{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003093","ANALYSIS_ID":"AN005062","VERSION":"1","CREATED_ON":"February 20, 2024, 11:47 am"},

"PROJECT":{"PROJECT_TITLE":"Integrative Analysis of Cytokine and Lipidomics Datasets Fol-lowing Mild Traumatic Brain Injury in the Rat","PROJECT_SUMMARY":"Traumatic brain injury (TBI) is a significant source of disability in the United States and around the world and may lead to long-lasting cognitive deficits and decreased quality of life for patients across injury severities. Following the primary injury phase, TBI is characterized by com-plex secondary cascades that involve altered homeostasis and metabolism, faulty signaling, neu-roinflammation, and lipid dysfunction. The objectives of the present study were to (1) assess po-tential correlations between lipidome and cytokine changes after closed-head mild TBI (mTBI), and (2) examine reproducibility of our acute lipidomic profiles following TBI. Cortices from 54 Sprague Dawley male and female rats were analyzed by ultra-high-performance liquid chromatography mass spectrometry (LC-MS) in both positive and negative ionization modes and multiplex cytokine analysis after single (smTBI) or repetitive (rmTBI) closed-head impacts, or sham conditions. Tissue age was a variable, given that two cohorts (n= 26 and n=28) were initially run a year-and-a-half apart, creating inter-batch variations. We annotated the lipidome datasets using an in-house data dictionary based on exact masses of precursor and fragment ions and removed features with statis-tically significant differences between sham control batches. Our results indicate that lipids with high fold change between injury groups moderately correlate with the cytokines eotaxin, IP-10, and TNF-a. Additionally, we show a significant decrease of the pro-inflammatory markers, IL-1b and IP-10, TNF-a, and RANTES in the rmTBI samples relative to sham control. We discuss the major challenges in correlating high dimensional lipidomic data with functional cytokine profiles and the implications for understanding the biological significance of two related but disparate analysis modes in the study of TBI, an inherently heterogeneous neurological disorder.","INSTITUTE":"Georgia Institute of Technology","DEPARTMENT":"The Wallace H. Coulter Department of Biomedical Engineering","LABORATORY":"Michelle LaPlaca","LAST_NAME":"Pulliam","FIRST_NAME":"Alexis","ADDRESS":"313 Ferst Dr. NW, Atlanta, GA, 30332","EMAIL":"apulliam3@gatech.edu","PHONE":"404.385.0629"},

"STUDY":{"STUDY_TITLE":"Integrative Analysis of Cytokine and Lipidomics Datasets Following Mild Traumatic Brain Injury in the Rat","STUDY_SUMMARY":"Traumatic brain injury (TBI) is a significant source of disability in the United States and around the world and may lead to long-lasting cognitive deficits and decreased quality of life for patients across injury severities. Following the primary injury phase, TBI is characterized by com-plex secondary cascades that involve altered homeostasis and metabolism, faulty signaling, neu-roinflammation, and lipid dysfunction. The objectives of the present study were to (1) assess po-tential correlations between lipidome and cytokine changes after closed-head mild TBI (mTBI), and (2) examine reproducibility of our acute lipidomic profiles following TBI. Cortices from 54 Sprague Dawley male and female rats were analyzed by ultra-high-performance liquid chromatography mass spectrometry (LC-MS) in both positive and negative ionization modes and multiplex cytokine analysis after single (smTBI) or repetitive (rmTBI) closed-head impacts, or sham conditions. Tissue age was a variable, given that two cohorts (n= 26 and n=28) were initially run a year-and-a-half apart, creating inter-batch variations. We annotated the lipidome datasets using an in-house data dictionary based on exact masses of precursor and fragment ions and removed features with statis-tically significant differences between sham control batches. Our results indicate that lipids with high fold change between injury groups moderately correlate with the cytokines eotaxin, IP-10, and TNF-a. Additionally, we show a significant decrease of the pro-inflammatory markers, IL-1b and IP-10, TNF-a, and RANTES in the rmTBI samples relative to sham control. We discuss the major challenges in correlating high dimensional lipidomic data with functional cytokine profiles and the implications for understanding the biological significance of two related but disparate analysis modes in the study of TBI, an inherently heterogeneous neurological disorder.","INSTITUTE":"Georgia Institute of Technology","DEPARTMENT":"The Wallace H. Coulter Department of Biomedical Engineering","LABORATORY":"Michelle LaPlaca","LAST_NAME":"Pulliam","FIRST_NAME":"Alexis","ADDRESS":"313 Ferst Dr. NW, Atlanta, GA, 30332","EMAIL":"apulliam3@gatech.edu","PHONE":"404.385.0629","NUM_GROUPS":"3","TOTAL_SUBJECTS":"54","NUM_MALES":"27","NUM_FEMALES":"27"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Rattus norvegicus","TAXONOMY_ID":"10116","WEIGHT_OR_WEIGHT_RANGE":"400g","GENDER":"Male and female","ANIMAL_ANIMAL_SUPPLIER":"Charles River","ANIMAL_HOUSING":"Double Housed","ANIMAL_LIGHT_CYCLE":"Reverse Light Cycle","SPECIES_GROUP":"Sprague Dawley"},
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"COLLECTION":{"COLLECTION_SUMMARY":"Brain samples were harvested and collected following transcardial perfusion with phosphate buffer (0.1 M, pH 7.4) 24 hr post-TBI. The perfused whole brains were rapidly removed, and flash frozen in an isopentane-methanol ice slurry. Pieces of parietal cortices (5 mm x 2 mm) were dissected from partially thawed brains by removing the subcortical structures including the majority of white matter and stored at -80° C in microcentrifuge tubes. The cortices were then transferred to liquid nitrogen and manually pulverized with a pestle and mortar submerged in liquid nitrogen and aliquoted in ~10-30 mg tissue samples.","SAMPLE_TYPE":"Brain"},

"TREATMENT":{"TREATMENT_SUMMARY":"Experimental batch 1 contained female (n = 16) and male (n = 10) to either sham procedure (n = 10), 1X, single mild traumatic brain injury (mTBI) (n = 8), and 3X, repetitive mTBI (n = 8) groups. Experimental batch 2 contained female (n = 11) and male (n = 17) to either sham procedure (n = 8), smTBI(n = 9), and rmTBI (n = 11) groups."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Experimental batch 1 and 2 aliquoted tissue samples were thawed simultane-ously on ice prior to addition of solvent (IPA and Splash II Lipidomix in (1:3 v/v)) to sep-arate lipids and small non-polar metabolites. LC-MS grade water was used to prepare sample blanks, and pooled quality control (QC) samples were prepared from 5 µL ali-quoted supernatant of all samples in the study. The brain and solvent (1:4 w/v), and beads were placed in a Tissuelyser II for 8 min and centrifuged at 16000 g for 7 min. The supernatant was collected for LC-MS. Pooled quality control samples were formed from combining 6 µL aliquots of all brain sample extracts. Sample blanks were prepared with the same procedure except instead of a brain sample, 50 µL of LC-MS grade water was used."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"MS","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Accucore C30 (50 x 2.1mm,2.1um)","SOLVENT_A":"40% water/60% acetonitrile; 10 mM ammonium formate; 0.1% formic acid","SOLVENT_B":"10% acetonitrile/90% isopropanol; with 10 mM ammonium formate; 0.1% formic acid","FLOW_GRADIENT":"0 minutes 80% A; 1 minute 40% A; 5 minutes 30% A; 5.5 minutes 15% A; 8 minutes 10% A; held 8.2 minutes to 10.5 minutes 0% A; 10.7 minutes 80% A; and held until 12 minutes","FLOW_RATE":"0.40 mL/min","COLUMN_TEMPERATURE":"50"},

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

"MS":{"INSTRUMENT_NAME":"Thermo ID-X Orbitrap Tribrid","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"LCMS Pos","MS_RESULTS_FILE":"ST003093_AN005062_Results.txt UNITS:m/z Has m/z:Yes Has RT:No RT units:No RT data"}

}