Genome-wide CRISPR-Cas9 screen identifies SLC1A3 as a key contributor to L-asparaginase Resistance in Solid tumors
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ABSTRACT:
PROVIDER: PRJNA553692 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9665760.fastq.gz | Fastqsanger.gz | |||
| SRR9665761.fastq.gz | Fastqsanger.gz | |||
| SRR9665752.fastq.gz | Fastqsanger.gz | |||
| SRR9665762.fastq.gz | Fastqsanger.gz | |||
| SRR9665753.fastq.gz | Fastqsanger.gz |
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Project description:L-asparaginase (ASNase) has been incorporated in the treatment of acute lymphoblastic leukemia for decades. However, intolerable toxicity due to increasing ASNase dosage has been observed in clinical trials with solid tumors. Here, we performed a genome-wide CRISPR-Cas9 functional screen in ASNase-resistant PC3 prostate cancer cells and identified SLC1A3, an aspartate transporter highly expressed in brain tissues but also in several tumor types. Interestingly, combined ASNase treatment and SLC1A3 inhibition caused cell cycle arrest and metabolic alterations in the urea cycle, nucleotide synthesis, energy production by both TCA cycle and glycolysis, and impaired lipid metabolism. Additionally, the introduction of SLC1A3 into SLC1A3-negative mouse and human breast cancer cells increased tumor and metastasis burden, and promoted ASNase tolerance in vitro and in vivo. These findings uncover an important role of SLC1A3 in ASNase resistance and indicated limited aspartate uptake for enhancement of ASNase efficacy with solid tumors.
2019-07-11 | GSE134074 | GEO
Project description:Resistance to asparaginase, an antileukemic enzyme that depletes asparagine, is a common clinical problem. Using a genome-wide CRISPR/Cas9 screen, we found a synthetic lethal interaction between Wnt pathway activation and asparaginase in acute leukemias resistant to this enzyme. Wnt pathway activation induced asparaginase sensitivity in distinct treatment-resistant subtypes of acute leukemia, but not in normal hematopoietic progenitors. Sensitization to asparaginase was mediated by Wnt-dependent stabilization of proteins (Wnt/STOP), which inhibits GSK3-dependent protein ubiquitination and proteasomal degradation, a catabolic source of asparagine. Inhibiting the alpha isoform of GSK3 phenocopied this effect, and pharmacologic GSK3 inhibition profoundly sensitized drug-resistant leukemias to asparaginase. Our findings provide a molecular rationale for activation of Wnt/STOP signaling to improve the therapeutic index of asparaginase. To gain further insights into mechanisms of cytotoxicity of this combination, we applied unbiased mass spectrometry proteomics to CCRF-CEM cells, a human T-cell acute lymphoblastic leukemia cell line, treated with vehicle, asparaginase alone, the GSK3 inhibitor BRD0705 (which phenocopies Wnt/STOP pathway activation), or the combination of asparaginase and BRD0705.
2019-03-29 | PXD013061 | Pride
Project description:To identify genes affected by L-asparaginase, we treated with L-asparaginase 1U/ml. After 2 days, RNA was extracted, and then expression analysis was performed using agilent microarray.
2017-01-31 | GSE94289 | GEO
Project description:Abstract: To investigate the effect of l-asparaginase on acute lymphoblastic leukemia (ALL), we used cDNA microarrays to obtain a genome-wide view of gene expression both at baseline and after in vitro exposure to l-asparaginase in cell lines and pediatric ALL samples. In 16 cell lines, a baseline gene expression pattern distinguished l-asparaginase sensitivity from resistance. However, for 28 pediatric ALL samples, no consistent baseline expression pattern was associated with sensitivity to l-asparaginase. In particular, baseline expression of asparagine synthetase (ASNS) was not predictive of response to l-asparaginase. After exposure to l-asparaginase, 5 cell lines and 10 clinical samples exhibited very similar changes in the expression of a large number of genes. However, the gene expression changes occurred more slowly in the clinical samples. These changes included a consistent increase in expression of tRNA synthetases and solute transporters and activating transcription factor and CCAAT/enhancer binding protein family members, a response similar to that observed with amino acid starvation. There was also a consistent decrease in many genes associated with proliferation. Taken together, the changes seem to reflect a consistent coordinated response to asparagine starvation in both cell lines and clinical samples. Importantly, in the clinical samples, increased expression of ASNS after l-asparaginase exposure was not associated with in vitro resistance to l-asparaginase, indicating that ASNS-independent mechanisms of in vitro l-asparaginase resistance are common in ALL. These results suggest that targeting particular genes involved in the response to amino acid starvation in ALL cells may provide a novel way to overcome l-asparaginase resistance. This SuperSeries is composed of the SubSeries listed below.
2006-03-08 | GSE4397 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE4070: Clinical acute lymphoblastic leukemia samples (untreated) with known asparaginase LC50 values GSE4071: Clinical pediatric acute lymphoblastic leukemia samples after in vitro exposure to L-asparaginase GSE4072: L-asparaginase exposure in acute lymphoblastic leukemia cell lines time series Abstract: To investigate the effect of l-asparaginase on acute lymphoblastic leukemia (ALL), we used cDNA microarrays to obtain a genome-wide view of gene expression both at baseline and after in vitro exposure to l-asparaginase in cell lines and pediatric ALL samples. In 16 cell lines, a baseline gene expression pattern distinguished l-asparaginase sensitivity from resistance. However, for 28 pediatric ALL samples, no consistent baseline expression pattern was associated with sensitivity to l-asparaginase. In particular, baseline expression of asparagine synthetase (ASNS) was not predictive of response to l-asparaginase. After exposure to l-asparaginase, 5 cell lines and 10 clinical samples exhibited very similar changes in the expression of a large number of genes. However, the gene expression changes occurred more slowly in the clinical samples. These changes included a consistent increase in expression of tRNA synthetases and solute transporters and activating transcription factor and CCAAT/enhancer binding protein family members, a response similar to that observed with amino acid starvation. There was also a consistent decrease in many genes associated with proliferation. Taken together, the changes seem to reflect a consistent coordinated response to asparagine starvation in both cell lines and clinical samples. Importantly, in the clinical samples, increased expression of ASNS after l-asparaginase exposure was not associated with in vitro resistance to l-asparaginase, indicating that ASNS-independent mechanisms of in vitro l-asparaginase resistance are common in ALL. These results suggest that targeting particular genes involved in the response to amino acid starvation in ALL cells may provide a novel way to overcome l-asparaginase resistance. Refer to individual Series
2006-03-07 | E-GEOD-4397 | biostudies-arrayexpress
Project description:Genome-wide CRISPR-Cas9 knockout screen using TKOv1 sgRNA library was performed in isogenic RBM10-proficient and RBM10-deficient HCC827 cells.
2023-03-04 | E-MTAB-12724 | biostudies-arrayexpress
Project description:Clinical reports describing increased liver toxicity in adult versus pediatric patients treated with the anti-leukemic drug asparaginase suggest that hepatic stress responses differ with age. We utilized RNA sequencing to comparatively examine the liver transcriptomes of juvenile (2 wk old) and adult (8 and 16 wk old) mice following chronic exposure to asparaginase. Liver RNA from 2 and 16 week old mice were sent Sulzberger Columbia Genome Center for cDNA library preparation and sequencing at the same time as liver RNA from 8 week old mice (GSE92364). Asparaginase exposure altered the liver transcriptomes only modestly whereas age had a massive global influence. Unbiased exploration into the effect of age on drug responses revealed that the integrated stress response (ISR) represented a common, core molecular signature regardless of age. ISR engagement in juveniles corresponded with transcriptional signatures of downregulated lipid biosynthesis and increased sequestration of iron. In contrast, adults showed ISR activation alongside upregulation of Saa1 and Saa2 inflammatory markers, serine/glycine metabolism, and folate cycle suggesting mitochondrial stress. We also observed sporadic enrichment in RNA gene signatures reflecting altered nucleotide metabolism of adults in response to the drug. Taken together, our data show that maturity to adulthood does not alter the ISR gene signature to asparaginase. Instead, age-related changes in cellular resource capacity and turnover may be the determining factor in guiding hepatic stress responses to asparaginase.
2018-12-25 | GSE122243 | GEO
Project description:Time series of in vitro 2 IU/ml L-asparaginase exposure in acute lymphoblastic leukemia cell lines. Groups of assays that are related as part of a time series. Keywords: time_series_design
2006-01-21 | GSE4072 | GEO
Project description:We have shown that drug-resistant leukemias rely on protein degradation through the ubiquitin proteasome pathway to survive during asparaginase therapy. Our studies support the model that this catabolic source of amino acids is upregulated in response to amino acid starvation. To investigate whether this involves bulk protein degradation or the degradation of specific protein targets, we analyzed K48-ubiquitinated proteins using immunoprecipitation with an anti-K48-linked ubiquitin antibody (Millipore #05-1307) followed by mass spectrometry proteomics from Jurkat cells after treatment with vehicle vs asparaginase. We found no enrichment of specific proteins after asparaginase treatment, consistent with the possibility that asparaginase therapy stimulates bulk protein degradation, although these results do not rule out degradation of specific proteins below the limit of detection of this assay.
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Project description:primary ALL cells (B- and T-lineage) resistant to L-asparaginase by the MTT in vitro sensitivity assay
2008-06-14 | E-GEOD-645 | biostudies-arrayexpress