Selective mTORC1 inhibition prevents and treats NAFLD and NASH

We find that selective inhibition of one arm of mTORC1 signaling, via deletion of FLCN, promotes activation of the transcription factor TFE3 and profoundly protects against NAFLD and NASH in mice. (1) We performed genome-wide RNA-seq on livers from Control, liver-specific Flcn-null mice (LiFKO), and Flcn/Tfe3 double knock-out (DKO) mice fed either normal chow (NC) or a NAFLD-inducing diet (AMLN). We find TFE3-mediated induction of lysosomal and mitochondrial gene programs, and also suppression of de novo lipogenesis genes. (2) To understand whether TFE3 directly affects gene expression, we performed TFE3 ChIP-seq on livers from Control and LiFKO mice on normal chow. We find TFE3 occupancy on the chromatin at lysosomal genes, Ppargc1a (a driver of mitochondrial genes), and at de novo lipogenesis genes. (3) Finally, we wanted to test whether TFE3 antagonistically competes with the pro-lipogenic transcription factor SREBP-1c on chromatin. We therefore injected HA-tagged constitutively nuclear (active) SREBP-1c (nSREBP-1c), or a control virus, into control and LiFKO mice, treated them with a NAFLD-inducing diet (FPC diet), and collected liver tissue. We consequently performed HA-nSREBP-1c and TFE3 ChIP-seq experiments and observed no evidence of antagonistic competition. Flcn floxed mice were injected with AAV8-TBG-GFP or -Cre to yield Control and hepatocyte-specific Flcn-null (LiFKO) mice. Flcn floxed; Tfe3 -/Y (a whole body deletion of Tfe3) mice were also injected with either AAV8-TBG-GFP or -Cre to yield Tfe3 KO or Flcn/Tfe3 double knock-out (DKO) mice. (1) RNA-seq: Control, LiFKO, and DKO mice were placed on 17-18.5 weeks of normal chow or AMLN diet, and RNA-seq was performed on livers. (2) Normal chow TFE3 ChIP-seq: Control, LiFKO, and Tfe3 KO mice were fed normal chow, and livers were used for TFE3 ChIP-seq. (3) FPC diet TFE3 and HA-nSREBP-1c ChIP-seq: Control, LiFKO, and Tfe3 KO mice were additionally injected with either an AAV8 expressing HA-nSREBP-1c (“1c”) driven by a liver-specific ApoE/AAT promoter or a control virus (AAV8-TBG-GFP or -Cre) and treated with 9 days of FPC diet. Livers were then subjected to both TFE3 ChIP-seq and HA ChIP-seq.