Summary
A bioRxiv preprint describes a probe-based method for measuring lysosome acidity in living mouse brain immune cells. The researchers found substantial variation among meningeal phagocytes, with only about 5% reaching a pH below 5.0.
Researchers have used a fluorescent pH sensor called ApHID to measure the acidity of lysosomes inside living mouse-brain immune cells. The method revealed substantial cell-to-cell variation in lysosomal acidification among meningeal phagocytes, with only about 5% of the cells reaching pH values below 5.0.
The findings are reported in a bioRxiv preprint posted on September 18, 2026. The work was conducted in mice and provides a method for studying lysosome behaviour in the living brain rather than relying only on cultured cells or genetically modified animals.
Measuring lysosomes inside the living brain
Lysosomes are membrane-bound compartments that break down and recycle cellular material. Their interiors are acidic, and the degree of acidity affects how efficiently they process their contents. pH is a measure of acidity: lower values indicate a more acidic environment.
The researchers attached ApHID molecules to dextran polymers and delivered the labelled material systemically. The dextran was rapidly taken up by phagocytes in the meninges, the protective membranes surrounding the brain. The material accumulated in lysosomal compartments, allowing the researchers to image and quantify their pH through intravital imaging—microscopy performed in living tissue.
The approach enabled direct pH measurements without genetic manipulation. This is important because measurements from cells grown in culture may not reflect the conditions inside an intact brain. In the preprint, lysosomes in the meningeal phagocytes showed a broad range of acidity rather than a uniform value. Only approximately 5% reached pH levels below 5.0, contrasting with measurements reported by the researchers in macrophage cell cultures.
The cells examined were mainly macrophages located in the dura and subdural layers of the meninges. These resident phagocytes are part of the brain’s local myeloid immune system and can take up and process material in the tissue surrounding the central nervous system.
Injury and drug treatment changed lysosomal pH
The researchers also tested how lysosomal acidity changed under two experimental conditions. Photothrombotic ischemic lesions—localized injuries produced by a light-triggered clotting procedure—were associated with progressive acidification in phagocytes near the lesions.
In a separate experiment, acute treatment with chloroquine caused rapid alkalinization of the lysosomes. Alkalinization means that the lysosomal compartments became less acidic. Together, these observations show that the measured pH was responsive to local brain injury and to a pharmacological intervention known to affect lysosomal function.
The method could allow researchers to examine how the acidity of lysosomes changes across different brain regions, immune-cell states or disease models. The observed heterogeneity also provides a more detailed picture than treating all resident meningeal phagocytes as though their lysosomes operate under the same conditions.
What the preprint establishes
This is a preclinical study based on live mouse-brain imaging. It establishes a way to quantify lysosomal pH in meningeal phagocytes and reports differences associated with ischemic injury and acute chloroquine treatment. It does not yet establish how the same pattern occurs in human meningeal immune cells or whether altered lysosomal acidity contributes directly to neurological disease.
The report is a bioRxiv preprint rather than a peer-reviewed journal publication. The authors also disclose that the chemical synthesis and uses of ApHID are included in a pending patent application, with three authors listed as co-inventors. These points are relevant when interpreting the method and its future development.