Epigenetic erosion of selective autophagy enhancers reorders the cellular cannibalism hierarchy, driving stem cell aging

Hypothesis

In aged hematopoietic stem cells (HSCs), progressive loss of chromatin accessibility at enhancer regions governing selective autophagy receptors (e.g., BNIP3/NIX for mitophagy, SQSTM1/p62 for aggrephagy, LC3C for lipophagy) disrupts the innate hierarchical order of organelle degradation. This epigenetic rewiring causes a mis‑timed activation of the autophagy machinery: bulk autophagosome formation proceeds, but the preferential clearance of damaged mitochondria is delayed or skipped, while less critical cytosolic proteins are degraded first. The resulting accumulation of mitochondrial ROS and metabolic dysfunction underlies the functional decline of aged HSCs, independent of global ATG gene expression levels.

Mechanistic Reasoning

1. Hierarchy as a regulatory program – Selective autophagy is not a random cargo‑engulfment process; it follows a temporally defined sequence where mitochondria are prioritized under stress, followed by protein aggregates and lipid droplets. This order is encoded by differential promoter/enhancer accessibility of receptor genes and their upstream transcription factors (TFEB/TFE3, HIF‑1α, FOXO1).
2. Aging‑specific chromatin closure – Recent ATAC‑seq data show that aged HSCs exhibit increased global accessibility but also locus‑specific closing at key signaling promoters (Chen et al., 2025); (Zhang et al., 2018). We propose that autophagy‑receptor enhancers belong to the latter class, becoming refractory despite overall chromatin openness.
3. TFEB/TFE3 decoupling – TFEB drives lysosomal biogenesis and cooperates with receptor transcription. If TFEB binding sites lose accessibility earlier than ATG promoters, lysosomal capacity lags behind autophagosome formation, creating a bottleneck that selectively impairs clearance of cargos requiring rapid lysosomal fusion (e.g., depolarized mitochondria).
4. Functional consequence – Misordered autophagy leads to selective mitochondrial accumulation, elevated ROS, and biased differentiation toward myeloid lineages, phenotypes that persist after transplantation into young niches (Walter et al., 2022); (Mohrin et al., 2015).

Testable Predictions

• Prediction 1: ATAC‑seq on young vs. aged HSCs will reveal significant loss of accessibility at enhancer regions of BNIP3, NIX, SQSTM1, and LC3C, but not at core ATG promoters (e.g., ATG5, ATG7).
• Prediction 2: RNA‑seq will show unchanged or modestly altered mRNA levels of these receptors, yet protein levels and mitophagy flux (measured by mt‑Keima or mito‑QC) will be specifically reduced in aged HSCs.
• Prediction 3: CRISPR‑based activation (CRISPRa) of the closed enhancers in aged HSCs will restore receptor protein levels, rescue mitophagy flux, and improve competitive repopulation assays without altering global ATG expression.
• Prediction 4: Pharmacological induction of TFEB (e.g., with trehalose or ML‑S1) will not rescue mitophagy unless receptor enhancers are concurrently accessible, demonstrating that TFEB activity is necessary but not sufficient.

Experimental Approach

1. Isolate LT‑HSCs from 3‑month (young) and 24‑month (aged) mice; perform ATAC‑seq and RNA‑seq in parallel.
2. Use motif enrichment (HOMER/MEME) to pinpoint TFEB/FoxO1 sites within differentially accessible peaks; validate by ChIP‑qPCR.
3. Measure mitophagy flux via mt‑Keima staining and Seahorse OCR; assess aggrephagy using Hsp70‑GFP reporter.
4. Deliver CRISPRa (dCas9‑VP64) targeting the identified enhancers via lentiviral transduction; evaluate functional rescue in serial transplantation and colony‑forming assays.
5. As a control, overexpress TFEB alone to test whether lysosomal biogenesis without receptor enhancement fails to correct the hierarchy defect.

Falsification

If ATAC‑seq shows no selective loss of accessibility at autophagy‑receptor enhancers, or if restoring accessibility does not improve mitophagy flux and HSC function, the hypothesis would be refuted, suggesting that age‑related decline stems from other regulatory layers (e.g., post‑translational modification of ATG proteins or altered cytosolic cargo recognition).