PTM‑coded autophagy selectivity directs clonal evolution of copy‑number variants in aging
Hypothesis: PTM‑coded autophagy selectivity governs clonal evolution of copy‑number variants
Core idea – The autophagic “cannibalism ritual” uses a PTM‑dependent hierarchy on cargo receptors to decide which protein burdens are degraded first. In aging, dysregulation of the kinases/phosphatases that modify these receptors reshapes the hierarchy, causing preferential clearance of low‑burden (narrow) CNV‑derived aggregates while sparing high‑burden (broad) CNV proteotoxins. This shift permits expansion of the most genomically unstable clones, driving age‑related cancer risk.
Mechanistic rationale – Cargo receptors such as RB1CC1/FIP200 contain multiple serine residues that become phosphorylated by mTORC1‑dependent kinases upon nutrient stress, creating high‑affinity docking sites for ubiquitinated, aggregated proteins (https://febs.onlinelibrary.wiley.com/doi/10.1111/febs.15824). Broad CNVs impose stronger proteotoxic stress and predict poorer outcomes than focal alterations (https://elifesciences.org/articles/39217). These broad‑CNV genomes generate massive, heterogeneous protein aggregates that rely on these high‑avidity interactions for efficient sequestration into phagophores. Narrow CNVs produce fewer, more homogeneous aggregates that can be handled by lower‑affinity, ubiquitin‑independent routes mediated by receptors like p62/SQSTM1.
In aged tissues, chronic mTORC1 hypoactivity and elevated phosphatase activity (e.g., PP2A) reduce RB1CC1 phosphorylation (https://pmc.ncbi.nlm.nih.gov/articles/PMC11872960/). Consequently, the autophagy hierarchy flips: low‑affinity receptors dominate, clearing narrow‑CNV debris while broad‑CNV aggregates accumulate, aggravating proteotoxic stress and allowing those clones to evade immune surveillance.
Testable predictions
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Phospho‑mutant rescue – Expressing a phospho‑mimetic RB1CC1 (S518D) in aged mouse hematopoietic stem cells will restore preferential clearance of broad CNV‑associated aggregates and reduce the expansion of CHIP‑like clones bearing focal amplifications of oncogenes (e.g., Jak2). Assay: single‑cell CNV sequencing + flow cytometry for annexin V/LC3 II after oxidative stress.
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Phosphatase inhibition – Treating aged mice with a selective PP2A inhibitor will increase RB1CC1 phosphorylation, broaden the autophagic cargo spectrum, and decrease the proportion of cells harboring >5 Mb broad CNVs in liver tissue. Assay: low‑pass whole‑genome sequencing of microdissected hepatocytes; correlate with p‑RB1CC1 levels by immunoblot.
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In vitro reconstitution – Synthetic phagophore membranes bearing either phospho‑defective (S518A) or phospho‑mimetic RB1CC1 will show differential recruitment of ubiquitinated versus non‑ubiquitinated model aggregates in a TIRF‑based autophagy assay. Readout: fluorescence intensity of aggregate‑GFP versus mCherry‑LC3 over time.
Falsification – If manipulating RB1CC1 PTM status does not alter the relative clearance of broad versus narrow CNV aggregates, or if clonal dynamics remain unchanged despite restored autophagy hierarchy, the hypothesis is refuted. Likewise, if broad CNV clearance improves without changes in receptor phosphorylation, alternative mechanisms (e.g., lysosomal pH) must be considered.
Implications – Targeting the PTM code of autophagy receptors offers a precise way to reprogram clonal selection in aging tissues, potentially suppressing the most oncogenic mosaic genotypes while tolerating less harmful variants.