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Pesch T, Bonati L, Kelton W, Parola C, Ehling RA, Csepregi L, Kitamura D, Reddy ST. Molecular Design, Optimization, and Genomic Integration of Chimeric B Cell Receptors in Murine B Cells. Front Immunol 2019; 10:2630. [PMID: 31798579 PMCID: PMC6868064 DOI: 10.3389/fimmu.2019.02630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/23/2019] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Theresa Pesch
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Lucia Bonati
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - William Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich, Switzerland
| | - Roy A. Ehling
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Life Science Graduate School, Microbiology and Immunology, ETH Zürich, University of Zurich, Zurich, Switzerland
| | - Daisuke Kitamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Japan
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM, Reddy ST. Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells. MAbs 2019; 11:1367-1380. [PMID: 31478465 PMCID: PMC6816377 DOI: 10.1080/19420862.2019.1662691] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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 (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, we are able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, we could isolate a diverse panel of >40 unique antigen-binding variants. Additionally, we successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | | | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
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Mason DM, Weber CR, Parola C, Meng SM, Greiff V, Kelton WJ, Reddy ST. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis. Nucleic Acids Res 2018; 46:7436-7449. [PMID: 29931269 PMCID: PMC6101513 DOI: 10.1093/nar/gky550] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 12/26/2022] Open
Abstract
Antibody engineering is often performed to improve therapeutic properties by directed evolution, usually by high-throughput screening of phage or yeast display libraries. Engineering antibodies in mammalian cells offer advantages associated with expression in their final therapeutic format (full-length glycosylated IgG); however, the inability to express large and diverse libraries severely limits their potential throughput. To address this limitation, we have developed homology-directed mutagenesis (HDM), a novel method which extends the concept of CRISPR/Cas9-mediated homology-directed repair (HDR). HDM leverages oligonucleotides with degenerate codons to generate site-directed mutagenesis libraries in mammalian cells. By improving HDR to a robust efficiency of 15-35% and combining mammalian display screening with next-generation sequencing, we validated this approach can be used for key applications in antibody engineering at high-throughput: rational library construction, novel variant discovery, affinity maturation and deep mutational scanning (DMS). We anticipate that HDM will be a valuable tool for engineering and optimizing antibodies in mammalian cells, and eventually enable directed evolution of other complex proteins and cellular therapeutics.
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Affiliation(s)
- Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
- Life Science Graduate School, Systems Biology, ETH Zürich, University of Zurich, Zurich 8057, Switzerland
| | - Simon M Meng
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - William J Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel 4058, Switzerland
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Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2017; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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Kelton W, Waindok AC, Pesch T, Pogson M, Ford K, Parola C, Reddy ST. Reprogramming MHC specificity by CRISPR-Cas9-assisted cassette exchange. Sci Rep 2017; 7:45775. [PMID: 28374766 PMCID: PMC5379551 DOI: 10.1038/srep45775] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/02/2017] [Indexed: 11/20/2022] Open
Abstract
The development of programmable nucleases has enabled the application of new genome engineering strategies for cellular immunotherapy. While targeted nucleases have mostly been used to knock-out or knock-in genes in immune cells, the scarless exchange of entire immunogenomic alleles would be of great interest. In particular, reprogramming the polymorphic MHC locus could enable the creation of matched donors for allogeneic cellular transplantation. Here we show a proof-of-concept for reprogramming MHC-specificity by performing CRISPR-Cas9-assisted cassette exchange. Using murine antigen presenting cell lines (RAW264.7 macrophages), we demonstrate that the generation of Cas9-induced double-stranded breaks flanking the native MHC-I H2-Kd locus led to exchange of an orthogonal H2-Kb allele. MHC surface expression allowed for easy selection of reprogrammed cells by flow cytometry, thus obviating the need for additional selection markers. MHC-reprogrammed cells were fully functional as they could present H2-Kd-restricted peptide and activate cognate T cells. Finally, we investigated the role of various donor template formats on exchange efficiency, discovering that templates that underwent in situ linearization resulted in the highest MHC-reprogramming efficiency. These findings highlight a potential new approach for the correcting of MHC mismatches in cellular transplantation.
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Affiliation(s)
- William Kelton
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Ann Cathrin Waindok
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Theresa Pesch
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Mark Pogson
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Kyle Ford
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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Piper Jenks N, Pardos de la Gandara M, D'Orazio BM, Correa da Rosa J, Kost RG, Khalida C, Vasquez KS, Coffran C, Pastagia M, Evering TH, Parola C, Urban T, Salvato S, Barsanti F, Coller BS, Tobin JN. Differences in prevalence of community-associated MRSA and MSSA among U.S. and non-U.S. born populations in six New York Community Health Centers. Travel Med Infect Dis 2016; 14:551-560. [PMID: 27773780 DOI: 10.1016/j.tmaid.2016.10.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/22/2016] [Accepted: 10/11/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Staphylococcus aureus is the most common cause of Skin and Soft Tissue Infections (SSTIs) in the community in the United States of America. Community Health Centers (CHC) serve as primary care providers for thousands of immigrants in New York. METHODS As part of a research collaborative, 6 New York City-area CHCs recruited patients with SSTIs. Characterization was performed in all S. aureus isolates from wounds and nasal swabs collected from patients. Statistical analysis examined the differences in wound and nasal cultures among immigrant compared to native-born patients. RESULTS Wound and nasal specimens were recovered from 129 patients and tested for antibiotic susceptibility. 40 patients were immigrants from 15 different countries. Although not statistically significant, immigrants had lower rates of MRSA infections (n = 15) than did native-born participants, and immigrants showed significantly higher rates of MSSA wound cultures (n = 11) (OR = 3.5, 95% CI: 1.3, 9.7). CONCLUSIONS In our study, immigrants were more likely to present with SSTIs caused by MSSA than US-born patients. Immigants also reported lower frequencies of antibiotic prescription or consumption in the months prior to SSTI infection. This suggests that antibiotic resistance may vary regionally and that immigrants presenting with SSTIs may benefit from a broader range of antibiotics.
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Affiliation(s)
- N Piper Jenks
- Clinical Directors Network, Inc (CDN), 5 West 37th Street, 10th Floor, New York, NY 10018, USA; Hudson River HealthCare, 1037 Main Street, Peekskill, NY 10566, USA.
| | - M Pardos de la Gandara
- Laboratory of Microbiology & Infectious Diseases, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - B M D'Orazio
- Clinical Directors Network, Inc (CDN), 5 West 37th Street, 10th Floor, New York, NY 10018, USA.
| | - J Correa da Rosa
- Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - R G Kost
- Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - C Khalida
- Clinical Directors Network, Inc (CDN), 5 West 37th Street, 10th Floor, New York, NY 10018, USA.
| | - K S Vasquez
- Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - C Coffran
- Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - M Pastagia
- Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - T H Evering
- Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - C Parola
- Urban Health Plan, Inc., 1065 Southern Boulevard, Bronx, NY 10459, USA.
| | - T Urban
- Urban Health Plan, Inc., 1065 Southern Boulevard, Bronx, NY 10459, USA.
| | - S Salvato
- Urban Health Plan, Inc., 1065 Southern Boulevard, Bronx, NY 10459, USA.
| | - F Barsanti
- Urban Health Plan, Inc., 1065 Southern Boulevard, Bronx, NY 10459, USA.
| | - B S Coller
- Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - J N Tobin
- Clinical Directors Network, Inc (CDN), 5 West 37th Street, 10th Floor, New York, NY 10018, USA; Center for Clinical and Translational Science (CCTS), The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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Prandelli C, Parola C, Buizza L, Delbarba A, Marziano M, Salvi V, Zacchi V, Memo M, Sozzani S, Calza S, Uberti D, Bosisio D. Sulphurous thermal water increases the release of the anti-inflammatory cytokine IL-10 and modulates antioxidant enzyme activity. Int J Immunopathol Pharmacol 2014; 26:633-46. [PMID: 24067460 DOI: 10.1177/039463201302600307] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The beneficial effects of hot springs have been known for centuries and treatments with sulphurous thermal waters are recommended in a number of chronic pathologies as well as acute recurrent infections. However, the positive effects of the therapy are often evaluated in terms of subjective sense of wellbeing and symptomatic clinical improvements. Here, the effects of an S-based compound (NaSH) and of a specific sulphurous thermal water characterized by additional ions such as sodium chloride, bromine and iodine (STW) were investigated in terms of cytokine release and anti-oxidant enzyme activity in primary human monocytes and in saliva from 50 airway disease patients subjected to thermal treatments. In vitro, NaSH efficiently blocked the induction of pro-inflammatory cytokines and counterbalanced the formation of ROS. Despite STW not recapitulating these results, possibly due to the low concentration of S-based compounds reached at the minimum non-toxic dilution, we found that it enhanced the release of IL-10, a potent anti-inflammatory cytokine. Notably, higher levels of IL-10 were also observed in patients' saliva following STW treatment and this increase correlated positively with salivary catalase activity (r2 = 0.19, *p less than 0.01). To our knowledge, these results represent the first evidence suggesting that S-based compounds and STW may prove useful in facing chronic inflammatory and age-related illness due to combined anti-inflammatory and anti-oxidant properties.
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Affiliation(s)
- C Prandelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
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Galluzzo M, De Cicco ML, Andreoli C, Cortese A, Parola C, Miele V. [Radiologic and MR findings in a rare case of intermediate cuneiform osteonecrosis in a child]. Radiol Med 2001; 101:304-6. [PMID: 11398067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Affiliation(s)
- M Galluzzo
- Servizio di Radiologia Generale, Ospedale S. Camillo, Università degli Studi La Sapienza, Rome, Italy
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Landman D, Volkert F, Manikal V, Saurina G, Ruan Y, Oydna E, Parola C, Quale J. Vancomycin-resistant enterococci in Brooklyn, New York: a moment in time. Clin Infect Dis 1999; 29:1587-8. [PMID: 10585828 DOI: 10.1086/313536] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- D Landman
- Division of Infectious Diseases State University of New York Health Science Center at Brooklyn, Brooklyn, NY 11203, USA
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