Summary of Study ST004296
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 PR002702. The data can be accessed directly via it's Project DOI: 10.21228/M8D27Z This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004296 |
| Study Title | (MS data) Global metabolomics identifies new extracellular biomarkers of nanovibration-driven mesenchymal stem cells osteodifferentiation |
| Study Summary | This study characterizes the metabolic adaptations of mesenchymal stem cells (MSCs) to chemical-free nanovibration (nanokicking, NK)-induced osteodifferentiation. Upon reaching the cell numbers required for metabolomic analysis (500,000 cells per sample for LC–MS), day 0 samples were collected in triplicate prior to stimulation. The remaining 24-well plates were divided into unstimulated controls (CTR) and NK-stimulated groups. The NK bioreactor uses the reverse piezoelectric effect to generate 30 nm vertical displacements at a frequency of 1000 Hz, providing a purely mechanical stimulus without chemical induction. For intracellular lipidomics, CTR and NK cells were collected in triplicate on days 0, 7, and 21. Through the integration of conventional osteogenic gene markers with global metabolomics and lipidomics analyses, our findings reveal that NK stimulation promotes a slow-paced osteodifferentiation process characterized by subtle, partially reversible intracellular changes and pronounced, largely irreversible extracellular alterations, highlighting the metabolic reprogramming underlying mechanically induced osteogenesis. |
| Institute | University of Aveiro |
| Department | Chemistry |
| Laboratory | CICECO - Aveiro Institute of Materials |
| Last Name | Gil |
| First Name | Ana M. |
| Address | CICECO, Departamento de química, Campus de Santiago, Aveiro, Portugal |
| agil@ua.pt | |
| Phone | +351234370707 |
| Submit Date | 2025-09-11 |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-10-18 |
| Release Version | 1 |
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Project:
| Project ID: | PR002702 |
| Project DOI: | doi: 10.21228/M8D27Z |
| Project Title: | Global metabolomics identifies new extracellular biomarkers of nanovibration-driven mesenchymal stem cells osteodifferentiation |
| Project Summary: | Bone-related conditions are a leading cause of disability and rising healthcare costs, prompting interest in tissue engineering solutions using mesenchymal stem cells (MSC). As part of an effort to eliminate synthetic osteogenic compounds, this study characterizes the metabolic adaptations of MSC to chemical-free nanovibration (or nanokicking, NK)-induced osteodifferentiation. Through articulation of conventional gene markers and a global metabolomics/lipidomics strategy, our findings indicate successful slow-paced osteodifferentiation, expressed by subtle and partially reversible intracellular changes, and pronounced, largely irreversible, extracellular alterations. |
| Institute: | University of Aveiro |
| Department: | Chemistry |
| Laboratory: | CICECO - Aveiro Institute of Materials |
| Last Name: | Gil |
| First Name: | Ana M. |
| Address: | CICECO, Departamento de química, Campus de Santiago, Aveiro, Portugal |
| Email: | agil@ua.pt |
| Phone: | +351 234 370 707 |
| Funding Source: | This work was developed within the scope of the CICECO-Aveiro Institute of Materials, UIDB/50011/2020 project (doi: 10.54499/UIDB/50011/2020), UIDP/50011/2020 (doi: 10.54499/UIDP/ 50011/2020) and LA/P/0006/2020 (doi:10.54499/LA/P/0006/2020), financed by national funds through the FCT/MCTES (PIDDAC). We acknowledge funds from the Foundation for Science and Technology through the BetterBone project (2022.04286.PTDC, doi: 10.54499/2022.04286.PTDC), the Portuguese National NMR Network (RNRMN), supported by Infrastructure Project Nº 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL and FCT through PIDDAC); and FCT/SPQ PhD grant (DSCB) (SFRH/BD/150655/2020, doi: 10.54499/SFRH/BD/150655/2020). EPSRC grant EP/P001114/1. |
Subject:
| Subject ID: | SU004449 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Age Or Age Range: | 29 |
| Weight Or Weight Range: | Healthy |
| Gender: | Female |
| Cell Strain Details: | Human adipose tissue-derived stem cells |
| Cell Passage Number: | 3 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Treatment |
|---|---|---|---|
| SA504670 | NK_D7_S2 | hASCs | Osteogenic conditions |
| SA504671 | NK_D7_S1 | hASCs | Osteogenic conditions |
| SA504672 | NK_D7_S3 | hASCs | Osteogenic conditions |
| SA504673 | NK_D21_S1 | hASCs | Osteogenic conditions |
| SA504674 | NK_D21_S2 | hASCs | Osteogenic conditions |
| SA504675 | NK_D21_S3 | hASCs | Osteogenic conditions |
| SA504676 | CTR_D0_S1 | hASCs | Proliferation conditions |
| SA504677 | CTR_D0_S2 | hASCs | Proliferation conditions |
| SA504678 | CTR_D0_S3 | hASCs | Proliferation conditions |
| SA504679 | CTR_D7_S1 | hASCs | Proliferation conditions |
| SA504680 | CTR_D7_S2 | hASCs | Proliferation conditions |
| SA504681 | CTR_D7_S3 | hASCs | Proliferation conditions |
| SA504682 | CTR_D21_S1 | hASCs | Proliferation conditions |
| SA504683 | CTR_D21_S2 | hASCs | Proliferation conditions |
| SA504684 | CTR_D21_S3 | hASCs | Proliferation conditions |
| Showing results 1 to 15 of 15 |
Collection:
| Collection ID: | CO004442 |
| Collection Summary: | hAMSC were donated from Histocell (Bilbao, Spain), derived from a healthy 29-year-old female donor undergoing liposuction with written informed consent. |
| Collection Protocol ID: | Protocol no. E08-30 |
| Sample Type: | Stem cells |
| Storage Conditions: | -80℃ |
| Tissue Cell Identification: | Adipose Tissue |
Treatment:
| Treatment ID: | TR004458 |
| Treatment Summary: | Upon reaching the cell numbers necessary for metabolomics (> 1 million cells/sample for NMR, and 500 k cells/sample for LC-MS), day 0 cell samples were collected in triplicate prior to stimulation. The remaining cell culture T150 flasks (for NMR metabolomics) and 24-well plates (for MS lipidomics, Alamar blue (AB) assay and qRT-PCR) were split into unstimulated (control, CTR) and NK-stimulated groups. As previously described,[30,32] the NK bioreactor employs the reverse piezoelectric effect to induce mechanical expansions from applied voltages, enabling 30 nm vertical displacements to cell cultures at a frequency of 1000 Hz. To ensure consistent amplitudes across the growth surfaces while allowing for easy removal and maintenance, culture flasks/plates were firmly attached to the bioreactor using magnetic sheets. For intracellular NMR metabolomics (endometabolomics) and MS lipidomics, CTR and NK cells were trypsinized and collected in triplicate on days 0, 7 and 21. The resulting cell suspensions were filtered through 100 μm pore strainers, centrifuged (300 g, 5 min, 4°C) and rinsed twice with phosphate-buffered saline (PBS) solution. For extracellular NMR metabolomics (exometabolomics), media samples were collected on days 3, 6, 7, 10, 13, 17, 20 and 21. Blank media (not cell-exposed) was also obtained. Media and cell samples were stored (− 80°C) until analysis. |
| Cell Media: | α-MEM (Gibco™ 12000063, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics |
| Cell Harvesting: | Days 0, 7 and 21 |
| Cell Pct Confluence: | 100% |
Sample Preparation:
| Sampleprep ID: | SP004455 |
| Sampleprep Summary: | Lipids were analyzed by LC-MS using a Thermo Q-Exactive Orbitrap mass spectrometer equipped with a heated electrospray ionization (HESI) probe and interfaced with a Dionex UltiMate 3000 RSLC system (Thermo Fisher Scientific, Hemel Hempstead, UK). Samples (10 µL) were injected onto a Thermo Hypersil Gold C18 column (2.1 mm × 100 mm; 1.9 μm) maintained at 50°C. Mobile phase A consisted of water containing 10 mM ammonium formate and 0.1% (v/v) formic acid. Mobile phase B consisted of a 90/10 (v/v) mixture of isopropanol/acetonitrile containing 10 mM ammonium formate and 0.1% (v/v) formic acid. The initial conditions for analysis were 65% mobile phase A, 35% mobile phase B and the percentage of mobile phase B was increased from 35 to 65% over 4 min, followed by 65% to 100% over 15 min, with a hold for 2 min before re-equilibration to the starting conditions over 6 min. The flow rate was 400 μL/min. All samples were analyzed in positive and negative ionization modes over the mass-to-charge ratio (m/z) range of 250 to 2,000 at a resolution of 60,000. |
| Extraction Method: | methanol-chloroform-water extraction method |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH005426 |
| Instrument Name: | Thermo Q-Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific) |
| Column Name: | Thermo Hypersil Gold C18 (2.1 mm × 100 mm; 1.9 μm) |
| Column Temperature: | 50℃ |
| Flow Gradient: | 0–4 min: 35% → 65% B; 4–19 min: 65% → 100% B; 19–21 min: 100% B (hold); 21–27 min: re-equilibrate to 35% B |
| Flow Rate: | 400 µL/min |
| Solvent A: | 100% Water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 90% Isopropanol/10% Acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN007142 |
| Analysis Type: | MS |
| Chromatography ID: | CH005426 |
| Num Factors: | 2 |
| Num Metabolites: | 33 |
| Units: | Normalized abundance |
| Analysis ID: | AN007143 |
| Analysis Type: | MS |
| Chromatography ID: | CH005426 |
| Num Factors: | 2 |
| Num Metabolites: | 34 |
| Units: | Normalized abundance |
