Summary of Study ST002416
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 PR001555. The data can be accessed directly via it's Project DOI: 10.21228/M8PT4W 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 | ST002416 |
| Study Title | Proteomics and metabolomics of multiple sclerosis (Part 2) |
| Study Summary | Multiple sclerosis (MS) is a chronic autoimmune disease that affects the myelination of the neurons present in the central nervous system (CNS). The exact etiology of MS development is unclear, but various environmental and genetic factors might play a role in initiating the disease. Current treatments for MS enhance the quality of life and reduce the symptoms. One of these treatments is dimethyl fumarate (DMF), commercially known as Tecfidera. Experimental autoimmune encephalomyelitis (EAE) is a mouse model that is used to study the pathophysiology of MS disease as well as the effects of possible therapeutic agents. In this study, we investigated the effects of SIMR1707 which is a novel compound designed at Sharjah Institute for Medical Research (SIMR). . Single and multiple doses of SIMR1707 demonstrated high safety in mice studies. Treatment of EAE mice with SIMR1707 was able to reduce the EAE clinical scores and maintain their body weight similar to the MS FDA-approved (DMF, Tecfidera), when they were used preventively, prophylactically, or therapeutically. The histological and immunohistochemistry evaluations showed reduced clinical features such as signs of inflammation, demyelination, and infiltration of CD3-positive T cells into the brains of the EAE mice, as compared to vehicle-treated, or untreated EAE mice. Moreover, multi-OMICS experiments including Transcriptomics, Proteomics and Metabolomics were performed to gain insights into the relevant mechanism of action of the SIMR1707 in EAE and thus its therapeutic efficacy to treat MS. Same tissue samples extracted from the cerebellum part of the brain of normal, EAE vehicle-treated, and therapeutic SIMR1707 treated mice, were subjected for the whole RNA-sequencing for transcriptomics, Nano MS for proteomics analysis and LC-MS metabolomics analysis. The multi-OMICs integrative analysis showed that the treatment with SIMR1707 downregulated key biomarkers functionally associated with top pathways including calcium signaling, PI3K/AKT, and mTOR signaling pathways, which may play important roles in EAE and MS pathophysiology. Additionally, the metabolomics-based enriched-for-action pathway analysis showed that the top significantly activated metabolites (FC > 2, p < 0.05) are cholic acid, propionic acid, sphinganine, and nutriacholic acid. Consisting with the functional enrichment pathway analysis, two potent markers, Snta1 and Fscn1, involved in the actin-binding and cytoskeleton are commonly shared between transcriptomics and proteomics and showed mRNA-protein expression correlation in SIMR1707 treated compared to vehicle EAE mice. Importantly, these two markers are involved in the MT2/AKT/GSK3 pathway and may potentially play role in MS and EAE disease |
| Institute | Sharjah Institute for Medical Research |
| Last Name | Facility |
| First Name | Core |
| Address | M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah |
| tims-tof@sharjah.ac.ae | |
| Phone | 065057656 |
| Submit Date | 2022-12-19 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-06-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001555 |
| Project DOI: | doi: 10.21228/M8PT4W |
| Project Title: | Proteomics and metabolomics of multiple sclerosis |
| Project Summary: | Multiple sclerosis (MS) is a chronic autoimmune disease that affects the myelination of the neurons present in the central nervous system (CNS). The exact etiology of MS development is unclear, but various environmental and genetic factors might play a role in initiating the disease. Current treatments for MS enhance the quality of life and reduce the symptoms. One of these treatments is dimethyl fumarate (DMF), commercially known as Tecfidera. Experimental autoimmune encephalomyelitis (EAE) is a mouse model that is used to study the pathophysiology of MS disease as well as the effects of possible therapeutic agents. In this study, we investigated the effects of SIMR1707 which is a novel compound designed at Sharjah Institute for Medical Research (SIMR). . Single and multiple doses of SIMR1707 demonstrated high safety in mice studies. Treatment of EAE mice with SIMR1707 was able to reduce the EAE clinical scores and maintain their body weight similar to the MS FDA-approved (DMF, Tecfidera), when they were used preventively, prophylactically, or therapeutically. The histological and immunohistochemistry evaluations showed reduced clinical features such as signs of inflammation, demyelination, and infiltration of CD3-positive T cells into the brains of the EAE mice, as compared to vehicle-treated, or untreated EAE mice. Moreover, multi-OMICS experiments including Transcriptomics, Proteomics and Metabolomics were performed to gain insights into the relevant mechanism of action of the SIMR1707 in EAE and thus its therapeutic efficacy to treat MS. Same tissue samples extracted from the cerebellum part of the brain of normal, EAE vehicle-treated, and therapeutic SIMR1707 treated mice, were subjected for the whole RNA-sequencing for transcriptomics, Nano MS for proteomics analysis and LC-MS metabolomics analysis. The multi-OMICs integrative analysis showed that the treatment with SIMR1707 downregulated key biomarkers functionally associated with top pathways including calcium signaling, PI3K/AKT, and mTOR signaling pathways, which may play important roles in EAE and MS pathophysiology. Additionally, the metabolomics-based enriched-for-action pathway analysis showed that the top significantly activated metabolites (FC > 2, p < 0.05) are cholic acid, propionic acid, sphinganine, and nutriacholic acid. Consisting with the functional enrichment pathway analysis, two potent markers, Snta1 and Fscn1, involved in the actin-binding and cytoskeleton are commonly shared between transcriptomics and proteomics and showed mRNA-protein expression correlation in SIMR1707 treated compared to vehicle EAE mice. Importantly, these two markers are involved in the MT2/AKT/GSK3 pathway and may potentially play role in MS and EAE disease |
| Institute: | Sharjah Institute for Medical Research |
| Last Name: | Facility |
| First Name: | Core |
| Address: | M32, SIMR, College of Pharmacy, Health Sciences, University of Sharjah |
| Email: | tims-tof@sharjah.ac.ae |
| Phone: | 065057656 |
Subject:
| Subject ID: | SU002505 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA242049 | N03-02_9_1_1408 | Normal |
| SA242050 | N03-03_9_1_1409 | Normal |
| SA242051 | N02-03_8_1_1406 | Normal |
| SA242052 | N01-01_7_1_1401 | Normal |
| SA242053 | N03-01_9_1_1407 | Normal |
| SA242054 | N01-02_7_1_1402 | Normal |
| SA242055 | N02-01_8_1_1404 | Normal |
| SA242056 | N01-03_7_1_1403 | Normal |
| SA242057 | N02-02_8_1_1405 | Normal |
| SA242058 | Prev1707-03-01_22_1_1446 | Preventative1707 |
| SA242059 | Prev1707-03-02_22_1_1447 | Preventative1707 |
| SA242060 | Prev1707-03-03_22_1_1448 | Preventative1707 |
| SA242061 | Prev1707-02-03_21_1_1445 | Preventative1707 |
| SA242062 | Prev1707-01-02_20_1_1441 | Preventative1707 |
| SA242063 | Prev1707-01-01_20_1_1440 | Preventative1707 |
| SA242064 | Prev1707-02-02_21_1_1444 | Preventative1707 |
| SA242065 | Prev1707-01-03_20_1_1442 | Preventative1707 |
| SA242066 | Prev1707-02-01_21_1_1443 | Preventative1707 |
| SA242067 | Proph1707-02-03_29_1_1469 | Prophylactic1707 |
| SA242068 | Proph1707-02-02_29_1_1468 | Prophylactic1707 |
| SA242069 | Proph1707-01-01_28_1_1464 | Prophylactic1707 |
| SA242070 | Proph1707-02-01_29_1_1467 | Prophylactic1707 |
| SA242071 | Proph1707-01-02_28_1_1465 | Prophylactic1707 |
| SA242072 | Proph1707-01-03_28_1_1466 | Prophylactic1707 |
| SA242073 | Ther-1707-02-02_35_1_1486 | Therapeutic1707 |
| SA242074 | Ther-1707-02-01_35_1_1485 | Therapeutic1707 |
| SA242075 | Ther-1707-02-03_35_1_1487 | Therapeutic1707 |
| SA242076 | Ther-1707-01-03_34_1_1484 | Therapeutic1707 |
| SA242077 | Ther-1707-01-01_34_1_1482 | Therapeutic1707 |
| SA242078 | Ther-1707-01-02_34_1_1483 | Therapeutic1707 |
| SA242079 | Veh02-03_14_1_1424 | Vehicle |
| SA242080 | Veh02-02_14_1_1423 | Vehicle |
| SA242081 | Veh01-03_13_1_1421 | Vehicle |
| SA242082 | Veh01-01_13_1_1419 | Vehicle |
| SA242083 | Veh01-02_13_1_1420 | Vehicle |
| SA242084 | Veh02-01_14_1_1422 | Vehicle |
| Showing results 1 to 36 of 36 |
Collection:
| Collection ID: | CO002498 |
| Collection Summary: | The experiments on the mice were approved by the University of Sharjah animal care and use committee (ACUC) (ACUC approval number: ACUC-16-003-EAE and ACUC-21-09-06-01). The mice were housed at the University of Sharjah animal facility, in plastic cages under a controlled environment of 24 ± 2 °C, 50% ± 5% humidity, 12 h/12 h light-dark cycle with unlimited food and water access. |
| Sample Type: | Brain |
Treatment:
| Treatment ID: | TR002517 |
| Treatment Summary: | From Normal, EAE vehicle-treated, and therapeutic SIMR1707 treated mice, the cerebellum part of the brain was cut, and immediately snap frozen using liquid nitrogen. The samples then were weighed, made in powder form and homogenized using pistol method under liquid nitrogen. The cerebellum sample was lysed using 400 uL RIBA lysis buffer and let to set for 5-10 minutes to allow lysis. 50 ul of the homogenized sample was taken for RNA extraction using norgen biotek RNA/DNA purification kit (cat#:47700) according to the manufacturer’s instructions. The remaining 350 uL was processed for metabolites and proteins extraction. First, it was centrifuged for 5 minutes at 4 C, 13000 rpm. The supernatant was collected in a new 1.5 mL eppendorf tube. The supernatant was centrifuged again for 1 minute at 4 C, at maximum speed (>13000 rpm), and the supernatant was collected again in a new 1.5 mL tube and kept on ice as it was used in the following steps, while the pellet was discarded. |
Sample Preparation:
| Sampleprep ID: | SP002511 |
| Sampleprep Summary: | 400 uL of methanol, and 300 uL of chloroform were added to the protein sample, and centrifuged for 5 minutes, at 4 C, 13000 rpm. Three phases appeared: the upper phase is the metabolites, the middle is the protein, and the lower phase is other metabolites. The metabolites' upper phase was kept in a new eppendorf tube and kept at -20 C. 300 uL methanol was added to the middle and the lower phases then they were mixed and centrifuged for 1 minute at 13000 rpm. The supernatant was added to the metabolite tube and then it was kept at - 80C for longer storage. |
Combined analysis:
| Analysis ID | AN003937 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Bruker Elute |
| Column | Hamilton Intensity Solo 2 C18(100 x 2.1 mm, 1.8 um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Bruker timsTOF |
| Ion Mode | POSITIVE |
| Units | AU |
Chromatography:
| Chromatography ID: | CH002916 |
| Instrument Name: | Bruker Elute |
| Column Name: | Hamilton Intensity Solo 2 C18(100 x 2.1 mm, 1.8 um) |
| Column Temperature: | 35 |
| Flow Gradient: | 1%B to 99%B in 15 min |
| Flow Rate: | 250 uL/min |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS003675 |
| Analysis ID: | AN003937 |
| Instrument Name: | Bruker timsTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Metabolomics Data Processing. For metabolomic analysis, MetaboScape® 4.0 program (Bruker Daltonics, Billerica, MA, USA) was employed for data processing, feature extrac-tion and metabolite identification. The T-ReX 2D/3D workflow was used to identify the molecular features with the following settings: The minimum peak length was set to 7 spectra and the minimum intensity threshold was 1000 counts for peaks detection. The peak area was employed for quantification and the injected external calibrant in the in-terval of 0–0.3 min was used to recalibrate the mass spectra. The selected mass to charge ratio (m/z) and retention time for scanning were in the ranges of 20–1300 m/z and 0.3–30 min, respectively. MS/MS spectra for features were averaged on import and features found at least in 12 of the 40 injections were taken into further consideration. Metabolites were identified by matching to the human metabolome database (HMDB) by combined MS/MS, precursor m/z values, and isotopic pattern scores. Where multiple features matched a given database entry, the annotation quality score (AQ score) was used to select only the best matching feature. |
| Ion Mode: | POSITIVE |
