Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics analysis of lysosomes and whole cell lysates from H4 cellsLysosome, H4, glucocerebrosidase

ABSTRACT: Studies have shown that the majority of Parkinson's disease patients have at least one putative damaging variant in a lysosomal storage disorder gene (60%) and in about 10% of sporadic PD subjects, the disease is associated with mutations in GBA1, a gene coding for glucocerebrosidase, a lysosomal hydrolase. However, the precise cellular and lysosome-specific alterations upon loss of glucocerebrosidase are not established. The aim of this study is to characterize the proteome-wide changes at the cellular and lysosomal level in H4 cells upon loss of the GBA gene. Moreover, we tested if reinstating glucocerebrosidase activity by treating cells with our in-house GCase-BS (glucocerebrosidase-brain shuttle) can revert these changes, both at the cellular and lysosomal level.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Alexandra Gehrlein

LAB HEAD: Ravi Jagasia

PROVIDER: PXD036361 | Pride | 2023-03-24

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	L_D200110_S2519-Exp01-SPL-BID01_MHRM_R01_T0.raw	Raw
	L_D200110_S2519-Exp01-SPL-BID02_MHRM_R01_T0.raw	Raw
	L_D200110_S2519-Exp01-SPL-BID03_MHRM_R01_T0.raw	Raw
	L_D200110_S2519-Exp01-SPL-BID04_MHRM_R01_T0.raw	Raw
	L_D200110_S2519-Exp01-SPL-BID05_MHRM_R01_T0.raw	Raw

Items per page:

1 - 5 of 15

Similar Datasets

A PIKfyve Modulator Combined with an Integrated Stress Response Inhibitor to treat Lysosomal Storage Diseases

Project description:Lysosomal degradation pathways coordinate the clearance of superfluous and damaged cellular components. Compromised lysosomal degradation is a hallmark of many degenerative diseases, including lysosomal storage diseases, which are caused by loss-of-function mutations within both alleles of a lysosomal hydrolase, leading to lysosomal substrate accumulation. Gaucher’s disease, characterized by <15% of normal glucocerebrosidase function, is the most common lysosomal storage disease and is a prominent risk factor for developing Parkinson’s disease. Here, we show that either of two structurally distinct small molecules that modulate PIKfyve activity, discovered from a high-throughput cellular lipid droplet clearance screen, can improve glucocerebrosidase function in Gaucher patient–derived fibroblasts through an MiT/TFE transcription factor that promotes lysosomal gene translation. An ISR antagonist used in combination with a PIKfyve modulator further improves cellular glucocerebrosidase activity, likely because integrated stress response (ISR) signaling appears to also be slightly activated by treatment by either small molecule at the higher doses employed, This strategy of combining a PIKfyve modulator with an integrated stress response inhibitor improves mutant lysosomal hydrolase function in cellular models of additional lysosomal storage diseases.

2024-06-11 | GSE263252 | GEO

Cross-linking of the Endolysosomal System Reveals Potential Flotillin Structures and Cargo

Project description:Lysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyzed lysosomes and early endosomes. Based on the identification of 5,376 cross-links, we investigated protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and a heterodimeric structure of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identified >300 proteins presenting putative cargo, and confirmed several substrates for flotillin-dependent endocytosis, including the latrophilin family of adhesion G protein-coupled receptors.

2022-10-22 | PXD030532 | Pride

A quantitative proteomic profile revealed the crucial roles of lysosome in the microbial infection

Project description:Lysosome played vital roles for both innate and adaptive immunity. It has been widely accepted that lysosome functioned more than a digestive organelle. However, it was still largely unknown for the proteome changes of lysosome on various microbes, and the understanding of lysosomal proteome from the purified lysosome is another obstacle that needs to be resolved. Here, we performed a proteomic study on the enriched lysosomes from THP1 cells after infected by Listeria monocytogenes (L. m), Herpes Simplex Virus 1 (HSV-1) and Vesicular Stomatitis Virus (VSV). Combining with the GO analysis, we identified 284 lysosomal related proteins from the totally identified 4560 proteins. We also constructed the protein-protein interaction networks for the changed proteins and revealed the core lysosomal proteins in responding for diverse microbial infections. From this study, we not only revealed that lysosome responded in a different manner for the bacterial or virus infection, but also proposed a new way for the proteome research for the enriched organelles.

2017-05-04 | PXD005748 | Pride

USP32 regulates non-proteolytic LAMTOR1 ubiquitination and Ragulator function

Project description:Ubiquitination is among the most prevalent post-translational modifications regulating a great number of cellular functions, and defects in such processes contribute to many diseases. Deubiquitinating enzymes (DUBs) are essential to control the precise outcome of ubiquitin signals. The ubiquitin-specific protease 32 (USP32) differs from all other DUBs as it comprises in addition to its catalytic USP domain and the DUSP domain also multiple EF hands and a C-terminal prenylation site. This unique domain architecture offers various features for the regulation of specific signaling processes by USP32. A SILAC-based proteomic analysis of purified lysosomes revealed an increase in lysosomal hydrolases in organelles isolated from USP32 KO cells as compared to WT cells, suggesting that hydrolases are not sorted correctly to their destination in the absence of USP32.

2022-12-16 | PXD024227 | Pride

Targeting of non-phosphorylated lysosomal enzymes involves secretion and Lrp1-mediated recapture

Project description:Most lysosomal enzymes require mannose 6-phosphate (M6P) residues for efficient receptor-mediated lysosomal targeting. Although the lack of M6P results in missorting and hypersecretion, selected lysosomal enzymes reach normal levels in lysosomes of various cell types suggesting the existence of M6P-independent transport routes. SILAC-based analysis of purified lysosomes from M6P-deficient mouse fibroblasts (PTki) revealed unchanged amounts of 11 lysosomal enzymes, including cathepsin D and B (CtsD, CtsB), while demonstrating mossiorting of a variety of soluble lysosomal enzymes

2015-05-01 | PXD001221 | Pride

lysosome proteomics in Niemann-Pick Type C disease model cells (CHOwt and NPC1-null cells)

Project description:Increasing evidence implicates lysosomal dysfunction in the pathogenesis of neurodegenerative diseases, including the rare inherited lysosomal storage disorders (LSDs) and the most common neurodegenerative diseases, such as Alzheimer’s and Parkinson’s disease (AD and PD). The goal of this work was to analyze whether there are changes in the lysosomal glycocalyx in a cellular model of a LSD Niemann-Pick type C disease (NPC). Using the ferrofluid nanoparticles we isolated lysosomal organelles from NPC1-null and CHOwt cells. Mass spectrometry identification of lysosomal proteins was performed in order to determine the enrichment efficiency for N-glycome profiling of the lysosomal glycocalyx in NPC disease cellular model.

2018-03-21 | PXD008438 | Pride

Multi cell line comparison of lysosome enriched fractions reveals cell type specific features and novel lysosomal proteins

Project description:Lysosomes are the main degradative organelles of mammalian cells and are responsible for the breakdown of the majority of cellular macromolecules and the recycling of their building blocks. To accomplish this task, lysosomes contain ~60 hydrolases. Malfunction of these proteins, as well as other proteins responsible for the transport of small molecules or proteins, lead to the accumulation of their respective substrates. This accumulation of substrates results in heavy impairment of lysosomal function leading to ~70 lysosomal storage disorders (LSDs). A better understanding of lysosomal composition is of high importance not only for a better understanding of LSDs, but also for cellular function. Analysis of lysosomes by mass spectrometry-based proteomics presents an attractive approach to allow for a better characterization of lysosomes. In the current study, we investigated the lysosomal proteome from six different cell lines (HEK293, HeLa, HuH-7, SH-SY5Y, MEF and NIH3T3) by lysosome enrichment using SPIONs (superparamagnetic iron oxide nanoparticles) combined with mass spectrometry-based proteomics. Comparison of the individual proteomes revealed cell type specific characteristics in lysosomal protein expression. To allow for the discrimination of lysosomal from unspecific enriched proteins, we included a differentially SILAC (stable isotope labelling by amino acids in cell culture) labelled control sample. Afterwards, lysosomal proteins were identified using a bimodal distribution model. By combination of data from several cell lines, we were able to generate a high confidence list of putative novel lysosomal proteins of which several were confirmed by immunostaining.

2023-02-21 | PXD020600 | Pride

The Ragulator complex regulates NLRP3 inflammasome activation through interaction with HDAC6

Project description:The activation of the NLRP3 inflammasome is spatiotemporally orchestrated by various organelles, but the precise roles of lysosomes are still unclear. Here we show the vital role of the Ragulator complex, a lysosomal protein, in NLRP3 inflammasome activation. Deficiency of Lamtor1, an essential component of the Ragulator complex, abrogated NLRP3 inflammasome activation in murine macrophage and human monocytic cells. Myeloid-specific Lamtor1-deficient mice showed remarkable attenuation of the severity of NLRP3-associated inflammatory diseases, including LPS-induced sepsis, alum-induced peritonitis, and monosodium urate (MSU)-induced arthritis. Mechanistically, Lamtor1 interacted with histone deacetylase 6 (HDAC6) during NLRP3 inflammasome activation, and this interaction augmented the interaction between the Ragulator complex and NLRP3. Lack of HDAC6 attenuated the interaction between Lamtor1 and NLRP3, resulting in insufficient NLRP3 inflammasome activation. Furthermore, DL-all-rac-α-tocopherol inhibited Lamtor1–HDAC6 interaction, resulting in diminished NLRP3 inflammasome activation. DL-all-rac-α-tocopherol alleviated acute gouty arthritis and MSU-induced peritonitis. Our results provide insight into the role of lysosomes in providing a platform for the activation of NLRP3 inflammasomes by the Ragulator complex.

2022-11-29 | PXD033497 | Pride

Comparative Analysis of murine tritosomal fractions after different starvation times

Project description:Lysosomal fractions were isolated following Triton WR1339 injection. Additionally, Mice weresubjected to food deprivation of 6 or 24 hours prior to sacrifice. Tritosome were labelled with TMT 10-plex

2024-11-18 | PXD047158 | Pride

Transcriptional control of lysosomal homeostasis by the disease-related CLN3 membrane protein

Project description:CLN3 is a type II transmembrane protein localized in the late endosomal/lysosomal compartment. A deficiency of CLN3 leads to the development of a certain type of Neuronal Ceroid Lipofuscinosis, a neurodegenerative disorder of childhood caused by aggregation of undegraded material in the lysosomal compartment. Cultured, immortalized wild type and Cln3(Δex7/8) cerebellar granule cells were used in this project to determine the influence of Cln3 deficiency on the proteome of the lysosomal compartment. For this purpose, cells were labelled by stable amino acid labelling in cell culture and lysosomes were isolated by magnetic beads.

2019-05-13 | PXD004548 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data