Summary of Study ST004203

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 PR002638. The data can be accessed directly via it's Project DOI: 10.21228/M8NV8F 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	ST004203
Study Title	Cell state-specific metabolic networks govern ferroptosis versus apoptosis in small cell lung cancer
Study Type	LC/MS
Study Summary	LC/MS metabolomics was performed on neuroendocrine (ASCL1 high) and non-neuroendocrine (ASCL1 low) small cell lung cancer cells isolated from the RPR2 genetically engineered mouse model (Rb1 flox/flox; Trp53 flox/flox; Rbl2 flox/flox; Hes1GFP). Cancer cell states were separated based on in vivo Hes1 expression, with ASCL1 high neuroendocrine cells enriched as cells with low/no Hes1 expression and ASCL1 low non-neuroendocrine cells as cells with high Hes1. Agilent 1290 Infinity LC system coupled to an Agilent 6545 Q-TOF mass spectrometer with an Agilent Jet Stream Source was used to detect 1296 entities, of which 474 were significantly altered between the two cell states. Pathway analysis revealed differences in purine metabolism, sphingolipid metabolism, tRNA charging, and glutathione-related redox pathways. These data provide insights into metabolic heterogeneity and redox regulation in SCLC cell states.
Institute	Stanford University
Last Name	Julien
First Name	Sage
Address	265 Campus Drive Stanford, CA 94305-5457
Email	julsage@stanford.edu
Phone	1-650-498-6603
Submit Date	2025-09-05
Raw Data Available	Yes
Raw Data File Type(s)	mzML, d
Analysis Type Detail	LC-MS
Release Date	2025-10-10
Release Version	1

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Project:

Project ID:	PR002638
Project DOI:	doi: 10.21228/M8NV8F
Project Title:	Cell state-driven metabolic dependency in small cell lung cancer
Project Type:	Mechanistic Study
Project Summary:	Cellular heterogeneity and plasticity are critical traits of tumour evolution and resistance to therapy. Small cell lung cancer (SCLC), a paradigm for the role of tumoral heterogeneity in resistance to therapy, undergoes rampant plasticity between cellular states defined by transcription factors regulating neuroendocrine differentiation. Here, we describe distinct metabolic states associated with neuroendocrine plasticity, revealing key metabolic vulnerabilities underlying cellular states in SCLC. Using integrated transcriptomic and metabolomic approaches, we found that SCLC cells in all states are dependent on exogenous cysteine/cystine (Cys). This dependency is explained by a uniformly low expression of the GNMT enzyme in the cysteine anabolic pathway. Ferroptosis is the most prevalent mechanism of cell death upon Cys deprivation, and SCLC cells in an ASCL1-low state (NEUROD1-high, POU2F3-high, and YAP1-high) died from ferroptosis upon depletion of exogenous Cys; in contrast, cells in the ASCL1-high state were more resistant to ferroptosis and instead underwent late apoptosis. Mechanistically, ASCL1 induces the expression of the GCH1 enzyme, leading to elevated levels of the antioxidant metabolites BH4/BH2, thereby causing ferroptosis resistance. Consequently, inhibition of the BH4/BH2 synthesis pathway sensitizes ASCL1-high SCLC cells to ferroptosis. Accordingly, enzyme-mediated cysteine depletion in combination with inhibition of BH4/BH2 synthesis was effective at reducing tumour growth in patient-derived xenografts (PDXs). Our work identifies distinct metabolic states during SCLC plasticity and demonstrates that Cys dependency is a key metabolic bottleneck that can be exploited for therapeutic strategies in SCLC across various cell death pathways and cell states.
Institute:	CECAD Research Center
Last Name:	von Karstedt
First Name:	Silvia
Address:	Joseph-Stelzmann-Straße 26, 50931 Köln
Email:	s.vonkarstedt@uni-koeln.de
Phone:	+49 221 478 84340

Subject:

Subject ID:	SU004355
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	Hes1 expression	Sample source
SA484441	1157_1	High Hes1 expression	Mouse tumor cells
SA484442	1157_2	High Hes1 expression	Mouse tumor cells
SA484443	1157_3	High Hes1 expression	Mouse tumor cells
SA484444	Hes1_neg_1	Low Hes1 expression	Mouse tumor cells
SA484445	Hes1_neg_2	Low Hes1 expression	Mouse tumor cells
SA484446	Hes1_neg_3	Low Hes1 expression	Mouse tumor cells

Showing results 1 to 6 of 6

Showing results 1 to 6 of 6

Collection:

Collection ID:	CO004348
Collection Summary:	Small cell lung cancer cells were derived from the RPR2 genetically engineered mouse model (Rb flox/flox; p53 flox/flox; Rbl2 flox/flox). Two distinct cell populations were collected: ASCL1 high neuroendocrine cells (low Hes1 expression) and ASCL1 low non-neuroendocrine cells (high Hes1 expression). Cells were cultured in 6-well plates at 37°C, centrifuged at 300 rcf for 5 min at 4°C and washed twice with ice-cold PBS. The collected sample was stored at -80°C until further processed.
Sample Type:	Tumor cells

Treatment:

Treatment ID:	TR004364
Treatment Summary:	No pharmacological or dietary treatments were applied. Cells were cultured under standard growth conditions and separated into neuroendocrine (Hes1-low/ASCL1-high) and non-neuroendocrine (Hes1-high/ASCL1-low) states based on their phenotype.

Sample Preparation:

Sampleprep ID:	SP004361
Sampleprep Summary:	Small cell lung cancer cells were derived from the RPR2 genetically engineered mouse model (Rb flox/flox; p53 flox/flox; Rbl2 flox/flox). Two distinct cell populations were collected: ASCL1 high neuroendocrine cells (low Hes1 expression) and ASCL1 low non-neuroendocrine cells (high Hes1 expression). Cells were cultured in 6-well plates, centrifuged at 300 rcf for 5 min at 4°C and washed twice with ice-cold PBS. Metabolites were extracted by immediately adding 300 µL of precooled 80% MeOH/H2O to cell pellets. After keeping the cells in -80°C for 15 min, they were vortexed and centrifuged at 20,000 rcf for 10 min at 4°C. The supernatant was collected for LC-MS analysis.

Sampleprep ID:

SP004361

Sampleprep Summary:

Small cell lung cancer cells were derived from the RPR2 genetically engineered mouse model (Rb flox/flox; p53 flox/flox; Rbl2 flox/flox). Two distinct cell populations were collected: ASCL1 high neuroendocrine cells (low Hes1 expression) and ASCL1 low non-neuroendocrine cells (high Hes1 expression). Cells were cultured in 6-well plates, centrifuged at 300 rcf for 5 min at 4°C and washed twice with ice-cold PBS. Metabolites were extracted by immediately adding 300 µL of precooled 80% MeOH/H2O to cell pellets. After keeping the cells in -80°C for 15 min, they were vortexed and centrifuged at 20,000 rcf for 10 min at 4°C. The supernatant was collected for LC-MS analysis.

Chromatography:

Chromatography ID:	CH005306
Chromatography Summary:	Agilent InfinityLab Poroshell 120 HILIC-Z (2.1 mm × 150 mm, 2.7 µm) PEEK-lined
Instrument Name:	Agilent 1290 Infinity
Column Name:	Agilent InfinityLab Poroshell 120 HILIC-Z PEEK-lined (150 x 2.1mm, 2.7 um)
Column Temperature:	25
Flow Gradient:	0-3 min, 98% B; 3-11 min, 98% to 70% B; 11-12 min, 70%-60% B; 12-14 min, 60%B; 14-14.1min, 60%-98% B; 14.1-16 min, 98% B
Flow Rate:	0.25 mL/min
Solvent A:	100% water; 10 mM ammonium formate; with 0.1% formic acid
Solvent B:	90% acetonitrile/10% water; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:	HILIC

Analysis:

Analysis ID:	AN006989
Analysis Type:	MS
Chromatography ID:	CH005306
Num Factors:	2
Num Metabolites:	1296
Units:	Peak height