Neural crest cell signatures drive tumorigenesis in tuberous sclerosis complex and lymphangioleiomyomatosis.

Tuberous sclerosis complex (TSC) and lymphangioleiomyomatosis (LAM) lack well-defined cellular origins, limiting treatment options. In this report, scRNA-seq of Tsc2+/- mouse renal cystadenomas revealed an 80-fold increase in a tumor cell subpopulation with neural crest features, expressing known cranial neural crest genes as SRY box transcription factor 9 (Sox9), transcription factor activator protein (Tfap2a), and candidate neurocristopathy markers, osteopontin (Spp1), lipocalin-2 (Lcn2), clusterin (Clu), and cytokeratin 18 (Krt18). These signatures were validated in mouse tumors and LAM patient lesions and serum, identifying a tumor phenotype distinct from traditional VEGFD detection. Pathway analysis indicated activation of WNT/SHH signaling, nephric duct formation, and protumorigenic signals, with transcription factor 7 (Tcf7) and ephrin-A ligands as key upstream regulators. Spp1 KO in cranial neural crest cells (CNCCs) significantly reduced proliferation (28%-33%), migration (54%-76%), and invasion (29%-64%) without affecting viability, while Tsc2 KO increased viability 3- to 6-fold with minimal effect on chemotaxis. Elevated serum levels of SPP1 and KRT18 in 1 subset of patients with LAM, decreased LCN2 in nearly all cases, and distinct increases in VEGFD in a separate subset suggest complementary roles for these biomarkers. Overall, findings support a neurocristopathic model of tumor development in TSC and LAM and identify potential biomarkers and therapeutic targets beyond mTOR inhibition.