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SRX18421045: GSM6766358: 2 Control-002; Homo sapiens; RNA-Seq
1 ILLUMINA (NextSeq 2000) run: 100.7M spots, 15.2G bases, 5.5Gb downloads

External Id: GSM6766358_r1
Submitted by: Radiation Oncology, Moffitt Cancer Center
Study: Elevated methionine flux drives pyroptosis evasion in persister cancer cells
show Abstracthide Abstract
Induction of cell death represents a primary goal of most anti-cancer treatments. Despite the efficacy of such approaches, a small population of “persisters” develop evasion strategies to therapy-induced cell death. While previous studies have identified mechanisms of resistance to apoptosis, the mechanisms by which persisters dampen other forms of cell death, such as pyroptosis, remain to be elucidated. Pyroptosis is a form of inflammatory cell death that involves formation of membrane pores, ion gradient imbalance, water inflow and membrane rupture. Herein, we investigate mechanisms by which cancer persisters resist pyroptosis, survive, then proliferate in the presence of tyrosine kinase inhibitors (TKI). Lung, prostate and esophageal cancer persister cells remaining after treatments exhibited several hallmarks indicative of pyroptosis resistance. The inflammatory attributes of persisters included chronic activation of inflammasome, STING, and type I interferons. Comprehensive metabolomic characterization uncovered that TKI-induced pyroptotic persisters display high methionine consumption and excessive taurine production. Elevated methionine flux or exogenous taurine maintained plasma membrane integrity via osmolyte-mediated effects. Increased dependency on methionine flux decreased the level of one carbon metabolism intermediate S-(5'-adenosyl)-L-homocysteine, a determinant of cell methylation capacity. The consequent increase in methylation potential induced DNA hypermethylation of genes regulating metal ion balance and intrinsic immune response. This enabled thwarting TKI resistance by using the hypomethylating agent decitabine. In summary, the evolution of resistance to pyroptosis can occur via a stepwise process of physical acclimation and epigenetic changes without existing or recurrent mutations. Overall design: PC9 Cells were treated in 4 96 well plates with 2µM Erlotinib for 3, 19, 27, 75 days (one plate for each time point). Cells were monitored by Incucyte live-cell imaging to identify early expanding clones (EEs or named Lauria's clones), Persisters (P) in plates 2-3, and descendant of persisters (DPs) in plate 4. We then collected one plate at each time point. We then processed untreated, early expanding clones (EEs), Persisters (P), and descendant of persisters (DPs) for RNA seq profiling. Control PC9 cells were left untreated and were collected on day 3 (plate 1).
Sample: 2 Control-002
SAMN31933482 • SRS15903997 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: GSM6766358
Instrument: NextSeq 2000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Cells were washed with PBS then each plate containing cells was frozen at -80 °C until further collection of RNA. RNA and DNA were simultaneously isolated from the indicated clones from plates 1-4 using AllPrep DNA/RNA Kit (#catalogue: 80284, Qiagen) according to manufacturer's protocols. RNA extracted from cell lines was quantitated with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 (Agilent Technologies, Santa Clara, CA) The samples were then processed for RNA-sequencing using the NuGEN Universal RNA-Seq Library Preparation Kit with NuQuant (NuGEN Technologies, San Carlos, CA) The final libraries were normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer with the P3-200 cycle reagent kit in order to generate approximately 50M million 100-base read pairs per sample (Illumina, Inc., San Diego, CA)
Runs: 1 run, 100.7M spots, 15.2G bases, 5.5Gb
Run# of Spots# of BasesSizePublished
SRR22452271100,683,82915.2G5.5Gb2022-12-02

ID:
25445633

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