Active Autophagy Suppression in Aged B Cells Safeguards Genome Stability by Restraining Somatic Hypermutation

Hypothesis

In aged B cells, autophagy is not merely impaired; it is actively suppressed to limit chromatin accessibility and thereby curb excessive somatic hypermutation (SHM) that could generate autoreactive antibodies. This protective restraint comes at the expense of reduced antibody diversity and poorer vaccine responses.

Mechanistic Model

1. mTORC1 Hyperactivation – Persistent nutrient‑sensing signals in aged B cells keep mTORC1 active, leading to ULK1 phosphorylation and inhibition of autophagosome initiation [1].
2. SASP‑Driven NF‑κB/p38MAPK Signaling – Senescent B cells secrete IL‑6 and TNF‑α, activating NF‑κB and p38MAPK pathways that upregulate the autophagy inhibitor Rubicon and phosphorylate TFEB, sequestering it in the cytoplasm [3,4].
3. Chromatin Consequence – Reduced autophagy diminishes lysosomal degradation of damaged mitochondria, lowering ROS but also decreasing nuclear export of histone deacetylases. The resulting hyperacetylated chromatin state would normally promote SHM; however, the concurrent rise in Rubicon‑mediated autophagy block impairs the delivery of LC3‑associated chromatin remodelers needed for controlled AID targeting [5].
4. Outcome – The net effect is a restrained SHM landscape, limiting the generation of high‑affinity but potentially autoreactive clones, while preserving a pool of relatively naïve‑like B cells that avoid autoimmunity.

Predictions and Experimental Tests

• Prediction 1: Pharmacological inhibition of mTORC1 (e.g., rapamycin) or neutralization of SASP cytokines (anti‑IL‑6/TNF‑α) in aged B cells will increase autophagic flux, nuclear TFEB accumulation, and LC3‑chromatin association, leading to a measurable rise in SHM frequency within immunoglobulin variable regions.
• Prediction 2: Enhanced SHM under these conditions will correlate with an increase in autoreactive antibodies detectable by ELISA against self‑antigens (dsDNA, insulin) and a rise in autoantibody‑positive B cells in peripheral blood.
• Prediction 3: Genetic deletion of Rubicon specifically in B cells of aged mice should mimic the effects of mTORC1/SASP inhibition, restoring autophagy and increasing SHM without altering mTORC1 activity.

Experimental Approach

• Isolate splenic B cells from young (3‑mo) and aged (24‑mo) mice.
• Treat cultures with rapamycin, IL‑6/TNF‑α neutralizing antibodies, or transduce with Rubicon‑shRNA.
• Measure autophagy flux (LC3‑II/I ratio, p62 degradation via western blot), TFEB localization (immunofluorescence), and mitochondrial mass (MitoTracker).
• Quantify SHM by sequencing IgV regions from sorted germinal center B cells.
• Assess autoreactivity via ELISA for anti‑dsDNA, anti‑insulin antibodies and flow cytometry for Annexin V/7‑AAD to rule out increased apoptosis.

Falsifiability If restoring autophagy in aged B cells fails to increase SHM or autoantibody production, or if SHM rises without a concomitant increase in autoreactivity, the hypothesis that autophagy suppression serves to restrain potentially harmful SHM would be refuted. Conversely, observing the predicted increases in both SHM and autoantibody specificity would support the model that active autophagy inhibition is a safeguard mechanism in aging B cells.