A lysosome-plasma membrane-sphingolipid axis linking lysosomal storage to cell growth arrest
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ABSTRACT:
PROVIDER: PRJNA418450 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6293390_1.fastq.gz | Fastqsanger.gz | |||
| SRR6293390_2.fastq.gz | Fastqsanger.gz | |||
| SRR6293400_1.fastq.gz | Fastqsanger.gz | |||
| SRR6293400_2.fastq.gz | Fastqsanger.gz | |||
| SRR6293391_1.fastq.gz | Fastqsanger.gz |
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Project description:Nearly all cellular processes are pH dependent. The acidic pH inside the lysosome (vacuole in yeast) is essential for cellular content degradation, signaling, and autophagy. Defect in lysosome/vacuole acidification is a conserved hallmark of aging and age-related diseases. Traditionally, lysosome/vacuole is thought to import free protons (H⁺) from the surrounding neutral cytosol. In this study, we uncovered a previously unrecognized, conserved lysosome/vacuole acidification mechanism, involving lysosomal/vacuolar uptake of H+ pumped out by mitochondrial electron transport chain through membrane contacts between mitochondria and lysosomes/vacuoles. Aging/senescence-associated disruption of mitochondria-lysosome/vacuole contacts causes lysosomal/vacuolar de-acidification, which can be reversed by expressing a linker to connect these organelles and through an asymmetry-dependent rejuvenation process in daughter cells. Preserving lysosomal acidification in senescent human cells prevents the induction of major senescence-associated secretory phenotype factors and enhances autophagic flux. These findings reshape our current understanding of the mechanisms underlying lysosomal/vacuolar (de-)acidification in both young and aged/senescent cells.
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Project description:HDL particles are known to possess several anti-atherogenic properties that include the removal of excess cholesterol from peripheral tissues, the maintenance of endothelial integrity, antioxidant and antiinflammatory activities. ApoA-I overexpression in apoE-deficient (EKO) mice has been shown to increase HDL levels and to strongly reduce atherosclerosis development. The aim of the study was to investigate gene expression patterns associated with atherosclerosis development in the aorta of EKO mice and how HDL plasma levels relate to gene expression patterns at different stages of atherosclerosis development and with different dietary treatments. Methods Eight weeks old EKO mice, EKO mice overexpressing human apoA-I (EKO/hA-I) and wild-type mice as controls were fed either Chow or Western diet for 6 or 22 weeks. Cholesterol distribution among lipoproteins was evaluated and atherosclerosis of the aorta was quantified. High-throughput sequencing technologies were used to analyse the transcriptome of the aorta of the three genotypes in each experimental condition. Results: In addition to the well-known activation of inflammation and immune response, the impairment of sphingolipid metabolism, phagosome-lysosome system and osteoclast differentiation emerged as relevant players in atherosclerosis development. The reduced atherosclerotic burden in the aorta of EKO mice expressing high levels of apoA-I was accompanied by a reduced activation of the immune system markers, as well as reduced perturbation of lysosomal activity and a better regulation of the sphingolipid synthesis pathway Conclusions. ApoA-I modulates atherosclerosis development in the aorta of EKO mice affecting the expression of pathways additional to those associated with inflammation and immune response
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Project description:Lysosomal cathepsins regulate an exquisite range of biological functions, and their deregulation is associated with inflammatory, metabolic and degenerative disease in humans. Here, we identified a key cell-intrinsic role for cathepsin B as a negative feedback regulator of lysosomal biogenesis and autophagy. Mice and macrophages lacking cathepsin B activity had increased resistance to the cytosolic bacterial pathogen Francisella novicida. Genetic deletion or pharmacological inhibition of cathepsin B downregulated mTOR activity and prevented cleavage of the lysosomal calcium channel TRPML1. These events drove transcription of lysosomal and autophagy genes via the transcription factor TFEB, which increased lysosomal biogenesis and activation of autophagy-initiation kinase ULK1 for clearance of the bacteria. Our results identified a fundamental biological function of cathepsin B in providing a checkpoint for homeostatic maintenance of lysosome population and basic recycling functions in the cell. We used microarrays to explore the gene expression profiles differentially expressed in bone marrow-derived macrophages (BMDM) isolated from cathepsin B-/- and wild-type mice.
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Project description:Despite accumulating evidences linking defective lysosome function with autoimmune diseases, how the catabolic machinery is regulated for immune homeostasis remains largely unknown. Lamtor5 is a subunit of the Ragulator mediating mTORC1 activation in response to amino acids, but its action mode and physiological role are yet to be addressed. Here we unexpectedly found that myeloid Lamtor5 ablating mice developed spontaneous inflammation and systemic lupus erythematosus (SLE)-like manifestation. Loss of Lamtor5 in macrophages caused impaired vacuolar H⁺-ATPase (v-ATPase) activity, lysosome de-acidification, and aberrant mTORC1 activation, correlating with undesirable inflammatory responses. Mechanistically, we showed that Lamtor5 physically associated with ATP6V1A, an essential subunit of v-ATPase, and promoted the V0/V1 holoenzyme assembly for lysosome acidification. Notably, binding of Lamtor5 to v-ATPase substantially affected lysosomal tethering of Rag GTPase and weakened its interaction with mTORC1 for activation. Importantly, defective Lamtor5 expression, along with impaired lysosomal function and hyperactivation of mTORC1, was corroborated in peripheral blood mononuclear cells (PBMCs) of SLE patients and correlated with disease severity. Overall, our findings establish Lamtor5 as a new lysosome regulator, and elucidate an unappreciated mechanism that coordinates catabolic and anabolic pathways to bolster immune homeostasis preventing autoimmunity.
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Project description:Lysosomes are essential organelles that play vital roles in the degradation and recycling of a variety of biomolecules. To fully understand their molecular mechanisms, high spatiotemporal identification of the lysosome proteome in living cells is critical. Although photocatalytic proximity labeling is a powerful tool for profiling subcellular proteome, it often struggles with low labeling efficiency, particularly for low-abundance proteins. To overcome this, we introduced a novel strategy that integrates photocatalytic proximity labeling with cross-linking. This approach enabled difficult-to-label proteins to be linked to already labeled ones via cross-linking, thereby expanding the scope of pro-tein identification. Using this strategy, we successfully identified 238 lysosome-annotated proteins in living HeLa cells, a substantial in-crease compared to method without cross-linking (238 vs 197). The developed strategy enhanced lysosomal proteomic coverage via a high-precision integration platform, allowing systematic identification of both membrane-associated and luminal proteins within lysosome, thereby providing mechanistic insights into subcellular biology and unlocking new frontiers in cellular research.
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