DNASE1L3Deficiency Drives Age‑Associated Enlargement of cfDNA Fragments and Inflamm‑Methylation

Hypothesis

Aging reduces plasma DNASE1L3 activity, leading to incomplete cleavage of neutrophil-derived chromatin and an accumulation of >250 bp cfDNA fragments that carry a distinct methylation signature (elevated LINE-1 and inflammasome-related CpGs). This fragment shift drives the observed age‑associated cfDNA fragmentomics and contributes to the inflation of epigenetic clocks.

Mechanistic Basis

It's known that neutrophils increase in number and NETotic activity with age [1]. NETosis releases chromatin as large, loosely packaged structures that are substrates for DNASE1L3, the plasma nuclease that normally trims nucleosomal DNA to ~150 bp apoptotic fragments [2]. Oxidative modifications and autoantibodies that accumulate with aging inhibit DNASE1L3 catalytic efficiency [3]. When DNASE1L3 fails, these large NET‑derived fragments persist in circulation, preserving the methylation patterns of neutrophil hypermethylated loci (including LINE‑1 promoters and IL‑1β enhancers) that are otherwise erased during normal apoptotic processing. Consequently, the cfDNA pool becomes enriched for >250 bp fragments bearing an “inflam‑methylome” that correlates with biological age predictors [4].

Testable Predictions

1. Plasma DNASE1L3 activity will inversely correlate with the proportion of cfDNA fragments >250 bp across human cohorts (r < -0.4, p<0.01).
2. Recombinant DNASE1L3 administration to aged mice will reduce the >250 bp cfDNA fraction by ≥30% and shift methylation patterns toward those seen in young mice, decreasing epigenetic clock estimates by ≥4 years.
3. Neutrophil‑specific depletion (e.g., anti‑Ly6G) in aged mice will blunt the age‑related rise in long cfDNA fragments, even without altering DNASE1L3 levels.
4. Individuals with autoimmune DNASE1L3 deficiency (e.g., lupus patients with anti‑DNASE1L3 antibodies) will show premature accumulation of >250 bp cfDNA and accelerated epigenetic aging relative to age‑matched controls.

Experimental Design

• Human cohort: Measure DNASE1L3 activity (fluorogenic substrate assay), cfDNA fragment size distribution (low‑input EM‑seq + fragmentomics), and methylation at 48‑CpG clock sites in 200 participants stratified by age (20‑80 y). Use linear mixed models to test prediction 1.
• Mouse intervention: Treat 20‑month‑old C57BL/6 mice with recombinant human DNASE1L3 (1 mg/kg, i.p., twice weekly for 4 weeks). Controls receive PBS. Assess plasma cfDNA size, methylation, and biological age (Horvath mouse clock) before and after treatment. Expected outcome matches prediction 2.
• Neutrophil depletion: Apply anti‑Ly6G antibody to aged mice for 2 weeks; compare cfDNA fragment profiles to isotype control. Prediction 3.
• Patient cohort: Recruit 30 lupus patients with high anti‑DNASE1L3 titers and 30 age‑matched controls; quantify cfDNA >250 bp fraction and epigenetic age. Prediction 4.

Potential Confounds and Controls

• Variability in plasma collection (tube type, processing time) can affect nuclease activity; standardize using EDTA‑treated tubes processed within 30 min.
• Hemolysis releases genomic DNA that skews fragment size; exclude samples with hemoglobin >0.2 mg/dL.
• Complement activation can also degrade DNA; include complement‑inhibited controls to isolate DNASE1L3 effects.
• Cell‑free RNA or protein contaminants may interfere with fluorometric assays; validate activity with immunodepletion of DNASE1L3.

If the predictions hold, the hypothesis positions DNASE1L3‑mediated cfDNA trimming as a mechanistic link between neutrophil aging, inflamm‑methylome generation, and epigenetic clock acceleration. Failure to observe the predicted correlations or rescue effects would falsify the model, prompting investigation of alternative nucleases or clearance pathways.