Summary of Study ST002122

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 PR001346. The data can be accessed directly via it's Project DOI: 10.21228/M8QX47 This work is supported by NIH grant, U2C- DK119886.

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Study IDST002122
Study TitleFunctional metabolic molecules were identified as novel therapeutic targets to facilitate gemcitabine treatment against pancreatic cancer (Cells metabolomics)
Study SummaryWith the development of frontier technologies in system biology, traditional omics-drove phenotypic studies are insufficient to decipher the diseases. Therefore, for a thorough understanding of the molecular mechanisms of diseases to investigate novel drug targets, traditional phenotypic studies must be broken through to the functional exploration of molecules. Meanwhile, the intuitive role of small molecule compounds (metabolites) in pathogenesis, precision diagnosis and therapy are gradually recognized compared to macromolecules such as DNA, RNA and proteins. Therefore, we pioneeringly proposed Spatial Temporal Operative Real Metabolomics (STORM) strategy that established a relationship between metabolic phenotypes and functions to accurately character abnormal metabolisms and further identify operative functional molecules as novel therapeutic targets. Here, given the difficulty of pancreatic cancer (PC) treatment and the high resistance of clinical drugs, we were committed to explore new targets and drugs of pancreatic cancer from a small molecular functional perspective via STORM strategy. Fortunately, based on targeted metabolomics, we found that gemcitabine, one of the most effective clinical anti-PC drugs, served as a dual modulator that promote the accumulation of functional metabolic molecules in purine metabolism to activate down-streamed kinases. And the quantitative consequences of related enzymes annotated the unique molecular mechanisms of purine metabolism regulations by gemcitabine. Collectively, we broadened the cognitions of gemcitabine in tumor inhibition, providing potential strategies for treating PC with small molecules modification. Even more importantly, with the integration of multiple frontier technologies, the STORM strategy has proven to be well adapted to the phenotypic era of functional molecules devoted to innovate molecule mechanism annotation and therapeutic discovery.
Institute
Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
DepartmentShanghai Center for Systems Biomedicine
LaboratoryLu Group
Last NameLu
First NameHaitao
Address800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
Emailhaitao_lu@sjtu.edu.cn
Phone15221478139
Submit Date2022-03-25
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2022-04-20
Release Version1
Haitao Lu Haitao Lu
https://dx.doi.org/10.21228/M8QX47
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001346
Project DOI:doi: 10.21228/M8QX47
Project Title:Functional metabolic molecule were identified as novel therapeutic targets to facilitate gemcitabine treatment against pancreatic cancer
Project Type:Targeted MS quantitative analysis
Project Summary:Characteristics of pancreatic cancer metabolomics with gemcitabine treatment
Institute:Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University
Department:Shanghai Center for Systems Biomedicine
Laboratory:Lu Group
Last Name:Lu
First Name:Haitao
Address:800 Dongchuan RD. Minhang District, Shanghai, Shanghai, 200240, China
Email:haitao_lu@sjtu.edu.cn
Phone:15221478139

Subject:

Subject ID:SU002207
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 Treatment
SA204245ASPC-C-1After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h
SA204246ASPC-C-2After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h
SA204247ASPC-C-5After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h
SA204248ASPC-C-3After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h
SA204249ASPC-C-4After inoculating cells for 24h in 10cm dishes, treating cells with 25μl DMSO for 72h
SA204250ASPC-GI-3After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h
SA204251ASPC-GI-1After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h
SA204252ASPC-GI-2After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h
SA204253ASPC-GI-5After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h
SA204254ASPC-GI-4After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM and IBMX with a final concentration of 200μM for 72h
SA204255ASPC-G-3After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h
SA204256ASPC-G-1-r002After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h
SA204257ASPC-G-2After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h
SA204258ASPC-G-4After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h
SA204259ASPC-G-5After inoculating cells for 24h in 10cm dishes, treating cells with gemcitabine with a final concentration of 50μM for 72h
Showing results 1 to 15 of 15

Collection:

Collection ID:CO002200
Collection Summary:After 72 hours of drug treatment, the cells were washed twice with ice PBS and scraped in 80% ice methanol
Sample Type:Tumor cells

Treatment:

Treatment ID:TR002219
Treatment Summary:Cells were evenly divided into 3 groups of 6 discs each. 24h after cell inoculation, gemcitabine administration group was treated with gemcitabine with final concentration of 50μM for 72h, while the GI group was supplemented with an additional 200μM 3-isobutyl-1-methylxanthine (IBMX) in the culture medium. Meanwhile, the control group was given the same volume of DMSO. One plate of cells was taken from each group for counting, and the rest were collected for metabolite extraction

Sample Preparation:

Sampleprep ID:SP002213
Sampleprep Summary:The cells were cultured as described above and fixed with 1 ml of 80% ice-cold menthol after being washed twice with ice-cold PBS. The cells were scraped from the plates, and 0.5-mm beads were added to process the cells by grinding and shaking. The supernatants were collected after centrifugation and deproteinized by mixing with 800μL acetonitrile on ice. Then, the supernatants collected and spun down under nitrogen at room temperature. The samples were resuspended in 100 μL of distilled H2O, and 5 μL was used for LC-TQ-MS-based metabolome assay.

Combined analysis:

Analysis ID AN003474 AN003475
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters Acquity HSS T3 (100 x2.1mm,1.8um) Waters Acquity HSS T3 (100 x2.1mm,1.8um)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name Agilent 6495 QQQ Agilent 6495 QQQ
Ion Mode POSITIVE NEGATIVE
Units counts counts

Chromatography:

Chromatography ID:CH002564
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity HSS T3 (100 x2.1mm,1.8um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003235
Analysis ID:AN003474
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Agilent MassHunter Workstation Data Acquisition Agilent MassHunter
Ion Mode:POSITIVE
  
MS ID:MS003236
Analysis ID:AN003475
Instrument Name:Agilent 6495 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Agilent MassHunter Workstation Data Acquisition Agilent MassHunter
Ion Mode:NEGATIVE
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