SNPs associated with Metabolic Disorders Disrupt Structural Properties of DNA G-Quadruplexes in Regulatory Regions relevant during Tumor Development

Background. The global prevalence of metabolic diseases (MetDs) is constantly rising and is associated with an increased risk of cancer development. Genome-wide association studies have identified numerous single nucleotide polymorphisms (SNPs) linked to MetDs, some of which occur in genes also implicated in tumorigenesis. G-quadruplexes (G4s) are non-canonical DNA secondary structures that regulate gene expression by serving as binding platforms for transcription factors. Alterations in their structural properties can significantly impact transcriptional efficiency. Notably, disease-associated variants have been found within or near regulatory elements. In this study, we systematically assessed the overlap between MetD-associated SNPs and G4 motifs, their impact on G4 stability and topology, and their potential to modulate the regulatory activity of G4s. Results. Approximately 0.9–1.5% of all SNPs were located within G4 motifs (G4-SNPs), varying by prediction tool. On a global level, effect alleles tended to lower G4 stability, regardless of whether the SNPs were risk or protective. Several G4-SNPs were found in regulatory regions, including the destabilizing MICB rs2855804 C/T and stabilizing PLA2G6 rs2277844 G/A variants. In vivo G4 formation was confirmed by permanganate/S1 nuclease footprinting; while circular dichroism spectroscopy and AlphaFold 3 predictions revealed allele-specific changes in G4 topology. Hi-C data, histone modifications, transcription factor binding, and luciferase reporter assays validated regulatory effects of these G4-SNPs. Conclusions. Although G4-SNPs are unlikely to be sole drivers of disease onset or progression, they significantly influence transcriptional regulation and may help explain allele-specific gene expression changes observed in MetDs and their elevated risk for certain tumors.