Summary of Study ST002960
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 PR001842. The data can be accessed directly via it's Project DOI: 10.21228/M8MH8P 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 | ST002960 |
| Study Title | Analysis of Lipids Secreted from Fibroblast Young Cells |
| Study Summary | In this experimental study, we aimed to understand the potential factors within the secretions of young cells that could trigger the reverse aging of Mid-old cells. To investigate this phenomenon, we co-cultured young cells with Mid-old cells and observed a fascinating outcome: the Mid-old cells exhibited reverse aging and transformed into a more youthful state. To uncover the specific factors responsible for this reverse aging effect, we conducted a detailed analysis of the secreted factors from the young cells. Our analysis focused on a range of biomolecules, including lipids. However, despite our efforts, we did not identify any distinct factors that could be directly attributed to this remarkable reverse aging process. |
| Institute | Ajou University Medical Center |
| Last Name | Kim |
| First Name | Young Hwa |
| Address | 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea |
| skyblue32@nate.com | |
| Phone | +82-10-5153-3636 |
| Submit Date | 2023-11-01 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-22 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001842 |
| Project DOI: | doi: 10.21228/M8MH8P |
| Project Title: | Mid-Old Cells are Potential Target for Anti-aging Interventions in the Elderly |
| Project Summary: | The biological process of aging is thought to result in part from accumulation of senescent cells in organs. However, the present study identified a subset of fibroblasts and smooth muscle cells which are the major constituents of organ stroma neither proliferative nor senescent in tissues of the elderly, which we termed “mid-old status” cells. Upregulation of pro-inflammatory genes (IL1B and SAA1) and downregulation of anti-inflammatory genes (SLIT2 and CXCL12) were detected in mid-old cells. In the stroma, SAA1 promotes development of the inflammatory microenvironment via upregulation of MMP9, which decreases the stability of epithelial cells present on the basement membrane, decreasing epithelial cell function. Remarkably, the microenvironmental change and the functional decline of mid-old cells could be reversed by a young cell-originated protein, SLIT2. Our data identify functional reversion of mid-old cells as a potential method to prevent or ameliorate aspects of aging-related tissue dysfunction. |
| Institute: | Ajou University Medical Center |
| Last Name: | Kim |
| First Name: | Young Hwa |
| Address: | 206, World cup-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, Republic of Korea |
| Email: | skyblue32@nate.com |
| Phone: | +82-10-5153-3636 |
Subject:
| Subject ID: | SU003073 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample_type |
|---|---|---|
| SA322373 | 20210625_AJU_M3_lipidomics | Control sample |
| SA322374 | 20210625_AJU_M2_lipidomics | Control sample |
| SA322375 | 20210625_AJU_M1_lipidomics | Control sample |
| SA322376 | 20210625_AJU_Y2_lipidomics | Test sample |
| SA322377 | 20210625_AJU_Y3_lipidomics | Test sample |
| SA322378 | 20210625_AJU_Y1_lipidomics | Test sample |
| Showing results 1 to 6 of 6 |
Collection:
| Collection ID: | CO003066 |
| Collection Summary: | The experiment was initiated by seeding the cells in a 100mm cell culture dish, followed by a 2-day incubation period, during which the culture medium was carefully harvested from the cell culture dish. Use a sterile technique to minimize contamination. Transfer the harvested culture medium to a suitable container. |
| Collection Protocol Filename: | Sample_collection_lipid.pdf |
| Sample Type: | Cultured fibroblasts |
Treatment:
| Treatment ID: | TR003082 |
| Treatment Summary: | no treatment |
Sample Preparation:
| Sampleprep ID: | SP003079 |
| Sampleprep Summary: | For lipid extraction from samples, a two-step method involving neutral and acidic extraction were used. At first, in neutral extraction, lipids from the samples were extracted according to the Folch method using a mixture of chloroform and methanol (2:1, v/v). The samples were vortexed and incubated on ice for 10 min. The samples were centrifuged at 13,800×g for 2 min at 4°C, supernatant was transferred to a new 1.5 mL tube. Next, in Acidic extraction, 750 μL of chloroform:methanol:HCl (1N, 37%) (40:80:1, v/v/v) was added to the remaining samples. After incubating for 15 min at room temperature, 250 μL of cold chloroform and 450 μL of cold 0.1 M HCl were added to the sample. The mixture was vortexed for 1 min and centrifuged at 6,500×g for 2 min at 4°C. The lower organic phase was collected and combined with the prior extract. The sample was then dried using HyperVAC-MAX VC2200 centrifugal vacuum concentrator (Hanil Scientific Inc., Korea). Dried metabolite contents were reconstituted in 50 µL of mobile phase solvent A:solvent B (2 :1, v/v) and then subjected to LC-MS/MS analysis. |
| Sampleprep Protocol Filename: | Sample_prep_lipid.pdf |
Combined analysis:
| Analysis ID | AN004861 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 1290 Infinity UHPLC |
| Column | Thermo Hypersil GOLD C18 (100 x 2.1mm,1.9um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Q Exactive™ Hybrid Quadrupole-Orbitrap MS |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH003669 |
| Methods Filename: | LC_MS_Method_lipid.pdf |
| Instrument Name: | Agilent 1290 Infinity UHPLC |
| Column Name: | Thermo Hypersil GOLD C18 (100 x 2.1mm,1.9um) |
| Column Temperature: | 320℃ |
| Flow Gradient: | 0–5 min, 5% B; 5–15 min, 5–30% B; 15–22 min, 30–90% B; 22–25 min, 90% B; 25–26 min, 90–5% B; 26–30 min, 5% B. Parameters were set as follows: positive mode, spray voltage; 3.8 kV |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | Acetonitrile:Methanol:Water (19:19:2, v/v/v) + 20 mmol/L ammonium formate + 0.1% formic acid (v/v) |
| Solvent B: | 2-propanol + 20 mmol/L ammonium formate + 0.1% formic acid (v/v) |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004605 |
| Analysis ID: | AN004861 |
| Instrument Name: | Q Exactive™ Hybrid Quadrupole-Orbitrap MS |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Obtained UHPLC-Orbitrap-MS/MS RAW files were processed using Lipid Search 4.2TM (Thermo Fisher Scientific, Waltham, MA, USA). Lipid profiling under the following conditions: parent search; 0.2 Da, product search; 5.0 ppm, precursor ion mass tolerance; 8.0 ppm, M-score threshold; 2.0. |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | MS_Analysis_lipid.pdf |
