13 results on '"de Souza, Matheus Oliveira"'
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2. Large-scale antibody immune response mapping of splenic B cells and bone marrow plasma cells in a transgenic mouse model
- Author
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Pan, Xiaoli, López Acevedo, Sheila N., Cuziol, Camille, De Tavernier, Evelyn, Fahad, Ahmed S., Longjam, Priyobarta S., Rao, Sambasiva P., Aguilera-Rodríguez, David, Rezé, Mathilde, Bricault, Christine A., Gutiérrez-González, Matías F., de Souza, Matheus Oliveira, DiNapoli, Joshua M., Vigne, Emmanuelle, Shahsavarian, Melody A., DeKosky, Brandon J., Pan, Xiaoli, López Acevedo, Sheila N., Cuziol, Camille, De Tavernier, Evelyn, Fahad, Ahmed S., Longjam, Priyobarta S., Rao, Sambasiva P., Aguilera-Rodríguez, David, Rezé, Mathilde, Bricault, Christine A., Gutiérrez-González, Matías F., de Souza, Matheus Oliveira, DiNapoli, Joshua M., Vigne, Emmanuelle, Shahsavarian, Melody A., and DeKosky, Brandon J.
- Abstract
Molecular characterization of antibody immunity and human antibody discovery is mainly carried out using peripheral memory B cells, and occasionally plasmablasts, that express B cell receptors (BCRs) on their cell surface. Despite the importance of plasma cells (PCs) as the dominant source of circulating antibodies in serum, PCs are rarely utilized because they do not express surface BCRs and cannot be analyzed using antigen-based fluorescence-activated cell sorting. Here, we studied the antibodies encoded by the entire mature B cell populations, including PCs, and compared the antibody repertoires of bone marrow and spleen compartments elicited by immunization in a human immunoglobulin transgenic mouse strain. To circumvent prior technical limitations for analysis of plasma cells, we applied single-cell antibody heavy and light chain gene capture from the entire mature B cell repertoires followed by yeast display functional analysis using a cytokine as a model immunogen. We performed affinity-based sorting of antibody yeast display libraries and large-scale next-generation sequencing analyses to follow antibody lineage performance, with experimental validation of 76 monoclonal antibodies against the cytokine antigen that identified three antibodies with exquisite double-digit picomolar binding affinity. We observed that spleen B cell populations generated higher affinity antibodies compared to bone marrow PCs and that antigen-specific splenic B cells had higher average levels of somatic hypermutation. A degree of clonal overlap was also observed between bone marrow and spleen antibody repertoires, indicating common origins of certain clones across lymphoid compartments. These data demonstrate a new capacity to functionally analyze antigen-specific B cell populations of different lymphoid organs, including PCs, for high-affinity antibody discovery and detailed fundamental studies of antibody immunity.
- Published
- 2023
3. Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens
- Author
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de Souza, Matheus Oliveira, primary, Madan, Bharat, additional, Teng, I-Ting, additional, Huang, Aric, additional, Liu, Lihong, additional, Fahad, Ahmed S., additional, Lopez Acevedo, Sheila N., additional, Pan, Xiaoli, additional, Sastry, Mallika, additional, Gutierrez-Gonzalez, Matias, additional, Yin, Michael T., additional, Zhou, Tongqing, additional, Ho, David D., additional, Kwong, Peter D., additional, and DeKosky, Brandon J., additional
- Published
- 2022
- Full Text
- View/download PDF
4. Large-scale antibody immune response mapping of splenic B cells and bone marrow plasma cells in a transgenic mouse model.
- Author
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Xiaoli Pan, Acevedo, Sheila N. López, Cuziol, Camille, De Tavernier, Evelyn, Fahad, Ahmed S., Longjam, Priyobarta S., Rao, Sambasiva P., Aguilera-Rodríguez, David, Rezé, Mathilde, Bricault, Christine A., Gutiérrez-González, Matías F., de Souza, Matheus Oliveira, DiNapoli, Joshua M., Vigne, Emmanuelle, Shahsavarian, Melody A., and DeKosky, Brandon J.
- Subjects
BONE marrow cells ,ANTIBODY formation ,B cells ,IMMUNE response ,B cell receptors ,PSYCHONEUROIMMUNOLOGY - Abstract
Molecular characterization of antibody immunity and human antibody discovery is mainly carried out using peripheral memory B cells, and occasionally plasmablasts, that express B cell receptors (BCRs) on their cell surface. Despite the importance of plasma cells (PCs) as the dominant source of circulating antibodies in serum, PCs are rarely utilized because they do not express surface BCRs and cannot be analyzed using antigen-based fluorescence-activated cell sorting. Here, we studied the antibodies encoded by the entire mature B cell populations, including PCs, and compared the antibody repertoires of bone marrow and spleen compartments elicited by immunization in a human immunoglobulin transgenic mouse strain. To circumvent prior technical limitations for analysis of plasma cells, we applied single-cell antibody heavy and light chain gene capture from the entire mature B cell repertoires followed by yeast display functional analysis using a cytokine as a model immunogen. We performed affinity-based sorting of antibody yeast display libraries and large- scale next-generation sequencing analyses to follow antibody lineage performance, with experimental validation of 76 monoclonal antibodies against the cytokine antigen that identified three antibodies with exquisite double-digit picomolar binding affinity. We observed that spleen B cell populations generated higher affinity antibodies compared to bone marrow PCs and that antigen-specific splenic B cells had higher average levels of somatic hypermutation. A degree of clonal overlap was also observed between bone marrow and spleen antibody repertoires, indicating common origins of certain clones across lymphoid compartments. These data demonstrate a new capacity to functionally analyze antigen-specific B cell populations of different lymphoid organs, including PCs, for high-affinity antibody discovery and detailed fundamental studies of antibody immunity. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
5. Strategies to Screen Anti-AQP4 Antibodies from Yeast Surface Display Libraries
- Author
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Huang, Aric, primary, Jin, Wei, additional, Fahad, Ahmed S., additional, Mussman, Brooklyn K., additional, Nicchia, Grazia Paola, additional, Madan, Bharat, additional, de Souza, Matheus Oliveira, additional, Griffin, J. Daniel, additional, Bennett, Jeffrey L., additional, Frigeri, Antonio, additional, Berkland, Cory J., additional, and DeKosky, Brandon J., additional
- Published
- 2022
- Full Text
- View/download PDF
6. Strategies to Screen Anti-AQP4 Antibodies from Yeast Surface Display Libraries
- Author
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Massachusetts Institute of Technology. Department of Chemical Engineering, Huang, Aric, Jin, Wei, Fahad, Ahmed S, Mussman, Brooklyn K, Nicchia, Grazia Paola, Madan, Bharat, de Souza, Matheus Oliveira, Griffin, J Daniel, Bennett, Jeffrey L, Frigeri, Antonio, Berkland, Cory J, DeKosky, Brandon J, Massachusetts Institute of Technology. Department of Chemical Engineering, Huang, Aric, Jin, Wei, Fahad, Ahmed S, Mussman, Brooklyn K, Nicchia, Grazia Paola, Madan, Bharat, de Souza, Matheus Oliveira, Griffin, J Daniel, Bennett, Jeffrey L, Frigeri, Antonio, Berkland, Cory J, and DeKosky, Brandon J
- Abstract
- Published
- 2022
7. Molecular probes of spike ectodomain and its subdomains for SARS-CoV-2 variants, Alpha through Omicron
- Author
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Teng, I-Ting, primary, Nazzari, Alexandra F., additional, Choe, Misook, additional, Liu, Tracy, additional, de Souza, Matheus Oliveira, additional, Petrova, Yuliya, additional, Tsybovsky, Yaroslav, additional, Wang, Shuishu, additional, Zhang, Baoshan, additional, Artamonov, Mykhaylo, additional, Madan, Bharat, additional, Huang, Aric, additional, Lopez Acevedo, Sheila N., additional, Pan, Xiaoli, additional, Ruckwardt, Tracy J., additional, DeKosky, Brandon J., additional, Mascola, John R., additional, Misasi, John, additional, Sullivan, Nancy J., additional, Zhou, Tongqing, additional, and Kwong, Peter D., additional
- Published
- 2021
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8. Functional Profiling of Antibody Immune Repertoires in Convalescent Zika Virus Disease Patients
- Author
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Fahad, Ahmed S., primary, Timm, Morgan R., additional, Madan, Bharat, additional, Burgomaster, Katherine E., additional, Dowd, Kimberly A., additional, Normandin, Erica, additional, Gutiérrez-González, Matías F., additional, Pennington, Joseph M., additional, De Souza, Matheus Oliveira, additional, Henry, Amy R., additional, Laboune, Farida, additional, Wang, Lingshu, additional, Ambrozak, David R., additional, Gordon, Ingelise J., additional, Douek, Daniel C., additional, Ledgerwood, Julie E., additional, Graham, Barney S., additional, Castilho, Leda R., additional, Pierson, Theodore C., additional, Mascola, John R., additional, and DeKosky, Brandon J., additional
- Published
- 2021
- Full Text
- View/download PDF
9. Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses
- Author
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Banach, Bailey B., primary, Cerutti, Gabriele, additional, Fahad, Ahmed S., additional, Shen, Chen-Hsiang, additional, de Souza, Matheus Oliveira, additional, Katsamba, Phinikoula S., additional, Tsybovsky, Yaroslav, additional, Wang, Pengfei, additional, Nair, Manoj S., additional, Huang, Yaoxing, additional, Urdániz, Irene M. Francino, additional, Steiner, Paul J., additional, Gutiérrez-González, Matias, additional, Liu, Lihong, additional, López Acevedo, Sheila N., additional, Nazzari, Alexandra, additional, Wolfe, Jacy R., additional, Luo, Yang, additional, Olia, Adam S., additional, Teng, I-Ting, additional, Yu, Jian, additional, Zhou, Tongqing, additional, Reddem, Eswar R., additional, Bimela, Jude, additional, Pan, Xiaoli, additional, Madan, Bharat, additional, Laflin, Amy D., additional, Nimrania, Rajani, additional, Yuen, Kwon-Tung, additional, Whitehead, Timothy A., additional, Ho, David D., additional, Kwong, Peter D., additional, Shapiro, Lawrence, additional, and DeKosky, Brandon J., additional
- Published
- 2021
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10. Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes
- Author
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Zhou, Tongqing, primary, Teng, I-Ting, additional, Olia, Adam S., additional, Cerutti, Gabriele, additional, Gorman, Jason, additional, Nazzari, Alexandra, additional, Shi, Wei, additional, Tsybovsky, Yaroslav, additional, Wang, Lingshu, additional, Wang, Shuishu, additional, Zhang, Baoshan, additional, Zhang, Yi, additional, Katsamba, Phinikoula S., additional, Petrova, Yuliya, additional, Banach, Bailey B., additional, Fahad, Ahmed S., additional, Liu, Lihong, additional, Acevedo, Sheila N. Lopez, additional, Madan, Bharat, additional, de Souza, Matheus Oliveira, additional, Pan, Xiaoli, additional, Wang, Pengfei, additional, Wolfe, Jacy R., additional, Yin, Michael, additional, Ho, David D., additional, Phung, Emily, additional, DiPiazza, Anthony, additional, Chang, Lauren, additional, Abiona, Olubukula, additional, Corbett, Kizzmekia S., additional, DeKosky, Brandon J., additional, Graham, Barney S., additional, Mascola, John R., additional, Misasi, John, additional, Ruckwardt, Tracy, additional, Sullivan, Nancy J., additional, Shapiro, Lawrence, additional, and Kwong, Peter D., additional
- Published
- 2020
- Full Text
- View/download PDF
11. Antibody screening at reduced pH enables preferential selection of potently neutralizing antibodies targeting SARS‐CoV‐2.
- Author
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Madan, Bharat, Reddem, Eswar R., Wang, Pengfei, Casner, Ryan G., Nair, Manoj S., Huang, Yaoxing, Fahad, Ahmed S., de Souza, Matheus Oliveira, Banach, Bailey B., López Acevedo, Sheila N., Pan, Xiaoli, Nimrania, Rajani, Teng, I‐Ting, Bahna, Fabiana, Zhou, Tongqing, Zhang, Baoshan, Yin, Michael T., Ho, David D., Kwong, Peter D., and Shapiro, Lawrence
- Subjects
SARS-CoV-2 ,MONOCLONAL antibodies ,COVID-19 ,VIRAL antibodies ,IMMUNOGLOBULINS ,VIRAL antigens - Abstract
Antiviral monoclonal antibody (mAb) discovery enables the development of antibody‐based antiviral therapeutics. Traditional antiviral mAb discovery relies on affinity between antibody and a viral antigen to discover potent neutralizing antibodies, but these approaches are inefficient because many high affinity mAbs have no neutralizing activity. We sought to determine whether screening for anti‐SARS‐CoV‐2 mAbs at reduced pH could provide more efficient neutralizing antibody discovery. We mined the antibody response of a convalescent COVID‐19 patient at both physiological pH (7.4) and reduced pH (4.5), revealing that SARS‐CoV‐2 neutralizing antibodies were preferentially enriched in pH 4.5 yeast display sorts. Structural analysis revealed that a potent new antibody called LP5 targets the SARS‐CoV‐2 N‐terminal domain supersite via a unique binding recognition mode. Our data combine with evidence from prior studies to support antibody screening at pH 4.5 to accelerate antiviral neutralizing antibody discovery. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
12. Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses.
- Author
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Banach BB, Cerutti G, Fahad AS, Shen CH, de Souza MO, Katsamba PS, Tsybovsky Y, Wang P, Nair MS, Huang Y, Urdániz IMF, Steiner PJ, Gutiérrez-González M, Liu L, López Acevedo SN, Nazzari A, Wolfe JR, Luo Y, Olia AS, Teng IT, Yu J, Zhou T, Reddem ER, Bimela J, Pan X, Madan B, Laflin AD, Nimrania R, Yuen KT, Whitehead TA, Ho DD, Kwong PD, Shapiro L, and DeKosky BJ
- Abstract
Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 receptor binding site as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. We performed sequence and structural analyses to explore how antibody features correlate with SARS-CoV-2 neutralization. Cryo-EM structures of 910-30 bound to the SARS-CoV-2 spike trimer revealed its binding interactions and ability to disassemble spike. Despite heavy chain sequence similarity, biophysical analyses of IGHV3-53/3-66 antibodies highlighted the importance of native heavy:light pairings for ACE2 binding competition and for SARS-CoV-2 neutralization. We defined paired heavy:light sequence signatures and determined antibody precursor prevalence to be ~1 in 44,000 human B cells, consistent with public antibody identification in several convalescent COVID-19 patients. These data reveal key structural and functional neutralization features in the IGHV3-53/3-66 public antibody class to accelerate antibody-based medical interventions against SARS-CoV-2., Highlights: A molecular study of IGHV3-53/3-66 public antibody responses reveals critical heavy and light chain features for potent neutralizationCryo-EM analyses detail the structure of a novel public antibody class member, antibody 910-30, in complex with SARS-CoV-2 spike trimerCryo-EM data reveal that 910-30 can both bind assembled trimer and can disassemble the SARS-CoV-2 spikeSequence-structure-function signatures defined for IGHV3-53/3-66 class antibodies including both heavy and light chainsIGHV3-53/3-66 class precursors have a prevalence of 1:44,000 B cells in healthy human antibody repertoires.
- Published
- 2021
- Full Text
- View/download PDF
13. Structure-Based Design with Tag-Based Purification and In-Process Biotinylation Enable Streamlined Development of SARS-CoV-2 Spike Molecular Probes.
- Author
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Zhou T, Teng IT, Olia AS, Cerutti G, Gorman J, Nazzari A, Shi W, Tsybovsky Y, Wang L, Wang S, Zhang B, Zhang Y, Katsamba PS, Petrova Y, Banach BB, Fahad AS, Liu L, Lopez Acevedo SN, Madan B, de Souza MO, Pan X, Wang P, Wolfe JR, Yin M, Ho DD, Phung E, DiPiazza A, Chang L, Abiona O, Corbett KS, DeKosky BJ, Graham BS, Mascola JR, Misasi J, Ruckwardt T, Sullivan NJ, Shapiro L, and Kwong PD
- Abstract
Biotin-labeled molecular probes, comprising specific regions of the SARS-CoV-2 spike, would be helpful in the isolation and characterization of antibodies targeting this recently emerged pathogen. To develop such probes, we designed constructs incorporating an N-terminal purification tag, a site-specific protease-cleavage site, the probe region of interest, and a C-terminal sequence targeted by biotin ligase. Probe regions included full-length spike ectodomain as well as various subregions, and we also designed mutants to eliminate recognition of the ACE2 receptor. Yields of biotin-labeled probes from transient transfection ranged from ~0.5 mg/L for the complete ectodomain to >5 mg/L for several subregions. Probes were characterized for antigenicity and ACE2 recognition, and the structure of the spike ectodomain probe was determined by cryo-electron microscopy. We also characterized antibody-binding specificities and cell-sorting capabilities of the biotinylated probes. Altogether, structure-based design coupled to efficient purification and biotinylation processes can thus enable streamlined development of SARS-CoV-2 spike-ectodomain probes.
- Published
- 2020
- Full Text
- View/download PDF
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