E3 aptamer

Jun 7, 2024 • Zhizhong Lu, Ying Ao

Description

In 2018, Powell Gray, B. et al. used cell selection for aptamers with prostate cancer specificity yielded the E3 aptamer, which internalizes into prostate cancer cells without targeting normal prostate cells. Chemical conjugation of E3 to the drugs monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) yields a potent cytotoxic agent that efficiently kills prostate cancer cells in vitro but does not affect normal prostate epithelial cells. Importantly, the E3 aptamer targets tumors in vivo and treatment with the MMAF-E3 conjugate significantly inhibits prostate cancer growth in mice, demonstrating the in vivo utility of aptamer–drug conjugates^[1].

SELEX

Performed two Cell-Internalization SELEX using a 2′fluoro pyrimidine modified RNA library comprising a modified, nuclease-resistant RNA pool of ∼10¹⁴ different RNAs. Two different selection strategies were employed. In the first, positive selections targeting PC-3 prostate cancer cells were combined with a strong negative selection against normal prostate epithelial cells (PrEC) to deplete RNA molecules capable of internalizing into noncancerous cells. In the second, the cell target for the positive selection was varied and included toggling between the LNCaP, PC-3, DU 145, and 22Rv1 cell lines. Additionally, to exclude PSMA as a target, chose to select against both PSMA-positive (LNCaP and 22Rv1) and PSMA-negative (PC-3 and DU 145) cell lines. Here again, positive rounds of selection targeting these cells were combined with a strong negative selection against PrECs. For both selections, after incubating cells with the library of RNA variants and washing away nonbinding aptamers, cell-surface-bound RNA was degraded via treatment with a harsh RNase mixture that degrades 2′fluoro modified RNA, leaving only RNAs that had internalized into cells. Subsequent reverse transcription, PCR amplification, and transcription of the internalized RNA completed a round of internalization selection. After nine rounds of selection against PC-3 cells, 12 unique RNAs were evaluated^[1].
Detailed information are accessible on SELEX page.

Structure

The 2D structure of the figure is based on the article by ribodraw tool to draw.

5'-GGCUUUCGGGCUUUCGGCAACAUCAGCCCCUCAGCC-3'

Ligand information

SELEX ligand

Prostate cancer is the uncontrolled growth of cells in the prostate, a gland in the male reproductive system below the bladder. Abnormal growth of prostate tissue is usually detected through screening tests, typically blood tests that check for prostate-specific antigen (PSA) levels. Those with high levels of PSA in their blood are at increased risk for developing prostate cancer. Diagnosis requires a biopsy of the prostate. If cancer is present, the pathologist assigns a Gleason score, and a higher score represents a more dangerous tumor. Medical imaging is performed to look for cancer that has spread outside the prostate. Based on the Gleason score, PSA levels, and imaging results, a cancer case is assigned a stage 1 to 4. A higher stage signifies a more advanced, more dangerous disease.-----from Wiki

Name	GenBase gene	GenBase protein	Gene ID
Prostate Cancer Cells	LZ218388.1	CAE11953.1	101867536

Some isolated sequences bind to the affinity of the protein.

Name	Sequence	Ligand	Affinity
E3 aptamer	5'-GGCUUUCGGGCUUUCGGCAACAUCAGCCCCUCAGCC-3'	Prostate Cancer Cells	146-410 nM

References

[1] Tunable cytotoxic aptamer-drug conjugates for the treatment of prostate cancer.
Powell Gray, B., Kelly, L., Ahrens, D. P., Barry, A. P., Kratschmer, C., Levy, M., & Sullenger, B. A.
Proceedings of the National Academy of Sciences of the United States of America, 115(18), 4761–4766. (2018)