Summary of Study ST002959

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 PR001841. The data can be accessed directly via it's Project DOI: 10.21228/M8RB1J This work is supported by NIH grant, U2C- DK119886.

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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 IDST002959
Study TitleTranscriptional regulation of amino acid metabolism by KDM2B
Study SummaryEpigenetic and metabolic alterations in cancer cells are intertwined. The concentration of metabolites can influence the activity of chromatin modifiers, which in turn can act as metabolic sensors that translate changes in cellular metabolism to transcriptional reprogramming. In the present study, we investigated the role of histone demethylase KDM2B in the metabolic reprogramming of the triple-negative breast cancer (TNBC), in which KDM2B is selectively expressed at high levels. Knockdown of KDM2B in TNBC cell lines reduced their proliferation rate and tumor growth in vivo. Transcriptomic, proteomic, and metabolomic profiling demonstrated that the Serine-Glycine pathway and One Carbon metabolism (SGOC) and other amino acid biosynthetic and catabolic processes are downregulated by the knockdown of KDM2B. Additionally, we see reduction of metabolites produced via these pathways (purines, pyrimidines, formate, glutathione and NADPH). Importantly, the expression of the enzymes involved in the SGOC metabolic pathway (e.g. PHGDH, PSAT1, PSPH, SHMT2, MTHFD1L, MTHFD2 and DHFR) depends on c-MYC, NRF2, and ATF4 which our data show that they are under the positive regulatory control of KDM2B. The epistatic relationship between these factors, with the expression of the enzymes of the SGOC pathway and the effects of the KDM2B knockdown on chromatin occupancy and accessibility of the promoters of these factors is in progress and will be presented. Analysis of TCGA data showed positive and statistically significant correlations between KDM2B and the SGOC gene signature in TNBC patients. In addition, the metabolic pathway signature that distinguishes control and shKDM2B-transduced cells corresponds to the metabolic signature of a subset of TNBCs, which have been reported to carry poor prognosis. The present study highlights the role of the epigenetic factor KDM2B as an upstream regulator of the metabolic reprogramming of TNBC.
Institute
The Ohio State University
Last NameAldana
First NameJulian
Address460 W 12th Ave, Columbus, OH
Emailaldanaaroca.1@osu.edu
Phone6142180748
Submit Date2023-10-23
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-11-17
Release Version1
Julian Aldana Julian Aldana
https://dx.doi.org/10.21228/M8RB1J
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001841
Project DOI:doi: 10.21228/M8RB1J
Project Title:Transcriptional regulation of amino acid metabolism by KDM2B
Project Summary:Epigenetic and metabolic alterations in cancer cells are intertwined. The concentration of metabolites can influence the activity of chromatin modifiers, which in turn can act as metabolic sensors that translate changes in cellular metabolism to transcriptional reprogramming. In the present study, we investigated the role of histone demethylase KDM2B in the metabolic reprogramming of the triple-negative breast cancer (TNBC), in which KDM2B is selectively expressed at high levels. Knockdown of KDM2B in TNBC cell lines reduced their proliferation rate and tumor growth in vivo. Transcriptomic, proteomic, and metabolomic profiling demonstrated that the Serine-Glycine pathway and One Carbon metabolism (SGOC) and other amino acid biosynthetic and catabolic processes are downregulated by the knockdown of KDM2B. Additionally, we see reduction of metabolites produced via these pathways (purines, pyrimidines, formate, glutathione and NADPH). Importantly, the expression of the enzymes involved in the SGOC metabolic pathway (e.g. PHGDH, PSAT1, PSPH, SHMT2, MTHFD1L, MTHFD2 and DHFR) depends on c-MYC, NRF2, and ATF4 which our data show that they are under the positive regulatory control of KDM2B. The epistatic relationship between these factors, with the expression of the enzymes of the SGOC pathway and the effects of the KDM2B knockdown on chromatin occupancy and accessibility of the promoters of these factors is in progress and will be presented. Analysis of TCGA data showed positive and statistically significant correlations between KDM2B and the SGOC gene signature in TNBC patients. In addition, the metabolic pathway signature that distinguishes control and shKDM2B-transduced cells corresponds to the metabolic signature of a subset of TNBCs, which have been reported to carry poor prognosis. The present study highlights the role of the epigenetic factor KDM2B as an upstream regulator of the metabolic reprogramming of TNBC.
Institute:The Ohio State University
Last Name:Aldana
First Name:Julian
Address:460 W 12th Ave, Columbus, OH
Email:aldanaaroca.1@osu.edu
Phone:6142180748

Subject:

Subject ID:SU003072
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Female

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA322325NEG_EV2_2Empty vector
SA322326NEG_EV2_3Empty vector
SA322327NEG_EV2_1Empty vector
SA322328NEG_EV1_3Empty vector
SA322329NEG_EV1_2Empty vector
SA322330NEG_EV3_1Empty vector
SA322331NEG_EV3_2Empty vector
SA322332NEG_EV4_3Empty vector
SA322333NEG_EV4_2Empty vector
SA322334NEG_EV4_1Empty vector
SA322335NEG_EV3_3Empty vector
SA322336POS_EV1_1Empty vector
SA322337NEG_EV1_1Empty vector
SA322338POS_EV3_2Empty vector
SA322339POS_EV3_3Empty vector
SA322340POS_EV4_1Empty vector
SA322341POS_EV4_2Empty vector
SA322342POS_EV2_3Empty vector
SA322343POS_EV2_2Empty vector
SA322344POS_EV1_2Empty vector
SA322345POS_EV1_3Empty vector
SA322346POS_EV2_1Empty vector
SA322347POS_EV4_3Empty vector
SA322348POS_EV3_1Empty vector
SA322349NEG_SH2_3shKDM2B
SA322350NEG_SH3_1shKDM2B
SA322351NEG_SH2_2shKDM2B
SA322352NEG_SH2_1shKDM2B
SA322353NEG_SH1_3shKDM2B
SA322354NEG_SH3_2shKDM2B
SA322355NEG_SH3_3shKDM2B
SA322356POS_SH2_1shKDM2B
SA322357NEG_SH4_3shKDM2B
SA322358NEG_SH4_2shKDM2B
SA322359NEG_SH4_1shKDM2B
SA322360NEG_SH1_2shKDM2B
SA322361NEG_SH1_1shKDM2B
SA322362POS_SH4_1shKDM2B
SA322363POS_SH4_2shKDM2B
SA322364POS_SH4_3shKDM2B
SA322365POS_SH1_2shKDM2B
SA322366POS_SH3_3shKDM2B
SA322367POS_SH1_3shKDM2B
SA322368POS_SH2_2shKDM2B
SA322369POS_SH2_3shKDM2B
SA322370POS_SH3_1shKDM2B
SA322371POS_SH3_2shKDM2B
SA322372POS_SH1_1shKDM2B
Showing results 1 to 48 of 48

Collection:

Collection ID:CO003065
Collection Summary:70% confluent cultures of control and shKDM2B MDA-MB-231 cells (four biological replicates) were first washed rapidly three times with PBS at room temperature.
Sample Type:Breast cancer cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003081
Treatment Summary:shRNAs in the pLKO-puro lentiviral vector, were packaged in Lenti-X 293T Cells (Takara Bio, Cat. 632180) by transient transfection, in combination with the packaging constructs psPax2 (Addgene, Cat. 12260) and pMD2.G (Addgene, Cat. 12259). Transfections were carried out using the Lipofectamine 3000 Transfection Reagent (Thermo Fisher Scientific, Cat. L3000015) and the Opti-MEM Reduced Serum Medium (Fisher Scientific, Cat. 31–985-070), according to the manufacturer’s protocol. The supernatants were collected 48h and 72h after the transfection. MDA-MB-231 and MDA-MB-468 cells were infected with the viral supernatants, in the presence of 8 μg/mL polybrene (Millipore-Sigma, Cat. 107689). Infected cells were selected with puromycin for 48h (Gibco, Cat. A11138) (10 μg/mL).

Sample Preparation:

Sampleprep ID:SP003078
Sampleprep Summary:1.5–2×106 cells per sample were treated with ice-cold methanol (80% v/v) and they were snap frozen via submergence into liquid Nitrogen for 30 seconds. Subsequently, they were placed on dry ice and allowed to thaw. This step was repeated three times with 10 second vortex-mixing between cycles. At the end, the samples were centrifuged at 11,500 g for 10 min at 4 °C, and the supernatants were collected, lyophilized overnight (~14 h) and stored at −80 °C.

Combined analysis:

Analysis ID AN004859 AN004860
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity
Column Agilent InfityLab Poroshell 120 SB-C18 (100 x 2.1mm, 2.7um) Agilent InfityLab Poroshell 120 SB-C18 (100 x 2.1mm, 2.7um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Agilent 6545 QTOF Agilent 6545 QTOF
Ion Mode POSITIVE NEGATIVE
Units Relative intensity Relative intensity

Chromatography:

Chromatography ID:CH003668
Instrument Name:Agilent 1290 Infinity
Column Name:Agilent InfityLab Poroshell 120 SB-C18 (100 x 2.1mm, 2.7um)
Column Temperature:40
Flow Gradient:0 min, 5%B; 15 min 95%B; 16 min 95%B; 17 min 5%, 25 min 5%B
Flow Rate:0.2 mL/min
Solvent A:Water with 0.1 % formic acid
Solvent B:Methanol with 0.1 % formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004603
Analysis ID:AN004859
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:ESI configuration included a mass range from 100 to 1,200 m/z, full scan mode at a scan rate of 2 scans per second, 3000V of capillary, 10 L/min of nebulizer gas flow and 300 °C of gas temperature. MS/MS data were collected in data dependent acquisition (DDA) mode with a scan rate of 5 spectra/sec and dynamic exclusion of 30 seconds for precursor ion selection and fragmentation, using 10 to 30 V.
Ion Mode:POSITIVE
  
MS ID:MS004604
Analysis ID:AN004860
Instrument Name:Agilent 6545 QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:ESI configuration included a mass range from 100 to 1,200 m/z, full scan mode at a scan rate of 2 scans per second, 3000V of capillary, 10 L/min of nebulizer gas flow and 300 °C of gas temperature. MS/MS data were collected in data dependent acquisition (DDA) mode with a scan rate of 5 spectra/sec and dynamic exclusion of 30 seconds for precursor ion selection and fragmentation, using 10 to 30 V.
Ion Mode:NEGATIVE
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