{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001469","ANALYSIS_ID":"AN002445","VERSION":"1","CREATED_ON":"2020-08-19"},

"PROJECT":{"PROJECT_TITLE":"Metabolomics of lung injury after allogeneic hematopoietic cell transplantation","PROJECT_SUMMARY":"Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs.","INSTITUTE":"University of Kentucky","DEPARTMENT":"Markey Cancer Center, Hematology and Blood and Marrow Transplant","LAST_NAME":"Hildebrandt","FIRST_NAME":"Gerhard","ADDRESS":"Gerhard C. Hildebrandt, MD, Room no. CC401A, Ben Roach Building, Markey Cancer Center University of Kentucky, Lexington, 40536","EMAIL":"gerhard.hildebrandt@uky.edu","PHONE":"800-333-8874"},

"STUDY":{"STUDY_TITLE":"Metabolomics of lung injury after allogeneic hematopoietic cell transplantation - Lung DI-FTMS","STUDY_TYPE":"preliminary data","STUDY_SUMMARY":"Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative treatment option for a variety of hematological malignancies. Interactions between the donor immune system and the patient tissue result in a disease, called GVHD. The pathophysiology of acute GVHD can be hypothesized in three sequential phases: cytokine storm and activation of the antigen-presenting cells (APC), donor T cell activation and effector cell phase. Idiopathic pneumonia syndrome (IPS) is one of the most deleterious complications after allogeneic HCT and is considered not only to be related to conditioning regimen toxicity but also represents an end organ damage caused by allo-reactive T cells, therefore making the lung susceptible to a two-pronged attack, one of which overlaps with GVHD causing other target organ injury. IPS results in mortality of up to 90% of patients. We will use a murine model of IPS and GVHD which is well established in our group, and in which disease evolves either across disparities in major histocompatibility complex (MCH) class I and II, minor histocompatibility antigens (miHags) or both. Metabolomics changes following syngeneic and allogeneic HCT at post-transplantation Days +7 (cytokine storm phase) and Days +42 (cellular effector phase) are compared to baseline wild-type (naive) controls. Prior to analysis, naïve - and experimental mice (N=3 from each group) were fed with semi-liquid diet supplemented with tracers (13C6-glucose ) over 24 hours. At the end of 7 days or 42 days, respectively, feces and aGVHD target organs (colon, liver and lung) were collected from all groups and further processed and / or analyzed. We expect to reveal metabolic pathways affected after allo-HCT which contribute to immune cell mediated lung injury (IPS) and will potentially identify different metabolic pathways in other GVHD target organs.","INSTITUTE":"University of Kentucky","DEPARTMENT":"MCC","LAST_NAME":"Hildebrandt","FIRST_NAME":"Gerhard","ADDRESS":"CTW-453, 900 South Limestone street. UKY. Lexington, Kentucky-40536","EMAIL":"gerhard.hildebrandt@uky.edu","PHONE":"800-333-8874"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"24_C2-0_Lung_allogenic_42days_170427_UKy_GCH_rep1-lipid",
"Factors":{"Treatment Protocol":"allogenic"},
"Additional sample data":{"lineage_1":"09_C2-0_allogenic_42days_UKy_GCH_rep1","protocol.id":"['allogenic']","replicate":"1","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"42","lineage_2":"24_C2-0_Lung_allogenic_42days_170427_UKy_GCH_rep1","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"24_C2-0_Lung_allogenic_42days_170427_UKy_GCH_rep1-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage24']","type":"cell_extract","weight":"0.4932","weight%units":"g","lineage_4":"24_C2-0_Lung_allogenic_42days_170427_UKy_GCH_rep1-protein","protein_weight":"0.6075844437094541","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung09_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"27_B1-2_Lung_syngenic_7days_170427_UKy_GCH_rep3-lipid",
"Factors":{"Treatment Protocol":"syngenic"},
"Additional sample data":{"lineage_1":"12_B1-2_syngenic_7days_UKy_GCH_rep3","protocol.id":"['syngenic']","replicate":"3","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"7","lineage_2":"27_B1-2_Lung_syngenic_7days_170427_UKy_GCH_rep3","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"27_B1-2_Lung_syngenic_7days_170427_UKy_GCH_rep3-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage27']","type":"cell_extract","weight":"0.4871","weight%units":"g","lineage_4":"27_B1-2_Lung_syngenic_7days_170427_UKy_GCH_rep3-protein","protein_weight":"0.3397343460300001","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung12_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"29_C1-2_Lung_allogenic_7days_170427_UKy_GCH_rep2-lipid",
"Factors":{"Treatment Protocol":"allogenic"},
"Additional sample data":{"lineage_1":"14_C1-2_allogenic_7days_UKy_GCH_rep2","protocol.id":"['allogenic']","replicate":"2","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"7","lineage_2":"29_C1-2_Lung_allogenic_7days_170427_UKy_GCH_rep2","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"29_C1-2_Lung_allogenic_7days_170427_UKy_GCH_rep2-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage29']","type":"cell_extract","weight":"0.4915","weight%units":"g","lineage_4":"29_C1-2_Lung_allogenic_7days_170427_UKy_GCH_rep2-protein","protein_weight":"0.31985855339373337","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung14_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"26_B1-1_Lung_syngenic_7days_170427_UKy_GCH_rep2-lipid",
"Factors":{"Treatment Protocol":"syngenic"},
"Additional sample data":{"lineage_1":"11_B1-1_syngenic_7days_UKy_GCH_rep2","protocol.id":"['syngenic']","replicate":"2","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"7","lineage_2":"26_B1-1_Lung_syngenic_7days_170427_UKy_GCH_rep2","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"26_B1-1_Lung_syngenic_7days_170427_UKy_GCH_rep2-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage26']","type":"cell_extract","weight":"0.4911","weight%units":"g","lineage_4":"26_B1-1_Lung_syngenic_7days_170427_UKy_GCH_rep2-protein","protein_weight":"0.34798720067708344","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung11_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"19_B0_Lung_syngenic_42days_170427_UKy_GCH_rep1-lipid",
"Factors":{"Treatment Protocol":"syngenic"},
"Additional sample data":{"lineage_1":"04_B0_syngenic_42days_UKy_GCH_rep1","protocol.id":"['syngenic']","replicate":"1","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"42","lineage_2":"19_B0_Lung_syngenic_42days_170427_UKy_GCH_rep1","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"19_B0_Lung_syngenic_42days_170427_UKy_GCH_rep1-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage19']","type":"cell_extract","weight":"0.4989","weight%units":"g","lineage_4":"19_B0_Lung_syngenic_42days_170427_UKy_GCH_rep1-protein","protein_weight":"0.5600416771907997","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung04_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"16_A0_Lung_naive_0days_170427_UKy_GCH_rep1-lipid",
"Factors":{"Treatment Protocol":"naive"},
"Additional sample data":{"lineage_1":"01_A0_naive_0days_UKy_GCH_rep1","protocol.id":"['naive']","replicate":"1","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"0","lineage_2":"16_A0_Lung_naive_0days_170427_UKy_GCH_rep1","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"16_A0_Lung_naive_0days_170427_UKy_GCH_rep1-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage16']","type":"cell_extract","weight":"0.4947","weight%units":"g","lineage_4":"16_A0_Lung_naive_0days_170427_UKy_GCH_rep1-protein","protein_weight":"0.6757957582975501","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung01_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"22_C1-1_Lung_allogenic_42days_170427_UKy_GCH_rep1-lipid",
"Factors":{"Treatment Protocol":"allogenic"},
"Additional sample data":{"lineage_1":"07_C1-1_allogenic_42days_UKy_GCH_rep1","protocol.id":"['allogenic']","replicate":"1","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"42","lineage_2":"22_C1-1_Lung_allogenic_42days_170427_UKy_GCH_rep1","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"22_C1-1_Lung_allogenic_42days_170427_UKy_GCH_rep1-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage22']","type":"cell_extract","weight":"0.4983","weight%units":"g","lineage_4":"22_C1-1_Lung_allogenic_42days_170427_UKy_GCH_rep1-protein","protein_weight":"1.3767591694919588","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung07_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"30_C1-20_Lung_allogenic_7days_170427_UKy_GCH_rep3-lipid",
"Factors":{"Treatment Protocol":"allogenic"},
"Additional sample data":{"lineage_1":"15_C1-20_allogenic_7days_UKy_GCH_rep3","protocol.id":"['allogenic']","replicate":"3","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"7","lineage_2":"30_C1-20_Lung_allogenic_7days_170427_UKy_GCH_rep3","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"30_C1-20_Lung_allogenic_7days_170427_UKy_GCH_rep3-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage30']","type":"cell_extract","weight":"0.4835","weight%units":"g","lineage_4":"30_C1-20_Lung_allogenic_7days_170427_UKy_GCH_rep3-protein","protein_weight":"0.4930096320820004","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung15_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"20_B1_Lung_syngenic_42days_170427_UKy_GCH_rep2-lipid",
"Factors":{"Treatment Protocol":"syngenic"},
"Additional sample data":{"lineage_1":"05_B1_syngenic_42days_UKy_GCH_rep2","protocol.id":"['syngenic']","replicate":"2","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"42","lineage_2":"20_B1_Lung_syngenic_42days_170427_UKy_GCH_rep2","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"20_B1_Lung_syngenic_42days_170427_UKy_GCH_rep2-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage20']","type":"cell_extract","weight":"0.5013","weight%units":"g","lineage_4":"20_B1_Lung_syngenic_42days_170427_UKy_GCH_rep2-protein","protein_weight":"0.2959754761535626","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung05_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"21_B2_Lung_syngenic_42days_170427_UKy_GCH_rep3-lipid",
"Factors":{"Treatment Protocol":"syngenic"},
"Additional sample data":{"lineage_1":"06_B2_syngenic_42days_UKy_GCH_rep3","protocol.id":"['syngenic']","replicate":"3","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"42","lineage_2":"21_B2_Lung_syngenic_42days_170427_UKy_GCH_rep3","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"21_B2_Lung_syngenic_42days_170427_UKy_GCH_rep3-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage21']","type":"cell_extract","weight":"0.4917","weight%units":"g","lineage_4":"21_B2_Lung_syngenic_42days_170427_UKy_GCH_rep3-protein","protein_weight":"0.3382559813306206","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung06_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"18_A2_Lung_naive_0days_170427_UKy_GCH_rep3-lipid",
"Factors":{"Treatment Protocol":"naive"},
"Additional sample data":{"lineage_1":"03_A2_naive_0days_UKy_GCH_rep3","protocol.id":"['naive']","replicate":"3","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"0","lineage_2":"18_A2_Lung_naive_0days_170427_UKy_GCH_rep3","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"18_A2_Lung_naive_0days_170427_UKy_GCH_rep3-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage18']","type":"cell_extract","weight":"0.5126","weight%units":"g","lineage_4":"18_A2_Lung_naive_0days_170427_UKy_GCH_rep3-protein","protein_weight":"0.14664251664539998","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung03_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"23_C1-2_Lung_allogenic_42days_170427_UKy_GCH_rep2-lipid",
"Factors":{"Treatment Protocol":"allogenic"},
"Additional sample data":{"lineage_1":"08_C1-2_allogenic_42days_UKy_GCH_rep2","protocol.id":"['allogenic']","replicate":"2","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"42","lineage_2":"23_C1-2_Lung_allogenic_42days_170427_UKy_GCH_rep2","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"23_C1-2_Lung_allogenic_42days_170427_UKy_GCH_rep2-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage23']","type":"cell_extract","weight":"0.5067","weight%units":"g","lineage_4":"23_C1-2_Lung_allogenic_42days_170427_UKy_GCH_rep2-protein","protein_weight":"1.1547210188083492","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung08_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"28_C1-1_Lung_allogenic_7days_170427_UKy_GCH_rep1-lipid",
"Factors":{"Treatment Protocol":"allogenic"},
"Additional sample data":{"lineage_1":"13_C1-1_allogenic_7days_UKy_GCH_rep1","protocol.id":"['allogenic']","replicate":"1","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"7","lineage_2":"28_C1-1_Lung_allogenic_7days_170427_UKy_GCH_rep1","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"28_C1-1_Lung_allogenic_7days_170427_UKy_GCH_rep1-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage28']","type":"cell_extract","weight":"0.4913","weight%units":"g","lineage_4":"28_C1-1_Lung_allogenic_7days_170427_UKy_GCH_rep1-protein","protein_weight":"0.37226618572882475","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung13_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"17_A1_Lung_naive_0days_170427_UKy_GCH_rep2-lipid",
"Factors":{"Treatment Protocol":"naive"},
"Additional sample data":{"lineage_1":"02_A1_naive_0days_UKy_GCH_rep2","protocol.id":"['naive']","replicate":"2","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"0","lineage_2":"17_A1_Lung_naive_0days_170427_UKy_GCH_rep2","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"17_A1_Lung_naive_0days_170427_UKy_GCH_rep2-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage17']","type":"cell_extract","weight":"0.474","weight%units":"g","lineage_4":"17_A1_Lung_naive_0days_170427_UKy_GCH_rep2-protein","protein_weight":"0.6112704400619461","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung02_pos.raw"}
},
{
"Subject ID":"-",
"Sample ID":"25_B1-0_Lung_syngenic_7days_170427_UKy_GCH_rep1-lipid",
"Factors":{"Treatment Protocol":"syngenic"},
"Additional sample data":{"lineage_1":"10_B1-0_syngenic_7days_UKy_GCH_rep1","protocol.id":"['syngenic']","replicate":"1","species":"Mus musculus","species_type":"Mouse","taxonomy_id":"10090","time_point":"7","lineage_2":"25_B1-0_Lung_syngenic_7days_170427_UKy_GCH_rep1","protocol.id":"['mouse_tissue_collection', 'tissue_quench', 'frozen_tissue_grind']","lineage_3":"25_B1-0_Lung_syngenic_7days_170427_UKy_GCH_rep1-lipid","protocol.id":"['lipid_extraction', 'FTMS_file_storage25']","type":"cell_extract","weight":"0.4939","weight%units":"g","lineage_4":"25_B1-0_Lung_syngenic_7days_170427_UKy_GCH_rep1-protein","protein_weight":"0.47147932892528355","protein_weight%units":"mg","protocol.id":"['protein_extraction']","RAW_FILE_NAME":"Hildebrandt_Lung10_pos.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mouse is sacrificed and tissues are harvested.","COLLECTION_PROTOCOL_ID":"mouse_tissue_collection","SAMPLE_TYPE":"Multiple tissues"},

"TREATMENT":{"TREATMENT_SUMMARY":"Mouse with allogenic bone marrow transplant. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest. Mouse with no treatment. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest. Mouse with syngenic bone marrow transplant. Fed with semi-liquid diet supplemented with fully labeled glucose for 24 hours before harvest.","TREATMENT_PROTOCOL_ID":"allogenic naive syngenic"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Tissue is frozen in liquid nitrogen to stop metabolic processes. Lipid extraction from homogenate. Frozen tissue is ground in a SPEX grinder under liquid nitrogen to homogenize the sample. Protein extraction and quantification.","SAMPLEPREP_PROTOCOL_ID":"frozen_tissue_grind; lipid_extraction; protein_extraction; tissue_quench","SAMPLEPREP_PROTOCOL_FILENAME":"4D_17Jun4_Fan_Prot_Quant.pdf; 4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"None","CHROMATOGRAPHY_TYPE":"None (Direct infusion)","INSTRUMENT_NAME":"None","COLUMN_NAME":"None"},

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

"MS":"Units":"peak_height",

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