Integrative cell subtype-to-drug discovery technology for angiomyolipomas treatment

Tuberous sclerosis complex mutation renal angiomyolipomas (TSC-RAML) are benign tumors driven by abnormal growth of mesenchymal-derived cells. Although mTOR inhibitors are clinically used, drug resistance and incomplete tumour shrinkage highlight the need for new treatment approaches. Here, we developed a new strategy combining single-cell transcriptomics, network pharmacology, and functional experiments to identify targeted therapies for TSC-RAMLs. Single-cell RNA sequencing of tumour tissues from 4 TSC-RAML patients uncovered a distinct mesenchymal subpopulation (TSC-RAML-Cells) with upregulated pathways in adipogenesis and mTOR signalling. Using high-dimensional weighted gene co-expression network analysis (hdWGCNA) on TSC-RAML-Cells, we identified three disease-associated modules containing hub genes critical for tumour survival. Cross-referencing these modules with the Connectivity Map (CMAP) drug database prioritized AS-605240 as a potential therapeutic candidate. Protein-protein interaction (PPI) network analysis further revealed PI3KCA as a central target, and molecular dynamics simulations confirmed stable binding between AS-605240 and PI3KCA, with a binding free energy of −7.8 ​kcal/mol, supporting its mechanism of action. In vitro experiments using patient-derived TSC-RAML cells showed that AS-605240 suppressed cell growth in a dose-dependent manner (IC50 ​= ​7.8 ​μM) and increased apoptosis rates through inhibition of the PI3K/AKT pathway. This work not only proposes AS-605240 as a promising therapy for TSC-RAMLs but also provides a scalable “cell subtype-to-drug" discovery framework. By integrating single-cell omics and computational drug repurposing, this approach accelerates precision medicine development for rare diseases.