{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002827","ANALYSIS_ID":"AN004616","VERSION":"1","CREATED_ON":"August 24, 2023, 7:12 am"}, "PROJECT":{"PROJECT_TITLE":"Multi-assay nutritional metabolomics profiling of low vitamin A status versus adequacy is characterized by reduced plasma lipid mediators among lactating women in the Philippines: A pilot study","PROJECT_SUMMARY":"Low vitamin A (VA) status is common among lactating women in low-income countries. Lactation has substantial effects on mother’s metabolism and VA is required in multiple biological processes, including growth, vision, immunity, and reproduction. The objective of this pilot study was to utilize metabolomics profiling to conduct a broad, exploratory assessment of differences in plasma metabolites associated with low VA status versus VA adequacy in lactating women. Plasma samples from lactating women who participated in a survey in Samar, Philippines, were selected from a cross-sectional study based on plasma retinol concentrations indicating low (VA-; n=5) or adequate (VA+; n=5) VA status (plasma retinol <0.8 or >1.05 µmol/L). The plasma results collected from six metabolomics assays (oxylipins, endocannabinoids, bile acids, primary metabolomics, biogenic amines, and lipidomics) were compared by group using liquid chromatography mass spectrometry. Twenty-eight metabolites were altered in the VA- versus VA+ status groups, with 24 being lipid mediators (p<0.05). These lipid mediators included lower concentrations of arachidonic acid- and eicosapentaenoic acid-derived oxylipins, as well as lysophospholipids and sphingolipids, in the VA- group (p<0.05). Chemical similarity enrichment analysis identified HETEs, HEPEs, and DiHETEs as significantly altered oxylipin clusters (p<0.0001, false discovery rate (FDR) p<0.0001), as well as sphingomyelins, saturated lysophosphatidylcholines, phosphatidylcholines, and phosphatidylethanolamines (p<0.001, FDR p<0.01). The multi-assay nutritional metabolomics profiling of low VA status compared with adequacy in lactating women was characterized by reduced lipid mediator concentrations. Future studies with stronger study designs and larger sample size are needed to confirm and validate these preliminary results.","INSTITUTE":"Cal Poly St. Univ., San Luis Obispo","LAST_NAME":"La Frano","FIRST_NAME":"Michael","ADDRESS":"CALIFORNIA POLYTECHNIC STATE UNIVERSITY, 1 GRAND AVE, SAN LUIS OBISPO, CA, 93407, USA","EMAIL":"mlafrano@calpoly.edu","PHONE":"7143602022"}, "STUDY":{"STUDY_TITLE":"Multi-assay nutritional metabolomics profiling of low vitamin A status versus adequacy is characterized by reduced plasma lipid mediators among lactating women in the Philippines: A pilot study.","STUDY_TYPE":"Case-control","STUDY_SUMMARY":"Low vitamin A (VA) status is common among lactating women in low-income countries. Lactation has substantial effects on mother’s metabolism and VA is required in multiple biological processes, including growth, vision, immunity, and reproduction. The objective of this pilot study was to utilize metabolomics profiling to conduct a broad, exploratory assessment of differences in plasma metabolites associated with low VA status versus VA adequacy in lactating women. Plasma samples from lactating women who participated in a survey in Samar, Philippines, were selected from a cross-sectional study based on plasma retinol concentrations indicating low (VA-; n=5) or adequate (VA+; n=5) VA status (plasma retinol <0.8 or >1.05 µmol/L). The plasma results collected from six metabolomics assays (oxylipins, endocannabinoids, bile acids, primary metabolomics, biogenic amines, and lipidomics) were compared by group using liquid chromatography mass spectrometry. Twenty-eight metabolites were altered in the VA- versus VA+ status groups, with 24 being lipid mediators (p<0.05). These lipid mediators included lower concentrations of arachidonic acid- and eicosapentaenoic acid-derived oxylipins, as well as lysophospholipids and sphingolipids, in the VA- group (p<0.05). Chemical similarity enrichment analysis identified HETEs, HEPEs, and DiHETEs as significantly altered oxylipin clusters (p<0.0001, false discovery rate (FDR) p<0.0001), as well as sphingomyelins, saturated lysophosphatidylcholines, phosphatidylcholines, and phosphatidylethanolamines (p<0.001, FDR p<0.01). The multi-assay nutritional metabolomics profiling of low VA status compared with adequacy in lactating women was characterized by reduced lipid mediator concentrations. Future studies with stronger study designs and larger sample size are needed to confirm and validate these preliminary results.","INSTITUTE":"California Polytechnic State University, San Luis Obispo","DEPARTMENT":"Food Science and Nutrition","LABORATORY":"Cal Poly Metabolomics Service Center","LAST_NAME":"La Frano","FIRST_NAME":"Michael","ADDRESS":"Attn: Dr. Michael La Frano Bldg 11 Room 239 Cal Poly State University 1 Grand Avenue San Luis Obispo, CA 93407","EMAIL":"mlafrano@calpoly.edu","PHONE":"(805) 756 6233","NUM_GROUPS":"2","TOTAL_SUBJECTS":"10"}, "SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Female"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"226", "Sample ID":"9", "Factors":{"Case_Control":"LOW"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP9","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP9","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP9","Species":"Human"} }, { "Subject ID":"390", "Sample ID":"2", "Factors":{"Case_Control":"LOW"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP2","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP2","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP2","Species":"Human"} }, { "Subject ID":"255", "Sample ID":"5", "Factors":{"Case_Control":"LOW"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP5","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP5","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP5","Species":"Human"} }, { "Subject ID":"391", "Sample ID":"7", "Factors":{"Case_Control":"LOW"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP7","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP7","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP7","Species":"Human"} }, { "Subject ID":"223", "Sample ID":"3", "Factors":{"Case_Control":"LOW"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP3","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP3","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP3","Species":"Human"} }, { "Subject ID":"248", "Sample ID":"10", "Factors":{"Case_Control":"ADEQUATE"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP10","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP10","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP10","Species":"Human"} }, { "Subject ID":"326", "Sample ID":"6", "Factors":{"Case_Control":"ADEQUATE"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP6","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP6","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP6","Species":"Human"} }, { "Subject ID":"388", "Sample ID":"8", "Factors":{"Case_Control":"ADEQUATE"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP8","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP8","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP8","Species":"Human"} }, { "Subject ID":"271", "Sample ID":"1", "Factors":{"Case_Control":"ADEQUATE"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP1","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP1","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP1","Species":"Human"} }, { "Subject ID":"266", "Sample ID":"4", "Factors":{"Case_Control":"ADEQUATE"}, "Additional sample data":{"Lipidomics Sample ID":"Haskell Plasma Lipidomics HP4","Biogenic Amines Sample ID Identifier":"Haskell Plasma Biogenic Amines HP4","Metabolomics Sample ID":"Haskell Plasma Metabolomics HP4","Species":"Human"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"Plasma samples analyzed in this study were collected from the antecubital vein in 7 mL Vacutainer® tubes containing K2-EDTA (Beckton Dickinson, Franklin Lakes, NJ, USA).","COLLECTION_PROTOCOL_FILENAME":"La_Frano_Treatment_Protocol_v1[23].pdf","SAMPLE_TYPE":"Blood (plasma)"}, "TREATMENT":{"TREATMENT_SUMMARY":"The samples for this study were obtained from archived specimens from a cross-sectional survey that assessed the prevalence of VAD among a convenience sample of 207 lactating women in the province of Santa Margarita, Samar, Philippines. The original protocol was approved by the UC Davis IRB 290430-5 and the ethical committee of the local Ministry of Health in Eastern Visayas (Region VIII), Philippines. Excluded from the study were individuals who did not consent to further analysis of banked samples, had insufficient plasma remaining for metabolomics analysis, had samples that were not stored at the University of California, Davis, or had acute phase protein concentrations above normal range, including plasma C-reactive protein (CRP) > 5 mg/L or plasma α-1-acid glycoprotein (AGP) > 1.0 g/L (both measured by radial immunodiffusion). For the remaining samples eligible for metabolomics analysis, participants were divided into two groups with the lowest and highest concentrations based on their plasma VA concentrations. We selected 5 participants with plasma retinol ≤ 0.8 μmol/L and 5 participants with plasma retinol >1.05 μmol/L that were our low VA (VA-, < 0.8 μmol/L) or adequate VA (VA+, > 1.05 μmol/L) status groups, respectively. It must be noted that one participant in the VA- group had a plasma retinol concentration of 0.8 μmol/L, while the remaining four participants had plasma retinol ≤ 0.7 μmol/L, the cutoff for deficiency [8]. Casual breast milk retinol per gram of fat was also measured. Plasma samples analyzed in this study were collected from the antecubital vein in 7 mL Vacutainer® tubes containing K2-EDTA (Beckton Dickinson, Franklin Lakes, NJ, USA). Blood samples were shielded from light and placed in a cooler with ice packs prior to centrifugation to obtain plasma. Separated plasma samples were aliquoted into 2 ml cryovials and stored temporarily in a refrigerator until the end of data collection that day, and then frozen at -20⁰C for ~1-4 months, until transferred to Manila on dry ice, where they were stored first at -20 ºC and then later at -80ºC. Thereafter, samples were shipped on dry ice to the University of California, Davis and stored at -80ºC until analysis.","TREATMENT_PROTOCOL_FILENAME":"La_Frano_Treatment_Protocol_v1[23].pdf"}, "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolomics assays for primary metabolomics, biogenic amines, and lipidomics were performed using protein precipitation extraction with UPLC-MS using modified previously published methods [6]. Briefly, 25 µL of plasma were added to 1.5 mL tubes before the addition of 10 µL of 1 µM internal standard solution, followed by 750 µL chilled methanol. Samples were then vortexed 30 seconds prior to being centrifuged at 15,000 x G for 10 min. The supernatant was transferred to 1.5 mL high performance liquid chromatography (HPLC) amber glass vials, dried by centrifugal vacuum evaporation, and reconstituted in 100 µL 3:1 acetonitrile: methanol solution with CUDA solution. The reconstituted solution was vortexed 30 seconds and placed on ice for 10 minutes. The solution was then centrifuged at 10,000 x G for 3 minutes after being transferred to microfilter tubes. The supernatant was then transferred to a HPLC vial to be analyzed using the UPLC-MS.","SAMPLEPREP_PROTOCOL_FILENAME":"La_Frano_Lab_Methods_Doc_VA_v9[2].pdf"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters Acquity I-Class","COLUMN_NAME":"Prosphere HP C4 (150 x 3.0 mm, 3um)","SOLVENT_A":"95% water/5% methanol; 0.1% acetic acid; 10 mM ammonium acetate","SOLVENT_B":"100% methanol; 0.1% acetic acid","FLOW_GRADIENT":"0-2 min: 20%, 2-3 min: 20%, 3-7 min: 80%, 7-10 min: 100%, 10-11 min: 100%, 11-15 min: 20%","FLOW_RATE":"0.35 mL/min","COLUMN_TEMPERATURE":"30 °C","METHODS_FILENAME":"La_Frano_Lab_Methods_Doc_VA_v9[2].pdf","SAMPLE_INJECTION":"5µl","RANDOMIZATION_ORDER":"Excel generated"}, "ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Cal Poly Metabolomics Service Center","OPERATOR_NAME":"Rob Fanter","DETECTOR_TYPE":"Quadropule ion trap (QTrap)","SOFTWARE_VERSION":"Data acquisition:AB Sciex Analyst;Data processing: AB Sciex MultiQuant 3.0","PROCESSING_PARAMETERS_FILE":"La_Frano_Lab_Methods_Doc_VA_v9[2].pdf","DATA_FORMAT":".mzml"}, "MS":{"INSTRUMENT_NAME":"ABI Sciex API 4000 QTrap","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"API","ION_MODE":"POSITIVE","MS_COMMENTS":"La_Frano_Lab_Methods_Doc_VA_v9[2].pdf"}, "MS_METABOLITE_DATA":{ "Units":"Peak Area", "Data":[{"Metabolite":"C32:2 PC","9":"188193006.3","2":"147464344.1","5":"131569973.7","7":"223142964","3":"154736957.9","10":"214218128.5","6":"217062438.8","8":"209227005.2","1":"291511389.8","4":"237573112"},{"Metabolite":"C32:1 PC","9":"543997622.5","2":"451804237.6","5":"304851265.8","7":"568626718.5","3":"516823037.7","10":"512288563.5","6":"467119676","8":"408241464.2","1":"430583681.7","4":"467218540"},{"Metabolite":"C32:0 PC","9":"508179440.3","2":"372883854.2","5":"259879307.3","7":"474707504.2","3":"518114644.4","10":"520648478.1","6":"472064816","8":"334394485.1","1":"420106317.5","4":"533698730.1"},{"Metabolite":"C34:2 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