Dual Compartmental Acetyl-CoA Sequestration Enforces Autophagy Suppression in Aging

Hypothesis

Aged cells actively suppress autophagy not only by nuclear acetyl-CoA depletion but also by ectopic accumulation of acetyl-CoA in the endoplasmic reticulum, which acetylates key autophagy effectors (e.g., ATG9A, ULK1) and blocks their function. This dual‑lock mechanism couples transcriptional silencing with post‑translational inhibition, creating a reversible state that preserves cellular integrity under stress.

Mechanistic Rationale

Nuclear acetyl-CoA fuels histone acetylation at autophagy gene promoters via ACLY and ACSS2, sustaining TFEB‑driven lysosomal biogenesis 1. When glucose‑derived acetyl-CoA falls, HDAC activity rises, dampening transcription. Simultaneously, excess acetyl‑CoA shunted into the ER (as shown by AT‑1 overexpression causing progeria‑like phenotypes) can acetyl‑modify lysosomal membrane proteins required for autophagosome formation 3. Acetylation of ATG9A impairs its cycling between the ER and nascent phagophores, while acetyl‑ULK1 shows reduced kinase activity toward downstream autophagy initiators. Thus, the same metabolite shortage that starves the nucleus fuels a cytotoxic gain‑of‑function in the ER, coupling epigenetic repression with direct enzyme inhibition.

Testable Predictions

1. In aged tissues, nuclear acetyl-CoA levels will correlate inversely with H3K27ac at TFEB targets, whereas ER acetyl-CoA will correlate positively with acetyl‑ATG9A and acetyl‑ULK1.
2. Pharmacological ER‑specific depletion of acetyl‑CoA (e.g., ER‑targeted ACSS2 knockdown) will restore autophagosome formation without altering nuclear histone acetylation.
3. Conversely, nuclear‑restricted ACLY overexpression will rescue TFEB expression but not fully restore flux if ER acetyl‑CoA remains high.
4. Combined nuclear ACLY boost and ER ACSS2 inhibition will synergistically increase LC3‑II turnover and reduce p62 accumulation in aged mouse liver.

Experimental Approach

• Subcellular fractionation followed by LC‑MS/MS to quantify acetyl‑CoA in nucleus, cytosol, and ER from young vs. old mouse liver.
• Immunoprecipitation of ATG9A and ULK1 followed by anti‑acetyl‑lysine Western blot to assess acetylation status.
• Generate AAV vectors encoding nucleus‑targeted ACLY (NLS‑ACLY) and ER‑targeted ACSS2 shRNA (ER‑ACSS2‑shRNA); inject into aged mice and measure autophagic flux using tandem mCherry‑GFP‑LC3 reporter.
• Use class I HDAC inhibitor (e.g., entinostat) as a control to isolate transcriptional effects.
• Compare outcomes: (i) NLS‑ACLY alone, (ii) ER‑ACSS2‑shRNA alone, (iii) combination, predicting only the combination restores youthful flux.

This framework is falsifiable: if ER acetyl‑CoA manipulation fails to affect ATG9A/ULK1 acetylation or autophagic flux, the dual‑lock hypothesis would be refuted, supporting a purely nuclear epigenetic model.