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Thesis ; Online: Systems analysis of the physiological landscape of antibody repertoires following immunization

Csepregi, Lucia

2021

Keywords	info:eu-repo/classification/ddc/570 ; Life sciences
Language	English
Publisher	ETH Zurich
Publishing country	ch
Document type	Thesis ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recombinant lymphocytic choriomeningitis virus-based vaccine vector protects type I interferon receptor deficient mice from viral challenge.

Krolik, Michal / Csepregi, Lucia / Hartmann, Fabienne / Engetschwiler, Céline / Flatz, Lukas

Vaccine

2021 Volume 39, Issue 8, Page(s) 1257–1264

Abstract: Reverse genetically engineered recombinant lymphocytic choriomeningitis virus (rLCMV) is a novel vaccine vector platform. Here, we investigate the safety and efficacy of rLCMV in mice lacking a functional type I interferon system with high susceptibility ...

Abstract	Reverse genetically engineered recombinant lymphocytic choriomeningitis virus (rLCMV) is a novel vaccine vector platform. Here, we investigate the safety and efficacy of rLCMV in mice lacking a functional type I interferon system with high susceptibility to viral infections. Propagation-deficient rLCMV vector expressing ovalbumin as a model antigen is cleared from type I interferon receptor-deficient mice (Ifnar
MeSH term(s)	Animals ; CD8-Positive T-Lymphocytes ; Lymphocytic choriomeningitis virus ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Receptor, Interferon alpha-beta/genetics ; Vaccines, Synthetic/genetics ; Viral Vaccines
Chemical Substances	Vaccines, Synthetic ; Viral Vaccines ; Receptor, Interferon alpha-beta (156986-95-7)
Language	English
Publishing date	2021-01-29
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605674-x
ISSN	1873-2518 ; 0264-410X
ISSN (online)	1873-2518
ISSN	0264-410X
DOI	10.1016/j.vaccine.2021.01.047
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Zs.A 1930: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Synthetic and Systems Immunology Conference in Ascona, Switzerland.

Csepregi, Lucia / Neumeier, Daniel / Reddy, Sai T

European journal of immunology

2019 Volume 49, Issue 7, Page(s) 980–981

Language	English
Publishing date	2019-07-02
Publishing country	Germany
Document type	News ; Research Support, Non-U.S. Gov't
ZDB-ID	120108-6
ISSN	1521-4141 ; 0014-2980
ISSN (online)	1521-4141
ISSN	0014-2980
DOI	10.1002/eji.201970075
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Article ; Online: Immune Literacy: Reading, Writing, and Editing Adaptive Immunity.

Csepregi, Lucia / Ehling, Roy A / Wagner, Bastian / Reddy, Sai T

iScience

2020 Volume 23, Issue 9, Page(s) 101519

Abstract: Advances in reading, writing, and editing DNA are providing unprecedented insights into the complexity of immunological systems. This combination of systems and synthetic biology methods is enabling the quantitative and precise understanding of molecular ...

Abstract	Advances in reading, writing, and editing DNA are providing unprecedented insights into the complexity of immunological systems. This combination of systems and synthetic biology methods is enabling the quantitative and precise understanding of molecular recognition in adaptive immunity, thus providing a framework for reprogramming immune responses for translational medicine. In this review, we will highlight state-of-the-art methods such as immune repertoire sequencing, immunoinformatics, and immunogenomic engineering and their application toward adaptive immunity. We showcase novel and interdisciplinary approaches that have the promise of transforming the design and breadth of molecular and cellular immunotherapies.
Keywords	covid19
Language	English
Publishing date	2020-09-01
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2020.101519
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Article ; Online: Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells.

Neumeier, Daniel / Yermanos, Alexander / Agrafiotis, Andreas / Csepregi, Lucia / Chowdhury, Tasnia / Ehling, Roy A / Kuhn, Raphael / Cotet, Tudor-Stefan / Brisset-Di Roberto, Raphaël / Di Tacchio, Mariangela / Antonialli, Renan / Starkie, Dale / Lightwood, Daniel J / Oxenius, Annette / Reddy, Sai T

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 18, Page(s) e2113766119

Abstract: The capacity of humoral B cell-mediated immunity to effectively respond to and protect against pathogenic infections is largely driven by the presence of a diverse repertoire of polyclonal antibodies in the serum, which are produced by plasma cells (PCs). ...

Abstract	The capacity of humoral B cell-mediated immunity to effectively respond to and protect against pathogenic infections is largely driven by the presence of a diverse repertoire of polyclonal antibodies in the serum, which are produced by plasma cells (PCs). Recent studies have started to reveal the balance between deterministic mechanisms and stochasticity of antibody repertoires on a genotypic level (i.e., clonal diversity, somatic hypermutation, and germline gene usage). However, it remains unclear if clonal selection and expansion of PCs follow any deterministic rules or are stochastic with regards to phenotypic antibody properties (i.e., antigen-binding, affinity, and epitope specificity). Here, we report on the in-depth genotypic and phenotypic characterization of clonally expanded PC antibody repertoires following protein immunization. We find that clonal expansion drives antigen specificity of the most expanded clones (top ∼10), whereas among the rest of the clonal repertoire antigen specificity is stochastic. Furthermore, we report both on a polyclonal repertoire and clonal lineage level that antibody-antigen binding affinity does not correlate with clonal expansion or somatic hypermutation. Last, we provide evidence for convergence toward targeting dominant epitopes despite clonal sequence diversity among the most expanded clones. Our results highlight the extent to which clonal expansion can be ascribed to antigen binding, affinity, and epitope specificity, and they have implications for the assessment of effective vaccines.
MeSH term(s)	Animals ; Antibodies/genetics ; Antibody Affinity ; Antigens ; Epitopes/genetics ; Mice ; Plasma Cells
Chemical Substances	Antibodies ; Antigens ; Epitopes
Language	English
Publishing date	2022-04-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2113766119
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Article ; Online: Molecular Design, Optimization, and Genomic Integration of Chimeric B Cell Receptors in Murine B Cells.

Pesch, Theresa / Bonati, Lucia / Kelton, William / Parola, Cristina / Ehling, Roy A / Csepregi, Lucia / Kitamura, Daisuke / Reddy, Sai T

Frontiers in immunology

2019 Volume 10, Page(s) 2630

Abstract: Immune cell therapies based on the integration of synthetic antigen receptors comprise a powerful strategy for the treatment of diverse diseases, most notably T cells engineered to express chimeric antigen receptors (CAR) for targeted cancer therapy. In ... ...

Abstract	Immune cell therapies based on the integration of synthetic antigen receptors comprise a powerful strategy for the treatment of diverse diseases, most notably T cells engineered to express chimeric antigen receptors (CAR) for targeted cancer therapy. In addition to T lymphocytes, B lymphocytes may also represent valuable immune cells that can be engineered for therapeutic purposes such as protein replacement therapy or recombinant antibody production. In this article, we report a promising concept for the molecular design, optimization, and genomic integration of a novel class of synthetic antigen receptors, chimeric B cell receptors (CBCR). We initially optimized CBCR expression and detection by modifying the extracellular surface tag, the transmembrane regions and intracellular signaling domains. For this purpose, we stably integrated a series of CBCR variants using CRISPR-Cas9 into immortalized B cell hybridomas. Subsequently, we developed a reliable and consistent pipeline to precisely introduce cassettes of several kb size into the genome of primary murine B cells also using CRISPR-Cas9 induced HDR. Finally, we were able to show the robust surface expression and antigen recognition of a synthetic CBCR in primary B cells. We anticipate CBCRs and our approach for engineering primary B cells will be a valuable tool for the advancement of future B cell- based immune cell therapies.
MeSH term(s)	Animals ; B-Lymphocytes ; CRISPR-Cas Systems ; Gene Editing/methods ; Mice ; Protein Engineering/methods ; Receptors, Antigen, B-Cell/genetics ; Receptors, Antigen, B-Cell/immunology ; Receptors, Artificial/genetics ; Receptors, Artificial/immunology
Chemical Substances	Receptors, Antigen, B-Cell ; Receptors, Artificial
Language	English
Publishing date	2019-11-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2019.02630
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Article ; Online: Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells.

Parola, Cristina / Neumeier, Daniel / Friedensohn, Simon / Csepregi, Lucia / Di Tacchio, Mariangela / Mason, Derek M / Reddy, Sai T

mAbs

2019 Volume 11, Issue 8, Page(s) 1367–1380

Abstract: Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in ... ...

Abstract	Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in cellular engineering enabled by CRISPR-Cas9 genome editing have made it possible to expand the use of mammalian cells in biotechnological applications. Here, we describe an antibody engineering and screening approach where complete variable light (V
MeSH term(s)	Animals ; Clustered Regularly Interspaced Short Palindromic Repeats ; Female ; Gene Editing ; Gene Library ; Hybridomas/metabolism ; Mice ; Mice, Inbred BALB C ; Single-Chain Antibodies/genetics ; Single-Chain Antibodies/metabolism
Chemical Substances	Single-Chain Antibodies
Language	English
Publishing date	2019-09-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1942-0870
ISSN (online)	1942-0870
DOI	10.1080/19420862.2019.1662691
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Article ; Online: Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single-cell analysis.

Neumeier, Daniel / Pedrioli, Alessandro / Genovese, Alessandro / Sandu, Ioana / Ehling, Roy / Hong, Kai-Lin / Papadopoulou, Chrysa / Agrafiotis, Andreas / Kuhn, Raphael / Shlesinger, Danielle / Robbiani, Damiano / Han, Jiami / Hauri, Laura / Csepregi, Lucia / Greiff, Victor / Merkler, Doron / Reddy, Sai T / Oxenius, Annette / Yermanos, Alexander

European journal of immunology

2021 Volume 52, Issue 2, Page(s) 297–311

Abstract: Plasma cells and their secreted antibodies play a central role in the long-term protection against chronic viral infection. However, due to experimental limitations, a comprehensive description of linked genotypic, phenotypic, and antibody repertoire ... ...

Abstract	Plasma cells and their secreted antibodies play a central role in the long-term protection against chronic viral infection. However, due to experimental limitations, a comprehensive description of linked genotypic, phenotypic, and antibody repertoire features of plasma cells (gene expression, clonal frequency, virus specificity, and affinity) has been challenging to obtain. To address this, we performed single-cell transcriptome and antibody repertoire sequencing of the murine BM plasma cell population following chronic lymphocytic choriomeningitis virus infection. Our single-cell sequencing approach recovered full-length and paired heavy- and light-chain sequence information for thousands of plasma cells and enabled us to perform recombinant antibody expression and specificity screening. Antibody repertoire analysis revealed that, relative to protein immunization, chronic infection led to increased levels of clonal expansion, class-switching, and somatic variants. Furthermore, antibodies from the highly expanded and class-switched (IgG) plasma cells were found to be specific for multiple viral antigens and a subset of clones exhibited cross-reactivity to nonviral and autoantigens. Integrating single-cell transcriptome data with antibody specificity suggested that plasma cell transcriptional phenotype was correlated to viral antigen specificity. Our findings demonstrate that chronic viral infection can induce and sustain plasma cell clonal expansion, combined with significant somatic hypermutation, and can generate cross-reactive antibodies.
MeSH term(s)	Animals ; Antibodies, Viral/genetics ; Antibodies, Viral/immunology ; Chronic Disease ; Clonal Selection, Antigen-Mediated ; Female ; Immunoglobulin Heavy Chains/genetics ; Immunoglobulin Heavy Chains/immunology ; Immunoglobulin Light Chains/genetics ; Immunoglobulin Light Chains/immunology ; Lymphocytic Choriomeningitis/genetics ; Lymphocytic Choriomeningitis/immunology ; Lymphocytic choriomeningitis virus/immunology ; Mice ; Plasma Cells/immunology ; Single-Cell Analysis
Chemical Substances	Antibodies, Viral ; Immunoglobulin Heavy Chains ; Immunoglobulin Light Chains
Language	English
Publishing date	2021-11-23
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120108-6
ISSN	1521-4141 ; 0014-2980
ISSN (online)	1521-4141
ISSN	0014-2980
DOI	10.1002/eji.202149331
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Article ; Online: Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen.

Sesterhenn, Fabian / Galloux, Marie / Vollers, Sabrina S / Csepregi, Lucia / Yang, Che / Descamps, Delphyne / Bonet, Jaume / Friedensohn, Simon / Gainza, Pablo / Corthésy, Patricia / Chen, Man / Rosset, Stéphane / Rameix-Welti, Marie-Anne / Éléouët, Jean-François / Reddy, Sai T / Graham, Barney S / Riffault, Sabine / Correia, Bruno E

PLoS biology

2019 Volume 17, Issue 2, Page(s) e3000164

Abstract: Throughout the last several decades, vaccination has been key to prevent and eradicate infectious diseases. However, many pathogens (e.g., respiratory syncytial virus [RSV], influenza, dengue, and others) have resisted vaccine development efforts, ... ...

Abstract	Throughout the last several decades, vaccination has been key to prevent and eradicate infectious diseases. However, many pathogens (e.g., respiratory syncytial virus [RSV], influenza, dengue, and others) have resisted vaccine development efforts, largely because of the failure to induce potent antibody responses targeting conserved epitopes. Deep profiling of human B cells often reveals potent neutralizing antibodies that emerge from natural infection, but these specificities are generally subdominant (i.e., are present in low titers). A major challenge for next-generation vaccines is to overcome established immunodominance hierarchies and focus antibody responses on crucial neutralization epitopes. Here, we show that a computationally designed epitope-focused immunogen presenting a single RSV neutralization epitope elicits superior epitope-specific responses compared to the viral fusion protein. In addition, the epitope-focused immunogen efficiently boosts antibodies targeting the palivizumab epitope, resulting in enhanced neutralization. Overall, we show that epitope-focused immunogens can boost subdominant neutralizing antibody responses in vivo and reshape established antibody hierarchies.
MeSH term(s)	Animals ; Antibodies, Monoclonal, Humanized/chemistry ; Antibodies, Monoclonal, Humanized/immunology ; Antibodies, Neutralizing/biosynthesis ; Antibodies, Neutralizing/genetics ; Antibodies, Viral/biosynthesis ; Antibodies, Viral/genetics ; Cloning, Molecular ; Computer-Aided Design ; Epitopes/chemistry ; Epitopes/immunology ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Female ; Gene Expression ; Genetic Vectors/chemistry ; Genetic Vectors/metabolism ; Immunization/methods ; Immunogenicity, Vaccine ; Mice ; Mice, Inbred BALB C ; Nanoparticles/administration & dosage ; Nanoparticles/chemistry ; Palivizumab/chemistry ; Palivizumab/immunology ; Receptors, Antigen, B-Cell/chemistry ; Receptors, Antigen, B-Cell/genetics ; Receptors, Antigen, B-Cell/immunology ; Recombinant Fusion Proteins/administration & dosage ; Recombinant Fusion Proteins/chemistry ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/immunology ; Respiratory Syncytial Virus Vaccines/administration & dosage ; Respiratory Syncytial Virus Vaccines/biosynthesis ; Respiratory Syncytial Virus Vaccines/genetics ; Respiratory Syncytial Viruses/immunology ; Structural Homology, Protein ; Viral Fusion Proteins/administration & dosage ; Viral Fusion Proteins/chemistry ; Viral Fusion Proteins/genetics ; Viral Fusion Proteins/immunology
Chemical Substances	Antibodies, Monoclonal, Humanized ; Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Receptors, Antigen, B-Cell ; Recombinant Fusion Proteins ; Respiratory Syncytial Virus Vaccines ; Viral Fusion Proteins ; motavizumab (50Y163LK8Q) ; Palivizumab (DQ448MW7KS)
Language	English
Publishing date	2019-02-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3000164
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