Summary of Study ST003566
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 PR002200. The data can be accessed directly via it's Project DOI: 10.21228/M87Z47 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 | ST003566 |
Study Title | Unraveling cysteine deficiency-associated rapid weight loss |
Study Summary | Forty percent of the US population and 1 in 6 individuals worldwide are obese, with the incidence surging globally. Various dietary interventions, including carbohydrate, fat and more recently amino acid restriction, have been explored to combat this epidemic. We investigated the impact of removing individual amino acids on the weight profiles of mice. Here, we show that conditional cysteine restriction resulted in the most dramatic weight loss when compared to essential amino acid restriction, amounting to 30% within one week, which was readily reversed. We found that cysteine deficiency activated the integrated stress response and oxidative stress response, which amplify each other, leading to the induction of GDF15 and FGF21, which partly explained the phenotype. Surprisingly, we observed lower tissue coenzyme A (CoA), which has been considered to be extremely stable10, resulting in reduced mitochondrial functionality and metabolic rewiring. This results in energetically inefficient anaerobic glycolysis and defective TCA cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen rich compounds, and amino acids In summary, our investigation reveals that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism, and stress signaling compared to other amino acid restrictions. These findings suggest novel strategies for addressing a range of metabolic diseases and the growing obesity crisis. |
Institute | NYU Grossman School of Medicine |
Last Name | Varghese |
First Name | Alan |
Address | 550 First Avenue, NY, NY 10016 |
Alan.Varghese@nyulangone.org | |
Phone | 212-263-7520 |
Submit Date | 2024-10-22 |
Raw Data Available | Yes |
Raw Data File Type(s) | mzXML |
Analysis Type Detail | LC-MS |
Release Date | 2025-02-03 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
Project ID: | PR002200 |
Project DOI: | doi: 10.21228/M87Z47 |
Project Title: | Unraveling cysteine deficiency-associated rapid weight loss |
Project Summary: | Forty percent of the US population and 1 in 6 individuals worldwide are obese, with the incidence surging globally. Various dietary interventions, including carbohydrate, fat and more recently amino acid restriction, have been explored to combat this epidemic. We investigated the impact of removing individual amino acids on the weight profiles of mice. Here, we show that conditional cysteine restriction resulted in the most dramatic weight loss when compared to essential amino acid restriction, amounting to 30% within one week, which was readily reversed. We found that cysteine deficiency activated the integrated stress response and oxidative stress response, which amplify each other, leading to the induction of GDF15 and FGF21, which partly explained the phenotype. Surprisingly, we observed lower tissue coenzyme A (CoA), which has been considered to be extremely stable10, resulting in reduced mitochondrial functionality and metabolic rewiring. This results in energetically inefficient anaerobic glycolysis and defective TCA cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen rich compounds, and amino acids In summary, our investigation reveals that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism, and stress signaling compared to other amino acid restrictions. These findings suggest novel strategies for addressing a range of metabolic diseases and the growing obesity crisis. |
Institute: | NYU Grossman School of Medicine |
Last Name: | Varghese |
First Name: | Alan |
Address: | 550 First Avenue, NY, NY 10016 |
Email: | Alan.Varghese@nyulangone.org |
Phone: | 212-263-7520 |
Subject:
Subject ID: | SU003695 |
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 | Factor | Sample source |
---|---|---|---|
SA389468 | SQ1615_Blank_0 | Blank | blank |
SA389469 | SQ1441_Blank_2 | Blank | blank |
SA389470 | SQ1441_Blank_3 | Blank | blank |
SA389471 | SQ1441_Blank_4 | Blank | blank |
SA389472 | SQ1441_Blank_5 | Blank | blank |
SA389473 | SQ1441_Blank_6 | Blank | blank |
SA389474 | SQ1441_Blank_7 | Blank | blank |
SA389475 | SQ1441_Blank_8 | Blank | blank |
SA389476 | SQ1441_Blank_9 | Blank | blank |
SA389477 | SQ1432_Blank_1 | Blank | blank |
SA389478 | SQ1432_Blank_2 | Blank | blank |
SA389479 | SQ1432_Blank_3 | Blank | blank |
SA389480 | SQ1432_Blank_4 | Blank | blank |
SA389481 | SQ1432_Blank_5 | Blank | blank |
SA389482 | SQ1615_Blank_1 | Blank | blank |
SA389483 | SQ1441_Blank_0 | Blank | blank |
SA389484 | SQ1615_Blank_2 | Blank | blank |
SA389485 | SQ1615_Blank_3 | Blank | blank |
SA389486 | SQ1615_Blank_4 | Blank | blank |
SA389487 | SQ1615_Blank_5 | Blank | blank |
SA389488 | SQ1615_Blank_6 | Blank | blank |
SA389489 | SQ1615_Blank_7 | Blank | blank |
SA389490 | SQ1616_Blank_0 | Blank | blank |
SA389491 | SQ1616_Blank_1 | Blank | blank |
SA389492 | SQ1616_Blank_2 | Blank | blank |
SA389493 | SQ1616_Blank_3 | Blank | blank |
SA389494 | SQ1616_Blank_4 | Blank | blank |
SA389495 | SQ1616_Blank_5 | Blank | blank |
SA389496 | SQ1616_Blank_6 | Blank | blank |
SA389497 | SQ1616_Blank_7 | Blank | blank |
SA389498 | SQ1441_Blank_1 | Blank | blank |
SA389499 | SQ1432_Blank_0 | Blank | blank |
SA389500 | SQ1403_Blank_2 | Blank | blank |
SA389501 | SQ1403_Blank_6 | Blank | blank |
SA389502 | SQ1403_Blank_5 | Blank | blank |
SA389503 | SQ1403_Blank_4 | Blank | blank |
SA389504 | SQ1403_Blank_3 | Blank | blank |
SA389505 | SQ1403_Blank_0 | Blank | blank |
SA389506 | SQ1403_Blank_7 | Blank | blank |
SA389507 | SQ1403_Blank_1 | Blank | blank |
SA389508 | F3 | Food | food |
SA389509 | F1 | Food | food |
SA389510 | F2 | Food | food |
SA389511 | SQ1616_U5 | Het 2 hr | urine |
SA389512 | SQ1616_U6 | Het 2 hr | urine |
SA389513 | SQ1616_U9 | Het 2 hr | urine |
SA389514 | SQ1616_U1 | Het 2 hr | urine |
SA389515 | SQ1616_U2 | Het 2 hr | urine |
SA389516 | SQ1616_U8 | Het 2 hr | urine |
SA389517 | SQ1615_L6 | Het 45 min | liver |
SA389518 | SQ1615_L5 | Het 45 min | liver |
SA389519 | SQ1615_L2 | Het 45 min | liver |
SA389520 | SQ1615_L1 | Het 45 min | liver |
SA389521 | SQ1615_ISTD_0 | ISTD | standard |
SA389522 | SQ1615_ISTD_1 | ISTD | standard |
SA389523 | SQ1615_ISTD_2 | ISTD | standard |
SA389524 | SQ1615_ISTD_3 | ISTD | standard |
SA389525 | SQ1403_ISTD_0 | ISTD | standard |
SA389526 | SQ1432_ISTD_1 | ISTD | standard |
SA389527 | SQ1432_ISTD_2 | ISTD | standard |
SA389528 | SQ1616_ISTD_3 | ISTD | standard |
SA389529 | SQ1616_ISTD_2 | ISTD | standard |
SA389530 | SQ1432_ISTD_0 | ISTD | standard |
SA389531 | SQ1403_ISTD_1 | ISTD | standard |
SA389532 | SQ1616_ISTD_1 | ISTD | standard |
SA389533 | SQ1616_ISTD_0 | ISTD | standard |
SA389534 | SQ1403_ISTD_2 | ISTD | standard |
SA389535 | SQ1403_ISTD_3 | ISTD | standard |
SA389544 | AMP KO3 | Knockout | urine |
SA389545 | AMP KO2 | Knockout | urine |
SA389546 | AMP KO1 | Knockout | urine |
SA389536 | SQ1616_U10 | KO 2 hr | urine |
SA389537 | SQ1616_U3 | KO 2 hr | urine |
SA389538 | SQ1616_U4 | KO 2 hr | urine |
SA389539 | SQ1616_U7 | KO 2 hr | urine |
SA389540 | SQ1615_L8 | KO 45 min | liver |
SA389541 | SQ1615_L7 | KO 45 min | liver |
SA389542 | SQ1615_L4 | KO 45 min | liver |
SA389543 | SQ1615_L3 | KO 45 min | liver |
SA389547 | SQ1432_L13 | No Cys KO | liver |
SA389548 | SQ1432_L12 | No Cys KO | liver |
SA389549 | SQ1432_L14 | No Cys KO | liver |
SA389550 | SQ1441_U23 | No Cys KO | urine |
SA389551 | SQ1441_U22 | No Cys KO | urine |
SA389552 | SQ1441_U8 | No Cys KO | urine |
SA389553 | SQ1441_U21 | No Cys KO | urine |
SA389554 | SQ1441_U20 | No Cys KO | urine |
SA389555 | SQ1441_U10 | No Cys KO | urine |
SA389556 | SQ1441_U9 | No Cys KO | urine |
SA389557 | SQ1432_L9 | No Cys WT | liver |
SA389558 | SQ1432_L8 | No Cys WT | liver |
SA389559 | SQ1432_L10 | No Cys WT | liver |
SA389560 | SQ1432_L11 | No Cys WT | liver |
SA389561 | SQ1441_U6 | No Cys WT | urine |
SA389562 | SQ1441_U16 | No Cys WT | urine |
SA389563 | SQ1441_U17 | No Cys WT | urine |
SA389564 | SQ1441_U18 | No Cys WT | urine |
SA389565 | SQ1441_U19 | No Cys WT | urine |
SA389566 | SQ1441_U7 | No Cys WT | urine |
SA389567 | AMP WT3 | Wild Type | urine |
Collection:
Collection ID: | CO003688 |
Collection Summary: | Food pellets were weighed into bead blaster tubes containing zircon beads. Extraction buffer containing 80% methanol with 500nM Metabolomics amino acid standard mix (Cambridge Isotopes Laboratory, MA) was added to each to reach a final concentration of 10 mg/mL. Samples were homogenized using D2400 BeadBlaster homogenizer (Benchmark Scientific, NJ) then spun at 21 kg for 3min. Then, 450uL of metabolite extract was transferred to a new 1.5mL Eppendorf tube and dried using Speedvac. Samples were reconstituted in 50uL of MS grade water and sonicated for 2 mins. Then, samples were spun at 21,000 g for 3 mins. Samples were transferred to glass LC vials for analysis by LCMS. Liver Samples Approximately 300 mg of liver was homogenized in 1 mL of PBS and then subjected to three freeze-thaw cycles. Liver samples were filtered using a 10kDa filter. Protein concentrations prior to deproteinization were measured using BSA standard curve and found to be between 12.8 – 42.0 mg/mL. For metabolomics extracts, on average protein concentration was determined to be 28.58 mg/mL per 300 mg of tissue. This value was used to scale all liver extracts to each other. Scaled liver extracts were transferred to bead blaster tubes with zircon beads and homogenized using D2400 BeadBlaster homogenizer (Benchmark Scientific, NJ) in cold 80% methanol spiked with 500 nM Metabolomics amino acid standard mix (Cambridge Isotopes Laboratory, MA). Samples were centrifuged at 21,000 g for 3 min to pellet any insoluble materials. Then, 450 µL of metabolite extract was transferred to a new 1.5mL Eppendorf tube and dried down using Speedvac. Samples were reconstituted in 50uL of MS grade water and sonicated for 2 mins. Then, samples were spun at 21,000 g for 3 min. Samples were transferred to glass LC vials for analysis by LCMS. Urine Samples Urine samples were collected and stored as frozen aliquots between ~5-7 µL. For metabolite extraction, 5µL of urine was transferred to a glass insert and extracted using 195 µL of cold 80% methanol spiked with 500nM Metabolomics amino acid standard mix (Cambridge Isotopes Laboratory, MA). Glass inserts were transferred into 1.5 mL Eppendorf tubes and spun at 3 kg for 10 min to pellet insoluble material. Then, 180 µL of extract was transferred to a 1.5 mL Eppendorf tube and dried down completely using Speedvac. To each, 20 µL of MS grade water was added to reconstitute metabolites. Samples were sonicated for 2 mins and then centrifuged for 3 min at 21 kg. Then 15 µL of samples was transferred to a glass LCMS vial for analysis. |
Sample Type: | urine, liver, food |
Treatment:
Treatment ID: | TR003704 |
Treatment Summary: | All custom diets were procured from TestDiet. All diets were based on the defined amino acid diet 5CC7. For individual or dual amino acid depleted diets, the specific amino acid(s) was completely removed, and all other amino acids were increased in proportion. For pantothenic acid-deficient diet, it was removed from the same 5CC7 defined diet. Unless specified control diet refers to the 5CC7 diet. D-Galactose (Sigma G0750) and D-Glucose (Sigma G8270) were purchased from Sigma and were dissolved in water and filter sterilized. A list of diet names is available on request. |
Sample Preparation:
Sampleprep ID: | SP003702 |
Sampleprep Summary: | Food pellets were weighed into bead blaster tubes containing zircon beads. Extraction buffer containing 80% methanol with 500nM Metabolomics amino acid standard mix (Cambridge Isotopes Laboratory, MA) was added to each to reach a final concentration of 10 mg/mL. Samples were homogenized using D2400 BeadBlaster homogenizer (Benchmark Scientific, NJ) then spun at 21 kg for 3min. Then, 450 µL of metabolite extract was transferred to a new 1.5 mL Eppendorf tube and dried using Speedvac. Samples were reconstituted in 50 µL of MS grade water and sonicated for 2 mins. Then, samples were spun at 21,000 g for 3 mins. Samples were transferred to glass LC vials for analysis by LCMS. Liver Samples Approximately 300 mg of liver was homogenized in 1 mL of PBS and then subjected to three freeze-thaw cycles. Liver samples were filtered using a 10 kDa filter. Protein concentrations prior to deproteinization were measured using BSA standard curve and found to be between 12.8 – 42.0 mg/mL. For metabolomics extracts, on average protein concentration was determined to be 28.58 mg/mL per 300 mg of tissue. This value was used to scale all liver extracts to each other. Scaled liver extracts were transferred to bead blaster tubes with zircon beads and homogenized using D2400 BeadBlaster homogenizer (Benchmark Scientific, NJ) in cold 80% methanol spiked with 500 nM Metabolomics amino acid standard mix (Cambridge Isotopes Laboratory, MA). Samples were centrifuged at 21,000 g for 3 min to pellet any insoluble materials. Then, 450 µL of metabolite extract was transferred to a new 1.5mL Eppendorf tube and dried down using Speedvac. Samples were reconstituted in 50uL of MS grade water and sonicated for 2 mins. Then, samples were spun at 21,000 g for 3 min. Samples were transferred to glass LC vials for analysis by LCMS. Urine Samples Urine samples were collected and stored as frozen aliquots between ~5-7 µL. For metabolite extraction, 5µL of urine was transferred to a glass insert and extracted using 195µL of cold 80% methanol spiked with 500nM Metabolomics amino acid standard mix (Cambridge Isotopes Laboratory, MA). Glass inserts were transferred into 1.5mL Eppendorf tubes and spun at 3 kg for 10 min to pellet insoluble material. Then, 180 µL of extract was transferred to a 1.5 mL Eppendorf tube and dried down completely using Speedvac. To each, 20 µL of MS grade water was added to reconstitute metabolites. Samples were sonicated for 2 mins and then centrifuged for 3 min at 21 kg. Then 15 µL of samples was transferred to a glass LCMS vial for analysis. |
Combined analysis:
Analysis ID | AN005859 |
---|---|
Analysis type | MS |
Chromatography type | HILIC |
Chromatography system | Thermo Ultimate 3000 RS |
Column | SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap |
Ion Mode | UNSPECIFIED |
Units | absolute intensity |
Chromatography:
Chromatography ID: | CH004450 |
Instrument Name: | Thermo Ultimate 3000 RS |
Column Name: | SeQuant ZIC-HILIC (150 x 2.1mm,5um) |
Column Temperature: | 25 |
Flow Gradient: | 80-20%B (0-30 min), 20-80%B (30-31 min), 80-80%B (31-42 min) |
Flow Rate: | 0.1 mL/min |
Solvent A: | 100% Water; 10 mM ammonium carbonate in water, pH 9.0 |
Solvent B: | 100% Acetonitrile |
Chromatography Type: | HILIC |
MS:
MS ID: | MS005579 |
Analysis ID: | AN005859 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | both positive and negative polarities were collected in the same acquisition during polarity switching mechanism |
Ion Mode: | UNSPECIFIED |