Summary of Study ST003102

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 PR001925. The data can be accessed directly via it's Project DOI: 10.21228/M8WM7T 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	ST003102
Study Title	Cellular adaptation to cancer therapy along a resistance continuum
Study Summary	Recent research has shed light on the role of non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell state transitions occurring in the adaptation to cancer therapies remain elusive and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell state transitions accompanied by a progressive increase in cell fitness, which we denote the ‘resistance continuum’. This cellular adaptation involves a step-wise assembly of gene expression programs and epigenetically reinforced cell states underpinned by phenotypic plasticity stress adaptation and metabolic reprogramming. Through systematic genetic perturbations, we identify an acquisition of progressive metabolic dependencies, exposing a spectrum of vulnerabilities that can be potentially exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell state transitions.
Institute	NYU Langone Health
Last Name	Starvaggi Franca
First Name	Gustavo
Address	430 East 29th Street, NY NY 10016
Email	Gustavo.StarvaggiFranca@nyulangone.org
Phone	6465015151
Submit Date	2024-02-13
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2024-04-02
Release Version	1

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Project:

Project ID:	PR001925
Project DOI:	doi: 10.21228/M8WM7T
Project Title:	Cellular adaptation to cancer therapy along a resistance continuum
Project Summary:	Recent research has shed light on the role of non-genetic plasticity in transient drug tolerance and the acquisition of stable resistance. However, the dynamics of cell state transitions occurring in the adaptation to cancer therapies remain elusive and require a systems-level longitudinal framework. Here we demonstrate that resistance develops through trajectories of cell state transitions accompanied by a progressive increase in cell fitness, which we denote the ‘resistance continuum’. This cellular adaptation involves a step-wise assembly of gene expression programs and epigenetically reinforced cell states underpinned by phenotypic plasticity stress adaptation and metabolic reprogramming. Through systematic genetic perturbations, we identify an acquisition of progressive metabolic dependencies, exposing a spectrum of vulnerabilities that can be potentially exploited therapeutically. The concept of the resistance continuum highlights the dynamic nature of cellular adaptation and calls for complementary therapies directed at the mechanisms underlying adaptive cell state transitions.
Institute:	NYU Langone Health
Last Name:	Starvaggi Franca
First Name:	Gustavo
Address:	430 E 29th Street
Email:	Gustavo.StarvaggiFranca@nyulangone.org
Phone:	646-501-4603
Funding Source:	NIH grants: P50 CA225450

Subject:

Subject ID:	SU003217
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	Sample source	Treatment
SA333491	S25059	Ovarian cancer cells	C
SA333492	S25061	Ovarian cancer cells	C
SA333493	S25060	Ovarian cancer cells	C
SA333494	S25064	Ovarian cancer cells	C_drug
SA333495	S25062	Ovarian cancer cells	C_drug
SA333496	S25063	Ovarian cancer cells	C_drug
SA333497	S25067	Ovarian cancer cells	T320
SA333498	S25065	Ovarian cancer cells	T320
SA333499	S25066	Ovarian cancer cells	T320
SA333500	S25070	Ovarian cancer cells	T320_drug
SA333501	S25069	Ovarian cancer cells	T320_drug
SA333502	S25068	Ovarian cancer cells	T320_drug

Showing results 1 to 12 of 12

Showing results 1 to 12 of 12

Collection:

Collection ID:	CO003210
Collection Summary:	To generate drug-induced PARPi resistant populations, 1×106 Kuramochi drug-naïve cells (C) were initially seeded in 150 mm plates.
Sample Type:	Ovarian cancer cells

Treatment:

Treatment ID:	TR003226
Treatment Summary:	Twenty four hours after seeding, 1 uM of olaparib (Selleckchem, S1060) was added and cells were maintained under treatment until reaching confluency (> 70%), thus characterizing resistance at this dose. Cells were harvested (0.25% Trypsin/EDTA for 5 min at 37°C) and a fraction of the surviving population (1×106 cells) was seeded again and treated with 2.5 uM until cells reached confluency. This process was repeated sequentially by doubling the drug concentrations until the cell populations were able to achieve confluency at 320 uM of olaparib (T320). The initial dose was determined by cell viability assays, indicating a low starting dose (< IC30). At each step, aliquots of the adapted populations were frozen (10% DMSO, 50% FBS, 40% media) for further experiments

Treatment ID:

TR003226

Treatment Summary:

Twenty four hours after seeding, 1 uM of olaparib (Selleckchem, S1060) was added and cells were maintained under treatment until reaching confluency (> 70%), thus characterizing resistance at this dose. Cells were harvested (0.25% Trypsin/EDTA for 5 min at 37°C) and a fraction of the surviving population (1×106 cells) was seeded again and treated with 2.5 uM until cells reached confluency. This process was repeated sequentially by doubling the drug concentrations until the cell populations were able to achieve confluency at 320 uM of olaparib (T320). The initial dose was determined by cell viability assays, indicating a low starting dose (< IC30). At each step, aliquots of the adapted populations were frozen (10% DMSO, 50% FBS, 40% media) for further experiments

Sample Preparation:

Sampleprep ID:	SP003223
Sampleprep Summary:	Kuramochi cells (C and T320) were cultured until ~80% confluence either on 320 uM of olaparib for 24h or off treatment in triplicates per condition. Cell pellets were collected and frozen with liquid nitrogen for submission to the NYU Metabolomics Core Resource Laboratory. Samples were subjected to an LCMS analysis to detect and quantify known peaks. A metabolite extraction was carried out on each sample based on a previously described method116.

Sampleprep ID:

SP003223

Sampleprep Summary:

Kuramochi cells (C and T320) were cultured until ~80% confluence either on 320 uM of olaparib for 24h or off treatment in triplicates per condition. Cell pellets were collected and frozen with liquid nitrogen for submission to the NYU Metabolomics Core Resource Laboratory. Samples were subjected to an LCMS analysis to detect and quantify known peaks. A metabolite extraction was carried out on each sample based on a previously described method116.

Combined analysis:

Analysis ID	AN005076
Analysis type	MS
Chromatography type	HILIC
Chromatography system	Ulitmate 3000
Column	SeQuant ZIC-pHILIC (150 x 4.6mm,5um)
MS Type	ESI
MS instrument type	Triple quadrupole
MS instrument name	Thermo Q Exactive Orbitrap
Ion Mode	UNSPECIFIED
Units	Arbitrary units

Chromatography:

Chromatography ID:	CH003833
Methods Filename:	L12
Chromatography Comments:	The LC column was a MilliporeTM ZIC-pHILIC (2.1 x150 mm, 5 μm) coupled to a Dionex Ultimate 3000TM system and the column oven temperature was set to 25oC for the gradient elution. A flow rate of 100 μL/min was used with the following buffers; A) 10 mM ammonium carbonate in water, pH 9.0, and B) neat acetonitrile. The gradient profile was as follows; 80-20%B (0-30 min), 20-80%B (30-31 min), 80-80%B (31-42 min). Injection volume was set to 2 μL for all analyses (42 min total run time per injection).
Instrument Name:	Ulitmate 3000
Column Name:	SeQuant ZIC-pHILIC (150 x 4.6mm,5um)
Column Pressure:	1800
Column Temperature:	25
Flow Gradient:	80-20%B (0-30 min), 20-80%B (30-31 min), 80-80%B (31-42 min)
Flow Rate:	0.1mL/min
Injection Temperature:	4
Internal Standard:	ISTD (500nM amino acid cocktail)
Sample Injection:	2uL
Solvent A:	100% water; 10 mM ammonium carbonate, pH 9.0
Solvent B:	100% acetonitrile
Analytical Time:	30m
Oven Temperature:	28
Chromatography Type:	HILIC

MS:

MS ID:	MS004814
Analysis ID:	AN005076
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Triple quadrupole
MS Type:	ESI
MS Comments:	M.13 Polar metabolites (pHILIC Hybrid). MS analyses were carried out by coupling the LC system to a Thermo Q Exactive HFTM mass spectrometer operating in heated electrospray ionization mode (HESI). Method duration was 30 min with a polarity switching data-dependent Top 5 method for both positive and negative modes. Spray voltage for both positive and negative modes was 3.5kV and capillary temperature was set to 320oC with a sheath gas rate of 35, aux gas of 10, and max spray current of 100 μA. The full MS scan for both polarities utilized 120,000 resolution with an AGC target of 3e6 and a maximum IT of 100 ms, and the scan range was from 67-1000 m/z. Tandem MS spectra for both positive and negative mode used a resolution of 15,000, AGC target of 1e5, maximum IT of 50 ms, isolation window of 0.4 m/z, isolation offset of 0.1 m/z, fixed first mass of 50 m/z, and 3-way multiplexed normalized collision energies (nCE) of 10, 35, 80. The minimum AGC target was 1e4 with an intensity threshold of 2e5. All data were acquired in profile mode.
Ion Mode:	UNSPECIFIED