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Allen-Coyle TJ, Roca BC, Costello A, Barron N, Keenan J, Clynes M, O’Neill F, O’Sullivan F. miRNA- and Cell Line-Specific Constraints on Precursor miRNA Processing of Stably Transfected Pancreatic Cancer and Other Mammalian Cells. Int J Mol Sci 2024; 25:5666. [PMID: 38891854 PMCID: PMC11172344 DOI: 10.3390/ijms25115666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
MicroRNAs (miRNAs) regulate approximately one-third of all human genes. The dysregulation of miRNAs has been implicated in the development of numerous human diseases, including cancers. In our investigation focusing on altering specific miRNA expression in human pancreatic cancer cells, we encountered an interesting finding. While two expression vector designs effectively enhanced miR-708 levels, they were unable to elevate mature forms of miR-29b, -1290, -2467, and -6831 in pancreatic cancer cell lines. This finding was also observed in a panel of other non-pancreatic cancer cell lines, suggesting that miRNA processing efficiency was cell line specific. Using a step-by-step approach in each step of miRNA processing, we ruled out alternative strand selection by the RISC complex and transcriptional interference at the primary miRNA (pri-miRNA) level. DROSHA processing and pri-miRNA export from the nucleus also appeared to be occurring normally. We observed precursor (pre-miRNA) accumulation only in cell lines where mature miRNA expression was not achieved, suggesting that the block was occurring at the pre-miRNA stage. To further confirm this, synthetic pre-miRNA mimics that bypass DICER processing were processed into mature miRNAs in all cases. This study has demonstrated the distinct behaviours of different miRNAs with the same vector in the same cell line, the same miRNA between the two vector designs, and with the same miRNA across different cell lines. We identified a stable vector pre-miRNA processing block. Our findings on the structural and sequence differences between successful and non-successful vector designs could help to inform future chimeric miRNA design strategies and act as a guide to other researchers on the intricate processing dynamics that can impact vector efficiency. Our research confirms the potential of miRNA mimics to surmount some of these complexities.
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Affiliation(s)
- Taylor J. Allen-Coyle
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Berta Capella Roca
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Alan Costello
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Niall Barron
- Cell Engineering Group, National Institute for Bioprocessing Research and Training (NIBRT), A94 X099 Dublin, Ireland
| | - Joanne Keenan
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Martin Clynes
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Fiona O’Neill
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
| | - Finbarr O’Sullivan
- The SFI Research Centre for Pharmaceuticals (SSPC), Bernal Institute, University of Limerick, V94 T9PX Limerick, Ireland; (T.J.A.-C.); (F.O.)
- SSPC Research Group, National Institute for Cellular Biotechnology, Life Sciences Institute, Dublin City University, D09 E432 Dublin, Ireland
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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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Chen Q, Wang Y, Dang H, Wu X. MicroRNA-148a-3p inhibits the proliferation of cervical cancer cells by regulating the expression levels of DNMT1 and UTF1. Oncol Lett 2021; 22:617. [PMID: 34257725 DOI: 10.3892/ol.2021.12878] [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: 01/31/2021] [Accepted: 05/21/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRs) serve a key role in carcinogenesis. miR-148a-3p has been demonstrated to act as a tumor suppressor in several tumors, such as epithelial ovarian cancer and esophageal cancer. However, to the best of our knowledge, the role of miR-148a-3p in cervical cancer remains unclear. In the present study, the expression levels of miR-148a-3p measured by reverse transcription-quantitative PCR were significantly decreased in cervical cancer tissues compared with that in normal cervical tissues. Furthermore, overexpression of miR-148a-3p markedly suppressed the proliferation of cervical cancer cells. The luciferase reporter assay demonstrated that DNA methyltransferase 1 (DNMT1) was the target gene of miR-148a-3p and that its expression measured by western blotting was inhibited by miR-148a-3p in cervical cancer cells. Correlation analysis highlighted that the expression levels of the undifferentiated embryonic cell transcription factor-1 (UTF1) were negatively associated with the expression levels of DNMT1 in cervical cancer tissues. Furthermore, DNMT1 knockdown increased the expression of UTF1 and decreased the methylation level of UTF1 promoter. These data demonstrated the expression levels of UTF1 were regulated by DNMT1 methylation in cervical cancer cells. Collectively, the results of the present study suggested that miR-148a-3p may inhibit the proliferation of cervical cancer cells by regulating the expression levels of DNMT1/UTF1, which provides potential therapeutic targets for cervical cancer.
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Affiliation(s)
- Qing Chen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Yidong Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Huimin Dang
- Department of Integrated Traditional Chinese and Western Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
| | - Xiaoling Wu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710004, P.R. China
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Costello A, Parker J, Clynes M, Murphy R. Development of whole-cell and cell-free biosensors for the detection and differentiation of organic and inorganic forms of copper. Metallomics 2020; 12:1729-1734. [PMID: 33029604 DOI: 10.1039/d0mt00146e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The modern world has seen exposure of bacterial communities to toxic metals at selective levels. This manifests itself both intentionally, through medicines and un-intentionally through waste streams. There is growing concern that selective exposure to metals may be linked to microbial resistance to antibiotics. For a microbe to become resistant to a specific metal it must first come in contact with it. The transition metal copper has the ability to enter bacterial cells without need for a copper specific uptake mechanism. Copper is commonly used as an antimicrobial in the healthcare industry, consumer products and as a growth promoter of livestock in the agricultural sector. Here we report a study into the uptake of different organic and inorganic sources of copper. A whole-cell bacterial biosensor was developed to quantify the specific uptake of copper from various sources. Furthermore, a cell-free sensor was utilized to investigate the response to copper sources when uptake is eliminated as a factor. The data within suggest inorganic copper to have greatly reduced uptake compared to organic sources and that there is significant difference between copper oxides, Cu2O and CuO.
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Affiliation(s)
- Alan Costello
- National Institute for Cellular Biotechnology and SSPC-SFI Centre for Pharmaceuticals, Dublin City University, Dublin 9, Ireland.
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Capella Roca B, Lao NT, Clynes M, Doolan P. Investigation and circumvention of transfection inhibition by ferric ammonium citrate in serum-free media for Chinese hamster ovary cells. Biotechnol Prog 2019; 36:e2954. [PMID: 31850663 DOI: 10.1002/btpr.2954] [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: 08/30/2019] [Revised: 11/13/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022]
Abstract
While reliable transfection methods are essential for Chinese hamster ovary (CHO) cell line engineering, reduced transfection efficiencies have been observed in several commercially prepared media. In this study, we aimed to assess common media additives that impede efficiency mediated by three chemical transfection agents: liposomal-based (Lipofectamine 2000), polymer-based (TransIT-X2), and lipopolyplex-based (TransIT-PRO). An in-house GFP-expressing vector and serum-free medium (BCR-F12: developed for the purposes of this study) were used to analyze transient transfection efficiencies of three CHO cell lines (CHO-K1, DG44, DP12). Compared to a selection of commercially available media, BCR-F12 displayed challenges associated with transfection in vendor-prepared formulations, with no detection when liposomal-based methods were used, reduced (<3%) efficiency observed when polymer-based methods were used and only limited efficiency (25%) with lipopolyplexes. Following a stepwise removal protocol, ferric ammonium citrate (FAC) was identified as the critical factor impeding transfection, with transfection enabled with the liposomal- and polymer-based methods and a 1.3- to 7-fold increased lipopolyplex efficiency observed in all cell lines in FAC-depleted media (-FAC), although lower viabilities were observed. Subsequent early addition of FAC (0.5-5 hr post-transfection) revealed 0.5 hr post-transfection as the optimal time to supplement in order to achieve transfection efficiencies similar to -FAC medium while retaining optimal cellular viabilities. In conclusion, FAC was observed to interfere with DNA transfection acting at early stages in all transfection agents and all cell lines studied, and a practical strategy to circumvent this problem is suggested.
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Affiliation(s)
- Berta Capella Roca
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland.,SSPC-SFI Centre for Pharmaceuticals, Dublin City University, Dublin 9, Ireland
| | - Nga T Lao
- National Institute for Bioprocessing Research and Training, University College Dublin, Dublin, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland.,SSPC-SFI Centre for Pharmaceuticals, Dublin City University, Dublin 9, Ireland
| | - Padraig Doolan
- National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland
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Chassin H, Müller M, Tigges M, Scheller L, Lang M, Fussenegger M. A modular degron library for synthetic circuits in mammalian cells. Nat Commun 2019; 10:2013. [PMID: 31043592 PMCID: PMC6494899 DOI: 10.1038/s41467-019-09974-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 04/04/2019] [Indexed: 01/26/2023] Open
Abstract
Tight control over protein degradation is a fundamental requirement for cells to respond rapidly to various stimuli and adapt to a fluctuating environment. Here we develop a versatile, easy-to-handle library of destabilizing tags (degrons) for the precise regulation of protein expression profiles in mammalian cells by modulating target protein half-lives in a predictable manner. Using the well-established tetracycline gene-regulation system as a model, we show that the dynamics of protein expression can be tuned by fusing appropriate degron tags to gene regulators. Next, we apply this degron library to tune a synthetic pulse-generating circuit in mammalian cells. With this toolbox we establish a set of pulse generators with tailored pulse lengths and magnitudes of protein expression. This methodology will prove useful in the functional roles of essential proteins, fine-tuning of gene-expression systems, and enabling a higher complexity in the design of synthetic biological systems in mammalian cells.
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Affiliation(s)
- Hélène Chassin
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Marius Müller
- Cilag AG, Hochstrasse 201, CH-8200, Schaffhausen, Switzerland
| | - Marcel Tigges
- Cilag AG, Hochstrasse 201, CH-8200, Schaffhausen, Switzerland
| | - Leo Scheller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Moritz Lang
- Institute of Science and Technology Austria, A-3400, Klosterneuburg, Austria
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, CH-4058, Basel, Switzerland.
- Faculty of Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland.
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Depletion of endogenous miRNA-378-3p increases peak cell density of CHO DP12 cells and is correlated with elevated levels of ubiquitin carboxyl-terminal hydrolase 14. J Biotechnol 2018; 288:30-40. [DOI: 10.1016/j.jbiotec.2018.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/27/2018] [Accepted: 10/28/2018] [Indexed: 01/01/2023]
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Costello A, Lao NT, Gallagher C, Capella Roca B, Julius LAN, Suda S, Ducrée J, King D, Wagner R, Barron N, Clynes M. Leaky Expression of the TET-On System Hinders Control of Endogenous miRNA Abundance. Biotechnol J 2018; 14:e1800219. [PMID: 29989353 DOI: 10.1002/biot.201800219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/08/2018] [Indexed: 12/12/2022]
Abstract
With the ability to affect multiple genes and fundamental pathways simultaneously, miRNA engineering of Chinese Hamster Ovary (CHO) cells has significant advantages over single gene expression or repression. Tight control of these molecular triggers is desirable as it could in theory allow on/off or even tunable regulation of desirable cellular phenotypes. The present study investigated the potential of employing a tetracycline inducible (TET-On) system for conditional knockdown of specific miRNAs but encountered several challenges. The authors show a significant reduction in cell proliferation and culture viability when maintained in media supplemented with the TET-On induction agent Doxycycline at concentrations commonly reported. Calculation of a mature miRNA and miRNA sponge mRNA copy number demonstrates that leaky basal transgene expression in the un-induced state, is sufficient for significant miRNA knockdown. This work highlights challenges of the TET-On inducible expression system for controlled manipulation of endogenous miRNAs with two examples; miR-378 and miR-455. The authors suggest a solution involving isolation of highly inducible clones and use a single cell analysis platform to demonstrate the heterogeneity of basal expression and inducibility. Finally, the authors describe numerous strategies to minimize leaky transgene expression and alterations to current miRNA sponge design.
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Affiliation(s)
- Alan Costello
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58, Dublin, Ireland
| | - Nga T Lao
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58, Dublin, Ireland
| | - Clair Gallagher
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58, Dublin, Ireland
| | - Berta Capella Roca
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58, Dublin, Ireland
| | | | - Srinivas Suda
- National Institute for Bioprocessing Research and Training, University College Dublin, Dublin, Ireland
| | - Jens Ducrée
- Fraunhofer Project Centre, Dublin City University, Dublin, Ireland
| | - Damien King
- Fraunhofer Project Centre, Dublin City University, Dublin, Ireland
| | | | - Niall Barron
- National Institute for Bioprocessing Research and Training, University College Dublin, Dublin, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University, D09 NR58, Dublin, Ireland
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