Summary of Study ST002055

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 PR001300. The data can be accessed directly via it's Project DOI: 10.21228/M8P69K This work is supported by NIH grant, U2C- DK119886.

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Study IDST002055
Study TitleMetabolomic Profiling of Human Pluripotent Stem Cell Differentiation into Lung Progenitors
Study SummaryMetabolism is vital to cellular function and tissue homeostasis during human lung development. In utero, embryonic pluripotent stem cells undergo endodermal differentiation towards a lung progenitor cell fate that can be mimicked in vitro using induced human pluripotent stem cells (hiPSCs) to study genetic mutations. To identify differences between wild type and surfactant protein B (SFTPB)-deficient cell lines during endoderm specification towards lung, we used an untargeted metabolomics approach to evaluate the developmental changes in metabolites. We found that the metabolites most enriched during the differentiation from pluripotent stem cell to lung progenitor cell, regardless of cell line, were sphingomyelins and phosphatidylcholines, two important lipid classes in fetal lung development. The SFTPB mutation had no metabolic impact on early endodermal lung development. The identified metabolite signatures during lung progenitor cell differentiation may be utilized as biomarkers for normal embryonic lung development.
Institute
The Hospital for Sick Children
Last NamePost
First NameMartin
Address555 University Avenue
Emailmartin.post@sickkids.ca
Phone4168136772
Submit Date2021-06-29
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS/MS(Dir. Inf.)
Release Date2022-01-13
Release Version1
Martin Post Martin Post
https://dx.doi.org/10.21228/M8P69K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001300
Project DOI:doi: 10.21228/M8P69K
Project Title:Metabolomic Profiling of Human Pluripotent Stem Cell Differentiation into Lung Progenitors
Project Type:Developmental metabolites and Biomarker discovery
Project Summary:Metabolism is vital to cellular function and tissue homeostasis during human lung development. In utero, embryonic pluripotent stem cells undergo endodermal differentiation towards a lung progenitor cell fate that can be mimicked in vitro using induced human pluripotent stem cells (hiPSCs) to study genetic mutations. To identify differences between wild type and surfactant protein B (SFTPB)-deficient cell lines during endoderm specification towards lung, we used an untargeted metabolomics approach to evaluate the developmental changes in metabolites. We found that the metabolites most enriched during the differentiation from pluripotent stem cell to lung progenitor cell, regardless of cell line, were sphingomyelins and phosphatidylcholines, two important lipid classes in fetal lung development. The SFTPB mutation had no metabolic impact on early endodermal lung development. The identified metabolite signatures during lung progenitor cell differentiation may be utilized as biomarkers for normal embryonic lung development.
Institute:The Hospital for Sick Children
Last Name:Post
First Name:Martin
Address:555 University Avenue
Email:martin.post@sickkids.ca
Phone:4168136772

Subject:

Subject ID:SU002137
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 Differentiation stage
SA19372660 - ICE 12Anterior Foregut Endoderm
SA19372728 - NCRM1 12Anterior Foregut Endoderm
SA19372826 - NCRM1 10Anterior Foregut Endoderm
SA19372925 - NCRM1 9Anterior Foregut Endoderm
SA19373059 - ICE 11Anterior Foregut Endoderm
SA19373142 - ICD 10Anterior Foregut Endoderm
SA19373257 - ICE 9Anterior Foregut Endoderm
SA19373358 - ICE 10Anterior Foregut Endoderm
SA19373444 - ICD 12Anterior Foregut Endoderm
SA19373543 - ICD 11Anterior Foregut Endoderm
SA19373641 - ICD 9Anterior Foregut Endoderm
SA19373727 - NCRM1 11Anterior Foregut Endoderm
SA19373810 - CA1 10Anterior Foregut Endoderm
SA1937399 - CA1 9Anterior Foregut Endoderm
SA19374011 - CA1 11Anterior Foregut Endoderm
SA19374112 - CA1 12Anterior Foregut Endoderm
SA1937427 - CA1 7Definitive Endoderm
SA19374356 - ICE 8Definitive Endoderm
SA1937446 - CA1 6Definitive Endoderm
SA19374540 - ICD 8Definitive Endoderm
SA19374639 - ICD 7Definitive Endoderm
SA19374737 - ICD 5Definitive Endoderm
SA1937488 - CA1 8Definitive Endoderm
SA19374955 - ICE 7Definitive Endoderm
SA1937505 - CA1 5Definitive Endoderm
SA19375154 - ICE 6Definitive Endoderm
SA19375222 - NCRM1 6Definitive Endoderm
SA19375321 - NCRM1 5Definitive Endoderm
SA19375453 - ICE 5Definitive Endoderm
SA19375523 - NCRM1 7Definitive Endoderm
SA19375624 - NCRM1 8Definitive Endoderm
SA19375738 - ICD 6Definitive Endoderm
SA19377833 - ICD 1iPSC
SA19377920 - NCRM1 4iPSC
SA19378019 - NCRM1 3iPSC
SA19378118 - NCRM1 2iPSC
SA19378217 - NCRM1 1iPSC
SA19378334 - ICD 2iPSC
SA19378435 - ICD 3iPSC
SA19378551 - ICE 3iPSC
SA19378650 - ICE 2iPSC
SA19378749 - ICE 1iPSC
SA19378836 - ICD 4iPSC
SA19378952 - ICE 4iPSC
SA19375845 - ICD 13Lung Progenitor Cell
SA19375946 - ICD 14Lung Progenitor Cell
SA19376047 - ICD 15Lung Progenitor Cell
SA19376148 - ICD 16Lung Progenitor Cell
SA19376231 - NCRM1 15Lung Progenitor Cell
SA19376364 - ICE 16Lung Progenitor Cell
SA19376413 - CA1 13Lung Progenitor Cell
SA19376516 - CA1 16Lung Progenitor Cell
SA19376615 - CA1 15Lung Progenitor Cell
SA19376763 - ICE 15Lung Progenitor Cell
SA19376862 - ICE 14Lung Progenitor Cell
SA19376914 - CA1 14Lung Progenitor Cell
SA19377032 - NCRM1 16Lung Progenitor Cell
SA19377130 - NCRM1 14Lung Progenitor Cell
SA19377229 - NCRM1 13Lung Progenitor Cell
SA19377361 - ICE 13Lung Progenitor Cell
SA1937741 - CA1 1PSC
SA1937754 - CA1 4PSC
SA1937763 - CA1 3PSC
SA1937772 - CA1 2PSC
Showing results 1 to 64 of 64

Collection:

Collection ID:CO002130
Collection Summary:Samples were analyzed for 180 metabolites using the AbsoluteIDQ® p180 kit from Biocrates Life Sciences AG at the Analytical Facility for Bioactive Molecules (The Hospital for Sick Children, Toronto, Canada). Collected cell pellets were resuspended in 15 % ice-cold 10 mM Phosphate Buffer (PB) + 85 % EtOH as per AbsoluteIDQ® p180 kit protocol. Resuspended cells were subjected to three rounds of sonication and rapid freeze thawing. Final suspension was then centrifuged at 20,000 x g for 10 minutes at 4°C. A small aliquot was taken for protein assay, and the remainder of the supernatant was used for metabolic analysis. Samples, standards, and controls (10 mL each) were added to the Biocrates 96-well filter plate with internal standard, dried under nitrogen, derivatized with phenyl isothiocyanate, and then extracted with methanol, as per kit instructions.
Sample Type:human cells

Treatment:

Treatment ID:TR002149
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP002143
Sampleprep Summary:At each differentiation step, DE, AFE and LPC, cells were analyzed by FACS for stage specific markers. The differentiated cells were harvested with TrypLE at 37 °C for 5-10 minutes and collected by centrifugation at 300 g for 5 minutes at room temperature. The cell pellets were resuspended in 3% (v/v) FBS in PBS, cell aggregates were removed using a cell strainer with a 40-µm pore size and single cells were collected. For surface antigens, the cells were incubated with primary antibodies for 30 minutes on ice with gentle shaking, washed twice with 3% (v/v) FBS in PBS, and if necessary, incubated with the secondary antibodies for 30 minutes followed by two more rinses with 3% (v/v) FBS in PBS. For DE cells, we used PE conjugated mouse anti-human CXCR4 and APC conjugated mouse anti-human cKit antibodies; AFE cells were stained with PE-conjugated mouse anti-human CD56 and APC conjugated mouse anti-human CD271 antibodies and LPCs we identified using mouse anti-human CPM antibody. Alexa Fluor 488 donkey anti-mouse IgG was used as the secondary antibody against primary CPM antibody. The cells were either sorted using the BD aria FACS sorter at the Sick Kids FACS core and/or analyzed using a Beckman Coulter Gallios flow cytometer. Unstained controls were used to set up gates for FSC and SSC and double stained cells underwent fluorescence minus one (FMO) to ensure accurate gating. Sorted cells were collected and the spun down into a cell pellet and stored in -80C degrees for further processing. The endodermal differentiations and cell sorts were repeated at four different times with two biological repeats.

Combined analysis:

Analysis ID AN003346 AN003347
Analysis type MS MS
Chromatography type Reversed phase None (Direct infusion)
Chromatography system Agilent 1290 Infinity -
Column Agilent Eclipse XDB-C18 (100 x 3.0mm) -
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap ABI Sciex 5500 QTrap
Ion Mode POSITIVE UNSPECIFIED
Units uM uM

Chromatography:

Chromatography ID:CH002477
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent Eclipse XDB-C18 (100 x 3.0mm)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002478
Instrument Name:-
Column Name:-
Chromatography Type:None (Direct infusion)

MS:

MS ID:MS003115
Analysis ID:AN003346
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Analyst1.7 (Sciex); MetIDQ (Biocrates)
Ion Mode:POSITIVE
  
MS ID:MS003116
Analysis ID:AN003347
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Analyst1.7 (Sciex); MetIDQ (Biocrates)
Ion Mode:UNSPECIFIED
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