1
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Palladini G, Liedtke M, Zago W, Dolan P, Kinney GG, Gertz MA. The mechanism of action, pharmacological characteristics, and clinical utility of the amyloid depleter birtamimab for the potential treatment of AL amyloidosis. Leuk Lymphoma 2024:1-11. [PMID: 38600883 DOI: 10.1080/10428194.2024.2337803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/27/2024] [Indexed: 04/12/2024]
Abstract
Amyloid light chain (AL) amyloidosis is a progressive plasma cell disorder caused by amyloid deposition resulting in organ damage and failure. Current standard-of-care treatments target clonal plasma cells, the source of misfolded light chains (amyloid precursors), yet only half of patients with advanced disease survive ≥6 months. The amyloid depleter birtamimab is an investigational humanized monoclonal antibody that binds misfolded κ and λ light chains with high specificity and was designed to neutralize soluble toxic light chain aggregates and promote phagocytic clearance of deposited amyloid. Post hoc analyses from the Phase 3 VITAL trial suggested birtamimab plus standard of care confers a survival benefit in patients with advanced (Mayo Stage IV) AL amyloidosis. AFFIRM-AL (NCT04973137), a Phase 3 confirmatory trial of birtamimab plus standard of care in patients with Mayo Stage IV AL amyloidosis, is ongoing. This review summarizes birtamimab's mechanism of action, attributes, and potential clinical utility.
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Affiliation(s)
- Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS, Policlinico San Matteo, Pavia, Italy
| | | | | | - Phil Dolan
- Prothena Biosciences Inc, Brisbane, CA, USA
| | | | - Morie A Gertz
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
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2
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Barton J, Gaspariunas A, Galson JD, Leem J. Building Representation Learning Models for Antibody Comprehension. Cold Spring Harb Perspect Biol 2024; 16:a041462. [PMID: 38012013 PMCID: PMC10910360 DOI: 10.1101/cshperspect.a041462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Antibodies are versatile proteins with both the capacity to bind a broad range of targets and a proven track record as some of the most successful therapeutics. However, the development of novel antibody therapeutics is a lengthy and costly process. It is challenging to predict the functional and biophysical properties of antibodies from their amino acid sequence alone, requiring numerous experiments for full characterization. Machine learning, specifically deep representation learning, has emerged as a family of methods that can complement wet lab approaches and accelerate the overall discovery and engineering process. Here, we review advances in antibody sequence representation learning, and how this has improved antibody structure prediction and facilitated antibody optimization. We discuss challenges in the development and implementation of such models, such as the lack of publicly available, well-curated antibody function data and highlight opportunities for improvement. These and future advances in machine learning for antibody sequences have the potential to increase the success rate in developing new therapeutics, resulting in broader access to transformative medicines and improved patient outcomes.
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Affiliation(s)
- Justin Barton
- Alchemab Therapeutics Ltd, London N1C 4AX, United Kingdom
| | | | - Jacob D Galson
- Alchemab Therapeutics Ltd, London N1C 4AX, United Kingdom
| | - Jinwoo Leem
- Alchemab Therapeutics Ltd, London N1C 4AX, United Kingdom
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3
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Schaffer AM, Fiala GJ, Hils M, Natali E, Babrak L, Herr LA, Romero-Mulero MC, Cabezas-Wallscheid N, Rizzi M, Miho E, Schamel WWA, Minguet S. Kidins220 regulates the development of B cells bearing the λ light chain. eLife 2024; 13:e83943. [PMID: 38271217 PMCID: PMC10810608 DOI: 10.7554/elife.83943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
The ratio between κ and λ light chain (LC)-expressing B cells varies considerably between species. We recently identified Kinase D-interacting substrate of 220 kDa (Kidins220) as an interaction partner of the BCR. In vivo ablation of Kidins220 in B cells resulted in a marked reduction of λLC-expressing B cells. Kidins220 knockout B cells fail to open and recombine the genes of the Igl locus, even in genetic scenarios where the Igk genes cannot be rearranged or where the κLC confers autoreactivity. Igk gene recombination and expression in Kidins220-deficient B cells is normal. Kidins220 regulates the development of λLC B cells by enhancing the survival of developing B cells and thereby extending the time-window in which the Igl locus opens and the genes are rearranged and transcribed. Further, our data suggest that Kidins220 guarantees optimal pre-BCR and BCR signaling to induce Igl locus opening and gene recombination during B cell development and receptor editing.
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Affiliation(s)
- Anna-Maria Schaffer
- Faculty of Biology, Albert-Ludwigs-University of FreiburgFreiburgGermany
- Signalling Research Centers BIOSS and CIBSS, University of FreiburgFreiburgGermany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical FacultyFreiburgGermany
| | - Gina Jasmin Fiala
- Faculty of Biology, Albert-Ludwigs-University of FreiburgFreiburgGermany
- Signalling Research Centers BIOSS and CIBSS, University of FreiburgFreiburgGermany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical FacultyFreiburgGermany
| | - Miriam Hils
- Faculty of Biology, Albert-Ludwigs-University of FreiburgFreiburgGermany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical FacultyFreiburgGermany
- Department of Dermatology and Allergy Biederstein, School of Medicine, Technical University of MunichMunichGermany
| | - Eriberto Natali
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW 15 University of Applied Sciences and Arts Northwestern SwitzerlandMuttenzSwitzerland
| | - Lmar Babrak
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW 15 University of Applied Sciences and Arts Northwestern SwitzerlandMuttenzSwitzerland
| | - Laurenz Alexander Herr
- Faculty of Biology, Albert-Ludwigs-University of FreiburgFreiburgGermany
- Signalling Research Centers BIOSS and CIBSS, University of FreiburgFreiburgGermany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical FacultyFreiburgGermany
| | - Mari Carmen Romero-Mulero
- Faculty of Biology, Albert-Ludwigs-University of FreiburgFreiburgGermany
- Max Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Nina Cabezas-Wallscheid
- Max Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
- CIBSS – Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
| | - Marta Rizzi
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical FacultyFreiburgGermany
- CIBSS – Centre for Integrative Biological Signalling Studies, University of FreiburgFreiburgGermany
- Division of Clinical and Experimental Immunology, Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of ViennaViennaAustria
- Department of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Faculty of Medicine, University of FreiburgFreiburgGermany
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW 15 University of Applied Sciences and Arts Northwestern SwitzerlandMuttenzSwitzerland
- aiNET GmbHBaselSwitzerland
- SIB Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Wolfgang WA Schamel
- Faculty of Biology, Albert-Ludwigs-University of FreiburgFreiburgGermany
- Signalling Research Centers BIOSS and CIBSS, University of FreiburgFreiburgGermany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical FacultyFreiburgGermany
| | - Susana Minguet
- Faculty of Biology, Albert-Ludwigs-University of FreiburgFreiburgGermany
- Signalling Research Centers BIOSS and CIBSS, University of FreiburgFreiburgGermany
- Center of Chronic Immunodeficiency CCI, University Clinics and Medical FacultyFreiburgGermany
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4
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Raybould MIJ, Turnbull OM, Suter A, Guloglu B, Deane CM. Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling. Commun Biol 2024; 7:62. [PMID: 38191620 PMCID: PMC10774428 DOI: 10.1038/s42003-023-05744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/26/2023] [Indexed: 01/10/2024] Open
Abstract
Antibodies with lambda light chains (λ-antibodies) are generally considered to be less developable than those with kappa light chains (κ-antibodies). Though this hypothesis has not been formally established, it has led to substantial systematic biases in drug discovery pipelines and thus contributed to kappa dominance amongst clinical-stage therapeutics. However, the identification of increasing numbers of epitopes preferentially engaged by λ-antibodies shows there is a functional cost to neglecting to consider them as potential lead candidates. Here, we update our Therapeutic Antibody Profiler (TAP) tool to use the latest data and machine learning-based structure prediction, and apply it to evaluate developability risk profiles for κ-antibodies and λ-antibodies based on their surface physicochemical properties. We find that while human λ-antibodies on average have a higher risk of developability issues than κ-antibodies, a sizeable proportion are assigned lower-risk profiles by TAP and should represent more tractable candidates for therapeutic development. Through a comparative analysis of the low- and high-risk populations, we highlight opportunities for strategic design that TAP suggests would enrich for more developable λ-antibodies. Overall, we provide context to the differing developability of κ- and λ-antibodies, enabling a rational approach to incorporate more diversity into the initial pool of immunotherapeutic candidates.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Oliver M Turnbull
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Annabel Suter
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
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5
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Zou L, Zhang D, Ha CM, Wende AR, Chatham JC. Best practices in assessing cardiac protein O-GlcNAcylation by immunoblot. Am J Physiol Heart Circ Physiol 2023; 325:H601-H616. [PMID: 37539459 PMCID: PMC10642998 DOI: 10.1152/ajpheart.00104.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/27/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
The modification of serine and threonine amino acids of proteins by O-linked N-acetylglucosamine (O-GlcNAc) regulates the activity, stability, function, and subcellular localization of proteins. Dysregulation of O-GlcNAc homeostasis is well established as a hallmark of various cardiac diseases, including cardiac hypertrophy, heart failure, complications associated with diabetes, and responses to acute injuries such as oxidative stress and ischemia-reperfusion. Given the limited availability of site-specific O-GlcNAc antibodies, studies of changes in O-GlcNAcylation in the heart frequently use pan-O-GlcNAc antibodies for semiquantitative evaluation of overall O-GlcNAc levels. However, there is a high degree of variability in many published cardiac O-GlcNAc blots. For example, many blots often have regions that lack O-GlcNAc positive staining of proteins either below 50 or above 100 kDa. In some O-GlcNAc blots, only a few protein bands are detected, while in others, intense bands around 75 kDa dominate the gel due to nonspecific IgM band staining, making it difficult to visualize less intense bands. Therefore, the goal of this study was to develop a modifiable protocol that optimizes O-GlcNAc positive banding of proteins in cardiac tissue extracts. We showed that O-GlcNAc blots using CTD110.6 antibody of proteins ranging from <30 to ∼450 kDa could be obtained while also limiting nonspecific staining. We also show that some myofilament proteins are recognized by the CTD110.6 antibody. Therefore, by protocol optimization using the widely available CTD110.6 antibody, we found that it is possible to obtain pan-O-GlcNAc blots of cardiac tissue, which minimizes common limitations associated with this technique.NEW & NOTEWORTHY The post-translational modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc) is recognized as mediating cardiac pathophysiology. However, there is considerable variability in the quality of O-GlcNAc immunoblots used to evaluate changes in cardiac O-GlcNAc levels. Here we show that with relatively minor changes to a commonly used protocol it is possible to minimize the intensity of nonspecific bands while also reproducibly generating O-GlcNAc immunoblots covering a range of molecular weights from <30 to ∼450 kDa.
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Affiliation(s)
- Luyun Zou
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Dingguo Zhang
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Chae-Myeong Ha
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Adam R Wende
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - John C Chatham
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
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6
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Singh S, Tian W, Severance ZC, Chaudhary SK, Anokhina V, Mondal B, Pergu R, Singh P, Dhawa U, Singha S, Choudhary A. Proximity-inducing modalities: the past, present, and future. Chem Soc Rev 2023; 52:5485-5515. [PMID: 37477631 DOI: 10.1039/d2cs00943a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Living systems use proximity to regulate biochemical processes. Inspired by this phenomenon, bifunctional modalities that induce proximity have been developed to redirect cellular processes. An emerging example of this class is molecules that induce ubiquitin-dependent proteasomal degradation of a protein of interest, and their initial development sparked a flurry of discovery for other bifunctional modalities. Recent advances in this area include modalities that can change protein phosphorylation, glycosylation, and acetylation states, modulate gene expression, and recruit components of the immune system. In this review, we highlight bifunctional modalities that perform functions other than degradation and have great potential to revolutionize disease treatment, while also serving as important tools in basic research to explore new aspects of biology.
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Affiliation(s)
- Sameek Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Wenzhi Tian
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Zachary C Severance
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santosh K Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Viktoriya Anokhina
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Basudeb Mondal
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Rajaiah Pergu
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Prashant Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Uttam Dhawa
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santanu Singha
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
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7
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Guloglu B, Deane CM. Specific attributes of the V L domain influence both the structure and structural variability of CDR-H3 through steric effects. Front Immunol 2023; 14:1223802. [PMID: 37564639 PMCID: PMC10410447 DOI: 10.3389/fimmu.2023.1223802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
Antibodies, through their ability to target virtually any epitope, play a key role in driving the adaptive immune response in jawed vertebrates. The binding domains of standard antibodies are their variable light (VL) and heavy (VH) domains, both of which present analogous complementarity-determining region (CDR) loops. It has long been known that the VH CDRs contribute more heavily to the antigen-binding surface (paratope), with the CDR-H3 loop providing a major modality for the generation of diverse paratopes. Here, we provide evidence for an additional role of the VL domain as a modulator of CDR-H3 structure, using a diverse set of antibody crystal structures and a large set of molecular dynamics simulations. We show that specific attributes of the VL domain such as subtypes, CDR canonical forms and genes can influence the structural diversity of the CDR-H3 loop, and provide a physical model for how this effect occurs through inter-loop contacts and packing of CDRs against each other. Our results indicate that the rigid minor loops fine-tune the structure of CDR-H3, thereby contributing to the generation of surfaces complementary to the vast number of possible epitope topologies, and provide insights into the interdependent nature of CDR conformations, an understanding of which is important for the rational antibody design process.
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Affiliation(s)
- Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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8
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Tolmacheva AS, Onvumere MK, Sedykh SE, Timofeeva AM, Nevinsky GA. Catalase Activity of IgGs of Patients Infected with SARS-CoV-2. Int J Mol Sci 2023; 24:10081. [PMID: 37373231 DOI: 10.3390/ijms241210081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/29/2023] Open
Abstract
Coronavirus disease (COVID-19), caused by the SARS-CoV-2 coronavirus, leads to various manifestations of the post-COVID syndrome, including diabetes, heart and kidney disease, thrombosis, neurological and autoimmune diseases and, therefore, remains, so far, a significant public health problem. In addition, SARS-CoV-2 infection can lead to the hyperproduction of reactive oxygen species (ROS), causing adverse effects on oxygen transfer efficiency, iron homeostasis, and erythrocytes deformation, contributing to thrombus formation. In this work, the relative catalase activity of the serum IgGs of patients recovered from COVID-19, healthy volunteers vaccinated with Sputnik V, vaccinated with Sputnik V after recovering from COVID-19, and conditionally healthy donors were analyzed for the first time. Previous reports show that along with canonical antioxidant enzymes, the antibodies of mammals with superoxide dismutase, peroxidase, and catalase activities are involved in controlling reactive oxygen species levels. We here show that the IgGs from patients who recovered from COVID-19 had the highest catalase activity, and this was statistically significantly higher each compared to the healthy donors (1.9-fold), healthy volunteers vaccinated with Sputnik V (1.4-fold), and patients vaccinated after recovering from COVID-19 (2.1-fold). These data indicate that COVID-19 infection may stimulate the production of antibodies that degrade hydrogen peroxide, which is harmful at elevated concentrations.
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Affiliation(s)
- Anna S Tolmacheva
- Institute of Chemical Biology and Fundamental Medicine, SB of the RAS, 630090 Novosibirsk, Russia
| | - Margarita K Onvumere
- Institute of Chemical Biology and Fundamental Medicine, SB of the RAS, 630090 Novosibirsk, Russia
| | - Sergey E Sedykh
- Institute of Chemical Biology and Fundamental Medicine, SB of the RAS, 630090 Novosibirsk, Russia
| | - Anna M Timofeeva
- Institute of Chemical Biology and Fundamental Medicine, SB of the RAS, 630090 Novosibirsk, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, SB of the RAS, 630090 Novosibirsk, Russia
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9
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Crescioli S, Correa I, Ng J, Willsmore ZN, Laddach R, Chenoweth A, Chauhan J, Di Meo A, Stewart A, Kalliolia E, Alberts E, Adams R, Harris RJ, Mele S, Pellizzari G, Black ABM, Bax HJ, Cheung A, Nakamura M, Hoffmann RM, Terranova-Barberio M, Ali N, Batruch I, Soosaipillai A, Prassas I, Ulndreaj A, Chatanaka MK, Nuamah R, Kannambath S, Dhami P, Geh JLC, MacKenzie Ross AD, Healy C, Grigoriadis A, Kipling D, Karagiannis P, Dunn-Walters DK, Diamandis EP, Tsoka S, Spicer J, Lacy KE, Fraternali F, Karagiannis SN. B cell profiles, antibody repertoire and reactivity reveal dysregulated responses with autoimmune features in melanoma. Nat Commun 2023; 14:3378. [PMID: 37291228 PMCID: PMC10249578 DOI: 10.1038/s41467-023-39042-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 05/23/2023] [Indexed: 06/10/2023] Open
Abstract
B cells are known to contribute to the anti-tumor immune response, especially in immunogenic tumors such as melanoma, yet humoral immunity has not been characterized in these cancers to detail. Here we show comprehensive phenotyping in samples of circulating and tumor-resident B cells as well as serum antibodies in melanoma patients. Memory B cells are enriched in tumors compared to blood in paired samples and feature distinct antibody repertoires, linked to specific isotypes. Tumor-associated B cells undergo clonal expansion, class switch recombination, somatic hypermutation and receptor revision. Compared with blood, tumor-associated B cells produce antibodies with proportionally higher levels of unproductive sequences and distinct complementarity determining region 3 properties. The observed features are signs of affinity maturation and polyreactivity and suggest an active and aberrant autoimmune-like reaction in the tumor microenvironment. Consistent with this, tumor-derived antibodies are polyreactive and characterized by autoantigen recognition. Serum antibodies show reactivity to antigens attributed to autoimmune diseases and cancer, and their levels are higher in patients with active disease compared to post-resection state. Our findings thus reveal B cell lineage dysregulation with distinct antibody repertoire and specificity, alongside clonally-expanded tumor-infiltrating B cells with autoimmune-like features, shaping the humoral immune response in melanoma.
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Affiliation(s)
- Silvia Crescioli
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Isabel Correa
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Joseph Ng
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
- Research Department of Structural and Molecular Biology, University College London, London, UK
| | - Zena N Willsmore
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Roman Laddach
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, London, UK
| | - Alicia Chenoweth
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Jitesh Chauhan
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Ashley Di Meo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Alexander Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Eleni Kalliolia
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Elena Alberts
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Rebecca Adams
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Robert J Harris
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Silvia Mele
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Giulia Pellizzari
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Anna B M Black
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Heather J Bax
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Anthony Cheung
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Mano Nakamura
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Ricarda M Hoffmann
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Manuela Terranova-Barberio
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Niwa Ali
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
- Centre for Gene Therapy and Regenerative Medicine, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Ihor Batruch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Ioannis Prassas
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Antigona Ulndreaj
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miyo K Chatanaka
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Rosamund Nuamah
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Shichina Kannambath
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Genomics Facility, Institute of Cancer Research, London, UK
| | - Pawan Dhami
- Biomedical Research Centre, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Jenny L C Geh
- St John's Institute of Dermatology, Guy's, King's, and St. Thomas' Hospitals NHS Foundation Trust, London, UK
- Department of Plastic Surgery at Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | | | - Ciaran Healy
- Department of Plastic Surgery at Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - David Kipling
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Panagiotis Karagiannis
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Eleftherios P Diamandis
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, ON, Canada
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, London, UK
| | - James Spicer
- School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK
| | - Katie E Lacy
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Franca Fraternali
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
- Research Department of Structural and Molecular Biology, University College London, London, UK
| | - Sophia N Karagiannis
- St John's Institute of Dermatology, School of Basic & Medical Biosciences, King's College London, Guy's Hospital, London, UK.
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King's College London, Guy's Hospital, London, UK.
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10
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Friman V, Quinti I, Davydov AN, Shugay M, Farroni C, Engström E, Pour Akaber S, Barresi S, Mohamed A, Pulvirenti F, Milito C, Granata G, Giorda E, Ahlström S, Karlsson J, Marasco E, Marcellini V, Bocci C, Cascioli S, Scarsella M, Phad G, Tilevik A, Tartaglia M, Bemark M, Chudakov DM, Carsetti R, Grimsholm O. Defective peripheral B cell selection in common variable immune deficiency patients with autoimmune manifestations. Cell Rep 2023; 42:112446. [PMID: 37119135 DOI: 10.1016/j.celrep.2023.112446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/15/2023] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
Common variable immune deficiency (CVID) is a heterogeneous disorder characterized by recurrent infections, low levels of serum immunoglobulins, and impaired vaccine responses. Autoimmune manifestations are common, but B cell central and peripheral selection mechanisms in CVID are incompletely understood. Here, we find that receptor editing, a measure of central tolerance, is increased in transitional B cells from CVID patients and that these cells have a higher immunoglobulin κ:λ ratio in CVID patients with autoimmune manifestations than in those with infection only. Contrariwise, the selection pressure in the germinal center on CD27bright memory B cells is decreased in CVID patients with autoimmune manifestations. Finally, functionally, T cell-dependent activation showed that naive B cells in CVID patients are badly equipped for activation and induction of mismatch repair genes. We conclude that central tolerance is functional whereas peripheral selection is defective in CVID patients with autoimmune manifestations, which could underpin the development of autoimmunity.
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Affiliation(s)
- Vanda Friman
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Chiara Farroni
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy; B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Erik Engström
- Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Shirin Pour Akaber
- Institute of Pathophysiology and Allergy Research, Centre for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Ahmed Mohamed
- Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Federica Pulvirenti
- Centre for Primary Immune Deficiency, AUO Policlinico Umberto I, Rome, Italy
| | - Cinzia Milito
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Guido Granata
- Clinical and Research Department for Infectious Diseases, National Institute for Infectious Diseases L. Spallanzani (IRCCS), 00149 Rome, Italy
| | - Ezio Giorda
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Sara Ahlström
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johanna Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Emiliano Marasco
- Division of Rheumatology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Chiara Bocci
- B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Simona Cascioli
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Marco Scarsella
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ganesh Phad
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Immunology and Transfusion Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Brno, Czech Republic
| | - Rita Carsetti
- B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy; Unit of Diagnostic Immunology, Department of Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ola Grimsholm
- Institute of Pathophysiology and Allergy Research, Centre for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria; Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy.
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11
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Saporiti S, Laurenzi T, Guerrini U, Coppa C, Palinsky W, Benigno G, Palazzolo L, Ben Mariem O, Montavoci L, Rossi M, Centola F, Eberini I. Effect of Fc core fucosylation and light chain isotype on IgG1 flexibility. Commun Biol 2023; 6:237. [PMID: 36869088 PMCID: PMC9982779 DOI: 10.1038/s42003-023-04622-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
N-glycosylation plays a key role in modulating the bioactivity of monoclonal antibodies (mAbs), as well as the light chain (LC) isotype can influence their physicochemical properties. However, investigating the impact of such features on mAbs conformational behavior is a big challenge, due to the very high flexibility of these biomolecules. In this work we investigate, by accelerated molecular dynamics (aMD), the conformational behavior of two commercial immunoglobulins G1 (IgG1), representative of κ and λ LCs antibodies, in both their fucosylated and afucosylated forms. Our results show, through the identification of a stable conformation, how the combination of fucosylation and LC isotype modulates the hinge behavior, the Fc conformation and the position of the glycan chains, all factors potentially affecting the binding to the FcγRs. This work also represents a technological enhancement in the conformational exploration of mAbs, making aMD a suitable approach to clarify experimental results.
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Affiliation(s)
- Simona Saporiti
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Tommaso Laurenzi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Uliano Guerrini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Crescenzo Coppa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Sezione di Chimica Generale e Organica "A. Marchesini", Via Venezian, 21, 20133, Milano, Italy
| | - Wolf Palinsky
- Biotech Development Programme, Merck Biopharma, Aubonne, Switzerland
| | - Giulia Benigno
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Luca Palazzolo
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Omar Ben Mariem
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Linda Montavoci
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
| | - Mara Rossi
- Global Analytical Pharmaceutical Science and Innovation, Merck Serono S.p.A., Rome, Italy
| | - Fabio Centola
- Global Analytical Pharmaceutical Science and Innovation, Merck Serono S.p.A., Rome, Italy.
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari & DSRC, Università degli Studi di Milano, Via Balzaretti, 9, 20133, Milan, Italy
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12
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Absmeier RM, Rottenaicher GJ, Svilenov HL, Kazman P, Buchner J. Antibodies gone bad - the molecular mechanism of light chain amyloidosis. FEBS J 2023; 290:1398-1419. [PMID: 35122394 DOI: 10.1111/febs.16390] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/19/2022] [Accepted: 02/03/2022] [Indexed: 12/19/2022]
Abstract
Light chain amyloidosis (AL) is a systemic disease in which abnormally proliferating plasma cells secrete large amounts of mutated antibody light chains (LCs) that eventually form fibrils. The fibrils are deposited in various organs, most often in the heart and kidney, and impair their function. The prognosis for patients diagnosed with AL is generally poor. The disease is set apart from other amyloidoses by the huge number of patient-specific mutations in the disease-causing and fibril-forming protein. The molecular mechanisms that drive the aggregation of mutated LCs into fibrils have been enigmatic, which hindered the development of efficient diagnostics and therapies. In this review, we summarize our current knowledge on AL amyloidosis and discuss open issues.
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Affiliation(s)
- Ramona M Absmeier
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Georg J Rottenaicher
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Hristo L Svilenov
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Pamina Kazman
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Functional Protein Assemblies and Department of Chemistry, Technische Universität München, Garching, Germany
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13
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Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun 2023; 24:21-31. [PMID: 36539592 PMCID: PMC10041605 DOI: 10.1038/s41435-022-00188-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 12/24/2022]
Abstract
Immunoglobulins (IGs), crucial components of the adaptive immune system, are encoded by three genomic loci. However, the complexity of the IG loci severely limits the effective use of short read sequencing, limiting our knowledge of population diversity in these loci. We leveraged existing long read whole-genome sequencing (WGS) data, fosmid technology, and IG targeted single-molecule, real-time (SMRT) long-read sequencing (IG-Cap) to create haplotype-resolved assemblies of the IG Lambda (IGL) locus from 6 ethnically diverse individuals. In addition, we generated 10 diploid assemblies of IGL from a diverse cohort of individuals utilizing IG-Cap. From these 16 individuals, we identified significant allelic diversity, including 36 novel IGLV alleles. In addition, we observed highly elevated single nucleotide variation (SNV) in IGLV genes relative to IGL intergenic and genomic background SNV density. By comparing SNV calls between our high quality assemblies and existing short read datasets from the same individuals, we show a high propensity for false-positives in the short read datasets. Finally, for the first time, we nucleotide-resolved common 5-10 Kb duplications in the IGLC region that contain functional IGLJ and IGLC genes. Together these data represent a significant advancement in our understanding of genetic variation and population diversity in the IGL locus.
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14
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Kilgore R, Chu W, Bhandari D, Fischler D, Carbonell RG, Crapanzano M, Menegatti S. Development of peptide affinity ligands for the purification of polyclonal and monoclonal Fabs from recombinant fluids. J Chromatogr A 2023; 1687:463701. [PMID: 36502645 DOI: 10.1016/j.chroma.2022.463701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Engineered multi-specific monoclonal antibodies (msAbs) and antibody fragments offer valuable therapeutic options against metabolic disorders, aggressive cancers, and viral infections. The advancement in molecular design and recombinant expression of these next-generation drugs, however, is not equaled by the progress in downstream bioprocess technology. The purification of msAbs and fragments requires affinity adsorbents with orthogonal biorecognition of different portions of the antibody structure, namely its Fc (fragment crystallizable) and Fab (fragment antigen-binding) regions or the CH1-3 and CL chains. Current adsorbents rely on protein ligands that, while featuring high binding capacity and selectivity, need harsh elution conditions and suffer from high cost, limited biochemical stability, and potential release of immunogenic fragments. Responding to these challenges, we undertook the de novo discovery of peptide ligands that target different regions of human Fab and enable product release under mild conditions. The ligands were discovered by screening a focused library of 12-mer peptides against a feedstock comprising human Fab and Chinese hamster ovary host cell proteins (CHO HCPs). The identified ligands were evaluated via binding studies as well as molecular docking simulations, returning excellent values of binding capacity (Qmax ∼ 20 mg of Fab per mL of resin) and dissociation constant (KD = 2.16·10-6 M). Selected ligand FRWNFHRNTFFP and commercial Protein L ligands were further characterized by measuring the dynamic binding capacity (DBC10%) at different residence times (RT) and performing the purification of polyclonal and monoclonal Fabs from CHO-K1 cell culture fluids. The peptide ligand featured DBC10% ∼ 6-16 mg/mL (RT of 2 min) and afforded values of yield (93-96%) and purity (89-96%) comparable to those provided by Protein L resins.
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Affiliation(s)
- Ryan Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Dipendra Bhandari
- LigaTrap Technologies, 1791 Varsity Dr., Suite 150, Raleigh, NC 27606, United States
| | - David Fischler
- LigaTrap Technologies, 1791 Varsity Dr., Suite 150, Raleigh, NC 27606, United States
| | - Ruben G Carbonell
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, United States
| | - Michael Crapanzano
- LigaTrap Technologies, 1791 Varsity Dr., Suite 150, Raleigh, NC 27606, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States; LigaTrap Technologies, 1791 Varsity Dr., Suite 150, Raleigh, NC 27606, United States; Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, NC 27695, United States.
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15
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Okoreeh MK, Kennedy DE, Emmanuel AO, Veselits M, Moshin A, Ladd RH, Erickson S, McLean KC, Madrigal B, Nemazee D, Maienschein-Cline M, Mandal M, Clark MR. Asymmetrical forward and reverse developmental trajectories determine molecular programs of B cell antigen receptor editing. Sci Immunol 2022; 7:eabm1664. [PMID: 35930652 PMCID: PMC9636592 DOI: 10.1126/sciimmunol.abm1664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
During B lymphopoiesis, B cell progenitors progress through alternating and mutually exclusive stages of clonal expansion and immunoglobulin (Ig) gene rearrangements. Great diversity is generated through the stochastic recombination of Ig gene segments encoding heavy and light chain variable domains. However, this commonly generates autoreactivity. Receptor editing is the predominant tolerance mechanism for self-reactive B cells in the bone marrow (BM). B cell receptor editing rescues autoreactive B cells from negative selection through renewed light chain recombination first at Igκ then Igλ loci. Receptor editing depends on BM microenvironment cues and key transcription factors such as NF-κB, FOXO, and E2A. The specific BM factor required for receptor editing is unknown. Furthermore, how transcription factors coordinate these developmental programs to promote usage of the λ chain remains poorly defined. Therefore, we used two mouse models that recapitulate pathways by which Igλ light chain-positive B cells develop. The first has deleted J kappa (Jκ) genes and hence models Igλ expression resulting from failed Igκ recombination (Igκdel). The second models autoreactivity by ubiquitous expression of a single-chain chimeric anti-Igκ antibody (κ-mac). Here, we demonstrated that autoreactive B cells transit asymmetric forward and reverse developmental trajectories. This imparted a unique epigenetic landscape on small pre-B cells, which opened chromatin to transcription factors essential for Igλ recombination. The consequences of this asymmetric developmental path were both amplified and complemented by CXCR4 signaling. These findings reveal how intrinsic molecular programs integrate with extrinsic signals to drive receptor editing.
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Affiliation(s)
- Michael K. Okoreeh
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
- Growth, Development, Disabilities Training program (GDDTP), Pritzker School of Medicine, University of Chicago, IL, 60637, USA
| | - Domenick E. Kennedy
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
- Present Address: Drug Discovery Science and Technology, Discovery Platform Technologies, Chemical Biology and Emerging Therapeutics, AbbVie, North Chicago, IL, United States
| | - Akinola Olumide Emmanuel
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
| | - Margaret Veselits
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
| | - Azam Moshin
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
| | - Robert H. Ladd
- Cytometry and Antibody Technologies Facility, University of Chicago, Chicago, IL, 60637, USA
| | - Steven Erickson
- Department of Pathology, University of Chicago, Chicago, IL, 60637, USA
| | - Kaitlin C. McLean
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
| | - Brianna Madrigal
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Malay Mandal
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
| | - Marcus R. Clark
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL, 60637, USA
- Gwen Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL, 60637, USA
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16
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Gao H, Yu L, Yan F, Zheng Y, Huang H, Zhuang X, Zeng Y. Landscape of B Cell Receptor Repertoires in COVID-19 Patients Revealed Through CDR3 Sequencing of Immunoglobulin Heavy and Light Chains. Immunol Invest 2022; 51:1994-2008. [PMID: 35797435 DOI: 10.1080/08820139.2022.2092407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The outbreak and persistence of coronavirus disease 2019 (COVID-19) threaten human health. B cells play a vital role in fighting the infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite many studies on the immune responses in COVID-19 patients, it is still unclear how B cell receptor (BCR) constituents, including immunoglobulin heavy (IGHs) and light chains (IGLs), respond to SARS-CoV-2 in patients with varying symptoms. In this study, we conducted complementarity-determining region 3 (CDR3) sequencing of BCR IGHs and IGLs from the peripheral blood of COVID-19 patients and healthy donors. The results showed significantly reduced clonal diversity, more expanded clones, and longer CDR3 lengths of IGH and IGL in COVID-19 patients than those in healthy individuals. The IGLs had a much higher percentage of VJ skew usage (47.83% IGLV and 42.86% IGLJ were significantly regulated) than the IGHs (12.09% IGHV and 0% IGHJ) between the healthy individuals and patients, which indicated the importance of BCR light chains. Furthermore, we found a largely expanded IGLV3-25 gene cluster mostly pairing with IGLJ1 and ILGJ2 in COVID-19 patients and a newly identified upregulated IGLJ1 gene and IGLJ2+IGLV13-21 recombination, both of which are potential sources of SARS-CoV-2-targeting antibodies. Our findings on specific immune B-cell signatures associated with COVID-19 have clinical implications for vaccine and biomarker development for disease diagnosis.
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Affiliation(s)
- Hongzhi Gao
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.,Department of Respiratory Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liying Yu
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Furong Yan
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Youxian Zheng
- Department of Microbiology, Quanzhou Municipal Center for Disease Control and Prevention, Fujian Province, Quanzhou, China
| | - Hongbo Huang
- Department of Pulmonary and Critical Care Medicine, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xibin Zhuang
- Department of Pulmonary and Critical Care Medicine, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China
| | - Yiming Zeng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
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17
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Meyerholz DK, Leidinger MR, Goeken JA, Businga TR, Akers A, Vizuett S, Kaemmer CA, Kohlmeyer JL, Dodd RD, Quelle DE. Utility of CD138/syndecan-1 immunohistochemistry for localization of plasmacytes is tissue-dependent in B6 mice. BMC Res Notes 2022; 15:219. [PMID: 35752869 PMCID: PMC9233769 DOI: 10.1186/s13104-022-06100-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Objective Inflammation is present in many diseases and identification of immune cell infiltration is a common assessment. CD138 (syndecan-1) is a recommended immunohistochemical marker for human plasmacytes although it is also expressed in various epithelia and tumors. Similarly, CD138 is a marker for murine plasmacytes, but its tissue immunostaining is not well-defined. Endogenous CD138 expression is an important confounding factor when evaluating plasmacyte infiltration. We studied two plasmacyte markers (CD138 and Kappa light chains) for endogenous immunostaining in five organs and one tumor from B6 mice. Results Plasmacytes in Peyer’s patches were positive for CD138 and Kappa markers without endogenous immunostaining. Endogenous CD138 immunostaining was widespread in liver, kidney, lung and a malignant peripheral nerve sheath tumor (MPNST) versus regionalized immunostaining in skin and small intestine wall. Endogenous Kappa immunostaining was absent in all tissues except for plasmacytes. Tissues with widespread endogenous CD138 immunostaining were contrasted by absence of endogenous Kappa immunostaining. Here, plasmacytes would not be distinguished by CD138, but would be obvious by Kappa immunostaining. Our study suggests that utility of immunostaining for plasmacytes by CD138 is tissue dependent in mice. Additionally, Kappa immunostaining may be a useful alternative in mouse tissues with confounding endogenous CD138 immunostaining.
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Affiliation(s)
| | | | - J Adam Goeken
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | | | - Allison Akers
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | | | - Courtney A Kaemmer
- Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA, USA
| | | | - Rebecca D Dodd
- Department of Internal Medicine, University of Iowa, Iowa City, IA, USA
| | - Dawn E Quelle
- Department of Pathology, University of Iowa, Iowa City, IA, USA.,Department of Neuroscience and Pharmacology, University of Iowa, Iowa City, IA, USA
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18
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Wu M, Zhao H, Tang X, Zhao W, Yi X, Li Q, Sun X. Organization and Complexity of the Yak (Bos Grunniens) Immunoglobulin Loci. Front Immunol 2022; 13:876509. [PMID: 35615368 PMCID: PMC9124968 DOI: 10.3389/fimmu.2022.876509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/11/2022] [Indexed: 12/03/2022] Open
Abstract
As important livestock in Qinghai-Tibet Plateau, yak provides meat and other necessities for Tibetans living. Plateau yak has resistance to diseases and stress, yet is nearly unknown in the structure and expression mechanism of yak immunoglobulin loci. Based on the published immunoglobulin genes of bovids (cattle, sheep and goat), the genomic organization of the yak immunoglobulin heavy chain (IgH) and immunoglobulin light chain (IgL) were described. The assemblage diversity of IgH, Igλ and Igκ in yak was similar to that in bovids, and contributes little to the antibody lineage compared with that in humans and mice. Somatic hypermutation (SHM) had a greater effect on immunoglobulin diversity in yak than in goat and sheep, and in addition to the complementarity-determining region (CDR), some loci in the framework region (FR) also showed high frequency mutations. CDR3 diversity showed that immunological lineages in yak were overwhelmingly generated through linkage diversity in IgH rearrangements. The emergence of new high-throughput sequencing technologies and the yak whole genome (2019) publication have greatly improved our understanding of the immune response in yaks. We had a more comprehensive analysis of yak immunoglobulin expression diversity by PE300, which avoided the disadvantage of missing low-frequency recombination in traditional Sanger sequencing. In summary, we described the schematic structure of the genomic organization of yak IgH loci and IgL loci. The analysis of immunoglobulin expression diversity showed that yak made up for the deficiency of V(D)J recombinant diversity by junctional diversity and CDR3 diversity. In addition, yak, like cattle, also had the same ultra-long IgH CDR3 (CDR3H), which provided more contribution to the diverse expression of yak immunoglobulin. These findings might provide a theoretical basis for disease resistance breeding and vaccine development in yak.
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Affiliation(s)
- Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wanxia Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiuzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
- *Correspondence: Xiuzhu Sun,
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19
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Stewart A, Sinclair E, Ng JCF, O’Hare JS, Page A, Serangeli I, Margreitter C, Orsenigo F, Longman K, Frampas C, Costa C, Lewis HM, Kasar N, Wu B, Kipling D, Openshaw PJM, Chiu C, Baillie JK, Scott JT, Semple MG, Bailey MJ, Fraternali F, Dunn-Walters DK. Pandemic, Epidemic, Endemic: B Cell Repertoire Analysis Reveals Unique Anti-Viral Responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus. Front Immunol 2022; 13:807104. [PMID: 35592326 PMCID: PMC9111746 DOI: 10.3389/fimmu.2022.807104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/15/2022] [Indexed: 11/17/2022] Open
Abstract
Immunoglobulin gene heterogeneity reflects the diversity and focus of the humoral immune response towards different infections, enabling inference of B cell development processes. Detailed compositional and lineage analysis of long read IGH repertoire sequencing, combining examples of pandemic, epidemic and endemic viral infections with control and vaccination samples, demonstrates general responses including increased use of IGHV4-39 in both Zaire Ebolavirus (EBOV) and COVID-19 patient cohorts. We also show unique characteristics absent in Respiratory Syncytial Virus or yellow fever vaccine samples: EBOV survivors show unprecedented high levels of class switching events while COVID-19 repertoires from acute disease appear underdeveloped. Despite the high levels of clonal expansion in COVID-19 IgG1 repertoires there is a striking lack of evidence of germinal centre mutation and selection. Given the differences in COVID-19 morbidity and mortality with age, it is also pertinent that we find significant differences in repertoire characteristics between young and old patients. Our data supports the hypothesis that a primary viral challenge can result in a strong but immature humoral response where failures in selection of the repertoire risk off-target effects.
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Affiliation(s)
- Alexander Stewart
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Emma Sinclair
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Joseph Chi-Fung Ng
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, United Kingdom
| | - Joselli Silva O’Hare
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Audrey Page
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Ilaria Serangeli
- Dipartimento di Biologia e Biotecnologie Charles Darwin, Sapienza Università di Roma, Rome, Italy
| | | | - Federica Orsenigo
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
- Department of Biotechnology and Biosciences, Università degli Studi di Milano-Bicocca, Milan, Italy
| | - Katherine Longman
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Cecile Frampas
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Catia Costa
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Holly-May Lewis
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Nora Kasar
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Bryan Wu
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - David Kipling
- School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Peter JM Openshaw
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Christopher Chiu
- Faculty of Medicine, Imperial College London, London, United Kingdom
| | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Janet T. Scott
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, United Kingdom
| | - Malcolm G. Semple
- Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Melanie J. Bailey
- Department of Chemistry, University of Surrey, Guildford, United Kingdom
| | - Franca Fraternali
- Randall Centre for Cell & Molecular Biophysics, King’s College London, London, United Kingdom
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20
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Du AX, Gniadecki R, Osman M. Biomarkers of B cell activation in autoimmune connective tissue diseases: More than markers of disease activity. Clin Biochem 2021; 100:1-12. [PMID: 34822848 DOI: 10.1016/j.clinbiochem.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/25/2022]
Abstract
B cells play a central role in the pathogenesis of many autoimmune diseases, acting as antigen-presenting cells, producing inflammatory cytokines, and acting as a source of autoantibodies after differentiating into plasma cells. In this review, we aim to summarize and synthesize the literature for the utility of biomarkers of B cell activation (plasma immunoglobulins (Ig), free light chains (FLCs), and beta-2 microglobulin (β2M)) in monitoring inflammatory rheumatic connective tissue diseases, such as Sjogren's syndrome (SS), systemic lupus erythematosus (SLE), dermatomyositis (DM), and systemic sclerosis (SSc). Clinically, it is quite difficult to gauge prognosis in these conditions as there, historically, have not been many quantitative markers of disease activity available. From our extensive literature review, Ig, FLC, and β2M may function as invaluable prognostic markers of ongoing disease activity, and potentially as biomarkers for response to therapy or disease relapse. They are inexpensive and unsophisticated tests that are vastly underused in the setting of autoimmune disease. However, clinicians still need to be aware of the potential of false positives in times of infection or plasma cell dyscrasia, as these disease states can artificially increase these biomarkers. Ultimately, the utility of serum Ig, FLCs, and β2M is clearly delineated in SS and SLE, and least investigated in DM, and additional prospective studies utilizing these biomarkers, and specific B cell targeted therapies are still needed.
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Affiliation(s)
- Amy X Du
- Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Robert Gniadecki
- Division of Dermatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Mohamed Osman
- Division of Rheumatology, Department of Medicine, University of Alberta, Edmonton, AB, Canada.
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21
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Near-germline human monoclonal antibodies neutralize and protect against multiple arthritogenic alphaviruses. Proc Natl Acad Sci U S A 2021; 118:2100104118. [PMID: 34507983 DOI: 10.1073/pnas.2100104118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 12/11/2022] Open
Abstract
Arthritogenic alphaviruses are globally distributed, mosquito-transmitted viruses that cause rheumatological disease in humans and include Chikungunya virus (CHIKV), Mayaro virus (MAYV), and others. Although serological evidence suggests that some antibody-mediated heterologous immunity may be afforded by alphavirus infection, the extent to which broadly neutralizing antibodies that protect against multiple arthritogenic alphaviruses are elicited during natural infection remains unknown. Here, we describe the isolation and characterization of MAYV-reactive alphavirus monoclonal antibodies (mAbs) from a CHIKV-convalescent donor. We characterized 33 human mAbs that cross-reacted with CHIKV and MAYV and engaged multiple epitopes on the E1 and E2 glycoproteins. We identified five mAbs that target distinct regions of the B domain of E2 and potently neutralize multiple alphaviruses with differential breadth of inhibition. These broadly neutralizing mAbs (bNAbs) contain few somatic mutations and inferred germline-revertants retained neutralizing capacity. Two bNAbs, DC2.M16 and DC2.M357, protected against both CHIKV- and MAYV-induced musculoskeletal disease in mice. These findings enhance our understanding of the cross-reactive and cross-protective antibody response to human alphavirus infections.
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22
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Fernández-Quintero ML, Kroell KB, Bacher LM, Loeffler JR, Quoika PK, Georges G, Bujotzek A, Kettenberger H, Liedl KR. Germline-Dependent Antibody Paratope States and Pairing Specific V H-V L Interface Dynamics. Front Immunol 2021; 12:675655. [PMID: 34447370 PMCID: PMC8382685 DOI: 10.3389/fimmu.2021.675655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/24/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies have emerged as one of the fastest growing classes of biotherapeutic proteins. To improve the rational design of antibodies, we investigate the conformational diversity of 16 different germline combinations, which are composed of 4 different kappa light chains paired with 4 different heavy chains. In this study, we systematically show that different heavy and light chain pairings strongly influence the paratope, interdomain interaction patterns and the relative VH-VL interface orientations. We observe changes in conformational diversity and substantial population shifts of the complementarity determining region (CDR) loops, resulting in distinct dominant solution structures and differently favored canonical structures. Additionally, we identify conformational changes in the structural diversity of the CDR-H3 loop upon different heavy and light chain pairings, as well as upon changes in sequence and structure of the neighboring CDR loops, despite having an identical CDR-H3 loop amino acid sequence. These results can also be transferred to all CDR loops and to the relative VH-VL orientation, as certain paratope states favor distinct interface angle distributions. Furthermore, we directly compare the timescales of sidechain rearrangements with the well-described transition kinetics of conformational changes in the backbone of the CDR loops. We show that sidechain flexibilities are strongly affected by distinct heavy and light chain pairings and decipher germline-specific structural features co-determining stability. These findings reveal that all CDR loops are strongly correlated and that distinct heavy and light chain pairings can result in different paratope states in solution, defined by a characteristic combination of CDR loop conformations and VH-VL interface orientations. Thus, these results have broad implications in the field of antibody engineering, as they clearly show the importance of considering paired heavy and light chains to understand the antibody binding site, which is one of the key aspects in the design of therapeutics.
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Affiliation(s)
- Monica L Fernández-Quintero
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Katharina B Kroell
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Lisa M Bacher
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Johannes R Loeffler
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Patrick K Quoika
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Hubert Kettenberger
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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23
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Harris RJ, Cheung A, Ng JCF, Laddach R, Chenoweth AM, Crescioli S, Fittall M, Dominguez-Rodriguez D, Roberts J, Levi D, Liu F, Alberts E, Quist J, Santaolalla A, Pinder SE, Gillett C, Hammar N, Irshad S, Van Hemelrijck M, Dunn-Walters DK, Fraternali F, Spicer JF, Lacy KE, Tsoka S, Grigoriadis A, Tutt ANJ, Karagiannis SN. Tumor-Infiltrating B Lymphocyte Profiling Identifies IgG-Biased, Clonally Expanded Prognostic Phenotypes in Triple-Negative Breast Cancer. Cancer Res 2021; 81:4290-4304. [PMID: 34224371 PMCID: PMC7611538 DOI: 10.1158/0008-5472.can-20-3773] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/23/2021] [Accepted: 06/14/2021] [Indexed: 12/29/2022]
Abstract
In breast cancer, humoral immune responses may contribute to clinical outcomes, especially in more immunogenic subtypes. Here, we investigated B lymphocyte subsets, immunoglobulin expression, and clonal features in breast tumors, focusing on aggressive triple-negative breast cancers (TNBC). In samples from patients with TNBC and healthy volunteers, circulating and tumor-infiltrating B lymphocytes (TIL-B) were evaluated. CD20+CD27+IgD- isotype-switched B lymphocytes were increased in tumors, compared with matched blood. TIL-B frequently formed stromal clusters with T lymphocytes and engaged in bidirectional functional cross-talk, consistent with gene signatures associated with lymphoid assembly, costimulation, cytokine-cytokine receptor interactions, cytotoxic T-cell activation, and T-cell-dependent B-cell activation. TIL-B-upregulated B-cell receptor (BCR) pathway molecules FOS and JUN, germinal center chemokine regulator RGS1, activation marker CD69, and TNFα signal transduction via NFκB, suggesting BCR-immune complex formation. Expression of genes associated with B lymphocyte recruitment and lymphoid assembly, including CXCL13, CXCR4, and DC-LAMP, was elevated in TNBC compared with other subtypes and normal breast. TIL-B-rich tumors showed expansion of IgG but not IgA isotypes, and IgG isotype switching positively associated with survival outcomes in TNBC. Clonal expansion was biased toward IgG, showing expansive clonal families with specific variable region gene combinations and narrow repertoires. Stronger positive selection pressure was present in the complementarity determining regions of IgG compared with their clonally related IgA in tumor samples. Overall, class-switched B lymphocyte lineage traits were conspicuous in TNBC, associated with improved clinical outcomes, and conferred IgG-biased, clonally expanded, and likely antigen-driven humoral responses. SIGNIFICANCE: Tumor-infiltrating B lymphocytes assemble in clusters, undergoing B-cell receptor-driven activation, proliferation, and isotype switching. Clonally expanded, IgG isotype-biased humoral immunity associates with favorable prognosis primarily in triple-negative breast cancers.
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MESH Headings
- Antigens, CD/biosynthesis
- Antigens, CD20/biosynthesis
- Antigens, Differentiation, T-Lymphocyte/biosynthesis
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Base Sequence
- Cell Line, Tumor
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Immunoglobulin D/biosynthesis
- Immunoglobulin G/immunology
- Immunohistochemistry
- Lectins, C-Type/biosynthesis
- Lymphocytes/cytology
- Models, Statistical
- Phenotype
- Prognosis
- RNA-Seq
- Receptors, Antigen, B-Cell/metabolism
- Single-Cell Analysis
- Transcriptome
- Triple Negative Breast Neoplasms/immunology
- Triple Negative Breast Neoplasms/metabolism
- Tumor Necrosis Factor Receptor Superfamily, Member 7/biosynthesis
- Tumor Necrosis Factor-alpha/biosynthesis
- User-Computer Interface
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Affiliation(s)
- Robert J Harris
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- King's Health Partners Cancer Research UK Cancer Center, King's College London, London, United Kingdom
| | - Anthony Cheung
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Joseph C F Ng
- Randall Center for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - Roman Laddach
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Alicia M Chenoweth
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Silvia Crescioli
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
| | - Matthew Fittall
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Diana Dominguez-Rodriguez
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
| | - James Roberts
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Dina Levi
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Fangfang Liu
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Elena Alberts
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Jelmar Quist
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Aida Santaolalla
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- School of Cancer and Pharmaceutical Studies, Translational Oncology and Urology Research (TOUR), King's College London, London, United Kingdom
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, King's College London, Comprehensive Cancer Center, Guy's Hospital, London, United Kingdom
- King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
| | - Cheryl Gillett
- School of Cancer and Pharmaceutical Sciences, King's College London, Comprehensive Cancer Center, Guy's Hospital, London, United Kingdom
- King's Health Partners Cancer Biobank, King's College London, London, United Kingdom
| | - Niklas Hammar
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sheeba Irshad
- School of Cancer and Pharmaceutical Sciences, King's College London, Comprehensive Cancer Center, Guy's Hospital, London, United Kingdom
| | - Mieke Van Hemelrijck
- Unit of Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- School of Cancer and Pharmaceutical Studies, Translational Oncology and Urology Research (TOUR), King's College London, London, United Kingdom
| | | | - Franca Fraternali
- Randall Center for Cell and Molecular Biophysics, King's College London, London, United Kingdom
| | - James F Spicer
- School of Cancer and Pharmaceutical Sciences, King's College London, Comprehensive Cancer Center, Guy's Hospital, London, United Kingdom
| | - Katie E Lacy
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural and Mathematical Sciences, King's College London, London, United Kingdom
| | - Anita Grigoriadis
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
| | - Andrew N J Tutt
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
- Breast Cancer Now Toby Robins Research Center, Institute of Cancer Research, London, United Kingdom
| | - Sophia N Karagiannis
- St. John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom.
- NIHR Biomedical Research Center at Guy's and St. Thomas' Hospitals and King's College London, Guy's Hospital, King's College London, London, United Kingdom
- Breast Cancer Now Research Unit, School of Cancer and Pharmaceutical Sciences, King's College London, Guy's Cancer Center, London, United Kingdom
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24
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Immunofocusing humoral immunity potentiates the functional efficacy of the AnAPN1 malaria transmission-blocking vaccine antigen. NPJ Vaccines 2021; 6:49. [PMID: 33824336 PMCID: PMC8024329 DOI: 10.1038/s41541-021-00309-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/24/2021] [Indexed: 11/08/2022] Open
Abstract
Malaria transmission-blocking vaccines (TBVs) prevent the completion of the developmental lifecycle of malarial parasites within the mosquito vector, effectively blocking subsequent infections. The mosquito midgut protein Anopheline alanyl aminopeptidase N (AnAPN1) is the leading, mosquito-based TBV antigen. Structure-function studies identified two Class II epitopes that can induce potent transmission-blocking (T-B) antibodies, informing the design of the next-generation AnAPN1. Here, we functionally screened new immunogens and down-selected to the UF6b construct that has two glycine-linked copies of the T-B epitopes. We then established a process for manufacturing UF6b and evaluated in outbred female CD1 mice the immunogenicity of the preclinical product with the human-safe adjuvant Glucopyranosyl Lipid Adjuvant in a liposomal formulation with saponin QS21 (GLA-LSQ). UF6b:GLA-LSQ effectively immunofocused the humoral response to one of the key T-B epitopes resulting in potent T-B activity, underscoring UF6b as a prime TBV candidate to aid in malaria elimination and eradication efforts.
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25
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Fernández-Quintero ML, Heiss MC, Pomarici ND, Math BA, Liedl KR. Antibody CDR loops as ensembles in solution vs. canonical clusters from X-ray structures. MAbs 2021; 12:1744328. [PMID: 32264741 PMCID: PMC7153821 DOI: 10.1080/19420862.2020.1744328] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In the past decade, the relevance of antibodies as therapeutics has increased substantially. Therefore, structural and functional characterization, in particular of the complementarity-determining regions (CDRs), is crucial to the design and engineering of antibodies with unique binding properties. Various studies have focused on classifying the CDR loops into a small set of main-chain conformations to facilitate antibody design by assuming that certain sequences can only adopt a limited number of conformations. Here, we present a kinetic classification of CDR loop structures as ensembles in solution. Using molecular dynamics simulations in combination with strong experimental structural information, we observe conformational transitions between canonical clusters and additional dominant solution structures in the micro-to-millisecond timescale for all CDR loops, independent of length and sequence composition. Besides identifying all relevant conformations in solution, our results revealed that various canonical cluster medians actually belong to the same kinetic minimum. Additionally, we reconstruct the kinetics and probabilities of the conformational transitions between canonical clusters, and thereby extend the model of static canonical structures to reveal a dynamic conformational ensemble in solution as a new paradigm in the field of antibody structure design. Abbreviations: CDR: Complementary-determining region; Fv: Antibody variable fragment; PCCA: Perron cluster analysis; tICA: Time-lagged independent component analysis; VH: Heavy chain variable region; VL: Light chain variable region
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Affiliation(s)
- Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Martin C Heiss
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Nancy D Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Barbara A Math
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innsbruck, Austria
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26
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Matz H, Munir D, Logue J, Dooley H. The immunoglobulins of cartilaginous fishes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 115:103873. [PMID: 32979434 PMCID: PMC7708420 DOI: 10.1016/j.dci.2020.103873] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/12/2020] [Accepted: 09/16/2020] [Indexed: 05/12/2023]
Abstract
Cartilaginous fishes, comprising the chimeras, sharks, skates, and rays, split from the common ancestor with other jawed vertebrates approx. 450 million years ago. Being the oldest extant taxonomic group to possess an immunoglobulin (Ig)-based adaptive immune system, examination of this group has taught us much about the evolution of adaptive immunity, as well as the conserved and taxon-specific characteristics of Igs. Significant progress has been made analyzing sequences from numerous genomic and transcriptomic data sets. These findings have been supported by additional functional studies characterizing the Igs and humoral response of sharks and their relatives. This review will summarize what we have learned about the genomic organization, protein structure, and in vivo function of these Ig isotypes in cartilaginous fishes and highlight the areas where our knowledge is still lacking.
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Affiliation(s)
- Hanover Matz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Institute of Marine and Environmental Technology, Baltimore, MD, USA
| | - Danish Munir
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - James Logue
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Helen Dooley
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA; Institute of Marine and Environmental Technology, Baltimore, MD, USA.
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Broad specificity of immune helminth scFv library to identify monoclonal antibodies targeting Strongyloides. Sci Rep 2021; 11:2502. [PMID: 33510342 PMCID: PMC7843650 DOI: 10.1038/s41598-021-82125-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022] Open
Abstract
Antibodies have different chemical properties capable of targeting a diverse nature of antigens. Traditionally, immune antibody libraries are perceived to be disease-specific with a skewed repertoire. The complexity during the generation of a combinatorial antibody library allows for a skewed but diverse repertoire to be generated. Strongyloides stercoralis is a parasite that causes strongyloidiasis, a potentially life-threatening disease with a complex diagnosis that impedes effective control and treatment of the disease. This study describes the isolation of monoclonal antibodies against S. stercoralis NIE recombinant protein using an immune antibody phage display library derived from lymphatic filaria-infected individuals. The isolated antibody clones showed both lambda and kappa light chains gene usage, with diverse amino acid distributions. Structural analysis showed that electropositivity and the interface area could determine the binding affinity of the clones with NIE. The successful identification of S. stercoralis antibodies from the filarial immune library highlights the breadth of antibody gene diversification in an immune antibody library that can be applied for closely related infections.
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Min TT, Yamabhai M. Human Hexa-Histidine-Tagged Single-Chain Variable Fragments for Bioimaging of Bacterial Infections. ACS OMEGA 2021; 6:762-774. [PMID: 33458528 PMCID: PMC7808144 DOI: 10.1021/acsomega.0c05340] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 12/11/2020] [Indexed: 06/12/2023]
Abstract
The single-chain variable fragment (scFv) of monoclonal antibodies is a promising recombinant nanostructure for various medical applications, including bioimaging and targeted therapy. While numerous scFv antibodies against eukaryotic cell surface proteins (especially cancer biomarkers) have been generated and engineered to suit various purposes, only a few specific scFv against bacterial cell surfaces have been developed, especially those of human origin. Recent incidents of emerging multidrug-resistant pathogenic bacteria and the realization of the importance of a balanced microbiota on the health of the host has led to more interests in the development of recombinant antibacterial antibodies as a detection probe or targeted therapy for bacterial infections. This study reports the generation of two specific human antibacterial scFv using phage display antibody technology. The recombinant scFv fragments of about 30 kDa and a diameter of 5 nm were produced and purified from engineered Escherichia coli that can enhance cytosolic disulfide bond formation. As a proof of principle, Propionibacterium acnes and Pseudomonas aeruginosa were used as model Gram-positive and Gram-negative bacteria, respectively. Specificity at the strain and species level to both planktonic and biofilm forms of these bacteria were demonstrated in various assay formats, namely, ELISA, flow cytometry, western blot, immunofluorescence, and electron microscopy via the hexa-histidine tag. This recombinant scFv generation platform can be applied for other bacteria, and since the scFv obtained has a benefit of being a human origin, it could be conveniently engineered for various therapeutic or theranostic applications with minimized adverse immunoreaction.
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Fernández-Quintero ML, Kroell KB, Heiss MC, Loeffler JR, Quoika PK, Waibl F, Bujotzek A, Moessner E, Georges G, Liedl KR. Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments. Front Mol Biosci 2020; 7:609088. [PMID: 33330636 PMCID: PMC7732698 DOI: 10.3389/fmolb.2020.609088] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Fab consist of a heavy and light chain and can be subdivided into a variable (V H and V L ) and a constant region (C H 1 and C L ). The variable region contains the complementarity-determining region (CDR), which is formed by six hypervariable loops, shaping the antigen binding site, the paratope. Apart from the CDR loops, both the elbow angle and the relative interdomain orientations of the V H -V L and the C H 1-C L domains influence the shape of the paratope. Thus, characterization of the interface and elbow angle dynamics is essential to antigen specificity. We studied nine antigen-binding fragments (Fab) to investigate the influence of affinity maturation, antibody humanization, and different light-chain types on the interface and elbow angle dynamics. While the CDR loops reveal conformational transitions in the micro-to-millisecond timescale, both the interface and elbow angle dynamics occur on the low nanosecond timescale. Upon affinity maturation, we observe a substantial rigidification of the V H and V L interdomain and elbow-angle flexibility, reflected in a narrower and more distinct distribution. Antibody humanization describes the process of grafting non-human CDR loops onto a representative human framework. As the antibody framework changes upon humanization, we investigated if both the interface and the elbow angle distributions are changed or shifted. The results clearly showed a substantial shift in the relative V H -V L distributions upon antibody humanization, indicating that different frameworks favor distinct interface orientations. Additionally, the interface and elbow angle dynamics of five antibody fragments with different light-chain types are included, because of their strong differences in elbow angles. For these five examples, we clearly see a high variability and flexibility in both interface and elbow angle dynamics, highlighting the fact that Fab interface orientations and elbow angles interconvert between each other in the low nanosecond timescale. Understanding how the relative interdomain orientations and the elbow angle influence antigen specificity, affinity, and stability has broad implications in the field of antibody modeling and engineering.
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Affiliation(s)
- Monica L. Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Katharina B. Kroell
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Martin C. Heiss
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes R. Loeffler
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Patrick K. Quoika
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Ekkehard Moessner
- Roche Pharma Research and Early Development, Large Molecular Research, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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30
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Production of a full chimeric mouse x pig anti-porcine DEC205 receptor recombinant antibody. J Immunol Methods 2020; 489:112911. [PMID: 33186587 DOI: 10.1016/j.jim.2020.112911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 11/01/2020] [Accepted: 11/02/2020] [Indexed: 11/23/2022]
Abstract
Recombinant hybrid antibodies are commonly used in antigen-targeting assays to reduce the immunogenic potential associated with using classic mouse antibodies in other species. The DEC205 receptor has become an attractive target due to its effectiveness in activating the immune response and is considered a promising vaccination target. The aim of this study was to produce a fully chimeric mouse x pig anti-porcine DEC205 recombinant antibody (rAb). Based on a mouse anti-porcine DEC205 monoclonal antibody (mAb), we designed and expressed a chimeric mouse x pig rAb using the Expi293f system. The resulting rAb maintained the recognition capacity of the native mouse mAb toward the porcine DEC205 receptor, as evidenced by western blot analysis. By using flow cytometry, we evaluated the ability of the rAb to recognize DEC205+ dendritic cells. In conclusion, the chimeric mouse x pig anti-DEC205 rAb can be used in antigen-targeting assays as a vaccination strategy in pigs.
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31
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Fernández-Quintero ML, Pomarici ND, Math BA, Kroell KB, Waibl F, Bujotzek A, Georges G, Liedl KR. Antibodies exhibit multiple paratope states influencing V H-V L domain orientations. Commun Biol 2020; 3:589. [PMID: 33082531 PMCID: PMC7576833 DOI: 10.1038/s42003-020-01319-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
Abstract
In the last decades, antibodies have emerged as one of the most important and successful classes of biopharmaceuticals. The highest variability and diversity of an antibody is concentrated on six hypervariable loops, also known as complementarity determining regions (CDRs) shaping the antigen-binding site, the paratope. Whereas it was assumed that certain sequences can only adopt a limited set of backbone conformations, in this study we present a kinetic classification of several paratope states in solution. Using molecular dynamics simulations in combination with experimental structural information we capture the involved conformational transitions between different canonical clusters and additional dominant solution structures occurring in the micro-to-millisecond timescale. Furthermore, we observe a strong correlation of CDR loop movements. Another important aspect when characterizing different paratope states is the relative VH/VL orientation and the influence of the distinct CDR loop states on the VH/VL interface. Conformational rearrangements of the CDR loops do not only have an effect on the relative VH/VL orientations, but also influence in some cases the elbow-angle dynamics and shift the respective distributions. Thus, our results show that antibodies exist as several interconverting paratope states, each contributing to the antibody's properties.
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Affiliation(s)
- Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Nancy D Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Barbara A Math
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Katharina B Kroell
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria.
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32
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Nouri N, Kleinstein SH. Somatic hypermutation analysis for improved identification of B cell clonal families from next-generation sequencing data. PLoS Comput Biol 2020; 16:e1007977. [PMID: 32574157 PMCID: PMC7347241 DOI: 10.1371/journal.pcbi.1007977] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 07/09/2020] [Accepted: 05/21/2020] [Indexed: 01/11/2023] Open
Abstract
Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune responses. Members of a B cell clone are descended from a common ancestor and share the same initial V(D)J rearrangement, but their B cell receptor (BCR) sequence may differ due to the accumulation of somatic hypermutations (SHMs). Clonal relationships are learned from AIRR-seq data by analyzing the BCR sequence, with the most common methods focused on the highly diverse junction region. However, clonally related cells often share SHMs which have been accumulated during affinity maturation. Here, we investigate whether shared SHMs in the V and J segments of the BCR can be leveraged along with the junction sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture junction similarity and shared mutations, and combine these in a spectral clustering framework to infer the BCR clonal relationships. Using both simulated and experimental data, we show that this model improves both the sensitivity and specificity for identifying B cell clones. Source code for this method is freely available in the SCOPer (Spectral Clustering for clOne Partitioning) R package (version 0.2 or newer) in the Immcantation framework: www.immcantation.org under the AGPLv3 license.
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Affiliation(s)
- Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Center for Medical Informatics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
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33
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Ling WL, Lua WH, Gan SKE. Sagacity in antibody humanization for therapeutics, diagnostics and research purposes: considerations of antibody elements and their roles. Antib Ther 2020; 3:71-79. [PMID: 33928226 PMCID: PMC7990220 DOI: 10.1093/abt/tbaa005] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/27/2020] [Accepted: 04/07/2020] [Indexed: 12/15/2022] Open
Abstract
The humanization of antibodies for therapeutics is a critical process that can determine the success of antibody drug development. However, the science underpinning this process remains elusive with different laboratories having very different methods. Well-funded laboratories can afford automated high-throughput screening methods to derive their best binder utilizing a very expensive initial set of equipment affordable only to a few. Often within these high-throughput processes, only standard key parameters, such as production, binding and aggregation are analyzed. Given the lack of suitable animal models, it is only at clinical trials that immunogenicity and allergy adverse effects are detected through anti-human antibodies as per FDA guidelines. While some occurrences that slip through can be mitigated by additional desensitization protocols, such adverse reactions to grafted humanized antibodies can be prevented at the humanization step. Considerations such as better antibody localization, avoidance of unspecific interactions to superantigens and the tailoring of antibody dependent triggering of immune responses, the antibody persistence on cells, can all be preemptively considered through a holistic sagacious approach, allowing for better outcomes in therapy and for research and diagnostic purposes.
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Affiliation(s)
- Wei-Li Ling
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Wai-Heng Lua
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Samuel Ken-En Gan
- Antibody & Product Development Lab, Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- p53 Laboratory, ASTAR, 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648
- Experimental Drug Development Center, ASTAR, 10 Biopolis Road, #05-01, Chromos, Singapore 138670
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34
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Mitsunaga EM, Snyder MP. Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing. Mol Cell Proteomics 2020; 19:278-293. [PMID: 31767621 PMCID: PMC7000125 DOI: 10.1074/mcp.ra119.001633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
Human antibody response studies are largely restricted to periods of high immune activity (e.g. vaccination). To comprehensively understand the healthy B cell immune repertoire and how this changes over time and through natural infection, we conducted immune repertoire RNA sequencing on flow cytometry-sorted B cell subsets to profile a single individual's antibodies over 11 months through two periods of natural viral infection. We found that 1) a baseline of healthy variable (V) gene usage in antibodies exists and is stable over time, but antibodies in memory cells consistently have a different usage profile relative to earlier B cell stages; 2) a single complementarity-determining region 3 (CDR3) is potentially generated from more than one VJ gene combination; and 3) IgG and IgA antibody transcripts are found at low levels in early human B cell development, suggesting that class switching may occur earlier than previously realized. These findings provide insight into immune repertoire stability, response to natural infections, and human B cell development.
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Affiliation(s)
- Erin M Mitsunaga
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305.
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35
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Abstract
In vertebrates, immunoglobulins (Igs), commonly known as antibodies, play an integral role in the armamentarium of immune defense against various pathogens. After an antigenic challenge, antibodies are secreted by differentiated B cells called plasma cells. Antibodies have two predominant roles that involve specific binding to antigens to launch an immune response, along with activation of other components of the immune system to fight pathogens. The ability of immunoglobulins to fight against innumerable and diverse pathogens lies in their intrinsic ability to discriminate between different antigens. Due to this specificity and high affinity for their antigens, antibodies have been a valuable and indispensable tool in research, diagnostics and therapy. Although seemingly a simple maneuver, the association between an antibody and its antigen, to make an antigen-antibody complex, is comprised of myriads of non-covalent interactions. Amino acid residues on the antigen binding site, the epitope, and on the antibody binding site, the paratope, intimately contribute to the energetics needed for the antigen-antibody complex stability. Structural biology methods to study antigen-antibody complexes are extremely valuable tools to visualize antigen-antibody interactions in detail; this helps to elucidate the basis of molecular recognition between an antibody and its specific antigen. The main scope of this chapter is to discuss the structure and function of different classes of antibodies and the various aspects of antigen-antibody interactions including antigen-antibody interfaces-with a special focus on paratopes, complementarity determining regions (CDRs) and other non-CDR residues important for antigen binding and recognition. Herein, we also discuss methods used to study antigen-antibody complexes, antigen recognition by antibodies, types of antigens in complexes, and how antigen-antibody complexes play a role in modern day medicine and human health. Understanding the molecular basis of antigen binding and recognition by antibodies helps to facilitate the production of better and more potent antibodies for immunotherapy, vaccines and various other applications.
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Affiliation(s)
- A Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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36
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Leitch S, Charlewood R. Paraprotein implicated in hardware failures in nucleic acid testing of blood donors. Vox Sang 2019; 115:140-147. [PMID: 31777099 DOI: 10.1111/vox.12870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND OBJECTIVES Analyser blockage due to gel formation by paraproteins leading to invalid results is a rare problem in viral nucleic acid testing (NAT) at New Zealand Blood Service (NZBS) despite many blood samples tested without problems from individuals with known paraproteins. This study aimed to identify common factors in samples causing blockages. METHOD Retrospective data were gathered on blood samples known to have blocked analysers at NZBS testing sites. Patients with plasma cell dyscrasia undergoing haematopoietic stem cell (HSC) harvest formed the comparator arm. These patients were identified from registry data of individuals undergoing autologous stem cell transplantation at Auckland City Hospital between 2013 and 2017. RESULTS Four individuals were identified as having blocked analysers between 2010 and 2018. A total of 184 HSC transplant patients were identified, with contemporaneous paraprotein levels available for 177 (96%). Patients with intact immunoglobulin subtypes (134, 73%) were further analysed. Of these, 119 patients (65%) also had total protein and globulin levels available. Mean paraprotein (37.5 g/l), total protein (95.3 g/l), globulin levels (51.5 g/l) and proportion of lambda subtype (75%) were higher in the blocker group compared with non-blocking comparators (4.7 g/l, 66.8 g/l, 27.7 g/l, 36.6% respectively) (P = 0·03, 0·02, 0·007, 0·12). The highest paraprotein and total protein levels from the non-blocking cohort overlapped with the lowest of the blocker group. DISCUSSION High protein levels (paraprotein >20 g/l, total protein >75 g/l) and a trend towards lambda subtype were associated with NAT analyser blockage. The overlap with non-blocking donor samples suggests factors in addition to protein quantity that are also important.
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37
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Fernández-Quintero ML, Math BA, Loeffler JR, Liedl KR. Transitions of CDR-L3 Loop Canonical Cluster Conformations on the Micro-to-Millisecond Timescale. Front Immunol 2019; 10:2652. [PMID: 31803187 PMCID: PMC6877499 DOI: 10.3389/fimmu.2019.02652] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 10/25/2019] [Indexed: 01/02/2023] Open
Abstract
Sequence and structural diversity of antibodies are concentrated on six hypervariable loops, also known as the complementarity determining regions (CDRs). Five of six antibody CDR loops presumably adopt a so-called canonical structure out of a limited number of conformations. However, here we show for four antibody CDR-L3 loops differing in length and sequence, that each loop undergoes conformational transitions between different canonical structures. By extensive sampling in combination with Markov-state models we reconstruct the kinetics and probabilities of the transitions between canonical structures. Additionally, for these four CDR-L3 loops, we identify all relevant conformations in solution. Thereby we extend the model of static canonical structures to a dynamic conformational ensemble as a new paradigm in the field of antibody structure design.
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Affiliation(s)
| | | | | | - Klaus R. Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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38
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Quiroz JA, Malonis RJ, Thackray LB, Cohen CA, Pallesen J, Jangra RK, Brown RS, Hofmann D, Holtsberg FW, Shulenin S, Nyakatura EK, Durnell LA, Rayannavar V, Daily JP, Ward AB, Aman MJ, Dye JM, Chandran K, Diamond MS, Kielian M, Lai JR. Human monoclonal antibodies against chikungunya virus target multiple distinct epitopes in the E1 and E2 glycoproteins. PLoS Pathog 2019; 15:e1008061. [PMID: 31697791 PMCID: PMC6837291 DOI: 10.1371/journal.ppat.1008061] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/01/2019] [Indexed: 01/31/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that causes persistent arthritis in a subset of human patients. We report the isolation and functional characterization of monoclonal antibodies (mAbs) from two patients infected with CHIKV in the Dominican Republic. Single B cell sorting yielded a panel of 46 human mAbs of diverse germline lineages that targeted epitopes within the E1 or E2 glycoproteins. MAbs that recognized either E1 or E2 proteins exhibited neutralizing activity. Viral escape mutations localized the binding epitopes for two E1 mAbs to sites within domain I or the linker between domains I and III; and for two E2 mAbs between the β-connector region and the B-domain. Two of the E2-specific mAbs conferred protection in vivo in a stringent lethal challenge mouse model of CHIKV infection, whereas the E1 mAbs did not. These results provide insight into human antibody response to CHIKV and identify candidate mAbs for therapeutic intervention.
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Affiliation(s)
- Jose A. Quiroz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Ryan J. Malonis
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Larissa B. Thackray
- Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
| | - Courtney A. Cohen
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Jesper Pallesen
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Rohit K. Jangra
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Rebecca S. Brown
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Daniel Hofmann
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | | | - Sergey Shulenin
- Integrated Biotherapeutics Inc., Rockville, Maryland, United States of America
| | - Elisabeth K. Nyakatura
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Lorellin A. Durnell
- Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
| | - Vinayak Rayannavar
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Johanna P. Daily
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - M. Javad Aman
- Integrated Biotherapeutics Inc., Rockville, Maryland, United States of America
| | - John M. Dye
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Michael S. Diamond
- Department of Medicine, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
- Department of Molecular Microbiology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
- Department of Pathology & Immunology, Washington University in St. Louis, School of Medicine, St. Louis, Missouri, United States of America
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jonathan R. Lai
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, United States of America
- * E-mail:
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39
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Goulet DR, Atkins WM. Considerations for the Design of Antibody-Based Therapeutics. J Pharm Sci 2019; 109:74-103. [PMID: 31173761 DOI: 10.1016/j.xphs.2019.05.031] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/02/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023]
Abstract
Antibody-based proteins have become an important class of biologic therapeutics, due in large part to the stability, specificity, and adaptability of the antibody framework. Indeed, antibodies not only have the inherent ability to bind both antigens and endogenous immune receptors but also have proven extremely amenable to protein engineering. Thus, several derivatives of the monoclonal antibody format, including bispecific antibodies, antibody-drug conjugates, and antibody fragments, have demonstrated efficacy for treating human disease, particularly in the fields of immunology and oncology. Reviewed here are considerations for the design of antibody-based therapeutics, including immunological context, therapeutic mechanisms, and engineering strategies. First, characteristics of antibodies are introduced, with emphasis on structural domains, functionally important receptors, isotypic and allotypic differences, and modifications such as glycosylation. Then, aspects of therapeutic antibody design are discussed, including identification of antigen-specific variable regions, choice of expression system, use of multispecific formats, and design of antibody derivatives based on fragmentation, oligomerization, or conjugation to other functional moieties. Finally, strategies to enhance antibody function through protein engineering are reviewed while highlighting the impact of fundamental biophysical properties on protein developability.
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Affiliation(s)
- Dennis R Goulet
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195.
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195
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Lim CC, Woo PCY, Lim TS. Development of a Phage Display Panning Strategy Utilizing Crude Antigens: Isolation of MERS-CoV Nucleoprotein human antibodies. Sci Rep 2019; 9:6088. [PMID: 30988390 PMCID: PMC6465254 DOI: 10.1038/s41598-019-42628-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
Antibody phage display has been pivotal in the quest to generate human monoclonal antibodies for biomedical and research applications. Target antigen preparation is a main bottleneck associated with the panning process. This includes production complexity, downstream purification, quality and yield. In many instances, purified antigens are preferred for panning but this may not be possible for certain difficult target antigens. Here, we describe an improved procedure of affinity selection against crude or non-purified antigen by saturation of non-binders with blocking agents to promote positive binder enrichment termed as Yin-Yang panning. A naïve human scFv library with kappa light chain repertoire with a library size of 109 was developed. The improved Yin-Yang biopanning process was able to enrich monoclonal antibodies specific to the MERS-CoV nucleoprotein. Three unique monoclonal antibodies were isolated in the process. The Yin-Yang biopanning method highlights the possibility of utilizing crude antigens for the isolation of monoclonal antibodies by phage display.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia
| | - Patrick C Y Woo
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11800, Penang, Malaysia.
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Leishmania infantum β-Tubulin Identified by Reverse Engineering Technology through Phage Display Applied as Theranostic Marker for Human Visceral Leishmaniasis. Int J Mol Sci 2019; 20:ijms20081812. [PMID: 31013713 PMCID: PMC6514782 DOI: 10.3390/ijms20081812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/30/2019] [Accepted: 04/04/2019] [Indexed: 12/27/2022] Open
Abstract
Two Leishmania infantum mimotopes (B10 and C01) identified by phage display showed to be antigenic and immunogenic for visceral (VL) and tegumentary (TL) leishmaniasis; however, their biological targets in the parasites have not been identified. The aim of the present study was to investigate the native antigens expressing both mimotopes, and to use them in distinct immunological assays. For this, a subtractive phage display technology was used, where a combinatorial library of single-chain variable fragments (scFv) was employed and the most reactive monoclonal antibodies for each target were captured, being the target antigens identified by mass spectrometry. Results in immunoblotting and immunoprecipitation assays showed that both monoclonal scFvs antibodies identified the β-tubulin protein as the target antigen in L. infantum. To validate these findings, the recombinant protein was cloned, purified and tested for the serodiagnosis of human leishmaniasis, and its immunogenicity was evaluated in PBMC derived from healthy subjects and treated or untreated VL patients. Results showed high diagnostic efficacy, as well as the development of a specific Th1 immune response in the cell cultures, since higher IFN-γ and lower IL-10 production was found.
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42
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Kaleli NE, Karadag M, Kalyoncu S. Phage display derived therapeutic antibodies have enriched aliphatic content: Insights for developability issues. Proteins 2019; 87:607-618. [DOI: 10.1002/prot.25685] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/07/2019] [Accepted: 03/13/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Nazlı Eda Kaleli
- Izmir Biomedicine and Genome Center Izmir Turkey
- Izmir Biomedicine and Genome Institute, Dokuz Eylül University Izmir Turkey
| | - Murat Karadag
- Izmir Biomedicine and Genome Center Izmir Turkey
- Izmir Biomedicine and Genome Institute, Dokuz Eylül University Izmir Turkey
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Dunn‐Walters D, Townsend C, Sinclair E, Stewart A. Immunoglobulin gene analysis as a tool for investigating human immune responses. Immunol Rev 2018; 284:132-147. [PMID: 29944755 PMCID: PMC6033188 DOI: 10.1111/imr.12659] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self-reactive B cells removed. Later antigen-dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases, and cancer. It can also be used to identify antigen-specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub-speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action.
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Affiliation(s)
| | | | - Emma Sinclair
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
| | - Alex Stewart
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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Ling WL, Lua WH, Poh JJ, Yeo JY, Lane DP, Gan SKE. Effect of VH-VL Families in Pertuzumab and Trastuzumab Recombinant Production, Her2 and FcγIIA Binding. Front Immunol 2018; 9:469. [PMID: 29593727 PMCID: PMC5857972 DOI: 10.3389/fimmu.2018.00469] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/21/2018] [Indexed: 11/15/2022] Open
Abstract
Many therapeutic antibodies are humanized from animal sources. In the humanization process, complementarity determining region grafting is tedious and highly prone to failure. With seven known VH families, and up to six known κ VL families, there are choices aplenty. However, the functions of these families remain largely enigmatic. To study the role of these V-region families, we made 84 recombinant combinations of the various VH and VL family whole IgG1 variants of both Trastuzumab and Pertuzumab. We managed to purify 66 of these to investigate the biophysical characteristics: recombinant protein production, and both Her2 and FcγIIA binding. Our findings revealed combinations that showed improved recombinant antibody production and both antigen and receptor binding kinetics. These findings show the need to rethink antibodies as a whole protein, relooking of the functions of the antibody domains, and the need to include immunoglobulin receptor investigations for effective antibody therapeutics development.
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Affiliation(s)
- Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Wai-Heng Lua
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Jun-Jie Poh
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Joshua Yi Yeo
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - David Philip Lane
- p53 Laboratory, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,p53 Laboratory, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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Gomez-Tourino I, Kamra Y, Baptista R, Lorenc A, Peakman M. T cell receptor β-chains display abnormal shortening and repertoire sharing in type 1 diabetes. Nat Commun 2017; 8:1792. [PMID: 29176645 PMCID: PMC5702608 DOI: 10.1038/s41467-017-01925-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 10/25/2017] [Indexed: 01/10/2023] Open
Abstract
Defects in T cell receptor (TCR) repertoire are proposed to predispose to autoimmunity. Here we show, by analyzing >2 × 108TCRB sequences of circulating naive, central memory, regulatory and stem cell-like memory CD4+ T cell subsets from patients with type 1 diabetes and healthy donors, that patients have shorter TCRB complementarity-determining region 3s (CDR3), in all cell subsets, introduced by increased deletions/reduced insertions during VDJ rearrangement. High frequency of short CDR3s is also observed in unproductive TCRB sequences, which are not subjected to thymic culling, suggesting that the shorter CDR3s arise independently of positive/negative selection. Moreover, TCRB CDR3 clonotypes expressed by autoantigen-specific CD4+ T cells are shorter compared with anti-viral T cells, and with those from healthy donors. Thus, early events in thymic T cell development and repertoire generation are abnormal in type 1 diabetes, which suggest that short CDR3s increase the potential for self-recognition, conferring heightened risk of autoimmune disease. T cell receptors are generated by somatic gene recombination, and are normally selected against autoreactivity. Here the authors show that CD4 T cells from patients with autoimmune type 1 diabetes have shorter TCRβ sequences, broader repertoire diversity, and more repertoire sharing than those from healthy individuals.
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Affiliation(s)
- Iria Gomez-Tourino
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK.,National Institute for Health Research, Biomedical Research Centre at Guy's and St Thomas' Hospital Foundation Trust and King's College London, Guy's Hospital, London, SE1 9RT, UK.,Immunology Laboratory, Biomedical Research Center (CINBIO), Centro Singular de Investigación de Galicia, University of Vigo, Campus Universitario de Vigo, Pontevedra, 36310, Spain
| | - Yogesh Kamra
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Roman Baptista
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK.,National Institute for Health Research, Biomedical Research Centre at Guy's and St Thomas' Hospital Foundation Trust and King's College London, Guy's Hospital, London, SE1 9RT, UK
| | - Anna Lorenc
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Mark Peakman
- Department of Immunobiology, Faculty of Life Sciences & Medicine, King's College London, 2nd Floor, Borough Wing, Guy's Hospital, London, SE1 9RT, UK. .,National Institute for Health Research, Biomedical Research Centre at Guy's and St Thomas' Hospital Foundation Trust and King's College London, Guy's Hospital, London, SE1 9RT, UK.
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Abstract
Immune tolerance hinders the potentially destructive responses of lymphocytes to host tissues. Tolerance is regulated at the stage of immature B cell development (central tolerance) by clonal deletion, involving apoptosis, and by receptor editing, which reprogrammes the specificity of B cells through secondary recombination of antibody genes. Recent mechanistic studies have begun to elucidate how these divergent mechanisms are controlled. Single-cell antibody cloning has revealed defects of B cell central tolerance in human autoimmune diseases and in several human immunodeficiency diseases caused by single gene mutations, which indicates the relevance of B cell tolerance to disease and suggests possible genetic pathways that regulate tolerance.
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47
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Martin VG, Wu YCB, Townsend CL, Lu GHC, O'Hare JS, Mozeika A, Coolen ACC, Kipling D, Fraternali F, Dunn-Walters DK. Transitional B Cells in Early Human B Cell Development - Time to Revisit the Paradigm? Front Immunol 2016; 7:546. [PMID: 27994589 PMCID: PMC5133252 DOI: 10.3389/fimmu.2016.00546] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/16/2016] [Indexed: 01/08/2023] Open
Abstract
The B cell repertoire is generated in the adult bone marrow by an ordered series of gene rearrangement processes that result in massive diversity of immunoglobulin (Ig) genes and consequently an equally large number of potential specificities for antigen. As the process is essentially random, the cells exhibiting excess reactivity with self-antigens are generated and need to be removed from the repertoire before the cells are fully mature. Some of the cells are deleted, and some will undergo receptor editing to see if changing the light chain can rescue an autoreactive antibody. As a consequence, the binding properties of the B cell receptor are changed as development progresses through pre-B ≫ immature ≫ transitional ≫ naïve phenotypes. Using long-read, high-throughput, sequencing we have produced a unique set of sequences from these four cell types in human bone marrow and matched peripheral blood, and our results describe the effects of tolerance selection on the B cell repertoire at the Ig gene level. Most strong effects of selection are seen within the heavy chain repertoire and can be seen both in gene usage and in CDRH3 characteristics. Age-related changes are small, and only the size of the CDRH3 shows constant and significant change in these data. The paucity of significant changes in either kappa or lambda light chain repertoires implies that either the heavy chain has more influence over autoreactivity than light chain and/or that switching between kappa and lambda light chains, as opposed to switching within the light chain loci, may effect a more successful autoreactive rescue by receptor editing. Our results show that the transitional cell population contains cells other than those that are part of the pre-B ≫ immature ≫ transitional ≫ naïve development pathway, since the population often shows a repertoire that is outside the trajectory of gene loss/gain between pre-B and naïve stages.
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Affiliation(s)
- Victoria G Martin
- Division of Infection, Immunity and Inflammatory Disease, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Yu-Chang Bryan Wu
- Randall Division of Cell and Molecular Biophysics, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Catherine L Townsend
- Division of Infection, Immunity and Inflammatory Disease, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Grace H C Lu
- Randall Division of Cell and Molecular Biophysics, Faculty of Life Sciences & Medicine, King's College London , London , UK
| | - Joselli Silva O'Hare
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey , Guildford, Surrey , UK
| | - Alexander Mozeika
- Faculty of Life Sciences & Medicine, Institute for Mathematical and Molecular Biomedicine, King's College London , London , UK
| | - Anthonius C C Coolen
- Faculty of Life Sciences & Medicine, Institute for Mathematical and Molecular Biomedicine, King's College London , London , UK
| | - David Kipling
- Institute of Cancer and Genetics, School of Medicine, Cardiff University , Cardiff , UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, Faculty of Life Sciences & Medicine, King's College London, London, UK; Faculty of Life Sciences & Medicine, Institute for Mathematical and Molecular Biomedicine, King's College London, London, UK
| | - Deborah K Dunn-Walters
- Division of Infection, Immunity and Inflammatory Disease, Faculty of Life Sciences & Medicine, King's College London, London, UK; Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, UK
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