Summary of Study ST000530
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 PR000389. The data can be accessed directly via it's Project DOI: 10.21228/M8S02S 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 | ST000530 |
| Study Title | Effects of herb DG and KK01 on Type 2 Diabetes Mellitus (T2DM) through Lipidomics |
| Study Type | LC-MS lipidomics |
| Study Summary | According to the results in animal test, KK01 is effective in controlling blood glucose increase with comparable effect as metformin and rosiglitazone. This study will conduct lipid profile comparison for serum samples generated from the animal tests. The comparison will be based on the following groups: 1) db/db mice + DG-high dose; 2) db/db mice +DG-low dose; 3) db/db mice + KK01-high dose; 4) db/db mice + KK01-low dose; 5) db/db mice + metformin; 6) db/db mice + rosiglitazone; 7) db/db mice + saline (disease model); and 8) wild type mice + saline (healthy model). The determined lipid marker(s) will be applied to elucidate the drug target(s) and mechanisms of DG and KK01. Furthermore, comparison of target(s) between KK01 and the first line drugs in diabetic treatment, e.g., metformin and rosiglitazone, will facilitate the finding of featured pathway(s) of KK01 differentiated from the established drugs. Comparison of drug target(s) between KK01 and DG can help to understand the synergistic effects of multiple constituents in the herb. |
| Institute | University of North Carolina |
| Department | Systems and Translational Sciences |
| Laboratory | Sumner Lab |
| Last Name | Sumner |
| First Name | Susan |
| Address | Eastern Regional Comprehensive Metabolomics Resource Core, UNC Nutrition Research Institute, 500 Laureate Way, Kannapolis, NC, 28081 |
| susan_sumner@unc.edu | |
| Phone | 704-250-5066 |
| Submit Date | 2016-12-30 |
| Num Groups | 10 |
| Total Subjects | 93 samples for positive mode and 80 samples for negative mode |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-02-07 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000389 |
| Project DOI: | doi: 10.21228/M8S02S |
| Project Title: | Effects of herb DG and KK01 on Type 2 Diabetes Mellitus (T2DM) |
| Project Type: | LC-MS Lipidomics |
| Project Summary: | The long-term goal of this research is to use a system pharmacology approach to investigate novel drugs for type 2 diabetes based on the experience of Traditional Chinese Medicine (TCM). The aim of the current study is to use lipidomics to evaluate the anti-diabetic efficacy of DG extract and its major compounds and to interpret the drug targets and mechanisms. DG is a typical “heat clearing” herb in TCM, and has long been used as a treatment for type 2 diabetes. Phytochemicals with KK structure are the predominant constituents in DG extract, and KK01 is the major form, with a content of around 2% of dry herb. To verify that KK01 is the bioactive compound responsible for the effect of DG, we designed an animal experiment to investigate the efficacies of DG and KK01 on db/db mice in comparison to two first-line anti-diabetic drugs, metformin and rosiglitazone. It was found that after 9 weeks of treatments, KK01 was effective in inhibiting the increase of blood glucose of db/db mice, with effects comparable to metformin and rosiglitazone. To understand the mechanism, the mice blood was collected in fasting status, and the serum was separated and divided into three aliquots for lipidomics, cytokine array and Biocrates analysis. This study will focus on lipidomics analysis. |
| Institute: | RTI International |
| Department: | Systems and Translational Sciences |
| Laboratory: | RTI Eastern Regional Comprehensive Metabolomics Resource Core (RTI ERCMRC) |
| Last Name: | Li |
| First Name: | Yuanyuan |
| Address: | 3040 East Cornwallis Road, Research Triangle Park, NC 27709, USA |
| Email: | yli@rti.org |
| Phone: | 9199908327 |
Subject:
| Subject ID: | SU000552 |
| Subject Type: | Serum |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BLKsJ-db/db (disease model) and C57BLKsJ wild type (wild type) |
| Age Or Age Range: | 14 weeks; drug administration since the 5th week |
| Weight Or Weight Range: | 37-58 g for db/db mice; 18-25 g for wild type mice |
| Gender: | Male |
| Species Group: | Mammals |
Factors:
Subject type: Serum; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Gene type | Phenotypic grouping and treaments |
|---|---|---|---|
| SA027878 | S_53 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027879 | S_60 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027880 | S_47 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027881 | S_56 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027882 | S_67 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027883 | S_7 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027884 | S_19 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027875 | S_28 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027876 | S_34 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027877 | S_42 | C57BLKsJ-db/db | Group1, DG extract high dose |
| SA027813 | S_3 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027814 | S_36 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027815 | S_57 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027816 | S_38 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027817 | S_54 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027818 | S_25 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027819 | S_77 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027820 | S_4 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027821 | S_16 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027822 | S_73 | C57BLKsJ-db/db | Group 2, DG extract low dose |
| SA027823 | S_33 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027824 | S_76 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027825 | S_51 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027826 | S_5 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027827 | S_61 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027828 | S_48 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027829 | S_20 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027830 | S_15 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027831 | S_59 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027832 | S_66 | C57BLKsJ-db/db | Group 3, KK 01 high dose |
| SA027833 | S_79 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027834 | S_23 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027835 | S_14 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027836 | S_82 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027837 | S_50 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027838 | S_29 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027839 | S_37 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027840 | S_43 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027841 | S_39 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027842 | S_12 | C57BLKsJ-db/db | Group 4, KK 01 low dose (i.p.) |
| SA027843 | S_44 | C57BLKsJ-db/db | Group 5, metformin |
| SA027844 | S_71 | C57BLKsJ-db/db | Group 5, metformin |
| SA027845 | S_13 | C57BLKsJ-db/db | Group 5, metformin |
| SA027846 | S_75 | C57BLKsJ-db/db | Group 5, metformin |
| SA027847 | S_58 | C57BLKsJ-db/db | Group 5, metformin |
| SA027848 | S_49 | C57BLKsJ-db/db | Group 5, metformin |
| SA027849 | S_1 | C57BLKsJ-db/db | Group 5, metformin |
| SA027850 | S_74 | C57BLKsJ-db/db | Group 5, metformin |
| SA027851 | S_8 | C57BLKsJ-db/db | Group 5, metformin |
| SA027852 | S_46 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027853 | S_18 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027854 | S_52 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027855 | S_2 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027856 | S_45 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027857 | S_69 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027858 | S_21 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027859 | S_32 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027860 | S_65 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027861 | S_72 | C57BLKsJ-db/db | Group 6, rosiglitazone |
| SA027862 | S_68 | C57BLKsJ-db/db | Group 7, saline |
| SA027863 | S_70 | C57BLKsJ-db/db | Group 7, saline |
| SA027864 | S_22 | C57BLKsJ-db/db | Group 7, saline |
| SA027865 | S_41 | C57BLKsJ-db/db | Group 7, saline |
| SA027866 | S_24 | C57BLKsJ-db/db | Group 7, saline |
| SA027867 | S_64 | C57BLKsJ-db/db | Group 7, saline |
| SA027868 | S_40 | C57BLKsJ-db/db | Group 7, saline |
| SA027869 | S_27 | C57BLKsJ-db/db | Group 7, saline |
| SA027870 | S_62 | C57BLKsJ-db/db | Group 7, saline |
| SA027871 | S_35 | C57BLKsJ-db/db | Group 8, saline |
| SA027872 | S_81 | C57BLKsJ-db/db | Group 9, saline (i.p.) |
| SA027873 | S_83 | C57BLKsJ-db/db | Group 9, saline (i.p.) |
| SA027874 | S_10 | C57BLKsJ-db/db | Group 9, saline (i.p.) |
| SA027803 | S_55 | C57BLKsJ (WT) | Group 8, saline |
| SA027804 | S_9 | C57BLKsJ (WT) | Group 8, saline |
| SA027805 | S_17 | C57BLKsJ (WT) | Group 8, saline |
| SA027806 | S_30 | C57BLKsJ (WT) | Group 8, saline |
| SA027807 | S_78 | C57BLKsJ (WT) | Group 8, saline |
| SA027808 | S_11 | C57BLKsJ (WT) | Group 8, saline |
| SA027809 | S_26 | C57BLKsJ (WT) | Group 8, saline |
| SA027810 | S_80 | C57BLKsJ (WT) | Group 8, saline |
| SA027811 | S_63 | C57BLKsJ (WT) | Group 8, saline |
| SA027812 | S_6 | C57BLKsJ (WT) | Group 8, saline |
| SA027885 | P_8 | Pool serum from Sigma | - |
| SA027886 | P_9 | Pool serum from Sigma | - |
| SA027887 | P_11 | Pool serum from Sigma | - |
| SA027888 | P_7 | Pool serum from Sigma | - |
| SA027889 | P_10 | Pool serum from Sigma | - |
| SA027890 | P_2 | Pool serum from Sigma | - |
| SA027891 | P_1 | Pool serum from Sigma | - |
| SA027892 | P_3 | Pool serum from Sigma | - |
| SA027893 | P_4 | Pool serum from Sigma | - |
| SA027894 | P_5 | Pool serum from Sigma | - |
| SA027895 | P_6 | Pool serum from Sigma | - |
| Showing results 1 to 93 of 93 |
Collection:
| Collection ID: | CO000546 |
| Collection Summary: | Mice were fasting over night and then sacrified to collect blood. |
| Sample Type: | Serum |
| Collection Location: | Wuhan Institute of Drug and Device Control, China |
| Storage Conditions: | Frozen -80oC |
| Collection Vials: | Eppendorf tube 1 mL |
| Storage Vials: | Eppendorf tube 0.5 mL |
| Collection Tube Temp: | Room temperature |
| Blood Serum Or Plasma: | Serum |
Treatment:
| Treatment ID: | TR000566 |
| Treatment Summary: | C57BLKsJ-db/db mice were classified randomly into 8 groups. Seven groups were with 9~10 mice for each and one group with 4 mice. Mice were treated with DG extract (5 g/Kg), DG extract (1 g/Kg), KK01 (50 mg/Kg), KK01 (20 mg/Kg), metformin (5 mg/Kg); rotaglitazone (5 mg/Kg); and saline. Group treated with KK01(20 mg/Kg) and the group with 4 mice treated by saline were used intraperitoneal injection. Other groups were in intragastric administration. Also, a group with ten C57BLKsJ mice fedding with saline was used as healthy control. The drug administration were started with the 5th week of the age and lasted for 9 weeks. |
| Treatment Route: | Intragastric administration for all except for group of KK01 low-dose (20 mg/Kg), and 4 db/db mice treated with saline which were treated by intraperitoneal injection. |
| Treatment Dose: | 5 g/Kg for DG high dose; 1 g/Kg for DG low dose; 50 mg/Kg for KK01 high dose; 20 mg/Kg (i.p.) for KK01 low dose; 5 mg/Kg for metformin, 5 mg /Kg for rosiglitazone |
| Treatment Dosevolume: | 0.5 mL |
| Treatment Doseduration: | 9 weeks |
| Treatment Vehicle: | saline |
| Animal Fasting: | Over night |
| Animal Endp Tissue Coll List: | liver, kidney, brain, white fat, brown fat, pancreas |
Sample Preparation:
| Sampleprep ID: | SP000559 |
| Sampleprep Summary: | In lipidomics analysis, samples were first thawed on ice, and then mixed by vortex for 4 min at 4,000 rpm, followed by centrifugation for 4 min at 4, 000 rcf to spin down particulate. Pooled mouse serum from Sigma Aldrich (S7273) were used as QC samples. A 30 µL aliquot of each serum sample (including QC sample and real sample) was transferred to a 2.0 mL Eppendorf Lo-Bind tube and extracted by 600 µL of 2:1 dichloromethane: methanol (DCM) via vortex-mixing for 2 min at 4,000 rpm. Then, 120 µL of H2O was added and repeated the vortex-mixing for 1 min at 4,000 rpm. After placing the sample at room temperature for 10 min, the tube was centrifuged at 16,000 rcf for 10 minutes at 10 °C. A 370 µL aliquot of the lower lipid-rich DCM layer was transferred to a new labeled 2.0 mL Eppendorf Lo-Bind tubes and then lyophilized to complete dryness overnight. For immediate analysis, 300 µL of acetonitrile:isopropanol:H2O (65:30:5, v/v/v) was added to reconstitute the dried tissue extract, and the samples were thoroughly mixed on a multi-tube vortexer for 10 min at 5000 rpm and centrifuged at 16,000 rcf for 4 min. The supernatants were transferred to labeled autosampler vials for data acquisition by LC-MS. |
| Extraction Method: | cold 2:1 dichloromethane: methanol vortex extraction |
| Extract Storage: | -80 oC |
| Sample Resuspension: | acetonitrile:isopropanol:H2O (65:30:5, v/v/v) |
| Sample Spiking: | 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine |
Combined analysis:
| Analysis ID | AN000808 | AN000809 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Waters Acquity | Waters Acquity |
| Column | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap | Thermo Orbitrap |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | m/z | m/z |
Chromatography:
| Chromatography ID: | CH001295 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity CSH C18 (100 x 2.1mm,1.7um) |
| Column Pressure: | 6000-10000 |
| Column Temperature: | 50C |
| Flow Rate: | 0.25 mL/min |
| Injection Temperature: | 4C |
| Internal Standard: | 1,2-diheptadecanoyl-sn-glycero-3-phosphocholine |
| Solvent A: | 60% acetonitrile/40% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 90% isopropanol/10% acetonitrile; 0.1% formic acid; 10 mM ammonium formate |
| Analytical Time: | 30 min |
| Weak Wash Solvent Name: | 60:40 water/acetonitrile in 10 mM ammonium formate with 0.1% formic acid |
| Weak Wash Volume: | 1200 uL |
| Strong Wash Solvent Name: | 90:10 isopropanol/acetonitrile in 10 mM ammonium formate with 0.1% formic acid |
| Strong Wash Volume: | 600 uL |
| Sample Loop Size: | 10 uL |
| Sample Syringe Size: | 100 uL |
| Randomization Order: | Yes |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000715 |
| Analysis ID: | AN000808 |
| Instrument Name: | Thermo Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 250 oC |
| Collision Energy: | 35 |
| Fragmentation Method: | CID |
| Ion Source Temperature: | 400 oC |
| Ion Spray Voltage: | 4.0 kV |
| Ionization: | ES+ |
| Mass Accuracy: | 10 ppm |
| Desolvation Gas Flow: | 50 arbitary unit |
| Desolvation Temperature: | 400 oC |
| Resolution Setting: | 30000 |
| Scan Range Moverz: | 120-2000 m/s |
| MS ID: | MS000716 |
| Analysis ID: | AN000809 |
| Instrument Name: | Thermo Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Capillary Temperature: | 250 oC |
| Collision Energy: | 35 |
| Fragmentation Method: | CID |
| Ion Source Temperature: | 400 oC |
| Ion Spray Voltage: | 4.0 kV |
| Ionization: | ES- |
| Mass Accuracy: | 10 ppm |
| Desolvation Gas Flow: | 50 arbitary unit |
| Desolvation Temperature: | 400 oC |
| Resolution Setting: | 30000 |
| Scan Range Moverz: | 120-2000 m/s |
