Part:BBa_K5237100
Cathepsin B
Cathepsin B is a lysosomal protease present in the cytosol of various cancer types. We overexpressed wild-type cathepsin B in HEK293T cells to investigate cathepsin B induced cleavage of different peptide linkers via a fluorescence readout assay. We showed that the linker GFLG was efficiently cleaved by cathepsin B in vivo. Furthermore, we were able to demonstrate that wild-type cathepsin B matured into its active forms when overexpressed in HEK293T cells. Together, these findings enable the functionalization of our PICasSO system for a wide range of therapeutic and synthetic biology applications.
1. Sequence Overview
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 626
Illegal BglII site found at 725 - 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 56
Illegal NgoMIV site found at 127
Illegal NgoMIV site found at 979
Illegal AgeI site found at 811 - 1000COMPATIBLE WITH RFC[1000]
2. Usage and Biology
Cathepsin B is a cysteine protease typically located in lysosomes or secreted outside the cell, where it degrades proteins of the extracellular matrix (Ruan et al., 2015). The significance of cathepsin B in cancer progression is well-documented, with studies showing elevated cathepsin B levels in cancerous tissues compared with noncancerous tissues (Ruan et al., 2015). Given its important role in tumor progression, cathepsin B is considered a potential therapeutic target (Ruan et al., 2015) or prodrug-activating enzyme (Zhong et al., 2013).
To explore the potential of our PICasSO platform approach for therapeutic applications, we designed protein-based DNA staples that are responsive to the overexpression of cathepsin B in cancerous tissues. We were able to demonstrate doxorubicin-dependent cathepsin B cleavage of one out of five documented linkers (Jin et al., 2022; Shim et al., 2022; Wang et al., 2024) in HEK293T cells.
3. Assembly and Part Evolution
The protein sequence of human cathepsin B was obtained from UniProt (P07858). The corresponding nucleotide sequence was optimized for expression in human cells. Restriction cloning was used to insert the cathepsin B open reading frame into the mammalian expression vector pcDNA3.1 (BBa_K5237011). Plasmids were propagated in E. coli Top10 cells and used for transfection of HEK293T cells.
4. Results
4.1 The Peptide Linker GFLG Is Cleaved by Cathepsin B in Vivo
We performed a fluorescence readout assay in HEK293T cells to investigate cathepsin B cleavage of different peptide linkers. 24 hours after transfection, we added doxorubicin in a final concentration of 500 nM to the cell supernatant. Figure 1 shows the fluorescence intensity of mCherry for five different peptide linkers (GFLG, FFRG, FRRL, VA, FK). The negative control was not transfected with the plasmid encoding cathepsin B. We investigated two different test conditions, in which we either transfected 30 ng or 60 ng of the plasmid encoding cathepsin B. The fluorescence intensity of mCherry was normalized by the measured fluorescence intensity of eGFP in each condition. Additionally, the values for 30 ng and 60 ng cathepsin B were normalized against the corresponding negative controls. One data point for the VA linker, transfected with 60 ng of the plasmid encoding cathepsin B, was excluded due to severe deviation from the other values. We conducted a two-way analysis of variance (ANOVA) to assess the significance of the observed differences between the negative control and the test conditions for each linker. As the negative control did not contain the plasmid encoding cathepsin B, we expected the measured fluorescence intensity of mCherry to be the highest in these conditions. However, this was only observed for the GFLG and FK linkers. Contrary to our expectations, the fluorescence intensity of the negative control was the lowest out of the three conditions tested for the remaining linkers. It appears that the addition of the plasmid encoding cathepsin B increases mCherry fluorescence intensity when the linker is not cleaved. However, this increase is only significant for the FFRG linker in the 60 ng condition. For the GFLG linker, we observed significant decreases in fluorescence intensity between the negative control and both test conditions, with no difference between the 30 ng and 60 ng conditions. For the FK linker, no significant decreases in fluorescence intensity between the negative control and the test conditions were observed.
4.2 mCherry and eGFP Can be Used as a Reporter System to Measure Cleavage Efficiency
Figure 2 shows micrographs taken with a fluorescence microscope of three different conditions: the null control, the negative control and the test sample. All samples were transfected with plasmids encoding eGFP and mCherry. The null control and the negative control were not transfected with the plasmid encoding cathepsin B. The null control was also not transfected with any of the plasmids encoding Gal4-Linker-VP64 constructs. The test sample was transfected with 30 ng of the plasmid encoding cathepsin B and with the plasmid encoding Gal4-GFLG-VP64. As expected, the null control showed no detectable mCherry signal, since no plasmid encoding a Gal4-V64 construct was transfected. Consequently, mCherry overexpression via VP64 could not be induced. However, we observed a high fluorescence intensity for eGFP, indicating that the transfection was successful. The negative control showed strong signals of both mCherry and eGFP. Therefore, it can be assumed that the transfection was successful and that our mCherry readout system is functional. Interestingly, there are some cells which either seem to only express mCherry or eGFP and some cells that show no fluorescence signal. The test sample showed less eGFP and mCherry fluorescence compared to the negative control. We expected to observe reduced fluorescence intensity of mCherry, as the transfected cells would express cathepsin B, which cleaves the linker, thereby decreasing mCherry expression.
4.3 Mature Cathepsin B Is Expressed in HEK293T Cells
Figure 3 shows a western blot of the wild-type (wt) version of cathepsin B as well as the truncated and mutated version of cathepsin B (Δ1-20, D22A, H110A, R116A). Cells of both cathepsin B versions were treated with 500 nM doxorubicin (dox) 24 hours post-transfection and incubated for additional 24 hours. For each condition, three replicates were blotted. We observed no differences in protein expression levels between the dox-treated and untreated wt versions of cathepsin B. For the truncated and mutated version of cathepsin B, however, only the untreated samples showed the corresponding band at approximately 36 kDa expected for this version of cathepsin B. Additionally, the bands of the truncated and mutated version appeared much weaker than the ones of the wt, indicating poorer protein expression. The household protein β-tubulin is visible in all samples at approximately 55 kDa. The wt cathepsin B additionally showed bands for pro-cathepsin B at approximately 42 kDa, a mature single-chain version of cathepsin B at approximately 33 kDa and a mature double-chain version at approximately 26 kDa.
4.4 Conclusion
All in all, these findings demonstrate that our fluorescence-based readout assay can reliably detect cathepsin B-mediated cleavage of peptide linkers, with the GFLG linker showing particular susceptibility to cleavage. This makes GFLG a promising candidate for targeted applications in environments with upregulated cathepsin B activity, such as in cancerous tissues. Additionally, our cathepsin B-cleavable linker can be combined with caged inteins (Gramespacher et al., 2017) conjugated to a dead Cas9 to selectively induce Cas-stapling in the presence of cathepsin B.
5. References
Gramespacher, J. A., Stevens, A. J., Nguyen, D. P., Chin, J. W., & Muir, T. W. (2017). Intein Zymogens: Conditional Assembly and Splicing of Split Inteins via Targeted Proteolysis. J Am Chem Soc, 139(24), 8074-8077. https://doi.org/10.1021/jacs.7b02618
Jin, C., EI-Sagheer, A. H., Li, S., Vallis, K. A., Tan, W., & Brown, T. (2022). Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers. Angewandte Chemie International Edition, 61(13), e202114016. https://doi.org/10.1002/anie.202114016
Ruan, H., Hao, S., Young, P., & Zhang, H. (2015). Targeting Cathepsin B for Cancer Therapies. Horiz Cancer Res, 56, 23-40.
Shim, N., Jeon, S. I., Yang, S., Park, J. Y., Jo, M., Kim, J., Choi, J., Yun, W. S., Kim, J., Lee, Y., Shim, M. K., Kim, Y., & Kim, K. (2022). Comparative study of cathepsin B-cleavable linkers for the optimal design of cathepsin B-specific doxorubicin prodrug nanoparticles for targeted cancer therapy. Biomaterials, 289, 121806. https://doi.org/10.1016/j.biomaterials.2022.121806
Wang, J., Liu, M., Zhang, X., Wang, X., Xiong, M., & Luo, D. (2024). Stimuli-responsive linkers and their application in molecular imaging. Exploration, 4(4), 20230027. https://doi.org/10.1002/EXP.20230027
Zhong, Y.-J., Shao, L.-H., & Li, Y. (2013). Cathepsin B-cleavable doxorubicin prodrugs for targeted cancer therapy (Review). Int J Oncol, 42(2), 373-383. https://doi.org/10.3892/ijo.2012.1754
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