Decoding cancer heterogeneity through super-enhancer landscapes: from subtype discovery to therapeutic opportunity.

Super-enhancers (SEs) are clusters of enhancers with potent regulatory capabilities. They play a crucial role in shaping cellular identity and driving the progression of various diseases, including cancer. SEs exhibit significant heterogeneity across different cell types and cancer subtypes. Analysis of SE landscapes can recapitulate existing classification systems and unveil novel SE-driven epigenetic subtypes. In this review, we summarized the latest advancements in cancer subtype identification based on SE-related characteristics, outlined the typical analytical workflows adopted in such studies, and explored the biological and clinical significance of SE-driven subtypes. Furthermore, we discussed the field's key challenges and emerging technologies to highlight future research directions. SE analysis provides a robust framework for dissecting cancer heterogeneity. This approach offers novel epigenetic perspectives and support for the realization of personalized medicine.