Summary of Study ST002980

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 PR001856. The data can be accessed directly via it's Project DOI: 10.21228/M8T42G 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.

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Study IDST002980
Study TitleWater soluble metabolomics in mice upon loss of SHMT
Study SummaryThe enzyme SHMT interconverts the amino acids serine and glycine as part of the folate cycle. To explore the role of SHMT in amino acid homeostasis, Mice were treated with a small molecule inhibitor of SHMT (SHIN2) or had Shmt2 genetically knocked-out in a liver specific manner. Serum and liver samples were collected and underwent LC-MS metabolomics analysis.
Institute
Princeton University
Last NameMcBride
First NameMatthew
AddressCarl Icahn Lab, South Drive, Princeton, NJ 08544
Emailmatthewmcbride@princeton.edu
Phone8567457389
Submit Date2023-11-14
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2023-12-12
Release Version1
Matthew McBride Matthew McBride
https://dx.doi.org/10.21228/M8T42G
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001856
Project DOI:doi: 10.21228/M8T42G
Project Title:Glycine homeostasis requires reverse SHMT flux
Project Type:LCMS metabolomics
Project Summary:The folate-dependent enzyme serine hydroxymethyltransferase (SHMT) reversibly converts serine into glycine and a tetrahydrofolate-bound one-carbon unit. Such one-carbon unit production plays a critical role in development, the immune system, and cancer. Using rodent models, here we show that the whole-body SHMT flux acts to net consume rather than produce glycine. Pharmacological inhibition of whole-body SHMT1/2 and genetic knockout of liver SHMT2 elevated circulating glycine levels up to eight-fold. Stable isotope tracing revealed that the liver converts glycine to serine, which is then converted by serine dehydratase into pyruvate and burned in the tricarboxylic acid cycle. In response to diets deficient in serine and glycine, de novo biosynthetic flux was unaltered but SHMT2- and serine dehydratase-mediated catabolic flux was lower. Thus, glucose-derived serine synthesis does not respond to systemic demand. Instead, circulating serine and glycine homeostasis is maintained through variable consumption, with liver SHMT2 a major glycine-consuming enzyme.
Institute:Princeton University
Department:Department of Chemistry
Laboratory:Josh Rabinowitz
Last Name:McBride
First Name:Matthew
Address:Carl Icahn Lab, South Drive, Princeton, NJ 08544
Email:matthewmcbride@princeton.edu
Phone:8567457389

Subject:

Subject ID:SU003093
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 Sample type Genotype Treatment
SA323395SHMT2flox_KO_22_liverLiver Liver KO None
SA323396SHMT2flox_KO_23_liverLiver Liver KO None
SA323397SHMT2flox_KO_21_liverLiver Liver KO None
SA323398SHMT2flox_KO_35_liverLiver Liver KO None
SA323399SHMT2flox_KO_43_liverLiver Liver KO None
SA323400SHMT2flox_KO_45_liverLiver Liver KO None
SA323401SHMT2flox_KO_44_liverLiver Liver KO None
SA323402SHMT2flox_WT_46_liverLiver Wild-type None
SA323403SHMT2flox_WT_15_liverLiver Wild-type None
SA323404SHMT2flox_WT_20_liverLiver Wild-type None
SA323405SHMT2flox_WT_34_liverLiver Wild-type None
SA323406SHMT2flox_WT_37_liverLiver Wild-type None
SA323407SHIN2_2_liverLiver Wild-type SHIN2
SA323408SHIN2_3_liverLiver Wild-type SHIN2
SA323409SHIN2_1_liverLiver Wild-type SHIN2
SA323410Veh_1_liverLiver Wild-type Vehicle
SA323411Veh_2_liverLiver Wild-type Vehicle
SA323412Veh_3_liverLiver Wild-type Vehicle
SA323413SHMT2flox_KO_45_serumSerum Liver KO None
SA323414SHMT2flox_KO_44_serumSerum Liver KO None
SA323415SHMT2flox_KO_22_serumSerum Liver KO None
SA323416SHMT2flox_KO_21_serumSerum Liver KO None
SA323417SHMT2flox_KO_43_serumSerum Liver KO None
SA323418SHMT2flox_KO_23_serumSerum Liver KO None
SA323419SHMT2flox_KO_35_serumSerum Liver KO None
SA323420SHMT2flox_WT_20_serumSerum Wild-type None
SA323421SHMT2flox_WT_15_serumSerum Wild-type None
SA323422SHMT2flox_WT_34_serumSerum Wild-type None
SA323423SHMT2flox_WT_37_serumSerum Wild-type None
SA323424SHMT2flox_WT_46_serumSerum Wild-type None
SA323425SHIN2_2_serumSerum Wild-type SHIN2
SA323426SHIN2_1_serumSerum Wild-type SHIN2
SA323427SHIN2_3_serumSerum Wild-type SHIN2
SA323428Veh_2_serumSerum Wild-type Vehicle
SA323429Veh_3_serumSerum Wild-type Vehicle
SA323430Veh_1_serumSerum Wild-type Vehicle
Showing results 1 to 36 of 36

Collection:

Collection ID:CO003086
Collection Summary:For pharmacological inhibition of SHMT, mice were treated with Vehicle or SHIN2 for 12 hours and then blood serum and liver samples were collected. For genetic loss of Shmt2, blood serum and liver samples were collected from mice 21 days after liver-specific gene knockout.
Sample Type:Blood (serum) and Liver

Treatment:

Treatment ID:TR003102
Treatment Summary:For pharmacological inhibition of SHMT, mice (C57BL/6N) were divided into two groups and received Vehicle (20% 2-hydroxypropyl-β-cyclodextrin) or SHIN2 (200 mg/kg) for 12 hours. For genetic loss of Shmt2, Shmt2(flox/flox) mice and wild-type litter mate controls were injected with AAV8-TBG-Cre viral particles to induce liver-specific gene knockout and samples were harvested 21 days later.

Sample Preparation:

Sampleprep ID:SP003099
Sampleprep Summary:Water soluble metabolites were extracted from serum and liver samples. 3ul of serum was extracted with 120 ul (40X) of 100% methanol, cooled on ice for 10 minutes, centrifuged at 16,000 x g for 30 minutes, and supernatant collected. 20mg of ground liver tissue was extracted with 800ul of 40:40:20 methanol:acetonitrile:water, cooled on ice for 10 minutes, centrifuged at 16,000 x g for 30 minutes, and supernatant collected.

Combined analysis:

Analysis ID AN004897 AN004898
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters XBridge BEH Amide (100 x 2.1mm,2.5um) Waters XBridge BEH Amide (100 x 2.1mm,2.5um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap Thermo Q Exactive Plus Orbitrap
Ion Mode NEGATIVE POSITIVE
Units Peak area Peak area

Chromatography:

Chromatography ID:CH003695
Instrument Name:Thermo Vanquish
Column Name:Waters XBridge BEH Amide (100 x 2.1mm,2.5um)
Column Temperature:25°C
Flow Gradient:0 minutes, 85% B; 2 minutes, 85% B; 3 minutes, 80% B; 5 minutes, 80% B; 6 minutes, 75% B; 7 minutes, 75% B; 8 minutes, 70% B; 9 minutes, 70% B; 10 minutes, 50% B; 12 minutes, 50% B; 13 minutes, 25% B; 16 minutes, 25% B; 18 minutes, 0% B; 23 minutes, 0% B; 24 minutes, 85% B; 30 minutes, 85% B
Flow Rate:150 μl/min
Solvent A:95% water/5% acetonitrile with 20 mM ammonium acetate, 20 mM ammonium hydroxide, pH 9.4
Solvent B:100% acetonitrile
Chromatography Type:HILIC

MS:

MS ID:MS004641
Analysis ID:AN004897
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS full scans were in negative ion mode with a resolution of 140,000 at m/z 200 and scan range of 70–1,000 m/z. The automatic gain control (AGC) target was 1 × 10^6. LC-MS peak files were analyzed and visualized with El-MAVEN (Elucidata) using 5 ppm ion extraction window, minimum peak intensity of 1 x 10^5 ions, and minimum signal to background blank ratio of 2.
Ion Mode:NEGATIVE
  
MS ID:MS004642
Analysis ID:AN004898
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS full scans were in positive ion mode with a resolution of 140,000 at m/z 200 and scan range of 70–1,000 m/z. The automatic gain control (AGC) target was 1 × 10^6. LC-MS peak files were analyzed and visualized with El-MAVEN (Elucidata) using 5 ppm ion extraction window, minimum peak intensity of 1 x 10^5 ions, and minimum signal to background blank ratio of 2.
Ion Mode:POSITIVE
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