Summary of Study ST003162

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 PR001967. The data can be accessed directly via it's Project DOI: 10.21228/M8G72D This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 IDST003162
Study TitleLoss of dihydroceramide desaturase drives neurodegeneration by disrupting endoplasmic reticulum and lipid droplet homeostasis in glial cells
Study TypeUntargeted Metabolomics & Lipidomics
Study SummaryDihydroceramide desaturases convert dihydroceramides to ceramides, the precursors of all complex sphingolipids. Reduction of DEGS1 dihydroceramide desaturase function causes pediatric neurodegenerative disorder hypomyelinating leukodystrophy-18 (HLD-18). We discovered that infertile crescent (ifc), the Drosophila DEGS1 homolog, is expressed primarily in glial cells to promote CNS development by guarding against neurodegeneration. Loss of ifc causes massive dihydroceramide accumulation and severe morphological defects in cortex glia, including endoplasmic reticulum (ER) expansion, failure of neuronal ensheathment, and lipid droplet depletion. RNAi knockdown of the upstream ceramide synthase schlank in glia of ifc mutants rescues ER expansion, suggesting dihydroceramide accumulation in the ER drives this phenotype. RNAi knockdown of ifc in glia but not neurons drives neuronal cell death, suggesting that ifc function in glia promotes neuronal survival. Our work identifies glia as the primary site of disease progression in HLD-18 and may inform on juvenile forms of ALS, which also feature elevated dihydroceramide levels.
Institute
Washington University in St. Louis
DepartmentGenetics, Medicine, Chemistry
LaboratorySkeath and Patti Laboratories
Last NameCho
First NameKevin
Address1 Brookings Drive, Campus Box 1134, St. Louis, MO, 63130, USA
Emailkevin.cho@wustl.edu
Phone314-935-8813
Submit Date2024-04-09
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-04-12
Release Version1
Kevin Cho Kevin Cho
https://dx.doi.org/10.21228/M8G72D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001967
Project DOI:doi: 10.21228/M8G72D
Project Title:Loss of dihydroceramide desaturase drives neurodegeneration by disrupting endoplasmic reticulum and lipid droplet homeostasis in glial cells
Project Type:Untargeted Metabolomics and Lipidomics
Project Summary:Dihydroceramide desaturases convert dihydroceramides to ceramides, the precursors of all complex sphingolipids. Reduction of DEGS1 dihydroceramide desaturase function causes pediatric neurodegenerative disorder hypomyelinating leukodystrophy-18 (HLD-18). We discovered that infertile crescent (ifc), the Drosophila DEGS1 homolog, is expressed primarily in glial cells to promote CNS development by guarding against neurodegeneration. Loss of ifc causes massive dihydroceramide accumulation and severe morphological defects in cortex glia, including endoplasmic reticulum (ER) expansion, failure of neuronal ensheathment, and lipid droplet depletion. RNAi knockdown of the upstream ceramide synthase schlank in glia of ifc mutants rescues ER expansion, suggesting dihydroceramide accumulation in the ER drives this phenotype. RNAi knockdown of ifc in glia but not neurons drives neuronal cell death, suggesting that ifc function in glia promotes neuronal survival. Our work identifies glia as the primary site of disease progression in HLD-18 and may inform on juvenile forms of ALS, which also feature elevated dihydroceramide levels.
Institute:Washington University in St. Louis
Department:Genetics, Medicine, Chemistry
Laboratory:Skeath and Patti Laboratories
Last Name:Cho
First Name:Kevin
Address:1 Brookings Drive, Campus Box 1134, St. Louis, MO, 63130, USA
Email:kevin.cho@wustl.edu
Phone:314-935-8813

Subject:

Subject ID:SU003281
Subject Type:Insect
Subject Species:Drosophila melanogaster
Taxonomy ID:7227

Factors:

Subject type: Insect; Subject species: Drosophila melanogaster (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Sample source
SA342859CNS_RPLC_POS_ifc_5Knockout CNS
SA342860CNS_RPLC_POS_ifc_4Knockout CNS
SA342861CNS_RPLC_POS_ifc_2Knockout CNS
SA342862CNS_HILIC_NEG_ifc_1Knockout CNS
SA342863CNS_RPLC_POS_ifc_1Knockout CNS
SA342864CNS_HILIC_NEG_ifc_2Knockout CNS
SA342865CNS_HILIC_NEG_ifc_5Knockout CNS
SA342866CNS_HILIC_NEG_ifc_4Knockout CNS
SA342867CNS_HILIC_NEG_ifc_3Knockout CNS
SA342868CNS_RPLC_POS_ifc_3Knockout CNS
SA342869WL_HILIC_NEG_ifc_2Knockout Whole Larvae
SA342870WL_HILIC_NEG_ifc_5Knockout Whole Larvae
SA342871WL_RPLC_POS_ifc_1Knockout Whole Larvae
SA342872WL_HILIC_NEG_ifc_4Knockout Whole Larvae
SA342873WL_HILIC_NEG_ifc_3Knockout Whole Larvae
SA342874WL_HILIC_NEG_ifc_1Knockout Whole Larvae
SA342875WL_RPLC_POS_ifc_5Knockout Whole Larvae
SA342876WL_RPLC_POS_ifc_2Knockout Whole Larvae
SA342877WL_RPLC_POS_ifc_3Knockout Whole Larvae
SA342878WL_RPLC_POS_ifc_4Knockout Whole Larvae
SA342879CNS_HILIC_NEG_WT_2Wild-type CNS
SA342880CNS_RPLC_POS_WT_3Wild-type CNS
SA342881CNS_HILIC_NEG_WT_3Wild-type CNS
SA342882CNS_HILIC_NEG_WT_1Wild-type CNS
SA342883CNS_HILIC_NEG_WT_5Wild-type CNS
SA342884CNS_RPLC_POS_WT_4Wild-type CNS
SA342885CNS_RPLC_POS_WT_5Wild-type CNS
SA342886CNS_RPLC_POS_WT_2Wild-type CNS
SA342887CNS_RPLC_POS_WT_1Wild-type CNS
SA342888CNS_HILIC_NEG_WT_4Wild-type CNS
SA342889WL_HILIC_NEG_WT_4Wild-type Whole Larvae
SA342890WL_RPLC_POS_WT_3Wild-type Whole Larvae
SA342891WL_RPLC_POS_WT_4Wild-type Whole Larvae
SA342892WL_RPLC_POS_WT_5Wild-type Whole Larvae
SA342893WL_HILIC_NEG_WT_1Wild-type Whole Larvae
SA342894WL_HILIC_NEG_WT_2Wild-type Whole Larvae
SA342895WL_RPLC_POS_WT_2Wild-type Whole Larvae
SA342896WL_HILIC_NEG_WT_5Wild-type Whole Larvae
SA342897WL_HILIC_NEG_WT_3Wild-type Whole Larvae
SA342898WL_RPLC_POS_WT_1Wild-type Whole Larvae
Showing results 1 to 40 of 40

Collection:

Collection ID:CO003274
Collection Summary:Whole larvae and dissected CNS
Sample Type:Larvae, CNS

Treatment:

Treatment ID:TR003290
Treatment Summary:Untargeted lipidomics analysis was conducted on whole larva and dissected CNS of wild type and ifc-/- mutants at the late-third instar stage. Five replicates were prepared for each set of experiments. For whole larvae, at least 15 larvae of each genotype were used for each replicate. For the dissected CNS, at least 50 wild type and 60 ifc-/- CNS were used per replicate. Immediately following collection or dissection, larvae and the dissected CNS were flash frozen in liquid nitrogen and placed at -80°C.

Sample Preparation:

Sampleprep ID:SP003288
Sampleprep Summary:Whole larvae and CNS samples were extracted utilizing a tissue homogenizer, employing a solvent mixture of acetonitrile, methanol, and water in a 2:2:1 ratio, using 40 µL per mg of wet weight. The samples were then stored at -20°C overnight. Following centrifugation at 14,000 x g for 10 minutes at 4°C, the supernatant was transferred into an LC/MS vial and subsequently stored at -80°C until LC/MS analysis.

Combined analysis:

Analysis ID AN005187 AN005188 AN005189 AN005190
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Thermo Vanquish Flex UHPLC Systems Thermo Vanquish Flex UHPLC Systems Agilent 1290 Infinity II Agilent 1290 Infinity II
Column HILICON iHILIC-(P) Classic (100 x 2.1mm,5um) HILICON iHILIC-(P) Classic (100 x 2.1mm,5um) Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.7um) Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.7um)
MS Type ESI ESI ESI ESI
MS instrument type Orbitrap Orbitrap QTOF Orbitrap
MS instrument name Thermo Orbitrap ID-X Tribrid Thermo Orbitrap ID-X Tribrid Agilent 6545 QTOF Thermo Orbitrap ID-X Tribrid
Ion Mode NEGATIVE NEGATIVE POSITIVE POSITIVE
Units peak area peak area peak area peak area

Chromatography:

Chromatography ID:CH003924
Instrument Name:Thermo Vanquish Flex UHPLC Systems
Column Name:HILICON iHILIC-(P) Classic (100 x 2.1mm,5um)
Column Temperature:45
Flow Gradient:0–1 min: 90% B, 1–12 min: 90-35% B, 12–12.5 min: 35-25% B, 12.5–14.5 min: 25% B
Flow Rate:250 uL/min
Solvent A:water/acetonitrile (95/5); 20 mM ammonium bicarbonate; 0.1% ammonium hydroxide; 2.5 μM medronic acid
Solvent B:acetonitrile/water (95/5)
Chromatography Type:HILIC
  
Chromatography ID:CH003925
Instrument Name:Agilent 1290 Infinity II
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.7um)
Column Temperature:60
Flow Gradient:0-2min: 30% B, 2-17 min: 30%-75% B, 17-20 min: 75%-85% B, 20-23 min: 85%-100% B, 23-26 min: 100% B
Flow Rate:250 uL/min
Solvent A:acetronitrile/water (60/40); 10mM ammonium formate; 2.5 uM medronic acid; 0.1% formic acid
Solvent B:2-propanol/acetonitrile (90/10); 10mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004920
Analysis ID:AN005187
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were collected with the following MS source settings: spray voltage, -2.8 kV; sheath gas, 50; auxiliary gas, 10; sweep gas, 1; ion transfer tube temperature, 300°C; vaporizer temperature, 200°C; mass range, 67 – 1000 Da; resolution, 120,000; maximum injection time, 200 ms; isolation window, 1.6 Da. XCMS and Skyline software were used for data processing
Ion Mode:NEGATIVE
  
MS ID:MS004921
Analysis ID:AN005188
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were collected with the following MS source settings: spray voltage, -2.8 kV; sheath gas, 50; auxiliary gas, 10; sweep gas, 1; ion transfer tube temperature, 300°C; vaporizer temperature, 200°C; mass range, 67 – 1000 Da; resolution, 120,000; maximum injection time, 200 ms; isolation window, 1.6 Da. XCMS and Skyline software were used for data processing
Ion Mode:NEGATIVE
  
MS ID:MS004922
Analysis ID:AN005189
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:Data were collected with the following MS source settings: gas temp, 250°C; drying gas, 11 l/min; nebulizer, 35 psi; sheath gas temp, 300°C; sheath gas flow 12 l/min; capillary voltage, 3 kV; nozzle voltage, 500 V; isolation window, 1.3 Da. XCMS and Skyline software were used for data processing
Ion Mode:POSITIVE
  
MS ID:MS004923
Analysis ID:AN005190
Instrument Name:Thermo Orbitrap ID-X Tribrid
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Data were collected with the following MS source settings: spray voltage, -3 kV; sheath gas, 50; auxiliary gas, 10; sweep gas, 1; ion transfer tube temperature, 300°C; vaporizer temperature, 350°C; mass range, 100 – 1500 Da; resolution, 120,000; maximum injection time, 150 ms; isolation window, 1.6 Da. XCMS and Skyline software were used for data processing
Ion Mode:POSITIVE
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