Summary of Study ST002809
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 PR001756. The data can be accessed directly via it's Project DOI: 10.21228/M8QT46 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST002809 |
| Study Title | Role of cilia in mitochondrial function |
| Study Type | cultured cells |
| Study Summary | Autosomal dominant polycystic kidney disease (ADPKD), the most common potentially lethal genetic disease in humans and the fourth leading cause of kidney disease, exhibits features of both a ciliary and metabolic disorder. Our previous research revealed that cells overexpressing Exoc5 with elongated cilia demonstrate enhanced recovery from oxidative stress. To investigate the connection between primary cilia and metabolism, we conducted an unbiased metabolomics screen. Global metabolic profiling was performed on canine MDCK cells (Control, Exoc5 ciliary targeting sequence mutation (CTS-mut), Exoc5 knockdown (KD), Exoc5 overexpression (OE)) and murine cells (Ift88 knockout (KO), Ift88 rescue). Knockdown (KD) or ciliary targeting sequence mutation (CTS-mut) in Exoc5, a central exocyst component, resulted in cilia loss. Similarly, Ift88 knockout (KO) resulted in cilia loss. For each experimental group, we cultivated six independent replicates of Exoc5 OE, KD, CTS-mut, and control MDCK cells, as well as six independent replicates of murine Ift88 KO and rescue cells. Cell pellets were obtained from the cultures, and we analyzed the global metabolic profiles for all 36 cell pellets. The most significant findings from the metabolomics screen indicated defects in tryptophan metabolism. This discovery suggests a potential link between primary cilia function and tryptophan-related metabolic pathways. Further exploration of these findings may shed light on the underlying mechanisms and implications for ADPKD pathogenesis and metabolic disturbances. |
| Institute | Medical University of South Carolina |
| Department | Medicine |
| Last Name | Lipschutz |
| First Name | Josh |
| Address | 96 Jonathan Lucas St, Charleston, SC 29425 |
| lipschut@musc.edu | |
| Phone | 8437927659 |
| Submit Date | 2023-08-03 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-06-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Combined analysis:
| Analysis ID | AN004566 | AN004567 | AN004568 | AN004569 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH C18 (100 x 2mm, 1.7um) | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Normalized/scaled raw area counts | Normalized/scaled raw area counts | Normalized/scaled raw area counts | Normalized/scaled raw area counts |
Chromatography:
| Chromatography ID: | CH003431 |
| Chromatography Summary: | Low pH polar |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in methanol, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003432 |
| Chromatography Summary: | Low pH Lipophilic |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 40 % B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes |
| Flow Rate: | 0.60 mL/min |
| Solvent A: | 0.1% formic acid and 0.05% PFPA in water, pH ~2.5 |
| Solvent B: | 0.1% formic acid and 0.05% PFPA in 50% methanol/ 50% acetonitrile, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003433 |
| Chromatography Summary: | High pH |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH C18 (100 x 2mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99%B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 6.5 mM ammonium bicarbonate in water, pH 8 |
| Solvent B: | 6.5 mM ammonium bicarbonate in 95% methanol/ 5% water |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH003434 |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) |
| Column Temperature: | 65 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 10 mM ammonium formate in 15% water/ 5% methanol/ 80% acetonitrile (effective pH 10.16 with NH4OH) |
| Solvent B: | 10 mM ammonium formate in 50% water/ 50% acetonitrile (effective pH 10.60 with NH4OH) |
| Chromatography Type: | HILIC |
