Summary of Study ST002284

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 PR001464. The data can be accessed directly via it's Project DOI: 10.21228/M8GT5D 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 IDST002284
Study TitleGenetically defined human GBM organoids reveal principles of GBM development and actionable targets
Study SummaryRecent advances in glioblastoma (GBM) studies provide a comprehensive catalog of its genetic aberrations and cellular heterogeneity. However, a solid understanding of genotype-based analysis of cancer pathway dependency and actionable target identification is required to transform GBM treatment into a personalized era. Here, we generated a spectrum of mutant iPSCs harboring frequent GBM mutations with CRISPR/Cas9 and profiled the organoids (LEGO: Laboratory Engineered Glioblastoma Organoid) derived from these iPSCs temporally on transcriptome, methylome, metabolome, lipidome, proteome, and phospho-proteome levels. We found that LEGOs form brain tumors in vivo and recapitulate critical features of human GBM. The multi-omics analysis discovered essential milestones driven by genetic heterogeneity during GBM progressions, such as lineage alteration, methylome rewriting, and metabolome/lipidome reprogramming, in concordance with altered pathway activity and drug response. This study provides a tool and research path to realizing genome-based personalized GBM therapy using novel advanced models.
Institute
DKFZ
DepartmentMolecular Neurogenetics
LaboratoryMolecular Neurogenetics
Last NameWang
First NameChangwen
AddressIm Neuenheimer Feld 581
Emailc.wang@dkfz-heidelberg.de
Phone+49 6221 42 3455
Submit Date2022-09-17
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2024-01-26
Release Version1
Changwen Wang Changwen Wang
https://dx.doi.org/10.21228/M8GT5D
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001464
Project DOI:doi: 10.21228/M8GT5D
Project Title:Comparing water-soluble metabolites and lipid changes on human organoids and corresponding culture medium with different genotypes at different culturing stages
Project Summary:Quantitative metabolome and lipidome analysis of human brain organoids with different genetic mutations. Water-soluble metabolites were extracted from 1- and 4-month-old WT, PT, PTCC, and PTN organoids and their respective culture medium.
Institute:DKFZ
Department:Molecular Neurogenetics
Laboratory:Molecular Neurogenetics
Last Name:Wang
First Name:Changwen
Address:Im Neuenheimer Feld 581, Heidelberg, Baden-Wurttemberg, 69120, Germany
Email:c.wang@dkfz-heidelberg.de
Phone:+49 6221 42 3455
Publications:https://www.nature.com/articles/s41698-024-00500-5, https://pubmed.ncbi.nlm.nih.gov/38273014/

Subject:

Subject ID:SU002370
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Species Group:Mammals

Factors:

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

mb_sample_id local_sample_id Genotype Age Extracted Sample
SA218667LS21_049_Med_Lip_S22_1m_woCells_2"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218668LS21_049_Med_Lip_S23_1m_woCells_3"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218669LS21_049_Med_Lip_S24_1m_woCells_4"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218670LS21_049_Med_Lip_S21_1m_woCells_1"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218671LS21_049_Med_S21_1m_woCells_1"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218672LS21_049_Med_S22_1m_woCells_2"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218673LS21_049_Med_S25_1m_woCells_5"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218674LS21_049_Med_S24_1m_woCells_4"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218675LS21_049_Med_S23_1m_woCells_3"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218676LS21_049_Med_Lip_S25_1m_woCells_5"NA, blank medium control" "NA, same batch medium as 1-month-old" Culture medium
SA218677LS21_049_Med_Lip_S46_4m_woCells_1"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218678LS21_049_Med_S46_4m_woCells_1"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218679LS21_049_Med_Lip_S47_4m_woCells_2"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218680LS21_049_Med_S50_4m_woCells_5"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218681LS21_049_Med_Lip_S50_4m_woCells_5"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218682LS21_049_Med_Lip_S49_4m_woCells_4"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218683LS21_049_Med_Lip_S48_4m_woCells_3"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218684LS21_049_Med_S47_4m_woCells_2"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218685LS21_049_Med_S49_4m_woCells_4"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218686LS21_049_Med_S48_4m_woCells_3"NA, blank medium control" "NA, same batch medium as 4-month-old" Culture medium
SA218727LS21_049_Med_S12_1m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218728LS21_049_Med_S13_1m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218729LS21_049_Med_Lip_S12_1m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218730LS21_049_Med_Lip_S13_1m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218731LS21_049_Med_Lip_S15_1m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218732LS21_049_Med_Lip_S14_1m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218733LS21_049_Med_S14_1m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218734LS21_049_Med_Lip_S11_1m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218735LS21_049_Med_S15_1m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218736LS21_049_Med_S11_1m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Culture medium
SA218737LS21_049_Org_S14_1m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218738LS21_049_Org_S13_1m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218739LS21_049_Org_S12_1m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218740LS21_049_Org_S11_1m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218741LS21_049_Org_S15_1m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218742LS21_049_Lip_Org_S14_1m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218743LS21_049_Lip_Org_S13_1m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218744LS21_049_Lip_Org_S15_1m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218745LS21_049_Lip_Org_S12_1m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218746LS21_049_Lip_Org_S11_1m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 1-month-old Organoid
SA218747LS21_049_Med_Lip_S37_4m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218748LS21_049_Med_Lip_S36_4m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218749LS21_049_Med_S36_4m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218750LS21_049_Med_S38_4m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218751LS21_049_Med_S37_4m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218752LS21_049_Med_Lip_S38_4m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218753LS21_049_Med_Lip_S40_4m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218754LS21_049_Med_S39_4m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218755LS21_049_Med_Lip_S39_4m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218756LS21_049_Med_S40_4m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Culture medium
SA218757LS21_049_Org_S35_4m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218758LS21_049_Org_S33_4m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218759LS21_049_Lip_Org_S32_4m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218760LS21_049_Org_S34_4m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218761LS21_049_Lip_Org_S34_4m_PTCC_4PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218762LS21_049_Lip_Org_S33_4m_PTCC_3PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218763LS21_049_Org_S32_4m_PTCC_2PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218764LS21_049_Org_S31_4m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218765LS21_049_Lip_Org_S35_4m_PTCC_5PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218766LS21_049_Lip_Org_S31_4m_PTCC_1PTCC; PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/- 4-month-old Organoid
SA218767LS21_049_Med_Lip_S16_1m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218768LS21_049_Med_Lip_S19_1m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218769LS21_049_Med_Lip_S17_1m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218770LS21_049_Med_Lip_S18_1m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218771LS21_049_Med_S20_1m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218772LS21_049_Med_S18_1m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218773LS21_049_Med_S19_1m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218774LS21_049_Med_Lip_S20_1m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218775LS21_049_Med_S17_1m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218776LS21_049_Med_S16_1m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Culture medium
SA218777LS21_049_Org_S20_1m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218778LS21_049_Org_S19_1m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218779LS21_049_Org_S18_1m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218780LS21_049_Lip_Org_S18_1m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218781LS21_049_Org_S16_1m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218782LS21_049_Org_S17_1m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218783LS21_049_Lip_Org_S17_1m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218784LS21_049_Lip_Org_S16_1m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218785LS21_049_Lip_Org_S19_1m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218786LS21_049_Lip_Org_S20_1m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 1-month-old Organoid
SA218787LS21_049_Med_Lip_S44_4m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218788LS21_049_Med_Lip_S43_4m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218789LS21_049_Med_S43_4m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218790LS21_049_Med_Lip_S45_4m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218791LS21_049_Med_S44_4m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218792LS21_049_Med_Lip_S42_4m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218793LS21_049_Med_S45_4m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218794LS21_049_Med_Lip_S41_4m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218795LS21_049_Med_S41_4m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218796LS21_049_Med_S42_4m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Culture medium
SA218797LS21_049_Org_S36_4m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218798LS21_049_Org_S37_4m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218799LS21_049_Lip_Org_S37_4m_PTN_2PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218800LS21_049_Org_S38_4m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218801LS21_049_Org_S39_4m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218802LS21_049_Org_S40_4m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218803LS21_049_Lip_Org_S38_4m_PTN_3PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218804LS21_049_Lip_Org_S36_4m_PTN_1PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218805LS21_049_Lip_Org_S39_4m_PTN_4PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
SA218806LS21_049_Lip_Org_S40_4m_PTN_5PTN; PTEN-/-; TP53-/-; NF1-/- 4-month-old Organoid
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Collection:

Collection ID:CO002363
Collection Summary:Organoid samples were quickly washed with 154 mM ammonium acetate on ice and snap-frozen in liquid nitrogen. The medium samples were collected from each well and snap-frozen in liquid nitrogen. All samples were stored at -80°C before extraction.
Sample Type:Organoid
Storage Conditions:-80℃

Treatment:

Treatment ID:TR002382
Treatment Summary:Not applicable

Sample Preparation:

Sampleprep ID:SP002376
Sampleprep Summary:Water-soluble metabolites and lipids were extracted from the organoids and corresponding culture medium. Details are described in the Sampleprep Protocol Files (WSplusLipid.pdf)

Combined analysis:

Analysis ID AN003732 AN003733
Chromatography ID CH002765 CH002765
MS ID MS003480 MS003481
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Thermo Accucore HILIC (100 x 2.1mm,2.6um) Thermo Accucore HILIC (100 x 2.1mm,2.6um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode POSITIVE NEGATIVE
Units peak intensity peak intensity

Chromatography:

Chromatography ID:CH002765
Methods Filename:WSplusLipid.pdf
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Thermo Accucore HILIC (100 x 2.1mm,2.6um)
Chromatography Type:HILIC

MS:

MS ID:MS003480
Analysis ID:AN003732
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:-
Ion Mode:POSITIVE
Analysis Protocol File:WSplusLipid.pdf
  
MS ID:MS003481
Analysis ID:AN003733
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:-
Ion Mode:NEGATIVE
Analysis Protocol File:WSplusLipid.pdf
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