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Lopez-Morales J, Vanella R, Kovacevic G, Santos MS, Nash MA. Titrating Avidity of Yeast-Displayed Proteins Using a Transcriptional Regulator. ACS Synth Biol 2023; 12:419-431. [PMID: 36728831 PMCID: PMC9942200 DOI: 10.1021/acssynbio.2c00351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Yeast surface display is a valuable tool for protein engineering and directed evolution; however, significant variability in the copy number (i.e., avidity) of displayed variants on the yeast cell wall complicates screening and selection campaigns. Here, we report an engineered titratable display platform that modulates the avidity of Aga2-fusion proteins on the yeast cell wall dependent on the concentration of the anhydrotetracycline (aTc) inducer. Our design is based on a genomic Aga1 gene copy and an episomal Aga2-fusion construct both under the control of an aTc-dependent transcriptional regulator that enables stoichiometric and titratable expression, secretion, and display of Aga2-fusion proteins. We demonstrate tunable display levels over 2-3 orders of magnitude for various model proteins, including glucose oxidase enzyme variants, mechanostable dockerin-binding domains, and anti-PDL1 affibody domains. By regulating the copy number of displayed proteins, we demonstrate the effects of titratable avidity levels on several specific phenotypic activities, including enzyme activity and cell adhesion to surfaces under shear flow. Finally, we show that titrating down the display level allows yeast-based binding affinity measurements to be performed in a regime that avoids ligand depletion effects while maintaining small sample volumes, avoiding a well-known artifact in yeast-based binding assays. The ability to titrate the multivalency of proteins on the yeast cell wall through simple inducer control will benefit protein engineering and directed evolution methodology relying on yeast display for broad classes of therapeutic and diagnostic proteins of interest.
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Affiliation(s)
- Joanan Lopez-Morales
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Swiss
Nanoscience Institute, University of Basel, Basel 4056, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Rosario Vanella
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Gordana Kovacevic
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Mariana Sá Santos
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, Basel 4058, Switzerland,Swiss
Nanoscience Institute, University of Basel, Basel 4056, Switzerland,Department
of Biosystems Science and Engineering, ETH
Zurich, Basel 4058, Switzerland,
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Huo Z, Bilang R, Supuran CT, von der Weid N, Bruder E, Holland-Cunz S, Martin I, Muraro MG, Gros SJ. Perfusion-Based Bioreactor Culture and Isothermal Microcalorimetry for Preclinical Drug Testing with the Carbonic Anhydrase Inhibitor SLC-0111 in Patient-Derived Neuroblastoma. Int J Mol Sci 2022; 23:ijms23063128. [PMID: 35328549 PMCID: PMC8955558 DOI: 10.3390/ijms23063128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/04/2022] [Accepted: 03/05/2022] [Indexed: 12/23/2022] Open
Abstract
Neuroblastoma is a rare disease. Rare are also the possibilities to test new therapeutic options for neuroblastoma in clinical trials. Despite the constant need to improve therapy and outcomes for patients with advanced neuroblastoma, clinical trials currently only allow for testing few substances in even fewer patients. This increases the need to improve and advance preclinical models for neuroblastoma to preselect favorable candidates for novel therapeutics. Here we propose the use of a new patient-derived 3D slice-culture perfusion-based 3D model in combination with rapid treatment evaluation using isothermal microcalorimetry exemplified with treatment with the novel carbonic anhydrase IX and XII (CAIX/CAXII) inhibitor SLC-0111. Patient samples showed a CAIX expression of 18% and a CAXII expression of 30%. Corresponding with their respective CAIX expression patterns, the viability of SH-EP cells was significantly reduced upon treatment with SLC-0111, while LAN1 cells were not affected. The inhibitory effect on SH-SY5Y cells was dependent on the induction of CAIX expression under hypoxia. These findings corresponded to thermogenesis of the cells. Patient-derived organotypic slice cultures were treated with SLC-0111, which was highly effective despite heterogeneity of CAIX/CAXII expression. Thermogenesis, in congruence with the findings of the histological observations, was significantly reduced in SLC-0111-treated samples. In order to extend the evaluation time, we established a perfusion-based approach for neuroblastoma tissue in a 3D perfusion-based bioreactor system. Using this system, excellent tissue quality with intact tumor cells and stromal structure in neuroblastoma tumors can be maintained for 7 days. The system was successfully used for consecutive drug response monitoring with isothermal microcalorimetry. The described approach for drug testing, relying on an advanced 3D culture system combined with a rapid and highly sensitive metabolic assessment, can facilitate development of personalized treatment strategies for neuroblastoma.
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Affiliation(s)
- Zihe Huo
- Department of Pediatric Surgery, University Children’s Hospital Basel, 4031 Basel, Switzerland; (Z.H.); (R.B.); (S.H.-C.)
- Department of Clinical Research, University of Basel, 4031 Basel, Switzerland;
| | - Remo Bilang
- Department of Pediatric Surgery, University Children’s Hospital Basel, 4031 Basel, Switzerland; (Z.H.); (R.B.); (S.H.-C.)
- Department of Clinical Research, University of Basel, 4031 Basel, Switzerland;
| | - Claudiu T. Supuran
- Department Neurofarba, Sezione di Scienze Farmaceutiche, University of Florence, 50121 Florence, Italy;
| | - Nicolas von der Weid
- Department of Clinical Research, University of Basel, 4031 Basel, Switzerland;
- Department of Hematology and Oncology, University Children’s Hospital Basel, 4031 Basel, Switzerland
| | - Elisabeth Bruder
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland;
| | - Stefan Holland-Cunz
- Department of Pediatric Surgery, University Children’s Hospital Basel, 4031 Basel, Switzerland; (Z.H.); (R.B.); (S.H.-C.)
- Department of Clinical Research, University of Basel, 4031 Basel, Switzerland;
| | - Ivan Martin
- Tissue Engineering, Department of Biomedicine, University of Basel and University Hospital Basel, 4031 Basel, Switzerland; (I.M.); (M.G.M.)
| | - Manuele G. Muraro
- Tissue Engineering, Department of Biomedicine, University of Basel and University Hospital Basel, 4031 Basel, Switzerland; (I.M.); (M.G.M.)
| | - Stephanie J. Gros
- Department of Pediatric Surgery, University Children’s Hospital Basel, 4031 Basel, Switzerland; (Z.H.); (R.B.); (S.H.-C.)
- Department of Clinical Research, University of Basel, 4031 Basel, Switzerland;
- Correspondence:
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Santos MS, Liu H, Schittny V, Vanella R, Nash MA. Correlating single-molecule rupture mechanics with cell population adhesion by yeast display. BIOPHYSICAL REPORTS 2022; 2:None. [PMID: 35284851 PMCID: PMC8904261 DOI: 10.1016/j.bpr.2021.100035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022]
Affiliation(s)
- Mariana Sá Santos
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Systems Biology PhD program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Haipei Liu
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Valentin Schittny
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Rosario Vanella
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Michael A. Nash
- Institute for Physical Chemistry, Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- Corresponding author
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Pini N, Huo Z, Holland-Cunz S, Gros SJ. Increased Proliferation of Neuroblastoma Cells under Fructose Metabolism Can Be Measured by Isothermal Microcalorimetry. CHILDREN-BASEL 2021; 8:children8090784. [PMID: 34572216 PMCID: PMC8467942 DOI: 10.3390/children8090784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/28/2022]
Abstract
Neuroblastoma, like other cancer types, has an increased need for energy. This results in an increased thermogenic profile of the cells. How tumor cells optimize their energy efficiency has been discussed since Warburg described the fact that tumor cells prefer an anaerobic to an aerobic metabolism in the 1920s. An important question is how far the energy efficiency is influenced by the substrate. The aim of this study was to investigate how the metabolic activity of neuroblastoma cells is stimulated by addition of glucose or fructose to the medium and if this can be measured accurately by using isothermal microcalorimetry. Proliferation of Kelly and SH-EP Tet-21/N cells was determined in normal medium, in fructose-enriched, in glucose-enriched and in a fructose/glucose-enriched environment. Heat development of cells was measured by isothermal microcalorimetry. The addition of fructose, glucose or both to the medium led to increases in the metabolic activity of the cells, resulting in increased proliferation under the influence of fructose. These changes were reflected in an enhanced thermogenic profile, mirroring the results of the proliferation assay. The tested neuroblastoma cells prefer fructose metabolism over glucose metabolism, a quality that provides them with a survival benefit under unfavorable low oxygen and low nutrient supply when fructose is available. This can be quantified by measuring thermogenesis.
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Affiliation(s)
- Nicola Pini
- Department of Pediatric Surgery, University Children’s Hospital Basel, Spitalstr. 33, 4031 Basel, Switzerland; (N.P.); (Z.H.); (S.H.-C.)
- Department of Clinical Research, University of Basel, Schanzenstrasse 55, 4021 Basel, Switzerland
| | - Zihe Huo
- Department of Pediatric Surgery, University Children’s Hospital Basel, Spitalstr. 33, 4031 Basel, Switzerland; (N.P.); (Z.H.); (S.H.-C.)
- Department of Clinical Research, University of Basel, Schanzenstrasse 55, 4021 Basel, Switzerland
| | - Stefan Holland-Cunz
- Department of Pediatric Surgery, University Children’s Hospital Basel, Spitalstr. 33, 4031 Basel, Switzerland; (N.P.); (Z.H.); (S.H.-C.)
| | - Stephanie J. Gros
- Department of Pediatric Surgery, University Children’s Hospital Basel, Spitalstr. 33, 4031 Basel, Switzerland; (N.P.); (Z.H.); (S.H.-C.)
- Department of Clinical Research, University of Basel, Schanzenstrasse 55, 4021 Basel, Switzerland
- Correspondence:
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