1
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Woo HJ, Kim J, Kim SM, Kim D, Moon JY, Park D, Lee JS. Context-dependent genomic locus effects on antibody production in recombinant Chinese hamster ovary cells generated through random integration. Comput Struct Biotechnol J 2024; 23:1654-1665. [PMID: 38680870 PMCID: PMC11046053 DOI: 10.1016/j.csbj.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/30/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
High-yield production of therapeutic protein using Chinese hamster ovary (CHO) cells requires stable cell line development (CLD). CLD typically uses random integration of transgenes; however, this results in clonal variation and subsequent laborious clone screening. Therefore, site-specific integration of a protein expression cassette into a desired chromosomal locus showing high transcriptional activity and stability, referred to as a hot spot, is emerging. Although positional effects are important for therapeutic protein expression, the sequence-specific mechanisms by which hotspots work are not well understood. In this study, we performed whole-genome sequencing (WGS) to locate randomly inserted vectors in the genome of recombinant CHO cells expressing high levels of monoclonal antibodies (mAbs) and experimentally validated these locations and vector compositions. The integration site was characterized by active histone marks and potential enhancer activities, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated indel mutations in the region upstream of the integration site led to a significant reduction in specific antibody productivity by up to 30%. Notably, the integration site and its core region did not function equivalently outside the native genomic context, showing a minimal effect on the increase in exogenous protein expression in the host cell line. We also observed a superior production capacity of the mAb expressing cell line compared to that of the host cell line. Collectively, this study demonstrates that developing recombinant CHO cell lines to produce therapeutic proteins at high levels requires a balance of factors including transgene configuration, genomic locus landscape, and host cell properties.
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Affiliation(s)
- Hyun Jee Woo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jaehoon Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Molecular Science and Technology Research Center, Ajou University, Suwon 16499, Republic of Korea
| | - Seul Mi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Dongwoo Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Yun Moon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
| | - Daechan Park
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Biological Sciences, Ajou University, Suwon 16499, Republic of Korea
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon 16499, Republic of Korea
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2
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Isu S, Vinskus L, Silva D, Cunningham K, Elich T, Greenhalgh P, Sokolnicki A, Raghunath B. Leveraging bioanalytical characterization of fractionated monoclonal antibody pools to identify aggregation-prone and less filterable proteoforms during virus filtration. Biotechnol Prog 2024; 40:e3451. [PMID: 38450976 DOI: 10.1002/btpr.3451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/11/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024]
Abstract
Monoclonal antibodies (mAbs) are an essential class of biotherapeutics. A platform process is used for mAb development to ensure clinically safe and stable molecules. Regulatory authorities ensure that mAb production processes include sufficient viral clearance steps to achieve less than one virus particle per million doses of product. Virus filtration is used for size-based removal of enveloped and nonenveloped viruses during downstream processing of mAbs. Process development in mAb purification relies on empirical approaches and often includes adsorptive prefiltration to mitigate virus filter fouling. Opportunities for molecular-level prediction of mAb filterability are needed to plug the existing knowledge gap in downstream processing. A molecular-level approach to understanding the factors influencing mAb filterability may reduce process development time, material loss, and processing costs due to oversized virus filters. In this work, pH step gradient fractionation was applied on polished bulk mAb feed to obtain concentrated pools of fractionated mAb variants. Biophysical properties and quality attributes of fractionated pools, including oligomeric state (size), isoelectric point profile, diffusion interaction parameters, and glycoform profile, were determined using bioanalytical methods. Filterability (loading and throughput) of fractionated pools were evaluated. Statistical methods were used to obtain correlations between quality attributes of mAb fractions and filterability on the Viresolve Pro virus filter.
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Affiliation(s)
- Solomon Isu
- Process Solutions, MilliporeSigma, Burlington, Massachusetts, USA
| | - Lilia Vinskus
- Process Solutions, MilliporeSigma, Burlington, Massachusetts, USA
| | - Derek Silva
- Process Solutions, MilliporeSigma, Burlington, Massachusetts, USA
| | | | - Thomas Elich
- Process Solutions, MilliporeSigma, Burlington, Massachusetts, USA
| | | | - Adam Sokolnicki
- Process Solutions, MilliporeSigma, Burlington, Massachusetts, USA
| | - Bala Raghunath
- Process Solutions, MilliporeSigma, Burlington, Massachusetts, USA
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3
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Gavade A, Nagraj AK, Patel R, Pais R, Dhanure P, Scheele J, Seiz W, Patil J. Understanding the Specific Implications of Amino Acids in the Antibody Development. Protein J 2024; 43:405-424. [PMID: 38724751 DOI: 10.1007/s10930-024-10201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 06/01/2024]
Abstract
As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.
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Affiliation(s)
- Akshata Gavade
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Anil Kumar Nagraj
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Riya Patel
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Roylan Pais
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | - Pratiksha Dhanure
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India
| | | | | | - Jaspal Patil
- Innoplexus Consulting Services Pvt Ltd, 7Th Floor, Midas Tower, Hinjawadi, Pune, Maharashtra, 411057, India.
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4
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Aebischer-Gumy C, Moretti P, Brunstein Laplace T, Frank J, Grand Y, Mosbaoui F, Hily E, Galea A, Peltret M, Estoppey C, Ayoub D, Giovannini R, Bertschinger M. Alternative splicing for tuneable expression of protein subunits at desired ratios. MAbs 2024; 16:2342243. [PMID: 38650451 DOI: 10.1080/19420862.2024.2342243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
The controlled expression of two or more proteins at a defined and stable ratio remains a substantial challenge, particularly in the bi- and multispecific antibody field. Achieving an optimal ratio of protein subunits can facilitate the assembly of multimeric proteins with high efficiency and minimize the production of by-products. In this study, we propose a solution based on alternative splicing, enabling the expression of a tunable and predefined ratio of two distinct polypeptide chains from the same pre-mRNA under the control of a single promoter. The pre-mRNA used in this study contains two open reading frames situated on separate exons. The first exon is flanked by two copies of the chicken troponin intron 4 (cTNT-I4) and is susceptible to excision from the pre-mRNA by means of alternative splicing. This specific design enables the modulation of the splice ratio by adjusting the strength of the splice acceptor. To illustrate this approach, we developed constructs expressing varying ratios of GFP and dsRED and extended their application to multimeric proteins such as monoclonal antibodies, achieving industrially relevant expression levels (>1 g/L) in a 14-day fed-batch process. The stability of the splice ratio was confirmed by droplet digital PCR in a stable pool cultivated over a 28-day period, while product quality was assessed via intact mass analysis, demonstrating absence of product-related impurities resulting from undesired splice events. Furthermore, we showcased the versatility of the construct by expressing two subunits of a bispecific antibody of the BEAT® type, which contains three distinct subunits in total.
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Affiliation(s)
- Christel Aebischer-Gumy
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Pierre Moretti
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Timothee Brunstein Laplace
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Jana Frank
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Ysaline Grand
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Farid Mosbaoui
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Emilie Hily
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Anna Galea
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Megane Peltret
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Carole Estoppey
- Antibody Engineering, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Daniel Ayoub
- Analytical Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Roberto Giovannini
- Process Sciences, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
| | - Martin Bertschinger
- Drug Substance Development, Ichnos Sciences SA (formerly Glenmark Pharmaceuticals SA), La Chaux-de-Fonds, Switzerland
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5
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Yin Y, Romei MG, Sankar K, Pal LR, Hon Hoi K, Yang Y, Leonard B, De Leon Boenig G, Kumar N, Matsumoto M, Payandeh J, Harris SF, Moult J, Lazar GA. Antibody Interfaces Revealed Through Structural Mining. Comput Struct Biotechnol J 2022; 20:4952-4968. [PMID: 36147680 PMCID: PMC9474289 DOI: 10.1016/j.csbj.2022.08.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 11/15/2022] Open
Abstract
Antibodies are fundamental effectors of humoral immunity, and have become a highly successful class of therapeutics. There is increasing evidence that antibodies utilize transient homotypic interactions to enhance function, and elucidation of such interactions can provide insights into their biology and new opportunities for their optimization as drugs. Yet the transitory nature of weak interactions makes them difficult to investigate. Capitalizing on their rich structural data and high conservation, we have characterized all the ways that antibody fragment antigen-binding (Fab) regions interact crystallographically. This approach led to the discovery of previously unrealized interfaces between antibodies. While diverse interactions exist, β-sheet dimers and variable-constant elbow dimers are recurrent motifs. Disulfide engineering enabled interactions to be trapped and investigated structurally and functionally, providing experimental validation of the interfaces and illustrating their potential for optimization. This work provides first insight into previously undiscovered oligomeric interactions between antibodies, and enables new opportunities for their biotherapeutic optimization.
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6
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Preisendörfer S, Ishikawa Y, Hennen E, Winklmeier S, Schupp JC, Knüppel L, Fernandez IE, Binzenhöfer L, Flatley A, Juan-Guardela BM, Ruppert C, Guenther A, Frankenberger M, Hatz RA, Kneidinger N, Behr J, Feederle R, Schepers A, Hilgendorff A, Kaminski N, Meinl E, Bächinger HP, Eickelberg O, Staab-Weijnitz CA. FK506-Binding Protein 11 Is a Novel Plasma Cell-Specific Antibody Folding Catalyst with Increased Expression in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:1341. [PMID: 35456020 PMCID: PMC9027113 DOI: 10.3390/cells11081341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Antibodies are central effectors of the adaptive immune response, widespread used therapeutics, but also potentially disease-causing biomolecules. Antibody folding catalysts in the plasma cell are incompletely defined. Idiopathic pulmonary fibrosis (IPF) is a fatal chronic lung disease with increasingly recognized autoimmune features. We found elevated expression of FK506-binding protein 11 (FKBP11) in IPF lungs where FKBP11 specifically localized to antibody-producing plasma cells. Suggesting a general role in plasma cells, plasma cell-specific FKBP11 expression was equally observed in lymphatic tissues, and in vitro B cell to plasma cell differentiation was accompanied by induction of FKBP11 expression. Recombinant human FKBP11 was able to refold IgG antibody in vitro and inhibited by FK506, strongly supporting a function as antibody peptidyl-prolyl cis-trans isomerase. Induction of ER stress in cell lines demonstrated induction of FKBP11 in the context of the unfolded protein response in an X-box-binding protein 1 (XBP1)-dependent manner. While deficiency of FKBP11 increased susceptibility to ER stress-mediated cell death in an alveolar epithelial cell line, FKBP11 knockdown in an antibody-producing hybridoma cell line neither induced cell death nor decreased expression or secretion of IgG antibody. Similarly, antibody secretion by the same hybridoma cell line was not affected by knockdown of the established antibody peptidyl-prolyl isomerase cyclophilin B. The results are consistent with FKBP11 as a novel XBP1-regulated antibody peptidyl-prolyl cis-trans isomerase and indicate significant redundancy in the ER-resident folding machinery of antibody-producing hybridoma cells.
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Affiliation(s)
- Stefan Preisendörfer
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Yoshihiro Ishikawa
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; (Y.I.); (H.P.B.)
| | - Elisabeth Hennen
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Stephan Winklmeier
- Institute of Clinical Neuroimmunology, Biomedical Center and LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; (S.W.); (E.M.)
| | - Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
- Department of Respiratory Medicine, Hannover Medical School, Biomedical Research in End-Stage and Obstructive Lung Disease Hannover, Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Larissa Knüppel
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Isis E. Fernandez
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Leonhard Binzenhöfer
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Andrew Flatley
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Brenda M. Juan-Guardela
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
| | - Clemens Ruppert
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), 35392 Giessen, Germany; (C.R.); (A.G.)
| | - Andreas Guenther
- Department of Internal Medicine, Medizinische Klinik II, Member of the German Center of Lung Research (DZL), 35392 Giessen, Germany; (C.R.); (A.G.)
| | - Marion Frankenberger
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Rudolf A. Hatz
- Thoraxchirurgisches Zentrum, Klinik für Allgemeine-, Viszeral-, Transplantations-, Gefäß- und Thoraxchirurgie, LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany;
- Asklepios Fachkliniken München-Gauting, 82131 Gauting, Germany
| | - Nikolaus Kneidinger
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Jürgen Behr
- Department of Medicine V, LMU Klinikum, Ludwig-Maximilians-Universität München, Member of the German Center of Lung Research (DZL), 81377 Munich, Germany; (N.K.); (J.B.)
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Aloys Schepers
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, 85764 Neuherberg, Germany; (A.F.); (R.F.); (A.S.)
| | - Anne Hilgendorff
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA; (J.C.S.); (B.M.J.-G.); (N.K.)
| | - Edgar Meinl
- Institute of Clinical Neuroimmunology, Biomedical Center and LMU Klinikum, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; (S.W.); (E.M.)
| | - Hans Peter Bächinger
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA; (Y.I.); (H.P.B.)
| | - Oliver Eickelberg
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
| | - Claudia A. Staab-Weijnitz
- Institute of Lung Health and Immunity and Comprehensive Pneumology Center with the CPC-M bioArchive, Member of the German Center of Lung Research (DZL), Helmholtz-Zentrum München, 81377 Munich, Germany; (S.P.); (E.H.); (L.K.); (I.E.F.); (L.B.); (M.F.); (A.H.); (O.E.)
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7
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Feng Y, Quinnell SP, Lanzi AM, Vegas AJ. Alginate-Based Amphiphilic Block Copolymers as a Drug Codelivery Platform. NANO LETTERS 2021; 21:7495-7504. [PMID: 34495662 PMCID: PMC8768502 DOI: 10.1021/acs.nanolett.1c01525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Structured nanoassemblies are biomimetic structures that are enabling applications from nanomedicine to catalysis. One approach to achieve these spatially organized architectures is utilizing amphiphilic diblock copolymers with one or two macromolecular backbones that self-assemble in solution. To date, the impact of alternating backbone architectures on self-assembly and drug delivery is still an area of active research limited by the strategies used to synthesize these multiblock polymers. Here, we report self-assembling ABC-type alginate-based triblock copolymers with the backbones of three distinct biomaterials utilizing a facile conjugation approach. This "polymer mosaic" was synthesized by the covalent attachment of alginate with a PLA/PEG diblock copolymer. The combination of alginate, PEG, and PLA domains resulted in an amphiphilic copolymer that self-assembles into nanoparticles with a unique morphology of alginate domain compartmentalization. These particles serve as a versatile platform for co-encapsulation of hydrophilic and hydrophobic small molecules, their spatiotemporal release, and show potential as a drug delivery system for combination therapy.
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Affiliation(s)
- Yunpeng Feng
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Sean P. Quinnell
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Alison M. Lanzi
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Arturo J. Vegas
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Corresponding Author: Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States;
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8
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Wang Y, Li X, Chen X, Nielsen J, Petranovic D, Siewers V. Expression of antibody fragments in Saccharomyces cerevisiae strains evolved for enhanced protein secretion. Microb Cell Fact 2021; 20:134. [PMID: 34261490 PMCID: PMC8278646 DOI: 10.1186/s12934-021-01624-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/01/2021] [Indexed: 11/10/2022] Open
Abstract
Monoclonal antibodies, antibody fragments and fusion proteins derived thereof have revolutionized the practice of medicine. Major challenges faced by the biopharmaceutical industry are however high production costs, long processing times and low productivities associated with their production in mammalian cell lines. The yeast Saccharomyces cerevisiae, a well-characterized eukaryotic cell factory possessing the capacity of post-translational modifications, has been industrially exploited as a secretion host for production of a range of products, including pharmaceuticals. However, due to the incompatible surface glycosylation, few antibody molecules have been functionally expressed in S. cerevisiae. Here, three non-glycosylated antibody fragments from human and the Camelidae family were chosen for expression in a S. cerevisiae strain (HA) previously evolved for high α-amylase secretion. These included the Fab fragment Ranibizumab (Ran), the scFv peptide Pexelizumab (Pex), and a nanobody consisting of a single V-type domain (Nan). Both secretion and biological activities of the antibody fragments were confirmed. In addition, the secretion level of each protein was compared in the wild type (LA) and two evolved strains (HA and MA) with different secretory capacities. We found that the secretion of Ran and Nan was positively correlated with the strains' secretory capacity, while Pex was most efficiently secreted in the parental strain. To investigate the mechanisms for different secretion abilities in these selected yeast strains for the different antibody fragments, RNA-seq analysis was performed. The results showed that several bioprocesses were significantly enriched for differentially expressed genes when comparing the enriched terms between HA.Nan vs. LA.Nan and HA.Pex vs. LA.Pex, including amino acid metabolism, protein synthesis, cell cycle and others, which indicates that there are unique physiological needs for each antibody fragment secretion.
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Affiliation(s)
- Yanyan Wang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xin Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Dina Petranovic
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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9
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Xi Z, Liu X, Lin R, Persons JD, Ilina TV, Li W, Dimitrov DS, Ishima R. The reduced form of the antibody CH2 domain. Protein Sci 2021; 30:1895-1903. [PMID: 34107549 DOI: 10.1002/pro.4142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022]
Abstract
Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xianglei Liu
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rui Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Gastroenterology and Hepatology, Tianjin Medical University, General Hospital, Tianjin, China
| | - John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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10
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Fauser J, Itzen A, Gulen B. Current Advances in Covalent Stabilization of Macromolecular Complexes for Structural Biology. Bioconjug Chem 2021; 32:879-890. [PMID: 33861574 DOI: 10.1021/acs.bioconjchem.1c00118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Structural characterization of macromolecular assemblies is often limited by the transient nature of the interactions. The development of specific chemical tools to covalently tether interacting proteins to each other has played a major role in various fundamental discoveries in recent years. To this end, protein engineering techniques such as mutagenesis, incorporation of unnatural amino acids, and methods using synthetic substrate/cosubstrate derivatives were employed. In this review, we give an overview of both commonly used and recently developed biochemical methodologies for covalent stabilization of macromolecular complexes enabling structural investigation via crystallography, nuclear magnetic resonance, and cryo-electron microscopy. We divided the strategies into nonenzymatic- and enzymatic-driven cross-linking and further categorized them in either naturally occurring or engineered covalent linkage. This review offers a compilation of recent advances in diverse scientific fields where the structural characterization of macromolecular complexes was achieved by the aid of intermolecular covalent linkage.
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Affiliation(s)
- Joel Fauser
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Aymelt Itzen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Burak Gulen
- Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
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11
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Jang S, Song J, Kim N, Bak J, Jung K, Park YW, Park BC, Kim HM. Development of an antibody-like T-cell engager based on VH-VL heterodimer formation and its application in cancer therapy. Biomaterials 2021; 271:120760. [PMID: 33774526 DOI: 10.1016/j.biomaterials.2021.120760] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/25/2021] [Accepted: 03/13/2021] [Indexed: 10/21/2022]
Abstract
Following the clinical success of immunotherapeutic antibodies, bispecific antibodies for cytotoxic effector cell redirection, tumor-targeted immunomodulation and dual immunomodulation, have received particular attentions. Here, we developed a novel bispecific antibody platform, termed Antibody-Like Cell Engager (ALiCE), wherein the Fc domain of each heavy chain of immunoglobulin G (IgG) is replaced by the VH and VL domains of an IgG specific to a second antigen while retaining the N-terminal Fab of the parent antibody. Because of specific interactions between the substituted VH and VL domains, the C-terminal stem Fv enables ALiCE to assemble autonomously into hetero-tetramers, thus simultaneously binding to two distinct antigens but with different avidities. This design strategy was used to generate ACE-05 (two anti-PD-L1 Fab × anti-CD3 Fv) and ACE-31 (two anti-CD3 Fab × anti-PD-L1 Fv), both of which bound PD-L1 and CD3. However, ACE-05 was more effective than ACE-31 in reducing off-target toxicity caused by the indiscriminate activation of T cells. Moreover, in cell-based assays and PBMC-reconstituted humanized mice harboring human non-small-cell lung cancer tumors, ACE-05 showed marked antitumor efficacy, causing complete tumor regression at a dose of 0.05 mg/kg body weight. The dual roles of ACE-05 in immune checkpoint inhibition and T-cell redirection, coupled with reduced off-target toxicity, suggest that ACE-05 may be a promising anti-cancer therapeutic agent. Moreover, the bispecific ALiCE platform can be further used for tumor-targeted or multiple immunomodulation applications.
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Affiliation(s)
- Seil Jang
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea; Y-BIOLOGICS, Inc., 17 Techno 4-ro, Yuseong-gu, Daejeon, 34013, South Korea; CTCELLS, Inc., R7, 333 Techno Jungang-daero, Hyeonpung-eup, Dalseong-gun, Daegu, 42988, South Korea
| | - Jaeho Song
- Y-BIOLOGICS, Inc., 17 Techno 4-ro, Yuseong-gu, Daejeon, 34013, South Korea
| | - NaYoung Kim
- Y-BIOLOGICS, Inc., 17 Techno 4-ro, Yuseong-gu, Daejeon, 34013, South Korea
| | - Jeonghyeon Bak
- Y-BIOLOGICS, Inc., 17 Techno 4-ro, Yuseong-gu, Daejeon, 34013, South Korea
| | - Keehoon Jung
- Seoul National University College of Medicine, Seoul, 03080, South Korea
| | - Young Woo Park
- Y-BIOLOGICS, Inc., 17 Techno 4-ro, Yuseong-gu, Daejeon, 34013, South Korea
| | - Bum-Chan Park
- Y-BIOLOGICS, Inc., 17 Techno 4-ro, Yuseong-gu, Daejeon, 34013, South Korea.
| | - Ho Min Kim
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea; Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, South Korea; Center for Biomolecular & Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, South Korea.
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12
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Masiero A, Nelly L, Marianne G, Christophe S, Florian L, Ronan C, Claire B, Cornelia Z, Grégoire B, Eric L, Ludovic L, Dominique B, Sylvie A, Marie G, Francis D, Fabienne S, Cécile C, Isabelle A, Jacques D, Jérôme D, Bruno G, Katarina R, Jean-Michel M, Catherine P. The impact of proline isomerization on antigen binding and the analytical profile of a trispecific anti-HIV antibody. MAbs 2021; 12:1698128. [PMID: 31791173 PMCID: PMC8675452 DOI: 10.1080/19420862.2019.1698128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Proline cis-trans conformational isomerization is a mechanism that affects different types of protein functions and behaviors. Using analytical characterization, structural analysis, and molecular dynamics simulations, we studied the causes of an aberrant two-peak size-exclusion chromatography profile observed for a trispecific anti-HIV antibody. We found that proline isomerization in the tyrosine-proline-proline (YPP) motif in the heavy chain complementarity-determining region (CDR)3 domain of one of the antibody arms (10e8v4) was a component of this profile. The pH effect on the conformational equilibrium that led to these two populations was presumably caused by a histidine residue (H147) in the light chain that is in direct contact with the YPP motif. Finally, we demonstrated that, due to chemical equilibrium between the cis and trans proline conformers, the antigen-binding potency of the trispecific anti-HIV antibody was not significantly affected in spite of a potential structural clash of 10e8v4 YPtransPtrans conformers with the membrane-proximal ectodomain region epitope in the GP41 antigen. Altogether, these results reveal at mechanistic and molecular levels the effect of proline isomerization in the CDR on the antibody binding and analytical profiles, and support further development of the trispecific anti-HIV antibody.
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Affiliation(s)
| | - Lechat Nelly
- Biologics Development, SANOFI R&D, Vitry-sur-Seine, France
| | | | | | | | - Crépin Ronan
- Biologics Development, SANOFI R&D, Vitry-sur-Seine, France
| | - Borel Claire
- Biologics Development, SANOFI R&D, Vitry-sur-Seine, France
| | | | - Bisch Grégoire
- Biologics Development, SANOFI R&D, Vitry-sur-Seine, France
| | - Leclerc Eric
- Biologics Development, SANOFI R&D, Vitry-sur-Seine, France
| | | | | | | | | | | | | | | | | | - Dumas Jacques
- Biologics Research, SANOFI R&D, Vitry-sur-Seine, France
| | - Dabin Jérôme
- Biologics Development, SANOFI R&D, Vitry-sur-Seine, France
| | - Genet Bruno
- Biologics Development, SANOFI R&D, Vitry-sur-Seine, France
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13
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Gong D, Riley TP, Bzymek KP, Correia AR, Li D, Spahr C, Robinson JH, Case RB, Wang Z, Garces F. Rational selection of building blocks for the assembly of bispecific antibodies. MAbs 2021; 13:1870058. [PMID: 33397191 PMCID: PMC7808324 DOI: 10.1080/19420862.2020.1870058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Bispecific antibodies, engineered to recognize two targets simultaneously, demonstrate exceptional clinical potential for the therapeutic intervention of complex diseases. However, these molecules are often composed of multiple polypeptide chains of differing sequences. To meet industrial scale productivity, enforcing the correct quaternary assembly of these chains is critical. Here, we describe Chain Selectivity Assessment (CSA), a high-throughput method to rationally select parental monoclonal antibodies (mAbs) to make bispecific antibodies requiring correct heavy/light chain pairing. By deploying CSA, we have successfully identified mAbs that exhibit a native preference toward cognate chain pairing that enables the production of hetero-IgGs without additional engineering. Furthermore, CSA also identified rare light chains (LCs) that permit positive binding of the non-cognate arm in the common LC hetero-IgGs, also without engineering. This rational selection of parental mAbs with favorable developability characteristics is critical to the successful development of bispecific molecules with optimal manufacturability properties.
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Affiliation(s)
- Danyang Gong
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Timothy P Riley
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Krzysztof P Bzymek
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Ana R Correia
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Danqing Li
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Christopher Spahr
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - John H Robinson
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
| | - Ryan B Case
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., San Francisco, CA USA
| | - Zhulun Wang
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., San Francisco, CA USA
| | - Fernando Garces
- Department of Therapeutics Discovery, Amgen Research, Amgen Inc ., Thousand Oaks, CA USA
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14
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Plate L, Rius B, Nguyen B, Genereux JC, Kelly JW, Wiseman RL. Quantitative Interactome Proteomics Reveals a Molecular Basis for ATF6-Dependent Regulation of a Destabilized Amyloidogenic Protein. Cell Chem Biol 2019; 26:913-925.e4. [PMID: 31105062 DOI: 10.1016/j.chembiol.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/14/2019] [Accepted: 03/31/2019] [Indexed: 12/24/2022]
Abstract
Activation of the unfolded protein response (UPR)-associated transcription factor ATF6 has emerged as a promising strategy to reduce the secretion and subsequent toxic aggregation of destabilized, amyloidogenic proteins implicated in systemic amyloid diseases. However, the molecular mechanism by which ATF6 activation reduces the secretion of amyloidogenic proteins remains poorly defined. We employ a quantitative interactomics platform to define how ATF6 activation reduces secretion of a destabilized, amyloidogenic immunoglobulin light chain (LC) associated with light-chain amyloidosis (AL). Using this platform, we show that ATF6 activation increases the targeting of this destabilized LC to a subset of pro-folding ER proteostasis factors that retains the amyloidogenic LC within the ER, preventing its secretion. Our results define a molecular basis for the ATF6-dependent reduction in destabilized LC secretion and highlight the advantage for targeting this UPR-associated transcription factor to reduce secretion of destabilized, amyloidogenic proteins implicated in AL and related systemic amyloid diseases.
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Affiliation(s)
- Lars Plate
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bibiana Rius
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA
| | - Bianca Nguyen
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA
| | - Joseph C Genereux
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffery W Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, MB110, La Jolla, CA 92037, USA.
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15
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Bannas P, Koch-Nolte F. Perspectives for the Development of CD38-Specific Heavy Chain Antibodies as Therapeutics for Multiple Myeloma. Front Immunol 2018; 9:2559. [PMID: 30459772 PMCID: PMC6232533 DOI: 10.3389/fimmu.2018.02559] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/17/2018] [Indexed: 01/12/2023] Open
Abstract
The NAD+-metabolizing ectoenzyme CD38 is an established therapeutic target in multiple myeloma. The CD38-specific monoclonal antibodies daratumumab and isatuximab show promising results in the clinic. Nanobodies correspond to the single variable domains (VHH) derived from heavy chain antibodies that naturally occur in camelids. VHHs display high solubility and excellent tissue penetration in vivo. We recently generated a panel of CD38-specific nanobodies, some of which block or enhance the enzymatic activity of CD38. Fusion of such a nanobody to the hinge, CH2, and CH3 domains of human IgG1 generates a chimeric llama/human hcAb of about half the size of a conventional moAb (75 vs. 150 kDa). Similarly, a fully human CD38-specific hcAb can be generated using a CD38-specific human VH3 instead of a CD38-specific camelid nanobody. Here we discuss the advantages and disadvantages of CD38-specific hcAbs vs. conventional moAbs and provide an outlook for the potential use of CD38-specific hcAbs as novel therapeutics for multiple myeloma.
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Affiliation(s)
- Peter Bannas
- Deptartment of Radiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology University, Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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The structural basis of nanobody unfolding reversibility and thermoresistance. Sci Rep 2018; 8:7934. [PMID: 29784954 PMCID: PMC5962586 DOI: 10.1038/s41598-018-26338-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/10/2018] [Indexed: 12/17/2022] Open
Abstract
Nanobodies represent the variable binding domain of camelid heavy-chain antibodies and are employed in a rapidly growing range of applications in biotechnology and biomedicine. Their success is based on unique properties including their reported ability to reversibly refold after heat-induced denaturation. This view, however, is contrasted by studies which involve irreversibly aggregating nanobodies, asking for a quantitative analysis that clearly defines nanobody thermoresistance and reveals the determinants of unfolding reversibility and aggregation propensity. By characterizing nearly 70 nanobodies, we show that irreversible aggregation does occur upon heat denaturation for the large majority of binders, potentially affecting application-relevant parameters like stability and immunogenicity. However, by deriving aggregation propensities from apparent melting temperatures, we show that an optional disulfide bond suppresses nanobody aggregation. This effect is further enhanced by increasing the length of a complementarity determining loop which, although expected to destabilize, contributes to nanobody stability. The effect of such variations depends on environmental conditions, however. Nanobodies with two disulfide bonds, for example, are prone to lose their functionality in the cytosol. Our study suggests strategies to engineer nanobodies that exhibit optimal performance parameters and gives insights into general mechanisms which evolved to prevent protein aggregation.
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17
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Velázquez-López I, Valdés-García G, Romero Romero S, Maya Martínez R, Leal-Cervantes AI, Costas M, Sánchez-López R, Amero C, Pastor N, Fernández Velasco DA. Localized conformational changes trigger the pH-induced fibrillogenesis of an amyloidogenic λ light chain protein. Biochim Biophys Acta Gen Subj 2018; 1862:1656-1666. [PMID: 29669263 DOI: 10.1016/j.bbagen.2018.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 02/04/2018] [Accepted: 04/13/2018] [Indexed: 01/04/2023]
Abstract
Solvent conditions modulate the expression of the amyloidogenic potential of proteins. In this work the effect of pH on the fibrillogenic behavior and the conformational properties of 6aJL2, a model protein of the highly amyloidogenic variable light chain λ6a gene segment, was examined. Ordered aggregates showing the ultrastructural and spectroscopic properties observed in amyloid fibrils were formed in the 2.0-8.0 pH range. At pH <3.0 a drastic decrease in lag time and an increase in fibril formation rate were found. In the 4.0-8.0 pH range there was no spectroscopic evidence for significant conformational changes in the native state. Likewise, heat capacity measurements showed no evidence for residual structure in the unfolded state. However, at pH <3.0 stability is severely decreased and the protein suffers conformational changes as detected by circular dichroism, tryptophan and ANS fluorescence, as well as by NMR spectroscopy. Molecular dynamics simulations indicate that acid-induced conformational changes involve the exposure of the loop connecting strands E and F. These results are compatible with pH-induced changes in the NMR spectra. Overall, the results indicate that the mechanism involved in the acid-induced increase in the fibrillogenic potential of 6aJL2 is profoundly different to that observed in κ light chains, and is promoted by localized conformational changes in a region of the protein that was previously not known to be involved in acid-induced light chain fibril formation. The identification of this region opens the potential for the design of specific inhibitors.
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Affiliation(s)
- Isabel Velázquez-López
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México
| | - Gilberto Valdés-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, México
| | - Sergio Romero Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México
| | - Roberto Maya Martínez
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, México
| | - Ana I Leal-Cervantes
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, México
| | | | - Carlos Amero
- Centro de Investigaciones Químicas, IICBA, Universidad Autónoma del Estado de Morelos, México
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, México.
| | - D Alejandro Fernández Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, México.
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18
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Luz D, Shiga EA, Chen G, Quintilio W, Andrade FB, Maranhão AQ, Caetano BA, Mitsunari T, Silva MA, Rocha LB, Moro AM, Sidhu SS, Piazza RMF. Structural Changes in Stx1 Engineering Monoclonal Antibody Improves Its Functionality as Diagnostic Tool for a Rapid Latex Agglutination Test. Antibodies (Basel) 2018; 7:antib7010009. [PMID: 31544861 PMCID: PMC6698835 DOI: 10.3390/antib7010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 01/10/2018] [Accepted: 01/26/2018] [Indexed: 11/16/2022] Open
Abstract
Stx1 toxin is one of the AB5 toxins of Shiga toxin-producing Escherichia coli (STEC) responsible for foodborne intoxication during outbreaks. The single-chain variable fragment (scFv) is the most common recombinant antibody format; it consists of both variable chains connected by a peptide linker with conserved specificity and affinity for antigen. The drawbacks of scFv production in bacteria are the heterologous expression, conformation and stability of the molecule, which could change the affinity for the antigen. In this work, we obtained a stable and functional scFv-Stx1 in bacteria, starting from IgG produced by hybridoma cells. After structural modifications, i.e., change in protein orientation, vector and linker, its solubility for expression in bacteria was increased as well as the affinity for its antigen, demonstrated by a scFv dissociation constant (KD) of 2.26 × 10-7 M. Also, it was able to recognize purified Stx1 and cross-reacted with Stx2 toxin by ELISA (Enzyme-Linked Immunosorbent Assay), and detected 88% of Stx1-producing strains using a rapid latex agglutination test. Thus, the scFv fragment obtained in the present work is a bacteria-produced tool for use in a rapid diagnosis test, providing an alternative for STEC diagnosis.
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Affiliation(s)
- Daniela Luz
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Emerson A Shiga
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Gang Chen
- Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Wagner Quintilio
- Laboratório de Biofármacos em Células Animais, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Fernanda B Andrade
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Andrea Q Maranhão
- Laboratório de Imunologia, Universidade de Brasília, Brasília 70910-900, Brazil.
| | - Bruna A Caetano
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Thaís Mitsunari
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Míriam A Silva
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Letícia B Rocha
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Ana M Moro
- Laboratório de Biofármacos em Células Animais, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
| | - Sachdev S Sidhu
- Department of Molecular Genetics, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
| | - Roxane M F Piazza
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, SP 05503-900, Brazil.
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19
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Kim HS, Dunshee DR, Yee A, Tong RK, Kim I, Farahi F, Hongo JA, Ernst JA, Sonoda J, Spiess C. Tethered-variable CL bispecific IgG: an antibody platform for rapid bispecific antibody screening. Protein Eng Des Sel 2017; 30:627-637. [PMID: 28985411 PMCID: PMC5914367 DOI: 10.1093/protein/gzx034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022] Open
Abstract
Bispecific antibodies offer a clinically validated platform for drug discovery. In generating functionally active bispecific antibodies, it is necessary to identify a unique parental antibody pair to merge into a single molecule. However, technologies that allow high-throughput production of bispecific immunoglobulin Gs (BsIgGs) for screening purposes are limited. Here, we describe a novel bispecific antibody format termed tethered-variable CLBsIgG (tcBsIgG) that allows robust production of intact BsIgG in a single cell line, concurrently ensuring cognate light chain pairing and preserving key antibody structural and functional properties. This technology is broadly applicable in the generation of BsIgG from a variety of antibody isotypes, including human BsIgG1, BsIgG2 and BsIgG4. The practicality of the tcBsIgG platform is demonstrated by screening BsIgGs generated from FGF21-mimetic anti-Klotho-β agonistic antibodies in a combinatorial manner. This screen identified multiple biepitopic combinations with enhanced agonistic activity relative to the parental monoclonal antibodies, thereby demonstrating that biepitopic antibodies can acquire enhanced functionality compared to monospecific parental antibodies. By design, the tcBsIgG format is amenable to high-throughput production of large panels of bispecific antibodies and thus can facilitate the identification of rare BsIgG combinations to enable the discovery of molecules with improved biological function.
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Affiliation(s)
- Hok Seon Kim
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Diana Ronai Dunshee
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Angie Yee
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Raymond K Tong
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ingrid Kim
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Farzam Farahi
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jo-Anne Hongo
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James A Ernst
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Junichiro Sonoda
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christoph Spiess
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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20
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van den Bremer ETJ, Labrijn AF, van den Boogaard R, Priem P, Scheffler K, Melis JPM, Schuurman J, Parren PWHI, de Jong RN. Cysteine-SILAC Mass Spectrometry Enabling the Identification and Quantitation of Scrambled Interchain Disulfide Bonds: Preservation of Native Heavy-Light Chain Pairing in Bispecific IgGs Generated by Controlled Fab-arm Exchange. Anal Chem 2017; 89:10873-10882. [DOI: 10.1021/acs.analchem.7b02543] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Patrick Priem
- Genmab, Yalelaan 60, 3584CM, Utrecht, The Netherlands
| | - Kai Scheffler
- Thermo Fisher Scientific GmbH, Im Steingrund 4-6, 63303, Dreieich, Germany
| | | | | | - Paul W. H. I. Parren
- Department
of Immunohematology and Blood Transfusion, Leiden University Medical Center, Albinusdreef 2, 2333
ZA, Leiden, The Netherlands
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21
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Herold EM, John C, Weber B, Kremser S, Eras J, Berner C, Deubler S, Zacharias M, Buchner J. Determinants of the assembly and function of antibody variable domains. Sci Rep 2017; 7:12276. [PMID: 28947772 PMCID: PMC5613017 DOI: 10.1038/s41598-017-12519-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/12/2017] [Indexed: 01/17/2023] Open
Abstract
The antibody Fv module which binds antigen consists of the variable domains VL and VH. These exhibit a conserved ß-sheet structure and comprise highly variable loops (CDRs). Little is known about the contributions of the framework residues and CDRs to their association. We exchanged conserved interface residues as well as CDR loops and tested the effects on two Fvs interacting with moderate affinities (KDs of ~2.5 µM and ~6 µM). While for the rather instable domains, almost all mutations had a negative effect, the more stable domains tolerated a number of mutations of conserved interface residues. Of particular importance for Fv association are VLP44 and VHL45. In general, the exchange of conserved residues in the VL/VH interface did not have uniform effects on domain stability. Furthermore, the effects on association and antigen binding do not strictly correlate. In addition to the interface, the CDRs modulate the variable domain framework to a significant extent as shown by swap experiments. Our study reveals a complex interplay of domain stability, association and antigen binding including an unexpected strong mutual influence of the domain framework and the CDRs on stability/association on the one side and antigen binding on the other side.
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Affiliation(s)
- Eva Maria Herold
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany.,Sanofi-Aventis GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Christine John
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Benedikt Weber
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Stephan Kremser
- Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, 85747, Garching, Germany
| | - Jonathan Eras
- ETH Zürich, Otto-Stern-Weg 5, 8093, Zuerich, Switzerland
| | - Carolin Berner
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Sabrina Deubler
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, 85747, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany.
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22
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Wozniak-Knopp G, Stadlmayr G, Perthold JW, Stadlbauer K, Woisetschläger M, Sun H, Rüker F. Designing Fcabs: well-expressed and stable high affinity antigen-binding Fc fragments. Protein Eng Des Sel 2017; 30:657-671. [DOI: 10.1093/protein/gzx042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/16/2017] [Indexed: 01/15/2023] Open
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23
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Toughiri R, Wu X, Ruiz D, Huang F, Crissman JW, Dickey M, Froning K, Conner EM, Cujec TP, Demarest SJ. Comparing domain interactions within antibody Fabs with kappa and lambda light chains. MAbs 2016; 8:1276-1285. [PMID: 27454112 PMCID: PMC5058631 DOI: 10.1080/19420862.2016.1214785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
IgG antibodies are multi-domain proteins with complex inter-domain interactions. Human IgG heavy chains (HCs) associate with light chains (LCs) of the κ or λ isotype to form mature antibodies capable of binding antigen. The HC/LC interaction involves 4 domains: VH and CH1 from the HC and VL and CL from the LC. Human Fabs with κ LCs have been well characterized for their unfolding behaviors and demonstrate a significant level of cooperativity and stabilization when all 4 domains are intact. Very little is known regarding the thermodynamic properties of human Fabs with λ LCs. Here, we dissect the domain contributions to Fab stability for both κ and λ LC-containing Fabs. We find the cooperativity of unfolding between the constant domains, CH1/Cλ, and variable domains, VH/Vλ, within λ LC-containing Fabs is significantly weaker than that of κ LC-containing Fabs. The data suggests there may not be an evolutionary necessity for strong variable/constant domain cooperativity within λ LC-containing Fabs. After investigating the biophysical properties of Fabs with mismatched variable and constant domain subunits (e.g., VH/Vκ paired with CH1/Cλ or T cell receptor Cα/Cβ), the major role of the constant domains for both κ- and λ-containing Fabs may be to reduce the hydrophobic exposure at the VH/VL interface. Even though Fabs with these non-native pairings were thermodynamically less stable, they secreted well from mammalian cells as well behaved monodisperse proteins, which was in contrast to what was observed with the VH/Vκ and VH/Vλ scFvs that secreted as a mixture of monomer and aggregates.
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Affiliation(s)
- Raheleh Toughiri
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Xiufeng Wu
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Diana Ruiz
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Flora Huang
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - John W Crissman
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Mark Dickey
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Karen Froning
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Elaine M Conner
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Thomas P Cujec
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
| | - Stephen J Demarest
- a Eli Lilly and Company, Lilly Biotechnology Center , 10300 Campus Point Drive, San Diego , CA 92130 , USA
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24
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Schinn SM, Broadbent A, Bradley WT, Bundy BC. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA. N Biotechnol 2016; 33:480-7. [PMID: 27085957 DOI: 10.1016/j.nbt.2016.04.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022]
Abstract
A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems.
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Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - William T Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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25
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Direct Delivery of Antigens to Dendritic Cells via Antibodies Specific for Endocytic Receptors as a Promising Strategy for Future Therapies. Vaccines (Basel) 2016; 4:vaccines4020008. [PMID: 27043640 PMCID: PMC4931625 DOI: 10.3390/vaccines4020008] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/15/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022] Open
Abstract
Dendritic cells (DCs) are the most potent professional antigen presenting cells and are therefore indispensable for the control of immunity. The technique of antibody mediated antigen targeting to DC subsets has been the basis of intense research for more than a decade. Many murine studies have utilized this approach of antigen delivery to various kinds of endocytic receptors of DCs both in vitro and in vivo. Today, it is widely accepted that different DC subsets are important for the induction of select immune responses. Nevertheless, many questions still remain to be answered, such as the actual influence of the targeted receptor on the initiation of the immune response to the delivered antigen. Further efforts to better understand the induction of antigen-specific immune responses will support the transfer of this knowledge into novel treatment strategies for human diseases. In this review, we will discuss the state-of-the-art aspects of the basic principles of antibody mediated antigen targeting approaches. A table will also provide a broad overview of the latest studies using antigen targeting including addressed DC subset, targeted receptors, outcome, and applied coupling techniques.
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26
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Gaciarz A, Veijola J, Uchida Y, Saaranen MJ, Wang C, Hörkkö S, Ruddock LW. Systematic screening of soluble expression of antibody fragments in the cytoplasm of E. coli. Microb Cell Fact 2016; 15:22. [PMID: 26809624 PMCID: PMC4727284 DOI: 10.1186/s12934-016-0419-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/11/2016] [Indexed: 12/21/2022] Open
Abstract
Background Disulfide bonds are the most common structural, post-translational modification found in proteins. Antibodies contain up to 25 disulfide bonds depending on type, with scFv fragments containing two disulfides and Fab fragments containing five or six disulfide bonds. The production of antibody fragments that contain native disulfide bonds can be challenging, especially on a large scale. The protein needs to be targeted to prokaryotic periplasm or the eukaryotic endoplasmic reticulum. These compartments are specialised for disulfide bond formation, but both compartments have limitations. Results Here we show that the introduction into the cytoplasm of a catalyst of disulfide bond formation and a catalyst of disulfide bond isomerization allows the efficient formation of natively folded scFv and Fab antibody fragments in the cytoplasm of Escherichia coli with intact reducing pathways. Eleven scFv and eleven Fab fragments were screened and ten of each were obtained in yields of >5 mg/L from deep-well plates. Production of eight of the scFv and all ten of the Fab showed a strong dependence on the addition of the folding factors. Yields of purified scFv of up to 240 mg/L and yields of purified Fab fragments of up to 42 mg/L were obtained. Purified fragments showed circular dichroism spectra consistent with being natively folded and were biologically active. Conclusions Our results show that the efficient production of soluble, biologically active scFv and Fab antibody fragments in the cytoplasm of E. coli is not only possible, but facile. The required components can be easily transferred between different E. coli strains. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0419-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Gaciarz
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Johanna Veijola
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Yuko Uchida
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Mirva J Saaranen
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Chunguang Wang
- Department of Medical Microbiology and Immunology and Medical Research Center, University of Oulu, Oulu, Finland.
| | - Sohvi Hörkkö
- Department of Medical Microbiology and Immunology and Medical Research Center, University of Oulu, Oulu, Finland. .,Nordlab Oulu, Oulu University Hospital, Oulu, Finland.
| | - Lloyd W Ruddock
- Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu, Finland.
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27
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Abstract
Professional secretory cells produce and release abundant proteins. Particularly in case of mutations and/or insufficient chaperoning, these can aggregate and become toxic within or amongst cells. Immunoglobulins (Ig) are no exception. In the extracellular space, certain Ig-L chains form fibrils causing systemic amyloidosis. On the other hand, Ig variants lacking the first constant domain condense in dilated cisternae of the early secretory compartment, called Russell Bodies (RB), frequently observed in plasma cell dyscrasias, autoimmune diseases and chronic infections. RB biogenesis can be recapitulated in lymphoid and non-lymphoid cells by expressing mutant Ig-μ, providing powerful models to investigate the pathophysiology of endoplasmic reticulum storage disorders. Here we analyze the aggregation propensity and the biochemical features of the intra- and extra-cellular Ig deposits in human cells, revealing β-aggregated features for RB.
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Affiliation(s)
- Maria Francesca Mossuto
- Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Diletta Ami
- 1] Department of Physics, University of Milano-Bicocca [2] Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Tiziana Anelli
- 1] Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy [2] Vita-Salute San Raffaele University, Milan, Italy
| | - Claudio Fagioli
- Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Maria Doglia
- 1] Department of Physics, University of Milano-Bicocca [2] Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Roberto Sitia
- 1] Unit of Protein Transport and Secretion, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy [2] Vita-Salute San Raffaele University, Milan, Italy
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28
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Gershenson A, Gierasch LM, Pastore A, Radford SE. Energy landscapes of functional proteins are inherently risky. Nat Chem Biol 2014; 10:884-91. [PMID: 25325699 PMCID: PMC4416114 DOI: 10.1038/nchembio.1670] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 09/19/2014] [Indexed: 01/08/2023]
Abstract
Evolutionary pressure for protein function leads to unavoidable sampling of conformational states that are at risk of misfolding and aggregation. The resulting tension between functional requirements and the risk of misfolding and/or aggregation in the evolution of proteins is becoming more and more apparent. One outcome of this tension is sensitivity to mutation, in which only subtle changes in sequence that may be functionally advantageous can tip the delicate balance toward protein aggregation. Similarly, increasing the concentration of aggregation-prone species by reducing the ability to control protein levels or compromising protein folding capacity engenders increased risk of aggregation and disease. In this Perspective, we describe examples that epitomize the tension between protein functional energy landscapes and aggregation risk. Each case illustrates how the energy landscapes for the at-risk proteins are sculpted to enable them to perform their functions and how the risks of aggregation are minimized under cellular conditions using a variety of compensatory mechanisms.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Lila M Gierasch
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Annalisa Pastore
- Department of Clinical Neurosciences, King’s College London, Denmark Hill Campus, London, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
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