Lysosomal Cholesterol Accumulation Drives Active Suppression of Autophagy in Aging via the mTORC1‑TFEB Axis

Hypothesis

Age‑related buildup of free cholesterol within lysosomes sustains mTORC1 activation on the lysosomal surface, which in turn keeps TFEB phosphorylated and cytoplasmic, while also directly inhibiting the VPS34‑Beclin1 complex that nucleates autophagosomes. This creates a self‑reinforcing loop that actively suppresses autophagy, beyond the transcriptional and transport blocks already described.

Mechanistic Rationale

• Lysosomal cholesterol as a mTORC1 primer – Cholesterol enrichment in lysosomal membranes promotes Rag GTPase recruitment and activates mTORC1, a process shown to be sensitive to lysosomal lipid composition (mTORC1 hyperactivation).
• TFEB sequestration – Persistent mTORC1 activity phosphorylates TFEB at Ser142 and Ser212, enhancing its binding to cytosolic 14‑3‑3 proteins and preventing nuclear import, compounding the nuclear‑pore bottleneck described in (mTORC1 hyperactivation).
• Direct VPS34 inhibition – Free cholesterol can intercalate into the phosphatidylinositol‑3‑phosphate (PI3P) producing VPS34 complex, reducing its lipid kinase activity and impairing phagophore nucleation, a mechanism not captured by current transcriptional or transport models.
• Synergy with epigenetic silencing – Cholesterol‑activated mTORC1 can stimulate EZH2 activity, reinforcing H3K27me3‑mediated repression of autophagy genes (epigenetic silencing).

Testable Predictions

1. Correlation – Lysosomal free cholesterol levels will positively correlate with cytoplasmic TFEB retention and inversely with autophagic flux across tissues from young to old mice.
2. Rescue by cholesterol depletion – Pharmacological depletion of lysosomal cholesterol (e.g., cyclodextrin treatment) or genetic overexpression of NPC1 will reduce lysosomal cholesterol, decrease mTORC1 signaling, increase nuclear TFEB, restore VPS34 activity, and enhance autophagic flux in aged cells.
3. Lifespan extension dependence – The lifespan‑extending effects of lysosomal cholesterol lowering will be abolished in autophagy‑deficient (Atg5‑KO or TFEB‑KO) backgrounds, demonstrating that autophagy is required for the benefit.
4. Falsification – If cholesterol reduction fails to alter TFEB localization, mTORC1 activity, or autophagic flux despite verified cholesterol depletion, the hypothesis is falsified.

Experimental Approach

• Measure lysosomal cholesterol using filipin staining coupled with lysosomal markers (LAMP1) in liver, brain, and muscle of 3‑month vs. 24‑month mice.
• Manipulate cholesterol: treat primary fibroblasts or organoids with 2‑mM methyl‑β‑cyclodextrin for 24 h; alternatively, generate AAV‑NPC1 vectors for in vivo overexpression.
• Readouts: Western blot for phospho‑S6K (mTORC1 activity), phospho‑TFEB (Ser142/Ser212), nuclear vs. cytoplasmic TFEB fractionation, LC3‑II/I turnover with bafilomycin A1, and PI3P levels (using FYVE‑domain GFP).
• Functional assays: Seahorse extracellular flux analysis for metabolic health, senescence‑associated β‑galactosidase staining, and murine survival curves.
• Genetic controls: Atg5‑flox;Cre‑ERT2 and TFEB‑flox;Cre‑ERT2 mice to test autophagy dependence of cholesterol‑lowering benefits.

Implications

If validated, this hypothesis positions lysosomal cholesterol as a upstream metabolic checkpoint that actively enforces autophagy suppression in aging. It suggests that targeting lysosomal lipid homeostasis—not only mTORC1 or TFEB directly—could re‑engage autophagic clearance and improve healthspan, offering a novel avenue for interventions that complement rapamycin or caloric restriction.