1
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Beatriz M, Rodrigues RJ, Vilaça R, Egas C, Pinheiro PS, Daley GQ, Schlaeger TM, Raimundo N, Rego AC, Lopes C. Extracellular vesicles improve GABAergic transmission in Huntington's disease iPSC-derived neurons. Theranostics 2023; 13:3707-3724. [PMID: 37441602 PMCID: PMC10334823 DOI: 10.7150/thno.81981] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/22/2023] [Indexed: 07/15/2023] Open
Abstract
Background: Extracellular vesicles (EVs) carry bioactive molecules associated with various biological processes, including miRNAs. In both Huntington's disease (HD) models and human samples, altered expression of miRNAs involved in synapse regulation was reported. Recently, the use of EV cargo to reverse phenotypic alterations in disease models with synaptopathy as the end result of the pathophysiological cascade has become an interesting possibility. Methods: Here, we assessed the contribution of EVs to GABAergic synaptic alterations using a human HD model and studied the miRNA content of isolated EVs. Results: After differentiating human induced pluripotent stem cells into electrophysiologically active striatal-like GABAergic neurons, we found that HD-derived neurons displayed reduced density of inhibitory synapse markers and GABA receptor-mediated ionotropic signaling. Treatment with EVs secreted by control (CTR) fibroblasts reversed the deficits in GABAergic synaptic transmission and increased the density of inhibitory synapses in HD-derived neuron cultures, while EVs from HD-derived fibroblasts had the opposite effects on CTR-derived neurons. Moreover, analysis of miRNAs from purified EVs identified a set of differentially expressed miRNAs between manifest HD, premanifest, and CTR lines with predicted synaptic targets. Conclusion: The EV-mediated reversal of the abnormal GABAergic phenotype in HD-derived neurons reinforces the potential role of EV-miRNAs on synapse regulation.
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Affiliation(s)
- Margarida Beatriz
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Ricardo J. Rodrigues
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Rita Vilaça
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Conceição Egas
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
- Biocant- Transfer Technology Association, Biocant Park, Cantanhede, Portugal
| | - Paulo S. Pinheiro
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - George Q. Daley
- Division of Pediatric Hematology/Oncology, Children's Hospital Boston, Boston, MA USA
- Harvard Stem Cell Institute, Boston, MA USA
| | - Thorsten M. Schlaeger
- Division of Pediatric Hematology/Oncology, Children's Hospital Boston, Boston, MA USA
- Harvard Stem Cell Institute, Boston, MA USA
| | - Nuno Raimundo
- MIA - Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - A. Cristina Rego
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- FMUC - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Carla Lopes
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
- IIIUC - Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
- MIA - Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
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2
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Recent developments in miRNA based recombinant protein expression in CHO. Biotechnol Lett 2022; 44:671-681. [PMID: 35507207 DOI: 10.1007/s10529-022-03250-1] [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: 09/25/2021] [Accepted: 03/30/2022] [Indexed: 11/02/2022]
Abstract
It is widely accepted that the growing demand for recombinant therapeutic proteins has led to the expansion of the biopharmaceutical industry and the development of strategies to increase recombinant protein production in mammalian cell lines such as SP2/0 HEK and particularly Chinese hamster ovary cells. For a long time now, most investigations have been focused on increasing host cell productivity using genetic manipulating of cellular processes like cell cycle, apoptosis, cell growth, protein secretory and other pathways. In recent decades MicroRNAs beside different genetic engineering tools (e.g., TALEN, ZFN, and Crisper/Cas) have attracted further attention as a tool in the genetic engineering of host cells to increase protein expression levels. Their ability to simultaneously target multiple mRNAs involved in one or more cellular processes made them a favorable tool in this field. Accordingly, this study aimed to review the methods of selecting target miRNA for cell line engineering, miRNA gain- or loss-of-function strategies, examples of laboratory and pilot studies in this field and discussed advantages and disadvantages of this technology.
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3
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Quilang RC, Lui S, Forbes K. miR-514a-3p: a novel SHP-2 regulatory miRNA that modulates human cytotrophoblast proliferation. J Mol Endocrinol 2022; 68:99-110. [PMID: 34792485 PMCID: PMC8789026 DOI: 10.1530/jme-21-0175] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/18/2021] [Indexed: 11/08/2022]
Abstract
Src homology-2 domain-containing protein tyrosine phosphatase 2 (SHP-2), encoded by the PTPN11 gene, forms a central component of multiple signalling pathways and is required for insulin-like growth factor (IGF)-induced placental growth. Altered expression of SHP-2 is associated with aberrant placental and fetal growth indicating that drugs modulating SHP-2 expression may improve adverse pregnancy outcome associated with altered placental growth. We have previously demonstrated that placental PTPN11/SHP-2 expression is controlled by miRNAs. SHP-2 regulatory miRNAs may have therapeutic potential; however, the individual miRNA(s) that regulate SHP-2 expression in the placenta remain to be established. We performed in silico analysis of 3'UTR target prediction databases to identify libraries of Hela cells transfected with individual miRNA mimetics, enriched in potential SHP-2 regulatory miRNAs. Analysis of PTPN11 levels by quantitative (q) PCR revealed that miR-758-3p increased, while miR-514a-3p reduced PTPN11 expression. The expression of miR-514a-3p and miR-758-3p within the human placenta was confirmed by qPCR; miR-514a-3p (but not miR-758-3p) levels inversely correlated with PTPN11 expression. To assess the interaction between these miRNAs and PTPN11/SHP-2, specific mimetics were transfected into first-trimester human placental explants and then cultured for up to 4 days. Overexpression of miR-514a-3p, but not miR-758-3p, significantly reduced PTPN11 and SHP-2 expression. microRNA-ribonucleoprotein complex (miRNP)-associated mRNA assays confirmed that this interaction was direct. miR-514a-3p overexpression attenuated IGF-I-induced trophoblast proliferation (BrdU incorporation). miR-758-3p did not alter trophoblast proliferation. These data demonstrate that by modulating SHP-2 expression, miR-514a-3p is a novel regulator of IGF signalling and proliferation in the human placenta and may have therapeutic potential in pregnancies complicated by altered placental growth.
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Affiliation(s)
- Rachel C Quilang
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - Sylvia Lui
- Maternal and Fetal Health Research Centre, Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- St. Mary’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Karen Forbes
- Leeds Institute of Cardiovascular and Metabolic Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
- Maternal and Fetal Health Research Centre, Division of Developmental Biology and Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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4
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Abaandou L, Quan D, Shiloach J. Affecting HEK293 Cell Growth and Production Performance by Modifying the Expression of Specific Genes. Cells 2021; 10:cells10071667. [PMID: 34359846 PMCID: PMC8304725 DOI: 10.3390/cells10071667] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/22/2022] Open
Abstract
The HEK293 cell line has earned its place as a producer of biotherapeutics. In addition to its ease of growth in serum-free suspension culture and its amenability to transfection, this cell line’s most important attribute is its human origin, which makes it suitable to produce biologics intended for human use. At the present time, the growth and production properties of the HEK293 cell line are inferior to those of non-human cell lines, such as the Chinese hamster ovary (CHO) and the murine myeloma NSO cell lines. However, the modification of genes involved in cellular processes, such as cell proliferation, apoptosis, metabolism, glycosylation, secretion, and protein folding, in addition to bioprocess, media, and vector optimization, have greatly improved the performance of this cell line. This review provides a comprehensive summary of important achievements in HEK293 cell line engineering and on the global engineering approaches and functional genomic tools that have been employed to identify relevant genes for targeted engineering.
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Affiliation(s)
- Laura Abaandou
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
- Department of Chemistry and Biochemistry, College of Science, George Mason University, Fairfax, VA 22030, USA
| | - David Quan
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
| | - Joseph Shiloach
- Biotechnology Core Laboratory National Institutes of Diabetes, Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; (L.A.); (D.Q.)
- Correspondence:
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5
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Abaandou L, Sharma AK, Shiloach J. Knockout of the caspase 8-associated protein 2 gene improves recombinant protein expression in HEK293 cells through up-regulation of the cyclin-dependent kinase inhibitor 2A gene. Biotechnol Bioeng 2020; 118:186-198. [PMID: 32910455 DOI: 10.1002/bit.27561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/29/2020] [Accepted: 09/03/2020] [Indexed: 12/21/2022]
Abstract
Cell lines used in bioproduction are routinely engineered to improve their production efficiency. Numerous strategies, such as random mutagenesis, RNA interference screens, and transcriptome analyses have been employed to identify effective engineering targets. A genome-wide small interfering RNA screen previously identified the CASP8AP2 gene as a potential engineering target for improved expression of recombinant protein in the HEK293 cell line. Here, we validate the CASP8AP2 gene as an engineering target in HEK293 cells by knocking it out using CRISPR/Cas9 genome editing and assessing the effect of its knockout on recombinant protein expression, cell growth, cell viability, and overall gene expression. HEK293 cells lacking CASP8AP2 showed a seven-fold increase in specific expression of recombinant luciferase and a 2.5-fold increase in specific expression of recombinant SEAP, without significantly affecting cell growth and viability. Transcriptome analysis revealed that the deregulation of the cell cycle, specifically the upregulation of the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene, contributed to the improvement in recombinant protein expression in CASP8AP2 deficient cells. The results validate the CASP8AP2 gene is a viable engineering target for improved recombinant protein expression in the HEK293 cell line.
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Affiliation(s)
- Laura Abaandou
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA.,Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA, USA
| | - Ashish K Sharma
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland, USA
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6
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Amadi IM, Agrawal V, Christianson T, Bardliving C, Shamlou P, LeBowitz JH. Inhibition of endogenous miR-23a/miR-377 in CHO cells enhances difficult-to-express recombinant lysosomal sulfatase activity. Biotechnol Prog 2020; 36:e2974. [PMID: 31990124 DOI: 10.1002/btpr.2974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/11/2019] [Accepted: 01/22/2020] [Indexed: 11/10/2022]
Abstract
Difficult-to-express (DTE) recombinant proteins such as multi-specific proteins, DTE monoclonal antibodies, and lysosomal enzymes have seen difficulties in manufacturability using Chinese hamster ovary (CHO) cells or other mammalian cells as production platforms. CHO cells are preferably used for recombinant protein production for their ability to secrete human-like recombinant proteins with posttranslational modification, resistance to viral infection, and familiarity with drug regulators. However, despite huge progress made in engineering CHO cells for high volumetric productivity, DTE proteins like recombinant lysosomal sulfatase represent one of the poorly understood proteins. Furthermore, there is growing interest in the use of microRNA (miRNA) to engineer CHO cells expressing DTE proteins to improve cell performance of relevant bioprocess phenotypes. To our knowledge, no research has been done to improve CHO cell production of DTE recombinant lysosomal sulfatase using miRNA. We identified miR-23a and miR-377 as miRNAs predicted to target SUMF1, an activator of sulfatases, using in silico prediction tools. Transient inhibition of CHO endogenous miR-23a/miR-377 significantly enhanced recombinant sulfatase enzyme-specific activity by ~15-21% compared to scramble without affecting cell growth. Though inhibition of miR-23a/miR-377 had no significant effect on the mRNA and protein levels of SUMF1, overexpression of miR-23a/377 caused ~30% and ~27-29% significant reduction in endogenous SUMF1 protein and mRNA expression levels, respectively. In summary, our data demonstrate the importance of using miRNA to optimize the CHO cell line secreting DTE recombinant lysosomal sulfatase.
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Affiliation(s)
- Ifeanyi Michael Amadi
- BioMarin Pharmaceutical Inc., Novato, California.,Keck Graduate Institute, Claremont, California
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7
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Inwood S, Abaandou L, Betenbaugh M, Shiloach J. Improved protein expression in HEK293 cells by over-expressing miR-22 and knocking-out its target gene, HIPK1. N Biotechnol 2019; 54:28-33. [PMID: 31425885 DOI: 10.1016/j.nbt.2019.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/01/2019] [Accepted: 08/15/2019] [Indexed: 02/08/2023]
Abstract
Stable cell lines can continuously produce a recombinant protein without the need to repeatedly engineer the genome. In a previous study HIPK1, Homeodomain-interacting Protein Kinase 1, was found to be a target of the microRNA miR-22 that, when repressed, improved expression of both an intracellular and a secreted protein. In this report, HEK293 cells stably over-expressing miR-22 were compared with HEK293 with knockout of HIPK1, executed by CRISPR/Cas9, for their ability to improve recombinant protein expression. In this model case of luciferase, over-expression of miR-22 improved overall activity 2.4-fold while the HIPK1 knockout improved overall activity 4.7-fold.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA; Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Laura Abaandou
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering Johns Hopkins University, Baltimore, Maryland, 21218, USA
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892, USA.
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8
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Rodrigues Lopes I, Silva RJ, Caramelo I, Eulalio A, Mano M. Shedding light on microRNA function via microscopy-based screening. Methods 2019; 152:55-64. [DOI: 10.1016/j.ymeth.2018.09.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/13/2018] [Accepted: 09/28/2018] [Indexed: 12/24/2022] Open
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9
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Abaandou L, Shiloach J. Knocking out Ornithine Decarboxylase Antizyme 1 ( OAZ1) Improves Recombinant Protein Expression in the HEK293 Cell Line. Med Sci (Basel) 2018; 6:medsci6020048. [PMID: 29890687 PMCID: PMC6024716 DOI: 10.3390/medsci6020048] [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: 04/02/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 12/13/2022] Open
Abstract
Creating efficient cell lines is a priority for the biopharmaceutical industry, which produces biologicals for various uses. A recent approach to achieving this goal is the use of non-coding RNAs, microRNA (miRNA) and small interfering RNA (siRNA), to identify key genes that can potentially improve production or growth. The ornithine decarboxylase antizyme 1 (OAZ1) gene, a negative regulator of polyamine biosynthesis, was identified in a genome-wide siRNA screen as a potential engineering target, because its knock down by siRNA increased recombinant protein expression from human embryonic kidney 293 (HEK293) cells by two-fold. To investigate this further, the OAZ1 gene in HEK293 cells was knocked out using CRISPR genome editing. The OAZ1 knockout cell lines displayed up to four-fold higher expression of both stably and transiently expressed proteins, with comparable growth and metabolic activity to the parental cell line; and an approximately three-fold increase in intracellular polyamine content. The results indicate that genetic inactivation of OAZ1 in HEK293 cells is an effective strategy to improve recombinant protein expression in HEK293 cells.
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Affiliation(s)
- Laura Abaandou
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
- Department of Chemistry and Biochemistry, George Mason University, Fairfax, VA 22030, USA.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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10
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Weis BL, Guth N, Fischer S, Wissing S, Fradin S, Holzmann KH, Handrick R, Otte K. Stable miRNA overexpression in human CAP cells: Engineering alternative production systems for advanced manufacturing of biologics using miR-136 and miR-3074. Biotechnol Bioeng 2018; 115:2027-2038. [PMID: 29665036 DOI: 10.1002/bit.26715] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/15/2018] [Accepted: 04/09/2018] [Indexed: 01/06/2023]
Abstract
Chinese hamster ovary (CHO) cells still represent the major production host for therapeutic proteins. However, multiple limitations have been acknowledged leading to the search for alternative expression systems. CEVEC's amniocyte production (CAP) cells are human production cells demonstrated to enable efficient overexpression of recombinant proteins with human glycosylation pattern. However, CAP cells have not yet undergone any engineering approaches to optimize process parameters for a cheaper and more sustainable production of biopharmaceuticals. Thus, we assessed the possibility to enhance CAP cell production capacity via cell engineering using miRNA technology. Based on a previous high-content miRNA screen in CHO-SEAP cells, selected pro-productive miRNAs including, miR-99b-3p, 30a-5p, 329-3p, 483-3p, 370-3p, 219-1-3p, 3074-5p, 136-3p, 30e-5p, 1a-3p, and 484-5p, were shown to act pro-productive and product independent upon transient transfection in CAP and CHO antibody expressing cell lines. Stable expression of miRNAs established seven CAP cell pools with an overexpression of the pro-productive miRNA strand. Subsequent small-scale screening as well as upscaling batch experiments identified miR-136 and miR-3074 to significantly increase final mAb concentration in CAP-mAb cells. Transcriptomic changes analyzed by microarrays identified several lncRNAs as well as growth and apoptosis-related miRNAs to be differentially regulated in CAP-mAb-miR-136 and -miR-3074. This study presents the first engineering approach to optimize the alternative human expression system of CAP-cells.
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Affiliation(s)
- Benjamin L Weis
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Nadine Guth
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Simon Fischer
- Boehringer Ingelheim Pharma GmbH & Co KG, Cell Culture Development CMB, Biberach, Germany
| | | | | | | | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Biberach, Germany
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11
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Wu J, Ding J, Yang J, Guo X, Zheng Y. MicroRNA Roles in the Nuclear Factor Kappa B Signaling Pathway in Cancer. Front Immunol 2018; 9:546. [PMID: 29616037 PMCID: PMC5868594 DOI: 10.3389/fimmu.2018.00546] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 03/02/2018] [Indexed: 12/19/2022] Open
Abstract
Nuclear factor kappa B (NF-κB) is a pluripotent and crucial dimer transcription factor that orchestrates various physiological and pathological processes, especially cell proliferation, inflammation, and cancer development and progression. NF-κB expression is transient and tightly regulated in normal cells, but it is activated in cancer cells. Recently, numerous studies have demonstrated microRNAs (miRNAs) play a vital role in the NF-κB signaling pathway and NF-κB-associated immune responses, radioresistance and drug resistance of cancer, some acting as inhibitors and the others as activators. Although it is still in infancy, targeting NF-κB or the NF-κB signaling pathway by miRNAs is becoming a promising strategy of cancer treatment.
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Affiliation(s)
- Jin’en Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
| | - Juntao Ding
- College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Jing Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
| | - Xiaola Guo
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute (CAAS), Lanzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China
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12
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Methods for Using Small Non-Coding RNAs to Improve Recombinant Protein Expression in Mammalian Cells. Genes (Basel) 2018; 9:genes9010025. [PMID: 29315258 PMCID: PMC5793178 DOI: 10.3390/genes9010025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/19/2017] [Accepted: 01/03/2018] [Indexed: 12/27/2022] Open
Abstract
The ability to produce recombinant proteins by utilizing different “cell factories” revolutionized the biotherapeutic and pharmaceutical industry. Chinese hamster ovary (CHO) cells are the dominant industrial producer, especially for antibodies. Human embryonic kidney cells (HEK), while not being as widely used as CHO cells, are used where CHO cells are unable to meet the needs for expression, such as growth factors. Therefore, improving recombinant protein expression from mammalian cells is a priority, and continuing effort is being devoted to this topic. Non-coding RNAs are RNA segments that are not translated into a protein and often have a regulatory role. Since their discovery, major progress has been made towards understanding their functions. Non-coding RNA has been investigated extensively in relation to disease, especially cancer, and recently they have also been used as a method for engineering cells to improve their protein expression capability. In this review, we provide information about methods used to identify non-coding RNAs with the potential of improving recombinant protein expression in mammalian cell lines.
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13
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Inwood S, Buehler E, Betenbaugh M, Lal M, Shiloach J. Identifying HIPK1 as Target of miR-22-3p Enhancing Recombinant Protein Production From HEK 293 Cell by Using Microarray and HTP siRNA Screen. Biotechnol J 2017; 13. [PMID: 28987030 DOI: 10.1002/biot.201700342] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 09/11/2017] [Indexed: 01/20/2023]
Abstract
Protein expression from human embryonic kidney cells (HEK 293) is an important tool for structural and clinical studies. It is previously shown that microRNAs (small, noncoding RNAs) are effective means for improved protein expression from these cells, and by conducting a high-throughput screening of the human microRNA library, several microRNAs are identified as potential candidates for improving expression. From these, miR-22-3p is chosen for further study since it increased the expression of luciferase, two membrane proteins and a secreted fusion protein with minimal effect on the cells' growth and viability. Since each microRNA can interact with several gene targets, it is of interest to identify the repressed genes for understanding and exploring the improved expression mechanism for further implementation. Here, the authors describe a novel approach for identification of the target genes by integrating the differential gene expression analysis with information obtained from our previously conducted high-throughput siRNA screening. The identified genes were validated as being involved in improving luciferase expression by using siRNA and qRT-PCR. Repressing the target gene, HIPK1, is found to increase luciferase and GPC3 expression 3.3- and 2.2-fold, respectively.
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Affiliation(s)
- Sarah Inwood
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland 20892, USA.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Eugen Buehler
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Madhu Lal
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, MD 20850
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland 20892, USA
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14
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Meyer HJ, Reilly D, Martin SE, Wong AW. Identification of a novel miRNA that increases transient protein expression in combination with valproic acid. Biotechnol Prog 2017; 33:1139-1145. [DOI: 10.1002/btpr.2488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/18/2017] [Indexed: 12/29/2022]
Affiliation(s)
| | - Dorothea Reilly
- Dept. of Early Stage Cell Culture; 1 DNA Way South San Francisco CA 94080
| | - Scott E. Martin
- Department of Discovery Oncology; Genentech; 1 DNA Way South San Francisco CA 94080
| | - Athena W. Wong
- Dept. of Early Stage Cell Culture; 1 DNA Way South San Francisco CA 94080
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Xiao S, Chen YC, Buehler E, Mandal S, Mandal A, Betenbaugh M, Park MH, Martin S, Shiloach J. Genome-scale RNA interference screen identifies antizyme 1 (OAZ1) as a target for improvement of recombinant protein production in mammalian cells. Biotechnol Bioeng 2016; 113:2403-15. [PMID: 27215166 DOI: 10.1002/bit.26017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/15/2016] [Accepted: 05/16/2016] [Indexed: 12/18/2022]
Abstract
For the purpose of improving recombinant protein production from mammalian cells, an unbiased, high-throughput whole-genome RNA interference screen was conducted using human embryonic kidney 293 (HEK 293) cells expressing firefly luciferase. A 21,585 human genes were individually silenced with three different siRNAs for each gene. The screen identified 56 genes that led to the greatest improvement in luciferase expression. These genes were found to be included in several pathways involved in spliceosome formation and mRNA processing, transcription, metabolic processes, transport, and protein folding. The 10 genes that most enhanced protein expression when downregulated, were further confirmed by measuring the effect of their silencing on the expression of three additional recombinant proteins. Among the confirmed genes, OAZ1-the gene encoding the ornithine decarboxylase antizyme1-was selected for detailed investigation, since its silencing improved the reporter protein production without affecting cell viability. Silencing OAZ1 caused an increase of the ornithine decarboxylase enzyme and the cellular levels of putrescine and spermidine; an indication that increased cellular polyamines enhances luciferase expression without affecting its transcription. The study shows that OAZ1 is a novel target for improving expression of recombinant proteins. The genome-scale screening performed in this work can establish the foundation for targeted design of an efficient mammalian cell platform for various biotechnological applications. Biotechnol. Bioeng. 2016;113: 2403-2415. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Su Xiao
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Yu Chi Chen
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, Maryland, 20850
| | - Eugen Buehler
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, Maryland, 20850
| | - Swati Mandal
- Molecular and Cellular Biochemistry Section, NIDCR, NIH, Bethesda, Maryland
| | - Ajeet Mandal
- Molecular and Cellular Biochemistry Section, NIDCR, NIH, Bethesda, Maryland
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Myung Hee Park
- Molecular and Cellular Biochemistry Section, NIDCR, NIH, Bethesda, Maryland
| | - Scott Martin
- Chemical Genomics Center, National Center for Advancing Translational Sciences, NIH, Rockville, Maryland, 20850.
| | - Joseph Shiloach
- Biotechnology Core Laboratory NIDDK, NIH, Bethesda, Maryland, 20892.
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16
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Emmerling VV, Fischer S, Stiefel F, Holzmann K, Handrick R, Hesse F, Hörer M, Kochanek S, Otte K. Temperature-sensitive miR-483 is a conserved regulator of recombinant protein and viral vector production in mammalian cells. Biotechnol Bioeng 2015; 113:830-41. [DOI: 10.1002/bit.25853] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/15/2015] [Accepted: 10/08/2015] [Indexed: 01/19/2023]
Affiliation(s)
- Verena V. Emmerling
- Department of Gene Therapy; Ulm University; Ulm Germany
- Rentschler Biotechnologie GmbH; Erwin-Rentschler-Str. 21; Laupheim Germany
| | - Simon Fischer
- Institute of Applied Biotechnology; Biberach University of Applied Sciences; Hubertus-Liebrecht-Str. 35 88400 Biberach Germany
| | - Fabian Stiefel
- Institute of Applied Biotechnology; Biberach University of Applied Sciences; Hubertus-Liebrecht-Str. 35 88400 Biberach Germany
| | | | - René Handrick
- Institute of Applied Biotechnology; Biberach University of Applied Sciences; Hubertus-Liebrecht-Str. 35 88400 Biberach Germany
| | - Friedemann Hesse
- Institute of Applied Biotechnology; Biberach University of Applied Sciences; Hubertus-Liebrecht-Str. 35 88400 Biberach Germany
| | - Markus Hörer
- Rentschler Biotechnologie GmbH; Erwin-Rentschler-Str. 21; Laupheim Germany
- VBBio Consultant; Auf dem Berg 17; Laupheim Germany
| | | | - Kerstin Otte
- Institute of Applied Biotechnology; Biberach University of Applied Sciences; Hubertus-Liebrecht-Str. 35 88400 Biberach Germany
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