PhD.Dissertation Defense:Atike Nur Çimen
Application of Short Peptides For Enhanced Biomarker-Based Cancer Detection
Atike Nur Çimen
Molecular Biology, Genetics and Bioengineering, PhD Dissertation, 2024
Thesis Jury
Asst. Prof. Sibel Çetinel (Thesis Advisor)
Asst. Prof. Stuart James Lucas
Asst. Prof. Nur Mustafaoğlu Varol
Asst. Prof. Hasan Ümit Öztürk
Asst. Prof. Esra Yüca Yılmaz
Özlem Kutlu (Thesis Co-advisor)
Date & Time: December 20th, 2024 – 11.30 AM
Place: FASS G052
Keywords : phage display, peptide, cancer, cytokine
Abstract
Cancer remains one of the deadliest diseases worldwide due to the limitations of traditional, non-targeted diagnostic approaches, which often lack the sensitivity required for early detection and effective treatment. Tumor specific molecules with high affinity serve as targeting agents in combination with imaging probes or therapeutics. Phage display has revolutionized the discovery of novel peptide ligands as promising molecular tools against specific cancer biomarkers. Peptides selected through biopanning, typically 3-5 rounds, are widely utilized in cancer diagnosis and therapy, showing high affinity for tumor biomarkers. In this study, we performed phage display screening to identify high-affinity peptides against a cytokine recently reported to be elevated in various cancer cells, suggesting its potential as a novel biomarker. Following four rounds of biopanning with an initial negative selection against serum, we identified 31 unique peptide sequences. Among these, four candidate peptides including p25, p26, p29, and NGS-1 were selected based on phage ELISA, molecular docking and next-generation sequencing (NGS) analyses. SPR measurements revealed that p25 and p26 bound with Kd of 53.7 μM and 42.7 μM, respectively. Furthermore, especially p25 and p29 peptides, with NGS-1 peptide that has a lower effect, demonstrated inhibition of STAT3 translocation and signaling, along with the suppression of cancer cell migration in cell culture studies. Simulation studies and cluster analysis revealed possible binding regions of peptides on protein; resulting that p25, p29, and NGS-1 occupies gp130 binding sites of the protein with differing stabilities, showing that these peptides most likely demonstrate inhibitory effect in cells through eliminating gp130 interaction. These results underscore the potential of the selected peptides as promising candidates for targeted cancer diagnostics and therapeutics. Furthermore, their ability to inhibit signaling pathways suggests therapeutic potential, as these peptides may disrupt tumor growth and metastasis. With further optimization and validation, these peptides could be integrated into molecular imaging or therapeutic delivery systems, advancing precision oncology and offering a novel approach to cancer management.