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Phospho\u2010S6K, phospho\u2010S6, and phospho\u2010S6K\u2013activated proteins phospho\u2010STAT3 and phospho\u20104EBP1 were detected immunohistochemically in GCs, whereas only phospho\u2010S6 was observed in BCs. Expression of four candidate gene families (cell signaling, cell adhesion, growth factor\/receptor, and transcription factor mRNAs) was assayed in single, microdissected phospho\u2010S6\u2013immunolabeled BCs and GCs as a strategy to define whether BCs and GCs exhibit differential transcriptional profiles. Among 60 genes, differential expression of 24 mRNAs distinguished BCs from GCs and only 4 genes showed similar expression profiles between BCs and GCs. Tuberin mRNA levels were reduced in GCs from TSC patients with <jats:italic>TSC2<\/jats:italic> gene mutations but were unchanged in BCs. Phospho\u2010S6K, \u2010S6, \u2010STAT3, and \u20104EBP1 expression in GCs reflects loss of hamartin\u2010tuberin\u2013mediated mTOR pathway inhibition. Phospho\u2010S6 expression alone in BCs does not support mTOR cascade activation in FCD. Differential gene expression profiles in BCs and GCs supports the hypothesis that these cell types derive by distinct pathogenic mechanisms. 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