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von Mässenhausen A, Schlecht MN, Beer K, Maremonti F, Tonnus W, Belavgeni A, Gavali S, Flade K, Riley JS, Zamora Gonzalez N, Brucker A, Becker JN, Tmava M, Meyer C, Peitzsch M, Hugo C, Gembardt F, Angeli JPF, Bornstein SR, Tait SWG, Linkermann A. Treatment with siRNAs is commonly associated with GPX4 up-regulation and target knockdown-independent sensitization to ferroptosis. SCIENCE ADVANCES 2024; 10:eadk7329. [PMID: 38489367 PMCID: PMC10942120 DOI: 10.1126/sciadv.adk7329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Small interfering RNAs (siRNAs) are widely used in biomedical research and in clinical trials. Here, we demonstrate that siRNA treatment is commonly associated with significant sensitization to ferroptosis, independently of the target protein knockdown. Genetically targeting mitochondrial antiviral-signaling protein (MAVS) reversed the siRNA-mediated sensitizing effect, but no activation of canonical MAVS signaling, which involves phosphorylation of IkBα and interferon regulatory transcription factor 3 (IRF3), was observed. In contrast, MAVS mediated a noncanonical signal resulting in a prominent increase in mitochondrial ROS levels, and increase in the BACH1/pNRF2 transcription factor ratio and GPX4 up-regulation, which was associated with a 50% decrease in intracellular glutathione levels. We conclude that siRNAs commonly sensitize to ferroptosis and may severely compromise the conclusions drawn from silencing approaches in biomedical research. Finally, as ferroptosis contributes to a variety of pathophysiological processes, we cannot exclude side effects in human siRNA-based therapeutical concepts that should be clinically tested.
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Affiliation(s)
- Anne von Mässenhausen
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, 53127 Bonn, Germany
| | - Marlena Nastassja Schlecht
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Kristina Beer
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Francesca Maremonti
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Wulf Tonnus
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Alexia Belavgeni
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Shubhangi Gavali
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Karolin Flade
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Joel S. Riley
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1BD, UK
- Biocenter Innsbruck (CCB), Medical University Innsbruck, Division of Developmental Immunology, Innrain 80, 6020 Innsbruck, Austria
| | - Nadia Zamora Gonzalez
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Anne Brucker
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Jorunn Naila Becker
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Mirela Tmava
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Claudia Meyer
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Mirko Peitzsch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Christian Hugo
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Florian Gembardt
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
| | - Jose Pedro Friedmann Angeli
- Rudolf Virchow Center for Integrative and Translational Bioimaging, Chair of Translational Cell Biology, University of Würzburg, 97080 Würzburg, Germany
| | - Stefan R. Bornstein
- Department of Internal Medicine 3, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- Diabetes and Nutritional Sciences, King's College London, London, UK
- Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of Helmholtz Centre Munich at University Clinic Carl Gustav Carus of TU Dresden Faculty of Medicine, Dresden, Germany
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Stephen W. G. Tait
- Cancer Research UK Beatson Institute, Switchback Road, Glasgow G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow G61 1BD, UK
| | - Andreas Linkermann
- Division of Nephrology, Department of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, 01307 Dresden, Germany
- Division of Nephrology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
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Liu Z, Dai S, Bones J, Ray S, Cha S, Karger BL, Li JJ, Wilson L, Hinckle G, Rossomando A. A quantitative proteomic analysis of cellular responses to high glucose media in Chinese hamster ovary cells. Biotechnol Prog 2015; 31:1026-38. [PMID: 25857574 DOI: 10.1002/btpr.2090] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 03/11/2015] [Indexed: 12/12/2022]
Abstract
A goal in recombinant protein production using Chinese hamster ovary (CHO) cells is to achieve both high specific productivity and high cell density. Addition of glucose to the culture media is necessary to maintain both cell growth and viability. We varied the glucose concentration in the media from 5 to 16 g/L and found that although specific productivity of CHO-DG44 cells increased with the glucose level, the integrated viable cell density decreased. To examine the biological basis of these results, we conducted a discovery proteomic study of CHO-DG44 cells grown under batch conditions in normal (5 g/L) or high (15 g/L) glucose over 3, 6, and 9 days. Approximately 5,000 proteins were confidently identified against an mRNA-based CHO-DG44 specific proteome database, with 2,800 proteins quantified with at least two peptides. A self-organizing map algorithm was used to deconvolute temporal expression profiles of quantitated proteins. Functional analysis of altered proteins suggested that differences in growth between the two glucose levels resulted from changes in crosstalk between glucose metabolism, recombinant protein expression, and cell death, providing an overall picture of the responses to high glucose environment. The high glucose environment may enhance recombinant dihydrofolate reductase in CHO cells by up-regulating NCK1 and down-regulating PRKRA, and may lower integrated viable cell density by activating mitochondrial- and endoplasmic reticulum-mediated cell death pathways by up-regulating HtrA2 and calpains. These proteins are suggested as potential targets for bioengineering to enhance recombinant protein production.
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Affiliation(s)
- Zhenke Liu
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Shujia Dai
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Jonathan Bones
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Somak Ray
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Sangwon Cha
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Barry L Karger
- Barnett Inst. and Dept. of Chemistry and Chemical Biology, Northeastern University, Boston, MA, 02115
| | - Jingyi Jessica Li
- Dept. of Statistics, University of California, Los Angeles, CA, 90095
| | - Lee Wilson
- Alnylam Pharmaceuticals, Cambridge, MA, 02142
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Farrell A, McLoughlin N, Milne JJ, Marison IW, Bones J. Application of Multi-Omics Techniques for Bioprocess Design and Optimization in Chinese Hamster Ovary Cells. J Proteome Res 2014; 13:3144-59. [DOI: 10.1021/pr500219b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amy Farrell
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Niaobh McLoughlin
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - John J. Milne
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Ian W. Marison
- Laboratory
of Integrated Bioprocessing, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Jonathan Bones
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
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Li C, Rossomando A, Wu SL, Karger BL. Comparability analysis of anti-CD20 commercial (rituximab) and RNAi-mediated fucosylated antibodies by two LC-MS approaches. MAbs 2013; 5:565-75. [PMID: 23751726 DOI: 10.4161/mabs.24814] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In developing biosimilar or biobetter products, comparability to the reference product is required to claim similar integrity or intended purpose. In this work, an anti-CD20 monoclonal antibody developed using RNA interference to decrease core fucosylation (RNAi-mediated) was comprehensively characterized by LC-MS and compared with the commercially-available anti-CD20 rituximab (MabThera (®) ). As anticipated, < 30% core fucose was found within the RNAi-produced molecule (compared with > 90% in rituximab), and the reduction in fucose resulting in a significant improvement in FcγRΙΙΙa binding and antibody-dependent cell-mediated cytotoxicity. Two mutations, S258Y (fully mutated) and F174I/L (partially mutated), however, were detected in the production of the RNAi-mediated molecule. An alternative LC-MS approach using dimethyl labeling (i.e., 2CH 2 for rituximab and 2CD 2 for the RNAi-mediated molecule) was developed to additionally compare the two mAbs and confirm the full sequence with the two mutation sites. Furthermore, disulfide linkages were found to be the same for the two antibodies, with a small portion of unpaired cysteines in both products. Disulfides were correctly linked if the samples were prepared at low pH (i.e., enzymatic digestion by pepsin at pH 2); however, trace amounts of scrambling were found by trypsin digestion at pH 6.8, and this scrambling increased significantly at pH 8. Typical modifications, such as pyro-Glu formation at the N-terminus, K clipping at the C-terminus, oxidation at Met, and deamidation at Asn, were also detected with no significant differences between the two products. Using the LC-MS approaches for the comparability study, product integrity with critical structure information was revealed for confirmation of intended purpose (core fucosylation), identification of critical parameters (e.g., sample pH), and correction as needed (amino acid mutation).
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Affiliation(s)
- Chen Li
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
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