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Van Gool SW, Van de Vliet P, Kampers LFC, Kosmal J, Sprenger T, Reich E, Schirrmacher V, Stuecker W. Methods behind oncolytic virus-based DC vaccines in cancer: Toward a multiphase combined treatment strategy for Glioblastoma (GBM) patients. Methods Cell Biol 2023; 183:51-113. [PMID: 38548421 DOI: 10.1016/bs.mcb.2023.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Glioblastoma (GBM) remains an orphan cancer disease with poor outcome. Novel treatment strategies are needed. Immunotherapy has several modes of action. The addition of active specific immunotherapy with dendritic cell vaccines resulted in improved overall survival of patients. Integration of DC vaccination within the first-line combined treatment became a challenge, and immunogenic cell death immunotherapy during chemotherapy was introduced. We used a retrospective analysis using real world data to evaluate the complex combined treatment, which included individualized multimodal immunotherapy during and after standard of care, and which required adaptations during treatment, and found a further improvement of overall survival. We also discuss the use of real world data as evidence. Novel strategies to move the field of individualized multimodal immunotherapy forward for GBM patients are reviewed.
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Affiliation(s)
| | | | | | | | | | - Ella Reich
- Immun-onkologisches Zentrum Köln, Cologne, Germany
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Van Gool SW, Makalowski J, Kampers LFC, Van de Vliet P, Sprenger T, Schirrmacher V, Stücker W. Dendritic cell vaccination for glioblastoma multiforme patients: has a new milestone been reached? Transl Cancer Res 2023; 12:2224-2228. [PMID: 37701100 PMCID: PMC10493805 DOI: 10.21037/tcr-23-603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/10/2023] [Indexed: 09/14/2023]
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Van de Vliet P, Sprenger T, Kampers LFC, Makalowski J, Schirrmacher V, Stücker W, Van Gool SW. The Application of Evidence-Based Medicine in Individualized Medicine. Biomedicines 2023; 11:1793. [PMID: 37509433 PMCID: PMC10376974 DOI: 10.3390/biomedicines11071793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
The fundamental aim of healthcare is to improve overall health of the population by providing state-of-the-art healthcare for individuals at an affordable cost. The foundation for this system is largely referred to as "evidence-based medicine". Too often, evidence-based medicine is based solely on so-called "best research evidence", collected through randomized controlled trials while disregarding clinical expertise and patient expectations. As healthcare gravitates towards personalized and individualized medicine, such external clinical (research) evidence can inform, but never replace, individual clinical expertise. This applies in particular to orphan diseases, for which clinical trials are methodologically particularly problematic, and evidence derived from them is often questionable. Evidence-based medicine constitutes a complex process to allow doctors and patients to select the best possible solutions for each individual based on rapidly developing new therapeutic directions. This requires a revisit of the foundations of evidence-based medicine. A proposition as to how to manage evidence-based data in individualized immune-oncology is presented here.
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Affiliation(s)
| | - Tobias Sprenger
- Immune-Oncological Centre Cologne (IOZK), D-50674 Cologne, Germany
| | | | | | | | - Wilfried Stücker
- Immune-Oncological Centre Cologne (IOZK), D-50674 Cologne, Germany
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Asin-Garcia E, Robaey Z, Kampers LFC, Martins Dos Santos VAP. Exploring the Impact of Tensions in Stakeholder Norms on Designing for Value Change: The Case of Biosafety in Industrial Biotechnology. Sci Eng Ethics 2023; 29:9. [PMID: 36882674 PMCID: PMC9992083 DOI: 10.1007/s11948-023-00432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Synthetic biologists design and engineer organisms for a better and more sustainable future. While the manifold prospects are encouraging, concerns about the uncertain risks of genome editing affect public opinion as well as local regulations. As a consequence, biosafety and associated concepts, such as the Safe-by-design framework and genetic safeguard technologies, have gained notoriety and occupy a central position in the conversation about genetically modified organisms. Yet, as regulatory interest and academic research in genetic safeguard technologies advance, the implementation in industrial biotechnology, a sector that is already employing engineered microorganisms, lags behind. The main goal of this work is to explore the utilization of genetic safeguard technologies for designing biosafety in industrial biotechnology. Based on our results, we posit that biosafety is a case of a changing value, by means of further specification of how to realize biosafety. Our investigation is inspired by the Value Sensitive Design framework, to investigate scientific and technological choices in their appropriate social context. Our findings discuss stakeholder norms for biosafety, reasonings about genetic safeguards, and how these impact the practice of designing for biosafety. We show that tensions between stakeholders occur at the level of norms, and that prior stakeholder alignment is crucial for value specification to happen in practice. Finally, we elaborate in different reasonings about genetic safeguards for biosafety and conclude that, in absence of a common multi-stakeholder effort, the differences in informal biosafety norms and the disparity in biosafety thinking could end up leading to design requirements for compliance instead of for safety.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands.
- Bioprocess Engineering Group, Wageningen University & Research, 6700, AA, Wageningen, The Netherlands.
| | - Zoë Robaey
- Department of Social Sciences, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
| | - Linde F C Kampers
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708, WE, Wageningen, The Netherlands
- Bioprocess Engineering Group, Wageningen University & Research, 6700, AA, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
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Kampers LFC, Asin-Garcia E, Schaap PJ, Wagemakers A, Martins Dos Santos VAP. From Innovation to Application: Bridging the Valley of Death in Industrial Biotechnology. Trends Biotechnol 2021; 39:1240-1242. [PMID: 34024649 DOI: 10.1016/j.tibtech.2021.04.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 11/29/2022]
Abstract
Few biotechnology innovations make it through the Valley of Death to markets. Based on our experience with academia, technology transfer offices, and industry, we provide insights into differences in operating levels, how to best traverse the Valley of Death, and ways to foster more innovation towards market implementation.
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Affiliation(s)
- Linde F C Kampers
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, 6708, WE, The Netherlands
| | - Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, 6708, WE, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, 6708, WE, The Netherlands
| | - Annemarie Wagemakers
- Health and Society, Department of Social Sciences, Wageningen University and Research, Wageningen, 6700, EW, The Netherlands
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Wageningen, 6708, WE, The Netherlands; LifeGlimmer GmbH, Berlin, Germany.
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Kampers LFC, Koehorst JJ, van Heck RJA, Suarez-Diez M, Stams AJM, Schaap PJ. A metabolic and physiological design study of Pseudomonas putida KT2440 capable of anaerobic respiration. BMC Microbiol 2021; 21:9. [PMID: 33407113 PMCID: PMC7789669 DOI: 10.1186/s12866-020-02058-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pseudomonas putida KT2440 is a metabolically versatile, HV1-certified, genetically accessible, and thus interesting microbial chassis for biotechnological applications. However, its obligate aerobic nature hampers production of oxygen sensitive products and drives up costs in large scale fermentation. The inability to perform anaerobic fermentation has been attributed to insufficient ATP production and an inability to produce pyrimidines under these conditions. Addressing these bottlenecks enabled growth under micro-oxic conditions but does not lead to growth or survival under anoxic conditions. RESULTS Here, a data-driven approach was used to develop a rational design for a P. putida KT2440 derivative strain capable of anaerobic respiration. To come to the design, data derived from a genome comparison of 1628 Pseudomonas strains was combined with genome-scale metabolic modelling simulations and a transcriptome dataset of 47 samples representing 14 environmental conditions from the facultative anaerobe Pseudomonas aeruginosa. CONCLUSIONS The results indicate that the implementation of anaerobic respiration in P. putida KT2440 would require at least 49 additional genes of known function, at least 8 genes encoding proteins of unknown function, and 3 externally added vitamins.
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Affiliation(s)
- Linde F C Kampers
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Jasper J Koehorst
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Ruben J A van Heck
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708, WE, Wageningen, The Netherlands.
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Kampers LFC, van Heck RGA, Donati S, Saccenti E, Volkers RJM, Schaap PJ, Suarez-Diez M, Nikel PI, Martins Dos Santos VAP. In silico-guided engineering of Pseudomonas putida towards growth under micro-oxic conditions. Microb Cell Fact 2019; 18:179. [PMID: 31640713 PMCID: PMC6805499 DOI: 10.1186/s12934-019-1227-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 10/09/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Pseudomonas putida is a metabolically versatile, genetically accessible, and stress-robust species with outstanding potential to be used as a workhorse for industrial applications. While industry recognises the importance of robustness under micro-oxic conditions for a stable production process, the obligate aerobic nature of P. putida, attributed to its inability to produce sufficient ATP and maintain its redox balance without molecular oxygen, severely limits its use for biotechnology applications. RESULTS Here, a combination of genome-scale metabolic modelling and comparative genomics is used to pinpoint essential [Formula: see text]-dependent processes. These explain the inability of the strain to grow under anoxic conditions: a deficient ATP generation and an inability to synthesize essential metabolites. Based on this, several P. putida recombinant strains were constructed harbouring acetate kinase from Escherichia coli for ATP production, and a class I dihydroorotate dehydrogenase and a class III anaerobic ribonucleotide triphosphate reductase from Lactobacillus lactis for the synthesis of essential metabolites. Initial computational designs were fine-tuned by means of adaptive laboratory evolution. CONCLUSIONS We demonstrated the value of combining in silico approaches, experimental validation and adaptive laboratory evolution for microbial design by making the strictly aerobic Pseudomonas putida able to grow under micro-oxic conditions.
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Affiliation(s)
- Linde F C Kampers
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ruben G A van Heck
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Stefano Donati
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043, Marburg, Germany
| | - Edoardo Saccenti
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Rita J M Volkers
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Peter J Schaap
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Maria Suarez-Diez
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Kgs Lyngby, Denmark
| | - Vitor A P Martins Dos Santos
- Systems and Synthetic Biology, Wageningen University and Research Centre, Stippeneng 4, 6708 WE, Wageningen, The Netherlands. .,LifeGlimmer GmbH, Berlin, Germany.
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Kampers LFC, Volkers RJM, Martins dos Santos VAP. Pseudomonas putida KT2440 is HV1 certified, not GRAS. Microb Biotechnol 2019; 12:845-848. [PMID: 31199068 PMCID: PMC6680625 DOI: 10.1111/1751-7915.13443] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 05/16/2019] [Indexed: 01/13/2023] Open
Abstract
Pseudomonas putida is rapidly becoming a workhorse for industrial production due to its metabolic versatility, genetic accessibility and stress-resistance properties. The P. putida strain KT2440 is often described as Generally Regarded as Safe, or GRAS, indicating the strain is safe to use as food additive. This description is incorrect. P. putida KT2440 is classified by the FDA as HV1 certified, indicating it is safe to use in a P1 or ML1 environment.
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Affiliation(s)
- Linde F. C. Kampers
- Laboratory of Systems and Synthetic BiologyWageningen University and Research CentreStippeneng 46708WageningenThe Netherlands
| | - Rita J. M. Volkers
- Laboratory of Systems and Synthetic BiologyWageningen University and Research CentreStippeneng 46708WageningenThe Netherlands
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic BiologyWageningen University and Research CentreStippeneng 46708WageningenThe Netherlands
- Lifeglimmer GmbHMarkelstr. 3812163BerlinGermany
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