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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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Zeni A, Grasso M, Denti MA. Identification of miRNAs Bound to an RNA of Interest by MicroRNA Capture Affinity Technology (miR-CATCH). Methods Mol Biol 2022; 2404:207-218. [PMID: 34694611 DOI: 10.1007/978-1-0716-1851-6_11] [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] [Indexed: 06/13/2023]
Abstract
microRNA capture affinity technology (miR-CATCH) uses affinity capture biotinylated antisense oligonucleotides to co-purify a target transcript together with all its endogenously bound miRNAs. The miR-CATCH assay is performed to investigate miRNAs bound to a specific mRNA. This method allows to have a total vision of miRNAs bound not only to the 3'UTR but also to the 5'UTR and Coding Region of target messenger RNAs (mRNAs).
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Affiliation(s)
- Andrea Zeni
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
- Istituto Rainerum-SDB, Bolzano, Italy
| | - Margherita Grasso
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy
- L.N.Age Srl-Link Neuroscience and Healthcare, Pomezia (RM), Italy
| | - Michela A Denti
- Department of Cellular, Computational and Integrative Biology-CIBIO, University of Trento, Trento, Italy.
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Marranci A, D'Aurizio R, Vencken S, Mero S, Guzzolino E, Rizzo M, Pitto L, Pellegrini M, Chiorino G, Greene CM, Poliseno L. Systematic evaluation of the microRNAome through miR-CATCHv2.0 identifies positive and negative regulators of BRAF-X1 mRNA. RNA Biol 2019; 16:865-878. [PMID: 30929607 DOI: 10.1080/15476286.2019.1600934] [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] [Indexed: 12/14/2022] Open
Abstract
Here we present miR-CATCHv2.0, an implemented experimental method that allows the identification of the microRNA species directly bound to an RNA of interest. After cross-linking of microRNA::RNA::Ago2 complexes using formaldehyde, the RNA is fragmented using sonication and then subjected to affinity purification using two sets of biotinylated tiling probes (ODD and EVEN). Finally, enriched microRNA species are retrieved by means of small RNA sequencing coupled with an ad hoc analytical workflow. In BRAFV600E mutant A375 melanoma cells, miR-CATCHv2.0 allowed us to identify 20 microRNAs that target X1, the most abundant isoform of BRAF mRNA. These microRNAs fall into different functional classes, according to the effect that they exert (decrease/increase in BRAFV600E mRNA and protein levels) and to the mechanism they use to achieve it (destabilization/stabilization of X1 mRNA or decrease/increase in its translation). microRNA-induced variations in BRAFV600E protein levels are most of the times coupled to consistent variations in pMEK levels, in melanoma cell proliferation in vitro and in sensitivity to the BRAF inhibitor vemurafenib in a xenograft model in zebrafish. However, microRNAs exist that uncouple the degree of activation of the ERK pathway from the levels of BRAFV600E protein. Our study proposes miR-CATCHv2.0 as an effective tool for the identification of direct microRNA-target interactions and, by using such a tool, unveils the complexity of the post-transcriptional regulation to which BRAFV600E and the ERK pathway are subjected in melanoma cells.
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Affiliation(s)
- Andrea Marranci
- a Institute of Clinical Physiology , CNR , Pisa , Italy.,b Oncogenomics Unit, Core Research Laboratory , ISPRO , Pisa , Italy.,c Signal Transduction Unit, Core Research Laboratory , ISPRO , Siena , Italy
| | | | - Sebastian Vencken
- e Department of Clinical Microbiology , Royal College of Surgeon in Ireland , Dublin , Ireland
| | - Serena Mero
- a Institute of Clinical Physiology , CNR , Pisa , Italy.,b Oncogenomics Unit, Core Research Laboratory , ISPRO , Pisa , Italy
| | | | - Milena Rizzo
- a Institute of Clinical Physiology , CNR , Pisa , Italy
| | - Letizia Pitto
- a Institute of Clinical Physiology , CNR , Pisa , Italy
| | | | - Giovanna Chiorino
- f Cancer Genomics Lab , Fondazione Edo ed Elvo Tempia , Biella , Italy
| | - Catherine M Greene
- e Department of Clinical Microbiology , Royal College of Surgeon in Ireland , Dublin , Ireland
| | - Laura Poliseno
- a Institute of Clinical Physiology , CNR , Pisa , Italy.,b Oncogenomics Unit, Core Research Laboratory , ISPRO , Pisa , Italy
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Vito D, Smales CM. Engineering of the cellular translational machinery and non-coding RNAs to enhance CHO cell growth, recombinant product yields and quality. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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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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Affiliation(s)
- Nicole Borth
- Department of Biotechnology, Universität für Bodenkultur, Austria
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, USA
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