Full-thickness spatial transcriptomics of the human uterus reveals basalis niche architecture and regeneration gradients during menstrual breakdown

Technical Summary: Full-thickness Spatial Transcriptomics of the Human Uterus

Problem Statement
The human endometrium exhibits a unique capacity for cyclical, scarless breakdown and regeneration during the menstrual cycle. While it is established that progenitor cells retained within the deep basalis compartment drive this renewal, the full-depth spatiotemporal dynamics of the process have remained poorly understood. Previous research has been constrained by anatomical complexities and technical limitations, particularly regarding the underrepresentation of the menstrual and proliferative phases in existing datasets. Consequently, the precise molecular architecture of the basalis niche and the coordination between tissue shedding and repair have not been fully resolved.

Methodology
To address these gaps, the study employs an integrated multi-omics approach combining high-resolution spatial transcriptomics with single-cell transcriptomics. The researchers mapped spatial gene-expression gradients across the entire thickness of the human endometrium, extending from the myometrial-endometrial boundary to the luminal surface. The dataset encompasses over ten million cells derived from three distinct sources: biopsies, hysterectomy samples, and menstrual fluid. A critical methodological focus was the enrichment of samples from the menstrual and proliferative phases, which are typically scarce in prior studies, thereby enabling a comprehensive view of the regenerative cycle.

Key Contributions and Results
The study yields several high-resolution molecular insights:

• Concurrent Breakdown and Regeneration: Contrary to models suggesting temporally separated phases of shedding and repair, the data reveal that endometrial breakdown, regeneration, and rapid luminal re-epithelialisation occur concurrently. These processes are organized across distinct tissue compartments, operating simultaneously rather than sequentially.
• Basalis-to-Luminal Gradients: The analysis identifies continuous transcriptional gradients extending from the basalis to the luminal surface. These gradients link progenitor cell identity, niche signaling, and tissue remodeling, defining a coordinated regenerative axis that spans the full depth of the tissue.
• Resolution of the Basalis Niche: At unprecedented molecular resolution, the study resolves the basalis epithelial niche. It identifies a discrete, predominantly quiescent progenitor-like epithelial subset and a specialized population of supporting SFRP5+ fibroblasts. Both cell types are characterized by WNT inhibition.
• Multi-Component Architecture: The basalis niche is defined as a multi-component architecture that includes these progenitor and fibroblast populations alongside lymphoid aggregates. Notably, this architecture persists after menopause, suggesting it functions as a long-lived regenerative reservoir.

Significance
The paper establishes spatial transcriptional gradients as a central organizing principle of endometrial renewal. By providing a detailed molecular framework of the full-thickness endometrium, these findings offer a basis for understanding the mechanisms underlying disorders of menstruation, implantation failure, and impaired tissue repair. The identification of a persistent, quiescent progenitor niche provides a specific target for investigating the origins of endometrial pathologies and the mechanisms of scarless healing.