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.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST002097 |
| Study Title | Functional metabolomics-based molecular profiling of acute and chronic hepatitis (Liver Metabolomics) |
| Study Summary | Non-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 |
| 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 |
| haitao_lu@sjtu.edu.cn | |
| Phone | 15221478139 |
| Submit Date | 2022-03-09 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-03-25 |
| Release Version | 1 |
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 |
|---|---|---|
| SA201204 | A549 Ad-Mieap 3 | Ad-Mieap infection |
| SA201205 | A549 Ad-Mieap 4 | Ad-Mieap infection |
| SA201206 | LS174T Control 5 | Control |
| SA201207 | LS174T Control 6 | Control |
| SA201208 | LS174T Control 4 | Control |
| SA201209 | LS174T Control 3 | Control |
| SA201210 | LS174T Mieap-KD 6 | Mieap-knockdown |
| SA201211 | LS174T Mieap-KD 3 | Mieap-knockdown |
| SA201212 | LS174T Mieap-KD 5 | Mieap-knockdown |
| SA201213 | LS174T Mieap-KD 4 | Mieap-knockdown |
| SA201214 | A549 Non-infection 3 | Non-infection |
| SA201215 | A549 Non-infection 4 | Non-infection |
| SA201216 | 20210522-C-3 | 3 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil) |
| SA201217 | 20210522-C-7 | 3 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil) |
| SA201218 | 20210522-C-8 | 3 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil) |
| SA201219 | 20210522-C-6 | 3 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil) |
| SA201220 | 20210522-C-4 | 3 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil) |
| SA201221 | 20210522-C-5 | 3 times per week with 4 consecutive respectively intraperitoneal injection (10 mL/kg of olive oil) |
| SA201228 | 20210522-CH-4 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil) |
| SA201229 | 20210522-CH-2 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil) |
| SA201230 | 20210522-CH-5 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil) |
| SA201231 | 20210522-CH-3 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil) |
| SA201232 | 20210522-CH-6 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil) |
| SA201233 | 20210522-CH-8 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 10% CCl4 (10 mL/kg of olive oil) |
| SA201222 | 20210522-CL-3 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil) |
| SA201223 | 20210522-CL-5 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil) |
| SA201224 | 20210522-CL-8 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil) |
| SA201225 | 20210522-CL-7 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil) |
| SA201226 | 20210522-CL-6 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil) |
| SA201227 | 20210522-CL-1 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 1% CCl4 (10 mL/kg of olive oil) |
| SA201234 | 20210522-CM-3-2 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil) |
| SA201235 | 20210522-CM-4 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil) |
| SA201236 | 20210522-CM-6 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil) |
| SA201237 | 20210522-CM-2 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil) |
| SA201238 | 20210522-CM-5 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil) |
| SA201239 | 20210522-CM-1 | 3 times per week with 4 consecutive respectively intraperitoneal injection with 5% CCl4 (10 mL/kg of olive oil) |
| SA201240 | 20210522-AL-6 | Only 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. |
| SA201241 | 20210522-AL-1-0524 | Only 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. |
| SA201242 | 20210522-AL-5 | Only 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. |
| SA201243 | 20210522-AL-7 | Only 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. |
| SA201244 | 20210522-AL-4 | Only 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. |
| SA201245 | 20210522-AL-2 | Only 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. |
| SA201246 | 20210522-AH-5 | Only 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. |
| SA201247 | 20210522-AH-3 | Only 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. |
| SA201248 | 20210522-AH-8 | Only 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. |
| SA201249 | 20210522-AH-2 | Only 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. |
| SA201250 | 20210522-AH-1 | Only 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. |
| SA201251 | 20210522-AH-6 | Only 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 | Waters X-Bridge C18 (150 x 1.0mm,3.5um) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| 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: | Waters X-Bridge C18 (150 x 1.0mm,3.5um) |
| 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: | Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 40 |
| Flow Gradient: | 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 |
| Flow Rate: | 0.3 mL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| 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 |
