From rabbit antibody repertoires to rabbit monoclonal antibodies

Justus Weber; Haiyong Peng; Christoph Rader

doi:10.1038/emm.2017.23

Mining Naïve Rabbit Antibody Repertoires by Phage Display for Monoclonal Antibodies of Therapeutic Utility

Journal of Molecular Biology ◽

10.1016/j.jmb.2017.08.003 ◽

2017 ◽

Vol 429 (19) ◽

pp. 2954-2973 ◽

Cited By ~ 19

Author(s):

Haiyong Peng ◽

Thomas Nerreter ◽

Jing Chang ◽

Junpeng Qi ◽

Xiuling Li ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Phage Display ◽

Rabbit Antibody ◽

Antibody Repertoires ◽

Therapeutic Utility

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Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires

Frontiers in Immunology ◽

10.3389/fimmu.2021.728694 ◽

2021 ◽

Vol 12 ◽

Author(s):

Brian M. Petersen ◽

Sophia A. Ulmer ◽

Emily R. Rhodes ◽

Matias F. Gutierrez-Gonzalez ◽

Brandon J. Dekosky ◽

...

Keyword(s):

Monoclonal Antibodies ◽

High Frequency ◽

In Silico ◽

Sequence Data ◽

Antibody Repertoire ◽

Human Antibody ◽

Therapeutic Antibodies ◽

T Cell Epitopes ◽

Antibody Repertoires ◽

Dynamics Simulations

Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using baseline human antibody repertoire sequences. Our analysis shows that human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from baseline human antibody sequence data. We find that mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in baseline human antibody repertoires. In addition, high frequency mutations in baseline human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that baseline human antibody repertoires may be useful as predictive tools to guide mAb development in the future.

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Molecular Level Characterization of Circulating Aquaporin-4 Antibodies in Neuromyelitis Optica Spectrum Disorder

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000001034 ◽

2021 ◽

Vol 8 (5) ◽

pp. e1034

Author(s):

Jie Li ◽

Sam A. Bazzi ◽

Florian Schmitz ◽

Hidetaka Tanno ◽

Jonathan R. McDaniel ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Neuromyelitis Optica ◽

High Throughput Sequencing ◽

Cell Receptor ◽

Spectrum Disorder ◽

Aquaporin 4 ◽

Neuromyelitis Optica Spectrum Disorder ◽

Igg Antibody ◽

Antibody Repertoires

ObjectiveTo determine whether distinct aquaporin-4 (AQP4)-IgG lineages play a role in neuromyelitis optica spectrum disorder (NMOSD) pathogenesis, we profiled the AQP4-IgG polyclonal serum repertoire and identified, quantified, and functionally characterized distinct AQP4-IgG lineages circulating in 2 patients with NMOSD.MethodsWe combined high-throughput sequencing and quantitative immunoproteomics to simultaneously determine the constituents of both the B-cell receptor (BCR) and the serologic (IgG) anti-AQP4 antibody repertoires in the peripheral blood of patients with NMOSD. The monoclonal antibodies identified by this platform were recombinantly expressed and functionally characterized in vitro.ResultsMultiple antibody lineages comprise serum AQP4-IgG repertoires. Their distribution, however, can be strikingly different in polarization (polyclonal vs pauciclonal). Among the 4 serum AQP4-IgG monoclonal antibodies we identified in 2 patients, 3 induced complement-dependent cytotoxicity in a model mammalian cell line (p < 0.01).ConclusionsThe composition and polarization of AQP4-IgG antibody repertoires may play an important role in NMOSD pathogenesis and clinical presentation. Here, we present a means of coupling both cellular (BCR) and serologic (IgG) antibody repertoire analysis, which has not previously been performed in NMOSD. Our analysis could be applied in the future to clinical management of patients with NMOSD to monitor disease activity over time as well as applied to other autoimmune diseases to facilitate a deeper understanding of disease pathogenesis relative to autoantibody clones.

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Regulatory approved monoclonal antibodies contain framework mutations predicted from human antibody repertoires

10.1101/2021.06.22.449488 ◽

2021 ◽

Author(s):

Brian M Petersen ◽

Sophia A Ulmer ◽

Emily R Rhodes ◽

Matias F Gutierrez Gonzalez ◽

Brandon J Dekosky ◽

...

Keyword(s):

Monoclonal Antibodies ◽

High Frequency ◽

In Silico ◽

Sequence Data ◽

Antibody Repertoire ◽

Human Antibody ◽

Therapeutic Antibodies ◽

T Cell Epitopes ◽

Antibody Repertoires ◽

Dynamics Simulations

Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using natural human antibody repertoire sequences. Our analysis shows that natural human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from natural human antibody sequence data. mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in natural human antibody repertoires. In addition, high frequency mutations in natural human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that natural human antibody repertoires may be useful as predictive tools to guide mAb development in the future.

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Mouse Antibodies with Activity Against the SARS-CoV-2 D614G and B.1.351 Variants

10.1101/2021.07.05.451203 ◽

2021 ◽

Author(s):

Larisa Troitskaya ◽

Nelson Lap Shun Chan ◽

Brendon Frank ◽

Daniel Capon ◽

Brian A. Zabel ◽

...

Keyword(s):

Monoclonal Antibodies ◽

Severe Disease ◽

Human Antibody ◽

Human Antibodies ◽

Rapid Spread ◽

Antibody Repertoires ◽

Murine Monoclonal Antibodies

With the rapid spread of SARS-CoV-2 variants, including those that are resistant to antibodies authorized for emergency use, it is apparent that new antibodies may be needed to effectively protect patients against more severe disease. Differences between the murine and human antibody repertoires may allow for the isolation of murine monoclonal antibodies that recognize a different or broader range of SARS-CoV-2 variants than the human antibodies that have been characterized so far. We describe mouse antibodies B13 and O24 that demonstrate neutralizing potency against SARS-CoV-2 Wuhan (D614G) and B.1.351 variants. Such murine antibodies may have advantages in protecting against severe symptoms when individuals are exposed to new SARS-CoV-2 variants.

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Ultrastructural analysis of unique glycoconjugates in the rat olfactory system

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100124859 ◽

1992 ◽

Vol 50 (1) ◽

pp. 890-891

Author(s):

James E. Crandall ◽

Linda C. Hassinger ◽

Gerald A. Schwarting

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Monoclonal Antibodies ◽

Olfactory System ◽

Olfactory Bulbs ◽

Temporal And Spatial Patterns ◽

Carbohydrate Epitopes ◽

Olfactory Systems ◽

Temporal And Spatial ◽

Cell Surface Glycoconjugates

Cell surface glycoconjugates are considered to play important roles in cell-cell interactions in the developing central nervous system. We have previously described a group of monoclonal antibodies that recognize defined carbohydrate epitopes and reveal unique temporal and spatial patterns of immunoreactivity in the developing main and accessory olfactory systems in rats. Antibody CC2 reacts with complex α-galactosyl and α-fucosyl glycoproteins and glycolipids. Antibody CC1 reacts with terminal N-acetyl galactosamine residues of globoside-like glycolipids. Antibody 1B2 reacts with β-galactosyl glycolipids and glycoproteins. Our light microscopic data suggest that these antigens may be located on the surfaces of axons of the vomeronasal and olfactory nerves as well as on some of their target neurons in the main and accessory olfactory bulbs.

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Structural and Chemical Studies of Pathological Fibers in Human Neurofibrillary Degeneration

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010012031x ◽

1985 ◽

Vol 43 ◽

pp. 726-729

Author(s):

K.S. Kosik ◽

L.K. Duffy ◽

S. Bakalis ◽

C. Abraham ◽

D.J. Selkoe

Keyword(s):

Monoclonal Antibodies ◽

Alzheimer Disease ◽

Human Brain ◽

Neurofibrillary Tangles ◽

Morphological Analysis ◽

High Specificity ◽

Cytoskeletal Proteins ◽

Neuritic Plaque ◽

Protein Chemistry ◽

Chemical Studies

The major structural lesions of the human brain during aging and in Alzheimer disease (AD) are the neurofibrillary tangles (NFT) and the senile (neuritic) plaque. Although these fibrous alterations have been recognized by light microscopists for almost a century, detailed biochemical and morphological analysis of the lesions has been undertaken only recently. Because the intraneuronal deposits in the NFT and the plaque neurites and the extraneuronal amyloid cores of the plaques have a filamentous ultrastructure, the neuronal cytoskeleton has played a prominent role in most pathogenetic hypotheses.The approach of our laboratory toward elucidating the origin of plaques and tangles in AD has been two-fold: the use of analytical protein chemistry to purify and then characterize the pathological fibers comprising the tangles and plaques, and the use of certain monoclonal antibodies to neuronal cytoskeletal proteins that, despite high specificity, cross-react with NFT and thus implicate epitopes of these proteins as constituents of the tangles.

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