Polycomb-mediatedsilencing of TFEB enhancers drives autophagy arrest in aged hematopoietic stem cells

Hypothesis

In aged hematopoietic stem cells (HSCs) autophagy stalls not because the machinery wears out, but because Polycomb repressive complex 2 (PRC2) deposits H3K27me3 at enhancers bound by the master autophagy regulator TFEB. This targeted silencing occurs despite a global rise in chromatin accessibility, creating a paradox where the genome is more open yet key autophagy loci are locked down. We propose that expansion of pericentric heterochromatin in old HSCs sequesters EZH2, the catalytic subunit of PRC2, and redirects its activity to TFEB-associated enhancers, thereby suppressing lysosomal biogenesis and autophagic flux as a protective response to limit catabolic stress amid heightened DNA damage.

Mechanistic Rationale

1. Global chromatin opening vs. local closure – Aged HSCs show increased ATAC‑seq signal genome‑wide [1], yet autophagy‑gene expression falls [2]. This mirrors patterns in aged muscle satellite cells where H3K27me3 spreads and represses specific loci [3], and in aged memory CD8+ T cells where promoter closing correlates with reduced transcription [4].
2. PRC2 redistribution – Loss of lamin B1 and increased heterochromatin foci in aging nuclei can alter EZH2 availability [5]. We predict that in aged HSCs EZH2 is relocalized from constitutive heterochromatin to TFEB‑occupied enhancers, imposing H3K27me3 marks that block transcription.
3. Functional consequence – H3K27me3 at TFEB enhancers diminishes TFEB binding, reducing expression of lysosomal and autophagosome genes (e.g., LAMP1, MAP1LC3B). Consequently, autophagic flux declines, leading to accumulation of damaged proteins and organelles, which further fuels senescence.
4. Reversibility – Mechanical chromatin remodeling can reverse senescence‑associated gene expression in aged mesenchymal stem cells [5], indicating that epigenetic states are pliable. Likewise, pharmacological EZH2 inhibition or HDAC inhibition should reduce H3K27me3 at TFEB enhancers, restore TFEB occupancy, and rescue autophagy.

Testable Predictions

• Prediction 1: ATAC‑seq combined with H3K27me3 ChIP‑seq in young vs. aged HSCs will reveal increased accessibility globally but specific loss of accessibility and gain of H3K27me3 at TFEB‑bound enhancers in aged cells.
• Prediction 2: TFEB ChIP‑seq will show reduced occupancy at its target enhancers in aged HSCs, concomitant with decreased mRNA levels of lysosomal/autophagy genes.
• Prediction 3: Treating aged HSCs with an EZH2 inhibitor (e.g., GSK126) or an HDAC inhibitor (e.g., Vorinostat) will decrease H3K27me3 at TFEB enhancers, increase TFEB binding, and restore autophagic flux measured by LC3‑II turnover and lysosomal activity.
• Prediction 4: Forced expression of a TFEB mutant resistant to repression (e.g., TFEB‑ΔNLS) in aged HSCs will bypass the epigenetic block and rescue autophagy without altering global chromatin accessibility.

Falsifiable Outcomes

If EZH2 inhibition fails to increase TFEB binding or autophagic flux, or if H3K27me3 does not accumulate at TFEB enhancers in aged HSCs, the hypothesis would be refuted. Similarly, if TFEB overexpression does not improve autophagy despite the epigenetic block, alternative mechanisms (e.g., post‑translational inhibition of TFEB) would need consideration.

Broader Implications

Confirming this model would reposition autophagy decline in aging as an epigenetically programmed adaptation rather than inevitable wear‑and‑tear. It would also highlight PRC2‑TFEB axis as a leverage point for rejuvenating stem‑cell function, with potential applications in age‑related hematopoietic decline and regenerative medicine.