Summary of Study ST002059

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 PR001303. The data can be accessed directly via it's Project DOI: 10.21228/M89135 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	ST002059
Study Title	4T1 and SkM cells
Study Summary	4T1-parental and 4T1-SkM cells were analyzed by metabolomics
Institute	University of Colorado Anschutz Medical Campus
Last Name	Nemkov
First Name	Travis
Address	12801 E 17th Avenue, RC-1 South, Rm 9403G, Aurora, CO, 80045, USA
Email	travis.nemkov@cuanschutz.edu
Phone	303-724-3253
Submit Date	2022-01-12
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2022-02-14
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001303
Project DOI:	doi: 10.21228/M89135
Project Title:	Unchecked oxidative stress is an insurmountable barrier for tumour cells that disseminate to skeletal muscle
Project Summary:	Skeletal muscle has been recognized as an inhospitable site for disseminated tumour cells (DTCs) for decades, yet its antimetastatic nature has eluded a thorough mechanistic description. Here, we show that DTCs traffic to and persist within skeletal muscle, raising the question as to how this tissue suppresses colonization. We employed mouse and organotypic culture models along with metabolomic profiling and ultimately find that oxidative stress is a principal suppressor of DTC proliferation in skeletal muscle. DTCs bypassed this oxidative constraint upon colonization of more fertile sites, but were unable to in muscle. Functional studies demonstrated that disrupting redox homeostasis via chemogenetic induction of reactive oxygen species slowed proliferation in lung. Conversely, enhancing antioxidant potential of tumour cells via ectopic expression of catalase allowed robust colonization of skeletal muscle. These findings reveal a profound metabolic bottleneck imposed on DTCs and sustained by skeletal muscle. Understanding this biology could reveal novel DTC vulnerabilities.
Institute:	University of Colorado Anschutz Medical Campus
Last Name:	Nemkov
First Name:	Travis
Address:	12801 E 17th Avenue, RC-1 South, Rm 9403G, Aurora, CO, 80045, USA
Email:	travis.nemkov@cuanschutz.edu
Phone:	303-724-3253

Subject:

Subject ID:	SU002141
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606

Factors:

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

mb_sample_id	local_sample_id	Genotype
SA193933	P2-50K_R6-	4T1-Parental
SA193934	P3-50K_R7-	4T1-Parental
SA193935	P1-50K_R14+	4T1-Parental
SA193936	P1-50K_R14-	4T1-Parental
SA193937	P2-50K_R6+	4T1-Parental
SA193938	P3-50K_R7+	4T1-Parental
SA193939	SK3-50K_R5-	4T1-SkM
SA193940	SK2-50K_R10+	4T1-SkM
SA193941	SK2-50K_R10-	4T1-SkM
SA193942	SK1-50K_R15-	4T1-SkM
SA193943	SK3-50K_R5+	4T1-SkM
SA193944	SK1-50K_R15+	4T1-SkM

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO002134
Collection Summary:	. 4T1-parental and 4T1-SkM cells were plated in 6-well plates at an initial density of 50,000 cells/well and collected 48h later (final density ~275,000 cells/well). Wells were washed twice with 1x PBS and cells were scraped into 1.5 mL microcentrifuge tubes and spun at 16,000 x g for 3 minutes. Samples were then flash frozen and stored at -80°C until ready to process.
Sample Type:	Breast cancer cells

Treatment:

Treatment ID:	TR002153
Treatment Summary:	A 4T1 subline derived from a rare skeletal muscle metastasis cells was serially passaged through Balb/c mice to achieve a 4T1 derivative that effectively colonized skeletal muscle (termed “4T1-SkM”)

Sample Preparation:

Sampleprep ID:	SP002147
Sampleprep Summary:	Prior to LC-MS analysis, tissue samples were weighed and resuspended in pre-chilled (-20°C) methanol:acetonitrile:water (5:3:2, v:v) to a final concentration of 30 mg/ml, cell samples were placed on ice and re-suspended with methanol:acetonitrile:water (5:3:2, v:v) at a concentration of 2x106 cells/mL, and media samples were extracted with the same solution at a dilution of 1:25 (v/v). Suspensions were vortexed continuously for 30 min at 4°C. Insoluble material was removed by centrifugation at 18,000 g for 10 min at 4°C and supernatants were isolated for metabolomics analysis by UHPLC-MS.

Sampleprep ID:

SP002147

Sampleprep Summary:

Prior to LC-MS analysis, tissue samples were weighed and resuspended in pre-chilled (-20°C) methanol:acetonitrile:water (5:3:2, v:v) to a final concentration of 30 mg/ml, cell samples were placed on ice and re-suspended with methanol:acetonitrile:water (5:3:2, v:v) at a concentration of 2x106 cells/mL, and media samples were extracted with the same solution at a dilution of 1:25 (v/v). Suspensions were vortexed continuously for 30 min at 4°C. Insoluble material was removed by centrifugation at 18,000 g for 10 min at 4°C and supernatants were isolated for metabolomics analysis by UHPLC-MS.

Combined analysis:

Analysis ID	AN003352	AN003353
Analysis type	MS	MS
Chromatography type	Reversed phase	Reversed phase
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Q Exactive Orbitrap	Thermo Q Exactive Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	AU	AU

Chromatography:

Chromatography ID:	CH002482
Instrument Name:	Thermo Vanquish
Column Name:	Phenomenex Kinetex C18 (150 x 2.1mm,2.6um)
Chromatography Type:	Reversed phase

MS:

MS ID:	MS003121
Analysis ID:	AN003352
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)
Ion Mode:	POSITIVE

MS ID:	MS003122
Analysis ID:	AN003353
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The Q Exactive mass spectrometer (ThermoFisher) was operated independently in positive or negative ion mode, scanning in Full MS mode (2 scans) from 60 to 900 m/z at 70,000 resolution, with 4 kV spray voltage, 45 sheath gas, 15 auxiliary gas. Calibration was performed prior to analysis using the PierceTM Positive and Negative Ion Calibration Solutions (ThermoFisher). Acquired data was then converted from raw to mzXML file format using Mass Matrix (Cleveland, OH). Samples were analyzed in randomized order with a technical mixture injected periodically through analysis to qualify instrument performance. Metabolite assignments, isotopologue distributions, and correction for expected natural abundances of deuterium, 13C, and 15N isotopes were performed using MAVEN (Princeton, NJ)
Ion Mode:	NEGATIVE