Summary of Study ST003093
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001922. The data can be accessed directly via it's Project DOI: 10.21228/M88T6X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
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.
| Study ID | ST003093 |
| 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 |
| apulliam3@gatech.edu | |
| Phone | 404.385.0629 |
| Submit Date | 2024-02-16 |
| Num Groups | 3 |
| Total Subjects | 54 |
| Num Males | 27 |
| Num Females | 27 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-02-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001922 |
| Project DOI: | doi: 10.21228/M88T6X |
| 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 |
Subject:
| Subject ID: | SU003208 |
| 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 |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Injury severity | Sex | Batches |
|---|---|---|---|---|---|
| SA333248 | 01_010 | Norm. Area 01_10.raw (F77) | 1X | M | Batch 1 |
| SA333249 | 01_011 | Norm. Area 01_11.raw (F78) | 3X | M | Batch 1 |
| SA333250 | 01_012 | Norm. Area 01_12.raw (F54) | 3X | M | Batch 1 |
| SA333251 | 01_013 | Norm. Area 01_13.raw (F32) | 1X | F | Batch 1 |
| SA333252 | 01_014 | Norm. Area 01_14.raw (F38) | SHAM | F | Batch 1 |
| SA333253 | 01_017 | Norm. Area 01_17.raw (F50) | 1X | F | Batch 1 |
| SA333254 | 01_018 | Norm. Area 01_18.raw (F51) | SHAM | F | Batch 1 |
| SA333255 | 01_019 | Norm. Area 01_19.raw (F53) | SHAM | F | Batch 1 |
| SA333247 | 01_001 | Norm. Area 01_1.raw (F81) | SHAM | M | Batch 1 |
| SA333257 | 01_020 | Norm. Area 01_20.raw (F63) | 3X | F | Batch 1 |
| SA333258 | 01_021 | Norm. Area 01_21.raw (F28) | SHAM | F | Batch 1 |
| SA333259 | 01_022 | Norm. Area 01_22.raw (F46) | 1X | F | Batch 1 |
| SA333260 | 01_023 | Norm. Area 01_23.raw (F82) | 3X | F | Batch 1 |
| SA333261 | 01_024 | Norm. Area 01_24.raw (F29) | 1X | F | Batch 1 |
| SA333262 | 01_025 | Norm. Area 01_25.raw (F41) | SHAM | M | Batch 1 |
| SA333263 | 01_026 | Norm. Area 01_26.raw (F80) | SHAM | M | Batch 1 |
| SA333264 | 01_027 | Norm. Area 01_27.raw (F59) | 1X | F | Batch 1 |
| SA333265 | 01_028 | Norm. Area 01_28.raw (F55) | 3X | F | Batch 1 |
| SA333266 | 01_029 | Norm. Area 01_29.raw (F34) | 3X | M | Batch 1 |
| SA333256 | 01_002 | Norm. Area 01_2.raw (F44) | SHAM | M | Batch 1 |
| SA333267 | 01_030 | Norm. Area 01_30.raw (F74) | 3X | F | Batch 1 |
| SA333268 | 01_031 | Norm. Area 01_31.raw (F56) | SHAM | F | Batch 1 |
| SA333269 | 01_032 | Norm. Area 01_32.raw (F73) | 3X | F | Batch 1 |
| SA333270 | 01_006 | Norm. Area 01_6.raw (F79) | 1X | M | Batch 1 |
| SA333271 | 01_007 | Norm. Area 01_7.raw (F57) | SHAM | M | Batch 1 |
| SA333272 | 01_008 | Norm. Area 01_8.raw (F76) | 1X | M | Batch 1 |
| SA333273 | 02_010 | Norm. Area 02_10.raw (F43) | 1X | F | Batch 2 |
| SA333274 | 02_011 | Norm. Area 02_11.raw (F27) | 1X | M | Batch 2 |
| SA333275 | 02_012 | Norm. Area 02_12.raw (F60) | SHAM | M | Batch 2 |
| SA333276 | 02_013 | Norm. Area 02_13.raw (F30) | SHAM | F | Batch 2 |
| SA333277 | 02_014 | Norm. Area 02_14.raw (F37) | 1X | F | Batch 2 |
| SA333278 | 02_015 | Norm. Area 02_15.raw (F33) | 3X | M | Batch 2 |
| SA333279 | 02_016 | Norm. Area 02_16.raw (F47) | 3X | M | Batch 2 |
| SA333280 | 02_017 | Norm. Area 02_17.raw (F68) | 3X | M | Batch 2 |
| SA333281 | 02_018 | Norm. Area 02_18.raw (F26) | 3X | M | Batch 2 |
| SA333282 | 02_019 | Norm. Area 02_19.raw (F31) | SHAM | M | Batch 2 |
| SA333284 | 02_020 | Norm. Area 02_20.raw (F35) | 1X | M | Batch 2 |
| SA333285 | 02_021 | Norm. Area 02_21.raw (F67) | 1X | M | Batch 2 |
| SA333286 | 02_022 | Norm. Area 02_22.raw (F65) | 3X | M | Batch 2 |
| SA333287 | 02_023 | Norm. Area 02_23.raw (F66) | 3X | M | Batch 2 |
| SA333288 | 02_025 | Norm. Area 02_25.raw (F69) | SHAM | F | Batch 2 |
| SA333289 | 02_026 | Norm. Area 02_26.raw (F45) | 1X | F | Batch 2 |
| SA333290 | 02_027 | Norm. Area 02_27.raw (F64) | 3X | F | Batch 2 |
| SA333291 | 02_028 | Norm. Area 02_28.raw (F70) | SHAM | F | Batch 2 |
| SA333292 | 02_029 | Norm. Area 02_29.raw (F25) | 3X | M | Batch 2 |
| SA333283 | 02_002 | Norm. Area 02_2.raw (F48) | SHAM | M | Batch 2 |
| SA333294 | 02_031 | Norm. Area 02_31.raw (F75) | 3X | M | Batch 2 |
| SA333293 | 02_003 | Norm. Area 02_3.raw (F62) | SHAM | F | Batch 2 |
| SA333295 | 02_004 | Norm. Area 02_4.raw (F42) | 1X | M | Batch 2 |
| SA333296 | 02_005 | Norm. Area 02_5.raw (F58) | 3X | F | Batch 2 |
| SA333297 | 02_006 | Norm. Area 02_6.raw (F39) | SHAM | M | Batch 2 |
| SA333298 | 02_007 | Norm. Area 02_7.raw (F71) | 1X | F | Batch 2 |
| SA333299 | 02_008 | Norm. Area 02_8.raw (F52) | 1X | M | Batch 2 |
| SA333300 | 02_009 | Norm. Area 02_9.raw (F40) | 3X | F | Batch 2 |
| Showing results 1 to 54 of 54 |
Collection:
| Collection ID: | CO003201 |
| 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 ID: | TR003217 |
| 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. |
Sample Preparation:
| Sampleprep ID: | SP003214 |
| 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. |
Combined analysis:
| Analysis ID | AN005062 | AN005063 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Thermo Accucore C30 (50 x 2.1mm,2.1um) | Thermo Accucore C30 (50 x 2.1mm,2.1um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo ID-X Orbitrap Tribrid | Thermo ID-X Orbitrap Tribrid |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | m/z | m/z |
Chromatography:
| Chromatography ID: | CH003822 |
| Chromatography Summary: | MS |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (50 x 2.1mm,2.1um) |
| Column Temperature: | 50 |
| 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 |
| 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 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003823 |
| Chromatography Summary: | MS |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (50 x 2.1mm,2.1um) |
| Column Temperature: | 50 |
| 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 |
| 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 |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004800 |
| Analysis ID: | AN005062 |
| Instrument Name: | Thermo ID-X Orbitrap Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LCMS Pos |
| Ion Mode: | POSITIVE |
| MS ID: | MS004801 |
| Analysis ID: | AN005063 |
| Instrument Name: | Thermo ID-X Orbitrap Tribrid |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | LCMS Neg |
| Ion Mode: | NEGATIVE |
