Summary of Study ST002097

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 PR001330. The data can be accessed directly via it's Project DOI: 10.21228/M8ST3F 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 IDST002097
Study TitleFunctional metabolomics-based molecular profiling of acute and chronic hepatitis (Liver Metabolomics)
Study SummaryNon-alcoholic steatohepatitis (NASH) is a metabolic dysregulation triggered by an overload disrupting the hepatic tolerance to external molecules. With the complexity and diversity of hepatitis triggers, no effective clinical classification and treatment are available, and even using the same strategies or approaches for acute and chronic hepatitis. For us, it is really difficult to precisely diagnose and treat hepatitis accordingly. To overcome this challenge, we integrated metabolomic, lipidomics, transcriptomics and other life science frontier technologies for functional metabolomics studies, and pioneered the redefinition of hepatitis at the molecular level. Our findings suggested that acute hepatitis mainly interferes with purine metabolism and amino acids metabolism, while chronic hepatitis mainly causes disruption of hepatic bile acids and lipidome, especially glycerolipids. Based on the liver-gut axis, we also found that the metabolic regulation of the gut microbiota is another key factor for chronic hepatitis development. In conclusion, functional metabolomics enables the cognition of disease occurrence, development and regression from small molecule metabolic modifications and modulations, realizing the ultimate goal of treating diseases and improving population health through regulation of dysregulated metabolism
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 Date2022-03-09
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2022-03-25
Release Version1
Haitao Lu Haitao Lu
https://dx.doi.org/10.21228/M8ST3F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001330
Project DOI:doi: 10.21228/M8ST3F
Project Title:Functional metabolomics-based molecular profiling of acute and chronic hepatitis
Project Type:Targeted MS quantitative analysis
Project Summary:Characteristics of liver metabolomics in acute and chronic hepatitis
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:SU002181
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Biosource Or Supplier:American Type Culture Collection
Cell Strain Details:A549 (tissue, lung cancer; gender, male), LS174T (tissue, colon cancer; gender, female)
Cell Counts:10,000,000
  
Subject ID:SU002182
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id Genotype/Treatment
SA201204A549 Ad-Mieap 3Ad-Mieap infection
SA201205A549 Ad-Mieap 4Ad-Mieap infection
SA201206LS174T Control 5Control
SA201207LS174T Control 6Control
SA201208LS174T Control 4Control
SA201209LS174T Control 3Control
SA201210LS174T Mieap-KD 6Mieap-knockdown
SA201211LS174T Mieap-KD 3Mieap-knockdown
SA201212LS174T Mieap-KD 5Mieap-knockdown
SA201213LS174T Mieap-KD 4Mieap-knockdown
SA201214A549 Non-infection 3Non-infection
SA201215A549 Non-infection 4Non-infection
SA20121620210522-C-33 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil)
SA20121720210522-C-73 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil)
SA20121820210522-C-83 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil)
SA20121920210522-C-63 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil)
SA20122020210522-C-43 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil)
SA20122120210522-C-53 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil)
SA20122820210522-CH-43 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil)
SA20122920210522-CH-23 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil)
SA20123020210522-CH-53 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil)
SA20123120210522-CH-33 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil)
SA20123220210522-CH-63 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil)
SA20123320210522-CH-83 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil)
SA20122220210522-CL-33 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil)
SA20122320210522-CL-53 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil)
SA20122420210522-CL-83 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil)
SA20122520210522-CL-73 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil)
SA20122620210522-CL-63 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil)
SA20122720210522-CL-13 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil)
SA20123420210522-CM-3-23 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil)
SA20123520210522-CM-43 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil)
SA20123620210522-CM-63 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil)
SA20123720210522-CM-23 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil)
SA20123820210522-CM-53 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil)
SA20123920210522-CM-13 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil)
SA20124020210522-AL-6Only intraperitoneally (i.p) injected with 1% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124120210522-AL-1-0524Only intraperitoneally (i.p) injected with 1% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124220210522-AL-5Only intraperitoneally (i.p) injected with 1% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124320210522-AL-7Only intraperitoneally (i.p) injected with 1% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124420210522-AL-4Only intraperitoneally (i.p) injected with 1% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124520210522-AL-2Only intraperitoneally (i.p) injected with 1% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124620210522-AH-5Only intraperitoneally (i.p) injected with 5% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124720210522-AH-3Only intraperitoneally (i.p) injected with 5% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124820210522-AH-8Only intraperitoneally (i.p) injected with 5% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20124920210522-AH-2Only intraperitoneally (i.p) injected with 5% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20125020210522-AH-1Only intraperitoneally (i.p) injected with 5% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
SA20125120210522-AH-6Only intraperitoneally (i.p) injected with 5% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil.
Showing results 1 to 48 of 48

Collection:

Collection ID:CO002174
Collection Summary:Cells were collected using trypsin-EDTA. The cells were snap-frozen in liquid nitrogen after cell count, and subsequently stored at -80°C until lipidomic analysis.
Sample Type:Cultured cells
Volumeoramount Collected:10,000,000 cells/tube
Storage Conditions:-80℃
  
Collection ID:CO002175
Collection Summary:Animals were killed at 24h post the last CCl4 treatment and the liver tissue samples were harvested for further assays.
Sample Type:Liver

Treatment:

Treatment ID:TR002193
Treatment Summary:Infection of the A549 cell line was carried out by adding viral solution (Ad-Mieap) to A549 cell monolayers, and incubating at 37°C for 120 min with brief agitation every 20 min. This was followed by the addition of culture medium and the return of the infected cells to the 37°C incubator. We established a Mieap-KD cell line using LS174T. Mieap expression was inhibited in the cell line by retroviral expression of short-hairpin RNA (shRNA) against the Mieap sequence. We also established LS174T-cont cells using the retroviral vector with target sequence for EGFP. The LS174T-cont and Mieap-KD cells were incubated under normal condition.
Treatment Doseduration:A549 cells: 24 h; LS174T-cont and Mieap-KD cells: none (incubated under normal condition)
Treatment Vehicle:A549 cells: viral solution (Ad-Mieap); LS174T-cont and Mieap-KD cells: none (incubated under normal condition)
Cell Storage:stored at -80°C
  
Treatment ID:TR002194
Treatment Summary:Prior to experimental, animals were acclimatized breeding to laboratory conditions for 1 week. The mice were randomly allocated into 6 groups (n=8 each), as follows: a control group (C); two acute hepatitis groups, low and high concentrations (AL/ AH); three chronic hepatitis groups, low, middle and high concentration (CL/ CM/ CH). Mice in chronic groups were treated 3 times per week with 4 consecutive respectively intraperitoneal (i.p) injection with 1% / 5% / 10% CCl4 (10 mL/kg, dissolved in olive oil). However, in the acute groups, mice were only intraperitoneally (i.p) injected with 1% / 5% CCl4 (10 mL/kg, dissolved in olive oil) at the 12th injection. During the previous 11 times they were treated the same as the healthy controls with an equal volume of olive oil. Animals were killed at 24h post the last CCl4 treatment and serum, stool and liver tissue samples were harvested for further assays.

Sample Preparation:

Sampleprep ID:SP002187
Sampleprep Summary:Total lipids were extracted from samples using the Bligh-Dyer method. An aliquot of the organic phase was added to an equal volume of methanol before being loaded onto a DEAE-cellulose column (Wako Chemical) pre-equilibrated with chloroform. After successive washes with chloroform/methanol (1:1, v/v), acidic phospholipids were eluted with chloroform/methanol/HCl/water (12:12:1:1, v/v), followed by evaporation to dryness to yield a residue was soluble in methanol.
Extraction Method:the Bligh-Dyer method
  
Sampleprep ID:SP002188
Sampleprep Summary:100-130 mg liver tissue samples were weighted, 1.2 mL of 80% ice-cold aqueous methanol, which contains 0.001 mg/mL internal standard, and approximately 1 g of glass beads (1.0 mm i.d.) was added into a 2 mL screw-cap plastic microvial. The Mini-BeadBeater-16 (Biospec Products, USA) was used for tissue disruption. Samples were homogenized 3 times for 2 min each, with cooling procedure in between, centrifuged at 20,000 g for 10 min at 4 °C, and the supernatants were mixed with 800 μL of ice-cold acetonitrile and centrifuged again for protein precipitation. The supernatant was filtered through a 0.22 µm organic phase membrane, blown dry in nitrogen, reconstituted in 100 µL of water and transferred to vials for metabolomics assay.

Combined analysis:

Analysis ID AN003425 AN003426 AN003427
Analysis type MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase
Chromatography system UltiMate 3000 (Thermo Fisher Scientific) Agilent 1290 Infinity Agilent 1290 Infinity
Column X-Bridge C18 column (3.5 μm, 150 mm × 1.0 mm i.d.) (Waters) ACQUITY UPLC HSS T3 column (2.1 mm i.d. × 100 mm, 1.8 μm; Waters) ACQUITY UPLC HSS T3 column (2.1 mm i.d. × 100 mm, 1.8 μm; Waters)
MS Type ESI ESI ESI
MS instrument type Orbitrap Triple quadrupole Triple quadrupole
MS instrument name Thermo Q Exactive Plus Orbitrap Agilent 6495 QQQ Agilent 6495 QQQ
Ion Mode NEGATIVE POSITIVE NEGATIVE
Units pmol/10,000,000 cells counts counts

Chromatography:

Chromatography ID:CH002533
Instrument Name:UltiMate 3000 (Thermo Fisher Scientific)
Column Name:X-Bridge C18 column (3.5 μm, 150 mm × 1.0 mm i.d.) (Waters)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002534
Chromatography Summary:In this study, a newly developed precision-targeted metabolomics method with a UPLC-TQ/MS system (Agilent 1290 Infnity, Agilent Technologies, USA; Agilent 6495 QQQ, Agilent Technologies, USA) in a DMRM scan-mode was applied to analyze the metabolome of interest from trial samples (serum, liver tissues and stool). Briefly, the method was performed with an ACQUITY UPLC HSS T3 column (2.1 mm i.d. × 100 mm, 1.8 μm; Waters); mobile phase A and B were water and acetonitrile with 0.1% formic acid (v/v) respectively. The flow rate was at 0.3 mL/min and the column temperature was maintained at 40 ℃. The samples were placed in an auto-sampler maintained at 4 °C with a 5 μL injection volume. The optimized gradient-elution program, as follows: 0-2 min, 98% A; 2-10 min, 98-65% A; 10-12 min, 65-20% A; 12-14 min, 20-2% A; 14-30 min, 2% A.
Instrument Name:Agilent 1290 Infinity
Column Name:ACQUITY UPLC HSS T3 column (2.1 mm i.d. × 100 mm, 1.8 μm; Waters)
Chromatography Type:Reversed phase

MS:

MS ID:MS003188
Analysis ID:AN003425
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:pmol/10,000,000 cells
Ion Mode:NEGATIVE
  
MS ID:MS003189
Analysis ID:AN003426
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:MS003190
Analysis ID:AN003427
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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