Summary of Study ST004175
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 PR002634. The data can be accessed directly via it's Project DOI: 10.21228/M85V83 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 | ST004175 |
| Study Title | The influence of implants on the amino acid metabolism of mesenchymal stem cells (MSCs) |
| Study Summary | To determine whether the modified titanium implant can regulate the glutamine metabolism of mesenchymal stem cells (MSC), the amino acid metabolism levels of each group were analyzed. |
| Institute | Chongqing University |
| Laboratory | College of Bioengineering, Chongqing University |
| Last Name | Li |
| First Name | Xuan |
| Address | 174 Shazheng St., Shapingba,, Chongqing, 400044, China |
| 201919021061@cqu.edu.cn | |
| Phone | 15310893373 |
| Submit Date | 2025-09-04 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-09-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002634 |
| Project DOI: | doi: 10.21228/M85V83 |
| Project Title: | Directed Rescue Strategy for Enhanced Implant Osteointegration in Aged Rats |
| Project Summary: | Senolytics, which involve the removal of senescent cells from tissues, have emerged as one of the most promising strategies for treating age-related degenerative diseases. In the context of orthopedic treatment, the elimination of senescent cells can also enhance to the osteointegration of implants in elderly patients. However, achieving specific clearance of senescent cells without adversely affecting the function of normal cell remains challenging. To overcome these challenges, we developed a novel implant surface modification technique to achieve specific clearance of locally senescent cells by modulating their metabolism. Our technique also involved modifying implants with BPTES, a glutaminase 1 (GLS1) inhibitor, through π-π stacking with dopamine. This modification effectively induced apoptosis in senescent mesenchymal stem cells (MSCs) through extensive inhibition of GLS1. This effect was attributed to intracellular acidosis resulting from the suppression of glutaminolysis in senescent MSCs. Simultaneously, poly(γ-glutamate) (PGA), modified by a layer-by-layer method, served as a high-density carbon source coating, continuously supporting glutamine metabolism in MSCs without ammonia production. Targeted metabolic analysis revealed that the modified titanium implants significantly altered the metabolic profile of MSCs, enhancing glutamine metabolism, the pentose phosphate pathway (PPP), aerobic glycolysis, and fatty acid oxidation (FAO), which collectively stimulated osteogenic differentiation. In vivo experiments showed that the surface modification significantly reduced the senescence level around implants and promoted osteointegration in aged rats. These findings offer promising insights into the design and application of orthopedic implants for elderly patients. |
| Institute: | Chongqing University |
| Laboratory: | College of Bioengineering, Chongqing University |
| Last Name: | Li |
| First Name: | Xuan |
| Address: | 174 Shazheng St., Shapingba, Chongqing, 400044, China |
| Email: | 201919021061@cqu.edu.cn |
| Phone: | 15310893373 |
| Funding Source: | The National Natural Science Foundation of China (Nos. 52333011, 52021004, 21734002 and 32171327), State Key Project of Research and Development (2022YFB3804400), and the Natural Science Foundation of Chongqing (No. cstc2021jcyj-cxttX0002) |
Subject:
| Subject ID: | SU004326 |
| Subject Type: | Cultured cells |
| Subject Species: | Rattus norvegicus |
| Genotype Strain: | wild type |
| Age Or Age Range: | 4 weeks old |
| Gender: | Male |
| Cell Biosource Or Supplier: | Primary cells from Rattus norvegicus |
| Cell Primary Immortalized: | Non-immortalized cells |
| Cell Passage Number: | Passage 3 |
| Cell Counts: | 0.5*10^7 cells |
Factors:
Subject type: Cultured cells; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Culture substrate |
|---|---|---|---|
| SA482188 | R3-2 | MSCs Primary cells | BPTES@MNT |
| SA482189 | R3-5 | MSCs Primary cells | BPTES@MNT |
| SA482190 | R3-4 | MSCs Primary cells | BPTES@MNT |
| SA482191 | R3-3 | MSCs Primary cells | BPTES@MNT |
| SA482192 | R3-1 | MSCs Primary cells | BPTES@MNT |
| SA482193 | R4-2 | MSCs Primary cells | BPTES@MNT/PGA |
| SA482194 | R4-1 | MSCs Primary cells | BPTES@MNT/PGA |
| SA482195 | R4-3 | MSCs Primary cells | BPTES@MNT/PGA |
| SA482196 | R4-4 | MSCs Primary cells | BPTES@MNT/PGA |
| SA482197 | R4-5 | MSCs Primary cells | BPTES@MNT/PGA |
| SA482198 | R2-2 | MSCs Primary cells | MT |
| SA482199 | R2-3 | MSCs Primary cells | MT |
| SA482200 | R2-4 | MSCs Primary cells | MT |
| SA482201 | R2-5 | MSCs Primary cells | MT |
| SA482202 | R2-1 | MSCs Primary cells | MT |
| SA482203 | R1-2 | MSCs Primary cells | Ti |
| SA482204 | R1-5 | MSCs Primary cells | Ti |
| SA482205 | R1-4 | MSCs Primary cells | Ti |
| SA482206 | R1-3 | MSCs Primary cells | Ti |
| SA482207 | R1-1 | MSCs Primary cells | Ti |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO004319 |
| Collection Summary: | MSCs were seeded onto different samples and cultured at 37°C under 5% CO₂. The culture medium was replaced with fresh medium every two days. After 7 days of culture, all cells were collected. |
| Sample Type: | Mesenchymal stem cells |
| Collection Method: | Cells were harvested via trypsin digestion. The cells were centrifuged at 500 × g and collected into a 15 mL centrifuge tube. After discarding the supernatant, the cell pellet was resuspended in 10 mL of pre-cooled PBS and centrifuged for washing (repeated 3 times). The cell pellet was then resuspended in 1 mL PBS, and the cell concentration was accurately quantified. 0.5 × 10^7 cells were transferred to a 1.5 mL centrifuge tube, centrifuged at 500 × g for 5 min, and the supernatant was completely removed. The cell pellet was flash-frozen in liquid nitrogen and stored at −80°C. |
| Collection Location: | Room 416, Cell Laboratory, School of Bioengineering, Chongqing University |
| Collection Frequency: | 5 times |
| Collection Duration: | 1 h |
| Volumeoramount Collected: | 0.5 * 10^7 cells |
| Storage Conditions: | -80℃ |
| Collection Vials: | 15 mL centrifuge tube |
| Storage Vials: | 1.5 mL centrifuge tube |
| Collection Tube Temp: | 4 |
Treatment:
| Treatment ID: | TR004335 |
| Treatment Summary: | Befere the collection, the cells were cultured on the surface of different substrates for 7 days as a treatment step. Ti means titanium foils which were purchased from Alfa Aesar Co. (Tianjin, China). MT was fabricated from Ti via acid etching. Briefly, the titanium was sequentially treated with 3 wt% hydrofluoric acid at room temperature for 2 min and then immersed in 66 wt% sulfuric acid at 80 °C for 5 min. The obtained MT was rinsed thoroughly by ultrasonic. Subsequently, MT was immersed in 3 % APTES solution (toluene as solvent) for 24 h, and then washed thoroughly for further use. BPTES@MNT was obtained by one-step polymerization of dopamine. Briefly, MT-NH2 was placed in a mixed solution (VTris-HCl buffer (10 mM, pH 8.5): VDMSO = 1:1) containing dopamine (1 mg/mL), CaCl2 (0.05 mg/mL), BPTES (0.05 mg/mL) and 1 % APS. The reaction mixture was under continuous shaking (40 rpm) at room temperature overnight and avoid light. The obtained samples were rinsed thoroughly with DI water. Subsequently, PGA coating was modified on the substrate of BPTES@MNT by layer-by-layer method. In short, the samples were alternately immersed into Chi (0.5 w/v%) and PGA (1 w/v%) solution (two repeats). The samples were sterilized with ultraviolet irradiation or prepared under an aseptic environment for subsequent in vitro and in vivo experiments. |
| Treatment: | different culture substrates |
| Treatment Compound: | Ti (R1), MT(R2), BPTES@MNT(R3), and BPTES@MNT/PGA(R4) |
| Treatment Route: | the cells were seeded in the different substrate (The sterile titanium substrate (different groups) was placed in a petri dish to fully cover the base) |
| Treatment Vehicle: | Ti (R1) |
| Cell Storage: | Primary cells |
| Cell Growth Container: | Cell Culture Dishes (Φ100mm) |
| Cell Growth Config: | spindle-shaped or elongated |
| Cell Inoc Proc: | The sterile titanium substrate (different groups) was placed in a petri dish to fully cover the base. Third-passage MSCs (0.5*10^6) were seeded on the titanium surface, followed by the addition of fresh culture medium. The cells were cultured at 37°C under 5% CO₂ atmosphere, and the medium was replaced with fresh medium every two days. |
| Cell Media: | DMEM Medium(Low Glucose, with 10 % fetal bovine serum) |
| Cell Envir Cond: | incubated at 37 °C under 5 % CO2 atmosphere |
| Cell Harvesting: | trypsin digestion |
| Cell Pct Confluence: | 90 % |
| Cell Media Lastchanged: | one day before collection |
Sample Preparation:
| Sampleprep ID: | SP004332 |
| Sampleprep Summary: | In this experiment, a certain mass of the sample was precisely measured. Then, the sample was added to the extraction solution (tissues, cells and other samples need to be ground first) in a low-temperature environment for metabolite extraction treatment. Standard solutions of different concentrations were prepared. The standard solutions and the sample to be tested were subjected to LC-MS analysis under the same conditions. The detailed steps are as follows: 0.5*10^7 cells were combined with 4 μL of internal standard solution (containing 100 μg/mL L-Trp-D5, L-Gln-D5, and L-Lys-D4), 216 μL purified water and 25 μL of 0.15 % DOC.The mixed solution was sonicated (40 kHz) for 10 min at 5 °C, and then 5 μL of trichloroacetic acid (10 M) were added. Before centrifugation, the sample was stored at -20 °C for 10 min. Then the sample was centrifuged at 14000 g for 10 min at 4 °C, and 50 μL of supernatant was collected. 350 μL purified water were added, and then the mixed solution was filtrated by a PTFE filter (0.2 μm, biotage) for further analysis. |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | 4℃ |
Chromatography:
| Chromatography ID: | CH005262 |
| Chromatography Summary: | In this experiment, LC-ESI-MS/MS (UHPLC-Qtrap) was used to conduct qualitative and quantitative detection of the target substances in the samples. The specific parameters are as follows: Chromatographic conditions: AdvanceBio MS Spent Media (2.1 * 50mm, 2.7 µm), column temperature 40℃, injection volume 1 μL. Mobile phase A (0.1% formic acid 10mM ammonium formate 95% water solution), mobile phase B (0.1% formic acid 10mM ammonium formate 95% acetonitrile solution). |
| Instrument Name: | ACQUITY UPLC |
| Column Name: | Agilent AdvanceBio MS Spent Media (50 x 2.1mm, 2.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0.0min 10% A; 3min 40% A; 4min 40% A; 4.1min 10% A; 6min 10% A |
| Flow Rate: | 0.5ml/min |
| Internal Standard: | 100 μg/mL L-Trp-D5, L-Gln-D5 and L-Lys-D4), 216 μL purified water (fisher) and 25 μL of 0.15 % DOC |
| Solvent A: | 100% water; 0.1% formic acid; 10 mM ammonium formate |
| Solvent B: | 95% acetonitrile/5% water0.1% formic acid; 10 mM ammonium formate |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN006930 |
| Analysis Type: | MS |
| Chromatography ID: | CH005262 |
| Num Factors: | 4 |
| Num Metabolites: | 21 |
| Units: | ng/ml |
