Identification of LncRNAs scaffolding a chromatin-associated gene regulatory complex in breast cancer cells comprising ERα, DOT1L and menin

In Estrogen Receptor (ER)-positive Breast Cancer (BC), the development of resistance to endocrine therapies remains a significant clinical challenge, often linked to transcriptional and epigenetic deregulations. The main hallmark in this neoplasm, the nuclear receptor ERα, drives oncogenesis by recruiting multiple coregulators, including the histone methyltransferase DOT1L and the scaffold protein menin, forming a pro-tumorigenic machinery. However, the precise mechanism of this complex assembly is not fully understood. Our study investigates the molecular basis of ERα-DOT1L-menin functional association, focusing on the potential scaffolding role of long non-coding RNAs (lncRNAs).To identify lncRNAs specifically involved in this network, we performed native nuclear immunoprecipitation coupled to RNA sequencing (RIP-Seq) for DOT1L and menin in MCF-7 BC cells. Cross comparison between these datasets and existing ERα-interacting RNA data revealed six common molecules. Among these, we focused on PVT1, a known oncogenic RNA previously characterized by our group and able to co-recruit ERα and PRC2 complex onto specific chromatin loci, whose high expression, along with ERα, DOT1L and menin, correlates with worse patients' survival. Functional experiments confirmed that PVT1 knock down reduces ERα, menin and DOT1L association, supporting its role as a molecular scaffold in this complex. Transcriptomic profiling upon ERα, DOT1L, menin, or PVT1 blockade uncovered a common gene signature enriched in pathways covering main BC hallmarks. Many of deregulated genes were directly bound by all three proteins, suggesting a coordinated transcriptional regulation, revealing a critical axis involving ERα, DOT1L, menin and PVT1. Targeting this RNA-dependent chromatin associated regulatory complex could offer novel therapeutic strategies for BC treatment.