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Hao S, Cong J, Ma Z, Xia Y, Zhang Y, Tong N, Tian J, Li Y. SPRR1B is Related to the Immune Microenvironment and Can Be Used as a Biomarker for the Diagnosis of Psoriasis. Int J Gen Med 2024; 17:401-418. [PMID: 38333021 PMCID: PMC10849920 DOI: 10.2147/ijgm.s439845] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/21/2024] [Indexed: 02/10/2024] Open
Abstract
Background Psoriasis, a chronic inflammatory disorder with an unknown cause, significantly impacts the physical and psychological well-being of patients. However, current biomarkers related to psoriasis lack clinical specificity, sensitivity, and predictive ability. Methods In this study, we collected skin lesion tissues from 20 psoriasis patients and 20 normal skin samples. Additionally, we obtained four datasets from the GEO database, which included human psoriasis and healthy specimens. We utilized SVM-RFE analysis and the LASSO regression model to identify potential biomarkers. Furthermore, we examined the composition of immune cell types in psoriasis and their correlation with specific genes. Results Our investigation revealed 57 differentially expressed genes (DEGs), and we identified significantly enriched pathways through KEGG pathway analysis. The results of machine learning and WGCNA suggested that LCE3D and SPRR1B could potentially be used as marker genes for diagnosing psoriasis. RT-PCR and immunohistochemical detection confirmed the abnormally high expression of the SPRR1B gene in psoriasis. Analysis of immune cell infiltration revealed a strong positive correlation between SPRR1B and Macrophages M0 and T cells follicular helper, while showing the strongest negative correlation with resting Mast cells. In addition, we found that silencing SPRR1B in IFN-γ-treated HaCat cells could significantly reduce the increase in IL-17, IL-22, KRT6, and KRT16 caused by IFN-γ. Conclusion These findings suggest that SPRR1B may have a significant role in the pathogenesis of psoriasis and could be employed as a novel immunomarker for its development.
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Affiliation(s)
- Siyu Hao
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, People’s Republic of China
| | - Jiuyi Cong
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
| | - Zhiqiang Ma
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, People’s Republic of China
| | - Yan Xia
- Scientific Research Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
| | - Yu Zhang
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
| | - Nannan Tong
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
| | - Jiangtian Tian
- Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, People’s Republic of China
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
| | - Yuzhen Li
- Department of Dermatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
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Matsuda T, Akazawa-Ogawa Y, Komaba LK, Kiyose N, Miyazaki N, Mizuguchi Y, Fukuta T, Ito Y, Hagihara Y. Prediction of antigen-responding VHH antibodies by tracking the evolution of antibody along the time course of immunization. Front Immunol 2024; 14:1335462. [PMID: 38292485 PMCID: PMC10825579 DOI: 10.3389/fimmu.2023.1335462] [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: 11/09/2023] [Accepted: 12/22/2023] [Indexed: 02/01/2024] Open
Abstract
Antibody maturation is the central function of the adaptive immune response. This process is driven by the repetitive selection of mutations that increase the affinity toward antigens. We hypothesized that a precise observation of this process by high-throughput sequencing along the time course of immunization will enable us to predict the antibodies reacting to the immunized antigen without any additional in vitro screening. An alpaca was immunized with IgG fragments using multiple antigen injections, and the antibody repertoire development was traced via high-throughput sequencing periodically for months. The sequences were processed into clusters, and the antibodies in the 16 most abundant clusters were generated to determine whether the clusters included antigen-binding antibodies. The sequences of most antigen-responsive clusters resembled those of germline cells in the early stages. These sequences were observed to accumulate significant mutations and also showed a continuous sequence turnover throughout the experimental period. The foregoing characteristics gave us >80% successful prediction of clusters composed of antigen-responding VHHs against IgG fragment. Furthermore, when the prediction method was applied to the data from other alpaca immunized with epidermal growth factor receptor, the success rate exceeded 80% as well, confirming the general applicability of the prediction method. Superior to previous studies, we identified the immune-responsive but very rare clusters or sequences from the immunized alpaca without any empirical screening data.
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Affiliation(s)
- Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Japan
| | - Yoko Akazawa-Ogawa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Lilian-Kaede Komaba
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda, Japan
| | - Norihiko Kiyose
- Division of Antibody Operations, ARK Resource. Co., Ltd., Kumamoto, Japan
| | - Nobuo Miyazaki
- Division of Antibody Operations, ARK Resource. Co., Ltd., Kumamoto, Japan
| | | | | | - Yuji Ito
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, Japan
| | - Yoshihisa Hagihara
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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Teodori L, Omer M, Kjems J. RNA nanostructures for targeted drug delivery and imaging. RNA Biol 2024; 21:1-19. [PMID: 38555519 PMCID: PMC10984137 DOI: 10.1080/15476286.2024.2328440] [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] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
The RNA molecule plays a pivotal role in many biological processes by relaying genetic information, regulating gene expression, and serving as molecular machines and catalyzers. This inherent versatility of RNA has fueled significant advancements in the field of RNA nanotechnology, driving the engineering of complex nanoscale architectures toward biomedical applications, including targeted drug delivery and bioimaging. RNA polymers, serving as building blocks, offer programmability and predictability of Watson-Crick base pairing, as well as non-canonical base pairing, for the construction of nanostructures with high precision and stoichiometry. Leveraging the ease of chemical modifications to protect the RNA from degradation, researchers have developed highly functional and biocompatible RNA architectures and integrated them into preclinical studies for the delivery of payloads and imaging agents. This review offers an educational introduction to the use of RNA as a biopolymer in the design of multifunctional nanostructures applied to targeted delivery in vivo, summarizing physical and biological barriers along with strategies to overcome them. Furthermore, we highlight the most recent progress in the development of both small and larger RNA nanostructures, with a particular focus on imaging reagents and targeted cancer therapeutics in pre-clinical models and provide insights into the prospects of this rapidly evolving field.
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Affiliation(s)
- Laura Teodori
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
| | - Marjan Omer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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4
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Leal-Lopes C, D'Angelo S, Erasmus MF, Teixeira AAR, Temples G, Zhou J, Bradbury ARM, Ferrara F. High throughput purification of monoclonal recombinant antibodies using a Protein-A coated membrane plate system. N Biotechnol 2023; 77:111-119. [PMID: 37648151 DOI: 10.1016/j.nbt.2023.08.003] [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: 06/27/2023] [Revised: 07/28/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
The therapeutic use of monoclonal antibodies (mAbs) ranges from cancer treatment to immune-mediated conditions, covering infectious and cardiovascular disorders, among others. The development of improved methods for therapeutic antibody discovery has accelerated the identification of numerous mAbs: a discovery campaign can be deeply mined, resulting in hundreds, even thousands, of potential antibody leads for a given target of interest. High throughput mAb expression and purification methods are required for the rapid validation of those leads. In this work, we describe the implementation of a Protein-A coated membrane plate system, the Purexa™ AHT membrane plate, for robust preparative purification of hundreds of recombinant mAbs, without the need for automation. The high efficiency (>80%) recovery generated sufficient mAb for downstream screening analyses such as ELISA and surface plasmon resonance (SPR). This new system allows the functional validation of hundreds of lead antibodies from discovery campaigns in a timely manner regardless of operational size.
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Affiliation(s)
- Camila Leal-Lopes
- New Mexico Consortium, 4200 W. Jemez Rd, Suite 301, Los Alamos, NM 87544, USA
| | - Sara D'Angelo
- Specifica Inc, a Q2 Solution Company, 1607 Alcaldesa Street, Santa Fe, NM 87501, USA
| | - M Frank Erasmus
- Specifica Inc, a Q2 Solution Company, 1607 Alcaldesa Street, Santa Fe, NM 87501, USA
| | - Andre A R Teixeira
- New Mexico Consortium, 4200 W. Jemez Rd, Suite 301, Los Alamos, NM 87544, USA
| | - Graham Temples
- Purilogics, a Donaldson Brand, 900B W Faris Rd., Greenville, SC 29605, USA
| | - Jinxiang Zhou
- Purilogics, a Donaldson Brand, 900B W Faris Rd., Greenville, SC 29605, USA
| | - Andrew R M Bradbury
- Specifica Inc, a Q2 Solution Company, 1607 Alcaldesa Street, Santa Fe, NM 87501, USA.
| | - Fortunato Ferrara
- Specifica Inc, a Q2 Solution Company, 1607 Alcaldesa Street, Santa Fe, NM 87501, USA.
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Diao Z, Wang X, Zhang J, Ge A, Xu T, Kan L, Li Y, Ji Y, Jing X, Xu J, Ma B. Optical-based microbubble for on-demand droplet release from static droplet array (SDA) for dispensing one droplet into one tube. Biosens Bioelectron 2023; 240:115639. [PMID: 37660461 DOI: 10.1016/j.bios.2023.115639] [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: 05/17/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Static droplet array (SDA) is a pivotal tool for high-capacity screening assays, yet extraction and collection the target droplets that contain unique analytes or cells from the SDA remains one major technical bottleneck that limits its broader application. Here we present an optical-based on-demand droplet release (OODR) system by incorporating a 1064 nm laser-responsive indium tin oxide (ITO) layer into a chamber array-based droplet microfluidic chip. By focusing the 1064 nm laser onto the ITO layer, microbubbles can be created via local heating to selectively push-out the droplets from the chamber. Then the released droplet is readily exported in a one-droplet-one-tube (ODOT) manner by the inherent capillary force into pipette tip. Releasing of the droplets containing fluorescein sodium demonstrated ∼100% successful rate (9 out of 6400 droplets were successfully released) and low residual (only ∼5% of the droplet volume remains in the chamber). White or fluorescence image-based releasing of single-cell-droplets directly after cell loading or multi-cells-droplets derived from on-chip single-cell cultivation for both E. coli and yeast cells further demonstrated the wide applicability of OODR. The present system is user-friendly and has the potential to be applied in various high-throughput screening assays, including single molecule/cell analysis, drug screening, and phenotype-based cell sorting.
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Affiliation(s)
- Zhidian Diao
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Xixian Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Jiaping Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Anle Ge
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Lingyan Kan
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yuandong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Qingdao Single-Cell Biotech., Co., Ltd., Qingdao, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China.
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China.
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Lubow J, Levoir LM, Ralph DK, Belmont L, Contreras M, Cartwright-Acar CH, Kikawa C, Kannan S, Davidson E, Duran V, Rebellon-Sanchez DE, Sanz AM, Rosso F, Doranz BJ, Einav S, Matsen IV FA, Goo L. Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses. PLoS Pathog 2023; 19:e1011722. [PMID: 37812640 PMCID: PMC10586629 DOI: 10.1371/journal.ppat.1011722] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 05/17/2023] [Revised: 10/19/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasures that avoid enhancement of infection associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following repeated DENV infections. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies.
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Affiliation(s)
- Jay Lubow
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Lisa M. Levoir
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Duncan K. Ralph
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Laura Belmont
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, United States of America
| | - Maya Contreras
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Catiana H. Cartwright-Acar
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Caroline Kikawa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Medical Scientist Training Program, University of Washington, Seattle, Washington, United States of America
| | - Shruthi Kannan
- Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America
| | - Edgar Davidson
- Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America
| | - Veronica Duran
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Ana M. Sanz
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
| | - Fernando Rosso
- Clinical Research Center, Fundación Valle del Lili, Cali, Colombia
- Department of Internal Medicine, Division of Infectious Diseases, Fundación Valle del Lili, Cali, Colombia
| | - Benjamin J. Doranz
- Integral Molecular, Inc., Philadelphia, Pennsylvania, United States of America
| | - Shirit Einav
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Frederick A. Matsen IV
- Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Leslie Goo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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Zhu J, Kou J, Ma L, Yu X, Li C, Wang Z, Shen J, Wen K, Yu W. Molecular Recognition Mechanism of an Anti-Amatoxins mAb and Its Application in Centrifugal Disk-Based Immunoassay. J Agric Food Chem 2023; 71:13889-13898. [PMID: 37695809 DOI: 10.1021/acs.jafc.3c03442] [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] [Indexed: 09/13/2023]
Abstract
Amatoxins are polypeptides that cause 90% of fatalities from accidental ingestion of poisonous mushrooms. Unfortunately, there are no specific antidotes against amatoxins poisoning, hence preparation of high-affinity antibodies, understanding the receptor (amatoxins) and ligand (antibody) mechanism, and establishing a straightforward screening approach are of great significance for confirming poison agents and clinical diagnosis. Here, anti-amatoxins monoclonal antibody (mAb) 9B2 was prepared and the recognition mechanism was investigated. The approach is useful for designing desirable immunogens, developing new antibodies with improved performance, and constructing effective immunoassays. Based on the mAb, we designed a centrifugal disk-like microfluidics chip and developed a fully automated immunoassay capable of detecting amatoxins poisoning in various samples including serum, urine, and mushrooms. The whole detection process could be automatically accomplished within 30 min, with a limit of detection of 0.08 to 0.12 μg/L for real samples, ∼30-fold more sensitive than conventional enzyme-linked immunosorbent assay (ELISA). Our platform not only provided a practical approach for performing poison agent confirmation and clinical diagnosis but also had important implications for improving the survival of patients with mushroom poisoning.
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Affiliation(s)
- Jianyu Zhu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
- School of Basic Medicine, Beihua University, 132013 Jilin, People's Republic of China
| | - Jiaqian Kou
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Licai Ma
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Xuezhi Yu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Chenglong Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
- College of Veterinary Medicine, Henan Agricultural University, 450002 Zhengzhou, People's Republic of China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Kai Wen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Wenbo Yu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, and Beijing Laboratory for Food Quality and Safety, China Agricultural University, 100193 Beijing, People's Republic of China
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8
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Beal KM, Bandara KR, Ali SR, Sonak RG, Barnes MR, Scarcelli JJ, Zhang L. The impact of expression vector position on transgene transcription allows for rational expression vector design in a targeted integration system. Biotechnol J 2023; 18:e2300038. [PMID: 37272404 DOI: 10.1002/biot.202300038] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/09/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023]
Abstract
Site-specific integration (SSI) technology has emerged as an effective approach by the pharmaceutical industry for the development of recombinant Chinese hamster ovary (CHO) cell lines. While SSI systems have been demonstrated to be effective for the development of CHO cell lines, they can be limiting in terms of both transgene expression and in the case of multi-specifics, the ability to generate the correct product of interest. To maximize the performance of Pfizer's dual SSI expression system for expressing monoclonal and multi-specific antibodies, we used a novel approach to investigate the positional effect of transgenes within expression vectors by engineering nucleotide polymorphisms (NP)s to use as biomarkers to track the level of transcript output from each expression vector position. We observed differences in transcript level for two different transgenes across all four expression vector positions interrogated. We then applied these learnings to rationally design expression vectors for six different mAbs and a multi-specific antibody. We showed enhanced productivity and optimal product quality when compared to a conventional expression vector topology. The learnings gained here can potentially aid in the determination of optimal vector topologies for several IgG-like multi-specific formats.
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Affiliation(s)
- Kathryn M Beal
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Kalpanie R Bandara
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Syed R Ali
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Renuka G Sonak
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Michael R Barnes
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - John J Scarcelli
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
| | - Lin Zhang
- Cell Line Development, Bioprocess R&D, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Andover, Massachusetts, USA
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9
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Huang X, Meng H, Shou Z, Yu J, Hu K, Chen L, Zhou H, Bai Z, Chen C. Identification of basement membrane-related biomarkers associated with the diagnosis of osteoarthritis based on machine learning. BMC Med Genomics 2023; 16:198. [PMID: 37612746 PMCID: PMC10464276 DOI: 10.1186/s12920-023-01601-z] [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: 01/09/2023] [Accepted: 07/05/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Osteoarthritis is a very common clinical disease in middle-aged and elderly individuals, and with the advent of ageing, the incidence of this disease is gradually increasing. There are few studies on the role of basement membrane (BM)-related genes in OA. METHOD We used bioinformatics and machine learning methods to identify important genes related to BMs in OA patients and performed immune infiltration analysis, lncRNA‒miRNA-mRNA network prediction, ROC analysis, and qRT‒PCR. RESULT Based on the results of machine learning, we determined that LAMA2 and NID2 were the key diagnostic genes of OA, which were confirmed by ROC and qRT‒PCR analyses. Immune analysis showed that LAMA2 and NID2 were closely related to resting memory CD4 T cells, mast cells and plasma cells. Two lncRNAs, XIST and TTTY15, were simultaneously identified, and lncRNA‒miRNA‒mRNA network prediction was performed. CONCLUSION LAMA2 and NID2 are important potential targets for the diagnosis and treatment of OA.
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Affiliation(s)
- Xiaojing Huang
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Hongming Meng
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Zeyu Shou
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Jiahuan Yu
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Kai Hu
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Liangyan Chen
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Han Zhou
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China
| | - Zhibiao Bai
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China.
| | - Chun Chen
- Department of Orthopedics, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China.
- Wenzhou Medical University, Wenzhou City, 325000, Zhejiang Province, China.
- Key Laboratory of Intelligent Treatment and Life Support for Critical Diseases of Zhejiang Province, Wenzhou, 325000, Zhejiang, China.
- Zhejiang Engineering Research Center for Hospital Emergency and Process Digitization, Wenzhou, 325000, Zhejiang, China.
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10
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Oksanen S, Saarinen R, Korkiakoski A, Lamminmäki U, Huovinen T. Genotyped functional screening of soluble Fab clones enables in-depth analysis of mutation effects. Sci Rep 2023; 13:13107. [PMID: 37567990 PMCID: PMC10421887 DOI: 10.1038/s41598-023-40241-2] [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: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Monoclonal antibodies (mAbs) and their fragments are widely used in therapeutics, diagnostics and basic research. Although display methods such as phage display offer high-throughput, affinities of individual antibodies need to be accurately measured in soluble format. We have developed a screening platform capable of providing genotyped functional data from a total of 9216 soluble, individual antigen binding fragment (Fab) clones by employing next-generation sequencing (NGS) with hierarchical indexing. Full-length, paired variable domain sequences (VL-VH) are linked to functional screening data, enabling in-depth analysis of mutation effects. The platform was applied to four phage display-selected scFv/Fab screening projects and one site-saturation VH affinity maturation project. Genotyped functional screening simultaneously enabled the identification of affinity improving mutations in the VH domain of Fab 49A3 recognizing Dengue virus non-structural protein 1 (NS1) serotype 2 and informed on VH residue positions which cannot be changed from wild-type without decreasing the affinity. Genotype-based identification revealed to us the extent of intraclonal signal variance inherent to single point screening data, a phenomenon often overlooked in the field. Moreover, genotyped screening eliminated the redundant selection of identical genotypes for further study and provided a new analysis tool to evaluate the success of phage display selections and remaining clonal diversity in the screened repertoires.
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Affiliation(s)
- Sami Oksanen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
| | - Roope Saarinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | | | - Urpo Lamminmäki
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
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11
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Robinson JP, Ostafe R, Iyengar SN, Rajwa B, Fischer R. Flow Cytometry: The Next Revolution. Cells 2023; 12:1875. [PMID: 37508539 PMCID: PMC10378642 DOI: 10.3390/cells12141875] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Unmasking the subtleties of the immune system requires both a comprehensive knowledge base and the ability to interrogate that system with intimate sensitivity. That task, to a considerable extent, has been handled by an iterative expansion in flow cytometry methods, both in technological capability and also in accompanying advances in informatics. As the field of fluorescence-based cytomics matured, it reached a technological barrier at around 30 parameter analyses, which stalled the field until spectral flow cytometry created a fundamental transformation that will likely lead to the potential of 100 simultaneous parameter analyses within a few years. The simultaneous advance in informatics has now become a watershed moment for the field as it competes with mature systematic approaches such as genomics and proteomics, allowing cytomics to take a seat at the multi-omics table. In addition, recent technological advances try to combine the speed of flow systems with other detection methods, in addition to fluorescence alone, which will make flow-based instruments even more indispensable in any biological laboratory. This paper outlines current approaches in cell analysis and detection methods, discusses traditional and microfluidic sorting approaches as well as next-generation instruments, and provides an early look at future opportunities that are likely to arise.
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Affiliation(s)
- J Paul Robinson
- Department of Basic Medical Sciences, Purdue University, West Lafayette, IN 47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Raluca Ostafe
- Molecular Evolution, Protein Engineering and Production Facility (PI4D), Purdue University, West Lafayette, IN 47907, USA
| | | | - Bartek Rajwa
- Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Rainer Fischer
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Diseases, Purdue University, West Lafayette, IN 47907, USA
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12
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Bao Y, Lu W. Targeting cerebral diseases with enhanced delivery of therapeutic proteins across the blood-brain barrier. Expert Opin Drug Deliv 2023; 20:1681-1698. [PMID: 36945117 DOI: 10.1080/17425247.2023.2193390] [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: 01/14/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]
Abstract
INTRODUCTION Cerebral diseases have been threatening public physical and psychological health in the recent years. With the existence of the blood-brain barrier (BBB), it is particularly hard for therapeutic proteins like peptides, enzymes, antibodies, etc. to enter the central nervous system (CNS) and function in diagnosis and treatment in cerebral diseases. Fortunately, the past decade has witnessed some emerging strategies of delivering macromolecular therapeutic proteins across the BBB. AREAS COVERED Based on the structure, functions, and substances transport mechanisms, various enhanced delivery strategies of therapeutic proteins were reviewed, categorized by molecule-mediated delivery strategies, carrier-mediated delivery strategies, and other delivery strategies. EXPERT OPINION As for molecule-mediated delivery strategies, development of genetic engineering technology, optimization of protein expression and purification techniques, and mature of quality control systems all help to realize large-scale production of recombinant antibodies, making it possible to apply to the clinical practice. In terms of carrier-mediated delivery strategies and others, although nano-carriers/adeno-associated virus (AAV) are also promising candidates for delivering therapeutic proteins or genes across the BBB, some issues still remain to be further investigated, including safety concerns related to applied materials, large-scale production costs, quality control standards, combination therapies with auxiliary delivery strategies like focused ultrasound, etc.
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Affiliation(s)
- Yanning Bao
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education, Shanghai, China
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education, Shanghai, China
- Shanghai Engineering Technology Research Center for Pharmaceutical Intelligent Equipment, and Shanghai Frontiers Science Center for Druggability of Cardiovascular non-coding RNA, Institute for Frontier Medical Technology, Shanghai University of Engineering Science, Shanghai, China
- Department of Research and Development, Shanghai Tayzen PharmLab Co., Ltd. Lingang of Shanghai, China
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13
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Wang Y, Huang J, Zhang J, Wang F, Tang X. Identifying biomarkers associated with the diagnosis of ulcerative colitis via bioinformatics and machine learning. Math Biosci Eng 2023; 20:10741-10756. [PMID: 37322958 DOI: 10.3934/mbe.2023476] [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] [Indexed: 06/17/2023]
Abstract
BACKGROUND Ulcerative colitis (UC) is an idiopathic inflammatory disease with an increasing incidence. This study aimed to identify potential UC biomarkers and associated immune infiltration characteristics. METHODS Two datasets (GSE87473 and GSE92415) were merged to obtain 193 UC samples and 42 normal samples. Using R, differentially expressed genes (DEGs) between UC and normal samples were filtered out, and their biological functions were investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. Promising biomarkers were identified using least absolute shrinkage selector operator regression and support vector machine recursive feature elimination, and their diagnostic efficacy was evaluated through receiver operating characteristic (ROC) curves. Finally, CIBERSORT was used to investigate the immune infiltration characteristics in UC, and the relationship between the identified biomarkers and various immune cells was examined. RESULTS We found 102 DEGs, of which 64 were significantly upregulated, and 38 were significantly downregulated. The DEGs were enriched in pathways associated with interleukin-17, cytokine-cytokine receptor interaction and viral protein interactions with cytokines and cytokine receptors, among others. Using machine learning methods and ROC tests, we confirmed DUOX2, DMBT1, CYP2B7P, PITX2 and DEFB1 to be essential diagnostic genes for UC. Immune cell infiltration analysis revealed that all five diagnostic genes were correlated with regulatory T cells, CD8 T cells, activated and resting memory CD4 T cells, activated natural killer cells, neutrophils, activated and resting mast cells, activated and resting dendritic cells and M0, M1 and M2 macrophages. CONCLUSIONS DUOX2, DMBT1, CYP2B7P, PITX2 and DEFB1 were identified as prospective biomarkers for UC. A new perspective on understanding the progression of UC may be provided by these biomarkers and their relationship with immune cell infiltration.
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Affiliation(s)
- Yuedan Wang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Jinke Huang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Jiaqi Zhang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Fengyun Wang
- Institute of Digestive Diseases, Xiyuan Hospital of China Academy of Chinese Medical Sciences, Beijing 100091, China
| | - Xudong Tang
- China Academy of Chinese Medical Sciences, Beijing 100091, China
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14
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Lubow J, Levoir LM, Ralph DK, Belmont L, Contreras M, Cartwright-Acar CH, Kikawa C, Kannan S, Davidson E, Doranz BJ, Duran V, Sanchez DE, Sanz AM, Rosso F, Einav S, Matsen FA, Goo L. Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses. bioRxiv 2023:2023.04.09.536175. [PMID: 37090561 PMCID: PMC10120628 DOI: 10.1101/2023.04.09.536175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasure strategies that avoid infection enhancement associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following secondary DENV infection. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies.
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15
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Xiao X, Wan Z, Liu X, Chen H, Zhao X, Ding R, Cao Y, Zhou F, Qiu E, Liang W, Ou J, Chen Y, Chen X, Zhang H. Screening of Therapeutic Targets for Pancreatic Cancer by Bioinformatics Methods. Horm Metab Res 2023. [PMID: 36599457 DOI: 10.1055/a-2007-2715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Pancreatic cancer (PC) has the lowest survival rate and the highest mortality rate among all cancers due to lack of effective treatments. The objective of the current study was to identify potential therapeutic targets in PC. Three transcriptome datasets, namely GSE62452, GSE46234, and GSE101448, were analyzed for differentially expressed genes (DEGs) between cancer and normal samples. Several bioinformatics methods, including functional analysis, pathway enrichment, hub genes, and drugs were used to screen therapeutic targets for PC. Fisher's exact test was used to analyze functional enrichments. To screen DEGs, the paired t-test was employed. The statistical significance was considered at p <0.05. Overall, 60 DEGs were detected. Functional enrichment analysis revealed enrichment of the DEGs in "multicellular organismal process", "metabolic process", "cell communication", and "enzyme regulator activity". Pathway analysis demonstrated that the DEGs were primarily related to "Glycolipid metabolism", "ECM-receptor interaction", and "pathways in cancer". Five hub genes were examined using the protein-protein interaction (PPI) network. Among these hub genes, 10 known drugs targeted to the CPA1 gene and CLPS gene were found. Overall, CPA1 and CLPS genes, as well as candidate drugs, may be useful for PC in the future.
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Affiliation(s)
- Xiaojie Xiao
- Department of Oncology and Vascular Interventional Radiology, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Zheng Wan
- Department of Oncology and Vascular Interventional Radiology, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Xinmei Liu
- Animal and Plant Inspection and Quarantine Technology Center Shenzhen Customs, Shenzhen Haiguan, Shenzhen, China
| | - Huaying Chen
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Xiaoyan Zhao
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Rui Ding
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Yajun Cao
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Fangyuan Zhou
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Enqi Qiu
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Wenrong Liang
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Juanjuan Ou
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Yifeng Chen
- Zhongshan Hospital of Xiamen University, Zhongshan Hospital Xiamen University, Xiamen, China
| | - Xueting Chen
- Wanbei Coal and Electricity Group General Hospital, Suzhou, China
| | - Hongjian Zhang
- Department of Oncology and Vascular Interventional Radiology, Zhongshan Hospital Xiamen University, Xiamen, China
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16
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Agrafiotis A, Neumeier D, Hong KL, Chowdhury T, Ehling R, Kuhn R, Sandu I, Kreiner V, Cotet TS, Shlesinger D, Laslo D, Anzböck S, Starkie D, Lightwood DJ, Oxenius A, Reddy ST, Yermanos A. Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen specificity. iScience 2023; 26:106055. [PMID: 36852274 DOI: 10.1016/j.isci.2023.106055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/07/2022] [Accepted: 01/20/2023] [Indexed: 01/26/2023] Open
Abstract
Although new genomics-based pipelines have potential to augment antibody discovery, these methods remain in their infancy due to an incomplete understanding of the selection process that governs B cell clonal selection, expansion, and antigen specificity. Furthermore, it remains unknown how factors such as aging and reduction of tolerance influence B cell selection. Here we perform single-cell sequencing of antibody repertoires and transcriptomes of murine B cells following immunizations with a model therapeutic antigen target. We determine the relationship between antibody repertoires, gene expression signatures, and antigen specificity across 100,000 B cells. Recombinant expression and characterization of 227 monoclonal antibodies revealed the existence of clonally expanded and class-switched antigen-specific B cells that were more frequent in young mice. Although integrating multiple repertoire features such as germline gene usage and transcriptional signatures failed to distinguish antigen-specific from nonspecific B cells, other features such as immunoglobulin G (IgG) subtype and sequence composition correlated with antigen specificity.
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17
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Abstract
Therapeutic peptides have revolutionized treatment for a number of human diseases. In particular, the past two decades have witnessed rapid progress of stapled helical peptides in drug discovery. Stapled helical peptides are chemically modified and constrained in their bioactive α-helical conformation. Compared to unstabilized linear peptides, stapled helical peptides exhibit superior binding affinity and selectivity, enhanced membrane permeability, and improved metabolic stability, presenting exciting promise for targeting otherwise challenging protein-protein interfaces. In this Perspective, we summarize recent applications of high-throughput screening technologies for identification of potent stapled helical peptides with optimized binding properties. We expect to provide a broad reference to accelerate the development of stapled helical peptides as the next generation of therapeutic peptides for various human diseases.
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Affiliation(s)
- Yiwei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiabei Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Zhenghua Zhang
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Fenghua Kang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
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18
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Chu HW, Chang KP, Yen WC, Liu HP, Chan XY, Liu CR, Hung CM, Wu CC. Identification of salivary autoantibodies as biomarkers of oral cancer with immunoglobulin A enrichment combined with affinity mass spectrometry. Proteomics 2023; 23:e2200321. [PMID: 36625099 DOI: 10.1002/pmic.202200321] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
Globally, oral cavity squamous cell carcinoma (OSCC) is one of the most common fatal illnesses. Its high mortality is ascribed to the fact that the disease is often diagnosed at a late stage, which indicates an urgent need for approaches for the early detection of OSCC. The use of salivary autoantibodies (autoAbs) as OSCC biomarkers has numerous advantages such as easy access to saliva samples and efficient detection of autoAbs using well-established secondary reagents. To improve OSCC screening, we identified OSCC-associated autoAbs with the enrichment of salivary autoAbs combined with affinity mass spectrometry (MS). The salivary IgA of healthy individuals and OSCC patients was purified with peptide M-conjugated beads and then applied to immunoprecipitated antigens (Ags) in OSCC cells. Using tandem MS analysis and spectral counting-based quantitation, the level of 10 Ags increased in the OSCC group compared with the control group. Moreover, salivary levels of autoAbs to the 10 Ags were determined by a multiplexed bead-based immunoassay. Among them, seven were significantly higher in early-stage OSCC patients than in healthy individuals. A marker panel consisting of autoAbs to LMAN2, PTGR1, RAB13, and UQCRC2 was further developed to improve the early diagnosis of OSCC.
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Affiliation(s)
- Hao-Wei Chu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kai-Ping Chang
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Chen Yen
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hao-Ping Liu
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Xiu-Ya Chan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chiao-Rou Liu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chu-Mi Hung
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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19
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Fahad AS, Madan B, DeKosky BJ. Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery. Methods Mol Biol 2023; 2552:447-463. [PMID: 36346608 DOI: 10.1007/978-1-0716-2609-2_25] [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: 06/16/2023]
Abstract
Next-generation DNA sequencing (NGS) of human antibody repertoires has been extensively implemented to discover novel antibody drugs, to analyze B-cell developmental features, and to investigate antibody responses to infectious diseases and vaccination. Because the antibody repertoire encoded by human B cells is highly diverse, NGS analyses of antibody genes have provided a new window into understanding antibody responses for basic immunology, biopharmaceutical drug discovery, and immunotherapy. However, many antibody discovery protocols analyze the heavy and light chains separately due to the short-read nature of most NGS technologies, whereas paired heavy and light chain data are required for complete antibody characterization. Here, we describe a computational workflow to process millions of paired antibody heavy and light chain DNA sequence reads using the Illumina MiSeq 2x300 NGS platform. In this workflow, we describe raw NGS read processing and initial quality filtering, the annotation and assembly of antibody clonotypes relating to paired heavy and light chain antibody lineages, and the generation of complete heavy+light consensus sequences for the downstream cloning and expression of human antibody proteins.
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Affiliation(s)
- Ahmed S Fahad
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Bharat Madan
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Brandon J DeKosky
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, USA.
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20
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Yanakieva D, Vollmer L, Kumar S, Becker S, Toleikis L, Pekar L, Kolmar H, Zielonka S, Krah S. One-Pot Droplet RT-OE-PCR for the Generation of Natively Paired Antibody Immune Libraries. Methods Mol Biol 2023; 2681:213-229. [PMID: 37405650 DOI: 10.1007/978-1-0716-3279-6_12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Classical yeast surface display (YSD) antibody immune libraries are generated by a separate amplification of heavy- and light-chain antibody variable regions (VH and VL, respectively) and subsequent random recombination during the molecular cloning procedure. However, each B cell receptor comprises a unique VH-VL combination, which has been selected and affinity matured in vivo for optimal stability and antigen binding. Thus, the native variable chain pairing is important for the functioning and biophysical properties of the respective antibody. Herein, we present a method for the amplification of cognate VH-VL sequences, compatible with both next-generation sequencing (NGS) and YSD library cloning. We employ a single B cell encapsulation in water-in-oil droplets, followed by a one-pot reverse transcription overlap extension PCR (RT-OE-PCR), resulting in a paired VH-VL repertoire from more than a million B cells in a single day.
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Affiliation(s)
- Desislava Yanakieva
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lena Vollmer
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Satyendra Kumar
- Protein Engineering and Antibody Technologies (PEAT), EMD Serono Research and Development Institute, Billerica, MA, USA
| | - Stefan Becker
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany.
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21
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Massey OW, Suphioglu C. Taking a Breather: Advances in Interleukin 5 Inhibition for Asthma Relief. Int J Mol Sci 2022; 23:ijms231911166. [PMID: 36232470 PMCID: PMC9569507 DOI: 10.3390/ijms231911166] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
Interleukin 5 (IL-5) is a major cytokine responsible for eosinophil proliferation, migration and degranulation. Eosinophils play a considerable role in the manifestation of type 2 asthma, and therefore this makes IL-5 a unique and clinically important target for therapeutic intervention. Due to the critical role that IL-5 plays in all areas of eosinophil activity, it has been identified and targeted by three therapeutics, Mepolizumab, Benralizumab and Reslizumab. This review describes the IL-5 pathway and presents the clinical trial history of the three IL-5 inhibitors, to provide insight into the role of IL-5 in clinical asthma presentation. Additionally, this review aims to foster further investigation into the IL-5 pathway by describing current novel therapeutic discovery strategies with monoclonal antibodies.
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Affiliation(s)
- Oliver William Massey
- NeuroAllergy Research Laboratory (NARL), School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
| | - Cenk Suphioglu
- NeuroAllergy Research Laboratory (NARL), School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, 75 Pigdons Road, Geelong, VIC 3216, Australia
- Correspondence:
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22
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Song C, Pan W, Brown B, Tang C, Huang Y, Chen H, Peng N, Wang Z, Weber D, Byrne-Steele M, Wu H, Liu H, Deng Y, He N, Li S. Immune repertoire analysis of normal Chinese donors at different ages. Cell Prolif 2022; 55:e13311. [PMID: 35929064 DOI: 10.1111/cpr.13311] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES This study investigated the characteristics of the immune repertoire in normal Chinese individuals of different ages. MATERIALS AND METHODS In this study, all seven receptor chains from both B and T cells in peripheral blood of 16 normal Chinese individuals from two age groups were analyzed using high-throughput sequencing and dimer-avoided multiplex PCR amplification. Normal in this study is defined as no chronic, infectious or autoimmune disease within 6 months prior to blood draw. RESULTS We found that compared with the younger group, the clonal expression of T-cell receptor repertoire increased in the older group, while diversity decreased. In addition, we found that the T-cell receptor repertoire was more significantly affected by age than the B-cell receptor repertoire, including significant differences in the use of the unique TCR-alpha and TCR-beta V-J gene combinations, in the two groups of normal participants. We further analyzed the degree of complementarity determining region 3 sequence sharing between the two groups, and found shared TCR-alpha, TCR-gamma, immunoglobulin-kappa and immunoglobulin-lambda chain complementarity determining region 3 sequences in all subjects. CONCLUSION Taken together, our study gives us a better understanding of the immune repertoire of different normal Chinese people, and these results can be applied to the treatment of age-related diseases. Immune repertoire analysis also allows us to observe participant's wellness, aiding in early-stage diagnosis.
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Affiliation(s)
- Cailing Song
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,Nanjing ARP Biotechnology Co., Ltd., Nanjing, China
| | | | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd., Nanjing, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Houao Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Nan Peng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Zhe Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,Guangdong Provincial Hospital of Chinese Medicine & Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | | | | | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Hunan Key Laboratory of Medical Epigenomics, Central South University, Changsha, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,Nanjing ARP Biotechnology Co., Ltd., Nanjing, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
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23
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Zhang K, Tang Y, Chen Q, Liu Y. The Screening of Therapeutic Peptides for Anti-Inflammation through Phage Display Technology. Int J Mol Sci 2022; 23:8554. [PMID: 35955688 PMCID: PMC9368796 DOI: 10.3390/ijms23158554] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
For the treatment of inflammatory illnesses such as rheumatoid arthritis and carditis, as well as cancer, several anti-inflammatory medications have been created over the years to lower the concentrations of inflammatory mediators in the body. Peptides are a class of medication with the advantages of weak immunogenicity and strong activity, and the phage display technique is an effective method for screening various therapeutic peptides, with a high affinity and selectivity, including anti-inflammation peptides. It enables the selection of high-affinity target-binding peptides from a complex pool of billions of peptides displayed on phages in a combinatorial library. In this review, we will discuss the regular process of using phage display technology to screen therapeutic peptides, and the peptides screened for anti-inflammation properties in recent years according to the target. We will describe how these peptides were screened and how they worked in vitro and in vivo. We will also discuss the current challenges and future outlook of using phage display to obtain anti-inflammatory therapeutic peptides.
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24
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Gao B, Han J, Reddy ST. Learning what not to select for in antibody drug discovery. Cell Rep Methods 2022; 2:100258. [PMID: 35880020 PMCID: PMC9308151 DOI: 10.1016/j.crmeth.2022.100258] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Identifying antibodies with high affinity and target specificity is crucial for drug discovery and development; however, filtering out antibody candidates with nonspecific or polyspecific binding profiles is also important. In this issue of Cell Reports Methods, Saksena et al. report a computational counterselection method combining deep sequencing and machine learning for identifying nonspecific antibody candidates and demonstrate that it has advantages over more established molecular counterselection methods.
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Affiliation(s)
- Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
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25
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Liang Y, Lin F, Huang Y. Identification of Biomarkers Associated with Diagnosis of Osteoarthritis Patients Based on Bioinformatics and Machine Learning. J Immunol Res 2022; 2022:5600190. [PMID: 35733917 DOI: 10.1155/2022/5600190] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 11/17/2022] Open
Abstract
Osteoarthritis (OA) is thought to be the most prevalent chronic joint disease. The incidence of OA is rising because of the ageing population and the epidemic of obesity. This research was designed for the identification of novel diagnostic biomarkers for OA and analyzing the possible association between critical genes and infiltrated immune cells. 10 OA samples from patients with spinal OA and 10 normal samples were collected. GSE55235 and GSE55457 datasets including human OA and normal samples were downloaded from the GEO datasets. Differentially expressed genes (DEGs) were identified between 20 OA and 20 controls. SVM-RFE analysis and LASSO regression model were carried out to screen possible markers. The compositional patterns of the 22 types of immune cell fraction in OA were determined by the use of CIBERSORT. The expression level of the biomarkers in OA was examined by the use of RT-PCR. In this study, an overall 44 DEGs were identified: 18 genes were remarkably upregulated and 26 genes were distinctly downregulated. KEGG pathway analyses revealed that pathways were significantly enriched including IL-17 signal path, rheumatoid arthritis, TNF signal path, and lipid and atherosclerosis. Based on the results of machine learning, we identified APOLD1 and EPYC as critical diagnostic genes in OA, which were further confirmed using ROC assays. Immune cell infiltration analysis revealed that APOLD1 was correlated with mastocytes stimulated, NK cells resting, T cells CD4 memory resting, DCs stimulated, T cells gamma delta, macrophages M0, NK cells stimulated, and mastocytes resting. Moreover, we found that EPYC was correlated with mastocytes stimulated, NK cells resting, T cells CD4 memory resting, DCs stimulated, T cells gamma delta, macrophages M0, NK cells stimulated, and mastocytes resting. Overall, our findings might provide some novel clue for the exploration of novel markers for OA diagnosis. The critical genes and their associations with immune infiltration may offer new insight into understanding OA developments.
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26
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Merkuleva YA, Shcherbakov DN, Ilyichev AA. Methods to Produce Monoclonal Antibodies for the Prevention and Treatment of Viral Infections. Russ J Bioorg Chem 2022; 48:256-272. [PMID: 35637780 PMCID: PMC9134727 DOI: 10.1134/s1068162022020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 11/23/2022]
Abstract
A viral threat can arise suddenly and quickly turn into a major epidemic or pandemic. In such a case, it is necessary to develop effective means of therapy and prevention in a short time. Vaccine development takes decades, and the use of antiviral compounds is often ineffective and unsafe. A quick response may be the use of convalescent plasma, but a number of difficulties associated with it forced researchers to switch to the development of safer and more effective drugs based on monoclonal antibodies (mAbs). In order to provide protection, such drugs must have a key characteristic-neutralizing properties, i.e., the ability to block viral infection. Currently, there are several approaches to produce mAbs in the researchers' toolkit, however, none of them may serve as a gold standard. Each approach has its own advantages and disadvantages. The choice of the method depends both on the characteristics of the virus and on time constraints and technical challenges. This review provides a comparative analysis of modern methods to produce neutralizing mAbs and describes current trends in the design of antibodies for therapy and prevention of viral diseases.
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Affiliation(s)
- Yu. A. Merkuleva
- Vector State Research Center of Virology and Biotechnology, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program for the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk oblast Russia
| | - D. N. Shcherbakov
- Vector State Research Center of Virology and Biotechnology, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program for the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk oblast Russia
| | - A. A. Ilyichev
- Vector State Research Center of Virology and Biotechnology, Rospotrebnadzor, World-Class Genomic Research Center for Biological Safety and Technological Independence, Federal Scientific and Technical Program for the Development of Genetic Technologies, 630559 Koltsovo, Novosibirsk oblast Russia
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27
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de Rutte J, Dimatteo R, Archang MM, van Zee M, Koo D, Lee S, Sharrow AC, Krohl PJ, Mellody M, Zhu S, Eichenbaum JV, Kizerwetter M, Udani S, Ha K, Willson RC, Bertozzi AL, Spangler J, Damoiseaux R, Di Carlo D. Suspendable Hydrogel Nanovials for Massively Parallel Single-Cell Functional Analysis and Sorting. ACS Nano 2022; 16:7242-7257. [PMID: 35324146 PMCID: PMC9869715 DOI: 10.1021/acsnano.1c11420] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [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] [Indexed: 05/26/2023]
Abstract
Techniques to analyze and sort single cells based on functional outputs, such as secreted products, have the potential to transform our understanding of cellular biology as well as accelerate the development of next-generation cell and antibody therapies. However, secreted molecules rapidly diffuse away from cells, and analysis of these products requires specialized equipment and expertise to compartmentalize individual cells and capture their secretions. Herein, we describe methods to fabricate hydrogel-based chemically functionalized microcontainers, which we call nanovials, and demonstrate their use for sorting single viable cells based on their secreted products at high-throughput using only commonly accessible laboratory infrastructure. These nanovials act as solid supports that facilitate attachment of a variety of adherent and suspension cell types, partition uniform aqueous compartments, and capture secreted proteins. Solutions can be exchanged around nanovials to perform fluorescence immunoassays on secreted proteins. Using this platform and commercial flow sorters, we demonstrate high-throughput screening of stably and transiently transfected producer cells based on relative IgG production. Chinese hamster ovary cells sorted based on IgG production regrew and maintained a high secretion phenotype over at least a week, yielding >40% increase in bulk IgG production rates. We also sorted hybridomas and B lymphocytes based on antigen-specific antibody production. Hybridoma cells secreting an antihen egg lysozyme antibody were recovered from background cells, enriching a population of ∼4% prevalence to >90% following sorting. Leveraging the high-speed sorting capabilities of standard sorters, we sorted >1 million events in <1 h. IgG secreting mouse B cells were also sorted and enriched based on antigen-specific binding. Successful sorting of antibody-secreting B cells combined with the ability to perform single-cell RT-PCR to recover sequence information suggests the potential to perform antibody discovery workflows. The reported nanovials can be easily stored and distributed among researchers, democratizing access to high-throughput functional cell screening.
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Affiliation(s)
- Joseph de Rutte
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- Partillion Bioscience Corporation, Los Angeles, CA 90095, USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Maani M. Archang
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Mark van Zee
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Doyeon Koo
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Sohyung Lee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Allison C. Sharrow
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Patrick J. Krohl
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Michael Mellody
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Sheldon Zhu
- Partillion Bioscience Corporation, Los Angeles, CA 90095, USA
| | - James V. Eichenbaum
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Monika Kizerwetter
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Shreya Udani
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
| | - Kyung Ha
- Department of Mathematics, University of California, Los Angeles, CA 90095, USA
| | - Richard C. Willson
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Andrea L. Bertozzi
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA
- Department of Mathematics, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Jamie Spangler
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Robert Damoiseaux
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA 90095, USA
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28
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Herbig M, Isozaki A, Di Carlo D, Guck J, Nitta N, Damoiseaux R, Kamikawaji S, Suyama E, Shintaku H, Wu AR, Nikaido I, Goda K. Best practices for reporting throughput in biomedical research. Nat Methods 2022; 19:633-634. [PMID: 35508736 DOI: 10.1038/s41592-022-01483-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Maik Herbig
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Mechanical Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jochen Guck
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | | | - Robert Damoiseaux
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Molecular and Medicinal Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Eigo Suyama
- Chugai Pharmaceutical Co., Ltd., Tokyo, Japan
| | | | - Angela Ruohao Wu
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China.,Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Itoshi Nikaido
- RIKEN Center for Biosystems Dynamics Research, Saitama, Japan.,Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Graduate School of Science and Technology, University of Tsukuba, Saitama, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan. .,Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA. .,Institute of Technological Sciences, Wuhan University, Wuhan, China.
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29
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Abstract
The need to consider an antibody's "developability" (immunogenicity, solubility, specificity, stability, manufacturability, and storability) is now well understood in therapeutic antibody design. Predicting these properties rapidly and inexpensively is critical to industrial workflows, to avoid devoting resources to non-productive candidates. Here, we describe a high-throughput computational developability assessment tool, the Therapeutic Antibody Profiler (TAP), which assesses the physicochemical "druglikeness" of an antibody candidate. Input variable domain sequences are converted to three-dimensional structural models, and then five developability-linked molecular surface descriptors are calculated and compared to advanced-stage clinical therapeutics. Values at the extremes of/outside of the distributions seen in therapeutics imply an increased risk of developability issues. Therefore, TAP, starting only from sequence information, provides a route to rapidly identifying drug candidate antibodies that are likely to have poor developability. Our web application ( opig.stats.ox.ac.uk/webapps/tap ) profiles input antibody sequences against a continually updated reference set of clinical therapeutics.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK.
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30
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Neumeier D, Pedrioli A, Genovese A, Sandu I, Ehling R, Hong KL, Papadopoulou C, Agrafiotis A, Kuhn R, Shlesinger D, Robbiani D, Han J, Hauri L, Csepregi L, Greiff V, Merkler D, Reddy ST, Oxenius A, Yermanos A. Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single-cell analysis. Eur J Immunol 2021; 52:297-311. [PMID: 34727578 PMCID: PMC9299196 DOI: 10.1002/eji.202149331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/02/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
Plasma cells and their secreted antibodies play a central role in the long-term protection against chronic viral infection. However, due to experimental limitations, a comprehensive description of linked genotypic, phenotypic, and antibody repertoire features of plasma cells (gene expression, clonal frequency, virus specificity, and affinity) has been challenging to obtain. To address this, we performed single-cell transcriptome and antibody repertoire sequencing of the murine BM plasma cell population following chronic lymphocytic choriomeningitis virus infection. Our single-cell sequencing approach recovered full-length and paired heavy- and light-chain sequence information for thousands of plasma cells and enabled us to perform recombinant antibody expression and specificity screening. Antibody repertoire analysis revealed that, relative to protein immunization, chronic infection led to increased levels of clonal expansion, class-switching, and somatic variants. Furthermore, antibodies from the highly expanded and class-switched (IgG) plasma cells were found to be specific for multiple viral antigens and a subset of clones exhibited cross-reactivity to nonviral and autoantigens. Integrating single-cell transcriptome data with antibody specificity suggested that plasma cell transcriptional phenotype was correlated to viral antigen specificity. Our findings demonstrate that chronic viral infection can induce and sustain plasma cell clonal expansion, combined with significant somatic hypermutation, and can generate cross-reactive antibodies.
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Affiliation(s)
- Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | - Ioana Sandu
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Roy Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Chrysa Papadopoulou
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Raphael Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Damiano Robbiani
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Laura Hauri
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Doron Merkler
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.,Division of Clinical Pathology, Geneva University Hospital, Geneva, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland.,Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
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31
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Mullen TE, Abdullah R, Boucher J, Brousseau AS, Dasuri NK, Ditto NT, Doucette AM, Emery C, Gabriel J, Greamo B, Patil KS, Rothenberger K, Stolte J, Souders CA. Accelerated antibody discovery targeting the SARS-CoV-2 spike protein for COVID-19 therapeutic potential. Antib Ther 2021; 4:185-196. [PMID: 34541454 PMCID: PMC8444149 DOI: 10.1093/abt/tbab018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Rapid deployment of technologies capable of high-throughput and high-resolution screening is imperative for timely response to viral outbreaks. Risk mitigation in the form of leveraging multiple advanced technologies further increases the likelihood of identifying efficacious treatments in aggressive timelines. Methods In this study, we describe two parallel, yet distinct, in vivo approaches for accelerated discovery of antibodies targeting the severe acute respiratory syndrome coronavirus-2 spike protein. Working with human transgenic Alloy-GK mice, we detail a single B-cell discovery workflow to directly interrogate antibodies secreted from plasma cells for binding specificity and ACE2 receptor blocking activity. Additionally, we describe a concurrent accelerated hybridoma-based workflow utilizing a DiversimAb™ mouse model for increased diversity. Results The panel of antibodies isolated from both workflows revealed binding to distinct epitopes with both blocking and non-blocking profiles. Sequence analysis of the resulting lead candidates uncovered additional diversity with the opportunity for straightforward engineering and affinity maturation. Conclusions By combining in vivo models with advanced integration of screening and selection platforms, lead antibody candidates can be sequenced and fully characterized within one to three months.
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Affiliation(s)
- Tracey E Mullen
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Rashed Abdullah
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Jacqueline Boucher
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Anna Susi Brousseau
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Narayan K Dasuri
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Noah T Ditto
- Product Development, Carterra, 825 N 300 W c309, Salt Lake City, UT 84103, USA
| | - Andrew M Doucette
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Chloe Emery
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Justin Gabriel
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Brendan Greamo
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Ketan S Patil
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Kelly Rothenberger
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Justin Stolte
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
| | - Colby A Souders
- Antibody Discovery, Abveris Inc., 480 Neponset St, Ste 10B, Canton, MA 02021, USA
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Ahmed L, Gupta P, Martin KP, Scheer JM, Nixon AE, Kumar S. Intrinsic physicochemical profile of marketed antibody-based biotherapeutics. Proc Natl Acad Sci U S A 2021; 118:e2020577118. [PMID: 34504010 DOI: 10.1073/pnas.2020577118] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 01/28/2023] Open
Abstract
Successful biologic drug discovery and development involves finding functional as well as developable candidates. Once a candidate has been demonstrated to be functional, the next step is to determine whether it can be translated into a drug product. This requires that the candidate can withstand stresses encountered during manufacturing, shipping, and storage. Additionally, it must be safe, efficacious, and possess good pharmacology. In silico analyses of the variable regions of 77 marketed antibody-based biotherapeutics have revealed five nonredundant physicochemical descriptors. Distributions of these descriptors, observed for marketed biotherapeutics, can help prioritize a drug candidate for experimental testing at early discovery stages, guide engineering efforts to further optimize it, and help increase the productivity of biologic drug discovery and development. Feeding biopharma pipelines with biotherapeutic candidates that possess desirable developability profiles can help improve the productivity of biologic drug discovery and development. Here, we have derived an in silico profile by analyzing computed physicochemical descriptors for the variable regions (Fv) found in 77 marketed antibody-based biotherapeutics. Fv regions of these biotherapeutics demonstrate significant diversities in their germlines, complementarity determining region loop lengths, hydrophobicity, and charge distributions. Furthermore, an analysis of 24 physicochemical descriptors, calculated using homology-based molecular models, has yielded five nonredundant descriptors whose distributions represent stability, isoelectric point, and molecular surface characteristics of their Fv regions. Fv regions of candidates from our internal discovery campaigns, human next-generation sequencing repertoires, and those in clinical-stages (CST) were assessed for similarity with the physicochemical profile derived here. The Fv regions in 33% of CST antibodies show physicochemical properties that are dissimilar to currently marketed biotherapeutics. In comparison, physicochemical characteristics of ∼29% of the Fv regions in human antibodies and ∼27% of our internal hits deviated significantly from those of marketed biotherapeutics. The early availability of this information can help guide hit selection, lead identification, and optimization of biotherapeutic candidates. Insights from this work can also help support portfolio risk assessment, in-licensing, and biopharma collaborations.
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Chen Q, Wang W, Khanal S, Han J, Zhang M, Chen Y, Li Z, Wang K, Paterson AH, Yu J, Chee PW, Wang B. Transcriptome analysis reveals genes potentially related to high fiber strength in a Gossypium hirsutum line IL9 with Gossypium mustelinum introgression. Genome 2021; 64:985-995. [PMID: 34253086 DOI: 10.1139/gen-2020-0177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cotton (Gossypium L.) is the most important fiber crop worldwide. Here, transcriptome analysis was conducted on developing fibers of a G. mustelinum introgression line, IL9, and its recurrent parent, PD94042, at 17 and 21 days post-anthesis (dpa). Differentially expressed genes (DEGs) of PD94042 and IL9 were identified. Gene Ontology (GO) enrichment analysis showed that the annotated DEGs were rich in two main biological processes and two main molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis likewise showed that the annotated DEGs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. In total, 52 DEGs were selected as candidate genes based on comparison of the DEGs and GO function annotation information. Quantitative real-time PCR (RT-qPCR) analysis results for 12 randomly selected DEGs were consistent with transcriptome analysis. SNP identification based on G. mustelinum chromatin segment introgression showed that 394 SNPs were identified in 268 DEGs, and two genes with known functions were identified within fiber strength quantitative trait loci (QTL) regions or near the confidence intervals. We identified 52 key genes potentially related to high fiber strength in a G. mustelinum introgression line and provided significant insights into the study of cotton fiber quality improvement.
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Affiliation(s)
- Qi Chen
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Wei Wang
- Jiangsu Coastal Area Institute of Agricultural Sciences/Jiangsu Collaborative Innovation Center for Modern Crop Production, Yancheng, Jiangsu 224002, P.R. China
| | - Sameer Khanal
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Jinlei Han
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Mi Zhang
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Yan Chen
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Zhenjiang Li
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, P.R. China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, 111 Riverbend Road, Athens, GA 30602, USA
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology/Chinese Academy of Agricultural Sciences Cotton Research Institute, Anyang, Henan 455000, P.R. China
| | - Peng W Chee
- Department of Crop and Soil Sciences, University of Georgia, 2356 Rainwater Road, Tifton, GA 31793, USA
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, Jiangsu 226019, P.R. China
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Fernandes CFC, Pereira SS, Luiz MB, Silva NKRL, Silva MCS, Marinho ACM, Fonseca MHG, Furtado GP, Trevizani R, Nicolete R, Soares AM, Zuliani JP, Stabeli RG. Engineering of single-domain antibodies for next-generation snakebite antivenoms. Int J Biol Macromol 2021; 185:240-250. [PMID: 34118288 DOI: 10.1016/j.ijbiomac.2021.06.043] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 12/29/2022]
Abstract
Given the magnitude of the global snakebite crisis, strategies to ensure the quality of antivenom, as well as the availability and sustainability of its supply are under development by several research groups. Recombinant DNA technology has allowed the engineering of monoclonal antibodies and recombinant fragments as alternatives to conventional antivenoms. Besides having higher therapeutic efficacy, with broad neutralization capacity against local and systemic toxicity, novel antivenoms need to be safe and cost-effective. Due to the biological and physical chemical properties of camelid single-domain antibodies, with high volume of distribution to distal tissue, their modular format, and their versatility, their biotechnological application has grown considerably in recent decades. This article presents the most up-to-date developments concerning camelid single-domain-based antibodies against major toxins from snake venoms, the main venomous animals responsible for reported envenoming cases and related human deaths. A brief discussion on the composition, challenges, and perspectives of antivenoms is presented, as well as the road ahead for next-generation antivenoms based on single-domain antibodies.
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Affiliation(s)
| | - Soraya S Pereira
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Marcos B Luiz
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Nauanny K R L Silva
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Marcela Cristina S Silva
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | | | | | | | | | | | - Andreimar M Soares
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil
| | - Juliana P Zuliani
- Fundação Oswaldo Cruz, Fiocruz Rondônia, and Instituto Nacional de Ciência e Tecnologia em Epidemiologia da Amazônia Ocidental, INCT-EpiAmO, Porto Velho, Rondônia, Brazil; Universidade Federal de Rondônia, UNIR, Porto Velho, Rondônia, Brazil
| | - Rodrigo G Stabeli
- Plataforma Bi-Institucional de Medicina Translacional (Fiocruz-USP), Ribeirão Preto, São Paulo, Brazil
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35
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Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community’s Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
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Affiliation(s)
- Johannes Trück
- University Children's Hospital and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi), Paris, France
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, United States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Davide Bagnara
- University of Genoa, Department of Experimental Medicine, Genoa, Italy
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, United States
| | - Jacob S Sherkow
- College of Law, University of Illinois, Champaign, United States.,Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of Law, Copenhagen, Denmark.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States
| | - Aimee S Payne
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France.,Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of Montpellier, Montpellier, France.,Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
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36
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Erasmus MF, D'Angelo S, Ferrara F, Naranjo L, Teixeira AA, Buonpane R, Stewart SM, Nastri HG, Bradbury ARM. A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol 2021; 4:350. [PMID: 33742103 DOI: 10.1038/s42003-021-01881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 109 human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
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37
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Zhang X, Wei C, Liang H, Han L. Polo-Like Kinase 4's Critical Role in Cancer Development and Strategies for Plk4-Targeted Therapy. Front Oncol 2021; 11:587554. [PMID: 33777739 PMCID: PMC7994899 DOI: 10.3389/fonc.2021.587554] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Polo-like kinases (Plks) are critical regulatory molecules during the cell cycle process. This family has five members: Plk1, 2, 3, 4, and 5. Plk4 has been identified as a master regulator of centriole replication, and its aberrant expression is closely associated with cancer development. In this review, we depict the DNA, mRNA, and protein structure of Plk4, and the regulation of Plk4 at a molecular level. Then we list the downstream targets of Plk4 and the hallmarks of cancer associated with these targets. The role of Plk4 in different cancers is also summarized. Finally, we review the inhibitors that target Plk4 in the hope of discovering effective anticancer drugs. From authors' perspective, Plk4 might represent a valuable tumor biomarker and critical target for cancer diagnosis and therapy.
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Affiliation(s)
| | | | | | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
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38
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Abstract
Antibodies represent a well-established class of clinical diagnostics for medical applications as well as essential research and biotechnological tools. Although both polyclonal and monoclonal antibodies are indispensable reagents in basic research and diagnostics but both of them have their limitations. Hence, there is urgent need to develop strategies aimed at production of alternative scaffolds and recombinant antibodies of smaller dimensions that could be easily produced, selected and manipulated. Unlike conventional antibodies, members of Camelidae and sharks produce antibodies composed only of heavy chains with small size, high solubility, thermal stability, refolding capacity and good tissue penetration in vivo. The discovery of these naturally occurring antibodies having only heavy-chain in Camelidae family and their further development into small recombinant nanobodies represents an attractive alternative in drug delivery, diagnostics and imaging. Nanobody derivatives are soluble, stable, versatile, have unique refolding capacities, reduced aggregation tendencies and high-target binding capabilities. They can be genetically customized to target enzymes, transmembrane proteins or molecular interactions. Their ability to recognize recessed antigenic sites has been attributed to their smaller size and the ability of the extended CDR3 loop to quickly penetrate into such epitopes. With the advent of molecular engineering and phage display technology, they can be of potential use in molecular imaging, drug delivery and therapeutics for several major diseases. In this review we present the recent advances in nanobodies for modulating immune functions, for targeting cancers, viruses, toxins and microbes as well as their utility as diagnostic and biosensor tools.
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39
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Crissman J, Lin Y, Separa K, Duquette M, Cohen M, Velasquez C, Cujec T. RNase H-dependent PCR enables highly specific amplification of antibody variable domains from single B-cells. PLoS One 2020; 15:e0241803. [PMID: 33152031 DOI: 10.1371/journal.pone.0241803] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/20/2020] [Indexed: 02/06/2023] Open
Abstract
Immunization-based antibody discovery platforms require robust and effective protocols for the amplification, cloning, expression, and screening of antibodies from large numbers of B-cells in order to effectively capture the diversity of an experienced Ig-repertoire. Multiplex PCR using a series of forward and reverse primers designed to recover antibodies from a range of different germline sequences is challenging because primer design requires the recovery of full length antibody sequences, low starting template concentrations, and the need for all the primers to function under the same PCR conditions. Here we demonstrate several advantages to incorporating RNase H2-dependent PCR (rh-PCR) into a high-throughput, antibody-discovery platform. Firstly, rh-PCR eliminated primer dimer synthesis to below detectable levels, thereby eliminating clones with a false positive antibody titer. Secondly, by increasing the specificity of PCR, the rh-PCR primers increased the recovery of cognate antibody variable regions from single B-cells, as well as downstream recombinant antibody titers. Finally, we demonstrate that rh-PCR primers provide a more homogeneous sample pool and greater sequence quality in a Next Generation Sequencing-based approach to obtaining DNA sequence information from large numbers of cloned antibody cognate pairs. Furthermore, the higher specificity of the rh-PCR primers allowed for a better match between native antibody germline sequences and the VL/VH fragments amplified from single B-cells.
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40
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Liu P, Guo Y, Jiao S, Chang Y, Liu Y, Zou R, Liu Y, Chen M, Guo Y, Zhu G. Characterization of Variable Region Genes and Discovery of Key Recognition Sites in the Complementarity Determining Regions of the Anti-Thiacloprid Monoclonal Antibody. Int J Mol Sci 2020; 21:E6857. [PMID: 32962080 PMCID: PMC7555632 DOI: 10.3390/ijms21186857] [Citation(s) in RCA: 2] [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: 07/20/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/27/2022] Open
Abstract
Sequence-defined recombinant antibodies (rAbs) have emerged as alternatives to hybridoma-secreted monoclonal antibodies (mAbs) for performing immunoassays. However, the polyploidy nature of hybridomas often leads to the coexistence of aberrant or non-specific functional variable region (VR) gene transcripts, which complicates the identification of correct VR sequences. Herein, we introduced the use of LC-MS/MS combined with next-generation sequencing to characterize VR sequences in an anti-thiacloprid mAb, which was produced by a hybridoma with genetic antibody diversity. The certainty of VR sequences was verified by the functional analysis based on the recombinant antibody (rAb) expressed by HEK293 mammalian cells. The performance of the rAb was similar to that of the parental mAb, with IC50 values of 0.73 and 0.46 μg/L as measured by ELISAs. Moreover, molecular docking analysis revealed that Ser52 (H-CDR2), Trp98, and Trp93 (L-CDR3) residues in the complementarity determining regions (CDRs) of the identified VR sequences predominantly contributed to thiacloprid-specific recognition through hydrogen bonds and the CH-π interaction. Through single-site-directed alanine mutagenesis, we found that Trp98 and Trp93 (L-CDR3) showed high affinity to thiacloprid, while Ser52 (H-CDR2) had an auxiliary effect on the specific binding. This study presents an efficient and reliable way to determine the key recognition sites of hapten-specific mAbs, facilitating the improvement of antibody properties.
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Affiliation(s)
- Pengyan Liu
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
| | - Yuanhao Guo
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
| | - Shasha Jiao
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
| | - Yunyun Chang
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
| | - Ying Liu
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
- Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Zhejiang University, Hangzhou 310058, China
| | - Rubing Zou
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
| | - Yihua Liu
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Mengli Chen
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of life sciences, China Jiliang University, Hangzhou 310018, China
| | - Yirong Guo
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
| | - Guonian Zhu
- Institute of Pesticide and Environmental Toxicology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; (P.L.); (Y.G.); (S.J.); (Y.C.); (Y.L.); (R.Z.); (M.C.); (G.Z.)
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41
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Smakaj E, Babrak L, Ohlin M, Shugay M, Briney B, Tosoni D, Galli C, Grobelsek V, D'Angelo I, Olson B, Reddy S, Greiff V, Trück J, Marquez S, Lees W, Miho E. Benchmarking immunoinformatic tools for the analysis of antibody repertoire sequences. Bioinformatics 2020; 36:1731-1739. [PMID: 31873728 PMCID: PMC7075533 DOI: 10.1093/bioinformatics/btz845] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/21/2019] [Accepted: 12/19/2019] [Indexed: 01/01/2023] Open
Abstract
Summary Antibody repertoires reveal insights into the biology of the adaptive immune system and empower diagnostics and therapeutics. There are currently multiple tools available for the annotation of antibody sequences. All downstream analyses such as choosing lead drug candidates depend on the correct annotation of these sequences; however, a thorough comparison of the performance of these tools has not been investigated. Here, we benchmark the performance of commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets. We analyzed changes in IMGT reference germline database in the last 10 years in order to assess the reproducibility of the annotation output. We found that only 73/183 (40%) V, D and J human genes were shared between the reference germline sets used by the tools. We found that the annotation results differed between tools. In terms of alignment accuracy, MiXCR had the highest average frequency of gene mishits, 0.02 mishit frequency and IgBLAST the lowest, 0.004 mishit frequency. Reproducibility in the output of complementarity determining three regions (CDR3 amino acids) ranged from 4.3% to 77.6% with preprocessed data. In addition, run time of the tools was assessed: MiXCR was the fastest tool for number of sequences processed per unit of time. These results indicate that immunoinformatic analyses greatly depend on the choice of bioinformatics tool. Our results support informed decision-making to immunoinformaticians based on repertoire composition and sequencing platforms. Availability and implementation All tools utilized in the paper are free for academic use. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Erand Smakaj
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Lmar Babrak
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund 223, Sweden
| | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Deniz Tosoni
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Christopher Galli
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland
| | - Vendi Grobelsek
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Igor D'Angelo
- One Amgen Center Drive, Amgen, Inc., Therapeutic Discovery/Molecular Engineering, Thousand Oaks, CA 91320, USA
| | - Branden Olson
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Department of Statistics, University of Washington, Seattle, WA 98195, USA
| | - Sai Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo 0372, Norway
| | - Johannes Trück
- Paediatric Immunology, Children's Research Center, University Children's Hospital, University of Zurich, Zurich 8032, Switzerland
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA
| | - William Lees
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, UK
| | - Enkelejda Miho
- Institute of Biomedical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz 4132, Switzerland.,aiNET GmbH, Switzerland Innovation Park Basel Area AG, Basel 4057, Switzerland
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Yermanos A, Dounas A, Greiff V, Stadler T, Oxenius A, Reddy ST. Inter- and intraspecies comparison of phylogenetic fingerprints and sequence diversity of immunoglobulin variable genes. Immunogenetics 2020; 72:279-94. [PMID: 32367185 DOI: 10.1007/s00251-020-01164-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/13/2020] [Indexed: 10/24/2022]
Abstract
Protection and neutralization of a vast array of pathogens is accomplished by the tremendous diversity of the B cell receptor (BCR) repertoire. For jawed vertebrates, this diversity is initiated via the somatic recombination of immunoglobulin (Ig) germline elements. While it is clear that the number of these germline segments differs from species to species, the extent of cross-species sequence diversity remains largely uncharacterized. Here we use extensive computational and statistical methods to investigate the sequence diversity and evolutionary relationship between Ig variable (V), diversity (D), and joining (J) germline segments across nine commonly studied species ranging from zebrafish to human. Metrics such as guanine-cytosine (GC) content showed low redundancy across Ig germline genes within a given species. Other comparisons, including amino acid motifs, evolutionary selection, and sequence diversity, revealed species-specific properties. Additionally, we showed that the germline-encoded diversity differs across antibody (recombined V-D-J) repertoires of various B cell subsets. To facilitate future comparative immunogenomics analysis, we created VDJgermlines, an R package that contains the germline sequences from multiple species. Our study informs strategies for the humanization and engineering of therapeutic antibodies.
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Yoo DK, Lee SR, Jung Y, Han H, Lee HK, Han J, Kim S, Chae J, Ryu T, Chung J. Machine Learning-Guided Prediction of Antigen-Reactive In Silico Clonotypes Based on Changes in Clonal Abundance through Bio-Panning. Biomolecules 2020; 10:E421. [PMID: 32182714 PMCID: PMC7175295 DOI: 10.3390/biom10030421] [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: 12/31/2019] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/07/2023] Open
Abstract
c-Met is a promising target in cancer therapy for its intrinsic oncogenic properties. However, there are currently no c-Met-specific inhibitors available in the clinic. Antibodies blocking the interaction with its only known ligand, hepatocyte growth factor, and/or inducing receptor internalization have been clinically tested. To explore other therapeutic antibody mechanisms like Fc-mediated effector function, bispecific T cell engagement, and chimeric antigen T cell receptors, a diverse panel of antibodies is essential. We prepared a chicken immune scFv library, performed four rounds of bio-panning, obtained 641 clones using a high-throughput clonal retrieval system (TrueRepertoireTM, TR), and found 149 antigen-reactive scFv clones. We also prepared phagemid DNA before the start of bio-panning (round 0) and, after each round of bio-panning (round 1-4), performed next-generation sequencing of these five sets of phagemid DNA, and identified 860,207 HCDR3 clonotypes and 443,292 LCDR3 clonotypes along with their clonal abundance data. We then established a TR data set consisting of antigen reactivity for scFv clones found in TR analysis and the clonal abundance of their HCDR3 and LCDR3 clonotypes in five sets of phagemid DNA. Using the TR data set, a random forest machine learning algorithm was trained to predict the binding properties of in silico HCDR3 and LCDR3 clonotypes. Subsequently, we synthesized 40 HCDR3 and 40 LCDR3 clonotypes predicted to be antigen reactive (AR) and constructed a phage-displayed scFv library called the AR library. In parallel, we also prepared an antigen non-reactive (NR) library using 10 HCDR3 and 10 LCDR3 clonotypes predicted to be NR. After a single round of bio-panning, we screened 96 randomly-selected phage clones from the AR library and found out 14 AR scFv clones consisting of 5 HCDR3 and 11 LCDR3 AR clonotypes. We also screened 96 randomly-selected phage clones from the NR library, but did not identify any AR clones. In summary, machine learning algorithms can provide a method for identifying AR antibodies, which allows for the characterization of diverse antibody libraries inaccessible by traditional methods.
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Affiliation(s)
- Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (D.K.Y.); (S.R.L.); (H.K.L.); (J.H.); (S.K.); (J.C.)
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Seung Ryul Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (D.K.Y.); (S.R.L.); (H.K.L.); (J.H.); (S.K.); (J.C.)
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yushin Jung
- Celemics, Inc., 131 Gasandigital 1-ro, Geumcheon-gu, Seoul 08506, Korea; (Y.J.); (H.H.)
| | - Haejun Han
- Celemics, Inc., 131 Gasandigital 1-ro, Geumcheon-gu, Seoul 08506, Korea; (Y.J.); (H.H.)
| | - Hwa Kyoung Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (D.K.Y.); (S.R.L.); (H.K.L.); (J.H.); (S.K.); (J.C.)
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jerome Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (D.K.Y.); (S.R.L.); (H.K.L.); (J.H.); (S.K.); (J.C.)
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Soohyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (D.K.Y.); (S.R.L.); (H.K.L.); (J.H.); (S.K.); (J.C.)
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jisu Chae
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (D.K.Y.); (S.R.L.); (H.K.L.); (J.H.); (S.K.); (J.C.)
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Taehoon Ryu
- Celemics, Inc., 131 Gasandigital 1-ro, Geumcheon-gu, Seoul 08506, Korea; (Y.J.); (H.H.)
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (D.K.Y.); (S.R.L.); (H.K.L.); (J.H.); (S.K.); (J.C.)
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
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44
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Magadán S. Adaptive immune receptor repertoires, an overview of this exciting field. Immunol Lett 2020; 221:49-55. [PMID: 32113899 DOI: 10.1016/j.imlet.2020.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/30/2022]
Abstract
The adaptive immune response in jawed vertebrates relies on the huge diversity and specificity of the B cell and T cell antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR), respectively. The high level of diversity has represented a barrier to a comprehensive analysis of the adaptive immune response before the emergence of high-throughput sequencing (HTS) technologies. The size and complexity of HTS data requires the generation of novel computational and analytical approaches, which are transforming how the adaptive immune responses are deciphered to understand the clonal dynamics and properties of antigen-specific B and T cells in response to different kind of antigens. This exciting and rapidly evolving field is not only impacting human and clinical immunology but also comparative immunology. We are now closer to understanding the evolution of adaptive immune response in jawed vertebrates. This review provides an overview about classical and current strategies developed to assess the IG/TR diversity and their applications in basic and clinical immunology.
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van Kruijsbergen I, Mulder MPC, Uckelmann M, van Welsem T, de Widt J, Spanjaard A, Jacobs H, El Oualid F, Ovaa H, van Leeuwen F. Strategy for Development of Site-Specific Ubiquitin Antibodies. Front Chem 2020; 8:111. [PMID: 32154221 PMCID: PMC7047734 DOI: 10.3389/fchem.2020.00111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Protein ubiquitination is a key post-translational modification regulating a wide range of biological processes. Ubiquitination involves the covalent attachment of the small protein ubiquitin to a lysine of a protein substrate. In addition to its well-established role in protein degradation, protein ubiquitination plays a role in protein-protein interactions, DNA repair, transcriptional regulation, and other cellular functions. Understanding the mechanisms and functional relevance of ubiquitin as a signaling system requires the generation of antibodies or alternative reagents that specifically detect ubiquitin in a site-specific manner. However, in contrast to other post-translational modifications such as acetylation, phosphorylation, and methylation, the instability and size of ubiquitin-76 amino acids-complicate the preparation of suitable antigens and the generation antibodies detecting such site-specific modifications. As a result, the field of ubiquitin research has limited access to specific antibodies. This severely hampers progress in understanding the regulation and function of site-specific ubiquitination in many areas of biology, specifically in epigenetics and cancer. Therefore, there is a high demand for antibodies recognizing site-specific ubiquitin modifications. Here we describe a strategy for the development of site-specific ubiquitin antibodies. Based on a recently developed antibody against site-specific ubiquitination of histone H2B, we provide detailed protocols for chemical synthesis methods for antigen preparation and discuss considerations for screening and quality control experiments.
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Affiliation(s)
- Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Monique P C Mulder
- Leiden Institute for Chemical Immunology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Michael Uckelmann
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - John de Widt
- Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Aldo Spanjaard
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Huib Ovaa
- Leiden Institute for Chemical Immunology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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Abbott RC, Cross RS, Jenkins MR. Finding the Keys to the CAR: Identifying Novel Target Antigens for T Cell Redirection Immunotherapies. Int J Mol Sci 2020; 21:E515. [PMID: 31947597 DOI: 10.3390/ijms21020515] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Oncology immunotherapy has been a significant advancement in cancer treatment and involves harnessing and redirecting a patient’s immune response towards their own tumour. Specific recognition and elimination of tumour cells was first proposed over a century ago with Paul Erlich’s ‘magic bullet’ theory of therapy. In the past decades, targeting cancer antigens by redirecting T cells with antibodies using either bispecific T cell engagers (BiTEs) or chimeric antigen receptor (CAR) T cell therapy has achieved impressive clinical responses. Despite recent successes in haematological cancers, linked to a high and uniformly expressed CD19 antigen, the efficacy of T cell therapies in solid cancers has been disappointing, in part due to antigen escape. Targeting heterogeneous solid tumours with T cell therapies will require the identification of novel tumour specific targets. These targets can be found among a range of cell-surface expressed antigens, including proteins, glycolipids or carbohydrates. In this review, we will introduce the current tumour target antigen classification, outline existing approaches to discover novel tumour target antigens and discuss considerations for future design of antibodies with a focus on their use in CAR T cells.
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Denis HL, David LS, Cicchetti F. Antibody-based therapies for Huntington’s disease: current status and future directions. Neurobiol Dis 2019; 132:104569. [DOI: 10.1016/j.nbd.2019.104569] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 12/12/2022] Open
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Parola C, Neumeier D, Friedensohn S, Csepregi L, Di Tacchio M, Mason DM, Reddy ST. Antibody discovery and engineering by enhanced CRISPR-Cas9 integration of variable gene cassette libraries in mammalian cells. MAbs 2019; 11:1367-1380. [PMID: 31478465 PMCID: PMC6816377 DOI: 10.1080/19420862.2019.1662691] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Antibody engineering in mammalian cells offers the important advantage of expression and screening of libraries in their native conformation, increasing the likelihood of generating candidates with more favorable molecular properties. Major advances in cellular engineering enabled by CRISPR-Cas9 genome editing have made it possible to expand the use of mammalian cells in biotechnological applications. Here, we describe an antibody engineering and screening approach where complete variable light (VL) and heavy (VH) chain cassette libraries are stably integrated into the genome of hybridoma cells by enhanced Cas9-driven homology-directed repair (HDR), resulting in their surface display and secretion. By developing an improved HDR donor format that utilizes in situ linearization, we are able to achieve >15-fold improvement of genomic integration, resulting in a screening workflow that only requires a simple plasmid electroporation. This proved suitable for different applications in antibody discovery and engineering. By integrating and screening an immune library obtained from the variable gene repertoire of an immunized mouse, we could isolate a diverse panel of >40 unique antigen-binding variants. Additionally, we successfully performed affinity maturation by directed evolution screening of an antibody library based on random mutagenesis, leading to the isolation of several clones with affinities in the picomolar range.
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Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Lucia Csepregi
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | | | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland
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49
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Abstract
Antibodies are considered the hallmark of the adaptive immune system in that they mediate various key biological functions, such as direct neutralization and recruitment of effector immune cells to eliminate invading pathogens. Antibodies exhibit several unique properties, including high diversity (enabling binding to a wide range of targets), high specificity and structural integrity. These properties and the understanding that antibodies can be utilized in a wide range of applications have motivated the scientific community to develop new approaches for antibody repertoire analysis and rapid monoclonal antibody discovery. Today, antibodies are key modules in the pharmaceutical and diagnostic industries. By virtue of their high affinity and specificity to their targets and the availability of technologies to engineer different antibodies to a wide range of targets, antibodies have become the most promising natural biological molecules in a range of biotechnological applications, such as: highly specific and sensitive nanobiosensors for the diagnostics of different biomarkers; nanoparticle-based targeted drug delivery systems to certain cells or tissues; and nanomachines, which are nanoscale mechanical devices that enable energy conversion into precise mechanical motions in response to specific molecular inputs. In this review, we start by describing the unique properties of antibodies, how antibody diversity is generated, and the available technologies for antibody repertoire analysis and antibody discovery. Thereafter, we provide an overview of some antibody-based nanotechnologies and discuss novel and promising approaches for the application of antibodies in the nanotechnology field. Overall, we aim to bridge the knowledge gap between the nanotechnology and antibody engineering disciplines by demonstrating how technological advances in the antibody field can be leveraged to develop and/or enhance new technological approaches in the nanotechnology field.
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Affiliation(s)
- Yaron Hillman
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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50
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Goulet DR, Atkins WM. Considerations for the Design of Antibody-Based Therapeutics. J Pharm Sci 2019; 109:74-103. [PMID: 31173761 DOI: 10.1016/j.xphs.2019.05.031] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/02/2019] [Accepted: 05/29/2019] [Indexed: 02/06/2023]
Abstract
Antibody-based proteins have become an important class of biologic therapeutics, due in large part to the stability, specificity, and adaptability of the antibody framework. Indeed, antibodies not only have the inherent ability to bind both antigens and endogenous immune receptors but also have proven extremely amenable to protein engineering. Thus, several derivatives of the monoclonal antibody format, including bispecific antibodies, antibody-drug conjugates, and antibody fragments, have demonstrated efficacy for treating human disease, particularly in the fields of immunology and oncology. Reviewed here are considerations for the design of antibody-based therapeutics, including immunological context, therapeutic mechanisms, and engineering strategies. First, characteristics of antibodies are introduced, with emphasis on structural domains, functionally important receptors, isotypic and allotypic differences, and modifications such as glycosylation. Then, aspects of therapeutic antibody design are discussed, including identification of antigen-specific variable regions, choice of expression system, use of multispecific formats, and design of antibody derivatives based on fragmentation, oligomerization, or conjugation to other functional moieties. Finally, strategies to enhance antibody function through protein engineering are reviewed while highlighting the impact of fundamental biophysical properties on protein developability.
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Affiliation(s)
- Dennis R Goulet
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195.
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195
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