bims-lypmec 2025-06-22 papers

Nat Struct Mol Biol. 2025 Jun 17.

DMXL1 promotes recruitment of V1-ATPase to lysosomes upon TRPML1 activation.

Chan Lee, Matthew J G Eldridge, Miguel A Gonzalez-Lozano, Thomas Bresnahan, Zachary Niday, Donato Del Camino, Tao Fu, Joao A Paulo, Magdalene M Moran, Sophie Helaine, J Wade Harper.

Lysosomes, central hydrolytic organelles, are regulated by ion flow, including calcium and protons, via transporters and channels to maintain an acidified lumen for hydrolytic activity. TRPML1, a lysosomal ion channel, effluxes cations upon activation, promoting rapid conjugation of ATG8 proteins to the lysosomal membrane in a process known as conjugation of ATG8 to single membranes (CASM). However, our understanding of how TRPML1 activation reorganizes the lysosomal proteome is poorly understood. Here, we identify DMXL1 as a key regulator of lysosomal homeostasis through quantitative proteomics of lysosomes during TRPML1 activation by the agonist MLSA5. DMXL1 is recruited to lysosomes and Salmonella-containing vacuoles, both in a CASM-dependent manner. As the mammalian ortholog of yeast Rav1, DMXL1 assembles with Rav2 ortholog ROGDI and WDR7, and associates with V0 and V1 subunits of the lysosomal V-ATPase. TRPML1 activation drives V1 subunit recruitment to lysosomes in a DMXL1- and DMXL2-dependent manner. DMXL1- and DMXL2-deficient cells display reduced V1-ATPase recruitment, increased lysosomal pH and diminished hydrolytic capacity. Using AlphaFold modeling supported by cross-linking proteomics, we identify interaction interfaces within the DMXL1-ROGDI-WDR7 complex, as well as an ATP6V1A binding interface in DMXL1, whose mutation affects interaction and function. Our findings suggest CASM-dependent DMXL1 recruitment, coupled with V-ATPase assembly, is critical for maintaining lumenal pH and lysosomal function in response to TRPML1 activation.

DOI: https://doi.org/10.1038/s41594-025-01581-x

ACS Chem Biol. 2025 Jun 16.

Biphasic Cellular Response Triggered by Tetrandrine-Mediated Dysfunction and Lysophagic Clearance of Lysosomes.

Zhe Yang, Tomoki Takahashi, Ayase Hoshino, Tatsuya Yamamoto, Hideyuki Shigemori, Yusaku Miyamae.

Lysosomes play an important role in the degradation of cellular components and are correlated with various other physiological phenomena. Lysophagy is a cellular quality control system that maintains homeostasis by removing damaged lysosomes through autophagy. The involvement of lysosomal dysfunction in the pathogenesis of certain illnesses (e.g., neurodegeneration) highlights the potential of small molecules that regulate lysophagy as drug candidates. Here, we found that tetrandrine, a bis-benzylisoquinoline alkaloid, induces lysophagy, leading to the clearance of damaged lysosomes in mammalian cells. To visualize the target organelles of tetrandrine, we synthesized a chimeric compound in which tetrandrine was connected to boron-dipyrromethene via a polyethylene glycol linker. Flow cytometry analysis confirmed the cellular uptake of the synthesized probe. An organelle-staining assay showed that the fluorescent signal of the probe was specifically colocalized with lysosomes. Tetrandrine transiently increased the lysosomal pH level, which returned to normal at 24 h post treatment. Consistently, the level of mCherry-tagged galectin-3, a marker protein for lysophagy, transiently increased and then diminished under treatment with tetrandrine. Tetrandrine also induced dephosphorylation of transcription factor EB, a regulator of lysosomal biogenesis, promoting its translocation from the cytosol to the nucleus. These results suggest that tetrandrine induces a biphasic cellular response, first disrupting lysosomal function before facilitating cellular lysosomal homeostasis through lysophagy and lysosomal biogenesis. This dual effect distinguishes tetrandrine from existing lysosomal modulators.

DOI: https://doi.org/10.1021/acschembio.5c00220

Autophagy. 2025 Jun 18. 1-20

Lysosomal membrane permeabilization enhances the anticancer effects of POLR1 (RNA polymerase I) transcription inhibitors.

Lucille Ferret, Jonathan G Pol, Allan Sauvat, Gautier Stoll, Karla Alvarez-Valadez, Alexandra Muller, Julie Le Naour, Felix Peyre, Gerasimos Anagnostopoulos, Isabelle Martins, Maria Chiara Maiuri, Harald Wodrich, Lionel Guittat, Jean-Louis Mergny, Guido Kroemer, Mojgan Djavaheri-Mergny.

Lysosomes contribute to the development of drug resistance through various mechanisms that include drug sequestration and the activation of adaptive stress pathways. While inhibitors of DNA-to-RNA transcription exhibit potent anticancer effects, the role of lysosomes in modulating responses to such transcription inhibitors remains largely unexplored. This study investigates this aspect in the context of two potent POLR1 (RNA polymerase I) transcription inhibitors, CX-3543 (quarfloxin) and CX-5461 (pidnarulex). Unexpectedly, CX-3543 was found to accumulate within lysosomes, leading to lysosomal membrane permeabilization (LMP) and the subsequent activation of cellular stress adaptation pathways, including those regulated by the transcription factor TFEB and autophagy. Disrupting TFEB or autophagy increased cell sensitivity to CX-3543, highlighting the cytoprotective role of these processes in counteracting CX-3543-induced cell death. Moreover, targeting lysosomal membranes with chloroquine derivatives or blue light exposure induced substantial LMP, releasing compound CX-3543 from lysosomes. This effect enhanced both the inhibition of DNA-to-RNA transcription and CX-3543-induced cell death. Similar effects were observed when chloroquine derivatives were combined with CX-5461. Additionally, combining CX-3543 with the chloroquine derivative DC661 more effectively reduced the fibrosarcoma growth in immunocompetent mice than either agent alone. Altogether, our results reveal an unanticipated lysosome-related mechanism that contributes to cancer cell resistance to POLR1 inhibitors and propose a strategy to overcome this resistance.Abbreviations: ATG7: autophagy related 7; ATG13: autophagy related 13; Baf A1: bafilomycin A1; CTSB: cathepsin B; DKO: double knockout; G4: Guanine quadruplex; KO: knockout; LAMP1: lysosomal associated membrane protein 1; LAMP2: lysosomal associated membrane protein 2; LGALS3: galectin 3; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MTORC1: mechanistic target of rapamycin kinase complex 1; NCL: nucleolin; POLR1: RNA polymerase I; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB; TFE3: transcription factor E3; ULK1: unc-51 like autophagy activating kinase 1.

Keywords: Autophagy; TFEB; cancer; cell death; guanine quadruplex ligands; resistance to therapy

DOI: https://doi.org/10.1080/15548627.2025.2497614

Compr Physiol. 2025 Jun;15(3): e70023

Lysosomal Acidification: A New Perspective on the Pathogenesis and Treatment of Pulmonary Fibrosis.

Kai Tian, Mengjiao Yu, Mengna Jiang, Zhengnan Gao, Dongnan Zheng, Weijian Shi, Demin Cheng, Xinyuan Zhao.

Pulmonary fibrosis is a complex pathophysiological process characterized by local pulmonary inflammation and fibrosis, along with systemic inflammation and distal organ damage. The acidic environment of lysosomes, as intracellular degradation and recycling centers, is important for cellular homeostasis and function. This review summarizes the potential role of lysosomal acidification in pulmonary fibrosis pathogenesis and its implications for cross-organ effects. Various proteins and ion channels, such as V-ATPase, ClC-7, CFTR, TRPML1, and NHE, regulate lysosomal acidification. Lung fibrosis involves many cells, including lung epithelial cells, endothelial cells, macrophages, fibroblasts, and myofibroblasts. Studies have shown that abnormal lysosomal acidification significantly contributes to the onset and progression of pulmonary fibrosis. Damaged epithelial cells activate inflammatory and fibrotic signals through lysosomal dysfunction; abnormal lysosomal acidification in endothelial cells causes tissue edema and inflammatory responses; macrophages exacerbate inflammatory responses due to impaired lysosomal acidification; and fibroblasts hyperproliferate and transform into myofibroblasts due to deficient lysosomal acidification. Chronic pulmonary inflammation increases blood-gas barrier permeability, facilitating extravasation of inflammatory mediators (e.g., IL-6, TNF-α, and TGF-β) into the circulation, where they act as endocrine signals affecting distant organs. These findings provide a rationale for exploring novel therapeutic targets; future pharmacologic modulation of lysosomal acidification and inhibition of key inflammatory mediators may represent important strategies for preventing and treating pulmonary fibrosis and its systemic complications.

Keywords: V‐ATPase; chronic inflammation; distal organ damage; lysosome acidification; pulmonary fibrosis

DOI: https://doi.org/10.1002/cph4.70023

Anal Chem. 2025 Jun 20.

An Aggregation/Monomer-Based Probe for Monitoring Mitochondria-Lysosome Interactions during Cuproptosis.

Cui Zhou, Jia-Tong Yan, Yi-Ting Chu, Jian Wang, Gui-Xue Tang, Shuo-Bin Chen, Zhi-Shu Huang, Jia-Heng Tan, Xiu-Cai Chen.

The interplay between lysosomes and mitochondria is essential for maintaining cellular function, and disruptions of their interaction have been implicated in the onset of various diseases. Small molecule fluorescent probes are powerful tools for monitoring these biological processes. However, a comprehensive strategy for designing small-molecule probes capable of dual-color visualization of both mitochondria and lysosomes remains lacking. In this study, we introduce MISO, a noninvasive small organic molecular probe, as an effective tool for tracking the dynamic interplay between mitochondria and lysosomes in living cells. Mechanistic studies revealed that MISO targets lysosomes in a monomeric state, exhibiting green fluorescence, and in an aggregated state within mitochondria, displaying red fluorescence. Using MISO, we were able to perform long-term tracking of dynamic mitochondria-lysosome interactions and identified several distinct types of interactions between these organelles. Notably, for the first time, MISO revealed changes in mitochondria-lysosome interactions during cuproptosis, suggesting that the modulation of these interactions may influence this form of cell death. This work presents a valuable tool for real-time monitoring of functional mitochondria-lysosome interactions in living cells and opens avenues for advancing our understanding of related cellular processes and disease mechanisms.

DOI: https://doi.org/10.1021/acs.analchem.5c00971

Cell Commun Signal. 2025 Jun 19. 23(1): 296

Lysosomal targeting of liposomes with acidic pH and Cathepsin B induces protein aggregate clearance.

Minsol Jeon, Da-Eun Kim, So Young Choi, Seoyoung Kim, Seongchan Kim, Hyojin Lee, Hyunkyung Kim.

The autophagy-lysosomal pathway is a cellular degradation mechanism that regulates protein quality by eliminating aggregates and maintaining normal protein function. It has been reported that aging itself reduces lysosomal proteolytic activity in age-related neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Reduction in lysosomal function may underlie the accumulation of protein aggregates such as amyloid beta (Aβ), tau, and α-synuclein. Some of these protein aggregates may cause additional lysosomal dysfunction and create a vicious cycle leading to a gradual increase in protein aggregation. In this study, liposome-based lysosomal pH-modulating particles (LPPs), containing a liquid solution to adjust lysosomal pH, have been developed to restore lysosomal function. The results demonstrate that acidic LPPs effectively restore lysosomal function by recovering lysosomal pH and facilitating the removal of protein aggregates. These findings demonstrated that acidic LPPs could effectively recover the abnormal lysosomal function via restoration of lysosomal pH and enhance the clearance of protein aggregates. Furthermore, the simultaneous introduction of Cathepsin B (CTSB) proteins and acidic LPP revealed a synergistic effect, promoting lysosomal pH recovery and enhancing aggregates removal. These findings suggest a novel strategy for improving lysosomal clearance activity in proteinopathies.

Keywords: Aggregate clearance; Autophagy; Cathepsin; Lysosome; Proteinopathy

DOI: https://doi.org/10.1186/s12964-025-02310-z