Decoding the lymphangioleiomyomatosis niche microenvironment via integrative analysis of single cell multiomics and spatial transcriptomics

Lymphangioleiomyomatosis (LAM) is a rare, destructive lung disease caused by mutations in tuberous sclerosis complex 1 (TSC1) or TSC2, leading to mammalian target of rapamycin complex 1 (mTORC1) hyperactivation. While mTOR inhibitor sirolimus, the only US Food and Drug Administration approved drug for this disease, stabilises lung function in most LAM patients, the drug does not eliminate LAM cells, underscoring a critical gap in our understanding of the tumour microenvironment and cellular heterogeneity that drive disease progression. This study provides the first comprehensive multiomics atlas of the human LAM niche, integrating single-cell/single-nucleus RNA-sequencing, single-nucleus ATAC-sequencing, and spatial transcriptomics to deconvolute its complex architecture. We elucidate LAM cellular heterogeneity by identifying three distinct subtypes: the canonical, uterine smooth muscle-like, mTORC1-hyperactive LAM^CORE1; a novel, fibroblast-like LAM^CORE2 subtype with potent extracellular matrix (ECM) remodelling activity; and LAM^CORE3, a substate of LAM^CORE1 that shares LAM and myogenic signatures, but is characterised by lower transcriptional activity and specific functional enrichment in protein translation. Our analysis reveals the transcriptomic heterogeneity of the LAM subtypes, orchestrated by distinct transcriptional drivers and networks. Furthermore, we uncover spatially resolved LAM-associated fibroblast (LAF) states, LAF-seed and LAF-niche, that coordinate transforming growth factor-β signalling, ECM deposition and remodelling, and niche expansion. Spatial mapping uncovers a structured ecosystem where LAM^CORE1 cells form a central core enmeshed with the lymphatic endothelium, which is surrounded by LAFs, LAM^CORE2 cells, and reprogrammed immune and epithelial cells. Findings were validated through multimodal imaging technologies. Present work advances the field by providing the first high-resolution blueprint of the LAM niche microenvironment, revealing novel cell states and crosstalk that identify promising novel therapeutic targets.