{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002207","ANALYSIS_ID":"AN003610","VERSION":"1","CREATED_ON":"July 6, 2022, 9:13 pm"},

"PROJECT":{"PROJECT_TITLE":"Metabolomic analysis to assess response to immunotherapy for malignant brain tumors: Part 1","PROJECT_TYPE":"Study of the urine and serum in mice treated with DC vaccine via 1H NMR","PROJECT_SUMMARY":"The objective of this project was to identify a peripheral metabolomic profile to serve as a biomarker of response to immunotherapy for the treatment of malignant brain tumors.","INSTITUTE":"University of Florida","DEPARTMENT":"Neurosurgery Department, Medical college, University of Florida","LAST_NAME":"Khattri","FIRST_NAME":"Ram","ADDRESS":"1200 Newell Dr., ARB 240, Gainesville, FL, 32611, USA","EMAIL":"rbk11@ufl.edu","PHONE":"3307856045","FUNDING_SOURCE":"This work was partially funded by the Florida Center for Brain Tumor Research (FCBTR), and by generous benefactors to the University of Florida, Peter and Angela Dziegielewski, who established the Eilzabeth Dziegielewski Glioblastoma Research Fund, and Rosalinde Wolfe, who established the Greg Wolfe Brain Tumor Research Fund. RK and MM were supported by funding from National Institutes of Health (U24-DK097209 and 5U2C-DK119889). All NMR portion of this study was performed in McKnight Brain Institute at National High Magnetic Field Laboratory’s Advanced Magnetic Resonance Imaging and Spectroscopy (AMRIS) Facility, which is funded by National Science Foundation Cooperative Agreement No. DMR-1644779 and the State of Florida.","PROJECT_COMMENTS":"Study of the urine and serum in mice treated with DC vaccine via 1H NMR","PUBLICATIONS":"Metabolomics journal (submitted)","CONTRIBUTORS":"Farhad Dastmalchi, Ram B. Khattri, Marc A. McLeod, Kaitlyn Melnick, Loic P. Deleyrolle, Yusuf Mehkri, Aida Karachi, Paul Kubilis, Shu Wang, Duane A. Mitchell, Matthew E. Merritt, Maryam Rahman"},

"STUDY":{"STUDY_TITLE":"Metabolomic analysis to assess response to immunotherapy for malignant brain tumors: Part 1","STUDY_SUMMARY":"An effective immune response in patients with cancer treated with immunotherapy includes dendritic cell (DC) activation and migration followed by stimulation of CD8 and CD4 T cells. This then leads to the activation, proliferation and further activation of other immune cell populations including NK cells or immunosuppressive populations such as Tregs and myeloid derived suppressor cells (MDSCs). These studies were carried out utilizing murine brain tumor models treated with an RNA DC vaccine platform. We hypothesized that metabolomic analyses of urines would be sensitive to the action of this diverse set of immune cells. The objective of this study was to evaluate the feasibility of using metabolomics to follow immune responses after immunotherapy. We chose NMR as our analytical technique of choice, as it has many favorable qualities that make it ideal for analyses of urine.","INSTITUTE":"University of Florida","DEPARTMENT":"Neurosurgery","LABORATORY":"Rm 042","LAST_NAME":"Khattri","FIRST_NAME":"Ram","ADDRESS":"1864 Stadium RD,","EMAIL":"rbk11@ufl.edu","NUM_GROUPS":"3","TOTAL_SUBJECTS":"15","NUM_MALES":"NA","NUM_FEMALES":"NA","STUDY_COMMENTS":"Metabolomic profiling of urine samples","PUBLICATIONS":"Metabolomics journal (submitted)","STUDY_TYPE":"Cancer surrogate biomarker discovery","PHONE":"330-785-6045"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","ANIMAL_ANIMAL_SUPPLIER":"Jackson Labs (Bar Harbor, ME)","ANIMAL_HOUSING":"Housed in a temperature of 22 oC","ANIMAL_LIGHT_CYCLE":"12-hour light/12-hour dark","ANIMAL_WATER":"free access to food and water (3-5 animals per cage)."},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_Control-1",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_Control-1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_Control-2",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_Control-2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_Control-3",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_Control-3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_Control-4",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_Control-4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_Control-5",
"Factors":{"Group":"Control"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_Control-5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_24hrs-1",
"Factors":{"Group":"24 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_24hrs-1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_24hrs-2",
"Factors":{"Group":"24 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_24hrs-2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_24hrs-3",
"Factors":{"Group":"24 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_24hrs-3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_24hrs-4",
"Factors":{"Group":"24 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_24hrs-4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_24hrs-5",
"Factors":{"Group":"24 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_24hrs-5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_48hrs-1",
"Factors":{"Group":"48 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_48hrs-1.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_48hrs-2",
"Factors":{"Group":"48 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_48hrs-2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_48hrs-3",
"Factors":{"Group":"48 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_48hrs-3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_48hrs-4",
"Factors":{"Group":"48 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_48hrs-4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"Maryam_1st-set_Urine_48hrs-5",
"Factors":{"Group":"48 hrs"},
"Additional sample data":{"RAW_FILE_NAME":"Maryam_1st-set_Urine_48hrs-5.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Intakt urine samples were collected from C57/Bl6 mice. Urine is collected from a clean surface after urination.","SAMPLE_TYPE":"Urine","COLLECTION_METHOD":"Naïve C57/BL6 mice received antigen-specific T cells through intravenous (IV) and the DC vaccine injection intradermally on the same day. Both antigen-specific T cells and DC vaccine were administered once. Urine or serum samples were collected after DC vaccination at several timepoints. Finally, animals were euthanized when they reached the endpoints","COLLECTION_LOCATION":"University of Florida, Neurosurgery Department, Medical college, University of Florida","COLLECTION_FREQUENCY":"Pre-vaccination, 24 hrs and 48 hrs of post DC vaccination.","COLLECTION_DURATION":"~30 minutes","STORAGE_CONDITIONS":"-80℃","COLLECTION_VIALS":"cryovials","STORAGE_VIALS":"cryovials"},

"TREATMENT":{"TREATMENT_SUMMARY":"Dendritic cell vaccine and anti-PD-1 immunotherapy. Bone marrow (BM) was harvested from the long bones and sternum of euthanized animals and the red blood cells (RBCs) were lysed. Then myeloid-derived cells were cultured in DC complete media including granulocyte macrophage colony stimulating factor (GM-CSF) and interleukin 4. Cells were cultured in six well plates for six days. On day seven, cells were re-plated in 60mm dishes. DCs were then electroporated with OVA-mRNA at day eight. On day nine, DCs were collected in phosphate buffered saline (PBS) for administration. DC vaccines were delivered once via intradermal injection in the inguinal area. Naïve C57/BL6 mice received antigen-specific T cells through intravenous (IV) and the DC vaccine injection intradermally on the same day. Both antigen-specific T cells and DC vaccine were administered once. Urine or serum samples were collected after DC vaccination at several timepoints. Finally, animals were euthanized when they reached the endpoints.","ANIMAL_ANESTHESIA":"isoflurane","ANIMAL_FASTING":"non-fasted","ANIMAL_ENDP_EUTHANASIA":"Euthanasia was carried out by thoracotomy followed by cervical dislocation."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"No filtration was performed for urine samples. The urine samples were centrifuged at 4 oC, with 13.2 K rpm speed before mixing it with an internal reference and phosphate buffer system.","SAMPLEPREP_PROTOCOL_FILENAME":"1. DC-Vaccine-treated-NMR urine Procedures","PROCESSING_METHOD":"None","PROCESSING_STORAGE_CONDITIONS":"-80℃","EXTRACTION_METHOD":"None","SAMPLE_RESUSPENSION":"In 500 microliter of 150 mM phosphate buffer (pH 7.2) with 2 mM EDTA, 10 mM TSP and 0.2% sodium azide for aqueous phase samples.","SAMPLE_SPIKING":"10 mM of TSP for urine samples"},

"ANALYSIS":{"ANALYSIS_TYPE":"NMR","LABORATORY_NAME":"McKnight Brain Institute","OPERATOR_NAME":"Ram Khattri","DETECTOR_TYPE":"Bruker 600 MHz","SOFTWARE_VERSION":"Topspin","ACQUISITION_DATE":"3/9/2016","ACQUISITION_PARAMETERS_FILE":"1. DC-Vaccine-treated-NMR urine Procedures","PROCESSING_PARAMETERS_FILE":"1. DC-Vaccine-treated-NMR urine Procedures","DATA_FORMAT":"fid, 1r"},

"NM":{"INSTRUMENT_NAME":"Bruker 600 MHz","INSTRUMENT_TYPE":"FT-NMR","NMR_EXPERIMENT_TYPE":"1D-1H","FIELD_FREQUENCY_LOCK":"Deuterium","STANDARD_CONCENTRATION":"10 mM TSP","SPECTROMETER_FREQUENCY":"600 MHz","NMR_PROBE":"5 mm CPTXI 1H/D-13C/15N Z-GRD Z44866/0026","NMR_SOLVENT":"Phosphate buffer (pH 7.2) + 2 mM EDTA + 10 mM TPS + 0.2% of sodium azide in deuterated environment","NMR_TUBE_SIZE":"5 mm O.D.","SHIMMING_METHOD":"Topshim","PULSE_SEQUENCE":"noesypr1d","WATER_SUPPRESSION":"presat","PULSE_WIDTH":"90-degree","RECEIVER_GAIN":"256","OFFSET_FREQUENCY":"4.77 ppm","CHEMICAL_SHIFT_REF_CPD":"TPS","TEMPERATURE":"300.2 oK","NUMBER_OF_SCANS":"256","DUMMY_SCANS":"8","ACQUISITION_TIME":"2.2719 s","RELAXATION_DELAY":"3 s","SPECTRAL_WIDTH":"7211.5 Hz","NUM_DATA_POINTS_ACQUIRED":"16384","REAL_DATA_POINTS":"65536","LINE_BROADENING":"0.22 Hz","ZERO_FILLING":"65,536 points","APODIZATION":"Exponential","BASELINE_CORRECTION_METHOD":"Spline","CHEMICAL_SHIFT_REF_STD":"0 ppm for TPS","BINNED_INCREMENT":"0.001 ppm","BINNED_DATA_EXCLUDED_RANGE":">9.5 ppm and < 0.5 ppm regions","NMR_RESULTS_FILE":"ST002207_AN003610_Results.txt UNITS:Peak intensity"}

}