Summary of Study ST002179
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 PR001387. The data can be accessed directly via it's Project DOI: 10.21228/M8FB0C 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 | ST002179 |
| Study Title | Impact of nitisinone on the cerebrospinal fluid metabolome of a murine model of alkaptonuria |
| Study Summary | Background: Nitisinone induced hypertyrosinaemia is well documented in Alkaptonuria (AKU), and there is uncertainty over whether it may contribute to a decline in cognitive function and or mood by altering neurotransmitter metabolism. The aim of this work was to evaluate the impact of nitisinone on the cerebrospinal fluid (CSF) metabolome in a murine model of AKU, with a view to providing additional insight into metabolic changes that occur following treatment with nitisinone. Methods: 17 CSF samples were collected from BALB/c Hgd-/-mice (n=8, treated with nitisinone – 4 mg/L and n=9, no treatment). Samples were diluted 1:1 with deionised water and analysed using a 1290 Infinity II liquid chromatography system coupled to a 6550 quadrupole time-of-flight mass spectrometry (Agilent, Cheadle, UK). Raw data were processed using a targeted feature extraction algorithm and an established in-house accurate mass retention time database. Matched entities (±10 ppm theoretical accurate mass and ±0.3 minutes retention time window) were filtered based on their frequency and variability. Experimental groups were compared using a moderated t-test with Benjamini-Hochberg false-discovery rate adjustment. Results: Tyrosine, acetyl-tyrosine, γ-glutamyl-tyrosine, p-hydroxyphenylacetic acid and 3-(4-hydroxyphenyl)lactic acid were shown to increase in abundance (log2 fold change 2.6-6.9, 3/5 were significant p<0.05) in the mice that received nitisinone. Several other metabolites of interest were matched but no significant differences were observed, including the aromatic amino acids phenylalanine and tryptophan, and monoamine metabolites adrenaline, 3-methoxy-4-hydroxyphenylglycol and octopamine. Conclusions: Evaluation of the CSF metabolome of a murine model of AKU showed a significant difference in the abundance of a limited number of metabolites. None of these have been reported in CSF from a murine model of AKU previously. Moreover this study confirms that some monoamine metabolites do not appear to be altered following nitisinone therapy. |
| Institute | University of Liverpool Institute of Life Course & Medical Sciences |
| Last Name | Davison |
| First Name | Andrew |
| Address | 1. Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; 2. Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK 3. School of Exercise Science, Liverpool John Moores University, Liverpool, UK |
| andrew.davison@liverpoolft.nhs.uk | |
| Phone | 0151 706 4011 |
| Submit Date | 2022-05-13 |
| Num Groups | 2 |
| Total Subjects | 17 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d, mzML |
| Analysis Type Detail | LC-MS |
| Release Date | 2022-06-08 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001387 |
| Project DOI: | doi: 10.21228/M8FB0C |
| Project Title: | Impact of nitisinone on the cerebrospinal fluid metabolome of a murine model of alkaptonuria |
| Project Summary: | Background: Nitisinone induced hypertyrosinaemia is well documented in Alkaptonuria (AKU), and there is uncertainty over whether it may contribute to a decline in cognitive function and or mood by altering neurotransmitter metabolism. The aim of this work was to evaluate the impact of nitisinone on the cerebrospinal fluid (CSF) metabolome in a murine model of AKU, with a view to providing additional insight into metabolic changes that occur following treatment with nitisinone. Methods: 17 CSF samples were collected from BALB/c Hgd-/-mice (n=8, treated with nitisinone – 4 mg/L and n=9, no treatment). Samples were diluted 1:1 with deionised water and analysed using a 1290 Infinity II liquid chromatography system coupled to a 6550 quadrupole time-of-flight mass spectrometry (Agilent, Cheadle, UK). Raw data were processed using a targeted feature extraction algorithm and an established in-house accurate mass retention time database. Matched entities (±10 ppm theoretical accurate mass and ±0.3 minutes retention time window) were filtered based on their frequency and variability. Experimental groups were compared using a moderated t-test with Benjamini-Hochberg false-discovery rate adjustment. Results: Tyrosine, acetyl-tyrosine, γ-glutamyl-tyrosine, p-hydroxyphenylacetic acid and 3-(4-hydroxyphenyl)lactic acid were shown to increase in abundance (log2 fold change 2.6-6.9, 3/5 were significant p<0.05) in the mice that received nitisinone. Several other metabolites of interest were matched but no significant differences were observed, including the aromatic amino acids phenylalanine and tryptophan, and monoamine metabolites adrenaline, 3-methoxy-4-hydroxyphenylglycol and octopamine. Conclusions: Evaluation of the CSF metabolome of a murine model of AKU showed a significant difference in the abundance of a limited number of metabolites. None of these have been reported in CSF from a murine model of AKU previously. Moreover this study confirms that some monoamine metabolites do not appear to be altered following nitisinone therapy. |
| Institute: | University of Liverpool Institute of Life Course & Medical Sciences |
| Last Name: | Davison |
| First Name: | Andrew |
| Address: | 1. Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; 2. Department of Musculoskeletal and Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK 3. School of Exercise Science, Liverpool John Moores University, Liverpool, UK |
| Email: | andrew.davison@liverpoolft.nhs.uk |
| Phone: | 0151 706 4011 |
| Contributors: | Davison AS1,2,*, Norman BP2, Sutherland H2,3, Milan AM1,2, Jarvis JC3, Gallagher JA2, Ranganath LR1,2 |
Subject:
| Subject ID: | SU002265 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment group |
|---|---|---|
| SA209243 | Hgd81.3 + Nitisinone POS | Nitisinone |
| SA209244 | Hgd81.2 + Nitisinone POS | Nitisinone |
| SA209245 | Hgd81.1 + Nitisinone POS | Nitisinone |
| SA209246 | Hgd82.1 + Nitisinone POS | Nitisinone |
| SA209247 | Hgd82.2 + Nitisinone POS | Nitisinone |
| SA209248 | Hgd83.2 - No treatment POS | Nitisinone |
| SA209249 | Hgd83.1 + Nitisinone POS | Nitisinone |
| SA209250 | Hgd81.1 + Nitisinone NEG | Nitisinone |
| SA209251 | Hgd80.2 + Nitisinone POS | Nitisinone |
| SA209252 | Hgd83.1 + Nitisinone NEG | Nitisinone |
| SA209253 | Hgd82.1 + Nitisinone NEG | Nitisinone |
| SA209254 | Hgd81.3 + Nitisinone NEG | Nitisinone |
| SA209255 | Hgd81.2 + Nitisinone NEG | Nitisinone |
| SA209256 | Hgd83.2 - No treatment NEG | Nitisinone |
| SA209257 | Hgd82.2 + Nitisinone NEG | Nitisinone |
| SA209258 | Hgd81.6 - No treatment POS | No Treatment (control) |
| SA209259 | Hgd81.5 - No treatment POS | No Treatment (control) |
| SA209260 | Hgd81.4 - No treatment POS | No Treatment (control) |
| SA209261 | Hgd82.3 - No treatment POS | No Treatment (control) |
| SA209262 | Hgd82.4 - No treatment POS | No Treatment (control) |
| SA209263 | Hgd81.6 - No treatment NEG | No Treatment (control) |
| SA209264 | Hgd83.4 - No treatment POS | No Treatment (control) |
| SA209265 | Hgd83.3 - No treatment POS | No Treatment (control) |
| SA209266 | Hgd80.4 - No treatment POS | No Treatment (control) |
| SA209267 | Hgd80.3 - No treatment POS | No Treatment (control) |
| SA209268 | Hgd83.4 - No treatment NEG | No Treatment (control) |
| SA209269 | Hgd80.3 - No treatment NEG | No Treatment (control) |
| SA209270 | Hgd80.4 - No treatment NEG | No Treatment (control) |
| SA209271 | Hgd83.3 - No treatment NEG | No Treatment (control) |
| SA209272 | Hgd81.5 - No treatment NEG | No Treatment (control) |
| SA209273 | Hgd82.3 - No treatment NEG | No Treatment (control) |
| SA209274 | Hgd82.4 - No treatment NEG | No Treatment (control) |
| SA209275 | Hgd81.4 - No treatment NEG | No Treatment (control) |
| Showing results 1 to 33 of 33 |
Collection:
| Collection ID: | CO002258 |
| Collection Summary: | A murine model of AKU was used for all experiments as described previously (Preston et al., 2014). Seventeen BALB/c Hgd-/- mice (Figure 5 for age and gender) were included in this study, 8 mice were administered nitisinone (4 mg/L) through their drinking water for 6 days, the remaining 9 mice received no nitisinone. All animals were housed in air conditioned rooms (with a 12 h dark/light cycle) at 20 °C and 53 % humidity, with access to food and water ad libitum at Liverpool John Moores University. All animal experiments complied with the ARRIVE guidelines and were carried out in accordance with the U.K. Animals (Scientific Procedures) Act, 1986 and associated guidelines, EU Directive 2010/63/EU for animal experiments. All mice were culled by carbon dioxide asphyxiation and CSF was removed from the cisterna magna following the puncture technique of Liu et al. (56), with some modifications. The cisterna magna was exposed by dissecting skin and overlaying muscles. Cauterisation was used to dry up any bleeding from surrounding tissues. A pulled glass pipette with an internal diameter of ~0.4 mm was attached to silicone tubing and connected to a 1 mL syringe with a 19 g needle. The tip of the glass pipette was used to puncture the membrane and held still just below the membrane by 1 person. Through a double-headed microscope a second person then used the 1 mL syringe to apply gentle pressure to encourage the CSF to flow up the capillary tube. Only clear CSF samples (i.e. non blood stained) were collected. Once collected CSF samples were transferred to clear Eppendorf tubes and stored at -80 °C until analysis. Samples were not acidified. The same glass pipette was used to collect CSF from each animal, and was washed with pure water between each animal. |
| Sample Type: | CSF |
Treatment:
| Treatment ID: | TR002277 |
| Treatment Summary: | 9 mice control 8 mice received 4 mg/L nitisinone for 6 days in drinking water |
Sample Preparation:
| Sampleprep ID: | SP002271 |
| Sampleprep Summary: | Murine CSF samples were prepared by diluting 2 µL CSF with 2 µL deionized water (DIRECT-Q 3UV Millipore water purification system). CSF samples were pipetted directly into a 150 µL glass insert with polymer feet, which sat in a 2 mL amber screw vial (Agilent, Cheadle, UK). These vials were used to ensure maximal recovery of sample. Deionised water was also added directly to the glass insert, and mixed with the CSF sample using a pipette. The glass vials were centrifuged at 600 rpm for 10 min to ensure the diluted sample was at the bottom of the vial for sampling. 1 µL of diluted CSF was analysed in negative and positive polarities, respectively. |
Chromatography:
| Chromatography ID: | CH002639 |
| Chromatography Summary: | Liquid chromatography (LC) was performed on an Agilent 1290 Infinity II LC system. An Atlantis dC18 column (3.0x100mm, 3µm, Waters, UK) was maintained at 60°C with a flow rate of 0.4mL/min. Mobile phases were (A) water and (B) methanol both containing 5mmol/L ammonium formate and 0.1% formic acid. The elution gradient started at 5% mobile phase B at 0-1 min increasing linearly to 100% B by 12 min, held at 100% B until 14 min, returning to 95% A for 5 min to recondition the column. Injection volume was 1µL. |
| Instrument Name: | Agilent Infinity II |
| Column Name: | Atlantis dC18 (3.0x100mm,3m,Waters,UK) |
| Column Temperature: | 60 |
| Flow Gradient: | The elution gradient started at 5% mobile phase B at 0-1 min increasing linearly to 100% B by 12 min, held at 100% B until 14 min, returning to 95% A for 5 min to recondition the column |
| Flow Rate: | 0.4mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 5 mM ammonium formate |
| Solvent B: | 100% acetonitrile; 0.1% formic acid;5 mM ammonium formate |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN003568 |
| Analysis Type: | MS |
| Chromatography ID: | CH002639 |
| Num Factors: | 2 |
| Num Metabolites: | 174 |
| Rt Units: | Minutes |
| Units: | area |
| Analysis ID: | AN003569 |
| Analysis Type: | MS |
| Chromatography ID: | CH002639 |
| Num Factors: | 2 |
| Num Metabolites: | 135 |
| Rt Units: | Minutes |
| Units: | area |
