Summary of Study ST002070

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 PR001312. The data can be accessed directly via it's Project DOI: 10.21228/M8499N 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 IDST002070
Study TitleLipidomic Comparison of 2D and 3D Colon Cancer Cell Culture Models
Study TypeUntargeted Lipidomics
Study SummaryAltered lipid metabolism is one of the hallmarks of cancer. Cellular proliferation and de novo synthesis of lipids are related to cancer progression. In this study, we evaluated the lipidomic profile of two-dimensional (2D) monolayer and multicellular tumor spheroids from the HCT 116 colon carcinoma cell line. We utilized serial trypsinization on the spheroid samples to generate three cellular populations representing the proliferative, quiescent, and necrotic regions of the spheroid. This analysis enabled a comprehensive identification and quantification of lipids produced in each of the spheroid layer and 2D cultures. We show that lipid subclasses associated with lipid droplets form in oxygen-restricted and acidic regions of spheroids and are produced at higher levels than in 2D cultures. Additionally, sphingolipid production, which is implicated in cell death and survival pathways, is higher in spheroids relative to 2D cells. Finally, we show that increased numbers of lipids comprised of polyunsaturated fatty acids (PUFAs) are produced in the quiescent and necrotic regions of the spheroid. The lipidomic signature for each region and cell culture type highlights the importance of understanding the spatial aspects of cancer biology. These results provide additional lipid biomarkers in the tumor microenvironment that can be further studied during potential therapeutic studies which target pivotal lipid production pathways.
Institute
The Ohio State University
Last NameTobias
First NameFernando
Address100 W 18th Avenue, Columbus, Ohio, 43210, USA
Emailtobias.62@osu.edu
Phone12345678907
Submit Date2022-01-30
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2022-02-14
Release Version1
Fernando Tobias Fernando Tobias
https://dx.doi.org/10.21228/M8499N
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001312
Project DOI:doi: 10.21228/M8499N
Project Title:Lipidomic Comparison of 2D and 3D Colon Cancer Cell Culture Models
Project Type:Untargeted Lipidomics
Project Summary:Altered lipid metabolism is one of the hallmarks of cancer. Cellular proliferation and de novo synthesis of lipids are related to cancer progression. In this study, we evaluated the lipidomic profile of two-dimensional (2D) monolayer and multicellular tumor spheroids from the HCT 116 colon carcinoma cell line. We utilized serial trypsinization on the spheroid samples to generate three cellular populations representing the proliferative, quiescent, and necrotic regions of the spheroid. This analysis enabled a comprehensive identification and quantification of lipids produced in each of the spheroid layer and 2D cultures. We show that lipid subclasses associated with lipid droplets form in oxygen-restricted and acidic regions of spheroids and are produced at higher levels than in 2D cultures. Additionally, sphingolipid production, which is implicated in cell death and survival pathways, is higher in spheroids relative to 2D cells. Finally, we show that increased numbers of lipids comprised of polyunsaturated fatty acids (PUFAs) are produced in the quiescent and necrotic regions of the spheroid. The lipidomic signature for each region and cell culture type highlights the importance of understanding the spatial aspects of cancer biology. These results provide additional lipid biomarkers in the tumor microenvironment that can be further studied during potential therapeutic studies which target pivotal lipid production pathways.
Institute:The Ohio State University
Department:Department of Chemistry and Biochemistry
Laboratory:Amanda B Hummon Research Group
Last Name:Tobias
First Name:Fernando
Address:100 W 18th Avenue, Columbus, Ohio, 43210, USA
Email:tobias.62@osu.edu
Phone:1234567890

Subject:

Subject ID:SU002152
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male
Cell Strain Details:HCT 116
Subject Comments:HCT 116 cell line was cultured as a 2D monolayer and 3D spheroids

Factors:

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

mb_sample_id local_sample_id GROUP TYPE
SA19471223 2D12D1_2 2D
SA19471341 2D12D1_3 2D
SA1947145 2D12D1 2D
SA1947159 2D22D2_1 2D
SA19472327 2D22D_2_2 2D
SA19471645 2D22D2_3 2D
SA19471714 2D32D3_1 2D
SA19471832 2D32D3_2 2D
SA19471950 2D32D3_3 2D
SA19472018 2D42D4_1 2D
SA19472136 2D42D4_2 2D
SA19472254 2D42D4_3 2D
SA1947248 P1CCore1_1 SPHEROID
SA19473526 P1CCore_1_2 SPHEROID
SA19472544 P1CCore1_3 SPHEROID
SA19472612 P2CCore2_1 SPHEROID
SA19472730 P2CCore2_2 SPHEROID
SA19472848 P2CCore2_3 SPHEROID
SA19472917 P3CCore3_1 SPHEROID
SA19473035 P3CCore3_2 SPHEROID
SA19473153 P3CCore3_3 SPHEROID
SA19473221 P4CCore4_1 SPHEROID
SA19473339 P4CCore4_2 SPHEROID
SA19473457 P4CCore4_3 SPHEROID
SA1947367 P1MMiddle1_1 SPHEROID
SA19473725 P1MMiddle1_2 SPHEROID
SA19473843 P1MMiddle1_3 SPHEROID
SA19473911 P2MMiddle2_1 SPHEROID
SA19474029 P2MMiddle2_2 SPHEROID
SA19474147 P2MMiddle2_3 SPHEROID
SA19474216 P3MMiddle3_1 SPHEROID
SA19474334 P3MMiddle3_2 SPHEROID
SA19474452 P3MMiddle3_3 SPHEROID
SA19474520 P4MMiddle4_1 SPHEROID
SA19474638 P4MMiddle4_2 SPHEROID
SA19474756 P4MMiddle4_3 SPHEROID
SA1947486 P1OOuter1_1 SPHEROID
SA19474942 P1OOuter1_3 SPHEROID
SA19475010 P2OOuter2_1 SPHEROID
SA19475128 P2OOuter2_2 SPHEROID
SA19475246 P2OOuter2_3 SPHEROID
SA19475924 P1OOuter_2 SPHEROID
SA19475315 P3OOuter3_1 SPHEROID
SA19475433 P3OOuter3_2 SPHEROID
SA19475551 P3OOuter3_3 SPHEROID
SA19475619 P4OOuter4_1 SPHEROID
SA19475737 P4OOuter4_2 SPHEROID
SA19475855 P4OOuter4_3 SPHEROID
SA19476059 QC20QC10 QC
SA19476160 QC40QC11 QC
SA1947622 QC10QC1 QC
SA1947633 QC20QC2 QC
SA1947644 QC40QC3 QC
SA19476513 QC10QC4 QC
SA19476622 QC20QC5 QC
SA19476731 QC40QC6 QC
SA19476840 QC20QC7 QC
SA19476949 QC40QC8 QC
SA19477058 QC10QC9 QC
Showing results 1 to 59 of 59

Collection:

Collection ID:CO002145
Collection Summary:Cell Lysates from 2D Monolayers and serially-trypsinized spheroids was subjected to lipid extraction
Sample Type:Cultured cells
Storage Conditions:-80℃
Collection Tube Temp:4
Additives:1X PBS

Treatment:

Treatment ID:TR002164
Treatment Summary:HCT 116 2D monolayers were cultured per ATCC protocol, while HCT 116 3D spheroids were cultured for 14 days. At Day 14, the spheroids were subjected to Serial Trypsinization in order to obtain discrete cell populations from spheroids representing the outer, middle, and core regions.

Sample Preparation:

Sampleprep ID:SP002158
Sampleprep Summary:Lipid extraction by MTBE/methanol/water solvent system
Processing Storage Conditions:On ice
Extraction Method:liquid-liquid extraction
Extract Storage:-80℃
Sample Resuspension:9:1 Methanol/Toluene
Sample Spiking:equiSPLASH LIPIDOMIX standards

Combined analysis:

Analysis ID AN003374 AN003375
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1260 Agilent 1260
Column Thermo Accucore C30 (100 x 2.1mm,2.6um) Thermo Accucore C30 (100 x 2.1mm,2.6um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6545 QTOF Agilent 6545 QTOF
Ion Mode POSITIVE NEGATIVE
Units pmol lipid/ ug protein pmol lipid/ ug protein

Chromatography:

Chromatography ID:CH002494
Instrument Name:Agilent 1260
Column Name:Thermo Accucore C30 (100 x 2.1mm,2.6um)
Column Temperature:50
Flow Rate:400uL/min
Injection Temperature:4
Internal Standard:equiSPLASH LIPIDOMIX
Sample Injection:2
Solvent A:50% water/50% acetonitrile; 10mM ammonium formate
Solvent B:90% isopropanol/10% acetonitrile; 10 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS003141
Analysis ID:AN003374
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS-Only on biological samples, Auto-MSMS on Pooled Sample
Ion Mode:POSITIVE
  
MS ID:MS003142
Analysis ID:AN003375
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:MS-Only on biological samples, Auto-MSMS on Pooled Sample
Ion Mode:NEGATIVE
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