Genomic features of the methylosome protein MEP50 and its implications in hormone signaling and cancer.

Graphical Abstract: Abstract: Dysfunction of several WD40 family proteins causes diverse endocrine diseases. Until recently, MEP50, a WD40 protein, was considered a gene of unknown significance because no inherited disease had been linked to its function. However, genetic inactivation of MEP50 in mouse models or somatic mutations in humans drives oncogenesis in several endocrine-related cancers, including those of the prostate, breast, and uterus. In this study, we generate new knowledge through a multi-tier integration of evolutionary genomics, sequence and structural analyses, molecular mechanic calculations, and dynamic simulations of wild-type and cancer-mutated MEP50 proteins. Indeed, we find that a conserved splicing event across evolution generates an alternative MEP50 isoform, which is smaller than the canonical MEP50 and lacks the final β-sheet of the first WD40 domain, the entirety of the second WD40 domain, and the first β-sheet of the third WD40 domain. Notably, we find that this novel, short MEP50 (s-MEP50) transcript encodes a 278 amino acid protein that retains aspects of the key regulatory and interaction sites, including those critical for androgen receptor and PRMT5 binding. Finally, we analyze the mutational landscape of MEP50 in endocrine-regulated cancers and use molecular mechanic calculations and dynamic simulations to reveal that cancer-associated mutations disrupt conserved bonding networks and induce widespread structural destabilization within the WD40 domain architecture. Thus, by combining evolutionary, structural, and biophysical approaches, we advance the understanding of MEP50 genomics, providing significant mechanistic and clinically relevant insights into endocrine-regulated tissues and their cancers.