Summary of Study ST004163

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002623. The data can be accessed directly via it's Project DOI: 10.21228/M8M26F This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST004163
Study TitleTargeted Lipid Profiling of HEK and iPSC derived iMG Cell Models with GBA1 Loss-of-Function
Study SummaryThe GBA1 gene encodes glucocerebrosidase (GCase), a lysosomal enzyme that degrades glucosylceramide and glucosylsphingosine, and whose dysfunction is linked to Gaucher disease and Parkinson’s disease. Targeted lipid profiling was performed in HEK (human embryonic kidney) cells and iPSC-derived iMG (microglial) cells with a GBA1 KO or loss-of-function variants E326K and L444P.
Institute
Denali Therapeutics
Last NameSuh
First NameJung
Address161 Oyster Point Blvd
Emailsuh@dnli.com
Phone+1 6507973837
Submit Date2025-08-29
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-09-02
Release Version1
Jung Suh Jung Suh
https://dx.doi.org/10.21228/M8M26F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002623
Project DOI:doi: 10.21228/M8M26F
Project Title:A Common PD-Risk GBA1 Variant Disrupts LIMP2 Interaction, Impairs Glucocerebrosidase Function, and Drives Lysosomal and Mitochondrial Dysfunction
Project Type:Preclinical Mouse and cellular studies
Project Summary:Variants in GBA1 cause Gaucher disease (GD) and are the most common genetic risk factor for Parkinson’s disease (PD). While some GBA1 variants are associated with both GD and PD, several coding mutations, including E326K, specifically confer risk for PD. The impact of these PD-specific variants on GCase activity and lysosomal and mitochondrial function relevant to PD remains poorly understood. We show the E326K variant reduces lysosomal GCase activity by impairing its delivery to lysosomes via altered interactions with its receptor, LIMP2. Structural analyses reveal that loss of a key salt bridge between E326 and R329 underlies disrupted GCase/LIMP2 interaction in cells, as reintroduction of a negative charge at R329 rescues LIMP2 binding. Functionally, the E326K variant produces greater deficits in PD-relevant pathways than GD-linked severe GCase LoF with effects reproduced in CNS cells and human E326K carriers, providing key insights into the nature of GCase dysfunction associated with GBA1-PD.
Institute:Denali Therapeutics
Last Name:Suh
First Name:Jung
Address:161 Oyster Point Blvd, South San Francisco, California, 94080, USA
Email:suh@dnli.com
Phone:+1 06507973837

Subject:

Subject ID:SU004314
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Treatment Sample type Sample source
SA481002HSA-000025515GBA1 KO none lysosome HEK293
SA481003HSA-000025516GBA1 KO none lysosome HEK293
SA481004HSA-000025541GBA1 KO none lysosome HEK293
SA481005HSA-000025527GBA1 KO none lysosome HEK293
SA481006HSA-000025539GBA1 KO none lysosome HEK293
SA481007HSA-000025528GBA1 KO none lysosome HEK293
SA481008HSA-000025517GBA1 KO none lysosome HEK293
SA481009HSA-000025540GBA1 KO none lysosome HEK293
SA481010HSA-000025529GBA1 KO none lysosome HEK293
SA481011HSA-000031088GBA1 KO none whole cell lysate HEK293
SA481012HSA-000031054GBA1 KO none whole cell lysate HEK293
SA481013HSA-000031102GBA1 KO none whole cell lysate HEK293
SA481014HSA-000031065GBA1 KO none whole cell lysate HEK293
SA481015HSA-000031078GBA1 KO none whole cell lysate HEK293
SA481016HSA-000031100GBA1 KO none whole cell lysate HEK293
SA481017HSA-000031066GBA1 KO none whole cell lysate HEK293
SA481018HSA-000031064GBA1 KO none whole cell lysate HEK293
SA481019HSA-000031076GBA1 KO none whole cell lysate HEK293
SA481020HSA-000031089GBA1 KO none whole cell lysate HEK293
SA481021HSA-000031077GBA1 KO none whole cell lysate HEK293
SA481022HSA-000031090GBA1 KO none whole cell lysate HEK293
SA481023HSA-000031053GBA1 KO none whole cell lysate HEK293
SA481024HSA-000031101GBA1 KO none whole cell lysate HEK293
SA481025HSA-000031052GBA1 KO none whole cell lysate HEK293
SA481026HSA-000038235GBA1 KO none whole cell lysate iMG
SA481027HSA-000038247GBA1 KO none whole cell lysate iMG
SA481028HSA-000038242GBA1 KO none whole cell lysate iMG
SA481029HSA-000038248GBA1 KO none whole cell lysate iMG
SA481030HSA-000038236GBA1 KO none whole cell lysate iMG
SA481031HSA-000038241GBA1 KO none whole cell lysate iMG
SA481032HSA-000037551GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481033HSA-000037555GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481034HSA-000037547GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481035HSA-000037561GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481036HSA-000037558GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481037HSA-000037548GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481038HSA-000037557GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481039HSA-000037556GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481040HSA-000037560GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481041HSA-000037552GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481042HSA-000037553GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481043HSA-000037559GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481044HSA-000037554GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481045HSA-000037549GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481046HSA-000037550GBA1-p.E326K imiglucerase whole cell lysate HEK293
SA481047HSA-000025522GBA1-p.E326K none lysosome HEK293
SA481048HSA-000025511GBA1-p.E326K none lysosome HEK293
SA481049HSA-000025534GBA1-p.E326K none lysosome HEK293
SA481050HSA-000025509GBA1-p.E326K none lysosome HEK293
SA481051HSA-000025510GBA1-p.E326K none lysosome HEK293
SA481052HSA-000025533GBA1-p.E326K none lysosome HEK293
SA481053HSA-000025521GBA1-p.E326K none lysosome HEK293
SA481054HSA-000025523GBA1-p.E326K none lysosome HEK293
SA481055HSA-000025535GBA1-p.E326K none lysosome HEK293
SA481056HSA-000031048GBA1-p.E326K none whole cell lysate HEK293
SA481057HSA-000031095GBA1-p.E326K none whole cell lysate HEK293
SA481058HSA-000037527GBA1-p.E326K none whole cell lysate HEK293
SA481059HSA-000037525GBA1-p.E326K none whole cell lysate HEK293
SA481060HSA-000031096GBA1-p.E326K none whole cell lysate HEK293
SA481061HSA-000031094GBA1-p.E326K none whole cell lysate HEK293
SA481062HSA-000037529GBA1-p.E326K none whole cell lysate HEK293
SA481063HSA-000037526GBA1-p.E326K none whole cell lysate HEK293
SA481064HSA-000031060GBA1-p.E326K none whole cell lysate HEK293
SA481065HSA-000037518GBA1-p.E326K none whole cell lysate HEK293
SA481066HSA-000031059GBA1-p.E326K none whole cell lysate HEK293
SA481067HSA-000037523GBA1-p.E326K none whole cell lysate HEK293
SA481068HSA-000037519GBA1-p.E326K none whole cell lysate HEK293
SA481069HSA-000037521GBA1-p.E326K none whole cell lysate HEK293
SA481070HSA-000037520GBA1-p.E326K none whole cell lysate HEK293
SA481071HSA-000031046GBA1-p.E326K none whole cell lysate HEK293
SA481072HSA-000037530GBA1-p.E326K none whole cell lysate HEK293
SA481073HSA-000037524GBA1-p.E326K none whole cell lysate HEK293
SA481074HSA-000037531GBA1-p.E326K none whole cell lysate HEK293
SA481075HSA-000037528GBA1-p.E326K none whole cell lysate HEK293
SA481076HSA-000037522GBA1-p.E326K none whole cell lysate HEK293
SA481077HSA-000037517GBA1-p.E326K none whole cell lysate HEK293
SA481078HSA-000031058GBA1-p.E326K none whole cell lysate HEK293
SA481079HSA-000031082GBA1-p.E326K none whole cell lysate HEK293
SA481080HSA-000031071GBA1-p.E326K none whole cell lysate HEK293
SA481081HSA-000031070GBA1-p.E326K none whole cell lysate HEK293
SA481082HSA-000031083GBA1-p.E326K none whole cell lysate HEK293
SA481083HSA-000031084GBA1-p.E326K none whole cell lysate HEK293
SA481084HSA-000031047GBA1-p.E326K none whole cell lysate HEK293
SA481085HSA-000031072GBA1-p.E326K none whole cell lysate HEK293
SA481086HSA-000038234GBA1-p.E326K none whole cell lysate iMG
SA481087HSA-000038233GBA1-p.E326K none whole cell lysate iMG
SA481088HSA-000038245GBA1-p.E326K none whole cell lysate iMG
SA481089HSA-000038239GBA1-p.E326K none whole cell lysate iMG
SA481090HSA-000038246GBA1-p.E326K none whole cell lysate iMG
SA481091HSA-000038240GBA1-p.E326K none whole cell lysate iMG
SA481092HSA-000025525GBA1-p.L444P none lysosome HEK293
SA481093HSA-000025536GBA1-p.L444P none lysosome HEK293
SA481094HSA-000025514GBA1-p.L444P none lysosome HEK293
SA481095HSA-000025513GBA1-p.L444P none lysosome HEK293
SA481096HSA-000025512GBA1-p.L444P none lysosome HEK293
SA481097HSA-000025526GBA1-p.L444P none lysosome HEK293
SA481098HSA-000025538GBA1-p.L444P none lysosome HEK293
SA481099HSA-000025524GBA1-p.L444P none lysosome HEK293
SA481100HSA-000025537GBA1-p.L444P none lysosome HEK293
SA481101HSA-000031085GBA1-p.L444P none whole cell lysate HEK293
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Collection:

Collection ID:CO004307
Collection Summary:HEK and iPSC derived iMG cells were harvested by aspirating medium then briefly washed with 1mL of ice-cold 0.9% saline solution and directly processed for lipidomic analysis. Lysosomes were isolated from HEK cells stably over-expressing the TMEM192-HAx3 tag. Cells were harvested and resuspended in KPBS+ buffer and then fractionated by passing the suspension through a 23g needle five total times. Intact nuclei and other heavy membranes were pelleted by centrifugation (800g, 10min), and lysosomes were immunoprecipitated from the resulting post-nuclear supernatant (PNS) by incubation with anti-HA magnetic beads (Thermo, 88837) with end-over-end rotation for 15 minutes. Lysosome-bound beads were washed 2x with KPBS+ buffer and 2x with KPBS buffer (3-minute incubation with end-over-end rotation in each wash). Lysosomes were eluted from beads for immunoblotting by resuspending beads in NuPAGE LDS sample buffer + NuPAGE Sample Reducing Agent, followed by incubation at 95ºC for 10 minutes. Lysosomes were eluted from beads for proteomic analysis by incubation in PBS supplemented with 5% SDS, with 2000rpm shaking for 15 minutes at room temperature. Lysosomal lipids were eluted from the beads and directly processed for lipidomic analysis.
Sample Type:HEK cells, iMG cells
Storage Conditions:-80℃
Collection Vials:Lobind 1.5 mL Eppendorf tubes
Storage Vials:Lobind 1.5 mL Eppendorf tubes

Treatment:

Treatment ID:TR004323
Treatment Summary:No treatment. Cells were treated for 72 hours with PBS or imiglucerase, followed by lipid extraction.

Sample Preparation:

Sampleprep ID:SP004320
Sampleprep Summary:Cells were harvested by aspirating medium then briefly washed with 1mL of ice-cold 0.9% saline solution. Cells and lysosomal fractions were directly lysed and extracted in 400 µL 9:1 methanol:water containing stable-isotope internal standards for 20 min at 4°C with shaking followed by 21,000 x g spin at 4°C for 5 min from which the supernatant was distributed for the LC-MS/MS analyses.
Processing Storage Conditions:On ice
Extract Storage:-20℃

Chromatography:

Chromatography ID:CH005247
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:55
Flow Gradient:0.0-8.0 min from 45% B to 99% B, 8.0-9.0 min at 99% B, 9.0-9.1 min to 45% B, and 9.1-10.0 min at 45% B.
Flow Rate:0.25 mL/min
Sample Injection:5
Solvent A:60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid
Solvent B:90% isopropyl alcohol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH005248
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um)
Column Temperature:55
Flow Gradient:0.0-8.0 min from 45% B to 99% B, 8.0-9.0 min at 99% B, 9.0-9.1 min to 45% B, and 9.1-10.0 min at 45% B.
Flow Rate:0.25 mL/min
Sample Injection:5
Solvent A:60% acetonitrile/40% water; 10 mM ammonium acetate; 0.1% acetic acid
Solvent B:90% isopropyl alcohol/10% acetonitrile; 10 mM ammonium acetate; 0.1% acetic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH005249
Instrument Name:Agilent 1290 Infinity II
Column Name:Advanced Materials Technology HALO HILIC column (150 x 3.0 mm, 2um); #91813
Column Temperature:45
Flow Gradient:0.0–2.0 min, 100% B; 2.1 min, 95% B; 4.5 min, 85% B; held at 85% B until 6.0 min; 6.1 min, 0% B; held at 0% B until 8.5 min
Flow Rate:0.45 mL/min
Sample Injection:8
Solvent A:92.5% acetonitrile/5% isopropanol/2.5% water; 5 mM ammonium formate; 0.5% formic acid
Solvent B:92.5% water/5% isopropanol/2.5% acetonitrile; 5 mM ammonium formate; 0.5% formic acid
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006908
Analysis Type:MS
Chromatography ID:CH005247
Num Factors:17
Num Metabolites:140
Units:normalized peak area
  
Analysis ID:AN006909
Analysis Type:MS
Chromatography ID:CH005248
Num Factors:17
Num Metabolites:118
Units:normalized peak area
  
Analysis ID:AN006910
Analysis Type:MS
Chromatography ID:CH005248
Num Factors:17
Num Metabolites:15
Units:normalized peak area
  
Analysis ID:AN006911
Analysis Type:MS
Chromatography ID:CH005249
Num Factors:17
Num Metabolites:39
Units:normalized peak area
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