Hypothesis

Aged cells actively suppress autophagy not merely through mTORC1 hyperactivation but because lysosomal calcium efflux fails, simultaneously disabling the calcineurin‑TFEB activation axis and removing calcium‑dependent inhibition of mTORC1 at the lysosomal surface. Restoring lysosomal calcium flux should reactivate TFEB nuclear translocation and dampen mTORC1 signaling, thereby rescuing autophagy flux even when the core machinery is intact.

Mechanistic Rationale

• Lysosomal calcium as a signaling hub – Lysosomal Ca²⁺ release via TRPML1 (MCOLN1) activates the phosphatase calcineurin, which dephosphorylates TFEB, promoting its nuclear translocation and transcription of autophagy‑lysosomal genes (3).
• Calcium‑dependent mTORC1 brake – Cytosolic Ca²⁺‑calcineurin also dephosphorylates and activates the TSC2 complex, which suppresses Rheb‑GTP and thus mTORC1 activity on the lysosomal surface. When lysosomal Ca²⁺ efflux declines, calcineurin activity drops, leaving TFEB phosphorylated (cytosolic) and TSC2 inactive, allowing mTORC1 to remain constitutively active (1, 2).
• Age‑related decline – Lysosomal Ca²⁺ release diminishes with age in multiple tissues due to oxidative modification of TRPML1 and altered lipid composition, a change not captured by transcriptional repressors like ZKSCAN3 (6).
• Functional autonomy of the core machinery – As shown, TFEB overexpression or constitutive activation can bypass the block and reduce aggregates (3, 4), indicating that the autophagic apparatus remains competent.

Testable Predictions

1. Lysosomal Ca²⁺ flux is reduced in aged human iPSC‑derived neurons and myotubes – measured with Fluo‑4 AM lysosome‑targeted probe.
2. Pharmacological activation of TRPML1 (e.g., ML‑SA1) will:
   • Increase lysosomal Ca²⁺ release.
   • Enhance calcineurin activity (dephosphorylated NFATc1 read‑out).
   • Promote TFEB dephosphorylation and nuclear accumulation.
   • Decrease p‑S6K and p‑4EBP1 (mTORC1 read‑outs).
   • Elevate autophagic flux (LC3‑II turnover in presence of bafilomycin A1) and reduce p62/SQSTM1 and insoluble ubiquitin‑positive aggregates.
3. Genetic rescue – Overexpressing wild‑type TRPML1 in aged cells should phenocopy ML‑SA1 effects, whereas a Ca²⁺‑dead TRPML1 mutant will not.
4. Falsification – If ML‑SA1 fails to alter mTORC1 signaling, TFEB localization, or autophagic flux despite restoring lysosomal Ca²⁺, the hypothesis is invalid.

Experimental Outline

• Cell models – iPSC‑derived dopaminergic neurons (aged >60 days in culture) and skeletal myotubes from older donors.
• Interventions – ML‑SA1 (10 µM, 6 h), vehicle control, Torin1 (mTORC1 inhibitor) as positive control for autophagy induction.
• Readouts – Western blot for p‑S6K, p‑4EBP1, total TFEB, phospho‑TFEB (Ser142), nuclear/cytosolic TFEB fractionation; immunofluorescence for LC3 puncta ± bafilomycin; Flow cytometry for lysosomal Fluo‑4 intensity; Filter‑trap assay for insoluble aggregates.
• Statistical analysis – Minimum n = 3 biological replicates; ANOVA with Tukey post‑hoc; effect size > 30 % change considered biologically significant.

Significance

Confirming that lysosomal Ca²⁺ loss couples mTORC1 hyperactivity to TFEB inhibition would reveal a unified upstream mechanism for the active suppression of autophagy in aging. It would also suggest that lysosomal ion channel pharmacology—already explored in lysosomal storage disorders—could be repurposed to rejuvenate aged stem cells and tissues without forcing transcriptional overdrive.