Biology subjects

Warren, J. D.

Publications and source records attributed to Warren, J. D..

4 recordsLinked to original sources

bioRxiv2026

Intravital pH Imaging using the sensor ApHID Reveals Incomplete Lysosomal Acidification in Resident Meningeal Phagocytes.

Tracking lysosomes and quantifying their pH in the living, intact brain has been challenging owing to the lack of suitable in vivo tools. Here we report the use of dextran polymers labeled with the pH sensor ApHID to visualize and quantify lysosomal pH in mouse brain resident phagocytes. ApHID-dextrans delivered systemically are rapidly endocytosed by phagocytes in the meninges -mainly dural and subdural macrophages- and accumulate in lysosomal compartments. Intravital pH imaging revealed a striking heterogeneity in lysosomal acidification, with only ~5% of meningeal phagocytes reaching pH values below 5.0, in marked contrast with measurements in macrophage cell cultures. Photothrombotic ischemic lesions induced progressive lysosomal acidification in local phagocytes, while acute chloroquine treatment led to rapid alkalinization. Our methodology enables direct, quantitative pH measurements without genetic manipulations, and unveils a previously unappreciated heterogeneity in lysosomal acidification among brain-resident myeloid cells.

neuroscience↗

bioRxiv2024

Ratiometric pH Imaging of Macrophage Lysosomes Using the Novel pH-sensitive Dye ApHID.

Lysosomes actively regulate their lumenal pH, which is necessary for optimal enzymatic activity. Endocytic processes are involved in many diseases, including Alzheimers disease, in which sub-optimal lysosomal function has been reported. To measure acidification, pH-sensitive probes can be delivered to endosomes and lysosomes using labeled dextran polymers or proteins. However, many commercially available probes have limited sensitivity in the acidic range of lysosomes, and their fluorescence is subject to enzymatic degradation and photobleaching. Herein, we describe the preparation, characterization, and use of a novel pH-sensitive probe, ApHID, a green-emitting fluorescent dye with optimal dynamic range within the acidity of endosomes and lysosomes. ApHID has a pKa near 5, increasing brightness with acidity, and it is robustly resistant to oxidation and photobleaching. We used ApHID ratiometric imaging to measure lysosomal pH in macrophages, yielding virtually identical results when compared with fluorescein and Oregon Green. Overall, ApHID circumvents limitations presented by most commercially available pH-sensitive probes and can be useful in demanding imaging applications such as intravital imaging of tissues.

biochemistry↗

bioRxiv2021

Kinetochores respond to subtle changes in the stability of microtubule attachments

Proper attachment of spindle microtubules to kinetochores is necessary to satisfy the spindle assembly checkpoint and ensure faithful chromosome segregation. Microtubules detach from kinetochores to correct improperly oriented attachments, and overall kinetochore-microtubule (k-MT) attachment stability is determined in response to regulatory enzymes and the activities of kinetochore-associated microtubule stabilizing and destabilizing proteins. However, it is unknown whether regulatory enzyme activity or kinetochore-associated protein localization respond to subtle changes in k-MT attachment stability. To test for this feedback response, we monitored Aurora B kinase activity and the localization of select kinetochore proteins in metaphase cells following treatments that subtly stabilize or destabilize k-MT attachments using low dose Taxol or UMK57 (an MCAK agonist), respectively. Increasing k-MT stability induced changes in the abundance of some kinetochore proteins. In contrast, reducing k-MT stability induced both increases in Aurora B kinase signaling and changes in the abundance of some kinetochore proteins. Thus, kinetochores dynamically respond to changes in the stability of their attached microtubules. This feedback control contributes to tuning k-MT attachment stability required for efficient error correction to facilitate faithful chromosome segregation. Summary StatementLive cell imaging demonstrates that kinetochore signaling responds to feedback from attached microtubules to tune their stability to ensure faithful chromosome segregation during cell division.

cell biology↗

bioRxiv2017

Uncovering the heterogeneity and temporal complexity of neurodegenerative diseases with Subtype and Stage Inference

The heterogeneity of neurodegenerative diseases is a key confound to disease understanding and treatment development, as study cohorts typically include multiple phenotypes on distinct disease trajectories. Here we present a new machine learning technique - Subtype and Stage Inference (SuStaIn) - able to uncover data-driven disease phenotypes with distinct temporal progression patterns, from widely available crosssectional patient studies. Results from imaging studies in two neurodegenerative diseases reveal new subgroups and their distinct trajectories of regional neurodegeneration. In genetic frontotemporal dementia, SuStaIn identifies genotypes from imaging alone, validating its ability to identify subtypes, and characterises within-group heterogeneity for the first time. In Alzheimers disease, SuStaIn uncovers three subtypes, uniquely revealing their temporal complexity. SuStaIn provides fine-grained patient stratification, which substantially enhances the ability to predict conversion between diagnostic categories over standard models that ignore subtype (p=7.18x10--4) or temporal stage (p=3.96x10-5). SuStaIn thus offers new promise for enabling disease subtype discovery and precision medicine.

neuroscience↗