bims-lycede 2024-11-03 papers

J Biol Chem. 2024 Oct 23. pii: S0021-9258(24)02431-1. [Epub ahead of print] 107929

TFEB agonist clomiphene citrate activates the autophagy-lysosomal pathway and ameliorates Alzheimer's disease symptoms in mice.

Jieru Lin, Yi Yuan, Chunhuan Huang, Jiayu Zi, Lu Li, Jiamiao Liu, Xiaoting Wu, Wei Li, Qing Zhao, Yuyin Li, Zhenxing Liu, Aipo Diao.

Autophagy is a conserved eukaryotic cellular clearance and recycling process through the lysosome-mediated degradation of damaged organelles and protein aggregates to maintain homeostasis. Impairment of the autophagy-lysosomal pathway is implicated in the pathogenesis of Alzheimer's disease (AD). Transcription factor EB (TFEB) is a master regulator of autophagy and lysosomal biogenesis. Therefore, activating TFEB and autophagy provides a novel strategy for AD treatment. We previously described that clomiphene citrate (CC) promotes nuclear translocation of TFEB and increases autophagy and lysosomal biogenesis. In this study, 7 and 3-month-old APP/PS1 mice were treated with TFEB agonist CC and assessed. The behavioral tests were performed using Morris water maze and open field test. Additional changes in Aβ pathology, autophagy and inflammatory response were determined. We found that CC activated TFEB and the autophagy-lysosomal pathway in neuronal cells. Moreover, using mouse model of Alzheimer's disease, CC treatment promoted clearance of Aβ plaques and ameliorated cognitive function in both 7 and 3-month-old APP/PS1 mice. The CC-induced activation of TFEB occurs by promoting acetylation of TFEB for nuclear translocation. These findings provide a molecular mechanism for the TFEB-mediated activation of the autophagy-lysosome pathway by CC, which has the potential to be repurposed and applied in the treatment or prevention of AD.

Keywords: Alzheimer's disease; TFEB; autophagy; clomiphene citrate; lysosome

DOI: https://doi.org/10.1016/j.jbc.2024.107929

bioRxiv. 2024 Oct 27. pii: 2024.10.25.620336. [Epub ahead of print]

Comprehensive Proteomic Characterization of Intra-Golgi Trafficking Intermediates.

Farhana Taher Sumya, Walter S Aragon-Ramirez, Vladimir V Lupashin.

The Conserved Oligomeric Golgi (COG) complex is critical for efficient intra-Golgi trafficking and glycosylation. Prior research has demonstrated that COG dysfunction or RNAi-induced depletion leads to the accumulation of non-tethered COG complex-dependent (CCD) vesicles. However, the precise connection between COG deficiency, degradation of Golgi enzymes, and its impact on vesicular trafficking has not been fully elucidated. In this study, we conducted a comprehensive proteomic analysis of Golgi-derived vesicles from both wild-type and COG-depleted cells. We specifically analyzed three distinct populations of vesicles immunoisolated with antibodies targeting transmembrane proteins from the cis, medial, and trans-Golgi sub-compartments. Our findings reveal that, while the vesicle content encompasses the entire Golgi proteome, the molecular signatures of vesicles derived from wild- type cells were markedly distinct, underscoring a robust recycling mechanism for Golgi- dependent proteins. Notably, these vesicles retained various vesicular coats, and COG depletion significantly accelerated their uncoating. Furthermore, the increased overlap in molecular signatures upon COG depletion indicates that persistent defects in vesicle tethering severely compromise intra-Golgi sorting mechanisms. Crucially, our analysis highlights that the entire Golgi glycosylation machinery recycles within CCD vesicles in a COG-dependent manner, while secretory proteins and components involved in ER-Golgi and Golgi-endosome trafficking were not enriched. These results strongly support a model of multi-step intra-Golgi vesicular recycling of the glycosylation machinery, orchestrated by the COG complex in concert with a cisternae-specific array of vesicular coats, coiled-coil tethers, Rabs, and SNARE proteins.

DOI: https://doi.org/10.1101/2024.10.25.620336

Dev Cell. 2024 Oct 21. pii: S1534-5807(24)00604-X. [Epub ahead of print]

An SLC12A9-dependent ion transport mechanism maintains lysosomal osmolarity.

Roni Levin-Konigsberg, Koushambi Mitra, Kaitlyn Spees, AkshatKumar Nigam, Katherine Liu, Camille Januel, Pravin Hivare, Sophia M Arana, Laura M Prolo, Anshul Kundaje, Manuel D Leonetti, Yamuna Krishnan, Michael C Bassik.

Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity cause ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium (NH4+). Ammonium buildup compromises lysosomal function, suggesting the existence of mechanisms that protect cells from ammonium toxicity. Here, we identified SLC12A9 as a lysosomal-resident protein that preserves organelle homeostasis by controlling ammonium and chloride levels. SLC12A9 knockout (KO) cells showed grossly enlarged lysosomes and elevated ammonium content. These phenotypes were reversed upon removal of the metabolic source of ammonium or dissipation of the lysosomal pH gradient. Lysosomal chloride increased in SLC12A9 KO cells, and chloride binding by SLC12A9 was required for ammonium transport. Our data indicate that SLC12A9 function is central for the handling of lysosomal ammonium and chloride, an unappreciated, fundamental mechanism of lysosomal physiology that may have special relevance in tissues with elevated ammonia, such as tumors.

Keywords: SLC12A9; ammonium; chloride; ion transport; lysosome metabolism; lysosome volume regulation

DOI: https://doi.org/10.1016/j.devcel.2024.10.003

Biomolecules. 2024 Oct 08. pii: 1268. [Epub ahead of print]14(10):

The Many Faces of Autophagy: Balancing Survival and Cell Death.

Barbara Canonico.

Autophagy and apoptosis are two fundamental biological mechanisms that may cooperate or be antagonistic, and both are involved in deciding the fate of cells in physiological or pathological conditions [...].

DOI: https://doi.org/10.3390/biom14101268

J Cell Biol. 2025 Jan 06. pii: e202403116. [Epub ahead of print]224(1):

Heterogeneity of late endosome/lysosomes shown by multiplexed DNA-PAINT imaging.

Charles Bond, Siewert Hugelier, Jiazheng Xing, Elena M Sorokina, Melike Lakadamyali.

Late endosomes/lysosomes (LELs) are crucial for numerous physiological processes and their dysfunction is linked to many diseases. Proteomic analyses have identified hundreds of LEL proteins; however, whether these proteins are uniformly present on each LEL, or if there are cell-type-dependent LEL subpopulations with unique protein compositions is unclear. We employed quantitative, multiplexed DNA-PAINT super-resolution imaging to examine the distribution of seven key LEL proteins (LAMP1, LAMP2, CD63, Cathepsin D, TMEM192, NPC1, and LAMTOR4). While LAMP1, LAMP2, and Cathepsin D were abundant across LELs, marking a common population, most analyzed proteins were associated with specific LEL subpopulations. Our multiplexed imaging approach identified up to eight different LEL subpopulations based on their unique membrane protein composition. Additionally, our analysis of the spatial relationships between these subpopulations and mitochondria revealed a cell-type-specific tendency for NPC1-positive LELs to be closely positioned to mitochondria. Our approach will be broadly applicable to determining organelle heterogeneity with single organelle resolution in many biological contexts.

DOI: https://doi.org/10.1083/jcb.202403116