Unveiling the biological effects of DNA G-quadruplex ligands through multi-omics data integration

G-quadruplexes (G4s) are non-canonical DNA structures that have proved to play a pivotal role in various biological processes, including telomere maintenance and gene expression regulation. Owing to their prevalence in tumor cells, G4s have emerged as promising targets for cancer therapy, with a substantial body of research demonstrating the potential of G4 ligands as anti-cancer tools. However, a more comprehensive understanding of G4 binders’ mode of action is imperative to successfully translate them into therapeutic agents. Herein, we employed a multi-omics approach, integrating transcriptomics, proteomics and metabolomics, to identify key signaling pathways that mediate the anti-cancer effects of well-characterized G4-binding agents (berberine, PDS and RHPS4) on HeLa cancer cells. Our results revealed that, under the investigated experimental conditions, berberine treatment only had negligible cellular effects, whereas PDS-treated HeLa cells underwent significant changes at the transcriptomic, proteomic and metabolomic levels, with marked impairment in glycolysis, antioxidant capacity, lipids and nucleotides biosynthetic processes. Notably, RHPS4 could selectively affect mitochondrial activity, possibly through the specific stabilization of mitochondrial G-quadruplex structures. Overall, our findings provide a valuable multi-omics perspective on the cellular changes driven by G-quadruplex binders, that may accelerate the development of G4-targeted therapies. mRNA-seq profiling of HeLa cells treated with three different G-quadruplex ligands (Berberine, Pyridostatin, and RHPS4), compared to mRNA-seq profiling of untreated cells