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Behboudi A, Minervini M, Badinger ZS, Haddad WW, Zydney AL. Addition of sodium malonate alters the morphology and increases the critical flux during tangential flow filtration of precipitated immunoglobulins. Protein Sci 2024; 33:e5010. [PMID: 38723172 PMCID: PMC11081521 DOI: 10.1002/pro.5010] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/13/2024]
Abstract
Recent studies have demonstrated that one can control the packing density, and in turn the filterability, of protein precipitates by changing the pH and buffer composition of the precipitating solution to increase the structure/order within the precipitate. The objective of this study was to examine the effect of sodium malonate, which is known to enhance protein crystallizability, on the morphology of immunoglobulin precipitates formed using a combination of ZnCl2 and polyethylene glycol. The addition of sodium malonate significantly stabilized the precipitate particles as shown by an increase in melting temperature, as determined by differential scanning calorimetry, and an increase in the enthalpy of interaction, as determined by isothermal titration calorimetry. The sodium malonate also increased the selectivity of the precipitation, significantly reducing the coprecipitation of DNA from a clarified cell culture fluid. The resulting precipitate had a greater packing density and improved filterability, enabling continuous tangential flow filtration with minimal membrane fouling relative to precipitates formed under otherwise identical conditions but in the absence of sodium malonate. These results provide important insights into strategies for controlling precipitate morphology to enhance the performance of precipitation-filtration processes for the purification of therapeutic proteins.
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Affiliation(s)
- Ali Behboudi
- Department of Chemical EngineeringThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Mirko Minervini
- Department of Chemical EngineeringThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Zachary S. Badinger
- Department of Chemical EngineeringThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - William W. Haddad
- Department of Chemical EngineeringThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Andrew L. Zydney
- Department of Chemical EngineeringThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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2
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Elofsson A, Han L, Bianchi E, Wright GJ, Jovine L. Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse. eLife 2024; 13:RP93131. [PMID: 38666763 PMCID: PMC11052572 DOI: 10.7554/elife.93131] [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] [Indexed: 04/28/2024] Open
Abstract
A crucial event in sexual reproduction is when haploid sperm and egg fuse to form a new diploid organism at fertilization. In mammals, direct interaction between egg JUNO and sperm IZUMO1 mediates gamete membrane adhesion, yet their role in fusion remains enigmatic. We used AlphaFold to predict the structure of other extracellular proteins essential for fertilization to determine if they could form a complex that may mediate fusion. We first identified TMEM81, whose gene is expressed by mouse and human spermatids, as a protein having structural homologies with both IZUMO1 and another sperm molecule essential for gamete fusion, SPACA6. Using a set of proteins known to be important for fertilization and TMEM81, we then systematically searched for predicted binary interactions using an unguided approach and identified a pentameric complex involving sperm IZUMO1, SPACA6, TMEM81 and egg JUNO, CD9. This complex is structurally consistent with both the expected topology on opposing gamete membranes and the location of predicted N-glycans not modeled by AlphaFold-Multimer, suggesting that its components could organize into a synapse-like assembly at the point of fusion. Finally, the structural modeling approach described here could be more generally useful to gain insights into transient protein complexes difficult to detect experimentally.
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Affiliation(s)
- Arne Elofsson
- Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm UniversitySolnaSweden
| | - Ling Han
- Department of Biosciences and Nutrition, Karolinska InstitutetHuddingeSweden
| | - Enrica Bianchi
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of YorkYorkUnited Kingdom
| | - Gavin J Wright
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of YorkYorkUnited Kingdom
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska InstitutetHuddingeSweden
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3
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Bianchi E, Jiménez-Movilla M, Cots-Rodríguez P, Viola C, Wright GJ. No evidence for a direct extracellular interaction between human Fc receptor-like 3 (MAIA) and the sperm ligand IZUMO1. Sci Adv 2024; 10:eadk6352. [PMID: 38381819 PMCID: PMC10881024 DOI: 10.1126/sciadv.adk6352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Fertilization involves the recognition and fusion of sperm and egg to form a previously unidentified organism. In mammals, surface molecules on the sperm and egg have central roles, and while adhesion is mediated by the IZUMO1-JUNO sperm-egg ligand-receptor pair, the molecule/s responsible for membrane fusion remain mysterious. Recently, MAIA/FCRL3 was identified as a mammalian egg receptor, which bound IZUMO1 and JUNO and might therefore have a bridging role in gamete recognition and fusion. Here, we use sensitive assays designed to detect extracellular protein binding to investigate the interactions between MAIA and both IZUMO1 and JUNO. Despite using reagents with demonstrable biochemical activity, we did not identify any direct binding between MAIA/FCRL3 and either IZUMO1 or JUNO. We also observed no fusogenic activity of MAIA/FCRL3 in a cell-based membrane fusion assay. Our findings encourage caution in further investigations on the role played by MAIA/FCRL3 in fertilization.
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Affiliation(s)
- Enrica Bianchi
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, UK
| | - Maria Jiménez-Movilla
- Department of Cell Biology and Histology, Medical School, University of Murcia, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - Paula Cots-Rodríguez
- Department of Cell Biology and Histology, Medical School, University of Murcia, Instituto Murciano de Investigación Biosanitaria (IMIB-Arrixaca), Murcia, Spain
| | - Cristina Viola
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, UK
| | - Gavin J. Wright
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, UK
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Indhuprakash ST, S P, C DR, Thirumalai D. Efficacy evaluation of anti-DEC-IgY against antibiotic-resistant diarrhoeagenic Escherichia coli. J Med Microbiol 2024; 73. [PMID: 38314672 DOI: 10.1099/jmm.0.001801] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2024] Open
Abstract
Introduction. The rise of multi-drug-resistant bacteria poses a global threat. In 2017, the World Health Organization identified 12 antibiotic-resistant 'priority pathogens', including Enterobacteriaceae, highlighting the menace of Gram-negative bacteria. Diarrhoeagenic Escherichia coli (DEC)-induced diarrhoea is particularly problematic for travellers and infants. In contrast to other antibiotic alternatives, passive immunotherapy is showing promise by providing immediate and precise protection. However, mammalian-sourced antibodies are costly, hindering large-scale production. Egg-laying chicken-derived IgY antibodies present a cost-effective, high-yield solution, revolutionizing antibody-based therapeutics compared to mammalian IgG.Hypothesis/Gap Statement. This study hypothesized that developing anti-DEC-IgY could combat DEC infections effectively.Aim. The primary aim was to develop anti-DEC-IgY and assess its potential in DEC-induced diarrhoeal management.Method. Chickens were immunized with DEC antigens to induce an immune response. IgY antibodies were extracted from immune eggs and purified using ion-exchange column chromatography. Anti-DEC-IgY's ability to inhibit DEC growth was evaluated through growth inhibition assays. Anti-DEC-IgY's capacity to prevent E. coli adhesion was assessed using mice intestinal mucosa. In vivo experiments measured pathogen colonization reduction and infection severity reduction. P values were calculated to confirm statistical significance.Result. The antibacterial efficacy of anti-DEC-IgY by growth inhibition assay demonstrated that 25 mg ml-1 of IgY could inhibit the DEC growth. The anti-adherence-property was tested using mice intestinal mucosa and found that anti-DEC-IgY could prevent the E. coli adhesion. In vivo results suggest that 12 mg ml-1 of IgY will reduce the pathogen colonization in intestine and reduce the severity of the infection. The P values between the experimental groups confirm the statistical significance of the findings.Conclusion. The study findings suggest that IgY-based passive immunotherapy could be a potential strategy for managing the risks associated with antibiotic-resistant bacterial infections. Additionally, this study paves the way for the development of IgY-related research and applications in India.
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Affiliation(s)
- Srichandrasekar Thuthikkadu Indhuprakash
- Centre for Research in Infectious Diseases (CRID), Bioengineering, School of Chemical and Biotechnology, SASTRA Deemed-to-be-University, Thanjavur 613401, Tamil Nadu, India
| | - Panchapakesan S
- Central Animal Facility, School of Chemical and Biotechnology, SASTRA Deemed-to-be-University, Thanjavur 613401, Tamil Nadu, India
| | - David Raj C
- Centre for Advanced Research in Indian System of Medicine, School of Chemical and Biotechnology, SASTRA Deemed-to-be-University, Thanjavur 613401, Tamil Nadu, India
| | - Diraviyam Thirumalai
- Centre for Research in Infectious Diseases (CRID), Bioengineering, School of Chemical and Biotechnology, SASTRA Deemed-to-be-University, Thanjavur 613401, Tamil Nadu, India
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Bajaj M, Muddassir M, Choi B, Singh P, Park JB, Singh S, Yadav M, Kumar R, Eom K, Sharma D. Single-molecule analysis of osmolyte-mediated nanomechanical unfolding behavior of a protein domain. Int J Biol Macromol 2023; 253:126849. [PMID: 37717878 DOI: 10.1016/j.ijbiomac.2023.126849] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/25/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
The small organic molecules, known as osmolytes being ubiquitously present in different cell types, affect protein folding, stability and aggregation. However, it is unknown how the osmolytes affect the nanomechanical unfolding behavior of protein domain. Here, we show the osmolyte-dependent mechanical unfolding properties of protein titin immunoglobulin-27 (I27) domain using an atomic force microscopy (AFM)-based single-molecule force spectroscopy. We found that amines and methylamines improved the mechanical stability of I27 domain, whereas polyols had no effect. Interestingly, glycine betaine (GB) or trimethylamine-N-oxide (TMAO) increased the average unfolding force of the protein domain. The kinetic parameters analyzed at single-molecule level reveal that stabilizing effect of osmolytes is due to a decrease in the unfolding rate constant of I27, which was confirmed by molecular dynamics simulations. Our study reveals different effects that diverse osmolytes have on the mechanical properties of the protein, and suggests the potential use of osmolytes in modulating the mechanical stability of proteins required for various nano-biotechnological applications.
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Affiliation(s)
- Manish Bajaj
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Mohd Muddassir
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bumjoon Choi
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea; Digial Bio R&D Center, Mediazen, Seoul 07789, Republic of Korea
| | - Priyanka Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Jong Bum Park
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea
| | - Surjeet Singh
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India
| | - Manisha Yadav
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Rajesh Kumar
- School of Basic and Applied Sciences, Central University of Punjab, Bathinda, India
| | - Kilho Eom
- Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University (SKKU), Suwon 16419, Republic of Korea.
| | - Deepak Sharma
- Council of Scientific and Industrial Research - Institute of Microbial Technology, Sector-39A, Chandigarh, India; Academy of Scientific & Innovative Research, India.
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Su Y, Luo Z, Sun D, Yang B, Li Q. The Force-Dependent Mechanism of an Integrin α4β7-MAdCAM-1 Interaction. Int J Mol Sci 2023; 24:16062. [PMID: 38003252 PMCID: PMC10670920 DOI: 10.3390/ijms242216062] [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: 09/13/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
The interaction between integrin α4β7 and mucosal vascular addressin cell-adhesion molecule-1 (MAdCAM-1) facilitates the adhesion of circulating lymphocytes to the surface of high endothelial venules in inflammatory bowel diseases (IBDs). Lymphocyte adhesion is a multistep cascade involving the tethering, rolling, stable adhesion, crawling, and migration of cells, with integrin α4β7 being involved in rolling and stable adhesions. Targeting the integrin α4β7-MAdCAM-1 interaction may help decrease inflammation in IBDs. This interaction is regulated by force; however, the underlying mechanism remains unknown. Here, we investigate this mechanism using a parallel plate flow chamber and atomic force microscopy. The results reveal an initial increase in the lifetime of the integrin α4β7-MAdCAM-1 interaction followed by a decrease with an increasing force. This was manifested in a two-state curve regulated via a catch-bond-slip-bond conversion regardless of Ca2+ and/or Mg2+ availability. In contrast, the mean rolling velocity of cells initially decreased and then increased with the increasing force, indicating the flow-enhanced adhesion. Longer tether lifetimes of single bonds and lower rolling velocities mediated by multiple bonds were observed in the presence of Mg2+ rather than Ca2+. Similar results were obtained when examining the adhesion to substrates co-coated with chemokine CC motif ligand 25 and MAdCAM-1, as opposed to substrates coated with MAdCAM-1 alone. In conclusion, the integrin α4β7-MAdCAM-1 interaction occurs via ion- and cytokine-dependent flow-enhanced adhesion processes and is regulated via a catch-bond mechanism.
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Affiliation(s)
- Youmin Su
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China; (Y.S.); (Z.L.); (D.S.)
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou 510006, China
| | - Zhiqing Luo
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China; (Y.S.); (Z.L.); (D.S.)
| | - Dongshan Sun
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China; (Y.S.); (Z.L.); (D.S.)
| | - Bishan Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China; (Y.S.); (Z.L.); (D.S.)
| | - Quhuan Li
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China; (Y.S.); (Z.L.); (D.S.)
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals, South China University of Technology, Guangzhou 510006, China
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7
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Han G, Li C, Zhang N, Liu Q, Huang L, Xia Y, Xu J. CmHem, a hemolin-like gene identified from Cnaphalocrocis medinalis, involved in metamorphosis and baculovirus infection. PeerJ 2023; 11:e16225. [PMID: 37810787 PMCID: PMC10559889 DOI: 10.7717/peerj.16225] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023] Open
Abstract
Background As a member of the immunoglobulin superfamily, hemolins play a vital role in insect development and defense against pathogens. However, the innate immune response of hemolin to baculovirus infection varies among different insects. Methods and results In this study, the hemolin-like gene from a Crambidae insect, Cnaphalocrocis medinalis, CmHem was cloned, and its role in insect development and baculovirus infection was analyzed. A 1,528 bp contig as potential hemolin-like gene of C. medinalis was reassembled from the transcriptome. Further, the complete hemolin sequence of C. medinalis (CmHem) was cloned and sequenced. The cDNA of CmHem was 1,515 bp in length and encoded 408 amino acids. The deduced amino acid of CmHem has relatively low identities (41.9-62.3%) to various insect hemolins. However, it contains four Ig domains similarity to other insect hemolins. The expression level of CmHem was the highest in eggs, followed by pupae and adults, and maintained a low expression level at larval stage. The synthesized siRNAs were injected into mature larvae, and the CmHem transcription decreased by 51.7%. Moreover, the abdominal somites of larvae became straightened, could not pupate normally, and then died. Infection with a baculovirus, C. medinalis granulovirus (CnmeGV), the expression levels of CmHem in the midgut and fat body of C. medinalis significantly increased at 12 and 24 h, respectively, and then soon returned to normal levels. Conclusions Our results suggested that hemolin may be related to the metamorphosis of C. medinalis. Exposure to baculovirus induced the phased expression of hemolin gene in the midgut and fat body of C. medinalis, indicated that hemolin involved in the immune recognition of Crambidae insects to baculovirus.
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Affiliation(s)
- Guangjie Han
- Lixiahe District Institute of Agricultural Sciences in Jiangsu, Yangzhou, China
| | - Chuanming Li
- Lixiahe District Institute of Agricultural Sciences in Jiangsu, Yangzhou, China
| | - Nan Zhang
- Lixiahe District Institute of Agricultural Sciences in Jiangsu, Yangzhou, China
| | - Qin Liu
- Lixiahe District Institute of Agricultural Sciences in Jiangsu, Yangzhou, China
| | - Lixin Huang
- Lixiahe District Institute of Agricultural Sciences in Jiangsu, Yangzhou, China
| | - Yang Xia
- Lixiahe District Institute of Agricultural Sciences in Jiangsu, Yangzhou, China
| | - Jian Xu
- Lixiahe District Institute of Agricultural Sciences in Jiangsu, Yangzhou, China
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8
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Sun Y, Papadaki GF, Devlin CA, Danon JN, Young MC, Winters TJ, Burslem GM, Procko E, Sgourakis NG. Xeno interactions between MHC-I proteins and molecular chaperones enable ligand exchange on a broad repertoire of HLA allotypes. Sci Adv 2023; 9:eade7151. [PMID: 36827371 PMCID: PMC9956121 DOI: 10.1126/sciadv.ade7151] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/19/2023] [Indexed: 06/01/2023]
Abstract
Immunological chaperones tapasin and TAP binding protein, related (TAPBPR) play key roles in antigenic peptide optimization and quality control of nascent class I major histocompatibility complex (MHC-I) molecules. The polymorphic nature of MHC-I proteins leads to a range of allelic dependencies on chaperones for assembly and cell-surface expression, limiting chaperone-mediated peptide exchange to a restricted set of human leukocyte antigen (HLA) allotypes. Here, we demonstrate and characterize xeno interactions between a chicken TAPBPR ortholog and a complementary repertoire of HLA allotypes, relative to its human counterpart. We find that TAPBPR orthologs recognize empty MHC-I with broader allele specificity and facilitate peptide exchange by maintaining a reservoir of receptive molecules. Deep mutational scanning of human TAPBPR further identifies gain-of-function mutants, resembling the chicken sequence, which can enhance HLA-A*01:01 expression in situ and promote peptide exchange in vitro. These results highlight that polymorphic sites on MHC-I and chaperone surfaces can be engineered to manipulate their interactions, enabling chaperone-mediated peptide exchange on disease-relevant HLA alleles.
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Affiliation(s)
- Yi Sun
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Georgia F. Papadaki
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Christine A. Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61820, USA
| | - Julia N. Danon
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Michael C. Young
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - Trenton J. Winters
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
| | - George M. Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL 61820, USA
| | - Nikolaos G. Sgourakis
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 3501 Civic Center Blvd., Philadelphia, PA 19104, USA
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Lefranc MP, Lefranc G. Antibody Sequence and Structure Analyses Using IMGT ®: 30 Years of Immunoinformatics. Methods Mol Biol 2023; 2552:3-59. [PMID: 36346584 DOI: 10.1007/978-1-0716-2609-2_1] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org , the global reference in immunogenetics and immunoinformatics, was created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS) to manage the huge diversity of the antigen receptors, immunoglobulins (IG) or antibodies, and T cell receptors (TR) of the adaptive immune responses. The founding of IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® standardized analysis of the IG, TR, and major histocompatibility (MH) genes and proteins bridges the gap between sequences and three-dimensional (3D) structures, for all jawed vertebrates from fish to humans. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY axioms, and primarily CLASSIFICATION (IMGT gene and allele nomenclature) and NUMEROTATION (IMGT unique numbering and IMGT Colliers de Perles). IMGT® comprises seven databases (IMGT/LIGM-DB for nucleotide sequences, IMGT/GENE-DB for genes and alleles, etc.), 17 tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST for NGS, etc.), and more than 20,000 Web resources. In this chapter, the focus is on the tools for amino acid sequences per domain (IMGT/DomainGapAlign and IMGT/Collier-de-Perles), and on the databases for receptors (IMGT/2Dstructure-DB and IMGT/3D-structure-DB) described per receptor, chain, and domain and, for 3D, with contact analysis, paratope, and epitope. The IMGT/mAb-DB is the query interface for monoclonal antibodies (mAb), fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA), and related proteins of interest (RPI) with links to IMGT® 2D and 3D databases and to the World Health Organization (WHO) International Nonproprietary Names (INN) program lists. The chapter includes the human IG allotypes and antibody engineered variants for effector properties used in the description of therapeutical mAb.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
| | - Gérard Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
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10
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McShan AC, Devlin CA, Papadaki GF, Sun Y, Green AI, Morozov GI, Burslem GM, Procko E, Sgourakis NG. TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules. Nat Chem Biol 2022; 18:859-868. [PMID: 35725941 PMCID: PMC9703140 DOI: 10.1038/s41589-022-01049-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 04/28/2022] [Indexed: 11/08/2022]
Abstract
Chaperones tapasin and transporter associated with antigen processing (TAP)-binding protein related (TAPBPR) associate with the major histocompatibility complex (MHC)-related protein 1 (MR1) to promote trafficking and cell surface expression. However, the binding mechanism and ligand dependency of MR1/chaperone interactions remain incompletely characterized. Here in vitro, biochemical and computational studies reveal that, unlike MHC-I, TAPBPR recognizes MR1 in a ligand-independent manner owing to the absence of major structural changes in the MR1 α2-1 helix between empty and ligand-loaded molecules. Structural characterization using paramagnetic nuclear magnetic resonance experiments combined with restrained molecular dynamics simulations reveals that TAPBPR engages conserved surfaces on MR1 to induce similar adaptations to those seen in MHC-I/TAPBPR co-crystal structures. Finally, nuclear magnetic resonance relaxation dispersion experiments using 19F-labeled diclofenac show that TAPBPR can affect the exchange kinetics of noncovalent metabolites with the MR1 groove, serving as a catalyst. Our results support a role of chaperones in stabilizing nascent MR1 molecules to enable loading of endogenous or exogenous cargo.
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Affiliation(s)
- Andrew C McShan
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Christine A Devlin
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Georgia F Papadaki
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Adam I Green
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Giora I Morozov
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, IL, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Zeneyedpour L, Stingl C, Kros JM, Sillevis Smitt PAE, Luider TM. Novel Antibody-Peptide Binding Assay Indicates Presence of Immunoglobulins against EGFR Phospho-Site S1166 in High-Grade Glioma. Int J Mol Sci 2022; 23:5061. [PMID: 35563452 PMCID: PMC9100080 DOI: 10.3390/ijms23095061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
We investigated the feasibility of detecting the presence of specific autoantibodies against potential tumor-associated peptide antigens by enriching these antibody-peptide complexes using Melon Gel resin and mass spectrometry. Our goal was to find tumor-associated phospho-sites that trigger immunoreactions and raise autoantibodies that are detectable in plasma of glioma patients. Such immunoglobulins can potentially be used as targets in immunotherapy. To that aim, we describe a method to detect the presence of antibodies in biological samples that are specific to selected clinically relevant peptides. The method is based on the formation of antibody-peptide complexes by mixing patient plasma with a glioblastoma multiforme (GBM) derived peptide library, enrichment of antibodies and antibody-peptide complexes, the separation of peptides after they are released from immunoglobulins by molecular weight filtration and finally mass spectrometric quantification of these peptides. As proof of concept, we successfully applied the method to dinitrophenyl (DNP)-labeled α-casein peptides mixed with anti-DNP. Further, we incubated human plasma with a phospho-peptide library and conducted targeted analysis on EGFR and GFAP phospho-peptides. As a result, immunoaffinity against phospho-peptide GSHQIS[+80]LDNPDYQQDFFPK (EGFR phospho-site S1166) was detected in high-grade glioma (HGG) patient plasma but not in healthy donor plasma. For the GFAP phospho-sites selected, such immunoaffinity was not observed.
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Affiliation(s)
- Lona Zeneyedpour
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (L.Z.); (C.S.); (P.A.E.S.S.)
| | - Christoph Stingl
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (L.Z.); (C.S.); (P.A.E.S.S.)
| | - Johan M. Kros
- Department of Pathology, Erasmus MC, 3015 GD Rotterdam, The Netherlands;
| | | | - Theo M. Luider
- Department of Neurology, Erasmus MC, 3015 GD Rotterdam, The Netherlands; (L.Z.); (C.S.); (P.A.E.S.S.)
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12
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Kasai Y, Gan SP, Funaki T, Ohashi‐Kumagai Y, Tominaga M, Shiu S, Suzuki D, Matsubara D, Sakamoto T, Sakurai‐Yageta M, Ito T, Murakami Y. Trans-homophilic interaction of CADM1 promotes organ infiltration of T-cell lymphoma by adhesion to vascular endothelium. Cancer Sci 2022; 113:1669-1678. [PMID: 35213073 PMCID: PMC9128163 DOI: 10.1111/cas.15307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/23/2022] [Accepted: 02/04/2022] [Indexed: 11/28/2022] Open
Abstract
The initial step of organ infiltration of malignant cells is the interaction with host vascular endothelial cells, which is often mediated by specific combinations of cell adhesion molecules. Cell adhesion molecule 1 (CADM1) is overexpressed in adult T-cell leukemia/lymphoma (ATL) and provides a cell-surface diagnostic marker. CADM1 promotes the adhesion of ATL cells to vascular endothelial cells and multiple organ infiltration in mice. However, its binding partner on host cells has not yet been identified. In this study, we show that CADM1 promotes transendothelial migration of ATL cells in addition to the adhesion to vascular endothelial cells. Moreover, CADM1 enhances liver infiltration of mouse T-cell lymphoma cells, EL4, after tail vein injection, whereas a CADM1 mutant lacking adhesive activity did not. Among the known CADM1-binding proteins expressed in primary endothelial cells, only CADM1 and CADM4 could induce morphological extension of ATL cells when plated onto glass coated with these proteins. Furthermore, CADM1-mediated liver infiltration of EL4 cells was canceled in conventional and vascular endothelium-specific Cadm1 knockout mice, whereas it was not canceled in Cadm4 knockout mice. These results suggest that CADM1 on host vascular endothelial cells is required for organ infiltration of ATL and other T-cell lymphomas expressing CADM1.
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Affiliation(s)
- Yutaka Kasai
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Siew Pey Gan
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Toko Funaki
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Yuki Ohashi‐Kumagai
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Mizuki Tominaga
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Shu‐Jen Shiu
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Daisuke Suzuki
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Daisuke Matsubara
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
- Department of Diagnostic PathologyUniversity of TsukubaTsukubaJapan
| | - Takeharu Sakamoto
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
- Department of Cancer BiologyInstitute of Biomedical ScienceKansai Medical UniversityHirakataJapan
| | - Mika Sakurai‐Yageta
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
- Tohoku Medical Megabank OrganizationTohoku UniversitySendaiJapan
| | - Takeshi Ito
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Yoshinori Murakami
- Division of Molecular PathologyThe Institute of Medical ScienceThe University of TokyoTokyoJapan
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13
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Štimac A, Kurtović T, Pavlović N, Halassy B. Development of Improved High-Performance Liquid Chromatography Method for the Determination of Residual Caprylic Acid in Formulations of Human Immunoglobulins. Molecules 2022; 27:molecules27051665. [PMID: 35268765 PMCID: PMC8912018 DOI: 10.3390/molecules27051665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 12/30/2022] Open
Abstract
Quality control of human immunoglobulin formulations produced by caprylic acid precipitation necessitates a simple, rapid, and accurate method for determination of residual caprylic acid. A high-performance liquid chromatography method for that purpose was developed and validated. The method involves depletion of immunoglobulins, the major interfering components that produce high background noise, by precipitation with acetonitrile (1:1, v/v). Chromatographic analysis of caprylic acid, preserved in supernatant with no loss, was performed using a reverse-phase C18 column (2.1 × 150 mm, 3 μm) as a stationary phase and water with 0.05% TFA–acetonitrile (50:50, v/v) as a mobile phase at a flow rate of 0.2 mL/min and run time of 10 min. The developed method was successfully validated according to the ICH guidelines. The validation parameters confirmed that method was linear, accurate, precise, specific, and able to provide excellent separation of peaks corresponding to caprylic acid and the fraction of remaining immunoglobulins. Furthermore, a 24−1 fractional factorial design was applied in order to test the robustness of developed method. As such, the method is highly suitable for the quantification of residual caprylic acid in formulations of human immunoglobulins for therapeutic use, as demonstrated on samples produced by fractionation of convalescent anti-SARS-CoV-2 human plasma at a laboratory scale. The obtained results confirmed that the method is convenient for routine quality control.
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Affiliation(s)
- Adela Štimac
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Rockefellerova 10, 10000 Zagreb, Croatia;
- Correspondence: (A.Š.); (B.H.)
| | - Tihana Kurtović
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Rockefellerova 10, 10000 Zagreb, Croatia;
| | - Nediljko Pavlović
- Institute of Immunology, Inc., Rockefellerova 10, 10000 Zagreb, Croatia;
| | - Beata Halassy
- Centre for Research and Knowledge Transfer in Biotechnology, University of Zagreb, Rockefellerova 10, 10000 Zagreb, Croatia;
- Correspondence: (A.Š.); (B.H.)
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14
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Peckert-Maier K, Royzman D, Langguth P, Marosan A, Strack A, Sadeghi Shermeh A, Steinkasserer A, Zinser E, Wild AB. Tilting the Balance: Therapeutic Prospects of CD83 as a Checkpoint Molecule Controlling Resolution of Inflammation. Int J Mol Sci 2022; 23:732. [PMID: 35054916 PMCID: PMC8775349 DOI: 10.3390/ijms23020732] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/05/2022] [Accepted: 01/08/2022] [Indexed: 12/15/2022] Open
Abstract
Chronic inflammatory diseases and transplant rejection represent major challenges for modern health care. Thus, identification of immune checkpoints that contribute to resolution of inflammation is key to developing novel therapeutic agents for those conditions. In recent years, the CD83 (cluster of differentiation 83) protein has emerged as an interesting potential candidate for such a "pro-resolution" therapy. This molecule occurs in a membrane-bound and a soluble isoform (mCD83 and sCD83, respectively), both of which are involved in resolution of inflammation. Originally described as a maturation marker on dendritic cells (DCs), mCD83 is also expressed by activated B and T cells as well as regulatory T cells (Tregs) and controls turnover of MHC II molecules in the thymus, and thereby positive selection of CD4+ T cells. Additionally, it serves to confine overshooting (auto-)immune responses. Consequently, animals with a conditional deletion of CD83 in DCs or regulatory T cells suffer from impaired resolution of inflammation. Pro-resolving effects of sCD83 became evident in pre-clinical autoimmune and transplantation models, where application of sCD83 reduced disease symptoms and enhanced allograft survival, respectively. Here, we summarize recent advances regarding CD83-mediated resolution of inflammatory responses, its binding partners as well as induced signaling pathways, and emphasize its therapeutic potential for future clinical trials.
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Affiliation(s)
- Katrin Peckert-Maier
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander Universität—Erlangen-Nürnberg, 91052 Erlangen, Germany; (D.R.); (P.L.); (A.M.); (A.S.); (A.S.S.); (A.S.); (E.Z.)
| | | | | | | | | | | | | | | | - Andreas B. Wild
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander Universität—Erlangen-Nürnberg, 91052 Erlangen, Germany; (D.R.); (P.L.); (A.M.); (A.S.); (A.S.S.); (A.S.); (E.Z.)
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15
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Abstract
Fertilization in mammals begins with the union of egg and sperm, an event that starts a cascade of cellular processes. The molecular-level understanding of these processes can guide the development of new strategies for controlling and/or promoting fertilization, and inform researchers and medical professional on the best choice of interventions. The proteins encoded by the IZUMO1 and JUNO genes form a ligand-receptor protein pair involved in the recognition of sperm and egg. Due to their role in the fertilization process, these proteins are potential targets for the development of novel anti-contraceptive, as well as infertility treatments. Here we present a comprehensive analysis of these gene sequences, with the objective of identifying evolutionary patterns that may support their relevance as targets for preventing or improving fertility among humans. JUNO and IZUMO1 gene sequences were identified within the genomes of over 2,000 humans sequenced in the 1000 Genomes Project. The human sequences were subjected to analyses of nucleotide diversity, deviation from neutrality of genetic variation, population-based differentiation (FST), haplotype inference, and whole chromosome scanning for signals of positive or of balancing selection. Derived alleles were determined by comparison to archaic hominin and other primate genomes. The potential effect of common non-synonymous variants on protein-protein interaction was also assessed. IZUMO1 displays higher variability among human individuals than JUNO. Genetic differentiation between continental population pairs was within whole-genome estimates for all but the JUNO gene in the African population group with respect to the other 4 population groups (American, East Asian, South Asian, and European). Tajima’s D values demonstrated deviation from neutrality for both genes in comparison to a group of genes identified in the literature as under balancing or positive selection. Tajima’s D for IZUMO1 aligns with values calculated for genes presumed to be under balancing selection, whereas JUNO’s value aligned with genes presumed to be under positive selection. These inferences on selection are both supported by SNP density, nucleotide diversity and haplotype analysis. A JUNO haplotype carrying 3 derived alleles out of 5, one of which is a missense mutation implicated in polyspermy, was found to be significant in a population of African ancestry. Polyspermy has a disadvantageous impact on fertility and its presence in approximately 30% of the population of African ancestry may be associated to a potentially beneficial role of this haplotype. This role has not been established and may be related to a non-reproductive role of JUNO. The high degree of conservation of the JUNO sequence combined with a dominant haplotype across multiple population groups supports JUNO as a potential target for the development of contraceptive treatments. In addition to providing a detailed account of human genetic diversity across these 2 important and related genes, this study also provides a framework for large population-based studies investigating protein-protein interactions at the genome level.
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Affiliation(s)
- Jessica Allingham
- Department of Chemistry, Lakehead University, Thunder Bay, Ontario, Canada
| | - Wely B. Floriano
- Department of Chemistry, Lakehead University, Thunder Bay, Ontario, Canada
- * E-mail:
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16
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da Silva MTL, Deodato RM, Villar LM. Exploring the potential usefulness of IgY for antiviral therapy: A current review. Int J Biol Macromol 2021; 189:785-791. [PMID: 34416265 DOI: 10.1016/j.ijbiomac.2021.08.078] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/08/2021] [Accepted: 08/10/2021] [Indexed: 11/18/2022]
Abstract
Immunoglobulin yolk (IgY) is therapeutic antibodies presented in yolk eggs of birds, reptiles, and amphibians. These proteins produced by the immune system of the animal, are capable of neutralizing antigenic molecules, including viral antigens, fulfilling a role in the body defense. The specificity of these antibodies and the facility for their production, make these molecules capable of being used as tools for diagnosis and immunotherapy. Regarding this last aspect, it is common knowledge that the field of virology, is racing against time in the development of new drugs and vaccines to try to contain pandemics and local epidemics and, in counterproposal, avian antibodies are neutralizing molecules that can help in the control and spread of disease. These molecules have been explored for years and currently chicken eggs are produced in large quantities from the animal's immunization against a specific pathogen. Thus, on this subject, this review made a survey of these researches and presents a summary of all the successful cases and perspectives in the use of IgYs as tools for viral immunization.
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Affiliation(s)
| | - Raissa Martins Deodato
- Viral Hepatitis Laboratory, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil
| | - Livia Melo Villar
- Viral Hepatitis Laboratory, Oswaldo Cruz Institute, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.
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17
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Ye H, Cheng L, Ju B, Xu G, Liu Y, Zhang S, Wang L, Zhang Z. SCIGA: Software for large-scale, single-cell immunoglobulin repertoire analysis. Gigascience 2021; 10:giab050. [PMID: 34585238 PMCID: PMC8478610 DOI: 10.1093/gigascience/giab050] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/19/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND B-cell immunoglobulin repertoires with paired heavy and light chain can be determined by means of 10X single-cell V(D)J sequencing. Precise and quick analysis of 10X single-cell immunoglobulin repertoires remains a challenge owing to the high diversity of immunoglobulin repertoires and a lack of specialized software that can analyze such diverse data. FINDINGS In this study, specialized software for 10X single-cell immunoglobulin repertoire analysis was developed. SCIGA (Single-Cell Immunoglobulin Repertoire Analysis) is an easy-to-use pipeline that performs read trimming, immunoglobulin sequence assembly and annotation, heavy and light chain pairing, statistical analysis, visualization, and multiple sample integration analysis, which is all achieved by using a 1-line command. Then SCIGA was used to profile the single-cell immunoglobulin repertoires of 9 patients with coronavirus disease 2019 (COVID-19). Four neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified from these repertoires. CONCLUSIONS SCIGA provides a complete and quick analysis for 10X single-cell V(D)J sequencing datasets. It can help researchers to interpret B-cell immunoglobulin repertoires with paired heavy and light chain.
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Affiliation(s)
- Haocheng Ye
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Gang Xu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lifei Wang
- Department of Radiology, National Clinical Research Center for Infectious Disease, Shenzhen, Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
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18
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Wang XX, Zhang S, Dong PP, Li YH, Zhang L, Shi SH, Yu ZQ, Chen S. MRCKβ links Dasm1 to actin rearrangements to promote dendrite development. J Biol Chem 2021; 296:100730. [PMID: 33933448 PMCID: PMC8191314 DOI: 10.1016/j.jbc.2021.100730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 01/12/2023] Open
Abstract
Proper dendrite morphogenesis and synapse formation are essential for neuronal development and function. Dasm1, a member of the immunoglobulin superfamily, is known to promote dendrite outgrowth and excitatory synapse maturation in vitro. However, the in vivo function of Dasm1 in neuronal development and the underlying mechanisms are not well understood. To learn more, Dasm1 knockout mice were constructed and employed to confirm that Dasm1 regulates dendrite arborization and spine formation in vivo. We performed a yeast two-hybrid screen using Dasm1, revealing MRCKβ as a putative partner; additional lines of evidence confirmed this interaction and identified cytoplasmic proline-rich region (823–947 aa) of Dasm1 and MRCKβ self-activated kinase domain (CC1, 410–744 aa) as necessary and sufficient for binding. Using co-immunoprecipitation assay, autophosphorylation assay, and BS3 cross-linking assay, we show that Dasm1 binding triggers a change in MRCKβ’s conformation and subsequent dimerization, resulting in autophosphorylation and activation. Activated MRCKβ in turn phosphorylates a class 2 regulatory myosin light chain, which leads to enhanced actin rearrangement, causing the dendrite outgrowth and spine formation observed before. Removal of Dasm1 in mice leads to behavioral abnormalities. Together, these results reveal a crucial molecular pathway mediating cell surface and intracellular signaling communication to regulate actin dynamics and neuronal development in the mammalian brain.
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Affiliation(s)
- Xiao-Xiao Wang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China; Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Si Zhang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ping-Ping Dong
- Department of Gastroenterology and Hepatology, Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, China; Department of Surgery, Faculty of Medicine, Centre for Cancer Research, The University of Hong Kong, Hong Kong, China
| | - Yao-Hua Li
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Li Zhang
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Song-Hai Shi
- IDG/McGovern Institute for Brain Research, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center of Biological Structure, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China; Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Zhi-Qiang Yu
- NHC Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China; Eye Department, Eye & ENT Hospital, Fudan University, Shanghai, China.
| | - She Chen
- NHC Key Laboratory of Glycoconjugate Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
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19
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Valdez-Cruz NA, García-Hernández E, Espitia C, Cobos-Marín L, Altamirano C, Bando-Campos CG, Cofas-Vargas LF, Coronado-Aceves EW, González-Hernández RA, Hernández-Peralta P, Juárez-López D, Ortega-Portilla PA, Restrepo-Pineda S, Zelada-Cordero P, Trujillo-Roldán MA. Integrative overview of antibodies against SARS-CoV-2 and their possible applications in COVID-19 prophylaxis and treatment. Microb Cell Fact 2021; 20:88. [PMID: 33888152 PMCID: PMC8061467 DOI: 10.1186/s12934-021-01576-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 01/27/2021] [Accepted: 04/03/2021] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2 is a novel β-coronavirus that caused the COVID-19 pandemic disease, which spread rapidly, infecting more than 134 million people, and killing almost 2.9 million thus far. Based on the urgent need for therapeutic and prophylactic strategies, the identification and characterization of antibodies has been accelerated, since they have been fundamental in treating other viral diseases. Here, we summarized in an integrative manner the present understanding of the immune response and physiopathology caused by SARS-CoV-2, including the activation of the humoral immune response in SARS-CoV-2 infection and therefore, the synthesis of antibodies. Furthermore, we also discussed about the antibodies that can be generated in COVID-19 convalescent sera and their associated clinical studies, including a detailed characterization of a variety of human antibodies and identification of antibodies from other sources, which have powerful neutralizing capacities. Accordingly, the development of effective treatments to mitigate COVID-19 is expected. Finally, we reviewed the challenges faced in producing potential therapeutic antibodies and nanobodies by cell factories at an industrial level while ensuring their quality, efficacy, and safety.
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Affiliation(s)
- Norma A Valdez-Cruz
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Laura Cobos-Marín
- Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Claudia Altamirano
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil N° 2950, Valparaíso, Chile
| | - Carlos G Bando-Campos
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Luis F Cofas-Vargas
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Enrique W Coronado-Aceves
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Ricardo A González-Hernández
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Pablo Hernández-Peralta
- Facultad de Medicina Veterinaria Y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Daniel Juárez-López
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Paola A Ortega-Portilla
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Sara Restrepo-Pineda
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Patricio Zelada-Cordero
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México
| | - Mauricio A Trujillo-Roldán
- Programa de Investigación de Producción de Biomoléculas, Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, México.
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20
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Oangkhana P, Amparyup P, Tassanakajon A, Preetham E, Wongpanya R. Characterization and functional analysis of fibrinogen-related protein (FreP) in the black tiger shrimp, Penaeus monodon. Fish Shellfish Immunol 2021; 109:87-96. [PMID: 33359206 DOI: 10.1016/j.fsi.2020.12.012] [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: 07/15/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Ficolin is classified as an immune related protein containing collagen-like and fibrinogen-related domain (FreD). In invertebrates, the functions of fibrinogen-related proteins (FrePs) are of importance to innate immunity. In this study, a FreP in the black tiger shrimp Penaeus monodon was identified and characterized. The PmFreP cDNA is 1,007 bp long with a 921 bp-open reading frame that encodes for 306 amino acids. The deduced PmFreP sequence consists of a signal peptide, an unknown region and the FreD. Phylogenetic analysis showed that PmFreP was clustered with fibrinogen-like proteins in crustaceans which was separated from vertebrate ficolin-like proteins. The deduced fibrinogen-like domain contains four conserved cysteine residues (Cys96, Cys127, Cys249, and Cys262) that are responsible for the formation of disulfide bridges. Gene expression analysis shows that Pmfrep is mainly expressed in the intestine and the expression is significantly upregulated after Vibrio harveyi and white spot syndrome virus (WSSV) challenge. Recombinant PmFreP (rPmFreP) were successfully expressed and purified, and forms a trimeric structure as judged by native-PAGE. Bacterial binding assay showed that the rPmFreD can bind and agglutinate Gram-negative and Gram-positive bacteria in the presence of calcium (Ca2+) ions. Moreover, the rPmFreP facilitates the clearance of V. harveyi in vivo. Overall, our results suggested that the PmFreP may serve as pattern recognition receptors implicated in shrimp innate immunity.
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Affiliation(s)
- Prawit Oangkhana
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10903, Thailand.
| | - Piti Amparyup
- Marine Biotechnology Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Paholyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand; Center of Excellence for Marine Biotechnology, Department of Marine Science, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok, 10330, Thailand.
| | - Elumalai Preetham
- School of Processing Technology, Kerala University of Fisheries and Ocean Studies, Panangad, Kerala, India.
| | - Ratree Wongpanya
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10903, Thailand; Department of Biochemistry, Faculty of Science, Kasetsart University, 50 Ngamwongwan Road, Bangkok, 10900, Thailand.
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21
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Murugesan G, Correia VG, Palma AS, Chai W, Li C, Feizi T, Martin E, Laux B, Franz A, Fuchs K, Weigle B, Crocker PR. Siglec-15 recognition of sialoglycans on tumor cell lines can occur independently of sialyl Tn antigen expression. Glycobiology 2021; 31:44-54. [PMID: 32501471 PMCID: PMC7799145 DOI: 10.1093/glycob/cwaa048] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 12/15/2022] Open
Abstract
Siglec-15 is a conserved sialic acid-binding Ig-like lectin expressed on osteoclast progenitors, which plays an important role in osteoclast development and function. It is also expressed by tumor-associated macrophages and by some tumors, where it is thought to contribute to the immunosuppressive microenvironment. It was shown previously that engagement of macrophage-expressed Siglec-15 with tumor cells expressing its ligand, sialyl Tn (sTn), triggered production of TGF-β. In the present study, we have further investigated the interaction between Siglec-15 and sTn on tumor cells and its functional consequences. Based on binding assays with lung and breast cancer cell lines and glycan-modified cells, we failed to see evidence for recognition of sTn by Siglec-15. However, using a microarray of diverse, structurally defined glycans, we show that Siglec-15 binds with higher avidity to sialylated glycans other than sTn or related antigen sequences. In addition, we were unable to demonstrate enhanced TGF-β secretion following co-culture of Siglec-15-expressing monocytic cell lines with tumor cells expressing sTn or following Siglec-15 cross-linking with monoclonal antibodies. However, we did observe activation of the SYK/MAPK signaling pathway following antibody cross-linking of Siglec-15 that may modulate the functional activity of macrophages.
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Affiliation(s)
- Gavuthami Murugesan
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Viviana G Correia
- Applied Molecular Biosciences Unit, Faculty of Science and Technology, NOVA University of Lisbon, Lisbon, Portugal
| | - Angelina S Palma
- Applied Molecular Biosciences Unit, Department of Chemistry, Faculty of Science and Technology, NOVA University of Lisbon, Lisbon, Portugal
| | - Wengang Chai
- Glycosciences Laboratory, Imperial College London, London, United Kingdom
| | - Chunxia Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy and Shandong Provincial Key laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao 266003, China
| | - Ten Feizi
- Glycosciences Laboratory, Imperial College London, London, United Kingdom
| | - Eva Martin
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397 Biberach/Riss, Germany
| | - Brigitte Laux
- Cancer Immunology & Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397 Biberach/Riss, Germany
| | - Alexandra Franz
- Cancer Immunology & Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397 Biberach/Riss, Germany
| | - Klaus Fuchs
- Biotherapeutics Discovery, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397 Biberach/Riss, Germany
| | - Bernd Weigle
- Cancer Immunology & Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Str. 65, 88397 Biberach/Riss, Germany
| | - Paul R Crocker
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
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22
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Mirete-Bachiller S, Olivieri DN, Gambón-Deza F. Immunoglobulin T genes in Actinopterygii. Fish Shellfish Immunol 2021; 108:86-93. [PMID: 33279606 DOI: 10.1016/j.fsi.2020.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 09/01/2020] [Revised: 11/21/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
In teleost fishes, there are three immunoglobulin isotypes named immunoglobulin M (IgM), D (IgD), and T (IgT). IgT was the last to be described in teleost fishes, and it is specific to them. From recent fish genomes, we identified and studied the immunoglobulin heavy chain genes in Actinopterygii. For this analysis, a custom bioinformatics and machine learning pipeline, we call CHfinder, was developed that identifies the exons coding for the CH domains of fish immunoglobulins. Some IgT in teleost and holostean fish found from this systematic study have not been previously described. Phylogenetic analysis of the deduced amino acid sequences of the IgT CH1 exons reveals they are similar to the CH1 of IgM. This analysis also shows that the other three domains (CH2, CH3, and CH4) were not the result of recent IgM duplication processes in Actinopterygii, demonstrating that it is an immunoglobulin of earlier origin. The bioinformatics program, CHfinder, is publicly available at https://github.com/compimmuno/CHfinder.
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Affiliation(s)
| | - David N Olivieri
- Centro de Intelixencia Artificial, Ourense, Spain; ESE Informatica, Universidade de Vigo, Spain.
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23
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Abstract
Basic neuroscience research employs antibodies as key reagents to label, capture, and modulate the function of proteins of interest. Antibodies are immunoglobulin proteins. Recombinant antibodies are immunoglobulin proteins whose nucleic acid coding regions, or fragments thereof, have been cloned into expression plasmids that allow for unlimited production. Recombinant antibodies offer many advantages over conventional antibodies including their unambiguous identification and digital archiving via DNA sequencing, reliable expression, ease and reliable distribution as DNA sequences and as plasmids, and the opportunity for numerous forms of engineering to enhance their utility. Recombinant antibodies exist in many different forms, each of which offers potential advantages and disadvantages for neuroscience research applications. I provide an overview of recombinant antibodies and their development. Examples of their emerging use as valuable reagents in basic neuroscience research are also discussed. Many of these examples employ recombinant antibodies in innovative experimental approaches that cannot be pursued with conventional antibodies. © 2020 Wiley Periodicals LLC.
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Affiliation(s)
- James S Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, California
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24
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Powell LA, Miller A, Fox JM, Kose N, Klose T, Kim AS, Bombardi R, Tennekoon RN, Dharshan de Silva A, Carnahan RH, Diamond MS, Rossmann MG, Kuhn RJ, Crowe JE. Human mAbs Broadly Protect against Arthritogenic Alphaviruses by Recognizing Conserved Elements of the Mxra8 Receptor-Binding Site. Cell Host Microbe 2020; 28:699-711.e7. [PMID: 32783883 PMCID: PMC7666055 DOI: 10.1016/j.chom.2020.07.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 03/25/2020] [Revised: 06/25/2020] [Accepted: 07/15/2020] [Indexed: 10/23/2022]
Abstract
Mosquito inoculation of humans with arthritogenic alphaviruses results in a febrile syndrome characterized by debilitating musculoskeletal pain and arthritis. Despite an expanding global disease burden, no approved therapies or licensed vaccines exist. Here, we describe human monoclonal antibodies (mAbs) that bind to and neutralize multiple distantly related alphaviruses. These mAbs compete for an antigenic site and prevent attachment to the recently discovered Mxra8 alphavirus receptor. Three cryoelectron microscopy structures of Fab in complex with Ross River (RRV), Mayaro, or chikungunya viruses reveal a conserved footprint of the broadly neutralizing mAb RRV-12 in a region of the E2 glycoprotein B domain. This mAb neutralizes virus in vitro by preventing virus entry and spread and is protective in vivo in mouse models. Thus, the RRV-12 mAb and its defined epitope have potential as a therapeutic agent or target of vaccine design against multiple emerging arthritogenic alphavirus infections.
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Affiliation(s)
- Laura A Powell
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew Miller
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Julie M Fox
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Nurgun Kose
- Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA
| | - Thomas Klose
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Arthur S Kim
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Robin Bombardi
- Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA
| | - Rashika N Tennekoon
- Genetech Research Institute, Colombo, Sri Lanka; Department of Paraclinical Sciences, Faculty of Medicine, Kotelawala Defence University, Colombo, Sri Lanka
| | - A Dharshan de Silva
- Genetech Research Institute, Colombo, Sri Lanka; Department of Paraclinical Sciences, Faculty of Medicine, Kotelawala Defence University, Colombo, Sri Lanka
| | - Robert H Carnahan
- Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Michael S Diamond
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael G Rossmann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Richard J Kuhn
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Markey Center for Structural Biology and Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Vaccine Center, Department of Pediatrics, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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25
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Buonocore F, Scapigliati G, Pallavicini A, Gerdol M. Identification of an IgD/IgT chimera in the European sea bass (Dicentrarchus labrax L.). Fish Shellfish Immunol 2020; 105:224-232. [PMID: 32711154 DOI: 10.1016/j.fsi.2020.07.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 05/31/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Three classes of immunoglobulins have been identified in Teleosts: IgM, IgT/Z and IgD. They are fundamental for fish immune responses and, therefore, their functional activities are heavily investigated. In this paper, we describe the identification of a new IgD/IgT chimera in sea bass (Dicentrarchus labrax) from a gills transcriptome. This transcript joined the first six constant domains of the IgD chain with the two terminal constant domains of IgT, generating a long in-frame coding sequence with a junction between the canonical δ6 exon splicing donor site and the τ3 exon splicing acceptor site. Studies performed on genomic DNA confirmed the presence of the sequence and identifies and intronic region of 656 bp within this joining region. The basal expression of the IgD/IgT chimera was investigated both in silico and in vivo: high level of expression was found in gills, gut and head kidney. Moreover, IgD/IgT transcripts were up-regulated after in vitro stimulation of sea bass HK leukocytes with LPS. The IgD/IgT chimera was found also in two congener species, Morone saxatilis and Morone chrysops. It is not possible to have a precise idea on the evolutionary scenario that lead to the appearance of this sequence due to the lack of genomic information, but we could speculate that an ancestral duplication of the entire IgH locus was followed by the chimerization of Cδ/Cτ in one of the two loci. Finally, the IgD/IgT high basal expression in tissues and organs fundamental for sea bass immune response and its modulation after LPS stimulation provide a very preliminary indication that this unusual Ig variant could have a functional activity.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100, Viterbo, VT, Italy.
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Largo dell'Università snc, 05100, Viterbo, VT, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127, Trieste, TS, Italy
| | - Marco Gerdol
- Department of Life Sciences, University of Trieste, Via Giorgieri 5, 34127, Trieste, TS, Italy
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26
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Schoenenwald AKJ, Gwee CP, Stiasny K, Hermann M, Vasudevan SG, Skern T. Development and characterization of specific anti-Usutu virus chicken-derived single chain variable fragment antibodies. Protein Sci 2020; 29:2175-2188. [PMID: 32829514 PMCID: PMC7586906 DOI: 10.1002/pro.3937] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/10/2020] [Accepted: 08/21/2020] [Indexed: 12/18/2022]
Abstract
Usutu virus belongs to the Japanese encephalitis serogroup within the Flaviviridae family. Mammals may become incidental hosts after the bite of an infected mosquito while birds act as the main reservoir. Human cases have become more common recently and elicit various outcomes ranging from asymptomatic to severe illness including encephalitis. Problematically, antisera against Usutu virus cross-react with other flaviviruses such as the co-circulating West Nile virus. As an approach to generate Usutu virus-specific antibodies, we immunized chickens with purified Usutu virus envelope protein domain III, isolated the spleen mRNA and generated an scFv phage display library. The most potent binders for Usutu virus domain III were selected via biopanning and their affinity to domain III was examined using SPR. Four scFvs bound the domain III of Usutu virus in the nanomolar region; two bound the protein over 40 times more strongly than West Nile virus domain III. We further characterized these scFv antibodies for suitability in standard laboratory tests such as western blots, ELISA, and neutralization tests. Four specific and one cross-reactive antibody performed well in western blots with domain III and the full-length envelope protein of Usutu virus and West Nile virus. All antibodies bound in virus ELISA assays to Usutu virus strain Vienna-2001. However, none of the antibodies neutralized either Usutu virus or West Nile virus. These antibody candidates could be crucial in future diagnostic tests to distinguish Usutu virus from other flaviviruses and might even offer virus neutralization after a conversion to Fab or IgG.
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Affiliation(s)
| | - Chin Piaw Gwee
- Programme in Emerging Infectious DiseasesDuke‐NUS Medical SchoolSingapore
| | - Karin Stiasny
- Center for VirologyMedical University of ViennaViennaAustria
| | - Marcela Hermann
- Max Perutz LabsMedical University of Vienna, Vienna BiocenterViennaAustria
| | - Subhash G. Vasudevan
- Programme in Emerging Infectious DiseasesDuke‐NUS Medical SchoolSingapore
- Department of Microbiology and ImmunologyNational University of SingaporeSingapore
- Institute for GlycomicsGriffith University, Gold Coast CampusQueenslandAustralia
| | - Tim Skern
- Max Perutz LabsMedical University of Vienna, Vienna BiocenterViennaAustria
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27
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Peplau E, De Rose F, Reder S, Mittelhäuser M, Scafetta G, Schwaiger M, Weber WA, Bartolazzi A, Skerra A, D'Alessandria C. Development of a Chimeric Antigen-Binding Fragment Directed Against Human Galectin-3 and Validation as an Immuno-Positron Emission Tomography Tracer for the Sensitive In Vivo Imaging of Thyroid Cancer. Thyroid 2020; 30:1314-1326. [PMID: 32200708 DOI: 10.1089/thy.2019.0670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Background: The lack of facile methods for the specific characterization of malignant thyroid nodules makes the diagnosis of thyroid cancer (TC) challenging. Due to its restricted expression in such nodules, the cell-associated lectin galectin-3 (Gal3) has emerged as a marker for TC with growing interest for in vivo imaging as well as targeted radionuclide therapy. To accelerate translation into clinical application, we have developed a cognate chimeric human antigen-binding fragment (Fab) derived from the rat anti-Gal3 monoclonal antibody M3/38. Methods: The variable immunoglobulin (Ig) light and heavy chain sequences were cloned from the hybridoma cell line, and the corresponding Fab carrying human IgG1/κ constant genes was functionally produced in the periplasm of Escherichia coli and purified to homogeneity. To moderately prolong its plasma half-life and, thus, increase tumor uptake, the recombinant Fab was fused with a long disordered amino acid chain comprising in total 200 Pro, Ala, and Ser residues (PASylation). This novel tracer was subjected to in vitro characterization and in vivo validation by using two thyroid cancer orthotopic murine models. To this end, the αGal3-Fab-PAS200 was conjugated with deferoxamine (Dfo), labeled with 89Zr under mild conditions and tested for binding on TC cell lines. Athymic nude mice were inoculated either with FRO82-1 or with CAL62 tumor cells into the left thyroid lobe. After intravenous injection with ∼3.0 MBq of 89Zr-Dfo-PAS200-Fab, these mice were subjected to positron emission tomography (PET)/computed tomography imaging followed by quantification of tumor accumulation and immunohistochemical analysis. Results: The αGal3-Fab-PAS200 revealed high affinity toward the recombinant Gal3 antigen, with a dissociation constant ≤1 nM as measured via enzyme-linked immunosorbent assay, surface plasmon resonance spectroscopy, and radioactive cell binding assay. The in vivo Gal3-targeting by the 89Zr(IV)-labeled protein tracer, as investigated by immuno-PET, demonstrated highly selective and fast accumulation in orthotopically implanted tumors, with strong contrast images achieved 24 hours postinjection, and no uptake in the tumor-free thyroid lobe, as also confirmed by biodistribution studies. Conclusions: The chimeric αGal3 89Zr-Dfo-PAS200-Fab tracer exhibits selective accumulation in the tumor-bearing thyroid lobe of xenograft mice. Thus, this novel radioactive probe offers potential to change TC management, in addition to current diagnostic procedures, and to reduce unnecessary thyroidectomies.
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Affiliation(s)
- Emanuel Peplau
- Lehrstuhl für Biologische Chemie, Technische Universität München, Freising, Germany
| | - Francesco De Rose
- Klinikum rechts der Isar, Department of Nuclear Medicine, Technical University Munich, Munich, Germany
| | - Sybille Reder
- Klinikum rechts der Isar, Department of Nuclear Medicine, Technical University Munich, Munich, Germany
| | - Markus Mittelhäuser
- Klinikum rechts der Isar, Department of Nuclear Medicine, Technical University Munich, Munich, Germany
| | - Giorgia Scafetta
- Pathology Research Laboratory, Sant'Andrea Hospital, University Sapienza, Rome, Italy
| | - Markus Schwaiger
- Klinikum rechts der Isar, Department of Nuclear Medicine, Technical University Munich, Munich, Germany
| | - Wolfgang A Weber
- Klinikum rechts der Isar, Department of Nuclear Medicine, Technical University Munich, Munich, Germany
| | - Armando Bartolazzi
- Pathology Research Laboratory, Sant'Andrea Hospital, University Sapienza, Rome, Italy
- Pathology Research Laboratory, Cancer Center Karolinska, Karolinska Hospital, Stockholm, Sweden
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, Freising, Germany
| | - Calogero D'Alessandria
- Klinikum rechts der Isar, Department of Nuclear Medicine, Technical University Munich, Munich, Germany
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28
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Foglierini M, Pappas L, Lanzavecchia A, Corti D, Perez L. AncesTree: An interactive immunoglobulin lineage tree visualizer. PLoS Comput Biol 2020; 16:e1007731. [PMID: 32649725 PMCID: PMC7375605 DOI: 10.1371/journal.pcbi.1007731] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 07/22/2020] [Accepted: 06/14/2020] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Moreover, phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. The Immcantation framework provides a start-to-finish set of analytical methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) data. Furthermore, Immcantation's Change-O package has developed IgPhyML, an algorithm designed to build specifically immunoglobulin (Ig) phylogenic trees. Meanwhile Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. To complement Ig lineages made by IgPhyML or Dnaml (Phylip), we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools. The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.
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Affiliation(s)
- Mathilde Foglierini
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Leontios Pappas
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Laurent Perez
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
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29
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Zhang W, Qin L, Cai X, Juma SN, Xu R, Wei L, Wu Y, Cui X, Chen G, Liu L, Lv Z, Jiang X. Sequence structure character of IgNAR Sec in whitespotted bamboo shark (Chiloscyllium plagiosum). Fish Shellfish Immunol 2020; 102:140-144. [PMID: 32311460 DOI: 10.1016/j.fsi.2020.04.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 01/04/2020] [Revised: 04/11/2020] [Accepted: 04/16/2020] [Indexed: 06/11/2023]
Abstract
Whitespotted bamboo shark (Chiloscyllium plagiosum) is a demersal cartilaginous fish with an adaptive immune system founded upon immunoglobulins. In this manuscript, we characterize the IgNAR of the whitespotted bamboo shark. A newly discovered alternative splicing form of IgNAR Sec (IgNARshort (ΔC2-C3) Sec) was identified, in which the C1 domain was spliced directly to the C4 domain, the process resulted in a molecule containing three constant domains. However, a single unpaired cysteine remains in the highly flexible hinge region, contributing in the formation of an interchain disulfide bond. Two types of C1 domain were found, and the one lacking a short α-helix showed lower proportion. This finding suggests that short α-helices might be important to the stability of IgNAR. High-throughput sequencing revealed that the percentage of VNAR types significantly vary between the diverse species of sharks. The variable region of IgNAR (the VNAR) with small size and stabilization is a potential candidate for immunotherapeutic agents. The structure and stability analysis in this manuscript may be useful in future biomedical applications.
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Affiliation(s)
- Wenjie Zhang
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Lanyi Qin
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Xinyi Cai
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Salma Nassor Juma
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Rong Xu
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Ling Wei
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Yixin Wu
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Xuan Cui
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Guiqian Chen
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Lili Liu
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Zhengbing Lv
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Xiaofeng Jiang
- College of Life Sciences, Zhejiang Sci-Tech University, 310018, Hangzhou, China; Zhejiang Provincial Key Laboratory of Silkworm Bioreactor and Biomedicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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30
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Verschueren E, Husain B, Yuen K, Sun Y, Paduchuri S, Senbabaoglu Y, Lehoux I, Arena TA, Wilson B, Lianoglou S, Bakalarski C, Franke Y, Chan P, Wong AW, Gonzalez LC, Mariathasan S, Turley SJ, Lill JR, Martinez-Martin N. The Immunoglobulin Superfamily Receptome Defines Cancer-Relevant Networks Associated with Clinical Outcome. Cell 2020; 182:329-344.e19. [PMID: 32589946 DOI: 10.1016/j.cell.2020.06.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 04/06/2020] [Accepted: 06/02/2020] [Indexed: 01/31/2023]
Abstract
Cell surface receptors and their interactions play a central role in physiological and pathological signaling. Despite its clinical relevance, the immunoglobulin superfamily (IgSF) remains uncharacterized and underrepresented in databases. Here, we present a systematic extracellular protein map, the IgSF interactome. Using a high-throughput technology to interrogate most single transmembrane receptors for binding to 445 IgSF proteins, we identify over 500 interactions, 82% previously undocumented, and confirm more than 60 receptor-ligand pairs using orthogonal assays. Our study reveals a map of cell-type-specific interactions and the landscape of dysregulated receptor-ligand crosstalk in cancer, including selective loss of function for tumor-associated mutations. Furthermore, investigation of the IgSF interactome in a large cohort of cancer patients identifies interacting protein signatures associated with clinical outcome. The IgSF interactome represents an important resource to fuel biological discoveries and a framework for understanding the functional organization of the surfaceome during homeostasis and disease, ultimately informing therapeutic development.
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Affiliation(s)
| | - Bushra Husain
- Deparment of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Kobe Yuen
- Oncology Biomarker Development, Genentech, South San Francisco, CA, USA
| | - Yi Sun
- University of Birmingham, Department Biochemistry, Birmingham, UK
| | | | | | - Isabelle Lehoux
- BioMolecular Resources Department, Genentech, South San Francisco, CA, USA
| | - Tia A Arena
- Research Materials group, Genentech, South San Francisco, CA, USA
| | - Blair Wilson
- Biochemistry and Molecular Pharmacology, Genentech, South San Francisco, CA, USA
| | | | - Corey Bakalarski
- Deparment of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Yvonne Franke
- BioMolecular Resources Department, Genentech, South San Francisco, CA, USA
| | - Pamela Chan
- Biochemistry and Molecular Pharmacology, Genentech, South San Francisco, CA, USA
| | - Athena W Wong
- Research Materials group, Genentech, South San Francisco, CA, USA
| | | | | | - Shannon J Turley
- Cancer Immunology Department, Genentech, South San Francisco, CA, USA
| | - Jennie R Lill
- Deparment of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA
| | - Nadia Martinez-Martin
- Deparment of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA, USA.
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31
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Grosche L, Knippertz I, König C, Royzman D, Wild AB, Zinser E, Sticht H, Muller YA, Steinkasserer A, Lechmann M. The CD83 Molecule - An Important Immune Checkpoint. Front Immunol 2020; 11:721. [PMID: 32362900 PMCID: PMC7181454 DOI: 10.3389/fimmu.2020.00721] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022] Open
Abstract
The CD83 molecule has been identified to be expressed on numerous activated immune cells, including B and T lymphocytes, monocytes, dendritic cells, microglia, and neutrophils. Both isoforms of CD83, the membrane-bound as well as its soluble form are topic of intensive research investigations. Several studies revealed that CD83 is not a typical co-stimulatory molecule, but rather plays a critical role in controlling and resolving immune responses. Moreover, CD83 is an essential factor during the differentiation of T and B lymphocytes, and the development and maintenance of tolerance. The identification of its interaction partners as well as signaling pathways have been an enigma for the last decades. Here, we report the latest data on the expression, structure, and the signaling partners of CD83. In addition, we review the regulatory functions of CD83, including its striking modulatory potential to maintain the balance between tolerance versus inflammation during homeostasis or pathologies. These immunomodulatory properties of CD83 emphasize its exceptional therapeutic potential, which has been documented in specific preclinical disease models.
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Affiliation(s)
- Linda Grosche
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ilka Knippertz
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Christina König
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Dmytro Royzman
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Andreas B. Wild
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Elisabeth Zinser
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Yves A. Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Alexander Steinkasserer
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Matthias Lechmann
- Department of Immune Modulation, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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32
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Schulz K, Pöhlmann C, Dietrich R, Märtlbauer E, Elßner T. An Electrochemical Fiveplex Biochip Assay Based on Anti-Idiotypic Antibodies for Fast On-Site Detection of Bioterrorism Relevant Low Molecular Weight Toxins. Toxins (Basel) 2019; 11:toxins11120696. [PMID: 31795179 PMCID: PMC6950599 DOI: 10.3390/toxins11120696] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/19/2022] Open
Abstract
Modern threats of bioterrorism force the need for multiple detection of biothreat agents to determine the presence or absence of such agents in suspicious samples. Here, we present a rapid electrochemical fiveplex biochip screening assay for detection of the bioterrorism relevant low molecular weight toxins saxitoxin, microcystin-LR, T-2 toxin, roridin A and aflatoxin B1 relying on anti-idiotypic antibodies as epitope-mimicking reagents. The proposed method avoids the use of potentially harmful toxin-protein conjugates usually mandatory for competitive immunoassays. The biochip is processed and analyzed on the automated and portable detection platform pBDi within 13.4 min. The fiveplex biochip assay revealed toxin group specificity to multiple congeners. Limits of detection were 1.2 ng/mL, 1.5 ng/mL, 0.4 ng/mL, 0.5 ng/mL and 0.6 ng/mL for saxitoxin, microcystin-LR, T-2 toxin, roridin A or aflatoxin B1, respectively. The robustness of the fiveplex biochip for real samples was demonstrated by detecting saxitoxin, microcystin-LR, HT-2 toxin, roridin A and aflatoxin B1 in contaminated human blood serum without elaborate sample preparation. Recovery rates were between 52–115% covering a wide concentration range. Thus, the developed robust fiveplex biochip assay can be used on-site to quickly detect one or multiple low molecular weight toxins in a single run.
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Affiliation(s)
- Katharina Schulz
- Bruker Daltonik GmbH, Permoserstr. 15, 04318 Leipzig, Germany; (K.S.); (C.P.); (T.E.)
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstr. 8, 85764 Oberschleißheim, Germany;
| | - Christopher Pöhlmann
- Bruker Daltonik GmbH, Permoserstr. 15, 04318 Leipzig, Germany; (K.S.); (C.P.); (T.E.)
| | - Richard Dietrich
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstr. 8, 85764 Oberschleißheim, Germany;
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität München, Schönleutnerstr. 8, 85764 Oberschleißheim, Germany;
- Correspondence:
| | - Thomas Elßner
- Bruker Daltonik GmbH, Permoserstr. 15, 04318 Leipzig, Germany; (K.S.); (C.P.); (T.E.)
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33
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Pereira EPV, van Tilburg MF, Florean EOPT, Guedes MIF. Egg yolk antibodies (IgY) and their applications in human and veterinary health: A review. Int Immunopharmacol 2019; 73:293-303. [PMID: 31128529 PMCID: PMC7106195 DOI: 10.1016/j.intimp.2019.05.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022]
Abstract
Egg yolk constitutes a relevant alternative source of antibodies. It presents some advantages over mammalian serum immunoglobulins regarding productivity, animal welfare and specificity. The main immunoglobulin present in avian blood (IgY) is transmitted to their offspring and accumulates in egg yolks, which enables the non-invasive harvesting of high amounts of antibodies. Moreover, due to structural differences and phylogenetic distance, IgY is more suitable for diagnostic purposes than mammalian antibodies, since it does not react with certain components of the human immune system and displays greater avidity for mammalian conserved proteins. IgY has been extensively used in health researches, as both therapeutic and diagnostic tool. This article aims to review its applications in both human and veterinary health.
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Affiliation(s)
- E P V Pereira
- Laboratory of Biotechnology and Molecular Biology - LBBM, Ceará State University, Brazil.
| | - M F van Tilburg
- Laboratory of Biotechnology and Molecular Biology - LBBM, Ceará State University, Brazil
| | - E O P T Florean
- Laboratory of Biotechnology and Molecular Biology - LBBM, Ceará State University, Brazil
| | - M I F Guedes
- Laboratory of Biotechnology and Molecular Biology - LBBM, Ceará State University, Brazil
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34
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Demers-Mathieu V, Huston RK, Markell AM, McCulley EA, Martin RL, Spooner M, Dallas DC. Differences in Maternal Immunoglobulins within Mother's Own Breast Milk and Donor Breast Milk and across Digestion in Preterm Infants. Nutrients 2019; 11:nu11040920. [PMID: 31022910 PMCID: PMC6521323 DOI: 10.3390/nu11040920] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/08/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023] Open
Abstract
Maternal antibody transfer to the newborn provides essential support for the infant’s naïve immune system. Preterm infants normally receive maternal antibodies through mother’s own breast milk (MBM) or, when mothers are unable to provide all the milk required, donor breast milk (DBM). DBM is pasteurized and exposed to several freeze–thaw cycles, which could reduce intact antibody concentration and the antibody’s resistance to digestion within the infant. Whether concentrations of antibodies in MBM and DBM differ and whether their survival across digestion in preterm infants differs remains unknown. Feed (MBM or DBM), gastric contents (MBM or DBM at 1-h post-ingestion) and stool samples (collected after a mix of MBM and DBM feeding) were collected from 20 preterm (26–36 weeks gestational age) mother–infant pairs at 8–9 and 21–22 days of postnatal age. Samples were analyzed via ELISA for the concentration of secretory IgA (SIgA), total IgA (SIgA/IgA), total IgM (SIgM/IgM) and IgG. Total IgA, SIgA, total IgM and IgG concentrations were 55.0%, 71.6%, 98.4% and 41.1% higher in MBM than in DBM, and were 49.8%, 32.7%, 73.9% and 39.7% higher in gastric contents when infants were fed with MBM than when infants were fed DBM, respectively. All maternal antibody isotypes present in breast milk were detected in the infant stools, of which IgA (not sIgA) was the most abundant.
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Affiliation(s)
- Veronique Demers-Mathieu
- Nutrition Program, School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - Robert K Huston
- Department of Pediatrics, Randall Children's Hospital at Legacy Emanuel, Portland, OR 97227, USA.
| | - Andi M Markell
- Department of Pediatrics, Randall Children's Hospital at Legacy Emanuel, Portland, OR 97227, USA.
| | - Elizabeth A McCulley
- Department of Pediatrics, Randall Children's Hospital at Legacy Emanuel, Portland, OR 97227, USA.
| | - Rachel L Martin
- Department of Pediatrics, Randall Children's Hospital at Legacy Emanuel, Portland, OR 97227, USA.
| | - Melinda Spooner
- Nutrition Program, School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - David C Dallas
- Nutrition Program, School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.
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35
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Zhou H, Liu S, Yin X, Li Z, Yang Z, Zhou R. Molecular Origin of the Stability Difference in Four Shark IgNAR Constant Domains. Biophys J 2019; 116:1907-1917. [PMID: 31060814 DOI: 10.1016/j.bpj.2019.04.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/27/2018] [Revised: 02/09/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Improving the stability of antibodies for manufacture and shelf life is one of the main focuses of antibody engineering. One stabilization strategy is to perform specific mutations in human antibodies based on highly stable antibodies in other species. To identify the key residues for mutagenesis, it is necessary to understand the roles of these residues in stabilizing the antibody. Here, we use molecular dynamics simulations to study the molecular origin of the four shark immunoglobulin new antigen receptors constant domains (C1-C4). According to the unfolding pathways and the conformational free energy surfaces in 8 M urea at 380 K, the C2 domain is the most stable, followed by C4, C1, and C3, which agrees with the experimental findings. The C1 and C3 domains follow a common unfolding pathway in which the unfolding starts from the edge strands, particularly strand g, and then gradually progresses to the inner strands. Detailed structural analysis of the C2 domain reveals a "sandwich-like" R339-E322-R341 salt-bridge cluster on strand g, which grants ultrahigh stability to the C2 domain. We further design two sets of mutations by mutating E322 to alanine or setting all atomic charges in E322 to zero to break the salt-bridge cluster in the C2 domain, which confirms the importance of the salt bridges in stability. In the C4 domain, the D80-K104 salt bridge on strand g also strengthens the stability. On the other hand, in the C1 and C3 domains, there is no salt bridge on strand g. In addition to the salt bridges, the overall hydrophobicity score of the hydrophobic core is also positively correlated with the domain stability. Our findings provide a detailed microscopic picture of the molecular origin of the four shark immunoglobulin new antigen receptors constant domains that not only explains the differences in their structural stability but also provides important insights into future antibody design.
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Affiliation(s)
- Hong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China
| | - Shengtang Liu
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China
| | - Xiuhua Yin
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China
| | - Zengpeng Li
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, China
| | - Zaixing Yang
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China.
| | - Ruhong Zhou
- Institute of Quantitative Biology and Medicine, State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Soochow University, Jiangsu, China; IBM Thomas J. Watson Research Center, Yorktown Heights, New York; Department of Chemistry, Columbia University, New York, New York.
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36
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Ehsani A, Naghibi SS, Aminzare M, Keykhosravi K, Hashemi M. Extraction of specific egg yolk antibodies and application in chitosan coating: effect on microbial and sensory properties of rainbow trout fillet during chilled storage. J Sci Food Agric 2019; 99:2356-2364. [PMID: 30367501 DOI: 10.1002/jsfa.9442] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/22/2018] [Revised: 08/30/2018] [Accepted: 09/27/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND This study investigated the effect of chitosan coating enriched with extracted egg yolk antibodies on microbial and sensory quality of rainbow trout fillet during refrigeration (4 ± 1 °C). Firstly, bacterial antigen suspensions (total psychrophilic bacteria, Pseudomonas fluorescens and Shewanella putrefaciens) were injected into the breast muscles of chickens. Eggs of immunized chickens were then collected to isolate immunoglobulin from egg yolks (IgY). Fresh fish fillets were coated by chitosan solution containing different types of IgY separately, at two concentrations (60 and 90 mg mL-1 ), refrigerated for 16 days and analysed for total viable count, psychrotrophic, Pseudomonas spp., P. fluorescens and S. putrefaciens count as well as sensorial properties. RESULTS The tested microbial values increased in all samples during the storage period; however, CH + IgY treated samples could significantly retard microbial growth compared to control. The shelf life of CH + IgY-P samples was extended for about 4 days, while it was extended for about 8 days in CH + IgY-S and CH + IgY-T samples, when they were compared to control (p < 0.05). Higher scores for sensory attributes were also observed in CH + IgY treated samples, especially in CH + IgY-S samples until the end of storage period. CONCLUSIONS Accordingly, use of chitosan coating containing IgY increases the microbial and sensory quality of fish flesh at 4 °C. Therefore, given the consumer interest in natural additives, chitosan coating containing IgY can be a promising candidate. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Ali Ehsani
- Department of Food Science and Technology, Faculty of Nutrition, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyedeh S Naghibi
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, Urmia University, Urmia, Iran
| | - Majid Aminzare
- Department of Food Safety and Hygiene, School of Public Health, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Kobra Keykhosravi
- Department of Food Hygiene and Aquaculture, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Hashemi
- Department of Nutrition, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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37
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Shevate R, Kumar M, Cheng H, Hong PY, Behzad AR, Anjum D, Peinemann KV. Rapid Size-Based Protein Discrimination inside Hybrid Isoporous Membranes. ACS Appl Mater Interfaces 2019; 11:8507-8516. [PMID: 30699293 DOI: 10.1021/acsami.8b20802] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Owing to their unique morphology, isoporous membranes derived from block copolymers (BCPs) have rapidly advanced the process of macromolecular separation. In such separations, fouling is the most daunting challenge, affecting both the permeability and selectivity of high-performance isoporous membranes. To overcome this, we increase the hydrophilicity of nanostructured BCP isoporous membranes by incorporating hydrophilic polymer-grafted graphene oxide nanosheets into them. Due to the synergy of these two highly functional components, the hybrid isoporous membranes show pH-responsive and alcohol-gating behaviors, along with improved bactericidal capabilities. Leveraging the high permeability and selectivity behavior of BCP isoporous membranes together with the antifouling capabilities imparted by the polymer-grafted graphene oxide nanosheets, we achieved the highest separation factor (33) ever obtained during the ultrafiltration of the common blood proteins bovine serum albumin and immunoglobulin. This was accompanied by a 60% enhanced flux compared to that of the pristine BCP membranes during this challenging size-based separation of a protein mixture. We surmise that such fouling-resistant hybrid isoporous membranes with rationally functionalized filler materials can be used to replace existing membranes for specific energy-efficient bioseparation applications with improved performance.
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38
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Abstract
The traditional classification of protein structures (with regard to their supersecondary and tertiary conformation) is based on an assessment of conformational similarities between various polypeptide chains and particularly on the presence of specific secondary structural motifs. Mutual relations between secondary folds determine the overall shape of the protein and may be used to assign proteins to specific families (such as the immunoglobulin-like family). An alternative means of conducting structural assessment focuses on the structure of the protein's hydrophobic core. In this case, the protein is treated as a quasi-micelle, which exposes hydrophilic residues on its surface while internalizing hydrophobic residues. The accordance between the actual distribution of hydrophobicity in a protein and its corresponding theoretical ("idealized") distribution can be determined quantitatively, which, in turn, enables comparative analysis of structures regarded as geometrically similar (as well as geometrically divergent structures which are nevertheless regarded as similar in the sense of the fuzzy oil drop model). In this scope, the protein may be compared to an "intelligent micelle," where local disorder is often intentional and related to biological function-unlike traditional surfactant micelles which remain highly symmetrical throughout and do not carry any encoded information.
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Affiliation(s)
- Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kraków, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University, Medical College, Kraków, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University, Medical College, Kraków, Poland.
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39
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Mukhopadhyay D, Gupta C, Theint T, Jaroniec CP. Peptide bond conformation in peptides and proteins probed by dipolar coupling-chemical shift tensor correlation solid-state NMR. J Magn Reson 2018; 297:152-160. [PMID: 30396157 PMCID: PMC6289736 DOI: 10.1016/j.jmr.2018.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 05/30/2023]
Abstract
Multidimensional magic-angle spinning solid-state NMR experiments are described that permit cis and trans peptide bonds in uniformly 13C,15N-labeled peptides and proteins to be unambiguously distinguished in residue-specific manner by determining the relative orientations of the amide 13C' CSA and 1H-15N dipolar coupling tensors. The experiments are demonstrated for model peptides glycylglycine and 2,5-diketopiperazine containing trans and cis peptide bonds, respectively. Subsequently, the measurements are extended to two representative proteins that contain exclusively trans peptide bonds, microcrystalline B3 immunoglobulin domain of protein G and Y145Stop human prion protein amyloid fibrils, to illustrate their applicability to a wide range of protein systems.
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Affiliation(s)
- Dwaipayan Mukhopadhyay
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Chitrak Gupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Theint Theint
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States
| | - Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, United States.
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40
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Abstract
Choice in the behavior of organisms involves novelty, which may be unpredictable. Yet in retrospect, we can usually provide a rationale for the choice. A deterministic view of life cannot explain this. The solution to this paradox is that organisms can harness stochasticity through which they can generate many possible solutions to environmental challenges. They must then employ a comparator to find the solution that fits the challenge. What therefore is unpredictable in prospect can become comprehensible in retrospect. Harnessing stochastic and/or chaotic processes is essential to the ability of organisms to have agency and to make choices.
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Affiliation(s)
- Raymond Noble
- Institute for Women's Health, University College London, London WC1E 6AU, UK
| | - Denis Noble
- Department of Physiology, Anatomy & Genetics, University of Oxford, Oxford OX1 3PT, UK
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Escuder-Vieco D, Espinosa-Martos I, Rodríguez JM, Fernández L, Pallás-Alonso CR. Effect of HTST and Holder Pasteurization on the Concentration of Immunoglobulins, Growth Factors, and Hormones in Donor Human Milk. Front Immunol 2018; 9:2222. [PMID: 30319659 PMCID: PMC6170621 DOI: 10.3389/fimmu.2018.02222] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023] Open
Abstract
Donor human milk (DHM) is submitted to Holder pasteurization (HoP) to ensure its microbiological safety in human milk banks but this treatment affects some of its bioactive compounds. The objective of this work was to compare the effects of HoP and high temperature short time (HTST) treatments on some bioactive compounds found in DHM. A total of 24 DHM batches were processed in a continuous HTST system (70, 72, and 75°C for 5-25 s) and by HoP (62.5°C for 30 min). The concentrations of immunoglobulins (Igs) A, G, and M, transforming growth factor-beta 2 (TGF-β2), adiponectine, ghrelin, and leptin were measured using a multiplex system, whereas the concentration of epidermal growth factor (EGF) was determined by ELISA. In relation to Igs, IgG showed the highest preservation rates (87-101%) after HTST treatments, followed by IgA (54-88%) and IgM (25-73%). Ig retention after any of the HTST treatments was higher than after HoP (p < 0.001). Treatment times required to reduce the concentration of IgM by 90% (D-value) were 130, 88, and 49 s at 70, 72, and 75°C, while the number of degrees Celsius required to change the D-value by one factor of 10 (z-value) was 11.79°C. None of the heat treatments had a significant effect on the concentrations of TGF-β2, EGF, adiponectin, and ghrelin. In contrast, leptin was detected only in 4 of the samples submitted to HoP, whereas it was present in all samples after the different HTST treatments, with retention rates ranging between 34 and 68%. Globally, the concentration of IgA, IgG, IgM, and leptin in DHM was significantly higher after HTST pasteurization performed in a continuous system designed to be used in human milk banks than after the HoP procedure that is routinely applied at present.
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Affiliation(s)
- Diana Escuder-Vieco
- Banco Regional de Leche Materna, Hospital Universitario 12 de Octubre, Instituto de Investigación i+12, Madrid, Spain
- *Correspondence: Diana Escuder-Vieco
| | | | - Juan M. Rodríguez
- Sección Departamental de Nutrición y Ciencia de los Alimentos (Veterinaria), Universidad Complutense de Madrid, Madrid, Spain
| | - Leónides Fernández
- Sección Departamental de Farmacia Galénica y Tecnología Alimentaria (Veterinaria), Universidad Complutense de Madrid, Madrid, Spain
| | - Carmen Rosa Pallás-Alonso
- Banco Regional de Leche Materna, Hospital Universitario 12 de Octubre, Instituto de Investigación i+12, Madrid, Spain
- Servicio de Neonatología, Hospital Universitario 12 de Octubre, Instituto de Investigación i+12, Universidad Complutense de Madrid, Madrid, Spain
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42
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Zhang Z, Li J, Chen Y, Xie H, Yang J. A robust heteronuclear dipolar recoupling method comparable to TEDOR for proteins in magic-angle spinning solid-state NMR. J Magn Reson 2017; 285:79-85. [PMID: 29126001 DOI: 10.1016/j.jmr.2017.10.012] [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: 08/04/2017] [Revised: 10/27/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
In this letter, we propose a robust heteronuclear dipolar recoupling method for proteins in magic-angle spinning (MAS) solid-state NMR. This method is as simple, robust and efficient as the well-known TEDOR in the aspect of magnetization transfer between 15N and 13C. Deriving from our recent band-selective dual back-to-back pulses (DBP) (Zhang et al., 2016), this method uses new phase-cycling schemes to realize broadband DBP (Bro-DBP). For broadband 15N-13C magnetization transfer (simultaneous 15N→13C' and 15N→13Cα), Bro-DBP has almost the same 15N→13Cα efficiency while offers 30-40% enhancement on 15N→13C' transfer, compared to TEDOR. Besides, Bro-DBP can also be used as a carbonyl (13C')-selected method, whose 15N→13C' efficiency is up to 1.7 times that of TEDOR and is also higher than that of band-selective DBP. The performance of Bro-DBP is demonstrated on the N-formyl-[U-13C,15N]-Met-Leu-Phe-OH (fMLF) peptide and the U-13C, 15N labeled β1 immunoglobulin binding domain of protein G (GB1) microcrystalline protein. Since Bro-DBP is as robust, simple and efficient as TEDOR, we believe it is very useful for protein studies in MAS solid-state NMR.
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Affiliation(s)
- Zhengfeng Zhang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China.
| | - Jianping Li
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Yanke Chen
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Huayong Xie
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jun Yang
- National Center for Magnetic Resonance in Wuhan, Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, PR China.
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43
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Abstract
Immunotherapy is becoming increasingly important in the fight against cancers, using and manipulating the body's immune response to treat tumors. Understanding the immune repertoire-the collection of immunological proteins-of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to miss identifications in a mass spectrometry search. We introduce a novel proteogenomic approach, AbScan, to identify these highly variable antibody peptides, by developing a customized antibody database construction method using RNA-seq reads aligned to immunoglobulin (Ig) genes.AbScan starts by filtering transcript (RNA-seq) reads that match the template for Ig genes. The retained reads are used to construct a repertoire graph using the "split" de Bruijn graph: a graph structure that improves on the standard de Bruijn graph to capture the high diversity of Ig genes in a compact manner. AbScan corrects for sequencing errors, and converts the graph to a format suitable for searching with MS/MS search tools. We used AbScan to create an antibody database from 90 RNA-seq colorectal tumor samples. Next, we used proteogenomic analysis to search MS/MS spectra of matched colorectal samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) against the AbScan generated database. AbScan identified 1,940 distinct antibody peptides. Correlating with previously identified Single Amino-Acid Variants (SAAVs) in the tumor samples, we identified 163 pairs (antibody peptide, SAAV) with significant cooccurrence pattern in the 90 samples. The presence of coexpressed antibody and mutated peptides was correlated with survival time of the individuals. Our results suggest that AbScan (https://github.com/csw407/AbScan.git) is an effective tool for a proteomic exploration of the immune response in cancers.
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Affiliation(s)
- Seong Won Cha
- From the ‡Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, California
| | | | - Seungjin Na
- ¶Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92037
| | - Pavel A Pevzner
- ¶Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92037
| | - Vineet Bafna
- ¶Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92037
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Jiang J, Natarajan K, Boyd LF, Morozov GI, Mage MG, Margulies DH. Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation. Science 2017; 358:1064-1068. [PMID: 29025991 PMCID: PMC6320693 DOI: 10.1126/science.aao5154] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Abstract
Central to CD8+ T cell-mediated immunity is the recognition of peptide-major histocompatibility complex class I (p-MHC I) proteins displayed by antigen-presenting cells. Chaperone-mediated loading of high-affinity peptides onto MHC I is a key step in the MHC I antigen presentation pathway. However, the structure of MHC I with a chaperone that facilitates peptide loading has not been determined. We report the crystal structure of MHC I in complex with the peptide editor TAPBPR (TAP-binding protein-related), a tapasin homolog. TAPBPR remodels the peptide-binding groove of MHC I, resulting in the release of low-affinity peptide. Changes include groove relaxation, modifications of key binding pockets, and domain adjustments. This structure captures a peptide-receptive state of MHC I and provides insights into the mechanism of peptide editing by TAPBPR and, by analogy, tapasin.
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Affiliation(s)
- Jiansheng Jiang
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kannan Natarajan
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lisa F Boyd
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giora I Morozov
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Hebrew University of Jerusalem, Robert H. Smith Faculty of Agriculture, Food and Environment, Rehovot 76100, Israel
| | - Michael G Mage
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David H Margulies
- Molecular Biology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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45
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Mo ZQ, Wang JL, Yang M, Ni LY, Wang HQ, Lao GF, Li YW, Li AX, Luo XC, Dan XM. Characterization and expression analysis of grouper (Epinephelus coioides) co-stimulatory molecules CD83 and CD80/86 post Cryptocaryon irritans infection. Fish Shellfish Immunol 2017; 67:467-474. [PMID: 28579524 DOI: 10.1016/j.fsi.2017.05.064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 02/23/2017] [Revised: 05/10/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
Co-stimulatory molecules (CD83, CD80 and CD86), belong to immunoglobulin superfamily, are type I membrane glycoprotein, which express on antigen presenting cells and provide the second signal for the activation of T lymphocytes. In the present study, we cloned the grouper's CD83 (675 bp) and CD80/86 (876 bp). Homology analysis showed that both EcCD83 and EcCD80/86 shares the highest amino acid similarity (51% and 47%) for the overall sequence with puffer fish (Takifugu rubripes). Some conserved features and important functional residues in mammalian CD83, CD80 and CD86 were also identified from these molecules of teleosts including grouper, suggesting the function of both molecules may be conserved among vertebrates. In transfected HEK293T cells, both molecules localized on the membrane surface. Tissue distribution analysis showed both EcCD83 and EcCD80/86 mRNAs were mainly expressed in immune organs, and EcCD80/86 was extremely higher expressed in mucosal immune tissues including skin and gill than systematic immune organs, which indicates these co-stimulatory molecules may prime T cell activation in local mucosal tissues. In Cryptocaryon irritans infected groupers, the expression level of EcCD83 and EcCD80/86 were both seen significant up-regulation in the skin at most tested time points.
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Affiliation(s)
- Ze-Quan Mo
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China
| | - Jiu-Le Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China
| | - Man Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China
| | - Lu-Yun Ni
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China
| | - Hai-Qing Wang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China
| | - Guo-Feng Lao
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China
| | - Yan-Wei Li
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China
| | - An-Xing Li
- State Key Laboratory of Biocontrol/ Key Laboratory of Aquatic Product Safety (Sun Yat-Sen University), Ministry of Education, The School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong Province, PR China
| | - Xiao-Chun Luo
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, PR China.
| | - Xue-Ming Dan
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, Guangdong Province, PR China.
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46
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Bakhshi M, Ebrahimi F, Nazarian S, Zargan J, Behzadi F, Gariz DS. Nano-encapsulation of chicken immunoglobulin (IgY) in sodium alginate nanoparticles: In vitro characterization. Biologicals 2017; 49:69-75. [PMID: 28693954 DOI: 10.1016/j.biologicals.2017.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/27/2017] [Accepted: 06/02/2017] [Indexed: 12/25/2022] Open
Abstract
Controlled delivery of therapeutic agents by alginate nanoparticles became an attractive issue in the gastric organ. Some therapeutic agents such as proteins could not tolerate in severe condition in the gastrointestinal tract. In the present study, four concentrations of a specific IgY as a prophylactic agent against E. coli O157: H7 was entrapped in 0.2% w/v sodium alginate nanoparticles by ionic gelation method. Depending on the IgY concentration entrapment efficacy was 28.31-99.84%. The physicochemical and structural characteristics of free and IgY-loaded Alg NPs revealed that the individual particles exhibited a spherical shape with a diameter of 45-85 nm, and a negatively charged surface with a zeta potential value of 26-36 mV. In vitro release study showed a high significant difference of released amounts of IgY at 10% and 99.84% in simulated gastric fluid (pH 1.2) and simulated intestine fluid (pH 6.8), respectively. Also, the quality and activity of released IgY from Alg NPs not changed. The cytotoxicity of different concentrations of Alg NPs on the Vero cells was measured. Our results indicated that Alg NPs prepared from 0.2%w/v stock solution could be appropriate candidates for efficient and safe delivery of IgY through the gastrointestinal tract.
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Affiliation(s)
- Mostafa Bakhshi
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - Firouz Ebrahimi
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran.
| | - Shahram Nazarian
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - Jamil Zargan
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
| | - Faeze Behzadi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Dawood Sadeghi Gariz
- Department of Biology, Faculty of Basic Science, Imam Hossein University, Tehran, Iran
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47
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Heilingloh CS, Klingl S, Egerer-Sieber C, Schmid B, Weiler S, Mühl-Zürbes P, Hofmann J, Stump JD, Sticht H, Kummer M, Steinkasserer A, Muller YA. Crystal Structure of the Extracellular Domain of the Human Dendritic Cell Surface Marker CD83. J Mol Biol 2017; 429:1227-1243. [PMID: 28315353 DOI: 10.1016/j.jmb.2017.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 02/10/2017] [Accepted: 03/05/2017] [Indexed: 11/27/2022]
Abstract
CD83 is a type-I membrane protein and an efficient marker for identifying mature dendritic cells. Whereas membrane-bound, full-length CD83 co-stimulates the immune system, a soluble variant (sCD83), consisting of the extracellular domain only, displays strong immune-suppressive activities. Besides a prediction that sCD83 adopts a V-set Ig-like fold, however, little is known about the molecular architecture of CD83 and the mechanism by which CD83 exerts its function on dendritic cells and additional immune cells. Here, we report the crystal structure of human sCD83 up to a resolution of 1.7Å solved in three different crystal forms. Interestingly, β-strands C', C″, and D that are typical for V-set Ig-domains could not be traced in sCD83. Mass spectrometry analyses, limited proteolysis experiments, and bioinformatics studies show that the corresponding segment displays enhanced main-chain accessibility, extraordinary low sequence conservation, and a predicted high disorder propensity. Chimeric proteins with amino acid swaps in this segment show unaltered immune-suppressive activities in a TNF-α assay when compared to wild-type sCD83. This strongly indicates that this segment does not participate in the biological activity of CD83. The crystal structure of CD83 shows the recurrent formation of dimers and trimers in the various crystal forms and reveals strong structural similarities between sCD83 and B7 family members and CD48, a signaling lymphocyte activation molecule family member. This suggests that CD83 exerts its immunological activity by mixed homotypic and heterotypic interactions as typically observed for proteins present in the immunological synapse.
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Affiliation(s)
- Christiane S Heilingloh
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Stefan Klingl
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Claudia Egerer-Sieber
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Benedikt Schmid
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Sigrid Weiler
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany
| | - Petra Mühl-Zürbes
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Jörg Hofmann
- Division of Biochemistry, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Joachim D Stump
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Heinrich Sticht
- Division of Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Mirko Kummer
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Alexander Steinkasserer
- Department of Immune Modulation, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Hartmannstr. 14, D-91052 Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-University Erlangen-Nürnberg, Henkestr. 91, D-91052 Erlangen, Germany.
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48
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Picchietti S, Nuñez-Ortiz N, Stocchi V, Randelli E, Buonocore F, Guerra L, Scapigliati G. Evolution of lymphocytes. Immunoglobulin T of the teleost sea bass (Dicentrarchus labrax): Quantitation of gene expressing and immunoreactive cells. Fish Shellfish Immunol 2017; 63:40-52. [PMID: 28167252 DOI: 10.1016/j.fsi.2017.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 11/15/2016] [Revised: 01/29/2017] [Accepted: 02/02/2017] [Indexed: 06/06/2023]
Abstract
Immunoglobulin T (IgT) is one of the key effector molecules of jawed vertebrate's adaptive immune system, and in this work we describe the quantitative distribution of IgT-expressing and IgT-producing cells in tissues of the European seabass Dicentrarchus labrax by using mRNA riboprobes and a specific anti-IgT antibody. A polyclonal antiserum (pAb) was prepared by immunizing rabbits with three synthetic peptides deduced from the full length IgT cDNA sequence and located in a surface-exposed CH3 domain of IgT constant region. The obtained antiserum, named RAIgT1, was able to recognize by ELISA immunization antigens and IgT from intestinal mucus and serum. In western blots of head kidney leukocytes lysates the antiserum recognized a 180 kDa polypeptide in non-reducing, and a 75 kDa peptide in reducing conditions. Interestingly, the RAIgT1 pAb crossreacted intensely in western blots with rainbow trout IgT purified from mucus and serum. Antisense mRNA IgT oligonucleotide sequences were employed in in situ hybridization to detect IgT-expressing cells in sections from lymphoid tissues, and positive cells were observed in head kidney, spleen, intestine and gills. By employing RAIgT1 in quantitative immunohistochemistry, the highest number of IgT-producing cells was observed in the gills (9.5 ± 0.7%), followed by intestine (8.4 ± 1.2%), head kidney (6.2 ± 1.4%), and spleen (4.1 ± 0.7%). Interestingly, the number of IgT-B cells showed a regionalization in the intestine, increasing from the proximal to the terminal part. By immunofluorescence and flow cytometry of live leukocytes, the percentages of RAIgT1 stained cells were 34 ± 11% in the intestine, 22 ± 5% in head kidney, 16 ± 7% in spleen, and 9 ± 5% in gills. At the fluorescence microscope, live cells from these tissues showed a typical membrane-associated positivity and a lymphocytic morphology, and no IgT/IgM double positive cells were detected. Immunoreactive cells have been purified from head kidney using magnetic beads, and IgT-enriched cells showed by RT-PCR an enhanced expression of the IgT gene, whereas IgT-depleted cells had an highest expression of IgM and TRβ genes. These data describe for the first time a quantitative panel of IgT-expressing and IgT-immunoreactive cells in tissues of a teleost fish species.
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Affiliation(s)
- S Picchietti
- Università della Tuscia, Dipartimento per l'Innovazione Biologica, Agroalimentare e Forestale, Viterbo, Italy
| | - N Nuñez-Ortiz
- Università della Tuscia, Dipartimento per l'Innovazione Biologica, Agroalimentare e Forestale, Viterbo, Italy
| | - V Stocchi
- Università della Tuscia, Dipartimento per l'Innovazione Biologica, Agroalimentare e Forestale, Viterbo, Italy
| | - E Randelli
- Università della Tuscia, Dipartimento per l'Innovazione Biologica, Agroalimentare e Forestale, Viterbo, Italy
| | - F Buonocore
- Università della Tuscia, Dipartimento per l'Innovazione Biologica, Agroalimentare e Forestale, Viterbo, Italy
| | - L Guerra
- Università della Tuscia, Dipartimento per l'Innovazione Biologica, Agroalimentare e Forestale, Viterbo, Italy
| | - G Scapigliati
- Università della Tuscia, Dipartimento per l'Innovazione Biologica, Agroalimentare e Forestale, Viterbo, Italy.
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49
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Coyne CP, Narayanan L. Gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R]: molecular design, synthetic organic chemistry reactions, and antineoplastic cytotoxic potency in populations of pulmonary adenocarcinoma (A549). Chem Biol Drug Des 2017; 89:379-399. [PMID: 27561602 PMCID: PMC5396302 DOI: 10.1111/cbdd.12845] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/12/2016] [Accepted: 08/19/2016] [Indexed: 02/06/2023]
Abstract
One molecular-based approach that increases potency and reduces dose-limited sequela is the implementation of selective 'targeted' delivery strategies for conventional small molecular weight chemotherapeutic agents. Descriptions of the molecular design and organic chemistry reactions that are applicable for synthesis of covalent gemcitabine-monophosphate immunochemotherapeutics have to date not been reported. The covalent immunopharmaceutical, gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R] was synthesized by reacting gemcitabine with a carbodiimide reagent to form a gemcitabine carbodiimide phosphate ester intermediate which was subsequently reacted with imidazole to create amine-reactive gemcitabine-(5'-phosphorylimidazolide) intermediate. Monoclonal anti-IGF-1R immunoglobulin was combined with gemcitabine-(5'-phosphorylimidazolide) resulting in the synthetic formation of gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R]. The gemcitabine molar incorporation index for gemcitabine-(5'-phosphoramidate)-[anti-IGF-R1] was 2.67:1. Cytotoxicity Analysis - dramatic increases in antineoplastic cytotoxicity were observed at and between the gemcitabine-equivalent concentrations of 10-9 M and 10-7 M where lethal cancer cell death increased from 0.0% to a 93.1% maximum (100.% to 6.93% residual survival), respectively. Advantages of the organic chemistry reactions in the multistage synthesis scheme for gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R] include their capacity to achieve high chemotherapeutic molar incorporation ratios; option of producing an amine-reactive chemotherapeutic intermediate that can be preserved for future synthesis applications; and non-dedicated organic chemistry reaction scheme that allows substitutions of either or both therapeutic moieties, and molecular delivery platforms.
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Affiliation(s)
- Cody P. Coyne
- Department of Basic SciencesCollege of Veterinary MedicineWise CenterMississippi State UniversityMississippi StateMSUSA
- College of Veterinary MedicineWise CenterMississippi State UniversityMississippi StateMSUSA
| | - Lakshmi Narayanan
- Department of Basic SciencesCollege of Veterinary MedicineWise CenterMississippi State UniversityMississippi StateMSUSA
- College of Veterinary MedicineWise CenterMississippi State UniversityMississippi StateMSUSA
- Present address: Fishery and Wildlife Research CenterMississippi State UniversityLocksley Way 201Mississippi StateMSUSA
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50
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Li C, Zhang Y, Eremin SA, Yakup O, Yao G, Zhang X. Detection of kanamycin and gentamicin residues in animal-derived food using IgY antibody based ic-ELISA and FPIA. Food Chem 2017; 227:48-54. [PMID: 28274457 DOI: 10.1016/j.foodchem.2017.01.058] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/21/2016] [Accepted: 01/13/2017] [Indexed: 11/19/2022]
Abstract
Our aim in this study is to show that IgY antibody based immunoassays could be used to detect antibiotic residues in animal-derived food. Briefly, full antigens of gentamicin (Gent) and kanamycin (Kana) were used to immunize the laying chickens to prepare IgY antibodies. Then, these antibodies were evaluated by FPIA and ic-ELISA to detect Gent/Kana in animal-derived samples. The IC50 of FPIA and ic-ELISA based anti-Gent IgY were 7.70±0.6μg/mL and 0.32±0.06μg/mL, respectively. The IC50 of FPIA and ic-ELISA based anti-Kana IgY were 7.97±0.9μg/mL and 0.15±0.01μg/mL. The limits of detection (LOD, IC10) for FPIA based anti-Gent/Kana IgY were 0.17 and 0.007μg/mL, respectively. The LOD for ic-ELISA were both 0.001μg/mL. These results indicated that the ic-ELISA might more suitable for antibiotic residues detection than FPIA.
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Affiliation(s)
- Cui Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Yaoyao Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 Shaanxi, China
| | - Sergei A Eremin
- Faculty of Chemistry, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; Federal Research Center «Fundamentals of Biotechnology» of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Omar Yakup
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Gang Yao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China
| | - Xiaoying Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 Shaanxi, China; College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China.
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