Summary of Study ST002208

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001410. The data can be accessed directly via it's Project DOI: 10.21228/M8G42C This work is supported by NIH grant, U2C- DK119886.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002208
Study TitleMetabolomic analysis to assess response to immunotherapy for malignant brain tumors: Part 2
Study TypeCancer surrogate biomarker discovery
Study SummaryAn 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.
University of Florida
DepartmentApplied Physiology and Kinesiology
LaboratoryRm 042
Last NameKhattri
First NameRam
Address1200 Newell Dr., ARB 240, Gainesville, FL, 32611, USA
Submit Date2022-06-09
Num Groups10
Total Subjects80
Num MalesNA
Num FemalesNA
Study CommentsMetabolomic profiling of urine samples
PublicationsMetabolomics journal (submitted)
Raw Data AvailableYes
Raw Data File Type(s)fid
Analysis Type DetailNMR
Release Date2023-06-16
Release Version1
Ram Khattri Ram Khattri application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001410
Project DOI:doi: 10.21228/M8G42C
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
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


Subject ID:SU002294
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J
Gender:Not applicable
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 type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Group
SA211407Maryam_2nd-set_Urine_Control_C6_PostControl_Day 0 to 1
SA211408Maryam_2nd-set_Urine_Control_C1_PostControl_Day 0 to 1
SA211409Maryam_2nd-set_Urine_Control_C5_PostControl_Day 0 to 1
SA211410Maryam_2nd-set_Urine_Control_C7_PostControl_Day 0 to 1
SA211411Maryam_2nd-set_Urine_Control_C4_PostControl_Day 0 to 1
SA211412Maryam_2nd-set_Urine_Control_C2_PostControl_Day 0 to 1
SA211413Maryam_2nd-set_Urine_Control_C3_PostControl_Day 0 to 1
SA211414Maryam_2nd-set_Urine_Control_C3_D12Control_Day 0 to 12
SA211415Maryam_2nd-set_Urine_Control_C2_D12Control_Day 0 to 12
SA211416Maryam_2nd-set_Urine_Control_C5_D12Control_Day 0 to 12
SA211417Maryam_2nd-set_Urine_Control_C7_D12Control_Day 0 to 12
SA211418Maryam_2nd-set_Urine_Control_C1_D12Control_Day 0 to 12
SA211419Maryam_2nd-set_Urine_Control_C6_D12Control_Day 0 to 12
SA211420Maryam_2nd-set_Urine_Control_C4_D12Control_Day 0 to 12
SA211421Maryam_2nd-set_Urine_Control_C2_D16Control_Day 0 to 16
SA211422Maryam_2nd-set_Urine_Control_C3_D16Control_Day 0 to 16
SA211423Maryam_2nd-set_Urine_Control_C4_D16Control_Day 0 to 16
SA211424Maryam_2nd-set_Urine_Control_C7_D16Control_Day 0 to 16
SA211425Maryam_2nd-set_Urine_Control_C1_D16Control_Day 0 to 16
SA211426Maryam_2nd-set_Urine_Control_C5_D16Control_Day 0 to 16
SA211427Maryam_2nd-set_Urine_Control_C3_D20Control_Day 0 to 20
SA211428Maryam_2nd-set_Urine_Control_C7_D20Control_Day 0 to 20
SA211429Maryam_2nd-set_Urine_Control_C1_D20Control_Day 0 to 20
SA211430Maryam_2nd-set_Urine_Control_C2_D20Control_Day 0 to 20
SA211431Maryam_2nd-set_Urine_Control_C7_D8Control_Day 0 to 8
SA211432Maryam_2nd-set_Urine_Control_C2_D8Control_Day 0 to 8
SA211433Maryam_2nd-set_Urine_Control_C1_D8Control_Day 0 to 8
SA211434Maryam_2nd-set_Urine_Control_C5_D8Control_Day 0 to 8
SA211435Maryam_2nd-set_Urine_Control_C4_D8Control_Day 0 to 8
SA211436Maryam_2nd-set_Urine_Control_C3_D8Control_Day 0 to 8
SA211437Maryam_2nd-set_Urine_Control_C6_D8Control_Day 0 to 8
SA211438Maryam_2nd-set_Urine_DC_Vaccine_D7_PostDC_Vaccine_Day 0 to 1
SA211439Maryam_2nd-set_Urine_DC_Vaccine_D8_PostDC_Vaccine_Day 0 to 1
SA211440Maryam_2nd-set_Urine_DC_Vaccine_D9_PostDC_Vaccine_Day 0 to 1
SA211441Maryam_2nd-set_Urine_DC_Vaccine_D6_PostDC_Vaccine_Day 0 to 1
SA211442Maryam_2nd-set_Urine_DC_Vaccine_D10_PostDC_Vaccine_Day 0 to 1
SA211443Maryam_2nd-set_Urine_DC_Vaccine_D5_PostDC_Vaccine_Day 0 to 1
SA211444Maryam_2nd-set_Urine_DC_Vaccine_D2_PostDC_Vaccine_Day 0 to 1
SA211445Maryam_2nd-set_Urine_DC_Vaccine_D1_PostDC_Vaccine_Day 0 to 1
SA211446Maryam_2nd-set_Urine_DC_Vaccine_D4_PostDC_Vaccine_Day 0 to 1
SA211447Maryam_2nd-set_Urine_DC_Vaccine_D3_PostDC_Vaccine_Day 0 to 1
SA211448Maryam_2nd-set_Urine_DC_Vaccine_D4_D12DC_Vaccine_Day 0 to 12
SA211449Maryam_2nd-set_Urine_DC_Vaccine_D2_D12DC_Vaccine_Day 0 to 12
SA211450Maryam_2nd-set_Urine_DC_Vaccine_D5_D12DC_Vaccine_Day 0 to 12
SA211451Maryam_2nd-set_Urine_DC_Vaccine_D3_D12DC_Vaccine_Day 0 to 12
SA211452Maryam_2nd-set_Urine_DC_Vaccine_D9_D12DC_Vaccine_Day 0 to 12
SA211453Maryam_2nd-set_Urine_DC_Vaccine_D10_D12DC_Vaccine_Day 0 to 12
SA211454Maryam_2nd-set_Urine_DC_Vaccine_D1_D12DC_Vaccine_Day 0 to 12
SA211455Maryam_2nd-set_Urine_DC_Vaccine_D7_D12DC_Vaccine_Day 0 to 12
SA211456Maryam_2nd-set_Urine_DC_Vaccine_D6_D12DC_Vaccine_Day 0 to 12
SA211457Maryam_2nd-set_Urine_DC_Vaccine_D8_D12DC_Vaccine_Day 0 to 12
SA211458Maryam_2nd-set_Urine_DC_Vaccine_D4_D16DC_Vaccine_Day 0 to 16
SA211459Maryam_2nd-set_Urine_DC_Vaccine_D3_D16DC_Vaccine_Day 0 to 16
SA211460Maryam_2nd-set_Urine_DC_Vaccine_D2_D16DC_Vaccine_Day 0 to 16
SA211461Maryam_2nd-set_Urine_DC_Vaccine_D5_D16DC_Vaccine_Day 0 to 16
SA211462Maryam_2nd-set_Urine_DC_Vaccine_D7_D16DC_Vaccine_Day 0 to 16
SA211463Maryam_2nd-set_Urine_DC_Vaccine_D10_D16DC_Vaccine_Day 0 to 16
SA211464Maryam_2nd-set_Urine_DC_Vaccine_D9_D16DC_Vaccine_Day 0 to 16
SA211465Maryam_2nd-set_Urine_DC_Vaccine_D8_D16DC_Vaccine_Day 0 to 16
SA211466Maryam_2nd-set_Urine_DC_Vaccine_D1_D16DC_Vaccine_Day 0 to 16
SA211467Maryam_2nd-set_Urine_DC_Vaccine_D6_D16DC_Vaccine_Day 0 to 16
SA211468Maryam_2nd-set_Urine_DC_Vaccine_D5_D20DC_Vaccine_Day 0 to 20
SA211469Maryam_2nd-set_Urine_DC_Vaccine_D4_D20DC_Vaccine_Day 0 to 20
SA211470Maryam_2nd-set_Urine_DC_Vaccine_D3_D20DC_Vaccine_Day 0 to 20
SA211471Maryam_2nd-set_Urine_DC_Vaccine_D7_D20DC_Vaccine_Day 0 to 20
SA211472Maryam_2nd-set_Urine_DC_Vaccine_D8_D20DC_Vaccine_Day 0 to 20
SA211473Maryam_2nd-set_Urine_DC_Vaccine_D10_D20DC_Vaccine_Day 0 to 20
SA211474Maryam_2nd-set_Urine_DC_Vaccine_D9_D20DC_Vaccine_Day 0 to 20
SA211475Maryam_2nd-set_Urine_DC_Vaccine_D2_D20DC_Vaccine_Day 0 to 20
SA211476Maryam_2nd-set_Urine_DC_Vaccine_D1_D20DC_Vaccine_Day 0 to 20
SA211477Maryam_2nd-set_Urine_DC_Vaccine_D5_D8DC_Vaccine_Day 0 to 8
SA211478Maryam_2nd-set_Urine_DC_Vaccine_D4_D8DC_Vaccine_Day 0 to 8
SA211479Maryam_2nd-set_Urine_DC_Vaccine_D3_D8DC_Vaccine_Day 0 to 8
SA211480Maryam_2nd-set_Urine_DC_Vaccine_D1_D8DC_Vaccine_Day 0 to 8
SA211481Maryam_2nd-set_Urine_DC_Vaccine_D10_D8DC_Vaccine_Day 0 to 8
SA211482Maryam_2nd-set_Urine_DC_Vaccine_D6_D8DC_Vaccine_Day 0 to 8
SA211483Maryam_2nd-set_Urine_DC_Vaccine_D9_D8DC_Vaccine_Day 0 to 8
SA211484Maryam_2nd-set_Urine_DC_Vaccine_D8_D8DC_Vaccine_Day 0 to 8
SA211485Maryam_2nd-set_Urine_DC_Vaccine_D7_D8DC_Vaccine_Day 0 to 8
SA211486Maryam_2nd-set_Urine_DC_Vaccine_D2_D8DC_Vaccine_Day 0 to 8
Showing results 1 to 80 of 80


Collection ID:CO002287
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:Each animal was in a separate chamber individually. The chamber bottom was covered with clean parafilm. Animals were kept in the chamber until urination. Urine drops were collected using sterile syringes. Samples were stored at -80 °C until further analysis.
Collection Location:University of Florida, Neurosurgery Department, Medical college, University of Florida
Collection Frequency:Post-vaccination day 1, day 8, day 12, day 16, and day 20
Collection Duration:~30 minutes
Volumeoramount Collected:~100 uL
Storage Conditions:-80℃
Collection Vials:cryovials
Storage Vials:cryovials


Treatment ID:TR002306
Treatment Summary:DC vaccine treatment Naïve C57/BL6 mice were used for tumor implantation. B16F10-OVA (2 × 104 cells/brain) tumor cell lines were injected intracranially. Antigen specific T cells (3 × 107 cells/50 µL of PBS) were infused into the animals intravenous (IV) five days after tumor implantation and the DC vaccine (1x106 cells/50 µL of PBS per animal) was injected intradermally on the same day. Both antigen-specific T cells and DC vaccine were administered once. Urine samples were collected after DC vaccination at several timepoints. Finally, animals were euthanized when they reached the endpoints. Sample collection Each animal was in a separate chamber individually. The chamber bottom was covered with clean parafilm. Animals were kept in the chamber until urination. Urine drops were collected using sterile syringes. Samples were stored at -80 °C until further analysis. Serum samples were collected from peripheral blood.
Animal Anesthesia:isoflurane
Animal Fasting:non-fasted
Animal Endp Euthanasia:Euthanasia was carried out by thoracotomy followed by cervical dislocation.

Sample Preparation:

Sampleprep ID:SP002300
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:DC_Vaccine_treated_NMR_urine_Procedures.docx
Processing Method:None
Processing Storage Conditions:-80℃
Extraction Method:None
Extract Storage:-80℃
Sample Resuspension:In 500 microliter of 150 mM phosphate buffer (pH 7.2) with 2 mM EDTA, 0.5 mM DSS and 0.2% sodium azide for aqueous phase samples.
Sample Spiking:0.5 mM DSS for urine samples


Analysis ID:AN003611
Laboratory Name:McKnight Brain Institute
Analysis Type:NMR
Acquisition Date:4/12/2018
Acquisition Parameters File:DC_Vaccine_treated_NMR_urine_Procedures.docx
Software Version:Topspin
Operator Name:Ram Khattri
Processing Parameters File:DC_Vaccine_treated_NMR_urine_Procedures.docx
Detector Type:Bruker 600 MHz
Data Format:fid, 1r
Num Factors:10
Num Metabolites:33


NMR ID:NM000244
Analysis ID:AN003611
Instrument Name:Bruker 600 MHz
Instrument Type:FT-NMR
NMR Experiment Type:1D-1H
Field Frequency Lock:Deuterium
Standard Concentration:0.5mM DSS
Spectrometer Frequency:600 MHz
NMR Probe:Z44866_0026 (CP TXI 600S3 H-C/N-D-05 Z)
NMR Solvent:Phosphate buffer (pH 7.2) + 2 mM EDTA + 0.5 mM DSS + 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:101
Offset Frequency:4.78 ppm
Chemical Shift Ref Cpd:DSS
Temperature:298.2 oK
Number Of Scans:64
Dummy Scans:8
Acquisition Time:4s
Relaxation Delay:1s
Spectral Width:7142.9 Hz
Num Data Points Acquired:28572
Real Data Points:65536
Line Broadening:0.22 Hz
Zero Filling:65,536 points
Baseline Correction Method:Spline
Chemical Shift Ref Std:0 ppm for DSS