Use of spatial transcriptomics to analyze the molecular landscape of tuberous sclerosis complex–associated angiomyolipoma: Implications for diagnosis and therapeutic targeting.

517 Background: Tuberous sclerosis complex–associated angiomyolipoma (TSC-AML) is often bilateral, multifocal, and sometimes massive or familial, with increased rupture/hemorrhage risk, complicating management vs sporadic AML. mTOR inhibitors are available but with limited efficacy, so deeper molecular understanding may guide therapy selection and new targeted approaches. We performed a pilot, hypothesis-generating spatial transcriptomic comparison of TSC-AML, sporadic AML, and renal cell carcinoma (RCC) to contextualize its biology. Methods: Formalin-fixed paraffin-embedded sections from one case each of TSC-AML, sporadic AML, and RCC underwent spatial gene expression profiling (CytAssist Visium). Unsupervised clustering and pathway analysis defined cell-type–specific programs and candidate targets. Results: Both TSC-AML and sporadic AML showed triphasic architecture (vascular, smooth muscle, adipose) and PEC markers (PMEL, MLANA, ACTB, DES). TSC-AML had TSC1/2 downregulation without significant mTOR, MLST8, or RPTOR upregulation, suggesting post-translational mTORC1 activation. RCC showed broad mTORC1 pathway upregulation. Vascular regions enriched angiogenesis/ECM remodeling (Wnt, NABA matrisome), adipose regions activated lipid metabolism (PPAR signaling, triglyceride synthesis). Comparative profiling found 42 genes uniquely upregulated in TSC-AML, including immune modulators (IL33, ABCC8), metabolic regulators (FABP4, APOC1), muscle genes (LDB3, SYNM), and neuronal genes (GRIA2, ASTN1), suggesting candidate biomarkers and therapeutic targets. Conclusions: This pilot study maps the spatial transcriptome of TSC-AML, identifies candidate biomarkers for precision diagnostics, and highlights angiogenic, ECM, and metabolic pathways as therapeutic targets. Comparative profiling vs RCC and sporadic AML revealed distinct pathway activation, underscoring TSC-AML’s unique biology. These findings warrant validation in larger cohorts and could inform clinical management. Forty-two genes upregulated in TSC-associated angiomyolipoma. Lipid metabolism / Adipogenesis FABP4, APOC1, ADIPOQ, PLIN1, CES1 Immune regulation / Inflammation IL33, APOBEC3C, IGSF21, LGALS1 Muscle structure / Cytoskeleton LDB3, SYNM, PGAM2, TPM2, PLN, MRVI1, ADRA1A Neuronal / Synaptic function GRIA2, ASTN1, SNCG, CELF2, AFF2, C14orf180, TRARG1 Metabolism / Stress response PDK1, STEAP4, NDRG4, DUOX2, NMNAT2 Other / Unclassified IGFN1, TMEM132C, ADGRL3, ABCC8, KCNQ4, PDE1B, PIL5