Summary of Study ST001527

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 PR001028. The data can be accessed directly via it's Project DOI: 10.21228/M8T99V This work is supported by NIH grant, U2C- DK119886.

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Study IDST001527
Study TitleLung cancer metabolomics analysis
Study SummaryThis study explored models predictive of staging and chemotherapy response based on metabolomic analysis of fresh, patient-derived non-small cell lung cancer (NSCLC) core biopsies. Prospectively collected tissue samples before initial treatment were evaluated with high-resolution 2DLC-MS/MS and 13C-glucose enrichment, and the data were comprehensively analyzed with machine learning techniques. Patients were categorized as Disease-Control (DC) [encompassing complete-response (CR), partial-response (PR), and stable-disease (SD)] and Progressive-Disease (PD). Four major types of learning methods (partial least squares discriminant analysis (PLS-DA), support vector machines (SVM), artificial neural networks, and random forests) were applied to differentiate between positive (DC and CR/PR) and poor (PD and SD/PD) responses, and between stage I/II/III and stage IV disease. Models were trained with forward feature selection based on variable importance and tested on validation subsets.
Institute
University of Louisville
DepartmentBioengineering
Last NameFrieboes
First NameHermann
AddressLutz Hall 419
Emailhbfrie01@louisville.edu
Phone502-852-3302
Submit Date2020-09-16
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-08-01
Release Version1
Hermann Frieboes Hermann Frieboes
https://dx.doi.org/10.21228/M8T99V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001028
Project DOI:doi: 10.21228/M8T99V
Project Title:Lung cancer metabolomics analysis
Project Type:MS untargeted analysis
Project Summary:This study explored models predictive of staging and chemotherapy response based on metabolomic analysis of fresh, patient-derived non-small cell lung cancer (NSCLC) core biopsies. Prospectively collected tissue samples before initial treatment were evaluated with high-resolution 2DLC-MS/MS and the data were comprehensively analyzed with machine learning techniques. Patients were categorized as Disease-Control (DC) [encompassing complete-response (CR), partial-response (PR), and stable-disease (SD)] and Progressive-Disease (PD). Four major types of learning methods (partial least squares discriminant analysis (PLS-DA), support vector machines (SVM), artificial neural networks, and random forests) were applied to differentiate between positive (DC and CR/PR) and poor (PD and SD/PD) responses, and between stage I/II/III and stage IV disease. Models were trained with forward feature selection based on variable importance and tested on validation subsets.
Institute:University of Louisville
Department:Bioengineering
Last Name:Frieboes
First Name:Hermann
Address:Lutz Hall 419
Email:hbfrie01@louisville.edu
Phone:502-852-3302
Funding Source:NIH/NCI R15CA203605

Subject:

Subject ID:SU001601
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

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

mb_sample_id local_sample_id Tumor_staging_before_chemo Chemo_response_numeric
SA128667CDSR01292-01_neg1 -
SA128668N032_neg1 -
SA128669N023_pos1 -
SA128670N032_pos1 -
SA128671N023_neg1 -
SA128672CDSR01292-01_pos1 -
SA128673CDSR00861_01_pos1 1
SA128674CDSR00861_01_neg1 1
SA128675N026_pos1 1
SA128676N026_neg1 1
SA128677CDSR01154-01_pos1 3
SA128678CDSR01154-01_neg1 3
SA128679CDSR01257-01_pos2 -
SA128680CDSR01257-01_neg2 -
SA128681N039_neg2 -
SA128682N051_pos2 -
SA128683N039_pos2 -
SA128684N051_neg2 -
SA128685CDSR01092-01_pos2 1
SA128686CDSR01092-01_neg2 1
SA128687CDSR00877_01_pos2 2
SA128688CDSR00877_01_neg2 2
SA128689CDSR01563-01_pos3 -
SA128690CDSR01563-01_neg3 -
SA128691CDSR01197-01_pos3 -
SA128692CDSR01197-01_neg3 -
SA128693N010_neg3 2
SA128694N020_neg3 2
SA128695N020_pos3 2
SA128696N003_pos3 2
SA128697N003_neg3 2
SA128698N010_pos3 2
SA128699CDSR01256-01_pos3 3
SA128700CDSR01382-01_pos3 3
SA128701CDSR00894_01_neg3 3
SA128702CDSR01042_01_pos3 3
SA128703CDSR01042_01_neg3 3
SA128704N034_pos3 3
SA128705CDSR01382-01_neg3 3
SA128706N034_neg3 3
SA128707CDSR00894_01_pos3 3
SA128708CDSR01256-01_neg3 3
SA128709CDSR01155-01_neg3 4
SA128710CDSR01155-01_pos3 4
SA128711N045_neg4 -
SA128712N045_pos4 -
SA128713CDSR01405-01_neg4 -
SA128714CDSR01156-01_pos4 -
SA128715CDSR01405-01_pos4 -
SA128716CDSR01156-01_neg4 -
SA128717CDSR01177-01_pos4 2
SA128718N035_pos4 2
SA128719CDSR01177-01_neg4 2
SA128720N046_pos4 2
SA128721N018_pos4 2
SA128722N046_neg4 2
SA128723N035_neg4 2
SA128724N018_neg4 2
SA128725N004_pos4 3
SA128726CDSR01192-01_neg4 3
SA128727N004_neg4 3
SA128728CDSR01192-01_pos4 3
SA128729CDSR01023_01_pos4 4
SA128730CDSR01023_01_neg4 4
SA128731CDSR01291-01_pos4 4
SA128732CDSR01202-02_neg4 4
SA128733CDSR01202-02_pos4 4
SA128734CDSR01291-01_neg4 4
SA128663N030_neg- -
SA128664N017_pos- -
SA128665N017_neg- -
SA128666N030_pos- -
Showing results 1 to 72 of 72

Collection:

Collection ID:CO001596
Collection Summary:Tumor tissue samples were placed in a 1.8mL cryovial with either DMEM or RPMI cell culture medium and kept on ice during transport. In the laboratory, they were immediately placed into 1mL 13C labeled glucose medium in 24-well cell culture plate and incubated at 5% CO2 and 37oC on a shaker for 24h.
Sample Type:Tumor cells

Treatment:

Treatment ID:TR001616
Treatment Summary:Patients received chemotherapy post tumor tissue collection. Chemotherapy varied based on patient-specific conditions. Information regarding chemotherapy outcome in terms of complete regression (1), partial regression (2), stable disease (3), or progressive disease (4) was collected after chemotherapy regimen was completed.

Sample Preparation:

Sampleprep ID:SP001609
Sampleprep Summary:After incubation, media and tissue sample were transferred to 1.5mL microcentrifuge tube and centrifuged for 5min. 13C-glucose media was aspirated and specimen was washed with PBS and centrifuged for 5min, twice. After wash, 500mL acetonitrile was added and tissue was homogenized with pellet mixer. After 2-3min homogenization, 376mL of DNase/RNase free water and 250mL chloroform were added. Contents were vortexed until milky-white color and centrifuged for 20min. Top (polar) layer was aspirated and frozen at -80oC. As control, a NSCLC tissue biopsy was incubated in unlabeled glucose media for 24h and processed likewise. Sample polar layers were flash frozen in liquid N2, then lyophilized for 24-48h until dried

Combined analysis:

Analysis ID AN002548 AN002549
Analysis type MS MS
Chromatography type Parallel 2DLC-MS Parallel 2DLC-MS
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 Single quadrupole Single quadrupole
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode NEGATIVE POSITIVE
Units peak intensity peak intensity

Chromatography:

Chromatography ID:CH001866
Chromatography Summary:Used a reversed phase chromatography (RPC) column and a hydrophilic interaction chromatography (HILIC) column configured to form a parallel 2DLC-MS system
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Thermo Accucore HILIC (100 x 2.1mm, 2.6um)
Chromatography Type:Parallel 2DLC-MS

MS:

MS ID:MS002366
Analysis ID:AN002548
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:-
Ion Mode:NEGATIVE
  
MS ID:MS002367
Analysis ID:AN002549
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Single quadrupole
MS Type:ESI
MS Comments:-
Ion Mode:POSITIVE
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