bims-lycede 2025-11-30 papers

Front Mol Biosci. 2025 ;12 1699266

Loss of ARF5 impairs recovery after lysosomal damage.

Martyna O Iwaniec, Christopher J Bott, James E Casanova.

Lysosomal dysfunction is a defining feature of aging and neurodegenerative diseases, where lysosomal membrane permeabilization and release of its contents can trigger cellular death pathways. To counteract this, cells rely on lysosomal quality control mechanisms, many of which depend on lipid delivery to repair damaged membranes. However, the regulatory pathways governing this process remain unclear. In this study, we investigated whether canonical ARF GTPases, best known for their roles in Golgi and endosomal vesicular trafficking, are recruited to damaged lysosomes and contribute to their repair. Using LysoIP-based lysosome isolation, super-resolution immunofluorescence imaging, and functional assays in HeLa and HEK293 cells, we found that ARF1, ARF5, and ARF6 localize to lysosomal membranes following L-leucyl-L-leucine methyl ester (LLOME)-induced permeabilization. While loss of ARF6 did not impair recovery, ARF5 depletion resulted in a nearly complete block of lysosomal repair. These findings identify ARF proteins as early responders to lysosomal damage and suggest isoform-specific roles in coordinating the pathways of lysosomal quality control.

Keywords: ARF; ORP; OSBP; lysosome; repair

DOI: https://doi.org/10.3389/fmolb.2025.1699266

J Cell Biol. 2026 Jan 05. pii: e202503081. [Epub ahead of print]225(1):

Homocysteine disrupts lysosomal function by V-ATPase inhibition.

Yang Yang, Qianjin Kong, Chaolian Liu, Fengyang Wang, Meijiao Li, Shalan Li, Yuehui Shi, Leonard Krall, Xin Wang, Shan He, Kai Jiang, Xuna Wu, Mei Yang, Chonglin Yang.

Lysosomes are degradation and signaling organelles central to metabolic homeostasis. It remains unclear whether and how harmful metabolites compromise lysosome function in the etiopathology of metabolic disorders. Combining Caenorhabditiselegans and mouse models, we demonstrate that homocysteine, an intermediate in methionine-cysteine metabolism and the cause of the life-threatening disease homocystinuria, disrupts lysosomal functions. In C. elegans, mutations in cystathionine β-synthase cause strong buildup of homocysteine and developmental arrest. We reveal that homocysteine binds to and homocysteinylates V-ATPase, causing its inhibition and consequently impairment of lysosomal degradative capacity. This leads to enormous enlargement of lysosomes with extensive cargo accumulation and lysosomal membrane damage in severe cases. Cbs-deficient mice similarly accumulate homocysteine, displaying abnormal or damaged lysosomes reminiscent of lysosomal storage diseases in multiple tissues. These findings not only uncover how a metabolite can damage lysosomes but also establish lysosomal impairment as a critical contributing factor to homocystinuria and homocysteine-related diseases.

DOI: https://doi.org/10.1083/jcb.202503081

bioRxiv. 2025 Nov 05. pii: 2025.11.04.686610. [Epub ahead of print]

Cell-line specific role of Cathepsin B in triple-negative breast cancer growth, invasion and response to chemotherapy.

Charlotte Kelley, Justinne R Guarin, Emily Henrich, Jackson P Fatherree, Claire M Dunn, Anna Yui, Madeleine J Oudin.

Cathepsins are papain-family cysteine proteases known to play a cell-intrinsic role in protein degradation in the lysosome, as well as in digesting ECM and surface proteins after being secreted. Both of these functions are known to mediate pro-tumorigenic effects of CTSB in a range of cancers. Here, we specifically investigate the role of CTSB in TNBC, an aggressive subtype of breast cancer, where we find that high expression of CTSB in TNBC is associated with better outcomes. We used CRISPR to knockout CTSB in two highly metastatic TNBC cell lines, MDA-MB-231 and MDA-MB-468, and find different effects. In MDA-MB-231 cells, knockout of CTSB has no effect on cell viability, increases tumor cell 3D invasion in an ECM-independent manner, and increases sensitivity to many standard of care chemotherapy drugs. However, in MDA-MB-468 cells, knockout of CTSB increases cell viability, decreases tumor cell 3D invasion, in an ECM-independent manner, and drives resistance to certain chemotherapy drugs without affecting response to others. We find that in these cells, CTSB is not secreted, and that differential downstream mTOR and Akt activation can explain the differences seen in these phenotypes. Overall, our studies demonstrate that CTSB can regulate TNBC cell phenotypes via its lysosomal cell-intrinsic role, but that effects are cell-line specific, suggesting potential heterogeneity in the role of CTSB in TNBC.

DOI: https://doi.org/10.1101/2025.11.04.686610

Front Genet. 2025 ;16 1679497

Epigenetic landscape in lysosomal storage disorders: mechanisms and modulation.

Andrés Felipe Leal, Harry Pachajoa, Shunji Tomatsu.

Lysosomal storage disorders (LSDs) are rare substrate-accumulating diseases primarily characterized by mutations in genes encoding proteins involved in lysosomal function, most of which have enzymatic activity. Resulting lysosomal dysfunction leads to the overaccumulation of non- or partially degraded substrates. While it is true that enzyme deficiency is the primary cause of LSDs, the epigenetic alterations in DNA methylation, miRNA expression, and histone modifications appear to be critical mechanisms involved in the pathogenesis of LSDs. As epigenetic marks are, in most cases, reversible, their study becomes vital to developing strategies aimed at reversing epigenome alterations. Although classical therapeutic alternatives aim to recover the lysosomal function by restoring the protein expression lost, the use of modifiers able to repair the epigenetic modifications in LSDs may become a promising strategy. This manuscript explores the most recent evidence on the epigenetic alterations in LSDs. It also discusses their modulation through epigenetic modulators, a novel and intriguing approach to treat LSDs, as well as the potential of the CRISPR/Cas9 system.

Keywords: epigenetics; histones; lysosomal storage disorders; methylation; miRNA

DOI: https://doi.org/10.3389/fgene.2025.1679497

Free Radic Biol Med. 2025 Nov 23. pii: S0891-5849(25)01390-5. [Epub ahead of print]243 398-413

TFEB-nuclear translocation promotes BNIP3-mediated mitophagy and alleviates oxidative stress and ferroptosis in acute pancreatitis.

Haoyu Zhang, Yuchen Jia, Zheng Wang, Jie Li, Xiaozhou Xie, Yixuan Ding, Feng Cao, Fei Li.

Mitophagy, oxidative stress, and ferroptosis are critical processes in the development of acute pancreatitis (AP). Transcription factor EB (TFEB), a key regulator of autophagy and lysosomal biogenesis, plays a central role in the pathogenesis of AP. However, its specific regulatory mechanisms within the mitophagy-oxidative stress-ferroptosis network remain incompletely understood. This study investigated the therapeutic potential of ginkgetin (GK), a natural TFEB activator, in AP. The results demonstrated that GK activated TFEB and subsequently significantly alleviated pathological damage in AP in vivo and effectively inhibited acinar cell death in vitro. Further mechanistic studies revealed that TFEB activation markedly improved impaired autophagic flux in AP, enhanced mitophagy, and simultaneously suppressed ferroptosis and oxidative stress. Specifically, TFEB upregulated the expression of the lysosomal marker LAMP1 to restore autophagy-lysosome function and induced the expression of BNIP3, a key mitophagy receptor, thereby enhancing mitochondrial quality control, restoring mitochondrial function, and ultimately mitigating oxidative stress and ferroptosis. Functional experiments confirmed that TFEB exerts its protective effects through nuclear translocation. When nuclear translocation was blocked by a C270S mutation-a mutation that disrupts TFEB dissociation from 14-3-3 proteins and subsequent nuclear localization-TFEB's regulatory roles in autophagy, mitophagy, ferroptosis, and oxidative stress were significantly inhibited. This study elucidates that TFEB, through nuclear translocation, not only restores basal autophagy but also enhances mitophagy, thereby collectively inhibiting oxidative stress and ferroptosis and alleviating the progression of AP. These findings provide a novel therapeutic strategy for AP.

Keywords: Acute pancreatitis; Ferroptosis; Ginkgetin; Mitophagy; Oxidative stress; TFEB

DOI: https://doi.org/10.1016/j.freeradbiomed.2025.11.045