1
|
Melo-Braga MN, Carvalho MB, Ferreira MCE, Lavinder J, Abbasi A, Palmisano G, Thaysen-Andersen M, Sajadi MM, Ippolito GC, Felicori LF. Unveiling the multifaceted landscape of N-glycosylation in antibody variable domains: Insights and implications. Int J Biol Macromol 2024; 257:128362. [PMID: 38029898 PMCID: PMC11003471 DOI: 10.1016/j.ijbiomac.2023.128362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/02/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
N-glycosylation at the antibody variable domain has emerged as an important modification influencing antibody function. Despite its significance, information regarding its role and regulation remains limited. To address this gap, we comprehensively explored antibody structures housing N-glycosylation within the Protein Data Bank, yielding fresh insights into this intricate landscape. Our findings revealed that among 208 structures, N-glycosylation was more prevalent in human and mouse antibodies containing IGHV1-8 and IGHV2-2 germline genes, respectively. Moreover, our research highlights the potential for somatic hypermutation to introduce N-glycosylation sites by substituting polar residues (Ser or Thr) in germline variable genes with asparagine. Notably, our study underscores the prevalence of N-glycosylation in antiviral antibodies, especially anti-HIV. Besides antigen-antibody interaction, our findings suggest that N-glycosylation may impact antibody specificity, affinity, and avidity by influencing Fab dimer formation and complementary-determining region orientation. We also identified different glycan structures in HIV and SARS-CoV-2 antibody proteomic datasets, highlighting disparities from the N-glycan structures between PDB antibodies and biological repertoires further highlighting the complexity of N-glycosylation patterns. Our findings significantly enrich our understanding of the N-glycosylation's multifaceted characteristics within the antibody variable domain. Additionally, they underscore the pressing imperative for a more comprehensive characterization of its impact on antibody function.
Collapse
Affiliation(s)
- Marcella Nunes Melo-Braga
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Milene Barbosa Carvalho
- Departamento de Ciência da Computação da Universidade Federal de São João Del Rei, São João Del Rei, MG, Brazil
| | - Manuela Cristina Emiliano Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Jason Lavinder
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Abdolrahim Abbasi
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil; School of Natural Sciences, Macquarie University, Sydney, Australia
| | - Morten Thaysen-Andersen
- School of Natural Sciences, Macquarie University, Sydney, Australia; Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Mohammad M Sajadi
- Division of Clinical Care and Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, TX, USA
| | - Liza F Felicori
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas da Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
| |
Collapse
|
2
|
Gervásio J, Ferreira A, Felicori LF. Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data. J Immunol Methods 2023; 523:113576. [PMID: 37966818 DOI: 10.1016/j.jim.2023.113576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
MOTIVATION The next-generation sequencing technologies have transformed our understanding of immunoglobulin (Ig) profiles in various immune states. Clonotyping, which groups Ig sequences into B cell clones, is crucial in investigating the diversity of repertoires and changes in antigen exposure. Despite its importance, there is no widely accepted method for clonotyping, and existing methods are computationally intensive for large sequencing datasets. RESULTS To address this challenge, we introduce YClon, a fast and efficient approach for clonotyping Ig repertoire data. YClon uses a hierarchical clustering approach, similar to other methods, to group Ig sequences into B cell clones in a highly sensitive and specific manner. Notably, our approach outperforms other methods by being more than 30 to 5000 times faster in processing the repertoires analyzed. Astonishingly, YClon can effortlessly handle up to 2 million Ig sequences on a standard laptop computer. This enables in-depth analysis of large and numerous antibody repertoires. AVAILABILITY AND IMPLEMENTATION YClon was implemented in Python3 and is freely available on GitHub.
Collapse
Affiliation(s)
- João Gervásio
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Alice Ferreira
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
| |
Collapse
|
3
|
Fernandes LP, Rocha MN, Duarte CG, Minozzo JC, do Monte-Neto RL, Felicori LF. Validation of a colorimetric LAMP to detect Loxosceles experimental envenomation. Toxicon 2022; 216:50-56. [PMID: 35787893 DOI: 10.1016/j.toxicon.2022.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/10/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022]
Abstract
Diagnostic tests for brown spider accidents are unavailable and impact treatment decisions, increasing costs and patient risks. In this work, we used for the first time a fast, simple, and visual method based on the loop-mediated isothermal amplification assay (LAMP) to detect Loxosceles envenomation. Using the DNA from L. similis legs, we observed a high sensitivity using this test since as low as 0.32 pg of DNA could be detected. This pH-dependent colorimetric assay was 64 times more sensitive than PCR to detect spider DNA. The test was specific for Loxosceles once no cross-reaction was observed when testing DNA from different agents that cause similar dermonecrotic injuries. The test allowed the detection of Loxosceles intermedia DNA from hair, serum, and exudate samples obtained from experimentally-envenomed rabbit within 72 h. The method sensitivity varied according to the sample and the collection time, reaching 100% sensitivity in serum and hair, respectively, 1 h and 24 h after the experimental envenomation. Due to its ease of execution, speed, sensitivity, and specificity, LAMP presents an excellent potential for identifying Loxosceles spp. Envenomation. This can reduce the burden on the Health System and the morbidity for the patient by implementing the appropriate therapy immediately.In addition, this work opens up the perspective to other venomous animal accident identification using LAMP.
Collapse
Affiliation(s)
- Luana Paula Fernandes
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Marcele Neves Rocha
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Clara Guerra Duarte
- Centro de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, 30510-010, Belo Horizonte, MG, Brazil
| | - João Carlos Minozzo
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Rubens L do Monte-Neto
- Biotechnology Applied to Patogens (BAP) - Instituto René Rachou - Fundação Oswaldo Cruz, Belo Horizonte, 30190-009, Minas Gerais, Brazil
| | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil.
| |
Collapse
|
4
|
Gervásio J, Sampaio Y, Muniz P, Yamada C, Felicori LF. BioSin UFMG Club: Engaging a multilevel and multidisciplinary community in synthetic biology. Biochem Mol Biol Educ 2022; 50:249-253. [PMID: 35150200 DOI: 10.1002/bmb.21609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 01/11/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Learning synthetic biology is often seen as a far distant possibility, restricted to those who have the privilege of an academic career. We propose a student-centered discussion group around synthetic biology, aimed at people from high school onwards with different backgrounds to interact and learn about synthetic biology. We developed a 14-week long program with three modules: "Leveling," "Introducing," and "Discussion." By completing the first two modules, the members should be more comfortable with biological names, structures, concepts, and techniques. The modules developed are available in Portuguese, Spanish, and English via the Open Lab Idea Real website (https://ideareal.org/clube-de-biologia-sintetica/) and can be used to implement the Club either in place or virtually around the world. We put it to practice at Universidade Federal de Minas Gerais (UFMG) creating the Club named BioSin. There are programs such as the International Genetically Engineered Machine (iGEM) competition focused on disseminating synthetic biology. Although iGEM is one fantastic way of learning about synthetic biology, there is a high cost. Because of that, a study and discussion Club is a tool to spread knowledge and engage with the study area.
Collapse
Affiliation(s)
- João Gervásio
- IdeaReal Open Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Yala Sampaio
- IdeaReal Open Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Paulo Muniz
- IdeaReal Open Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Camila Yamada
- IdeaReal Open Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Liza F Felicori
- IdeaReal Open Laboratory, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
5
|
Aires RB, Soares AADSM, Gomides APM, Nicola AM, Teixeira-Carvalho A, da Silva DLM, de Gois ET, Xavier FD, Martins FP, Santos GPJ, Schulte HL, Luz IS, Espindola LS, do Amaral LR, Felicori LF, Naves LA, de Carvalho MRM, Gomes MDS, Nóbrega OT, Albuquerque P, Fontes W, Gomes CM, Kurizky PS, Albuquerque CP, Martins-Filho OA, da Mota LMH. Thromboelastometry demonstrates endogenous coagulation activation in nonsevere and severe COVID-19 patients and has applicability as a decision algorithm for intervention. PLoS One 2022; 17:e0262600. [PMID: 35030224 PMCID: PMC8759688 DOI: 10.1371/journal.pone.0262600] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 12/28/2021] [Indexed: 12/17/2022] Open
Abstract
In patients with severe forms of COVID-19, thromboelastometry has been reported to display a hypercoagulant pattern. However, an algorithm to differentiate severe COVID-19 patients from nonsevere patients and healthy controls based on thromboelastometry parameters has not been developed. Forty-one patients over 18 years of age with positive qRT-PCR for SARS-CoV-2 were classified according to the severity of the disease: nonsevere (NS, n = 20) or severe (S, n = 21). A healthy control (HC, n = 9) group was also examined. Blood samples from all participants were tested by extrinsic (EXTEM), intrinsic (INTEM), non-activated (NATEM) and functional assessment of fibrinogen (FIBTEM) assays of thromboelastometry. The thrombodynamic potential index (TPI) was also calculated. Severe COVID-19 patients exhibited a thromboelastometry profile with clear hypercoagulability, which was significantly different from the NS and HC groups. Nonsevere COVID-19 cases showed a trend to thrombotic pole. The NATEM test suggested that nonsevere and severe COVID-19 patients presented endogenous coagulation activation (reduced clotting time and clot formation time). TPI data were significantly different between the NS and S groups. The maximum clot firmness profile obtained by FIBTEM showed moderate/elevated accuracy to differentiate severe patients from NS and HC. A decision tree algorithm based on the FIBTEM-MCF profile was proposed to differentiate S from HC and NS. Thromboelastometric parameters are a useful tool to differentiate the coagulation profile of nonsevere and severe COVID-19 patients for therapeutic intervention purposes.
Collapse
Affiliation(s)
- Rodrigo B. Aires
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Serviço de Anestesiologia, Hospital Santa Lúcia Sul, Brasília, Distrito Federal, Brazil
- * E-mail: (RBA); (PSK)
| | - Alexandre A. de S. M. Soares
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Ana Paula M. Gomides
- Faculdade de Ciências da Saúde, Centro Universitário de Brasília, Brasília, Distrito Federal, Brazil
| | - André M. Nicola
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Andréa Teixeira-Carvalho
- Grupo Integrado de Pesquisa em Biomarcadores, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Dayde Lane M. da Silva
- Departamento de Farmácia, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Eliana T. de Gois
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Unidade de Clínica Médica, Hospital Regional do Gama (HRG), Brasília, Distrito Federal, Brazil
| | - Flávia D. Xavier
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Francielle P. Martins
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Núcleo de Gestão Interna de Leitos, Hospital Regional da Asa Norte (HRAN), Brasília, Distrito Federal, Brazil
| | - Gabriela P. J. Santos
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Unidade de Medicina Interna, Hospital Regional de Taguatinga, Brasília, Distrito Federal, Brazil
| | - Heidi Luise Schulte
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Isabelle S. Luz
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Laila S. Espindola
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Laboratório de Farmacognosia, Faculdade de Ciências da Saúde, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Laurence R. do Amaral
- Laboratório de Bioinformática e Análises Moleculares, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia (RMPCT), Universidade Federal de Uberlândia, Patos de Minas, Minas Gerais, Brazil
| | - Liza F. Felicori
- Laboratório de Biologia Sintética e Biomiméticos, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Luciana A. Naves
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Serviço de Endocrinologia, Hospital Universitário de Brasília, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Maíra R. M. de Carvalho
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Unidade de Medicina Interna, Hospital Regional da Asa Norte (HRAN), Brasília, Distrito Federal, Brazil
| | - Matheus de S. Gomes
- Laboratório de Bioinformática e Análises Moleculares, Rede Multidisciplinar de Pesquisa, Ciência e Tecnologia (RMPCT), Universidade Federal de Uberlândia, Patos de Minas, Minas Gerais, Brazil
| | - Otávio T. Nóbrega
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Patrícia Albuquerque
- Faculdade UnB Ceilândia, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Wagner Fontes
- Laboratório de Bioquímica e Química de Proteínas, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Ciro M. Gomes
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Serviço de Dermatologia, Hospital Universitário de Brasília, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Patricia S. Kurizky
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Serviço de Dermatologia, Hospital Universitário de Brasília, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- * E-mail: (RBA); (PSK)
| | - Cleandro P. Albuquerque
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Serviço de Reumatologia, Hospital Universitário de Brasília, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Olindo A. Martins-Filho
- Grupo Integrado de Pesquisa em Biomarcadores, Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Minas Gerais, Brazil
| | - Licia Maria H. da Mota
- Programa de Pós-graduação em Ciências Médicas da Faculdade de Medicina da Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
- Serviço de Reumatologia, Hospital Universitário de Brasília, Universidade de Brasília (UnB), Brasília, Distrito Federal, Brazil
| |
Collapse
|
6
|
Carvalho MB, Molina F, Felicori LF. Yvis: antibody high-density alignment visualization and analysis platform with an integrated database. Nucleic Acids Res 2019; 47:W490-W495. [PMID: 31106372 PMCID: PMC6602444 DOI: 10.1093/nar/gkz387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/20/2019] [Accepted: 05/02/2019] [Indexed: 11/18/2022] Open
Abstract
As antibodies are a very important tool for diagnosis, therapy, and experimental biology, a large number of antibody structures and sequences have become available in recent years. Therefore, tools that allow the analysis, comparison, and visualization of this large amount of antibody data are crucially needed. We developed the antibody high-density alignment visualization and analysis (Yvis) platform to provide an innovative, robust and high-density data visualization of antibody sequence alignments, called Collier de Diamants. The Yvis platform also provides an integrated structural database, which is updated weekly, and many different search and filter options. This platform can help to formulate hypotheses concerning the key residues in antibody structures or interactions to improve the understanding of antibody properties. The Yvis platform is available at http://bioinfo.icb.ufmg.br/yvis/.
Collapse
Affiliation(s)
- Milene B Carvalho
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.,Departamento de Ciência da Computação, Universidade Federal de São João del Rei, São João del Rei, Minas Gerais, 36301-360, Brazil
| | - Franck Molina
- Sys2diag, UMR9005 CNRS Alcediag, Montpellier 34184, France
| | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| |
Collapse
|
7
|
Manso TC, Groenner-Penna M, Minozzo JC, Antunes BC, Ippolito GC, Molina F, Felicori LF. Next-generation sequencing reveals new insights about gene usage and CDR-H3 composition in the horse antibody repertoire. Mol Immunol 2018; 105:251-259. [PMID: 30562645 DOI: 10.1016/j.molimm.2018.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/11/2018] [Accepted: 11/30/2018] [Indexed: 12/26/2022]
Abstract
Horse serum antibodies have been used for greater than a century for the treatment and prophylaxis of infectious diseases and envenomations. Little is known, however, about the immunogenetic diversity that produces horse serum antibodies. Here, we employed next-generation sequencing for a first-in-kind comprehensive analysis of the equine B-cell repertoire. Nearly 45,000 and 30,000 clonotypes were obtained for the heavy-chain (IGH) and lambda light-chain (IGL) loci, respectively. We observed skewed use of the common subgroups IGHV2 (92.49%) and IGLV8 (82.50%), consistent with previous reports, but also novel use of the rare genes IGHV6S1 and IGLV4S2. CDR-H3 amino acid composition revealed different amino acid patterns at positions 106 and 116 compared to human, rabbit, and mouse, suggesting that an extended conformation predominates among horse CDR-H3 loops. Our analysis provides new insights regarding the mechanisms employed to generate antibody diversity in the horse, and could be applicable to the optimized design of synthetic antibodies intended for future therapeutic use.
Collapse
Affiliation(s)
- Taciana Conceição Manso
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michele Groenner-Penna
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - João Carlos Minozzo
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Bruno Cesar Antunes
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Stop A5000, Austin, TX, 78712, USA
| | | | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
| |
Collapse
|
8
|
Sharma R, Al-Saleem FH, Panzer J, Lee J, Puligedda RD, Felicori LF, Kattala CD, Rattelle AJ, Ippolito G, Cox RH, Lynch DR, Dessain SK. Monoclonal antibodies from a patient with anti-NMDA receptor encephalitis. Ann Clin Transl Neurol 2018; 5:935-951. [PMID: 30128318 PMCID: PMC6093837 DOI: 10.1002/acn3.592] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/01/2018] [Accepted: 05/09/2018] [Indexed: 12/28/2022] Open
Abstract
Objective Anti‐NMDA receptor encephalitis (ANRE) is a potentially lethal encephalitis attributed to autoantibodies against the N‐methyl‐D‐aspartate receptor (NMDAR). We sought to clone and characterize monoclonal antibodies (mAbs) from an ANRE patient. Methods We used a hybridoma method to clone two IgG mAbs from a female patient with ANRE without teratoma, and characterized their binding activities on NMDAR‐transfected cell lines, cultured primary rat neurons, and mouse hippocampus. We also assessed their effects on voluntary locomotor activity in mice and binding to NMDAR in vivo. Results The mAbs are structurally distinct and arose from distinct B‐cell lineages. They recognize different epitopes on the GluN1 amino terminal domain (ATD), yet both require amino acids important for post‐translational modification. Both mAbs bind subsets of GluN1 on cultured rat hippocampal neurons. The 5F5 mAb binds mouse brain hippocampal tissues, and the GluN1 recognized on cultured rat neurons was substantially extra‐synaptic. Antibody binding to primary hippocampal neurons induced receptor internalization. The NMDAR inhibitor MK‐801 inhibited internalization without preventing mAb binding; AP5 inhibited both mAb binding and internalization. Exposure of mice to the mAbs following permeabilization of the blood brain barrier increased voluntary wheel running activity, similar to low doses of the NMDAR inhibitor, MK‐801. Interpretation These mAbs recapitulate features demonstrated in previous studies of ANRE patient CSF, and exert effects on NMDAR in vitro and in vivo consistent with modulation of NMDAR activity.
Collapse
Affiliation(s)
- Rashmi Sharma
- Lankenau Institute for Medical Research Wynnewood Pennsylvania 19096
| | | | - Jessica Panzer
- Division of Neurology Children's Hospital of Pennsylvania Philadelphia Pennsylvania 19104
| | - Jiwon Lee
- Department of Chemical Engineering College of Natural Sciences University of Texas Austin Texas 78712
| | | | - Liza F Felicori
- Departamento de Bioquímica e Imunologia Universidade Federal de Minas Gerais Belo Horizonte MG Brazil.,Department of Molecular Biosciences College of Natural Sciences University of Texas Austin Texas 78712
| | | | - Amy J Rattelle
- Division of Neurology Children's Hospital of Pennsylvania Philadelphia Pennsylvania 19104
| | - Gregory Ippolito
- Department of Molecular Biosciences College of Natural Sciences University of Texas Austin Texas 78712
| | - Robert H Cox
- Lankenau Institute for Medical Research Wynnewood Pennsylvania 19096
| | - David R Lynch
- Division of Neurology Children's Hospital of Pennsylvania Philadelphia Pennsylvania 19104
| | - Scott K Dessain
- Lankenau Institute for Medical Research Wynnewood Pennsylvania 19096
| |
Collapse
|
9
|
Oliveira CFB, Vilela A, Coura LAM, Rodrigues FTG, Nagem RAP, Chávez-Olortegui C, Maioli TU, Felicori LF. Protective antibodies against a sphingomyelinase D from Loxosceles intermedia spider venom elicited in mice with different genetic background. Vaccine 2016; 34:3828-34. [PMID: 27265457 DOI: 10.1016/j.vaccine.2016.05.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/06/2016] [Accepted: 05/24/2016] [Indexed: 01/27/2023]
Abstract
In the present investigation we used a recombinant LiD1 toxin, named rLiD1his, from Loxosceles intermedia brown spider to elicit specific antibodies in mice carrying different Human Leukocyte Antigens class II (HLAII) {DRB1.0401 (DR4), DQB1.0601 (DQ6) and DQB1.0302 (DQ8)} as well as in BALB/C and C57BL/6 control mice. All mice strains produced high antibody titers against rLiD1his but DR4 mice antibodies (the lower responder mice) were not able to recognize L. intermedia crude venom. The anti-rLiD1his sera, except from DR4 mice, were able to neutralize dermonecrotic, hemorrhagic and edematogenic effects of rLiD1his in naïve rabbits. Overlapping peptides from the amino acid sequence of LiD1 toxin were prepared by SPOT method and differences in LiD1 epitope recognition were observed using different mice anti-rLiD1his sera. The region (160)DKVGHDFSGNDDISDVGK(177) was recognized by transgenic DQ8 and DQ6 mice sera. Other epitopes were recognized by at least two different animals' sera including (10)MGHMVNAIGQIDEFVNLG(27), (37)FDDNANPEYTYHGIP(51), (70)GLRSATTPGNSKYQEKLV(87) and (259)AAYKKKFRVATYDDN(273). Among these epitopes, the epitopes 37-51 and 160-177 have already been shown in previously studies as good candidates to be used alone or combined with other peptides to induce protective immune response against Loxosceles venoms. The results presented here highlight the importance of HLAII in antibody response and recognition of specific B-cell epitopes of rLiD1his spider toxin according to HLAII type and impact in the epitopic vaccine development against this spider.
Collapse
Affiliation(s)
| | - Andrea Vilela
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, UFMG, Brazil
| | - Luis Augusto M Coura
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, UFMG, Brazil
| | | | | | - Carlos Chávez-Olortegui
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, UFMG, Brazil
| | - Tatiani U Maioli
- Departamento de Nutrição, Escola de Enfermagem - EE, UFMG, Brazil
| | - Liza F Felicori
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, UFMG, Brazil
| |
Collapse
|
10
|
Hayashi MAF, Felicori LF, Fresqui MAC, Yonamine CM. Protein-Protein and Peptide-Protein Interactions of NudE-Like 1 (Ndel1): A Protein Involved in Schizophrenia. Curr Protein Pept Sci 2016; 16:754-67. [PMID: 25961396 DOI: 10.2174/1389203716666150505225251] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/01/2014] [Accepted: 12/23/2014] [Indexed: 11/22/2022]
Abstract
Schizophrenia (SCZ) is a devastating chronic mental disease determined by genetic and environmental factors, which susceptibility may involve an impaired neural migration during the neurodevelopmental process. Several candidate risk genes potentially associated with SCZ were related to the formation of protein complexes that ultimately mediate alterations in the neuroplasticity. The most studied SCZ risk gene is the Disrupted-in-Schizophrenia 1 (DISC1) gene, which functions seem to depend on the binding with cytoskeleton proteins, as the Nuclear-distribution gene E homolog like-1 (Ndel1) protein among others. Interestingly, Ndel1 is the only binding partner of DISC1 proteins with oligopeptidase activity, besides playing roles in multiple processes, including cytoskeletal organization, cell signaling, neuron migration, and neurite outgrowth. It is still not clear if the protein-protein interaction between Ndel1 and DISC1 is enough to explain all cellular functions attributed to these proteins, but there are several lines of evidence suggesting the importance of the catalytic activity of Ndel1 for the neurite outgrowth and neuron migration during embryogenesis. Recent works of the group have demonstrated the modulation of Ndel1 activity by DISC1, which is hypothetically impaired in SCZ patients. In fact, more recently, we also showed a lower Ndel1 activity in the plasma of SCZ patients compared to control health subjects, but the physiopathological significance of this feature is still unknown. Here we discuss Ndel1 ligands involved in protein-protein complex formations related to neurodevelopmental diseases, as (1) lissencephaly or Miller-Dieker Syndrome (MDS), which is characterized by the typical craniofacial features and abnormal smooth cerebral surface, and as (2) SCZ, since they both seem to be determined by defects in neuronal migration. Although impaired lissencephaly protein Lis1 complex formation with Ndel1 is the leading cause of lissencephaly, this binding does not affect Ndel1 oligopeptidase activity. On the other hand, although MDS and SCZ may be both determined by an abnormal neuronal migration, DISC1 complex formation with Ndel1 was shown to inhibit Ndel1 activity. Also differently of MDS, SCZ needs inputs from environmental factors, while lissencephaly is not likely dependent or affected by the environment. Several other proteins and peptide ligands were described for Ndel1, Lis1 and DISC1, thanks to the employment of biochemical, immunochemical, and biological (using cells or living animals) assays, including heterologous expression and also simply by purification from nature of these proteins in the complex form. Effects of the post-translational modifications of these proteins are also discussed here. Taken together, the data presented here show in essence how protein-protein and proteinpeptide interactions can underlie fundamental processes as cell division, maturation and migration, necessary for adequate formation of a complex structured tissue as the brain. A special attention was given to Ndel1 as this protein binds to either proteins or peptides, besides having proteolytic activity. Moreover, Ndel1 seems to be the key protein underlying two seemingly unrelated diseases with highly complex etiology, as lissencephaly and SCZ.
Collapse
Affiliation(s)
- M A F Hayashi
- Departamento de Farmacologia, Universidade Federal de Sao Paulo (UNIFESP/EPM), Rua 3 de maio 100, Ed. INFAR 3rd floor, CEP 04044-020, São Paulo, SP, Brazil.
| | | | | | | |
Collapse
|
11
|
Sanchez EF, Felicori LF, Chavez-Olortegui C, Magalhaes HBP, Hermogenes AL, Diniz MV, Junqueira-de-Azevedo IDLM, Magalhaes A, Richardson M. Biochemical characterization and molecular cloning of a plasminogen activator proteinase (LV-PA) from bushmaster snake venom. Biochim Biophys Acta Gen Subj 2006; 1760:1762-71. [PMID: 17034951 DOI: 10.1016/j.bbagen.2006.08.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2006] [Revised: 08/30/2006] [Accepted: 08/31/2006] [Indexed: 11/18/2022]
Abstract
The protein (LV-PA) from bushmaster (Lachesis muta muta) venom is a serine proteinase which specifically activates the inactive proenzyme plasminogen. LV-PA is a single chain glycoprotein with an apparent molecular mass of 33 kDa that fell to 28 kDa after treatment with N-Glycosidase F (PNGase F). Approximately 93% of its protein sequence was determined by automated Edman degradation of various fragments derived from a digestion with trypsin. A cDNA library of L. m. muta was constructed to generate expressed sequence tags (ESTs) and the plasminogen activator precursor cDNA was sequenced. The complete amino acid sequence of the enzyme was deduced from the cDNA sequence. LV-PA is composed of 234 residues and contains a single asparagine-linked glycosylation site, Asn-X-Ser, bearing sugars that account for approximately 10% of the enzyme's total molecular mass of 33 kDa. The sequence of LV-PA is highly similar to the plasminogen activators (PAs) TSV-PA from Trimeresurus stejnegeri venom and Haly-PA from Agkistrodon halys. Furthermore, the mature protein sequence of LV-PA exhibits significant similarity with other viperidae venom serine proteinases which affect many steps of hemostasis, ranging from the blood coagulation cascade to platelet function. The Michaelis constant (Km) and the catalytic rate constant (kcat) of LV-PA on four chromogenic substrates were obtained from Lineweaver-Burk plots. In addition, we used an indirect enzyme-linked immunoabsorbent assay (ELISA) to explore the phylogenetic range of immunological cross-reactivity (using antibodies raised against LV-PA) with analogous serine proteinases from two viperidae venoms and mammals.
Collapse
Affiliation(s)
- Eladio F Sanchez
- Research and Development Center, Ezequiel Dias Foundation, 30510-010, Belo Horizonte, MG, Brazil.
| | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Felicori LF, Chávez-Olórtegui C, Sánchez EF. Specific identification of Lachesis muta muta snake venom using antibodies against the plasminogen activator enzyme, LV-PA. Toxicon 2005; 45:803-6. [PMID: 15804530 DOI: 10.1016/j.toxicon.2004.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 12/07/2004] [Indexed: 11/16/2022]
Abstract
Sandwich-type enzyme linked immunosorbent assays (ELISA) were developed to detect Lachesis muta muta (bushmaster) snake venom using antibodies against the plasminogen activator enzyme (LV-PA). Antibodies to LV-PA were obtained by immunization of one rabbit with the purified enzyme. The IgG fraction was purified from rabbit blood in a single step on a column of Sepharose-L. m. muta venom and used to coat the microtiter plates. The specificity of the assay was demonstrated by its capacity to correctly discriminate between the circulating antigens in mice that were experimentally inoculated with L. m. muta venom from those in mice inoculated with venoms from Bothrops atrox, B. brazili, B. castelnaudi, Bothriopsis taeniata, B. bilineata, Crotalus durissus ruruima and the antigenic Bothrops (AgB) and Crotalus (AgC) pools venoms used to produce Bothropic and Crotalic antivenoms at Fundacao Ezequiel Dias (FUNED). Measurable absorbance signals were obtained with 1.5 ng of venom per assay. The ELISA was used to follow the kinetic distribution of antigens in experimentally envenomed mice.
Collapse
Affiliation(s)
- Liza F Felicori
- Centro de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, 30510-010 Belo Horizonte, MG, Brazil
| | | | | |
Collapse
|
13
|
Weinberg MLD, Felicori LF, Bello CA, Magalhães HPB, Almeida AP, Magalhães A, Sanchez EF. Biochemical properties of a bushmaster snake venom serine proteinase (LV-Ka), and its kinin releasing activity evaluated in rat mesenteric arterial rings. J Pharmacol Sci 2004; 96:333-42. [PMID: 15539759 DOI: 10.1254/jphs.fpj04005x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
A serine proteinase with kallikrein-like activity (LV-Ka) has been purified to homogeneity from bushmaster snake (Lachesis muta muta) venom. Physicochemical studies indicated that LV-Ka is a single chain glycoprotein with a molecular mass (Mr) of 33 kDa under reducing conditions which was reduced to 28 kDa after treatment with N-Glycosidase F (PNGase F). LV-Ka can be bounded and neutralized by serum alpha2-macroglobulin (alpha2-M), a prevalent mammalian protease inhibitor that is capable of forming a macromolecular complex with LV-Ka (Mr >180 kDa). Cleavage of alpha2-M by the enzyme resulted in the formation of 90-kDa fragments. The proteolytic activity of LV-Ka against dimethylcasein could be inhibited by alpha2-M, and the binding ratio of the inhibitor:enzyme complex was found to be 1:1. The Michaelis constant, Km, and catalytic rate constant, kcat, of LV-Ka on four selective chromogenic substrates were obtained from Lineweaver-Burk plots. LV-Ka exhibits substrate specificities not only for the glandular kallikrein H-D-Val-Leu-Arg-pNA (S-2266) but also for the plasmin substrates S-2251 and Tos-Gly-Pro-Lys-pNA. Bovine kininogen incubated with LV-Ka generated a polypeptide that dose dependently contracted mesenteric arterial rings from spontaneously hypertensive rats (SHR) in a similar way as bradykinin (BK) does. As it happens with BK, LV-Ka generated polypeptide was inhibited by HOE-140, a bradykinin B2-receptor antagonist and by indomethacin, a cyclo-oxygenase inhibitor. These results strongly suggest that the polypeptide generated by LV-Ka by cleavage of bovine kininogen is bradykinin. In addition, our studies may help to understand the mechanism of action involved in hypotension produced by envenomation of bushmaster snake.
Collapse
Affiliation(s)
- Maria L D Weinberg
- Vascular Smooth Muscle Laboratory, Department of Physiology and Biophysics, ICB, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | | | | | | |
Collapse
|
14
|
Felicori LF, Souza CT, Velarde DT, Magalhaes A, Almeida AP, Figueiredo S, Richardson M, Diniz CR, Sanchez EF. Kallikrein-like proteinase from bushmaster snake venom. Protein Expr Purif 2003; 30:32-42. [PMID: 12821319 DOI: 10.1016/s1046-5928(03)00053-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A kallikrein-like proteinase of Lachesis muta muta (bushmaster) venom, designated LV-Ka, was purified by gel filtration and anion exchange chromatographies. Physicochemical studies indicated that the purified enzyme is a 33 kDa monomeric glycoprotein, the Mr of which fell to 28 kDa after deglycosylation with PNGase F. Approximately 77% of the protein sequence was determined by sequencing the various fragments derived from digestions with endoproteases. The partial sequence obtained suggests that LV-Ka is of a similar size to other serine proteinases (i.e., approximately 234 amino acid residues). Sequence studies on the NH2-terminal region of the protein indicate that LV-Ka shares a high degree of sequence homology with the kallikrein-like enzymes EI and EII from Crotalus atrox, with crotalase from Crotalus adamanteus and significant homology with other serine proteinases from snake venoms and vertebrate serum enzymes. LV-Ka showed kallikrein-like activity, releasing bradikinin from kininogen as evidenced by guinea pig bioassay. In addition, intravenous injection of the proteinase (0.8 microg/g) was shown to lower blood pressure in experimental rats. In vitro, the isolated proteinase was shown to have neither fibrin(ogeno)lytic activity nor coagulant effect. LV-Ka was active upon the kallikrein substrates S-2266 and S-2302 (specific activity=13.0 and 31.5 U/mg, respectively; crude venom=0.25 and 6.0 U/mg) but had no proteolytic effect on dimethylcasein and insulin B chain. Its enzymatic activity was inhibited by NPGB and PMSF, indicating that the enzyme is a serine proteinase. Interestingly, one of the other reactions catalyzed by plasma kallikrein, the activation of plasminogen was one of the activities exhibited by LV-Ka.
Collapse
Affiliation(s)
- Liza F Felicori
- Centro de Pesquisa e Desenvolvimento, Fundação Ezequiel Dias, Rua Conde Pereira Carneiro # 80, Belo Horizonte, MG 30510-010, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|