Parts

Overview

Basic parts

Contribution

1. CEA N domain Part

This part is based on the CEA N domain sequence information revealed by Abdul-Wahid et al. [1]. The CEA protein is a biomarker for certain cancers, including colon and cervical cancer, and it is detectable in the serum [2,3]. This protein holds great promise as a biomarker in cancer research.

We conducted both Cell-free expression (CFE) and cell expression experiments to produce the CEA protein using this part. While the CFE experiments were not successful, we confirmed the expression of the protein in cell expression. Optimization of expression conditions and other factors may be necessary to utilize CFE effectively.

Although further investigation is needed for successful expression under cell-free conditions, we have verified that the protein is expressed sufficiently within cells.

This part can be valuable for future iGEM teams interested in cancer diagnosis, treatment, and related fields. It allows for the easy expression of the CEA protein when needed and opens the possibility of expressing CEA proteins with specific accessory proteins for their projects.

2. N56 Aptamer Part

This part is a single-stranded DNA aptamer reported to have a binding specificity to the CEA protein, according to the study by Dasari et al. [4]. This team has discovered this aptamer through the Systematic Evolution of Ligands by EXponential Enrichment (SELEX) experiment.

We further validated the binding of N56 to the CEA protein using experimental techniques such as EMSA and PAD. In particular, through PAD, we discovered that N56 binds to CEA perpendicularly, indicating its suitability for diagnostic systems like LFA.

N56 aptamer exhibits high specificity for CEA [4] and, being in aptamer form, has the advantage of greater accessibility compared to antibodies. Additionally, we have characterized the binding pattern of the N56-CEA complex. Therefore, future iGEM teams aiming to target this protein or utilize it as a biomarker may have a simpler and more convenient method at their disposal.

[1] A. Abdul-Wahid *et al.*, “Induction of antigen-specific TH9 immunity accompanied by mast cell activation blocks tumor cell engraftment,” *International Journal of Cancer*, vol. 139, no. 4, pp. 841–853, Apr. 2016, doi: https://doi.org/10.1002/ijc.30121.

[2] S. Dasari, R. Wudayagiri, and L. Valluru, “Cervical cancer: Biomarkers for diagnosis and treatment,” *Clinica Chimica Acta*, vol. 445, no. 7–11, pp. 7–11, May 2015, doi: https://doi.org/10.1016/j.cca.2015.03.005.

[3] V. L. Kankanala and S. K. R. Mukkamalla, “Carcinoembryonic Antigen,” *PubMed*, 2022. https://www.ncbi.nlm.nih.gov/books/NBK578172/

[4] E. W. Orava, Aws Abdul-Wahid, E. J. Huang, Amirul Islam Mallick, and J. Gariépy, “Blocking the attachment of cancer cells in vivo with DNA aptamers displaying anti-adhesive properties against the carcinoembryonic antigen,” *Molecular Oncology*, vol. 7, no. 4, pp. 799–811, Aug. 2013, doi: https://doi.org/10.1016/j.molonc.2013.03.005.