Abstract
Chromobodies are nanobodies genetically fused to fluorescent proteins, which were developed to visualize endogenous intracellular antigens. These versatile bioimaging nanotools can also be used to detect cell surface epitopes, and we describe here how we use them as an alternative to conjugated antibodies. This way, we routinely test the binding efficiency of nanobodies for their cognate cell surface antigens, before integrating them as sensing domains into complex synthetic receptor architectures.
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References
Harmansa S, Affolter M (2018) Protein binders and their applications in developmental biology. Development 145(2):dev148874. https://doi.org/10.1242/dev.148874. https://journals.biologists.com/dev/article/145/2/dev148874/48799/Protein-binders-and-their-applications-in
Sun Y, Huang T, Hammarström L, et al (2020) The immunoglobulins: new insights, implications, and applications. Annu Rev Anim Biosci 8(1):145–169. https://doi.org/10.1146/annurev-animal-021419-083720. https://www.annualreviews.org/doi/10.1146/annurev-animal-021419-083720
Jovčevska I, Muyldermans S (2020) The therapeutic potential of nanobodies. BioDrugs 34(1):11–26. https://doi.org/10.1007/s40259-019-00392-z. http://link.springer.com/10.1007/s40259-019-00392-z
Brunner JD, Schenck S (2020) Production and application of nanobodies for membrane protein structural biology. In: Methods in molecular biology, vol 2127. Humana Press Inc., Totowa, p 167–184. https://doi.org/10.1007/978-1-0716-0373-4_12. http://link.springer.com/10.1007/978-1-0716-0373-4_12
Tsumoto K, Isozaki Y, Yagami H, et al (2019) Future perspectives of therapeutic monoclonal antibodies. Immunotherapy 11(2):119–127. https://doi.org/10.2217/imt-2018-0130. https://www.futuremedicine.com/doi/10.2217/imt-2018-0130
Aoki W (2019) Engineering antibodies and alternative binders for therapeutic uses. In: Ueda M (ed) Yeast cell surface engineering. Springer, Singapore, p 123–147. https://doi.org/10.1007/978-981-13-5868-5_10. http://link.springer.com/10.1007/978-981-13-5868-5_10
Nordeen SA, Andersen KR, Knockenhauer KE, et al (2020) A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure. Nat Commun 11(1):6179. https://doi.org/10.1038/s41467-020-19884-6. https://www.nature.com/articles/s41467-020-19884-6
Wagner TR, Rothbauer U (2020) Nanobodies right in the middle: intrabodies as toolbox to visualize and modulate antigens in the living cell. Biomolecules 10(12):1701. https://doi.org/10.3390/biom10121701. https://www.mdpi.com/2218-273X/10/12/1701
Kang W, Ding C, Zheng D, et al (2021) Nanobody conjugates for targeted cancer therapy and imaging. Technol Cancer Res Treat 20:153303382110,101. https://doi.org/10.1177/15330338211010117. http://journals.sagepub.com/doi/10.1177/15330338211010117
Beghein E, Gettemans J (2017) Nanobody technology: a versatile toolkit for microscopic imaging, protein–protein interaction analysis, and protein function exploration. Front Immunol 8(JUL):771. https://doi.org/10.3389/fimmu.2017.00771. http://journal.frontiersin.org/article/10.3389/fimmu.2017.00771/full
Hassanzadeh-Ghassabeh G, Saerens D, Muyldermans S (2011) Generation of Anti-infectome/Anti-proteome Nanobodies. In: Methods in Molecular Biology, vol 790. Humana Press, Totowa, p 239–259. https://doi.org/10.1007/978-1-61779-319-6_19. https://link.springer.com/10.1007/978-1-61779-319-6_19
Bai X, Shim H (2017) Construction of a scFv library with synthetic, non-combinatorial CDR diversity. In: Methods in Molecular Biology, vol 1575. Humana Press Inc., Totowa, p 15–29. https://doi.org/10.1007/978-1-4939-6857-2_2. http://link.springer.com/10.1007/978-1-4939-6857-2_2
Desautels T, Zemla A, Lau E, et al (2020) Rapid in silico design of antibodies targeting SARS-CoV-2 using machine learning and supercomputing. bioRxiv p 2020.04.03.024885. https://doi.org/10.1101/2020.04.03.024885. https://www.biorxiv.org/content/10.1101/2020.04.03.024885v1
Norman RA, Ambrosetti F, Bonvin AMJJ, et al (2020) Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief Bioinform 21(5):1549–1567. https://doi.org/10.1093/bib/bbz095. https://academic.oup.com/bib/article/21/5/1549/5581643
Sormanni P, Aprile FA, Vendruscolo M (2018) Third generation antibody discovery methods: in silico rational design. Chem Soc Rev 47(24):9137–9157. https://doi.org/10.1039/C8CS00523K. http://xlink.rsc.org/?DOI=C8CS00523K
Zhao J, Nussinov R, Wu WJ, et al (2018) In Silico methods in antibody design. Antibodies 7(3):22. https://doi.org/10.3390/antib7030022. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6640671/
Scheller L (2021) Synthetic receptors for sensing soluble molecules with mammalian cells. In: Methods in molecular biology (Clifton, N.J.), vol 2312. Humana Press Inc., Totowa, p 15–33. https://doi.org/10.1007/978-1-0716-1441-9_2. https://link.springer.com/10.1007/978-1-0716-1441-9_2
Santorelli M, Lam C, Morsut L (2019) Synthetic development: building mammalian multicellular structures with artificial genetic programs. Curr Opin Biotechnol 59:130–140. https://doi.org/10.1016/j.copbio.2019.03.016. https://linkinghub.elsevier.com/retrieve/pii/S0958166918301617
Morsut L, Roybal K, Xiong X, et al (2016) Engineering customized cell sensing and response behaviors using synthetic notch receptors. Cell 164(4):780–791. https://doi.org/10.1016/j.cell.2016.01.012. https://linkinghub.elsevier.com/retrieve/pii/S0092867416000520
Daringer NM, Dudek RM, Schwarz KA, et al (2014) Modular extracellular sensor architecture for engineering mammalian cell-based devices. ACS Synth Biol 3(12):892–902. https://doi.org/10.1021/sb400128g. https://pubs.acs.org/doi/10.1021/sb400128g
Manhas J, Edelstein HI, Leonard JN, et al (2022) The evolution of synthetic receptor systems. Nat Chem Biol 18(3):244–255. https://doi.org/10.1038/s41589-021-00926-z. https://www.nature.com/articles/s41589-021-00926-z
Acknowledgements
This work was supported by the School of Biological Sciences at the University of Edinburgh. Flow cytometry data were generated within the Flow Cytometry and Cell Sorting Facility in King’s Buildings at the University of Edinburgh, with the help of Dr Martin Waterfall. Microscopy images were acquired on a microscope funded by the School of Biological Sciences, the Institute of Quantitative Biology, Biochemistry, and Biotechnology, and the UK Centre for Mammalian Synthetic Biology.
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Baronaite, U., Cachat, E. (2024). Preparation of Chromobodies for the Detection of Cell Surface Epitopes. In: Ceroni, F., Polizzi, K. (eds) Mammalian Synthetic Systems. Methods in Molecular Biology, vol 2774. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3718-0_20
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