Summary of Study ST001708
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 PR001093. The data can be accessed directly via it's Project DOI: 10.21228/M8DT31 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 | ST001708 |
Study Title | Oxylipin biosynthesis reinforces cellular senescence through a RAS/p53 feedback loop and allows detection of senolysis |
Study Summary | Cellular senescence is a stress or damage response that causes a permanent proliferative arrest and secretion of numerous factors with potent biological activities. This senescence-associated secretory phenotype (SASP) has been characterized largely for secreted proteins that participate in embryogenesis, wound healing, inflammation and many age-related pathologies. By contrast, lipid components of the SASP are understudied. We show that senescent cells activate the biosynthesis of several oxylipins that promote segments of the SASP and reinforce the proliferative arrest. Notably, senescent cells synthesize and accumulate an unstudied intracellular prostaglandin, 1a,1b-dihomo-15-deoxy-delta-12,14-prostaglandin J2. Released 15-deoxy-delta-12,14-prostaglandin J2 is a biomarker of senolysis in culture and in vivo. This and other prostaglandin D2-related lipids promote the senescence arrest and SASP by activating RAS signaling. These data identify an important aspect of cellular senescence and a method to detect senolysis |
Institute | Buck Institute for Research on Aging |
Last Name | Sharma |
First Name | Rishi |
Address | 8001 Redwood Blvd, Novato, CA, 94945, USA |
sharmarishi2004@yahoo.co.in | |
Phone | 5084392367 |
Submit Date | 2021-02-20 |
Raw Data Available | Yes |
Raw Data File Type(s) | d |
Analysis Type Detail | LC-MS |
Release Date | 2021-08-10 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR001093 |
Project DOI: | doi: 10.21228/M8DT31 |
Project Title: | Oxylipin biosynthesis reinforces cellular senescence through a RAS/p53 feedback loop and allows detection of senolysis |
Project Summary: | Cellular senescence is a stress or damage response that causes a permanent proliferative arrest and secretion of numerous factors with potent biological activities. This senescence-associated secretory phenotype (SASP) has been characterized largely for secreted proteins that participate in embryogenesis, wound healing, inflammation and many age-related pathologies. By contrast, lipid components of the SASP are understudied. We show that senescent cells activate the biosynthesis of several oxylipins that promote segments of the SASP and reinforce the proliferative arrest. Notably, senescent cells synthesize and accumulate an unstudied intracellular prostaglandin, 1a,1b-dihomo-15-deoxy-delta-12,14-prostaglandin J2. Released 15-deoxy-delta-12,14-prostaglandin J2 is a biomarker of senolysis in culture and in vivo. This and other prostaglandin D2-related lipids promote the senescence arrest and SASP by activating RAS signaling. These data identify an important aspect of cellular senescence and a method to detect senolysis. |
Institute: | Buck Institute for Research on Aging |
Last Name: | Sharma |
First Name: | Rishi |
Address: | 8001 Redwood Blvd, Novato, CA, 94945, USA |
Email: | sharmarishi2004@yahoo.co.in |
Phone: | 5084392367 |
Subject:
Subject ID: | SU001785 |
Subject Type: | Cultured cells |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
mb_sample_id | local_sample_id | Factor |
---|---|---|
SA159037 | IR_DOXOABT_1 | DOXOABT |
SA159038 | A-121 | Mouse plasma |
SA159039 | Ctl_61120 | SEN Cells_Ctls |
SA159040 | IR_15_60120 | SENCells_IR |
Showing results 1 to 4 of 4 |
Collection:
Collection ID: | CO001778 |
Collection Summary: | Cell culture: Human fetal lung fibroblasts (IMR-90) and HEPG2 cells were cultured in Dulbecco’s modified eagle medium (DMEM - Gibco) supplemented with 10% FBS and penicillin/streptomycin (Gibco). HUVEC cells were obtained from the ATCC and cultured using the ATCC protocol and culture media. Quiescence was induced by replacing culture media with media containing 0.2% FBS for 72 h before analysis. All cells were cultured at 3% O2, and used prior to 40 population doublings, other than replicative senescent cells, which were cultured until replicative exhaustion. All cells were mycoplasma free. Mouse Plasma: Animal experiments were conducted using a protocol approved by the Institutional Animal Care and Use Committee of the Buck Institute. For DOXO treatments, 10-16 wk old p16-3MR mice received one intraperitoneal (i.p.) injection of 10 mg/kg of doxorubicin hydrochloride in PBS, and treated 5 d later with GCV or vehicle. GCV was administered via daily i.p. injections for 5 consecutive days at 25 mg/kg in PBS. Control mice were injected with an equal volume of PBS. Mice were euthanized and tissues collected 10 d after DOXO challenge. For aging studies, C57BL/6 mice were aged for 6 or 24 mo, at which point mice were euthanized and tissues collected for analysis. For the biomarker studies, mice with challenged with DOXO as above, and given either vehicle or ABT-263 6 weeks after DOXO challenge. Whole blood was collected by cardiac puncture into EDTA-tubes (lavender caps – BD Biosciences) and spun at 2000g for 5 minutes. For urine collection, mice were placed in plastic containers prior to euthanasia. |
Sample Type: | Blood (plasma) |
Treatment:
Treatment ID: | TR001798 |
Treatment Summary: | Cell culture: Human fetal lung fibroblasts (IMR-90) and HEPG2 cells were cultured in Dulbecco’s modified eagle medium (DMEM - Gibco) supplemented with 10% FBS and penicillin/streptomycin (Gibco). HUVEC cells were obtained from the ATCC and cultured using the ATCC protocol and culture media. Quiescence was induced by replacing culture media with media containing 0.2% FBS for 72 h before analysis. All cells were cultured at 3% O2, and used prior to 40 population doublings, other than replicative senescent cells, which were cultured until replicative exhaustion. All cells were mycoplasma free. Mouse Plasma: Animal experiments were conducted using a protocol approved by the Institutional Animal Care and Use Committee of the Buck Institute. For DOXO treatments, 10-16 wk old p16-3MR mice received one intraperitoneal (i.p.) injection of 10 mg/kg of doxorubicin hydrochloride in PBS, and treated 5 d later with GCV or vehicle. GCV was administered via daily i.p. injections for 5 consecutive days at 25 mg/kg in PBS. Control mice were injected with an equal volume of PBS. Mice were euthanized and tissues collected 10 d after DOXO challenge. For aging studies, C57BL/6 mice were aged for 6 or 24 mo, at which point mice were euthanized and tissues collected for analysis. For the biomarker studies, mice with challenged with DOXO as above, and given either vehicle or ABT-263 6 weeks after DOXO challenge. Whole blood was collected by cardiac puncture into EDTA-tubes (lavender caps – BD Biosciences) and spun at 2000g for 5 minutes. For urine collection, mice were placed in plastic containers prior to euthanasia. |
Sample Preparation:
Sampleprep ID: | SP001791 |
Sampleprep Summary: | Protocol for Lipid Extraction (10.24.2019) Lipid Biomarker for Senolysis Study 1. 80% MeOH was added to each sample 500µL to plasma samples 100µL to urine sample 2. Transfer the contents to 9 mL glass tube and add 1.0 mL of CHCl3 (containing 200 ng/mL FA 17:0 Saturated). Vortex mix for 5 minutes. 3. Place the glass tube into a 15mL polypropylene culture tube with Kimi wipes inserted at bottom as a cushion. Wrap the culture tube with paraffin and place in centrifuge. This will prevent glass tube being shattered in the centrifuge. 4. Centrifuge at 4°C for 10 minutes 3000rpm. 5. After spinning there will be two distinct layers, the top layer is the aqueous layer containing the aqueous metabolites (80% MeOH) and bottom layer which contains lipids. 6. Transfer the lower layer into 1.5ml vials. 7. Transfer from the 1.5mL tube the exact amount of each sample into the MS/HPLC glass vial and dry down using nitrogen gas. 8. Reconstitute the lipids with 80µL chloroform. 9. Transfer upper layer (metabolites) into labeled vials and store at -80°C, if possible. Samples stored in -80°C. Sample volume submitted -Plasma samples=50µL Urine samples= 10µL Sample volume in each vial- Plasma samples µL and Urine samples µL -submitted to mass spec All samples were split in half ½ given to CW for further testing other 1/2 in -80°C |
Combined analysis:
Analysis ID | AN002782 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Agilent 6520 |
Column | Phenomenex Kinetex C18 (150 x 2.1mm,2.6um) |
MS Type | ESI |
MS instrument type | QToF |
MS instrument name | Agilent 6520 QTOF |
Ion Mode | NEGATIVE |
Units | Peak Area |
Chromatography:
Chromatography ID: | CH002058 |
Instrument Name: | Agilent 6520 |
Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,2.6um) |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS002578 |
Analysis ID: | AN002782 |
Instrument Name: | Agilent 6520 QTOF |
Instrument Type: | QToF |
MS Type: | ESI |
MS Comments: | Full scan mode was used. Data processed using profinder software |
Ion Mode: | NEGATIVE |