AggregationState Shapes cfDNA Fragment Size and Methylation: A Proteostasis‑Centric Biomarker Hypothesis

Hypothesis

Adaptive protein sequestration into ordered aggregates reduces proteotoxic stress and limits necrotic cell death, yielding plasma cfDNA that is enriched in longer fragments (>150 bp) and carries a methylation signature reflective of controlled turnover (e.g., preserved neutrophil‑specific CpGs). In contrast, maladaptive aggregation amplifies oxidative stress and chromatin destabilization, driving necrotic/apoptotic release of short cfDNA (<150 bp) with hypomethylation at inflammasome‑associated loci.

Mechanistic Basis

• Aggregate‑mediated ROS buffering – Amyloid‑like fibrils sequester redox‑active metals (Fe²⁺/Cu⁺) that would otherwise catalyze Fenton reactions, lowering nuclear DNA damage and preserving nucleosome spacing during apoptosis, thus generating longer cfDNA fragments.
• Histone chaperone sequestration – Proteostatic condensates capture histone‑binding proteins (e.g., NAC, CAF‑1) during adaptive aggregation, maintaining proper histone deposition and protecting CpG methylation patterns; toxic aggregates overwhelm this capacity, leading to passive demethylation.
• Inflammasome modulation – Soluble oligomers activate NLRP3, while mature fibrils are inert; the balance determines cfDNA‑TLR9 signaling strength and downstream MCP‑1 release, shaping the inflammatory cfDNA load.

Predictions

1. Individuals with high levels of protective aggregates (measured by PET‑ ligands that distinguish mature fibrils from soluble oligomers) will show a higher proportion of long cfDNA fragments and a methylation pattern resembling the "healthy aging" 48‑CpG clock (e.g., preserved methylation at neutrophil‑specific sites).
2. Those burdened by toxic oligomers will exhibit elevated short cfDNA fractions, global CpG hypomethylation at inflammatory loci (e.g., TLR9 pathway genes), and higher plasma MCP‑1.
3. Experimentally shifting the aggregation equilibrium toward fibrils (using small‑molecule stabilizers) in aged mice will increase long cfDNA and reduce inflamm‑aging markers, whereas oligomer‑promoting agents will have the opposite effect.

Experimental Design

• Human cohort – Recruit 120 participants stratified by amyloid‑PET SUVR and CSF oligomer levels. Collect plasma, isolate cfDNA, quantify fragment size distribution via Bioanalyzer, and perform targeted bisulfite sequencing of the 48‑CpG clock plus 20 inflammasome‑associated CpGs.
• Analysis – Use multivariate regression to test whether protective aggregate load predicts long cfDNA fraction (β>0, p<0.01) and methylation preservation, while toxic oligomer load predicts short cfDNA fraction and hypomethylation.
• Animal validation – Treat 24‑month‑old mice with an amyloid‑stabilizer (e.g., tafamidis) or an oligomer‑inducer (e.g., D‑KLVFF) for 8 weeks, then repeat cfDNA and methylation assays; monitor serum MCP‑1 and frailty index.

Potential Confounds and Controls

• Renal clearance affects cfDNA levels; include eGFR as covariate.
• Recent infection or trauma can spike cfDNA; exclude participants with acute illness within 2 weeks.
• Cell‑type deconvolution of cfDNA methylation will help distinguish neutrophil vs. epithelial contributions.

If the predicted correlations fail to emerge across both human and animal data, the hypothesis that aggregation state directly shapes cfDNA fragmentation and methylation would be falsified, pushing focus toward alternative sources of cfDNA heterogeneity.