Targeted degradation of SETDB1 by an Aptamer-CRBNL PROTAC as a novel therapeutic strategy for breast cancer

PROteolysis TArgeting Chimeras (PROTACs) represent a novel therapeutic strategy that leverages the ubiquitin-proteasome system for targeted protein degradation. Aptamers, with their high specificity and binding affinity, have recently been explored as alternative recognition elements in PROTAC design. Here, we developed an aptamer-based PROTAC targeting SET domain bifurcated histone lysine methyltransferase 1 (SETDB1), an epigenetic regulator implicated in breast Cancer progression. The SETDB1-specific aptamer identified in our previous work was conjugated to a CRBN E3 Ligase ligand via click chemistry, generating a serum-stable PROTAC, designated as P-SETDB1-4. P-SETDB1-4 effectively recruits CRBN to SETDB1, inducing proteasome-dependent degradation of SETDB1 in breast Cancer cells. Consequently, P-SETDB1-4 significantly inhibits the proliferation and migration of breast Cancer cells. Moreover, P-SETDB1-4 enhances the CD8⁺ T cells cytotoxicity against breast Cancer cells and suppresses tumor growth in vivo. RNA Sequencing analysis elucidates the molecular mechanism underlying P-SETDB1-4-mediated tumor suppression and promotion of CD8⁺ T cell-mediated killing. This study provides a promising therapeutic strategy for breast Cancer and highlights the potential of aptamer-CRBNL PROTACs for targeting Other challenging oncogenic proteins.