Spatial transcriptomics uncovers the hybrid molecular identity, ciliated phenotype, and immune signature of adenomyosis lesions

Adenomyosis is a common gynecological condition characterized by ectopic endometrial-like tissue deep within the myometrium, causing debilitating symptoms. Treatment options are limited to hormones that primarily focus on symptom management only or invasive hysterectomy. Despite its prevalence, the pathogenesis of adenomyosis remains poorly understood, considerably impeding the development of targeted, true disease modifying treatments. Here, through spatial transcriptomics analysis of full-thickness human uterine wall biopsies ( n  = 10), we demonstrate that adenomyosis lesions exhibit a distinct transcriptomic profile, intermediate between matched endometrium and myometrium, characterized by enhanced epithelial ciliation and altered biological pathways. We reveal that adenomyosis lesion transcriptome more closely resembles the endometrial basalis than the functionalis, marked by enriched olfactory signaling, dysregulated oxidative phosphorylation and adenosine triphosphate synthesis, and an altered immune microenvironment indicative of chronic inflammation. In silico drug screening identified candidate compounds capable of reversing the adenomyosis lesion transcriptomic signature. These findings offer previously unknown insights into the molecular landscape of adenomyosis lesions and lay the groundwork for development of targeted, lesion-specific therapies that may preserve the eutopic endometrium and offer alternatives to hysterectomy.