bims-lycede 2025-02-23 papers

Autophagy. 2025 Feb 17.

Calcium release from damaged lysosomes triggers stress granule formation for cell survival.

Aravinth Kumar Jayabalan, Aanuoluwakiitan Ayeni, Jingyue Jia.

Lysosomes are essential membrane-bound organelles that integrate intracellular needs and external signals through multiple functions, including autophagy-mediated degradation and MTORC1 signaling. The integrity of the lysosomal membrane is therefore crucial for maintaining cellular homeostasis. Various endogenous and exogenous factors can damage lysosomes, contributing to diseases such as infections, cancer, and neurodegeneration. In response, cells mount defensive mechanisms to cope with such stress, including the formation of stress granules (SGs) - membraneless organelles composed of RNAs and protein complexes. While SGs have emerged as key players in repairing damaged lysosomes, how lysosomal damage triggers their formation and influences cell fate remains unclear. Here we report that the calcium signal from damaged lysosomes mediates SG formation and protects cells from lysosomal damage-induced cell death. Mechanistically, calcium leakage from damaged lysosomes signals the recruitment of calcium-activating protein PDCD6IP/ALIX and its partner PDCD6/ALG2. This complex recruits protein kinase EIF2AK2/PKR and its activator PRKRA/PACT, which phosphorylates translation initiator factor EIF2S1, stalling global translation initiation. This translation arrest leads to the accumulation of inactive messenger ribonucleoprotein complexes (mRNPs), resulting in SG formation. Cells deficient in SG formation show increased cell death when exposed to lysosomal damage from disease-associated factors including SARS-CoV-2ORF3a, adenovirus, malarial pigment, proteopathic MAPT/tau, or environmental hazards. Collectively, this study reveals how damaged lysosomes signal through calcium to trigger SG assembly, promoting cell survival. This establishes a novel link between membrane-bound and membraneless organelles, with implications for diseases involving lysosomal damage and SG dysfunction.

Keywords: Calcium signaling; cell survival; lysosomal damage; stress granules

DOI: https://doi.org/10.1080/15548627.2025.2468910

Autophagy. 2025 Feb 19.

Lysosomal Quality Control.

Danielle Henn, Xi Yang, Ming Li.

Healthy cells need functional lysosomes to degrade cargo delivered by autophagy and endocytosis. Defective lysosomes can lead to severe conditions such as lysosomal storage diseases (LSDs) and neurodegeneration. To maintain lysosome integrity and functionality, cells have evolved multiple quality control pathways corresponding to different types of stress and damage. These can be divided into five levels: regulation, reformation, repair, removal, and replacement. The different levels of lysosome quality control often work together to maintain the integrity of the lysosomal network. This review summarizes the different quality control pathways and discusses the less-studied area of lysosome membrane protein regulation and degradation, highlighting key unanswered questions in the field.

Keywords: ESCRT; Lysophagy; lysosome membrane protein regulation; lysosome membrane repair; lysosome quality control

DOI: https://doi.org/10.1080/15548627.2025.2469206

J Clin Invest. 2025 Feb 17. pii: e188507. [Epub ahead of print]135(4):

Purifying and profiling lysosomes to expand understanding of lysosomal dysfunction-associated diseases.

Ali Shilatifard, Issam Ben-Sahra.

Lysosome storage dysfunction plays a central role in numerous human diseases, but a lack of appropriate tools has hindered lysosomal content profiling in clinical settings. In this issue of the JCI, Saarela et al. introduce a method called tagless LysoIP that enabled rapid isolation of intact lysosomes from blood and brain cells via immunoprecipitation of the endogenous protein TMEM192. Applied to the neurodegenerative lysosomal storage disorder known as Batten disease (caused by mutations in the CLN3 gene), tagless LysoIP revealed substantial accumulation of glycerophosphodiesters (GPDs) in patient lysosomes. These findings highlight the role of CLN3 in GPD clearance and present an innovative method that will enable biomarker discovery and therapeutic advancement in lysosomal diseases.

DOI: https://doi.org/10.1172/JCI188507

Int J Biol Macromol. 2025 Feb 12. pii: S0141-8130(25)01520-X. [Epub ahead of print] 140971

From protective enzyme to facilitator of amyloid propagation: Cathepsin D-mediated amyloid fibril fragmentation.

Maksim I Sulatsky, Olga V Stepanenko, Olesya V Stepanenko, Ekaterina V Mikhailova, Anna I Sulatskaya.

Amyloid fibrils, linked to severe pathologies such as neurodegenerative diseases, pose a significant challenge to modern medicine. Lysosomal proteases, particularly cathepsins, have attracted attention for their potential role in modulating amyloid pathologies, especially in the context of immunotherapy. However, the impact of these proteases on mature amyloids remains poorly understood. This study investigates the effects of cathepsin D (CTSD), a lysosomal aspartyl protease, on mature amyloid fibrils associated with local insulin and systemic lysozyme amyloidoses, as well as neurodegenerative Alzheimer's and Parkinson's diseases. Our results demonstrate that CTSD induces fragmentation of all examined fibril types, presumably by disrupting hydrogen bonds between the beta-strands forming the fibril backbone. This fragmentation occurs without depolymerizing or destructuring the amyloids and does not reduce their toxic effects on immortalized and primary cell lines. Furthermore, the size, structure, and properties of CTSD-induced amyloid degradation products suggest that the enzyme may contribute to the rapid accumulation and propagation of pathological amyloids at both intercellular and tissue levels in mammals. This finding is valuable for understanding physiological processes and developing immunotherapeutic strategies, as artificially stimulating the immune response may exacerbate pathological conditions.

Keywords: Amyloid fibril degradation; Amyloidosis and neurodegeneration; Anti-amyloid therapy; Degradation product toxicity; Lysosomal aspartyl protease cathepsin D (CTSD)

DOI: https://doi.org/10.1016/j.ijbiomac.2025.140971

Eur J Pharm Biopharm. 2025 Feb 13. pii: S0939-6411(25)00041-4. [Epub ahead of print] 114665

Mannose-6-phosphate-PEG-lipid conjugates improve liposomal uptake.

Boris Sevarika, Deniz Capri, Joël Frey, Margarita C Dinamarca, Daniel Häussinger, Scott McNeil.

Targeted liposomes are a keystone of nanomedicine, offering a precise and efficient means to deliver therapeutic agents directly to diseased tissues or cells. By incorporating targeting ligands on their surface, liposomes enhance the specificity of drug delivery, improving efficacy and reducing toxicity. Mannose-6-phosphate (M6P) is a crucial molecular tag for internalization and intracellular sorting of macromolecular structures to lysosomes. Taking advantage of this mechanism, we designed and developed liposomal systems to enhance therapeutic delivery to the lysosomes. The synthesized M6P-based targeting molecules were covalently coupled to a phospholipid using a polyethylene glycol (PEG) linker. The prepared ligands were successfully incorporated into the liposomes, yielding a size of roughly 100 nm and a zeta potential of around -40 mV. Incorporating the M6P-based ligand enhances the internalization of liposomes in a concentration-dependent manner, increasing uptake by up to 14-fold in several tested cell lines. In contrast, structurally similar monosaccharides and equally charged ligands failed to replicate this effect, highlighting the specificity of M6P-mediated internalization. Our studies demonstrate that M6P-mediated uptake predominantly occurs via a clathrin-mediated pathway, and once internalized, 72 % of the M6P-coated liposomes are associated with the lysosomal compartment. This study highlights the potential of M6P-based liposomal carriers as a modular platform for targeted lysosomal delivery, offering a promising therapeutic approach for lysosomal storage diseases.

Keywords: Enzyme replacement therapy; Liposomes; Lysosomal storage diseases; Lysosomal targeting; Mannose-6-phosphate

DOI: https://doi.org/10.1016/j.ejpb.2025.114665

ACS Sens. 2025 Feb 17.

Novel Nucleus-Oriented Quenched Activity-Based Probes Link Cathepsin Nuclear Localization with Mitosis.

Karin Reut Shannon, Tommy Weiss-Sadan, Emmanuelle Merquiol, Gourab Dey, Tamar Gilon, Boris Turk, Galia Blum.

Cysteine cathepsins are important proteases that are highly upregulated in cancers and other diseases. While their reported location is mostly endolysosomal, some evidence shows their nuclear localization and involvement in the cell cycle. We aim to generate tools to investigate the involvement of cathepsins in the cell cycle progression. To investigate nuclear cathepsin activity, we designed nucleus-directed quenched activity-based probes (qABPs) by attaching cell-penetrating peptides (CPPs). qABPs are active-site-directed compounds that enable direct real-time monitoring of enzyme activity by the covalent linkage between the probe and the enzyme's active site. Biochemical evaluation of the CPP-qABPs showed potent and selective probes; cell fractionation, multimodal flow cytometry-imaging, and time-lapse movies demonstrated nuclear cathepsin activity in living cells. Interestingly, these probes reveal a spatiotemporal pattern, a surge of nuclear cathepsin just before mitosis, suggesting yet unrevealed roles of cathepsin in cell division. In summary, these nuclear-directed qABPs serve as unique scientific tools to unlock the hidden features of cysteine proteases and to understand their involvement in cell division and cancer.

Keywords: cell-cycle; cell-penetrating peptides; imaging probes; mitosis; nuclear cathepsin; quenched-activity-based-probes

DOI: https://doi.org/10.1021/acssensors.4c03217