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Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity

ABSTRACT: Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome-enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Caenorhabditis Elegans (ncbitaxon:6239)

SUBMITTER: Meng Wang

PROVIDER: MSV000090909 | MassIVE | Thu Dec 15 14:31:00 GMT 2022

SECONDARY ACCESSION(S): PXD038865

REPOSITORIES: MassIVE

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Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity

Project description:Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome-enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity.

2023-11-11 | MSV000093375 | MassIVE

Lysosome Lipid Signaling from the Periphery to Neurons Regulates Longevity

Project description:<p>Lysosomes are key cellular organelles that metabolize extra- and intra-cellular substrates. Alterations in lysosomal metabolism are implicated in aging-associated metabolic and neurodegenerative diseases. However, how lysosomal metabolism actively coordinates the metabolic and nervous systems to regulate aging remains unclear. Here, we report a fat-to-neuron lipid signaling pathway induced by lysosomal metabolism and its longevity promoting role in <em>Caenorhabditis elegans</em>. We discovered that induced lysosomal lipolysis in peripheral fat storage tissue up-regulates the neuropeptide signaling pathway in the nervous system to promote longevity. This cell-non-autonomous regulation is mediated by a 47 specific polyunsaturated fatty acid, dihomo-gamma-linolenic acid (DGLA) and LBP-3 lipid chaperone protein transporting from the fat storage tissue to neurons. LBP-3 binds to DGLA, and acts through NHR-49 nuclear receptor and NLP-11 neuropeptide in neurons to extend lifespan. These results reveal lysosomes as a signaling hub to coordinate metabolism and aging, and lysosomal signaling mediated inter-tissue communication in promoting longevity.</p>

2022-05-06 | MTBLS4654 | MetaboLights

GNPS Metabolomics Profiling of Single Enlarged Lysosomes Defines the Molecular Signature of Lysosomal Heterogeneity

Project description:Lysosomes are critical for cellular metabolism and heterogeneously involved in various cellular processes such as endocytosis, autophagy and senescence. The ability to measure lysosomal metabolic heterogeneity is essential for understanding its physiological roles. We therefore built a single-lysosome mass spectrometry (SLMS) platform integrating lysosomal patch-clamp recording and induced nanoESI/MS that enabled concurrent metabolic and electrophysiological profiling of individual enlarged lysosomes.

2021-04-14 | MSV000087208 | GNPS

Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization (Microarray)

Project description:Differentiation is critical for epithelial cell fate decisions, but the signals involved remain unclear. The kidney proximal tubule (PT) cells reabsorb disulphide-rich proteins through endocytosis, generating cystine via lysosomal proteolysis. Here we report that defective cystine mobilization from lysosomes through cystinosin (CTNS), which is mutated in cystinosis, diverts PT cells towards growth and proliferation, disrupting their functions. Mechanistically, lysosomal cystine storage stimulates Ragulator-Rag GTPase-dependent recruitment of mechanistic target of Rapamycin complex 1 (mTORC1) and its constitutive activation. Re-introduction of CTNS restores nutrient-dependent regulation of mTORC1 in knockout cells, whereas cell-permeant analogues of L-cystine, accumulating within lysosomes, render wild-type cells resistant to nutrient withdrawal. Therapeutic mTORC1 inhibition corrects lysosome and differentiation downstream of cystine storage, and phenotypes in a zebrafish model of cystinosis. Thus, cystine serves as a lysosomal signal that tailors mTORC1 signaling and metabolism to direct epithelial cell fate decisions. These results identify mechanisms and therapeutic targets for dysregulated homeostasis in cystinosis.

2023-03-08 | GSE226396 | GEO

Lysosomal cystine export regulates mTORC1 signaling to guide kidney epithelial cell fate specialization (RNA-Seq)

2023-03-08 | GSE226397 | GEO

Peripheral positioning of lysosomes supports melanoma aggressiveness

Project description:Emerging evidences suggest that both function and position of organelles are pivotal for tumor cell dissemination. Among them, lysosomes stand out as they integrate metabolic sensing with gene regulation and secretion of proteases. Yet, how lysosomes function is linked to their position and thereby control metastatic progression remains elusive. Here, we analyzed lysosome subcellular distribution in micropatterned patient-derived melanoma cells and found that lysosome spreading scales with their aggressiveness. Peripheral lysosomes promote invadopodia-based matrix degradation and invasion of melanoma cells which is directly linked to their lysosomal and cell transcriptional programs. When controlling lysosomal positioning using chemo-genetical heterodimerization in melanoma cells, we demonstrated that perinuclear clustering impairs lysosomal secretion, matrix degradation and invasion. Impairing lysosomal spreading in a zebrafish metastasis model significantly reduces invasive outgrowth. Our study provides a mechanistic demonstration that lysosomal positioning controls cell invasion, illustrating the importance of organelle adaptation in carcinogenesis.

2023-07-31 | E-MTAB-13165 | biostudies-arrayexpress

NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin

Project description:Mitochondrial activity is critical for cellular vitality and organismal longevity, yet underlying regulatory mechanisms spanning these different levels of organization remain elusive. From RNAi screens for mitochondrial biogenesis, we discovered NFYB-1, a subunit of the NF-Y transcriptional complex, as an ancestral regulator of mitochondrial function. NFYB-1 loss leads to reduced mitochondrial gene expression and oxygen consumption, mitochondrial fragmentation, disruption of mitochondrial stress pathways, and abolition of organismal longevity triggered by mitochondrial impairment. Multi-omics analysis reveals that NFYB-1 is a potent repressor of the ER stress response, as well as lysosomal prosaposin. Surprisingly, limiting prosaposin expression alters ceramide and cardiolipin pools, restores mitochondrial fusion, gene expression and longevity. Thus, the NFYB-1/prosaposin axis coordinates lysosomal to mitochondrial communication to enhance cellular mitochondrial function and organismal health.

2020-03-11 | GSE127917 | GEO

NFYB-1 regulates mitochondrial function and longevity via lysosomal prosaposin

2020-03-11 | PXD013233 | Pride

Mouse tissue-resident macrophage expression profiles

Project description:We show that macrophages from murine spleen, liver and peritoneum display dramatically different expression profiles. Clusters of genes were found to represent unique biological functions related to adhesion, antigen presentation, phagocytosis, lipid metabolism and signal transduction. Some gene families, such as integrins, are differentially expressed among the macrophages resident in different tissues, suggesting that the tissue of residence influences their biological function.

2010-09-22 | GSE24258 | GEO

β2-adrenergic agonists rescue lysosome acidification and function in PSEN1 deficiency by reversing defective ER to lysosome delivery of ClC-7

Project description:Lysosomal dysfunction is considered pathogenic in Alzheimer Disease (AD). Loss of Presenilin-1(PSEN1) function causing early onset AD impedes acidification via defective vATPase V0a1 subunit delivery to lysosomes. We report that isoproterenol and related β2-adrenergic agonists re-acidify lysosomes in PSEN1 KO cells and fibroblasts from PSEN1 familial AD(FAD) patients, restores lysosomal calcium homeostasis and proteolysis, and reverses impaired autophagy flux. We identify a novel rescue mechanism involving PKA-mediated facilitated delivery of ClC-7 to lysosomes, which stimulates chloride influx and reverses markedly lowered Cl- content of PSEN1 KO lysosomes. Notably, PSEN1 loss-of-function impedes ER-to-lysosome delivery of ClC-7, thus accounting for lysosomal Cl- deficits that compound pH deficits due to deficient vATPase function. Transcriptomics of PSEN1-deficient cells reveal strongly down-regulated ER-to-lysosome transport pathways and reversibility by isoproterenol. Our findings uncover a broadened PSEN1 role in lysosomal ion homeostasis and novel pH modulation of lysosomes through β-adrenergic regulation of ClC-7, which can be therapeutically modulated.

2020-02-29 | GSE136894 | GEO

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