Ketone-Mediated Lysosomal Preservation Determines Autophagic Flux Quality During Time-Restricted Feeding

Lena V.· Mar 24, 2026

Mechanism: Ketone bodies (BHB) preserve lysosomal acidification and cathepsin activity by inhibiting mTORC1 and activating TFEB, ensuring quality autophagic flux during fasting. Readout: Readout: Ketone supplementation restores autophagic flux and lysosomal integrity, reducing DNA damage (γ-H2AX foci) that is elevated in prolonged fasting without ketones.

Hypothesis

Sustained nutritional ketosis, rather than fasting duration alone, ensures completion of autophagic flux by maintaining lysosomal acidification and protease activity, whereas prolonged fasting that exceeds ketone saturation increases oxidative lysosomal damage, impairing degradative capacity and promoting lipofuscin accumulation.

Mechanistic Rationale

Ketone bodies as lysosomal stabilizers – β‑hydroxybutyrate (BHB) inhibits mTORC1 signaling and activates TFEB, driving lysosomal biogenesis and V‑ATPase assembly, which preserves the acidic pH required for cathepsin activity[3]. This effect is independent of caloric deficit and plateaus once plasma ketones reach ~1–2 mmol/L.
Oxidative stress threshold – Fasts >20 h elevate mitochondrial ROS beyond the scavenging capacity of Nrf2‑mediated antioxidants, leading to peroxidation of lysosomal membrane lipids[4]. Damaged membranes compromise autophagosome‑lysosome fusion, causing stalled autophagosomes and increased LC3‑II turnover without concomitant p62 degradation.
Quality vs. quantity – Short fasts (16:8) induce autophagy initiation (↑LC3B, ATG5) while keeping ROS low, allowing efficient cargo degradation[1][2]. Longer fasts raise initiation markers but simultaneously impair the degradative step, producing a paradox of high marker signal and low functional clearance.
Implications for tumor risk – Impaired lysosomal function during refeeding may allow damaged organelles and protein aggregates to persist, increasing genomic instability in proliferating stem cells[5]. Preserving lysosomal integrity via ketosis could mitigate this risk.

Testable Predictions

Flux measurement – In a randomized crossover trial, participants will undergo two 7‑day interventions: (a) 16:8 time‑restricted eating (TRE) and (b) 20:4 TRE, each with and without exogenous BHB ketone ester to maintain plasma β‑hydroxybutyrate ≥1 mmol/L during the fasting window. Autophagic flux will be assessed in peripheral blood mononuclear cells using LC3‑II turnover in the presence/absence of lysosomal inhibitors (bafilomycin A1) and p62 degradation. We predict that 20:4 TRE alone will show ↑LC3‑II but ↓flux (reduced LC3‑II degradation) and ↑lipofuscin fluorescence, whereas ketone‑supplemented 20:4 will restore flux to levels comparable to 16:8.
Lysosomal health – Lysosomal cathepsin activity and LysoTracker intensity will be higher in ketone‑supplemented conditions regardless of fasting length, and inversely correlated with mitochondrial ROS (MitoSOX) levels.
Tumor‑risk surrogate – γ‑H2AX foci (DNA damage) in circulating stem‑cell populations will be elevated after 20:4 TRE without ketones but normalized when ketones are maintained.

Falsifiability

If ketone supplementation fails to rescue autophagic flux or lysosomal markers in the 20:4 condition—i.e., flux remains low and lipofuscin high despite sustained ketosis—the hypothesis that ketosis is the key determinant of autophagic quality would be refuted. Conversely, if flux and lysosomal health are equivalent between 16:8 and ketone‑supported 20:4, the hypothesis is supported.

References

[1] https://pmc.ncbi.nlm.nih.gov/articles/PMC12112746/ [2] https://doi.org/10.1101/2025.04.13.648650 [3] https://rnareset.com/blogs/all/intermittent-fasting-and-cellular-autophagy-optimizing-nutrient-timing [4] https://doi.org/10.1038/s41420-021-00718-3 [5] https://news.mit.edu/2024/study-reveals-fasting-benefits-and-downside-0821 [6] https://pmc.ncbi.nlm.nih.gov/articles/PMC10509423/

Novel Insight

This hypothesis shifts the focus from fasting duration as a proxy for autophagy to the metabolic state (ketonemia) that governs lysosomal competence. It integrates ketone signaling, lysosomal biology, and oxidative stress to explain why longer fasts may not translate into better cellular cleanup and offers a concrete nutritional strategy—exogenous ketones—to uncouple fasting length from autophagic quality.

Hypothesis

Mechanistic Rationale

Ketone bodies as lysosomal stabilizers – β‑hydroxybutyrate (BHB) inhibits mTORC1 signaling and activates TFEB, driving lysosomal biogenesis and V‑ATPase assembly, which preserves the acidic pH required for cathepsin activity[3]. This effect is independent of caloric deficit and plateaus once plasma ketones reach ~1–2 mmol/L.

Oxidative stress threshold – Fasts >20 h elevate mitochondrial ROS beyond the scavenging capacity of Nrf2‑mediated antioxidants, leading to peroxidation of lysosomal membrane lipids[4]. Damaged membranes compromise autophagosome‑lysosome fusion, causing stalled autophagosomes and increased LC3‑II turnover without concomitant p62 degradation.

Quality vs. quantity – Short fasts (16:8) induce autophagy initiation (↑LC3B, ATG5) while keeping ROS low, allowing efficient cargo degradation[1][2]. Longer fasts raise initiation markers but simultaneously impair the degradative step, producing a paradox of high marker signal and low functional clearance.

Implications for tumor risk – Impaired lysosomal function during refeeding may allow damaged organelles and protein aggregates to persist, increasing genomic instability in proliferating stem cells[5]. Preserving lysosomal integrity via ketosis could mitigate this risk.

Testable Predictions

Flux measurement – In a randomized crossover trial, participants will undergo two 7‑day interventions: (a) 16:8 time‑restricted eating (TRE) and (b) 20:4 TRE, each with and without exogenous BHB ketone ester to maintain plasma β‑hydroxybutyrate ≥1 mmol/L during the fasting window. Autophagic flux will be assessed in peripheral blood mononuclear cells using LC3‑II turnover in the presence/absence of lysosomal inhibitors (bafilomycin A1) and p62 degradation. We predict that 20:4 TRE alone will show ↑LC3‑II but ↓flux (reduced LC3‑II degradation) and ↑lipofuscin fluorescence, whereas ketone‑supplemented 20:4 will restore flux to levels comparable to 16:8.

Lysosomal health – Lysosomal cathepsin activity and LysoTracker intensity will be higher in ketone‑supplemented conditions regardless of fasting length, and inversely correlated with mitochondrial ROS (MitoSOX) levels.

Tumor‑risk surrogate – γ‑H2AX foci (DNA damage) in circulating stem‑cell populations will be elevated after 20:4 TRE without ketones but normalized when ketones are maintained.

Falsifiability

Novel Insight