Inflamed brain immune cells take up protein clumps, then clear them poorly

THE BRAIN'S RESIDENT immune cells, known as microglia, patrol tissue and clear debris. One job is to take up protein clumps that have left neurons and break those clumps down. Alpha-synuclein is the main protein packed into Lewy bodies, the inclusions seen in Parkinson's disease and related conditions. Tau is another protein that can form clumps in diseased brains. Outside cells, both can assemble into fibrils that neighboring microglia can take up.

Once inside a cell, those fibrils need an acidic digestive organelle, the lysosome, to finish the job. One of the enzymes that does the cutting inside that organelle is cathepsin D. Frederik Eikens, Hannah Scheiblich and colleagues at the Max Planck Institute for Biology of Ageing in Cologne ask what happens to this clearance when microglia are inflamed. Their preprint, posted to bioRxiv on November 3 and not yet reviewed by other scientists, reports that inflamed cells still take the clumps up, yet they degrade them more poorly, because lysosomal capacity does not keep up.

The group worked mainly in primary microglia from newborn C57BL/6N mouse pups, not adult human brain as the primary system. To drive inflammation they used LPS, a molecule from bacterial cell walls, at 10 nanograms per milliliter, acting through the receptor TLR4. After 24 hours of LPS, proteomics of eight independent cultures found 3,478 of 6,742 detected proteins changed in abundance (1,903 up, 1,575 down). Inflammatory signaling, protein synthesis and proteasome-linked pathways rose. Lysosome-associated proteins fell, including cathepsin D on western blot in four experiments.

They then tested whether autophagy, the ordinary route by which a cell sends its own worn material to lysosomes, had collapsed. Measured by LC3B-II after four hours of bafilomycin A1, that signal tended to be higher with LPS but was not statistically significant. The authors read the flux as largely intact. Proteomics also found less of a switch that expands lysosome capacity. That switch is TFEB, transcription factor EB. In 2011 Carmine Settembre, Chiara Di Malta, Vinicia Assunta Polito and colleagues showed in Science that TFEB is a master gene for lysosomal biogenesis that drives expression of autophagy and lysosomal genes.

To separate uptake from breakdown, the team gave the cells fluorescent pre-formed fibrils of alpha-synuclein at 1 micromolar for 24 hours, with LPS from 0 to 10 nanograms per milliliter, then washed the fibrils away and chased the cells for 24 to 72 hours without extracellular fibrils or LPS. Across three independent experiments, LPS caused only a modest reduction in uptake. Intracellular alpha-synuclein then persisted during the chase in a concentration-dependent way. Cell death and alpha-synuclein in the culture medium were unchanged. LPS at 10 nanograms per milliliter similarly left tau fibrils uncleared. Inflamed cells also showed less association of internalized alpha-synuclein with cathepsin D-positive compartments during the chase.

Cycloheximide, which stops new protein synthesis, restored alpha-synuclein breakdown while inflammatory signaling stayed on. If the limit is lysosomal capacity, expanding it should help. Treating the cells with TFEB activator 1, a putative TFEB activator used at 2 micromolar during inflammatory stimulation, restored degradation of both alpha-synuclein and tau after a 48-hour chase without significantly changing uptake, and kept cathepsin D-positive structures from shrinking during prolonged processing. That laboratory rescue is not evidence that a TFEB-activating drug would help patients.

The authors looked beyond mouse cultures. They reanalyzed published data from Snijders and colleagues in 2023 and from Hellén and colleagues in 2025 on human microglia under inflammatory stimulation. Both showed stronger inflammatory programs and weaker lysosomal ones. In chimeric brain-slice cultures, human stem-cell-derived microglia that had taken up alpha-synuclein after exposure to the fibrils and LPS likewise showed some of the protein outside cathepsin D-positive compartments. In post-mortem frontal cortex from one non-demented control and one patient with a dementia marked by Lewy bodies in the cortex, known as dementia with Lewy bodies (Braak stage 6), microglial alpha-synuclein deposits showed little spatial association with cathepsin D-positive structures. The stain is static. It cannot measure trafficking, prove that inflammation causes the disease, or show that the dish mechanism drives Parkinson's disease or Alzheimer's disease. The authors call the post-mortem analysis limited in scope.

LPS is a sharp experimental stimulus, not the chronic mix of signals in a living brain, and most of the quantitative clearance work rests on neonatal mouse microglia under one LPS regimen. Inflamed microglia still take up clumps of alpha-synuclein and tau yet degrade them more poorly when lysosomal capacity does not match the load, and the paper cannot say whether that mismatch matters in patients.