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Kumar V, Barwal A, Sharma N, Mir DS, Kumar P, Kumar V. Therapeutic proteins: developments, progress, challenges, and future perspectives. 3 Biotech 2024; 14:112. [PMID: 38510462 PMCID: PMC10948735 DOI: 10.1007/s13205-024-03958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Proteins are considered magic molecules due to their enormous applications in the health sector. Over the past few decades, therapeutic proteins have emerged as a promising treatment option for various diseases, particularly cancer, cardiovascular disease, diabetes, and others. The formulation of protein-based therapies is a major area of research, however, a few factors still hinder the large-scale production of these therapeutic products, such as stability, heterogenicity, immunogenicity, high cost of production, etc. This review provides comprehensive information on various sources and production of therapeutic proteins. The review also summarizes the challenges currently faced by scientists while developing protein-based therapeutics, along with possible solutions. It can be concluded that these proteins can be used in combination with small molecular drugs to give synergistic benefits in the future.
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Affiliation(s)
- Vimal Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Arti Barwal
- Department of Microbial Biotechnology, Panjab University, South Campus, Sector-25, Chandigarh, 160014 India
| | - Nitin Sharma
- Department of Biotechnology, Chandigarh Group of Colleges, Mohali, Punjab 140307 India
| | - Danish Shafi Mir
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 India
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
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Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up. Microb Cell Fact 2021; 20:124. [PMID: 34193127 PMCID: PMC8246677 DOI: 10.1186/s12934-021-01617-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
The manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.
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A Novel Methanol-Free Platform for Extracellular Expression of rhGM-CSF in Pichia pastoris. Mol Biotechnol 2019; 61:521-527. [PMID: 31054084 DOI: 10.1007/s12033-019-00182-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The production of the recombinant proteins under the control of AOX1 promoter is a one of the most common expression systems in the methylotrophic yeast Pichia pastoris which is induced by methanol. The application of this expression platform is restricted by the toxicity and inflammatory nature of methanol, especially in food and pharmaceutical products. Human granulocyte macrophage-colony stimulating factor (hGM-CSF) is an important pharmaceutical protein, playing a crucial role in the proliferation and differentiation of innate immune cells. In this study, a methanol-free expression platform for extracellular expression of hGM-CSF was developed. To attain this goal, a novel constructed expression vector pEP(α)101, carrying the FMD promoter regulating recombinant expression by glycerol derepression was designed. The optimized hGM-CSF gene was subcloned into pEP(α)101 and transformed into P. pastoris. The expression of rhGM-CSF in three different culture media were investigated. Based on the observed heterogeneous glycosylation pattern on SDS-PAGE and western blot, the glycoproteins were deglycosylated to remove carbohydrate units. According to the results, the novel methanol independent PFMD expression platform would be a suitable candidate for driving heterologous gene expression especially for the production of food-grade and therapeutically important recombinant proteins.
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Park YK, Vandermies M, Soudier P, Telek S, Thomas S, Nicaud JM, Fickers P. Efficient expression vectors and host strain for the production of recombinant proteins by Yarrowia lipolytica in process conditions. Microb Cell Fact 2019; 18:167. [PMID: 31601223 PMCID: PMC6785901 DOI: 10.1186/s12934-019-1218-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background The oleaginous yeast Yarrowia lipolytica is increasingly used as an alternative cell factory for the production of recombinant proteins. Recently, regulated promoters from genes EYK1 and EYD1, encoding an erythrulose kinase and an erythritol dehydrogenase, respectively, have been identified and characterized in this yeast. Hybrid promoters up-regulated by polyols such as erythritol and erythrulose have been developed based on tandem copies of upstream activating sequences from EYK1 (UAS1EYK1) and XPR2 (encoding extracellular protease, UAS1XPR2) promoters. Results The strength of native (pEYD1) and engineered promoters (pEYK1-3AB and pHU8EYK) was compared using the extracellular lipase CalB from Candida antarctica as a model protein and a novel dedicated host strain. This latter is engineered in polyol metabolism and allows targeted chromosomal integration. In process conditions, engineered promoters pEYK1-3AB and pHU8EYK yielded 2.8 and 2.5-fold higher protein productivity, respectively, as compared to the reference pTEF promoter. We also demonstrated the possibility of multicopy integration in the newly developed host strain. In batch bioreactor, the CalB multi-copy strain RIY406 led to a 1.6 fold increased lipase productivity (45,125 U mL−1) within 24 h as compared to the mono-copy strain. Conclusions The expression system described herein appears promising for recombinant extracellular protein production in Y. lipolytica.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Marie Vandermies
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Paul Soudier
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Samuel Telek
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, Gembloux, Belgium
| | - Stéphane Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France. .,Micalis Institute, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, INRA-AgroParisTech, Domaine de Vilvert, 78352, Jouy-en-Josas, France.
| | - Patrick Fickers
- Microbial Processes and Interactions, TERRA Teaching and Research Centre, University of Liège - Gembloux Agro-Bio Tech, Gembloux, Belgium
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Vandermies M, Fickers P. Bioreactor-Scale Strategies for the Production of Recombinant Protein in the Yeast Yarrowia lipolytica. Microorganisms 2019; 7:E40. [PMID: 30704141 PMCID: PMC6406515 DOI: 10.3390/microorganisms7020040] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 01/02/2023] Open
Abstract
Recombinant protein production represents a multibillion-dollar market. Therefore, it constitutes an important research field both in academia and industry. The use of yeast as a cell factory presents several advantages such as ease of genetic manipulation, growth at high cell density, and the possibility of post-translational modifications. Yarrowia lipolytica is considered as one of the most attractive hosts due to its ability to metabolize raw substrate, to express genes at a high level, and to secrete protein in large amounts. In recent years, several reviews have been dedicated to genetic tools developed for this purpose. Though the construction of efficient cell factories for recombinant protein synthesis is important, the development of an efficient process for recombinant protein production in a bioreactor constitutes an equally vital aspect. Indeed, a sports car cannot drive fast on a gravel road. The aim of this review is to provide a comprehensive snapshot of process tools to consider for recombinant protein production in bioreactor using Y. lipolytica as a cell factory, in order to facilitate the decision-making for future strain and process engineering.
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Affiliation(s)
- Marie Vandermies
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, University of Liège⁻Gembloux AgroBio Tech, 5030 Gembloux, Belgium.
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, University of Liège⁻Gembloux AgroBio Tech, 5030 Gembloux, Belgium.
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Celińska E, Nicaud JM. Filamentous fungi-like secretory pathway strayed in a yeast system: peculiarities of Yarrowia lipolytica secretory pathway underlying its extraordinary performance. Appl Microbiol Biotechnol 2018; 103:39-52. [PMID: 30353423 PMCID: PMC6311201 DOI: 10.1007/s00253-018-9450-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
Abstract
Microbial production of secretory proteins constitutes one of the key branches of current industrial biotechnology, earning billion dollar (USD) revenues each year. That industrial branch strongly relies on fluent operation of the secretory machinery within a microbial cell. The secretory machinery, directing the nascent polypeptide to its final destination, constitutes a highly complex system located across the eukaryotic cell. Numerous molecular identities of diverse structure and function not only build the advanced network assisting folding, maturation and secretion of polypeptides but also serve as sensors and effectors of quality control points. All these events must be harmoniously orchestrated to enable fluent processing of the protein traffic. Availability of these elements is considered to be the limiting factor determining capacity of protein traffic, which is of crucial importance upon biotechnological production of secretory proteins. The main purpose of this work is to review and discuss findings concerning secretory machinery operating in a non-conventional yeast species, Yarrowia lipolytica, and to highlight peculiarities of this system prompting its use as the production host. The reviewed literature supports the thesis that secretory machinery in Y. lipolytica is characterized by significantly higher complexity than a canonical yeast protein secretion pathway, making it more similar to filamentous fungi-like systems in this regard.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Jean-Marc Nicaud
- INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Micalis Institute, Domaine de Vilvert, 78352, Jouy-en-Josas, France
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Celińska E, Borkowska M, Białas W, Korpys P, Nicaud JM. Robust signal peptides for protein secretion in Yarrowia lipolytica: identification and characterization of novel secretory tags. Appl Microbiol Biotechnol 2018; 102:5221-5233. [PMID: 29704042 PMCID: PMC5959983 DOI: 10.1007/s00253-018-8966-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/13/2018] [Accepted: 03/24/2018] [Indexed: 12/18/2022]
Abstract
Upon expression of a given protein in an expression host, its secretion into the culture medium or cell-surface display is frequently advantageous in both research and industrial contexts. Hence, engineering strategies targeting folding, trafficking, and secretion of the proteins gain considerable interest. Yarrowia lipolytica has emerged as an efficient protein expression platform, repeatedly proved to be a competitive secretor of proteins. Although the key role of signal peptides (SPs) in secretory overexpression of proteins and their direct effect on the final protein titers are widely known, the number of reports on manipulation with SPs in Y. lipolytica is rather scattered. In this study, we assessed the potential of ten different SPs for secretion of two heterologous proteins in Y. lipolytica. Genomic and transcriptomic data mining allowed us to select five novel, previously undescribed SPs for recombinant protein secretion in Y. lipolytica. Their secretory potential was assessed in comparison with known, widely exploited SPs. We took advantage of Golden Gate approach, for construction of expression cassettes, and micro-volume enzymatic assays, for functional screening of large libraries of recombinant strains. Based on the adopted strategy, we identified novel secretory tags, characterized their secretory capacity, indicated the most potent SPs, and suggested a consensus sequence of a potentially robust synthetic SP to expand the molecular toolbox for engineering Y. lipolytica.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Monika Borkowska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Paulina Korpys
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Jean-Marc Nicaud
- INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Domaine de Vilvert, Micalis Institute, 78352, Jouy-en-Josas, France
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Tran AM, Nguyen TT, Nguyen CT, Huynh-Thi XM, Nguyen CT, Trinh MT, Tran LT, Cartwright SP, Bill RM, Tran-Van H. Pichia pastoris versus Saccharomyces cerevisiae: a case study on the recombinant production of human granulocyte-macrophage colony-stimulating factor. BMC Res Notes 2017; 10:148. [PMID: 28376863 PMCID: PMC5379694 DOI: 10.1186/s13104-017-2471-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/27/2017] [Indexed: 11/10/2022] Open
Abstract
Background Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) is a glycoprotein that has been approved by the FDA for the treatment of neutropenia and leukemia in combination with chemotherapies. Recombinant hGM-CSF is produced industrially using the baker’s yeast, Saccharomyces cerevisiae, by large-scale fermentation. The methylotrophic yeast, Pichia pastoris, has emerged as an alternative host cell system due to its shorter and less immunogenic glycosylation pattern together with higher cell density growth and higher secreted protein yield than S. cerevisiae. In this study, we compared the pipeline from gene to recombinant protein in these two yeasts. Results Codon optimization in silico for both yeast species showed no difference in frequent codon usage. However, rhGM-CSF expressed from S. cerevisiae BY4742 showed a significant discrepancy in molecular weight from those of P. pastoris X33. Analysis showed purified rhGM-CSF species with molecular weights ranging from 30 to more than 60 kDa. Fed-batch fermentation over 72 h showed that rhGM-CSF was more highly secreted from P. pastoris than S. cerevisiae (285 and 64 mg total secreted protein/L, respectively). Ion exchange chromatography gave higher purity and recovery than hydrophobic interaction chromatography. Purified rhGM-CSF from P. pastoris was 327 times more potent than rhGM-CSF from S. cerevisiae in terms of proliferative stimulating capacity on the hGM-CSF-dependent cell line, TF-1. Conclusion Our data support a view that the methylotrophic yeast P. pastoris is an effective recombinant host for heterologous rhGM-CSF production. Electronic supplementary material The online version of this article (doi:10.1186/s13104-017-2471-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anh-Minh Tran
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam
| | - Thanh-Thao Nguyen
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam
| | - Cong-Thuan Nguyen
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam
| | - Xuan-Mai Huynh-Thi
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam
| | - Cao-Tri Nguyen
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam
| | - Minh-Thuong Trinh
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam
| | - Linh-Thuoc Tran
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam
| | | | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Birmingham, UK
| | - Hieu Tran-Van
- Faculty of Biology and Biotechnology, University of Science, VNU-HCM, Ho Chi Minh, Vietnam.
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Single cell oil production on molasses by Yarrowia lipolytica strains overexpressing DGA2 in multicopy. Appl Microbiol Biotechnol 2015; 99:8065-74. [DOI: 10.1007/s00253-015-6733-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/15/2015] [Accepted: 05/27/2015] [Indexed: 01/30/2023]
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Lipiäinen T, Peltoniemi M, Sarkhel S, Yrjönen T, Vuorela H, Urtti A, Juppo A. Formulation and stability of cytokine therapeutics. J Pharm Sci 2014; 104:307-26. [PMID: 25492409 DOI: 10.1002/jps.24243] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/29/2014] [Accepted: 10/13/2014] [Indexed: 12/12/2022]
Abstract
Cytokines are messenger proteins that regulate the proliferation and differentiation of cells and control immune responses. Interferons, interleukins, and growth factors have applications in cancer, autoimmune, and viral disease treatment. The cytokines are susceptible to chemical and physical instability. This article reviews the structure and stability issues of clinically used cytokines, as well as formulation strategies for improved stability. Some general aspects for identifying most probable stability concerns, selecting excipients, and developing stable cytokine formulations are presented. The vast group of cytokines offers possibilities for new biopharmaceuticals. The formulation approaches of the current cytokine products could facilitate development of new biopharmaceuticals.
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Affiliation(s)
- Tiina Lipiäinen
- University of Helsinki, Faculty of Pharmacy, Helsinki, Finland
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Tao Z, Yang H, Jia D, Wan L, Cheng J, Lu X. Molecular cloning, recombinant expression and characterization of GMCSF from the rhesus monkey, Macaca mulatta. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 40:69-77. [PMID: 23352624 DOI: 10.1016/j.dci.2013.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 01/07/2013] [Accepted: 01/07/2013] [Indexed: 02/05/2023]
Abstract
Recent studies have found that, in addition to hematopoiesis, granulocyte-macrophage colony-stimulating factor (GMCSF) plays pivotal roles in multiple immune disorders. The gene encoding Macaca mulatta GMCSF (mmGMCSF) was cloned from stimulated peripheral blood mononuclear cells (PBMCs). Concanavalin A (Con A) and mismatched allogeneic antigen-stimulation significantly increased the production of mmGMCSF by monkey PBMCs. The gene encoding mature mmGMCSF was first expressed as a soluble fusion protein in Escherichia coli, and native mmGMCSF was further prepared by protease cleavage. The recombinant mmGMCSF induced antigen-presenting dendritic cells from monkey PBMCs, suggesting a central role of mmGMCSF in the immune system of the rhesus monkey. Although the predicted mature mmGMCSF protein differs from human GMCSF (hGMCSF) at six amino acid residues, mmGMCSF showed a strong ability to support human TF-1 cell survival. Additional co-immunoprecipitation experiments revealed that mmGMCSF cross reacts with the hGMCSF receptor (hGMCSFR). In addition, the hGMCSF-neutralizing agents hGMCSFR-Fc and anti-hGMCSF antibody reduced the biological effects of mmGMCSF on TF-1 cells. These results suggest that recombinant mmGMCSF might be used for the in vitro evaluation of novel hGMCSF-neutralizing agents prior to the in vivo preclinical evaluation of these agents in the rhesus monkey model.
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Affiliation(s)
- Ze Tao
- Key Lab of Transplant Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu 610041, China
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