G4-regulated IKBKB drives prostate cancer progression by activating NF-κB and remodeling the immune microenvironment

Prostate cancer remains a significant health challenge, with progression often linked to the tumor microenvironment and epigenetic dysregulation. G-quadruplex (G4) structures, non-canonical DNA secondary structures, act as crucial epigenetic regulators and represent promising therapeutic targets in various cancers. However, their specific role in prostate cancer progression, particularly how they interact with and influence the immune microenvironment, has been largely unexplored. Understanding this interplay could reveal novel vulnerabilities and therapeutic strategies beyond current standard-of-care limitations.

Researchers performed BG4 ChIP-seq to comprehensively map genome-wide G4 structures within the prostate cancer cell line C4-2. This genomic data was then integrated with immune pathway enrichment analyses and multiple machine learning algorithms (including LASSO, SVM-RFE, GBM, Naïve Bayes, and GLM) to pinpoint critical hub genes driving prostate cancer progression. Clinical relevance was assessed by analyzing gene expression and survival data from public datasets like GTEx, TCGA, and HPA. Functional validation of identified targets involved qPCR, CCK-8 assays for cell viability, colony formation, and wound-healing assays for migration. Druggability was evaluated using DrugnomeAI, and AI-assisted peptide inhibitors were designed using RFdiffusion and ProteinMPNN platforms.

The study identified 1,289 prostate cancer-specific G4 structures, predominantly located in promoter regions, suggesting a role in gene regulation. Through machine learning and immune enrichment, IKBKB emerged as a pivotal hub gene in prostate cancer progression. Clinical data showed IKBKB was significantly overexpressed in prostate cancer tissues, correlating with advanced disease stages and poor patient prognosis. Its expression was found to be regulated by promoter G4 structures, influenced by transcription factors AR and ERG. Functionally, IKBKB promoted genome instability, enhanced tumor stemness, and actively remodeled the immune microenvironment.

G4 stabilization specifically increased IKBKB expression and robustly activated the NF-κB pathway, which in turn significantly enhanced cancer cell viability, proliferation, and migration. Computational screening confirmed IKBKB's druggability, identifying existing inhibitors like Auranofin. Furthermore, AI-assisted design successfully generated novel peptide inhibitors specifically targeting IKBKB and proposed a CRISPR-dCas9 strategy for G4 disruption at the IKBKB promoter.