Summary of Study ST003517
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 PR002162. The data can be accessed directly via it's Project DOI: 10.21228/M8581K 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 | ST003517 |
| Study Title | Identify key lipid species in CAF-PDAC crosstalk under hypoxia |
| Study Summary | This study ran lipidomic profiling to identify the lipids enriched in CAF-conditioned media and depleted in PDAC cell culture under hypoxia at 72 hours. |
| Institute | University of Pennsylvania |
| Last Name | Han |
| First Name | Xu |
| Address | 421 Curie Blvd, #438, Philadelphia, PA 19104 |
| Xu.Han@pennmedicine.upenn.edu | |
| Phone | 2138060245 |
| Submit Date | 2024-10-10 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-11-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002162 |
| Project DOI: | doi: 10.21228/M8581K |
| Project Title: | Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment |
| Project Summary: | Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with abundant cancer-associated fibroblasts (CAFs) creating hallmark desmoplasia that limits oxygen and nutrient delivery. This study explores the importance of lipid homeostasis under stress. Exogenous unsaturated lipids, rather than de novo synthesis, sustain PDAC cell viability by relieving endoplasmic reticulum (ER) stress under nutrient scarcity. Furthermore, CAFs are less hypoxic than adjacent malignant cells in vivo, nominating them as a potential source of unsaturated lipids. CAF conditioned medium promotes PDAC cell survival upon nutrient and oxygen deprivation, an effect reversed by delipidation. Lysophosphatidylcholines (LPCs) are particularly enriched in CAF conditioned medium and preferentially taken up by PDAC cells, where they are converted to phosphatidylcholine (PC) to sustain membrane integrity. Blocking LPC to PC conversion inhibits PDAC cell survival and increases ER stress. These findings reveal a critical lipid “cross-feeding” mechanism that promotes PDAC cell survival, offering a potential metabolic target for treatment. |
| Institute: | University of Pennsylvania |
| Last Name: | Han |
| First Name: | Xu |
| Address: | 421 Curie Blvd, #438 |
| Email: | Xu.Han@pennmedicine.upenn.edu |
| Phone: | 213-806-0245 |
Subject:
| Subject ID: | SU003646 |
| Subject Type: | Mammal |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor | Sample source |
|---|---|---|---|
| SA386437 | Basemedia | 0.5% FBS in DMEM | media |
| SA386438 | Pre-PSC CM_Hypo | 5X concerntrated conditioned meida from PSC under 48H hypoxic culture | media |
| SA386439 | Pre-PSC CM_Norm | 5X concerntrated conditioned meida from PSC under 48H normoxic culture | media |
| SA386440 | Post-PSC CM_Norm_1 | Conditioned media (sample #3) after PANC1 cell culture after 72H under SO | media |
| SA386441 | Post-PSC CM_Norm_2 | Conditioned media (sample #3) after PANC1 cell culture after 72H under SO | media |
| SA386442 | Post-PSC CM_Norm_3 | Conditioned media (sample #3) after PANC1 cell culture after 72H under SO | media |
| SA386443 | Post-PSC CM_Hypo_1 | Conditioned media (sample #4) after PANC1 cell culture after 72H under SO | media |
| SA386444 | Post-PSC CM_Hypo_2 | Conditioned media (sample #4) after PANC1 cell culture after 72H under SO | media |
| SA386445 | Post-PSC CM_Hypo_3 | Conditioned media (sample #4) after PANC1 cell culture after 72H under SO | media |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO003639 |
| Collection Summary: | Media were collected after PSC culture under normoxia or hypoxia at 48 hours, and concentrated for LC-MS. PDAC supernatant is collected after culturing under hypoxia at 72 hours. |
| Sample Type: | Media |
Treatment:
| Treatment ID: | TR003655 |
| Treatment Summary: | Human CAFs were seeded in DMEM containing 10% FBS. Cell culture media were changed to DMEM with 0.5% BSA (Sigma, A1595) at 80% confluency and cultured for 48 hours under 21% O2 (oxygen) or 0.5% O2. Conditioned media were collected and centrifuged at 300 x g to remove cell debris and transferred to 3KDa Amicon Ultra Centrifugal Filter (Millipore, UFC900308) and concentrated ~30-fold. Control medium was collected and concentrated from 0.5% BSA, DMEM. Concentrated conditioned media or control media were resuspended in DMEM with 0.5% FBS and applied to PDAC cell culture with indicated conditions. |
Sample Preparation:
| Sampleprep ID: | SP003653 |
| Sampleprep Summary: | For media extraction, 1 mL media was spiked with same internal standards as the cells. 5 mL methyl tert-butyl ether (MTBE) was added to each of the tubes. After vortexing and shaking, to each tube was added 1.2 mL water, vortexed and centrifuged at 300 x g. The top layer was moved to clean glass Pyrex tubes and dried down under nitrogen. To each tube was added with 100 µL of MTBE/MeOH=1/3, vortexed for 30 seconds, spined for 10 minutes at room temperature at 300 x g. Samples were analysed with a Dionex 3000 coupled to QE Exactive-HF mass spectrometer (Thermo Fisher Scientific), exactly as described in PMCID: PMC9399481. |
Combined analysis:
| Analysis ID | AN005774 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | Thermo Accucore C18 (100 x 2.1mm, 2.6um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | AUC |
Chromatography:
| Chromatography ID: | CH004382 |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | Thermo Accucore C18 (100 x 2.1mm, 2.6um) |
| Column Temperature: | 55°C |
| Flow Gradient: | 10 % B at 0 min, 10 % B at 1 min, 40 % B at 4 min, 75 % B at 12 min, 99 % B at 21 min, 99 % B at 24 min, 10 % B at 24.5 min, 10 % at 30 min. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 40% Water/60% Acetonitrile; 0.1% Formic acid, 10 mM Ammonium formate |
| Solvent B: | 10% Acetonitrile/90% Isopropanol; 0.1% Formic acid and 10 mM Ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005494 |
| Analysis ID: | AN005774 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | For the HRMS analysis, a recently calibrated QE Exactive-HF mass spectrometer (Thermo Fisher Scientific) was used in positive ion mode with an HESI source. The operating conditions were: spray voltage at 3.5 kV; capillary temperature at 285°C; auxiliary temperature 370°C; tube lens 45. Nitrogen was used as the sheath gas at 45 units, the auxiliary gas at 10 units and sweep gas was 2 units. Same MS conditions were used in negative ionization mode, but with a spray voltage at 3.2 kV. Control extraction blanks were made in the same way using just the solvents instead of the tissue homogenate. The control blanks were used for the exclusion list with a threshold feature intensity set at 1e10^5. Untargeted analysis and targeted peak integration was conducted using LipidsSearch 4.2 (Thermo Fisher Scientific) as described by Wang et al ( DOI: 10.4155/bio-2021-0098). |
| Ion Mode: | POSITIVE |
