for high-throughput structural modeling of antibodies or TCRs using Repertoire Builder and its extensions. AbAdapt is an extension of Repertoire Builder for antibody-antigen docking from antibody and antigen sequences. ImmuneScape is a corresponding extension for TCR-pMHC 3D modeling. Together, these pipelines can help researchers to understand immune responses to infection from a structural point of view.
    MeSH term(s) Receptors, Antigen, T-Cell ; Antigens ; Immunity
    Chemical Substances Receptors, Antigen, T-Cell ; Antigens
    Language English
    Publishing date 2022-11-13
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-2609-2_15
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Landscape of infection enhancing antibodies in COVID-19 and healthy donors.

    Ismanto, Hendra S / Xu, Zichang / Saputri, Dianita S / Wilamowski, Jan / Li, Songling / Nugraha, Dendi K / Horiguchi, Yasuhiko / Okada, Masato / Arase, Hisashi / Standley, Daron M

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 6033–6040

    Abstract: To assess the frequency of SARS-CoV-2 infection in the general population, we searched over 64 million heavy chain antibody sequences from healthy unvaccinated, healthy BNT162b2 vaccinated and COVID-19 patient repertoires for sequences similar to 11 ... ...

    Abstract To assess the frequency of SARS-CoV-2 infection in the general population, we searched over 64 million heavy chain antibody sequences from healthy unvaccinated, healthy BNT162b2 vaccinated and COVID-19 patient repertoires for sequences similar to 11 previously reported enhancing antibodies. Although the distribution of sequence identities was similar in all three groups of repertoires, the COVID-19 and healthy vaccinated hits were significantly more clonally expanded than healthy unvaccinated hits. Furthermore, among the tested hits, 17 out of 94 from COVID-19 and 9 out of 59 from healthy vaccinated, compared with only 2 out of 96 from healthy unvaccinated, bound to the enhancing epitope. A total of 9 of the 28 epitope-binding antibodies enhanced ACE2 receptor binding to the spike protein. Together, this study revealed that infection enhancing-like antibodies are far more frequent in COVID-19 patients or healthy vaccinated donors than in healthy unvaccinated donors, but a reservoir of potential enhancing antibodies exists in healthy donors that could potentially mature to actual enhancing antibodies upon infection.
    Language English
    Publishing date 2022-11-04
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.11.001
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Landscape of infection enhancing antibodies in COVID-19 and healthy donors

    Ismanto, Hendra S / Xu, Zichang / Saputri, Dianita S / Wilamowski, Jan / Li, Songling / Nugraha, Dendi K / Horiguchi, Yasuhiko / Okada, Masato / Arase, Hisashi / Standley, Daron M

    bioRxiv

    Abstract: To assess the frequency of SARS-CoV-2 infection enhancing antibodies in the general population, we searched over 64 million heavy chain antibody sequences from healthy and COVID-19 patient repertoires for sequences similar to 11 previously reported ... ...

    Abstract To assess the frequency of SARS-CoV-2 infection enhancing antibodies in the general population, we searched over 64 million heavy chain antibody sequences from healthy and COVID-19 patient repertoires for sequences similar to 11 previously reported enhancing antibodies. Although the distribution of sequence identities was similar in COVID-19 and healthy repertoires, the COVID-19 hits were significantly more clonally expanded than healthy hits. Furthermore, among the tested hits, 17 out of 94 from COVID-19, compared with 2 out of 96 from healthy, bound to the enhancing epitope. A total of 6 of the 19 epitope-binding antibodies enhanced ACE2 receptor binding to the spike protein. Together, this study revealed that enhancing antibodies are far more frequent in COVID-19 patients than in healthy donors, but a reservoir of potential enhancing antibodies exists in healthy donors that could potentially mature to actual enhancing antibodies upon infection.
    Keywords covid19
    Language English
    Publishing date 2022-07-11
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2022.07.09.499414
    Database COVID19

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  6. Article: Flexible, Functional, and Familiar: Characteristics of SARS-CoV-2 Spike Protein Evolution.

    Saputri, Dianita S / Li, Songling / van Eerden, Floris J / Rozewicki, John / Xu, Zichang / Ismanto, Hendra S / Davila, Ana / Teraguchi, Shunsuke / Katoh, Kazutaka / Standley, Daron M

    Frontiers in microbiology

    2020  Volume 11, Page(s) 2112

    Abstract: The SARS-CoV-2 S protein is a major point of interaction between the virus and the human ... immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution ... in the S protein that vary greatly across closely related viruses but are conserved in the subset ...

    Abstract The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These "evolutionarily important" residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs.
    Keywords covid19
    Language English
    Publishing date 2020-09-17
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2020.02112
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Flexible, Functional, and Familiar

    Dianita S. Saputri / Songling Li / Floris J. van Eerden / John Rozewicki / Zichang Xu / Hendra S. Ismanto / Ana Davila / Shunsuke Teraguchi / Kazutaka Katoh / Daron M. Standley

    Frontiers in Microbiology, Vol

    Characteristics of SARS-CoV-2 Spike Protein Evolution

    2020  Volume 11

    Abstract: The SARS-CoV-2 S protein is a major point of interaction between the virus and the human ... immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution ... in the S protein that vary greatly across closely related viruses but are conserved in the subset ...

    Abstract The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These “evolutionarily important” residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs.
    Keywords flexibility ; host like ; molecular evolution ; phylogenetics ; SARS-CoV-2 ; spike protein ; Microbiology ; QR1-502 ; covid19
    Subject code 572
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Book ; Online: Table_1_Flexible, Functional, and Familiar

    Dianita S. Saputri / Songling Li / Floris J. van Eerden / John Rozewicki / Zichang Xu / Hendra S. Ismanto / Ana Davila / Shunsuke Teraguchi / Kazutaka Katoh / Daron M. Standley

    Characteristics of SARS-CoV-2 Spike Protein Evolution.DOCX

    2020  

    Abstract: The SARS-CoV-2 S protein is a major point of interaction between the virus and the human ... immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution ... in the S protein that vary greatly across closely related viruses but are conserved in the subset ...

    Abstract The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These “evolutionarily important” residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs.
    Keywords Microbiology ; Microbial Genetics ; Microbial Ecology ; Mycology ; flexibility ; host like ; molecular evolution ; phylogenetics ; SARS-CoV-2 ; spike protein ; structural modeling ; structure alignment ; covid19
    Subject code 572
    Publishing date 2020-09-17T04:06:55Z
    Publishing country uk
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Flexible, Functional, and Familiar

    Saputri, Dianita S. / Li, Songling / van Eerden, Floris J. / Rozewicki, John / Xu, Zichang / Ismanto, Hendra S. / Davila, Ana / Teraguchi, Shunsuke / Katoh, Kazutaka / Standley, Daron M.

    Frontiers in Microbiology

    Characteristics of SARS-CoV-2 Spike Protein Evolution

    2020  Volume 11

    Keywords Microbiology (medical) ; Microbiology ; covid19
    Publisher Frontiers Media SA
    Publishing country ch
    Document type Article ; Online
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2020.02112
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Methods for sequence and structural analysis of B and T cell receptor repertoires.

    Teraguchi, Shunsuke / Saputri, Dianita S / Llamas-Covarrubias, Mara Anais / Davila, Ana / Diez, Diego / Nazlica, Sedat Aybars / Rozewicki, John / Ismanto, Hendra S / Wilamowski, Jan / Xie, Jiaqi / Xu, Zichang / Loza-Lopez, Martin de Jesus / van Eerden, Floris J / Li, Songling / Standley, Daron M

    Computational and structural biotechnology journal

    2020  Volume 18, Page(s) 2000–2011

    Abstract: B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of ... ...

    Abstract B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.
    Keywords covid19
    Language English
    Publishing date 2020-07-17
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2020.07.008
    Database MEDical Literature Analysis and Retrieval System OnLINE

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