Summary of Study ST003054
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 PR001903. The data can be accessed directly via it's Project DOI: 10.21228/M8R14K 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 | ST003054 |
| Study Title | Integrated metabolomics and proteomics of symptomatic and early pre-symptomatic states of colitis |
| Study Summary | Colitis has a multifactorial pathogenesis with a strong cross-talk among microbiota, hypoxia and tissue metabolism. Here, we aimed to characterize the molecular signature of the disease in symptomatic and pre-symptomatic stages of the inflammatory process at the tissue and fecal level. The study is based on two different murine models for colitis. High-resolution Magic Angle Spinning NMR on cryopreserved “intact” colon tissues and LC-MS/MS on colon tissue extracts were used to derive untargeted metabolomics and proteomics information, respectively. Solution NMR was used to derive metabolomic profiles of fecal extracts. By combining metabolomic and proteomic analyses of the tissues, we found increased anaerobic glycolysis, accompanied by altered citric acid cycle and oxidative phosphorylation in inflamed colons; these changes associate with inflammation-induced hypoxia taking place in colon tissues. Pre-symptomatic states can be discriminated from healthy samples before macroscopic inflammation is observed. Different colitis states are characterized by significantly different metabolomic profiles of fecal extracts, attributable to both the dysbiosis characteristic of colitis, as well as the dysregulated tissue metabolism. Strong and distinctive fecal metabolomic signatures can be detected before onset of symptoms. Therefore, untargeted metabolomics of tissues and fecal extracts provides a comprehensive picture of the changes accompanying the disease onset already at pre-clinical stages, highlighting the diagnostic potential of global metabolomics for inflammatory diseases. |
| Institute | University of Florence |
| Last Name | Ghini |
| First Name | Veronica |
| Address | via Luigi Sacconi, 6, Sesto Fiorentino, Firenze, 50019, Italy |
| ghini@cerm.unifi.it | |
| Phone | +390554574266 |
| Submit Date | 2024-01-23 |
| Num Groups | 5 |
| Total Subjects | 50 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | fid |
| Analysis Type Detail | NMR |
| Release Date | 2024-02-28 |
| Release Version | 1 |
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Project:
| Project ID: | PR001903 |
| Project DOI: | doi: 10.21228/M8R14K |
| Project Title: | Integrated metabolomics and proteomics of symptomatic and early pre-symptomatic states of colitis |
| Project Type: | NMR-based metabolomics |
| Project Summary: | Colitis has a multifactorial pathogenesis with a strong cross-talk among microbiota, hypoxia and tissue metabolism. Here, we aimed to characterize the molecular signature of the disease in symptomatic and pre-symptomatic stages of the inflammatory process at the tissue and fecal level. The study is based on two different murine models for colitis. High-resolution Magic Angle Spinning NMR on cryopreserved “intact” colon tissues and LC-MS/MS on colon tissue extracts were used to derive untargeted metabolomics and proteomics information, respectively. Solution NMR was used to derive metabolomic profiles of fecal extracts. By combining metabolomic and proteomic analyses of the tissues, we found increased anaerobic glycolysis, accompanied by altered citric acid cycle and oxidative phosphorylation in inflamed colons; these changes associate with inflammation-induced hypoxia taking place in colon tissues. Pre-symptomatic states can be discriminated from healthy samples before macroscopic inflammation is observed. Different colitis states are characterized by significantly different metabolomic profiles of fecal extracts, attributable to both the dysbiosis characteristic of colitis, as well as the dysregulated tissue metabolism. Strong and distinctive fecal metabolomic signatures can be detected before onset of symptoms. Therefore, untargeted metabolomics of tissues and fecal extracts provides a comprehensive picture of the changes accompanying the disease onset already at pre-clinical stages, highlighting the diagnostic potential of global metabolomics for inflammatory diseases. |
| Institute: | University of Florence |
| Department: | Department of Chemistry |
| Laboratory: | Metabolomics |
| Last Name: | Ghini |
| First Name: | Veronica |
| Address: | via Luigi Sacconi, 6, Sesto Fiorentino, Firenze, 50019, Italy |
| Email: | ghini@cerm.unifi.it |
| Phone: | +390554574266 |
Subject:
| Subject ID: | SU003169 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Gender: | Male and female |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA331564 | WT_DSS_4 | Day_10_DSS |
| SA331565 | WT_DSS_3 | Day_10_DSS |
| SA331566 | WT_DSS_1 | Day_10_DSS |
| SA331567 | WT_DSS_5 | Day_10_DSS |
| SA331568 | WT_DSS_10 | Day_10_DSS |
| SA331569 | WT_DSS_2 | Day_10_DSS |
| SA331570 | WT_DSS_6 | Day_10_DSS |
| SA331571 | WT_DSS_9 | Day_10_DSS |
| SA331572 | WT_DSS_8 | Day_10_DSS |
| SA331573 | WT_DSS_7 | Day_10_DSS |
| SA331574 | WT_DSS4_3 | Day_4_DSS |
| SA331575 | WT_DSS4_2 | Day_4_DSS |
| SA331576 | WT_DSS4_10 | Day_4_DSS |
| SA331577 | WT_DSS4_4 | Day_4_DSS |
| SA331578 | WT_DSS4_8 | Day_4_DSS |
| SA331579 | WT_DSS4_1 | Day_4_DSS |
| SA331580 | WT_DSS4_9 | Day_4_DSS |
| SA331581 | WT_DSS4_7 | Day_4_DSS |
| SA331582 | WT_DSS4_6 | Day_4_DSS |
| SA331583 | WT_DSS4_5 | Day_4_DSS |
| SA331584 | IL10_KO_HC5 | Healthy_IL10-/- |
| SA331585 | IL10_KO_HC4 | Healthy_IL10-/- |
| SA331586 | IL10_KO_HC3 | Healthy_IL10-/- |
| SA331587 | IL10_KO_HC6 | Healthy_IL10-/- |
| SA331588 | IL10_KO_HC7 | Healthy_IL10-/- |
| SA331589 | IL10_KO_HC9 | Healthy_IL10-/- |
| SA331590 | IL10_KO_HC8 | Healthy_IL10-/- |
| SA331591 | IL10_KO_HC2 | Healthy_IL10-/- |
| SA331592 | IL10_KO_HC10 | Healthy_IL10-/- |
| SA331593 | IL10_KO_HC1 | Healthy_IL10-/- |
| SA331594 | IL10_KO_ILL6 | Ill_IL10-/- |
| SA331595 | IL10_KO_ILL7 | Ill_IL10-/- |
| SA331596 | IL10_KO_ILL8 | Ill_IL10-/- |
| SA331597 | IL10_KO_ILL10 | Ill_IL10-/- |
| SA331598 | IL10_KO_ILL9 | Ill_IL10-/- |
| SA331599 | IL10_KO_ILL2 | Ill_IL10-/- |
| SA331600 | IL10_KO_ILL3 | Ill_IL10-/- |
| SA331601 | IL10_KO_ILL4 | Ill_IL10-/- |
| SA331602 | IL10_KO_ILL5 | Ill_IL10-/- |
| SA331603 | IL10_KO_ILL1 | Ill_IL10-/- |
| SA331604 | WT_HC_5 | WT |
| SA331605 | WT_HC_2 | WT |
| SA331606 | WT_HC_10 | WT |
| SA331607 | WT_HC_1 | WT |
| SA331608 | WT_HC_3 | WT |
| SA331609 | WT_HC_4 | WT |
| SA331610 | WT_HC_8 | WT |
| SA331611 | WT_HC_7 | WT |
| SA331612 | WT_HC_6 | WT |
| SA331613 | WT_HC_9 | WT |
| Showing results 1 to 50 of 50 |
Collection:
| Collection ID: | CO003162 |
| Collection Summary: | Colons were harvested from euthanized mice and flash-frozen in liquid nitrogen. For all downstream analyses, the distal region of the colon (0.5-2 cm from rectum) was used, since it is where colitis is most pronounced in these models. |
| Sample Type: | Colon |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003178 |
| Treatment Summary: | Acute colitis was induced in wild type (WT) C57BL/6 mice via addition of 1.25% DSS into the drinking water for seven days. To gain insight on chronic intestinal inflammation, we used C57BL/6 IL-10-/- mice that spontaneously develop chronic colon inflammation. This inflammation is not chemically induced, but rather is considered to be a result of a dysregulated immune system, which more resembles the clinical manifestation of chronic UC and CD patients and mimics a monogenic form of IBD20. In order to synchronize and accelerate the onset of chronic colitis, mice were exposed to 200 ppm piroxicam (Sigma-Aldrich ltd.) via supplementation in normal murine chow for 14 days. With the described experimental procedures, we obtained five groups of mice (10 mice per group) for further analysis: 1) Healthy WT; 2) Day 4 of DSS (pre-symptomatic); 3) Day 10 of DSS (acute colitis); 4) Healthy IL-10-/- (pre-symptomatic); and 5) Ill IL-10-/- (chronic colitis). |
Sample Preparation:
| Sampleprep ID: | SP003175 |
| Sampleprep Summary: | Frozen colon samples were trimmed (15–20 mg) to fit HR-MAS ZrO2 rotor insert capacity (50 μL). Each insert was filled with 2H2O containing 5.8 mM sodium trimethylsilyl [2,2,3,3-2H4]propionate (TMSP). Inserts were covered with plug and plug-restraining screw and inserted into the 4 mm rotor for HR-MAS probe. |
Analysis:
| Analysis ID: | AN005008 |
| Analysis Type: | NMR |
| Num Factors: | 5 |
| Num Metabolites: | 22 |
| Units: | AU |
NMR:
| NMR ID: | NM000274 |
| Analysis ID: | AN005008 |
| Instrument Name: | Bruker 600 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | HR-MAS TXI 1H/13C/15N probe |
| NMR Solvent: | H2O |
| NMR Tube Size: | 4 mm rotor for HR-MAS probe |
| Pulse Sequence: | CPMG |
| Water Suppression: | water peak suppression-presaturation |
| Temperature: | 277 K |
| Number Of Scans: | 64 |
| Dummy Scans: | 4 |
| Acquisition Time: | 1.36s |
| Spectral Width: | 12 KHz |
| Num Data Points Acquired: | 32 k |
| Line Broadening: | 1 |
| Baseline Correction Method: | automatic |
| Chemical Shift Ref Std: | doublet at 5.24 ppm |
| Binned Increment: | 0.02 ppm |
| Binned Data Excluded Range: | 4.5-5.5 ppm |
