Summary of Study ST003912

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 PR002447. The data can be accessed directly via it's Project DOI: 10.21228/M8BG16 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	ST003912
Study Title	TANGO2 binds crystallin alpha B and its loss causes desminopathy
Study Type	Targeted LCMS metabolomics
Study Summary	Mutations in the TANGO2 gene cause an autosomal recessive disorder characterised by developmental delay, stress-induced episodic rhabdomyolysis, and cardiac arrhythmias along with severe metabolic crises. Although TANGO2 mutations result in a well characterised disease pathology, the function of TANGO2 is still unknown. To investigate the function of TANGO2, we knocked out the TANGO2 gene in human cells and mice. We identify that loss of TANGO2 impairs intermediate filament structure, resulting in fragmented mitochondrial networks and formation of cup-like mitochondria. In mice loss of TANGO2 caused heart defects, reduced muscle function and hypoglycemia that were caused by remodelling of intermediate filaments, resulting in changes in the mitochondrial and cytoplasmic proteomes and glycosylation. We identify that TANGO2 binds the small heat shock protein crystallin alpha B (CRYAB) to prevent the aggregation of the intermediate filament desmin and in the absence of TANGO2, mice develop desminopathy, which is consistent with features found in patients carrying mutations either in desmin or CRYAB. We analysed intra-cellular concentrations of central carbon metabolites to understand metabolic changes underpinning Cal51 human cell lines with TANGO2 present or knocked-out, finding in particular that knock-out cell lines had increased concentrations of glucose 6-phosphate and fructose 6-phosphate, that suggests glycolysis is required at the expense of reduced oxidative phosphorylation.
Institute	The Kids Research Institute Australia
Last Name	Filipovska
First Name	Aleksandra
Address	The Kids Research Institute Australia, Northern Entrance, Perth Children′s Hospital, 15 Hospital Avenue, Nedlands, Western Australia, 6009, Australia
Email	aleksandra.filipovska@uwa.edu.au
Phone	+61 8 6319 1000
Submit Date	2025-05-11
Num Groups	2
Total Subjects	10
Raw Data Available	Yes
Raw Data File Type(s)	lcd
Analysis Type Detail	LC-MS
Release Date	2025-05-14
Release Version	1

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Project:

Project ID:	PR002447
Project DOI:	doi: 10.21228/M8BG16
Project Title:	TANGO2 binds crystallin alpha B and its loss causes desminopathy
Project Type:	MS quantitative analysis
Project Summary:	Analysis of intra-cellular concentrations of central carbon metabolites to understand metabolic changes underpinning Cal51 human cell lines with TANGO2 present or knocked-out.
Institute:	The Kids Research Institute Australia
Last Name:	Filipovska
First Name:	Aleksandra
Address:	The Kids Research Institute Australia, Northern Entrance, Perth Children′s Hospital, 15 Hospital Avenue, Nedlands, Western Australia, 6009, Australia
Email:	aleksandra.filipovska@uwa.edu.au
Phone:	+61 8 6319 1000

Subject:

Subject ID:	SU004047
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Cell Strain Details:	CAL51 cell line

Factors:

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

mb_sample_id	local_sample_id	Genotype
SA430493	27_TA	CAL51-TANGO2KO
SA430494	26_TA	CAL51-TANGO2KO
SA430495	28_TA	CAL51-TANGO2KO
SA430496	29_TA	CAL51-TANGO2KO
SA430497	30_TA	CAL51-TANGO2KO
SA430498	1_TA	CAL51-WT
SA430499	2_TA	CAL51-WT
SA430500	3_TA	CAL51-WT
SA430501	4_TA	CAL51-WT
SA430502	5_TA	CAL51-WT

Showing results 1 to 10 of 10

Showing results 1 to 10 of 10

Collection:

Collection ID:	CO004040
Collection Summary:	CAL51 cells (breast carcinoma cell line, DMZ no. ACC 302) were cultured and maintained at 37˚C under humidified 95% air and 5% CO2 in Dulbecco’s modified Eagle’s medium containing 4.5 g/l glucose, 1 mM pyruvate, 2 mM glutamine, 10% fetal bovine serum (FBS) and 50 µg/ml uridine referred as high glucose media. Galactose media referred to Dulbecco’s modified Eagle’s medium deprived of glucose (DMEM, Gibco, Life Technologies) containing 10 mM galactose, 1 mM pyruvate and 10% FBS. For metabolomics samples, 1 million cells were pelleted and snap-frozen.
Sample Type:	CAL51 cell line

Treatment:

Treatment ID:	TR004056
Treatment Summary:	CAL51 cell line with (control/wild-type) or without TANGO2 knocked-out via CRISPR/Cas9 genome editing.

Sample Preparation:

Sampleprep ID:	SP004053
Sampleprep Summary:	500 µL ice cold 50% methanol was added to pellets of 1 million snap-frozen cells and the mixture was vortex, thawed on ice and sonicated for 5 min in an ice bath. 200 µL of 0.5 mm silica glass beads were added to samples which were loaded onto an OMNI Bead Ruptor Elite that was pre-chilled to -1 °C. Metabolites were extracted using 5 rounds of 45 s pulses at 4 m/s with a 30 s dwell time. Metabolites were purified by adding 250 µL chloroform, which was then vortexed and centrifuged at 16,000 RCF for 5 min at 4 °C. The supernatant was recovered and the organic phase reduced using a vacuum concentrator until approximately 200 µL remained. Samples were further diluted with 500 µL milliQ water, freeze-dried and reconstituted in 100 µL of 2% acetonitrile where 60 µL was taken and spiked with 2.5 µM azidothymidine as an internal standard for central carbon metabolite quantification.

Sampleprep ID:

SP004053

Sampleprep Summary:

500 µL ice cold 50% methanol was added to pellets of 1 million snap-frozen cells and the mixture was vortex, thawed on ice and sonicated for 5 min in an ice bath. 200 µL of 0.5 mm silica glass beads were added to samples which were loaded onto an OMNI Bead Ruptor Elite that was pre-chilled to -1 °C. Metabolites were extracted using 5 rounds of 45 s pulses at 4 m/s with a 30 s dwell time. Metabolites were purified by adding 250 µL chloroform, which was then vortexed and centrifuged at 16,000 RCF for 5 min at 4 °C. The supernatant was recovered and the organic phase reduced using a vacuum concentrator until approximately 200 µL remained. Samples were further diluted with 500 µL milliQ water, freeze-dried and reconstituted in 100 µL of 2% acetonitrile where 60 µL was taken and spiked with 2.5 µM azidothymidine as an internal standard for central carbon metabolite quantification.

Chromatography:

Chromatography ID:	CH004873
Chromatography Summary:	Solvent A: 7.5 mM tributylamine aqueous solution (pH to 4.95 with acetic acid); Solvent B: acetonitrile
Instrument Name:	Shimadzu Nexera X2
Column Name:	Phenomenex Gemini NX-C18 (50 x 2mm,3um)
Column Temperature:	45
Flow Gradient:	0-8 min (2% B), 8-22 min (20% B), 22-32 min (27% B), 32-47 min (50% B), 47-48 min (98% B), 48-54 min (98% B), 54-60 min (2% B).
Flow Rate:	300 uL/min
Solvent A:	100% water; 7.5 mM tributylamine; 0.0675% acetic acid
Solvent B:	100% acetonitrile
Chromatography Type:	Reversed phase

Analysis:

Analysis ID:	AN006424
Analysis Type:	MS
Chromatography ID:	CH004873
Num Factors:	2
Num Metabolites:	41
Units:	nanomoles/million cells