#METABOLOMICS WORKBENCH mjayaram_20230303_090215 DATATRACK_ID:3773 STUDY_ID:ST002555 ANALYSIS_ID:AN004208 VERSION 1 CREATED_ON 02-08-2024 #PROJECT PR:PROJECT_TITLE Ethnicity-Specific Differences in Ovarian Cancer Metabolic Signatures PR:PROJECT_TYPE Cell line analysis PR:PROJECT_SUMMARY Ovarian cancer is a leading cause of cancer-related deaths among women PR:PROJECT_SUMMARY worldwide. Cancer cell metabolism plays a critical role in tumor growth and PR:PROJECT_SUMMARY progression, and metabolic alterations in cancer cells have been implicated in PR:PROJECT_SUMMARY treatment resistance. In this study, we performed metabolomic analysis using PR:PROJECT_SUMMARY ovarian cancer cells derived from patients in the United States and Korea. Our PR:PROJECT_SUMMARY results reveal significant ethnic-specific differences in the metabolic PR:PROJECT_SUMMARY signatures of ovarian cancer cells, with differential regulation of metabolites PR:PROJECT_SUMMARY derived from glycolytic pathways, lipid metabolism, and microbiome modified PR:PROJECT_SUMMARY metabolites. These findings have important therapeutic implications, as PR:PROJECT_SUMMARY differences in ovarian cancer metabolism between ethnic groups may influence PR:PROJECT_SUMMARY treatment response and resistance. Targeting the unique metabolic signatures of PR:PROJECT_SUMMARY ovarian cancer cells based on ethnic specificity may improve the effectiveness PR:PROJECT_SUMMARY of precision medicine approaches in the treatment of ovarian cancer. This study PR:PROJECT_SUMMARY highlights the potential for personalized and targeted therapeutic options based PR:PROJECT_SUMMARY on the tumor metabolome and ethnic background of the patient. Overall, our PR:PROJECT_SUMMARY results suggest that investigating ethnic-specific differences in cancer PR:PROJECT_SUMMARY metabolism is critical for developing effective and personalized cancer PR:PROJECT_SUMMARY therapies. The identification of unique metabolic signatures in ovarian cancer PR:PROJECT_SUMMARY cells based on ethnic specificity provides a promising avenue for improving PR:PROJECT_SUMMARY treatment outcomes and advancing the field of precision medicine in ovarian PR:PROJECT_SUMMARY cancer. PR:INSTITUTE University of Oklahoma Health Sciences Center PR:DEPARTMENT Cell Biology PR:LABORATORY Danny N Dhanasekaran PR:LAST_NAME Jayaraman PR:FIRST_NAME Muralidharan PR:ADDRESS 975 NE 10th street BRC1468 Oklahoma City OK 73104 PR:EMAIL Muralidharan-Jayaraman@ouhsc.edu PR:PHONE 405-271-8001 x30492 PR:DOI http://dx.doi.org/10.21228/M8T413 PR:CONTRIBUTORS Danny N. Dhanasekaran, Jihee Ha, Yong Sang Song #STUDY ST:STUDY_TITLE Ethnicity-Specific Differences in Ovarian Cancer Metabolic Signatures ST:STUDY_TYPE Cultured cells ST:STUDY_SUMMARY Ovarian cancer is a leading cause of cancer-related deaths among women ST:STUDY_SUMMARY worldwide. Cancer cell metabolism plays a critical role in tumor growth and ST:STUDY_SUMMARY progression, and metabolic alterations in cancer cells have been implicated in ST:STUDY_SUMMARY treatment resistance. In this study, we performed metabolomic analysis using ST:STUDY_SUMMARY ovarian cancer cells derived from patients in the United States and Korea. Our ST:STUDY_SUMMARY results reveal significant ethnic-specific differences in the metabolic ST:STUDY_SUMMARY signatures of ovarian cancer cells, with differential regulation of metabolites ST:STUDY_SUMMARY derived from glycolytic pathways, lipid metabolism, and microbiome modified ST:STUDY_SUMMARY metabolites. These findings have important therapeutic implications, as ST:STUDY_SUMMARY differences in ovarian cancer metabolism between ethnic groups may influence ST:STUDY_SUMMARY treatment response and resistance. Targeting the unique metabolic signatures of ST:STUDY_SUMMARY ovarian cancer cells based on ethnic specificity may improve the effectiveness ST:STUDY_SUMMARY of precision medicine approaches in the treatment of ovarian cancer. This study ST:STUDY_SUMMARY highlights the potential for personalized and targeted therapeutic options based ST:STUDY_SUMMARY on the tumor metabolome and ethnic background of the patient. Overall, our ST:STUDY_SUMMARY results suggest that investigating ethnic-specific differences in cancer ST:STUDY_SUMMARY metabolism is critical for developing effective and personalized cancer ST:STUDY_SUMMARY therapies. The identification of unique metabolic signatures in ovarian cancer ST:STUDY_SUMMARY cells based on ethnic specificity provides a promising avenue for improving ST:STUDY_SUMMARY treatment outcomes and advancing the field of precision medicine in ovarian ST:STUDY_SUMMARY cancer. ST:INSTITUTE University of Oklahoma Health Sciences Center ST:DEPARTMENT Cell Biology ST:LABORATORY Danny N. Dhanasekaran ST:LAST_NAME Jayaraman ST:FIRST_NAME Muralidharan ST:ADDRESS 975 NE 10th street BRC1468 Oklahoma City OK 73104 ST:EMAIL Muralidharan-Jayaraman@ouhsc.edu ST:PHONE 405-271-8001 x30492 ST:SUBMIT_DATE 2023-03-03 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:GENDER Female SU:CELL_BIOSOURCE_OR_SUPPLIER SNU3297 and SNU3298, and patient-derived ovarian cancer cells, A#5, A#8, A#39 SU:CELL_BIOSOURCE_OR_SUPPLIER were from Seoul National University, Seoul, South Korea. Patient-derived ovarian SU:CELL_BIOSOURCE_OR_SUPPLIER cancer cells, ASC110515, ASC102315, ASC061616, ASC060915, ASC062915B and SU:CELL_BIOSOURCE_OR_SUPPLIER ASC011215 were from Stephenson Cancer Center, University of Oklahoma Health SU:CELL_BIOSOURCE_OR_SUPPLIER Sciences Center, Oklahoma City, Oklahoma, USA. SU:CELL_PASSAGE_NUMBER 3 to 5 SU:CELL_COUNTS 20 million cells #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS FTE188 OUHSCPD-1 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3298 OUHSCPD-10 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3298 OUHSCPD-11 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3298 OUHSCPD-12 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS FTE188 OUHSCPD-2 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS FTE188 OUHSCPD-3 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS FTE188 OUHSCPD-4 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3297 OUHSCPD-5 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3297 OUHSCPD-6 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3297 OUHSCPD-7 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3297 OUHSCPD-8 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS SNU3298 OUHSCPD-9 Genotype:FTE (Normal) SUBJECT_SAMPLE_FACTORS ASC110515 OUHSCPD-13 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC110515 OUHSCPD-14 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC110515 OUHSCPD-15 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC110515 OUHSCPD-16 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC102315 OUHSCPD-17 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC102315 OUHSCPD-18 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC102315 OUHSCPD-19 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC102315 OUHSCPD-20 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC061616 OUHSCPD-21 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC061616 OUHSCPD-22 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC061616 OUHSCPD-23 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC061616 OUHSCPD-24 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC060915 OUHSCPD-25 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC060915 OUHSCPD-26 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC060915 OUHSCPD-27 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC060915 OUHSCPD-28 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC062915B OUHSCPD-29 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC062915B OUHSCPD-30 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC062915B OUHSCPD-31 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC062915B OUHSCPD-32 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC011215 OUHSCPD-33 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC011215 OUHSCPD-34 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC011215 OUHSCPD-35 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS ASC011215 OUHSCPD-36 Genotype:SCC-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#5 OUHSCPD-37 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#5 OUHSCPD-38 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#5 OUHSCPD-39 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#5 OUHSCPD-40 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#8 OUHSCPD-41 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#8 OUHSCPD-42 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#8 OUHSCPD-43 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#8 OUHSCPD-44 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#39 OUHSCPD-45 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#39 OUHSCPD-46 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#39 OUHSCPD-47 Genotype:SNU-PDOCC (Cancer) SUBJECT_SAMPLE_FACTORS A#39 OUHSCPD-48 Genotype:SNU-PDOCC (Cancer) #COLLECTION CO:COLLECTION_SUMMARY Immortalized normal fallopian-tube-derived epithelial (FTE) cells, FTE188 were CO:COLLECTION_SUMMARY maintained in MCDB105: M199 (1:1) medium (Thermo Fisher Scientific, Waltham, CO:COLLECTION_SUMMARY MA), SNU3297 and SNU3298 were maintained in DMEM/F12 medium (Thermo Fisher CO:COLLECTION_SUMMARY Scientific, Waltham, MA). Patient-derived ovarian cancer cells isolated at CO:COLLECTION_SUMMARY Stephenson Cancer Center (SCC-PDOCC), ASC110515, ASC102315, ASC061616, CO:COLLECTION_SUMMARY ASC060915, ASC062915B and ASC011215, were maintained in MCDB105: DMEM (1:1) CO:COLLECTION_SUMMARY medium (Thermo Fisher Scientific, Waltham, MA). Patient-derived ovarian cancer CO:COLLECTION_SUMMARY cells isolated from Seoul National University (SNU-PDOCC), A#5, A#8, A#39 were CO:COLLECTION_SUMMARY maintained in DMEM/F12 medium. All cells were maintained at 37°C in a 5% CO2 CO:COLLECTION_SUMMARY incubator. All media were supplemented with 10% FBS (Gemini Bio-Products, West CO:COLLECTION_SUMMARY Sacramento, CA), 50 U/mL penicillin, 50 μg/ml streptomycin (Cellgro, Manassas, CO:COLLECTION_SUMMARY VA). Cells were grown to 20 million cells and washed with cold PBS. Cells were CO:COLLECTION_SUMMARY collected by scraping them off the plates. CO:SAMPLE_TYPE Cultured cells CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY No treatment was done. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Samples were prepared using the automated MicroLab STAR® system from Hamilton SP:SAMPLEPREP_SUMMARY Company. Several recovery standards were added prior to the first step in the SP:SAMPLEPREP_SUMMARY extraction process for QC purposes. In order to dissociate small molecules bound SP:SAMPLEPREP_SUMMARY to or trapped in proteins, lysate was precipitated with methanol under vigorous SP:SAMPLEPREP_SUMMARY shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The SP:SAMPLEPREP_SUMMARY resulting extract was divided into five fractions: two for analysis by two SP:SAMPLEPREP_SUMMARY separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode SP:SAMPLEPREP_SUMMARY electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative SP:SAMPLEPREP_SUMMARY ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, SP:SAMPLEPREP_SUMMARY and one sample was reserved for backup. Samples were placed briefly on a SP:SAMPLEPREP_SUMMARY TurboVap® (Zymark) to remove the organic solvent. The sample extracts were SP:SAMPLEPREP_SUMMARY stored overnight under nitrogen before preparation for analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Low pH Lipophilic (Metabolon). All methods utilized a Waters ACQUITY CH:CHROMATOGRAPHY_SUMMARY ultra-performance liquid chromatography (UPLC) and a Thermo Scientific CH:CHROMATOGRAPHY_SUMMARY Q-Exactive high resolution/accurate mass spectrometer interfaced with a heated CH:CHROMATOGRAPHY_SUMMARY electrospray ionization (HESI-II) source and Orbitrap mass analyzer operated at CH:CHROMATOGRAPHY_SUMMARY 35,000 mass resolution. The sample extract was dried then reconstituted in CH:CHROMATOGRAPHY_SUMMARY solvents compatible to each of the four methods. Each reconstitution solvent CH:CHROMATOGRAPHY_SUMMARY contained a series of standards at fixed concentrations to ensure injection and CH:CHROMATOGRAPHY_SUMMARY chromatographic consistency. One aliquot was analyzed using acidic positive ion CH:CHROMATOGRAPHY_SUMMARY conditions, chromatographically optimized for more hydrophilic compounds. In CH:CHROMATOGRAPHY_SUMMARY this method, the extract was gradient eluted from a C18 column (Waters UPLC BEH CH:CHROMATOGRAPHY_SUMMARY C18-2.1x100 mm, 1.7 µm) using water and methanol, containing 0.05% CH:CHROMATOGRAPHY_SUMMARY perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA). Another aliquot was CH:CHROMATOGRAPHY_SUMMARY also analyzed using acidic positive ion conditions, however it was CH:CHROMATOGRAPHY_SUMMARY chromatographically optimized for more hydrophobic compounds. In this method, CH:CHROMATOGRAPHY_SUMMARY the extract was gradient eluted from the same afore mentioned C18 column using CH:CHROMATOGRAPHY_SUMMARY methanol, acetonitrile, water, 0.05% PFPA and 0.01% FA and was operated at an CH:CHROMATOGRAPHY_SUMMARY overall higher organic content. Another aliquot was analyzed using basic CH:CHROMATOGRAPHY_SUMMARY negative ion optimized conditions using a separate dedicated C18 column. The CH:CHROMATOGRAPHY_SUMMARY basic extracts were gradient eluted from the column using methanol and water, CH:CHROMATOGRAPHY_SUMMARY however with 6.5mM Ammonium Bicarbonate at pH 8. The fourth aliquot was analyzed CH:CHROMATOGRAPHY_SUMMARY via negative ionization following elution from a HILIC column (Waters UPLC BEH CH:CHROMATOGRAPHY_SUMMARY Amide 2.1x150 mm, 1.7 µm) using a gradient consisting of water and acetonitrile CH:CHROMATOGRAPHY_SUMMARY with 10mM Ammonium Formate, pH 10.8. The MS analysis alternated between MS and CH:CHROMATOGRAPHY_SUMMARY data-dependent MSn scans using dynamic exclusion. The scan range varied slighted CH:CHROMATOGRAPHY_SUMMARY between methods but covered 70-1000 m/z. Raw data files are archived and CH:CHROMATOGRAPHY_SUMMARY extracted as described below. CH:INSTRUMENT_NAME Waters Acquity CH:COLUMN_NAME Waters Acquity BEH C18 (100 x 2mm, 1.7um) CH:COLUMN_TEMPERATURE 50 CH:FLOW_GRADIENT Linear gradient from 5% B to 80% B over 3.35 minutes. CH:FLOW_RATE 0.35 mL/min CH:SOLVENT_A 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 CH:SOLVENT_B 0.1% formic acid and 0.05% PFPA in 50% methanol/50% acetonitrile, pH ~2.5 CH:CHROMATOGRAPHY_TYPE Reversed phase #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE ESI MS:MS_COMMENTS A detailed description of data processing including chromatographic alignment, MS:MS_COMMENTS QC practices, and compound identification has been described previously (PMID: MS:MS_COMMENTS 19624122, 20955607, 30242936). Missing values, if any, were imputed with the MS:MS_COMMENTS minimum observed value for each compound and the resulting data was median MS:MS_COMMENTS scaled. MS:ION_MODE POSITIVE #END