bims-lycede 2025-07-27 papers

Autophagy. 2025 Jul 25.

TM9SF3 is a mammalian Golgiphagy receptor that safeguards Golgi integrity and glycosylation fidelity.

Selective autophagy of the Golgi apparatus, or Golgiphagy, depends on receptor proteins that recognize and deliver fragmented Golgi membranes into phagophores for lysosomal degradation. We recently identified TM9SF3, a Golgi-resident transmembrane protein, as a receptor mediating this process under nutrient stress and various Golgi stress conditions. TM9SF3 binds to all six mammalian Atg8 (ATG8) proteins via multiple N-terminal LC3-interacting regions (LIRs). Knockout of TM9SF3 inhibits nutrient stress-induced Golgi fragmentation, reduces autophagic delivery of Golgi components, and hinders Golgi protein degradation. In addition to nutrient stress, TM9SF3 is essential for Golgiphagy induced by monensin, brefeldin A, and glycosylation perturbations. Knockout or LIR mutation of TM9SF3 disrupts protein glycosylation, whereas its overexpression promotes the degradation of aberrantly glycosylated proteins. Notably, TM9SF3 promotes breast cancer cell proliferation, and its high expression correlates with poor patient prognosis. Our findings establish TM9SF3 as a Golgiphagy receptor essential for maintaining Golgi integrity and glycosylation fidelity, and implicate its role in supporting cancer progression.

Keywords: Atg8 (ATG8); TM9SF3; breast cancer; golgiphagy; protein glycosylation; receptor

DOI: https://doi.org/10.1080/15548627.2025.2539928

J Biol Chem. 2025 Jul 17. pii: S0021-9258(25)02324-5. [Epub ahead of print] 110474

Secretory autophagy mediates lysosomal and autophagic degradation for α-synuclein proteostasis.

Taiki Sawai, Yoshitsugu Nakamura, Shigeki Arawaka.

Autophagy has two distinct pathways, degradation and secretion. Autophagic degradation plays a pivotal role in proteostasis. However, the role of autophagic secretion in proteostasis maintenance is not fully understood. Here, we investigate how the blockade of autophagic secretion impairs proteostasis in SH-SY5Y cells. siRNA-mediated knockdown of a modulator for autophagosome formation, ATG5, BECN1 or FIP200 inhibited autophagic flux and secretion, causing accumulation of Triton X-100-insoluble α-synuclein, which is an aggregate-prone protein responsible for neuronal loss in Parkinson's disease. The blockade of autophagic secretion by knockdown of t-SNARE SNAP23 or STX4 increased autophagic flux for p62 degradation, but these knockdowns induced enlargement and membrane damage of lysosomes as well as lysosomal dysfunction. SNAP23 or STX4 knockdown caused accumulation of Triton X-100-insoluble α-synuclein against induction of lysophagy. GBA knockdown showed lysosomal damage with the increase in autophagic secretion. RAB8A, a small GTPase regulator of polarized sorting to the plasma membrane, knockdown blocked autophagic secretion and produced lysosomal damage. SNAP23, STX4 or RAB8A knockdown further accelerated accumulation of Triton X-100-insoluble α-synuclein caused by a lysosomal protease inhibitor cocktail. Collectively, these findings suggest that SNAP23, STX4 or RAB8A knockdown blocks autophagic secretion and upregulates autophagic flux as a compensatory response to help maintain degradation. However, these knockdowns impair α-synuclein proteostasis because of lysosomal damage that they induce, counteracting compensatory effects of autophagic degradation, including lysophagy. Autophagic secretion and degradation may collaboratively form the clearance pathway required for maintaining lysosomal function by reducing the burden of aggregate-prone protein cargo.

Keywords: Parkinson disease; autophagy; lysosome; protein secretion; proteostasis; synuclein

DOI: https://doi.org/10.1016/j.jbc.2025.110474

Methods Mol Biol. 2025 Jul 22.

Computational Approaches for Delineating Lysosomes and Related Intracellular Trafficking Vesicles in Confocal and Other Fluorescence Datasets.

Charles Ellis, David S Chatelet, J Arjuna Ratnayaka.

Fluorescence datasets from investigations into intracellular trafficking compartments produce images of variable quality, scales, and complexities. Investigators are therefore confronted with a choice of how to analyze this information. Here, we have used confocal immunofluorescence images of lysosomes from retinal pigment epithelial cells as an exemplar dataset, and employed three freely accessible computational approaches (Fiji, CellProfiler and Icy) to showcase their workings. A step-by-step workflow for each pipeline is described with non-specialist users in mind. These produce results including lysosomal number and shape, but also 3D outputs such as volume. Features of the three methods alongside their advantages and limitations are subsequently summarized. An important consideration, however, is that results generated from the different approaches are not necessarily comparable. Hence, users should adopt only a single method to analyze their dataset which best suit their specific requirements.

Keywords: 3D imaging; Computation; Confocal microscopy; Data integrity; Lysosome; Retinal pigment epithelium (RPE); Stem cells; Trafficking vesicles; Volume

DOI: https://doi.org/10.1007/7651_2025_657