{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002009","ANALYSIS_ID":"AN003275","VERSION":"1","CREATED_ON":"02-13-2024"},

"PROJECT":{"PROJECT_TITLE":"Metabolic profiles of murine stress erythroid progenitors","PROJECT_SUMMARY":"Inflammation alters hematopoiesis, skewing production to generate myeloid effector cells at the expense of steady state erythropoiesis. To compensate, stress erythropoiesis is induced to maintain homeostasis until the inflammation is resolved. Unlike the constant production of steady state erythropoiesis, stress erythropoiesis generates a bolus of new erythrocytes by first producing immature progenitor cells, which then transition to committed erythroid progenitors and differentiate. We hypothesize that the proliferation of early progenitor cells and their transition to differentiation is regulated by changes in metabolism. Metabolomics and isotope tracing analysis was performed to assess the intracellular metabolic profiles in proliferating progenitors isolated from in vitro stress erythropoiesis cultures. We observed an active engagement of glucose metabolism in glycolysis and anabolic biosynthesis, while the levels of TCA intermediates suggested that TCA cycle and mitochondrial respiration were blocked. Concomitantly, inducible nitric oxide synthase (iNOS) was induced in progenitor cells to increase the production of nitric oxide (NO), which was demonstrated to be crucial for proliferating progenitor metabolism. Inhibition or genetic mutation of iNOS decreased NO levels resulting in the suppression of progenitor proliferation in vitro and in vivo. As evaluated by RNA-seq, inhibition of iNOS suppressed cell proliferation-related pathways including cell cycle and nucleotide metabolism, while upregulating erythroid differentiation genes. These data suggest that iNOS-derived NO production establishes a metabolism that promotes the proliferation of progenitor cells while inhibiting their differentiation. In contrast, the transition to differentiation is marked by decreased Nos2 expression and a change in metabolism to support induction of the erythroid gene expression program. These data support a model where increased pro-inflammatory signals inhibit steady state erythropoiesis, while at the same time promoting stress erythropoiesis to maintain homeostasis.","INSTITUTE":"Pennsylvania State University","DEPARTMENT":"Veterinary and Biomedical Sciences","LABORATORY":"Paulson Lab","LAST_NAME":"Paulson","FIRST_NAME":"Robert","ADDRESS":"228 AVBS Building, Shortlidge Road, University Park, PA 16802","EMAIL":"rfp5@psu.edu","PHONE":"814-863-6306","DOI":"http://dx.doi.org/10.21228/M89402"},

"STUDY":{"STUDY_TITLE":"Metabolomics analysis of stress erythroid progenitors","STUDY_SUMMARY":"A time course study to assess the intracellular metabolic changes of progenitors isolated from stress erythropoiesis expansion culture.","INSTITUTE":"Pennsylvania State University","DEPARTMENT":"Veterinary and Biomedical Sciences","LABORATORY":"Paulson Lab","LAST_NAME":"Paulson","FIRST_NAME":"Robert","ADDRESS":"228 AVBS Building Shortlidge Road University Park, PA 16802","EMAIL":"rfp5@psu.edu","PHONE":"814-863-6306","SUBMIT_DATE":"2021-12-05"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"Mus musculus",
"Sample ID":"D1_1",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"1"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D1_1.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D1_2",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"1"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D1_2.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D1_3",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"1"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D1_3.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D1_4",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"1"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D1_4.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D1_5",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"1"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D1_5.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D3_1",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"3"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D3_1.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D3_2",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"3"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D3_2.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D3_3",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"3"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D3_3.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D3_4",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"3"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D3_4.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D3_5",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"3"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D3_5.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D5_1",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"5"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D5_1.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D5_2",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"5"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D5_2.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D5_3",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"5"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D5_3.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D5_4",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"5"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D5_4.mzML"}
},
{
"Subject ID":"Mus musculus",
"Sample ID":"D5_5",
"Factors":{"Mouse_strain":"wild type C57BL/6","Culture_stage":"Expansion stage","Time_point(days)":"5"},
"Additional sample data":{"Cell_type":"Stress erythroid progenitor cells","RAW_FILE_NAME":"D5_5.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Unfractionated wild-type bone marrow cells were cultured in stress erythropoiesis expansion medium (SEEM). At indicated time point, stress erythroid progenitor cells were counted, washed with PBS and snap frozen in liquid nitrogen.","SAMPLE_TYPE":"Stem cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"All cells are untreated."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Cell pellets were extracted with 1 ml pre-chilled 50:50 HPLC-grade water:methanol (v/v) containing 1 µM chlorpropamide as the internal standard. The samples were vortexed briefly followed by thorough homogenization. The samples were then snap frozen with liquid nitrogen and immediately thawed at room temperature. This step was repeated for three times followed by centrifuging for 10 min at 12,000 x g and 4 °C. The supernatants were transferred into fresh microfuge tubes. The remaining cell pellets were re-extracted with 0.5 ml 50% methanol containing 1 µM chlorpropamide, homogenized, frozen and thawed three times, spun down, and the supernatants were combined with the first extraction. Metabolites-containing supernatants were concentrated to dryness at room temperature in a SpeedVac concentrator and re-dissolved in 100 µl 97:3 water:methanol (v/v). After centrifuging for 10 min at 13000 × g and 4°C, 70 µl of supernatants were transferred into autosampler vials for LC-MS analysis. Two types of control were prepared in triplicates to run in concert with the experimental samples: the process blank control, and the pooled control containing an equal volume from each experimental sample."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The sample run order was randomized to reduce bias from instrument drift. 10 µl sample was subjected to LC-MS analysis on a Exactive Plus Orbitrap mass spectrometer (Thermo Fisher Scientific) coupled to an Ultimate 3000 UHPLC system (Thermo Fisher Scientific). Reversed-phase chromatography mode was used to separate compounds on a Xselect C18 HSS column (Waters) with solvent A (97:3 water:methanol (v/v), 10 mM tributylamine, and 15 mM acetic acid ) and solvent B (methanol). The flow rate was 200 µl/min, and the total run time was 25 min. The gradient was 0 min, 0% B; 5 min, 20% B; 7.5 min, 55% B; 15 min, 65% B; 17.5 min, 95% B; and 21 min, 0% B. The mass spectrometer was operated in a negative-ion mode at a resolution of 140,000 at m/z 200 and with a scan range of 85 to 1000 m/z.","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Waters SSelect HSS C18","FLOW_GRADIENT":"0 min, 0% B; 5 min, 20% B; 7.5 min, 55% B; 15 min, 65% B; 17.5 min, 95% B; and 21 min, 0% B.","FLOW_RATE":"200 µl/min","SOLVENT_A":"97% water/3% methanol; 15 mM acetic acid; 10 mM tributylamine","SOLVENT_B":"100% methanol","CHROMATOGRAPHY_TYPE":"Reversed phase"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Exactive Plus Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"Raw data files were converted to .mzML file format using the ProteoWizard software, and they were analyzed by the MS-DIAL software. Metabolites were identified by comparison to an in-house reference library of pure metabolite standards which included mass-to-charge ratio (m/z) and retention time. For quantification of metabolite abundance, peak areas of identified metabolites were first normalized to the internal standard chlorpropamide, and then normalized to cell numbers from each sample. Data were analyzed using R and Cytoscape software.","ION_MODE":"NEGATIVE"},

"MS_METABOLITE_DATA":{
"Units":"Normalized peak area",

"Data":[{"Metabolite":"2_3-Dihydroxybenzoic acid","D1_1":"0.9685","D1_2":"0.7181","D1_3":"0.9808","D1_4":"0.8208","D1_5":"1.5118","D3_1":"2.3243","D3_2":"1.6640","D3_3":"1.6175","D3_4":"2.2272","D3_5":"1.8140","D5_1":"2.6140","D5_2":"2.5111","D5_3":"3.0011","D5_4":"2.5153","D5_5":"2.3772"},{"Metabolite":"2_3-Diphosphoglyceric acid","D1_1":"1.3875","D1_2":"0.8520","D1_3":"0.8147","D1_4":"0.8978","D1_5":"1.0481","D3_1":"1.7485","D3_2":"1.3036","D3_3":"1.8834","D3_4":"1.2509","D3_5":"1.9552","D5_1":"0.8310","D5_2":"0.6492","D5_3":"0.6949","D5_4":"0.8262","D5_5":"0.9381"},{"Metabolite":"2-Aminooctanoic acid","D1_1":"1.0219","D1_2":"0.7749","D1_3":"0.6995","D1_4":"1.0398","D1_5":"1.4639","D3_1":"1.1428","D3_2":"0.7104","D3_3":"0.7969","D3_4":"1.4082","D3_5":"0.8416","D5_1":"1.5975","D5_2":"1.6445","D5_3":"1.5446","D5_4":"1.6836","D5_5":"1.5016"},{"Metabolite":"2-Isopropylmalic acid","D1_1":"0.9664","D1_2":"0.6939","D1_3":"0.9030","D1_4":"1.0524","D1_5":"1.3843","D3_1":"1.3131","D3_2":"0.8048","D3_3":"0.8563","D3_4":"1.3277","D3_5":"1.2600","D5_1":"1.3129","D5_2":"1.2872","D5_3":"1.3435","D5_4":"1.4582","D5_5":"1.3610"},{"Metabolite":"2-Keto-D-gluconate","D1_1":"0.7569","D1_2":"1.1071","D1_3":"0.9194","D1_4":"0.8274","D1_5":"1.3892","D3_1":"2.4883","D3_2":"2.1424","D3_3":"2.4661","D3_4":"2.2092","D3_5":"1.9662","D5_1":"4.1852","D5_2":"5.5116","D5_3":"6.2231","D5_4":"7.1965","D5_5":"4.1991"},{"Metabolite":"2-Keto-isovalerate","D1_1":"0.9755","D1_2":"0.6889","D1_3":"0.8758","D1_4":"1.0369","D1_5":"1.4229","D3_1":"1.4985","D3_2":"0.8491","D3_3":"0.8305","D3_4":"1.4362","D3_5":"1.1219","D5_1":"1.4212","D5_2":"1.4407","D5_3":"1.5665","D5_4":"1.5208","D5_5":"1.5963"},{"Metabolite":"2-Oxobutanoate","D1_1":"0.7702","D1_2":"0.6038","D1_3":"1.1316","D1_4":"1.3005","D1_5":"1.1938","D3_1":"1.2363","D3_2":"0.7006","D3_3":"0.7120","D3_4":"1.1291","D3_5":"0.9945","D5_1":"1.9222","D5_2":"1.2999","D5_3":"1.2966","D5_4":"1.3369","D5_5":"2.2033"},{"Metabolite":"3-Hydroxybutyric acid","D1_1":"0.8109","D1_2":"0.6591","D1_3":"0.8589","D1_4":"1.0919","D1_5":"1.5793","D3_1":"1.5513","D3_2":"0.9081","D3_3":"0.8923","D3_4":"1.4444","D3_5":"1.3004","D5_1":"1.6988","D5_2":"1.7836","D5_3":"1.8042","D5_4":"1.9354","D5_5":"1.9492"},{"Metabolite":"3-Methylphenylacetic acid","D1_1":"0.9583","D1_2":"0.7024","D1_3":"0.9128","D1_4":"1.1086","D1_5":"1.3179","D3_1":"1.6981","D3_2":"0.9799","D3_3":"0.8804","D3_4":"1.9142","D3_5":"1.5522","D5_1":"1.3243","D5_2":"1.5542","D5_3":"1.5485","D5_4":"1.5196","D5_5":"1.6564"},{"Metabolite":"3-Phosphoglycerate","D1_1":"0.5333","D1_2":"0.7456","D1_3":"1.2190","D1_4":"1.2342","D1_5":"1.2679","D3_1":"10.7805","D3_2":"13.0988","D3_3":"18.3099","D3_4":"10.2167","D3_5":"21.2654","D5_1":"1.8702","D5_2":"2.3372","D5_3":"3.8093","D5_4":"7.5261","D5_5":"2.0086"},{"Metabolite":"3-Phospho-serine","D1_1":"0.8109","D1_2":"0.3304","D1_3":"0.7982","D1_4":"1.1274","D1_5":"1.9331","D3_1":"0.3777","D3_2":"0.0701","D3_3":"","D3_4":"0.4655","D3_5":"0.3373","D5_1":"","D5_2":"0.1432","D5_3":"","D5_4":"0.1455","D5_5":""},{"Metabolite":"4-Aminobutyrate","D1_1":"0.8181","D1_2":"0.8049","D1_3":"0.9501","D1_4":"1.1047","D1_5":"1.3222","D3_1":"4.4278","D3_2":"3.4252","D3_3":"3.9964","D3_4":"4.6813","D3_5":"4.4411","D5_1":"3.3122","D5_2":"3.3164","D5_3":"3.3811","D5_4":"4.7040","D5_5":"3.2055"},{"Metabolite":"4-Phosphopantothenate","D1_1":"1.1896","D1_2":"0.6659","D1_3":"1.9490","D1_4":"0.8023","D1_5":"0.3932","D3_1":"1.1191","D3_2":"0.8867","D3_3":"1.0175","D3_4":"1.0415","D3_5":"1.3487","D5_1":"9.0271","D5_2":"9.3289","D5_3":"12.4721","D5_4":"6.2863","D5_5":"8.2904"},{"Metabolite":"4-Pyridoxic 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