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

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
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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