Single-Cell Transcriptomic Analysis Identifies a Unique Pulmonary Lymphangioleiomyomatosis Cell

Rationale: Lymphangioleiomyomatosis (LAM) is a metastatic neoplasm of reproductive-age women associated with mutations in tuberous sclerosis complex genes. LAM causes cystic remodeling of the lung and progressive respiratory failure. The sources and cellular characteristics of LAM cells underlying disease pathogenesis remain elusive. Objectives: Identification and characterization of LAM cells in human lung and uterus using a single-cell approach. Methods: Single-cell and single-nuclei RNA sequencing on LAM ( n  = 4) and control ( n  = 7) lungs, immunofluorescence confocal microscopy, ELISA, and aptamer proteomics were used to identify and validate LAM CORE cells and secreted biomarkers, predict cellular origins, and define molecular and cellular networks in LAM. Measurements and Main Results: A unique cell type termed LAM CORE was identified, which was distinct from, but closely related to, lung mesenchymal cells. LAM CORE cells expressing signature genes included known LAM markers such as PMEL , FIGF , CTSK , and MLANA and novel biomarkers validated by aptamer screening, ELISA, and immunofluorescence microscopy. LAM cells in lung and uterus are morphologically indistinguishable and share similar gene expression profiles and biallelic TSC2 mutations, supporting a potential uterine origin for the LAM CORE cell. Effects of LAM on resident pulmonary cell types indicated recruitment and activation of lymphatic endothelial cells. Conclusions: A unique population of LAM CORE cells was identified in lung and uterus of patients with LAM, sharing close transcriptomic identity. LAM cell selective markers, secreted biomarkers, and the predicted cellular molecular features provide new insights into the signaling and transcriptional programs that may serve as diagnostic markers and therapeutic targets to influence the pathogenesis of LAM.