Summary of Study ST002828
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 PR001770. The data can be accessed directly via it's Project DOI: 10.21228/M8XB0Q 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 | ST002828 |
| Study Title | Role of the Afferent Lymph as an Immunological Conduit to Analyze Tissue Antigenic and Inflammatory Load - metabolomics |
| Study Summary | The intestinal barrier, and the gut-associated lymphoid tissue, are the interface of the host-microbiome/pathogens interactions and, its disruption, has been associated with a series of inflammatory, autoimmune, and degenerative diseases. Herein we performed the analysis of the pre-nodal mesenteric lymph at steady state and following disruption of the intestinal barrier to map the antigenic and pro-inflammatory load in both mice and human subjects with inflammatory bowel disease. The antigenic signature of gastrointestinal tissue inflammation was reflected in the mesenteric nodal dendritic-cells (DC)-MHCII-eluted immunopeptidome, in a tissue specific manner, when compared to the DC-eluted-MHCII-peptidome from cervical lymph nodes. Pro-inflammatory and microbiome-derived by-products, such as amino acids, deoxy sugars, component of the bacterial wall and other immunomodulators of the gut-brain axis, were found in the afferent lymph following damage to the gut epithelium. Our data points to the relevance of the lymphatic fluid to probe the tissue-specific antigenic and inflammatory load transported to the draining lymph node. |
| Institute | University of Colorado Denver |
| Last Name | Haines |
| First Name | Julie |
| Address | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| julie.haines@cuanschutz.edu | |
| Phone | 3037243339 |
| Submit Date | 2023-08-21 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-21 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001770 |
| Project DOI: | doi: 10.21228/M8XB0Q |
| Project Title: | Role of the Afferent Lymph as an Immunological Conduit to Analyze Tissue Antigenic and Inflammatory Load - metabolomics |
| Project Summary: | The intestinal barrier, and the gut-associated lymphoid tissue, are the interface of the host-microbiome/pathogens interactions and, its disruption, has been associated with a series of inflammatory, autoimmune, and degenerative diseases. Herein we performed the analysis of the pre-nodal mesenteric lymph at steady state and following disruption of the intestinal barrier to map the antigenic and pro-inflammatory load in both mice and human subjects with inflammatory bowel disease. The antigenic signature of gastrointestinal tissue inflammation was reflected in the mesenteric nodal dendritic-cells (DC)-MHCII-eluted immunopeptidome, in a tissue specific manner, when compared to the DC-eluted-MHCII-peptidome from cervical lymph nodes. Pro-inflammatory and microbiome-derived by-products, such as amino acids, deoxy sugars, component of the bacterial wall and other immunomodulators of the gut-brain axis, were found in the afferent lymph following damage to the gut epithelium. Our data points to the relevance of the lymphatic fluid to probe the tissue-specific antigenic and inflammatory load transported to the draining lymph node. |
| Institute: | University of Colorado Denver |
| Laboratory: | Lab of Angelo D'Alessandro in collaboration with lab of Laura Santambrogio (Weill Cornell) |
| Last Name: | Haines |
| First Name: | Julie |
| Address: | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| Email: | julie.haines@cuanschutz.edu |
| Phone: | 3037243339 |
Subject:
| Subject ID: | SU002937 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Factor |
|---|---|---|
| SA305863 | 2A | control afferent |
| SA305864 | 9A | control afferent |
| SA305865 | 13A | control afferent |
| SA305866 | 14A | control afferent |
| SA305867 | 1A | control afferent |
| SA305868 | 13E | control efferent |
| SA305869 | 14E | control efferent |
| SA305870 | 2E | control efferent |
| SA305871 | 9E | control efferent |
| SA305872 | 1E | control efferent |
| SA305851 | 5A | DSS afferent |
| SA305852 | 6A | DSS afferent |
| SA305853 | 16A | DSS afferent |
| SA305854 | 3A | DSS afferent |
| SA305855 | 7A | DSS afferent |
| SA305856 | 4A | DSS afferent |
| SA305857 | 5E | DSS efferent |
| SA305858 | 4E | DSS efferent |
| SA305859 | 3E | DSS efferent |
| SA305860 | 6E | DSS efferent |
| SA305861 | 7E | DSS efferent |
| SA305862 | 16E | DSS efferent |
| Showing results 1 to 22 of 22 |
Collection:
| Collection ID: | CO002930 |
| Collection Summary: | Mice (C57BL/6J) mice were obtained from Jackson Laboratories and housed at Weill Cornell Medicine animal facilities. The mice were anesthetized using ketamine (80 mg/kg) and Xylazine (10 mg/kg), injected intraperitonially. Cannulation is performed 15-20 minutes post anesthetizing the mice, when the mice is no longer able to feel toe pinch. Mice are placed face up with paws stretched and pinned. Incision is made at the abdominal area, exposing the underlying gut and intestinal tissues. Pre-nodal / post-nodal lymphatic vessels are visualized and identified. The pre-nodal lymphatic vessels run from intestines to mesenteric lymph nodes, while post-nodal lymphatic runs behind the mesenteric lymph nodes and can be reached by clearing tissues. Fat tissues is carefully removed or move aside using forceps and Q-tips. Care is taken to keep the tissues hydrated using 1X PBS. Upon creating a small tear/cut on the lymphatic vessel, using a glass pipette (tip diameter of 40-60 uM) lymph is collected. This pipette is then flushed into a microcentrifuge containing 1X PBS and 2X protease inhibitor (Thermofisher Scientific (A32963). |
| Sample Type: | Lymph fluid |
Treatment:
| Treatment ID: | TR002946 |
| Treatment Summary: | C57Bl6 mice are given access to either sterile water or water supplemented with 40-50 kDa dextran sulfate sodium (DSS) for 7 days. |
Sample Preparation:
| Sampleprep ID: | SP002943 |
| Sampleprep Summary: | Frozen mouse lymph samples were provided as 3 uL lymph fluid in PBS to a final volume of 300 uL. Specimens were thawed on ice then 22.2 uL was transferred to a tube containing 200 uL of ice-cold 5:3:2 methanol:acetonitrile:water. Samples were agitated 30 min in a cold room then spun at 12,000 g, 10 min, 4 degrees C. Two 100 uL aliquots of supernatant from each tube were transferred into new (separate) tubes and dried under vacuum at room temperature. One set was resuspended in 100 uL of 0.1% formic acid for positive mode acquisition. The other set was resuspended in 100 uL of 1 mM ammonium acetate for negative mode acquisition. |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004617 | AN004618 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Thermo Vanquish | Thermo Vanquish |
| Column | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | peak area | peak area |
Chromatography:
| Chromatography ID: | CH003473 |
| Chromatography Summary: | Negative C18 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-0.5 min 0% B, 0.5-1.1 min 0-100% B, 1.1-2.75 min hold at 100% B, 2.75-3 min 100-0% B, 3-5 min hold at 0% B |
| Flow Rate: | 450 uL/min |
| Sample Injection: | 10 uL |
| Solvent A: | 95% water/5% acetonitrile; 1 mM ammonium acetate |
| Solvent B: | 95% acetonitrile/5% water; 1 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003474 |
| Chromatography Summary: | Positive C18 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
| Column Temperature: | 45 |
| Flow Gradient: | 0-0.5 min 5% B, 0.5-1.1 min 5-95% B, 1.1-2.75 min hold at 95% B, 2.75-3 min 95-5% B, 3-5 min hold at 5% B |
| Flow Rate: | 450 uL/min |
| Sample Injection: | 10 uL |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004363 |
| Analysis ID: | AN004617 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | NEGATIVE |
| MS ID: | MS004364 |
| Analysis ID: | AN004618 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
| Ion Mode: | POSITIVE |
