CD performed compound identification using built-in spectral libraries, including LipidBlast (VS 68) and mzCloud (2021B). Positive and negative ion mode data were processed separately. The data was archived and exported for statistical analysis in R (version 4.4.1). Total fatty acids were analyzed using Skyline (version 24.1.1.254) and normalized to the total sum area of all fatty acids in each sample.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["A 2 mL volume of each sample was injected onto an ACQUITY Premier CSH C18 column (2.1 x 100 mm, 1.7 mm particle size) maintained at 65°C in a Thermo Vanquish UHPLC system. Gradient elution utilized two mobile phases: A (60% acetonitrile, 38.9% water, 0.1% formic acid, and 1M ammonium formate) and B (88.9% 2-propanol, 10% acetonitrile, 0.1% formic acid, and 1M ammonium formate). Mobile phase flow rate was set to 0.25 mL/min, and the following mobile phase gradient was used: 0-1 min, 15% B; 1-2 min, 15-30% B; 3-3.5 min, 30-48% B; 3.5-12 min, 48-82% B; 12-13 min, 82-99% B; 13-13.1 min, 99-15% B; 13.1-17 min, 15% B.
"],"publication":["Characterizing ex vivo models for studying lipid metabolism in triple negative breast cancer. 10.1016/j.jlr.2026.101074. PMID:42242475"],"submitter_name":["Naruenan naruenan@student.ubc.ca"],"submitter_affiliation":["University of British Columbia"],"organism_part":["Triple-Negative Breast Carcinoma"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Lipids were extracted from frozen tumour fragments and slices using a modified Matyash method. Briefly, samples were suspended in ice-cold Milli-Q water and methanol (30:225, v/v) at a ratio of 1 mg per 60 mL. Samples were homogenized in bead-mill homogenizer for 2 cycles of 30s at 6.5 m/s, using zirconium beads (BioSpec). 750 mL of ice-cold methyl tert-butyl ether (MTBE) containing 0.5 mM C17-ceramide (internal standard) was subsequently added to 255 mL of homogenate. The samples were vortexed and incubated for 10 minutes (4°C, 650 rpm). 188 mL of Milli-Q water was added to followed by centrifugation for 20 minutes (16,000 x g, 4°C). 300 mL of MTBE-containing layer was pipetted into a glass tube and evaporated under nitrogen (TurboVap). Extracted lipids were reconstituted in 200 mL of isopropanol: acetonitrile (50:50, v/v) for LC-MS analysis. A pooled sample was prepared as a quality control (QC) by combining 5 mL from each sample. Samples were maintained at 12°C and were randomized. Pooled samples were injected every 10 samples.
"],"organism":["blank","Mus sp.","Chorioallantoic Membrane","ex vivo design","Quality Control"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS13377"],"author":["Chloe White. University of British Columbia. 2405 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3. chloew99@student.ubc.ca.","Thomas Velenosi. University of British Columbia. 2405 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3. thomas.velenosi@ubc.ca.","Naruenan Wongreatong. University of British Columbia. 2405 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3. naruenan@student.ubc.ca.","Karla Williams. University of British Columbia. 2405 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3. karla.williams@ubc.ca.","Yong Jin Lim. University of British Columbia. 2405 Wesbrook Mall, Vancouver, BC, Canada, V6T 1Z3. james.lim@ubc.ca."],"data_transformation_protocol":["Raw data were processed in Compound Discoverer (CD) 3.3 (Thermo). CD performed peak integration, retention time alignment, feature detection and grouping, and SERRF quality control correction.
"],"study_factor":["Preservation type","Tumour type","Time period"],"submitter_email":["naruenan@student.ubc.ca"],"sample_collection_protocol":["TNBC-PDX tumour bearing mice were euthanized, and tumours were excised aseptically. Tumours were cut in half along the major axis. One half was placed, flat side down, on a tissue chopper slide, covered in 2% low melting point agarose and sliced into 500 µm slices using a McIlwain Tissue Chopper (Ted Pella, Inc.), as previously described. TNBC tumour slices were and washed twice in PBS placed into a 6-well plate containing 3mL of prewarmed RPMI (Corning) containing 10% FBS and 100U/mL penicillin/streptomycin/antimycotic (Corning). Ex vivo slices were cultured on an orbital shaker in a humidified 37°C incubator under 5% CO2. Fresh media was provided to ex vivo slices every two days and harvested on day 2, 4, 7, and 9 for analysis. The remaining half of the excised TNBC-PDX tumours from above was segmented into ~2mm3 fragments and used for CAM-PDX engraftment. Fertilized eggs were obtained from Poultry Research centre (AB, Canada). The eggs were incubated for 2 days at 37°C with rotation. On embryonic day 3, the eggs were cracked followed by surface scoring and tumour fragment engraftment. Tumour engraftments were performed using fresh tumour (primary TM00099 and metastatic TM00096) and cryopreserved tumour fragments (metastatic TM00096). Tumour samples were collected over the engraftment period at day 2, 4, 7, and 9 for analysis.
"],"omics_type":["Metabolomics"],"study_design":["pooled quality control sample","triple-negative breast cancer","Triple-Negative Breast Carcinoma","blank","untargeted analysis","Thermo Scientific Orbitrap IQ-X Tribrid","ex vivo design","experimental sample","Thermo Scientific Vanquish UHPLC System","Mus sp.","untargeted metabolites","experimental blank","Chorioallantoic Membrane","Quality Control"],"curator_keywords":["pooled quality control sample","triple-negative breast cancer","Triple-Negative Breast Carcinoma","blank","untargeted analysis","Thermo Scientific Orbitrap IQ-X Tribrid","ex vivo design","experimental sample","Thermo Scientific Vanquish UHPLC System","Mus sp.","untargeted metabolites","experimental blank","Chorioallantoic Membrane","Quality Control"],"mass_spectrometry_protocol":["Mass spectrometry (MS) analysis was conducted using a Thermo Scientific Orbitrap IQ-X Tribid Mass Spectrometer with the following instrument conditions: 3.5 kV spray voltage for positive ion and 2.4k for negative ion, 300°C ion transfer tube, 350°C vaporizer temperature. Ions in MS1 were acquired between 250-1500 m/z in the orbitrap at 120k resolution. AcquireX workflow was used to generate fragmentation on pooled samples by alternating between stepped higher-energy collisional dissociation (HCD) with energies of 20%, 30%, and 40% and collision-induced dissociation (CID) at 30%. Total fatty acids were acquired in negative ionization mode using the same LCMS method.
"],"pubmed_abstract":["Lipid metabolism drives cancer progression but is difficult to model using conventional methods. In vivo models provide access to circulating lipids, but are costly and low throughput, while in vitro models lack sufficient lipid availability in culture media. Here, we evaluate the chick chorioallantoic membrane (CAM) patient-derived xenograft (PDX) and tissue slice models as ex vivo cancer models of lipid metabolism in triple-negative breast cancer (TNBC) over a 9-day incubation period using lipidomics analysis. Differences in the TNBC tumour lipidome were driven by inherent differences between primary and metastatic tumours, then by ex vivo model. Ether-linked phosphatidylcholine and phosphatidylcholine lipids accumulated in CAM xenografts from primary and metastatic TNBC tumours (q < 0.05) but were unchanged in ex vivo tumour slices. Conversely, elevated triacylglycerol, sphingomyelin, and phosphatidylglycerol lipids were prominent in ex vivo tumour slices from primary and metastatic TNBC models when compared to CAM-PDX. Cryopreserved tumour fragments were successfully reanimated, demonstrating a similar lipidome profile to freshly engrafted TNBC tumour fragments in the CAM-PDX model. Hierarchical clustering of total saponifiable fatty acids revealed ex vivo model dependent differences, suggesting that the lipids availability to the tumour environment may influence fatty acyl composition, but not the distribution of esterified lipids. Our findings define the time-dependent lipid subclass accumulation in CAM-PDX and ex vivo tumour slice models, and highlight their utility in the study of the TNBC lipidome."],"pubmed_title":["Characterizing ex vivo models for studying lipid metabolism in triple negative breast cancer."],"pubmed_authors":["Wongreantong Naruenan N, White Chloe A K CAK, Lim Yong Jin YJ, Williams Karla C KC, Velenosi Thomas J TJ"],"additional_accession":[]},"is_claimable":false,"name":"Characterizing ex vivo models for studying lipid metabolism in triple negative breast cancer","description":"Lipid metabolism drives cancer progression but is difficult to model using conventional methods. In vivo models provide circulating lipids, but are costly and low throughput, while in vitro models lack sufficient lipid availability in culture media. Here, we evaluate the chick chorioallantoic membrane (CAM) xenograft and tissue slice models over a 9-day incubation period as ex vivo cancer models of lipid metabolism in triple-negative breast cancer (TNBC) using lipidomics analysis. Differences in the TNBC tumour lipidome were driven by inherent differences between primary and metastatic tumours, then by ex vivo model. Ether-linked phosphatidylcholine (PC-O) and PC lipids accumulated in CAM xenografts from primary and metastatic TNBC tumours (q < 0.05) but were unchanged in ex vivo tumour slices. Conversely, elevated sphingomyelin (SM) and triacylglycerol (TG) lipids were prominent in ex vivo tumour slices from primary and metastatic TNBC models when compared to CAM xenograft samples. Cryopreserved tumour fragments were successfully reanimated, demonstrating a similar lipidome profile to freshly engrafted TNBC tumour fragments in the CAM-PDX model. Total fatty acid analysis revealed ex vivo model dependent differences, suggesting that the availability of lipids in the tumour microenvironment may influence fatty acyl composition, but not the distribution of esterified lipids. In conclusion, the CAM xenograft and tissue slice models serve as robust and cost-effective tools for studying cancer lipid metabolism over time. This study provides a foundation for characterizing unique lipid alterations that support TNBC tumour growth using ex vivo models.
","dates":{"publication":"2026-07-16","submission":"2025-11-25"},"accession":"MTBLS13377","cross_references":{"pubmed":["42242475"]}}