Summary of Study ST003869

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 PR002425. The data can be accessed directly via it's Project DOI: 10.21228/M85V7Q 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 IDST003869
Study TitleA long non-coding RNA (lncRNA}-mediated metabolic rewiring of cell senescence
Study SummaryDespite not proliferating, senescent cells remain metabolically active to maintain the senescence program. However, the mechanisms behind this metabolic reprogramming are not well understood. We identify sin-lncRNA, a previously uncharacterized long noncoding RNA (lncRNA), a key player in this response. While strongly activated in senescence by C/EBPβ, sin-lncRNA loss reinforces the senescence program by altering oxidative phosphorylation and rewiring mitochondrial metabolism. By interacting with dihydrolipoamide S-succinyltransferase (DLST), it facilitates its mitochondrial localization. DLST is an enzyme of the TCA cycle that regulates the conversion of -ketoglutarate to succinyl-CoA. Results of metabolomic experiment show that the TCA is strongly affected upon DLST knockdown as seen by reduction in intermediate metabolites. However, sin-lncRNA does not affect any of the metabolites detected. Alternatively, we have observed that a compensatory mechanism includes the upregulation of the GABA shunt pathway. Moreover, depletion of sin-lncRNA causes DLST nuclear translocation, leading to transcriptional changes in OXPHOS genes. While not expressed in highly proliferative cancer cells it is strongly induced upon cisplatin-induced senescence. Depletion of sin-lncRNA in ovarian cancer cells, reduces oxygen consumption and increases extracellular acidification, sensitizing cells to cisplatin treatment. Altogether, these results indicate that sin-lncRNA is specifically induced in senescence to maintain metabolic homeostasis, unveiling an RNA-dependent metabolic rewiring specific to senescent cells.
Institute
CIC bioGUNE - Centro de Investigación Cooperativa en Biociencias
Last Namevan Liempd
First NameSebastiaan
AddressParque Tecnológico de Vizcaya Ed. 800, Derio, Bizkaia, 48160, Spain
Emailsmvanliempd@cicbiogune.es
Phone944061317
Submit Date2025-04-02
Raw Data AvailableYes
Raw Data File Type(s)mzXML
Analysis Type DetailLC-MS
Release Date2025-05-12
Release Version1
Sebastiaan van Liempd Sebastiaan van Liempd
https://dx.doi.org/10.21228/M85V7Q
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002425
Project DOI:doi: 10.21228/M85V7Q
Project Title:Measuring TCA cycle metabolites in cells after labeling via 13C5-glutamine with high resolution LCMS.
Project Summary:Measuring TCA cycle metabolites in cells after labeling via 13C5-glutamine with high resolution LCMS. Cell treatments consisted of Linc and DLST knock down and controls.
Institute:CIC bioGUNE - Centro de Investigación Cooperativa en Biociencias
Last Name:van Liempd
First Name:Sebastiaan
Address:Parque Tecnológico de Vizcaya Ed. 800, Derio, Bizkaia, 48160, Spain
Email:smvanliempd@cicbiogune.es
Phone:944061317

Subject:

Subject ID:SU004003
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Strain Details:IMR90 ER:RAS fibroblasts

Factors:

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

mb_sample_id local_sample_id Precursor Knock.down Sample source
SA42477720230524_TCA_CELLS_UNAV_Marta_069a13C5-Glutamine CTL Fibroblasts
SA42477820230524_TCA_CELLS_UNAV_Marta_068a13C5-Glutamine CTL Fibroblasts
SA42477920230524_TCA_CELLS_UNAV_Marta_067a13C5-Glutamine CTL Fibroblasts
SA42478020230524_TCA_CELLS_UNAV_Marta_066a13C5-Glutamine CTL Fibroblasts
SA42478120230524_TCA_CELLS_UNAV_Marta_065a13C5-Glutamine CTL Fibroblasts
SA42478220230524_TCA_CELLS_UNAV_Marta_046a13C5-Glutamine CTL Fibroblasts
SA42478320230524_TCA_CELLS_UNAV_Marta_045a13C5-Glutamine CTL Fibroblasts
SA42478420230524_TCA_CELLS_UNAV_Marta_047a13C5-Glutamine CTL Fibroblasts
SA42478520230524_TCA_CELLS_UNAV_Marta_048a13C5-Glutamine CTL Fibroblasts
SA42478620230524_TCA_CELLS_UNAV_Marta_049a13C5-Glutamine CTL Fibroblasts
SA42478720230524_TCA_CELLS_UNAV_Marta_062a13C5-Glutamine DLST KD Fibroblasts
SA42478820230524_TCA_CELLS_UNAV_Marta_064a13C5-Glutamine DLST KD Fibroblasts
SA42478920230524_TCA_CELLS_UNAV_Marta_063a13C5-Glutamine DLST KD Fibroblasts
SA42479020230524_TCA_CELLS_UNAV_Marta_061a13C5-Glutamine DLST KD Fibroblasts
SA42479120230524_TCA_CELLS_UNAV_Marta_060a13C5-Glutamine DLST KD Fibroblasts
SA42479220230524_TCA_CELLS_UNAV_Marta_080a13C5-Glutamine DLST KD Fibroblasts
SA42479320230524_TCA_CELLS_UNAV_Marta_081a13C5-Glutamine DLST KD Fibroblasts
SA42479420230524_TCA_CELLS_UNAV_Marta_082a13C5-Glutamine DLST KD Fibroblasts
SA42479520230524_TCA_CELLS_UNAV_Marta_083a13C5-Glutamine DLST KD Fibroblasts
SA42479620230524_TCA_CELLS_UNAV_Marta_084a13C5-Glutamine DLST KD Fibroblasts
SA42479720230524_TCA_CELLS_UNAV_Marta_075a13C5-Glutamine Linc KD Fibroblasts
SA42479820230524_TCA_CELLS_UNAV_Marta_079a13C5-Glutamine Linc KD Fibroblasts
SA42479920230524_TCA_CELLS_UNAV_Marta_078a13C5-Glutamine Linc KD Fibroblasts
SA42480020230524_TCA_CELLS_UNAV_Marta_077a13C5-Glutamine Linc KD Fibroblasts
SA42480120230524_TCA_CELLS_UNAV_Marta_076a13C5-Glutamine Linc KD Fibroblasts
SA42480220230524_TCA_CELLS_UNAV_Marta_056a13C5-Glutamine Linc KD Fibroblasts
SA42480320230524_TCA_CELLS_UNAV_Marta_058a13C5-Glutamine Linc KD Fibroblasts
SA42480420230524_TCA_CELLS_UNAV_Marta_059a13C5-Glutamine Linc KD Fibroblasts
SA42480520230524_TCA_CELLS_UNAV_Marta_057a13C5-Glutamine Linc KD Fibroblasts
SA42480620230524_TCA_CELLS_UNAV_Marta_055a13C5-Glutamine Linc KD Fibroblasts
SA42473920230524_TCA_CELLS_UNAV_Marta_022a- - Blank
SA42474020230524_TCA_CELLS_UNAV_Marta_021a- - Blank
SA42474120230524_TCA_CELLS_UNAV_Marta_020a- - Blank
SA42474220230524_TCA_CELLS_UNAV_Marta_037a- - Curve
SA42474320230524_TCA_CELLS_UNAV_Marta_034a- - Curve
SA42474420230524_TCA_CELLS_UNAV_Marta_035a- - Curve
SA42474520230524_TCA_CELLS_UNAV_Marta_036a- - Curve
SA42474620230524_TCA_CELLS_UNAV_Marta_038a- - Curve
SA42474720230524_TCA_CELLS_UNAV_Marta_032a- - Curve
SA42474820230524_TCA_CELLS_UNAV_Marta_039a- - Curve
SA42474920230524_TCA_CELLS_UNAV_Marta_040a- - Curve
SA42475020230524_TCA_CELLS_UNAV_Marta_041a- - Curve
SA42475120230524_TCA_CELLS_UNAV_Marta_042a- - Curve
SA42475220230524_TCA_CELLS_UNAV_Marta_043a- - Curve
SA42475320230524_TCA_CELLS_UNAV_Marta_044a- - Curve
SA42475420230524_TCA_CELLS_UNAV_Marta_008a- - Curve
SA42475520230524_TCA_CELLS_UNAV_Marta_033a- - Curve
SA42475620230524_TCA_CELLS_UNAV_Marta_007a- - Curve
SA42475720230524_TCA_CELLS_UNAV_Marta_016a- - Curve
SA42475820230524_TCA_CELLS_UNAV_Marta_012a- - Curve
SA42475920230524_TCA_CELLS_UNAV_Marta_009a- - Curve
SA42476020230524_TCA_CELLS_UNAV_Marta_010a- - Curve
SA42476120230524_TCA_CELLS_UNAV_Marta_011a- - Curve
SA42476220230524_TCA_CELLS_UNAV_Marta_019a- - Curve
SA42476320230524_TCA_CELLS_UNAV_Marta_018a- - Curve
SA42476420230524_TCA_CELLS_UNAV_Marta_017a- - Curve
SA42476520230524_TCA_CELLS_UNAV_Marta_015a- - Curve
SA42476620230524_TCA_CELLS_UNAV_Marta_014a- - Curve
SA42476720230524_TCA_CELLS_UNAV_Marta_013a- - Curve
SA42476820230524_TCA_CELLS_UNAV_Marta_028a- - QC
SA42476920230524_TCA_CELLS_UNAV_Marta_029a- - QC
SA42477020230524_TCA_CELLS_UNAV_Marta_030a- - QC
SA42477120230524_TCA_CELLS_UNAV_Marta_031a- - QC
SA42477220230524_TCA_CELLS_UNAV_Marta_027a- - QC
SA42477320230524_TCA_CELLS_UNAV_Marta_026a- - QC_INIT
SA42477420230524_TCA_CELLS_UNAV_Marta_023a- - QC_INIT
SA42477520230524_TCA_CELLS_UNAV_Marta_024a- - QC_INIT
SA42477620230524_TCA_CELLS_UNAV_Marta_025a- - QC_INIT
SA42480720230524_TCA_CELLS_UNAV_Marta_072aUnlabelled CTL Fibroblasts
SA42480820230524_TCA_CELLS_UNAV_Marta_073aUnlabelled CTL Fibroblasts
SA42480920230524_TCA_CELLS_UNAV_Marta_074aUnlabelled CTL Fibroblasts
SA42481020230524_TCA_CELLS_UNAV_Marta_071aUnlabelled CTL Fibroblasts
SA42481120230524_TCA_CELLS_UNAV_Marta_070aUnlabelled CTL Fibroblasts
SA42481220230524_TCA_CELLS_UNAV_Marta_053aUnlabelled CTL Fibroblasts
SA42481320230524_TCA_CELLS_UNAV_Marta_050aUnlabelled CTL Fibroblasts
SA42481420230524_TCA_CELLS_UNAV_Marta_051aUnlabelled CTL Fibroblasts
SA42481520230524_TCA_CELLS_UNAV_Marta_054aUnlabelled CTL Fibroblasts
SA42481620230524_TCA_CELLS_UNAV_Marta_052aUnlabelled CTL Fibroblasts
Showing results 1 to 78 of 78

Collection:

Collection ID:CO003996
Collection Summary:CELLS: IMR90-ER:RAS fibroblasts were cultured in DMEM medium (GIBCO), supplemented with 10% fetal bovine serum (GIBCO) and 1x penicillin/streptomycin (GIBCO). Cells were maintained at 37 °C in the presence of 5% CO2. For the metabolic analysis, cells were transfected in 6- well plates in triplicates with siRNA control, siRNA against DLST or siRNA against sin-lncRNA using RNAiMax (Invitrogen). 24h later, they were treated with 500nM 4-OHT to induce senescence for 6 days. After that cells were washed and sent on dry ice for analysis. INCUBATIONS: The samples indicated with the "Precursor" parameter 13C5-Glutamine were incubated with 4mM uniformly 13C-labelled glutamine and the ones indicated with Glutamine were incubated with 4mM non-labelled glutamine. CURVE: Curve samples as defined in the study design were serial dilutions of the pooled analytes (alpha ketoglutarate, Citrate, Glutamate, Glutamine, Isocitrate, Malate) in water/MeOH (75/25 %v/v). The following concentrations in µM were used: 100, 50, 25, 10, 5, 2.5, 1, 0.5, 0.25, 0.1, 0.05, 0.025 and 0 (blank). Curve_12 has the highest concentration and Curve_00 is the blank.
Sample Type:Fibroblasts
Storage Conditions:-80℃
Collection Tube Temp:20

Treatment:

Treatment ID:TR004012
Treatment Summary:Cells were incubated either with non-labeled and 13C5-labeled glutamate. Knockdowns were performed with siRNA for the various genes.

Sample Preparation:

Sampleprep ID:SP004009
Sampleprep Summary:Cells from three wells (1E6 cells/well) were pooled to obtain one LCMS sample. Therefore, cells were extracted with 200 μL icecold extraction liquid per well. The volume from one well was transferred to the next and finally the resulting 600 μL volume was passed over the three wells two times. The extraction liquid consisted of a mixture of ice-cold methanol/water (50/50 %v/v). Subsequently 400 μL of the cell homogenate plus 400μL of chloroform was transferred to a new aliquot and shaken at 1400 rpm for 60 minutes at 4 °C. Next the aliquots were centrifuged for 30 minutes at 14000 rpm at 4 °C. 250μL of the aqueous phase was transferred to a fresh aliquot. The chilled supernatants were evaporated with a speedvac in approximately 2h. The resulting pellets were resuspended in 150 μL water/MeOH (75/25 %v/v).

Combined analysis:

Analysis ID AN006358
Chromatography ID CH004823
MS ID MS006059
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity I-Class
Column Waters ACQUITY UPLC BEH Phenyl (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type QTOF
MS instrument name Waters Synapt G2 S QTOF
Ion Mode NEGATIVE
Units Integrated peak area

Chromatography:

Chromatography ID:CH004823
Chromatography Summary:Samples were measured with a UPLC system (Acquity, Waters Inc., Manchester, UK) coupled to a Time-of-Flight mass spectrometer (ToF MS, SYNAPT G2S, Waters Inc.). A 2.1 x 100 mm, 1.7 μm Phenyl-Hexyl column (Waters Inc.), thermostated at 40 °C, was used to separate the analytes before entering the MS. Mobile phase solvent A (aqueous phase) consisted of 99.5% water and 0.5% FA while solvent B (organic phase) consisted of 99.5% MeCN and 0.5% FA. In order to obtain a good separation of the analytes the following gradient was used: from 98% A to 0% A in 2 minutes in a curved gradient (Curve 8, as defined by Waters), constant at 0% A for 1 minutes, back to 98% A in 0.2 minutes in a linear gradient (Curve 6, as defined by Waters). The flow rate was 0.250 mL/min and the injection volume was 3 μL. After every 6 injections sample was injected. The gradient curves are defined by Waters as: The convex curve set conforms to the following: C(t) = Cf – [ (Cf – Ci) * (X^N) ] Where X = (Tf – t) / (Tf – Ti), and where the notation X^N indicates the quantity X raised to the Nth power, where Curve 2 N = 8 Curve 3 N = 5 Curve 4 N = 3 Curve 5 N = 2 The concave curve set (including linear) conforms to the following: C(t) = Ci + [ (Cf – Ci) * (X^N) ] Where X = (t – Ti) / (Tf – Ti), and where the notation X^N indicates the quantity X raised to the Nth power, where Curve 6 N = 1 Curve 7 N = 2 Curve 8 N = 3 Curve 9 N = 5 Curve 10 N = 8.
Instrument Name:Waters Acquity I-Class
Column Name:Waters ACQUITY UPLC BEH Phenyl (100 x 2.1mm,1.7um)
Column Temperature:40
Flow Gradient:from 98% A to 0% A in 2 minutes in a curved gradient (Curve 8, as defined by Waters), constant at 0% A for 1 minutes, back to 98% A in 0.2 minutes in a linear gradient (Curve 6, as defined by Waters)
Flow Rate:0.25 mL/min
Solvent A:100% Water; 0.5% formic acid
Solvent B:100% Acetonitrile; 0.5% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS006059
Analysis ID:AN006358
Instrument Name:Waters Synapt G2 S QTOF
Instrument Type:QTOF
MS Type:ESI
MS Comments:mass corrected with Leu-Enk lock mass processed in TargetLynx. Data is reported as Integrated peak area of the extracted ion current for the specific m/z within a 0.01Da window in "single ion counts".
Ion Mode:NEGATIVE
Ion Source Temperature:450
Ion Spray Voltage:500V
Ionization:ESI
Mass Accuracy:3ppm
Source Temperature:120
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