The role of compensatory metabolic reprogramming in ensuring PDAC cell survival under the limitation of glutamine
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE229055 | GEO | 2024/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:To gain mechanistic insight into how Epigenetic factors reprogramming metabolism in response to glutamine starvation. we performed CUT&Tag sequencing in murine PDAC cells. KPC1199 cells were treated in Cont group or Low Gln group , and harvested after 72 hours. CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme). DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme).
2024-12-31 | GSE229903 | GEO
Project description:By a transcriptome analysis using RNA sequencing in H1299 cells, a non-small cell lung cancer cell line (NSCLC), we determined the response of lipogenic genes to absence vs. presence of glutamine (Gln) or glucose (Gluc). We found that neither glutamine nor glucose alone was able to activate the expression of genes regulating fatty acid and cholesterol synthesis, and uptake, including SREBF1, SREBF2, ACLY, ACACA, FASN, SCD1, HMGCR and LDLR, as compared to absence of both. And, activation of lipogenic genes required the presence of both glutamine and glucose, but SCAP gene expression was not affected by either glutamine or glucose. The RNA sequencing analysis in H1299 cells also confirmed that ammonia, similarly to glutamine, significantly activated the expression of genes controlling the fatty acid and cholesterol synthesis pathways as compared to glucose alone. This study detemines the intrinsic molecular connection between glutamine, glucose and lipid synthesis.
2022-04-30 | GSE199089 | GEO
Project description:Glutamine (gln) is an essential and versatile metabolite that feeds different cellular pathways and generates several derivatives. Alpha-ketoglutarate (aKG) is the gln derivative that feeds the TCA cycle, activates cellular growth, and is related to epigenetic changes. Despite gln importance, the specific role of gln – and not its derivatives – in gene expression is not clear. To address this question, U2OS cells were cultured in the presence of gln or its absence +/- aKG for 8 hours. Gln had an unique effect in the transcriptome of U2OS cells and the addition of aKG was not able to mimic the gln effect. In conclusion, gln affects gene expression independently of its derivative aKG.
2024-09-10 | GSE276327 | GEO
Project description:ICR mice, age 6-8 weeks.(Harlan, Indianapolis, IN, USA). Housed individually with controlled temperature, humidity, and light-dark cycle (0600h – 1800h). Pregnant mice were housed individually with ad libitum access to standard rodent chow (T.2018, Harlan Teklad, Indianapolis, IN, USA). On day 12.5 of pregnancy, dams were randomly assigned to either a control or undernutrition group. In the undernutrition group, food was restricted to 50% that of gestational day -matched controls for the remainder of pregnancy. After delivery, mothers were given ad libitum access to chow and 24 hours after birth, litters were equalized to eight. We studied mice from 2 groups: in utero undernourished offpring (U) and control offspring (C). Primary muscle cells were isolated from the quadriceps of U and C at 3 weeks old. Isolated primary muscle cells were grown on Matrigel coated flasks in low glucose (5.5 mmol/L) Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 20% FBS, 1X antibiotic-antimycotic, 2.5μg/ml gentamycin and 2.5ng/ml basic fibroblast growth factor. When cells reached approximately 90% confluency, they were differentiated in low glucose DMEM supplemented with 2% FBS, 1X antibiotic-antimycotic, and 2.5μg/ml gentamycin. Other cells were cultured overnight in substrate limited medium (glucose and glutamine free DMEM supplemented with 0.5mM glucose, 1mM glutamine, 0.5mM carnitine and 1% (v/v) FBS; pH 7.4).
2019-09-12 | GSE103689 | GEO
Project description:We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by glutamine in rice roots. Transcriptomic analysis of rice roots revealed that the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses was rapidly induced by glutamine within 30 minutes. Total RNA from –N and Gln-treated roots (2.5 mM Gln, 30 min) was extracted using a phenol extraction protocol. RNA samples from two biological repeats were sent to the Affymetrix Gene Expression Service Lab at Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/affy/) for target preparation, and hybridization to the GeneChip Rice Genome Array.
2015-06-30 | E-GEOD-56770 | biostudies-arrayexpress
Project description:In our previous work, we found that the root exudates of sgn3 myb36 promoted the colonization of CHA0 on roots. Through LC-MS, we identified a large amount of glutamine (Gln) in the root exudates of sgn3 myb36. Therefore, we aim to use RNA-seq to uncover whether the root exudates of sgn3 myb36 and Gln have the same regulatory effects on CHA0. By conducting differential analysis with the CK (CHA0 treated with wild-type root exudates), we hope to identify the specific regulatory mechanisms of sgn3 myb36 and Gln on CHA0.
2024-11-06 | GSE280681 | GEO
Project description:Glutamine (Gln) metabolism has been reported to play an essential role in cancer. However, a comprehensive analysis of its role in lung adenocarcinoma is still unavailable. This study established a novel system of quantification of Gln metabolism to predict the prognosis and immunotherapy efficacy in lung cancer. Further, the Gln metabolism in tumor microenvironment (TME) was characterized and the Gln metabolism-related genes were identified for targeted therapy. We comprehensively evaluated the patterns of Gln metabolism in 513 patients diagnosed with lung adenocarcinoma (LUAD) based on 73 Gln metabolism-related genes. Based on differentially expressed genes (DEGs), a risk model was constructed using Cox regression and Lasso regression analysis. The prognostic efficacy of the model was validated using an individual LUAD cohort form Shandong Provincial Hospital, an integrated LUAD cohort from GEO and pan-cancer cohorts from TCGA databases. Five independent immunotherapy cohorts were used to validate the model performance in predicting immunotherapy efficacy. Next, a series of single-cell sequencing analyses were used to characterize Gln metabolism in TME. Finally, single-cell sequencing analysis, transcriptome sequencing, and a series of in vitro experiments were used to explore the role of EPHB2 in LUAD. Patients with LUAD were eventually divided into low- and high-risk groups. Patients in low-risk group were characterized by low levels of Gln metabolism, survival advantage, “hot” immune phenotype and benefit from immunotherapy. Compared with other cells, tumor cells in TME exhibited the most active Gln metabolism. Among immune cells, tumor-infiltrating T cells exhibited the most active levels of Gln metabolism, especially CD8 T cell exhaustion and Treg suppression. EPHB2, a key gene in the model, was shown to promote LUAD cell proliferation, invasion and migration, and regulated the Gln metabolic pathway. Finally, we found that EPHB2 was highly expressed in macrophages, especially M2 macrophages. It may be involved in the M2 polarization of macrophages and mediate the negative regulation of M2 macrophages in NK cells. This study revealed that the Gln metabolism-based model played a significant role in predicting prognosis and immunotherapy efficacy in lung cancer. We further characterized the Gln metabolism of TME and investigated the Gln metabolism-related gene EPHB2 to provide a theoretical framework for anti-tumor strategy targeting Gln metabolism.
2022-07-31 | GSE209973 | GEO
Project description:Objective: This study aimed to explore the mechanisms of early-onset T2DM by analyzing proteomic changes at different stages of glucose metabolism. Methods: A total of 40 individuals undergoing routine physical health examinations between December 2016 and April 2017 were enrolled. Subjects were divided into four groups based on fasting blood glucose (FPG) levels: 10 cases with FPG <5.6 mmol/L (group A); 10 cases with FPG ≥5.6 mmol/L and <6.1 mmol/L (group B); 10 cases with FPG ≥6.1 mmol/L and <7.0 mmol/L (group C); and 10 cases with FPG ≥7.0 mmol/L (group D). Results of differential proteomic analysis performed by label-free quantification were compared with metabolites determined by metabolomics. Results: A total of 277 differentially expressed proteins were screened and were identified as mainly secreted proteins. Comparing group A with group B, 32 proteins were up-regulated (fold change >1.2; p <0.05) and 18 proteins were down-regulated (fold change <-1.2; p <0.05). Comparing group B with group C, 3 pro
2022-10-19 | PXD035367 |
Project description:Expression of PIK3CA WT and mutant colon cancer cells grown with (+ Gln)or without glutamine (-Gln)
| PRJNA659806 | ENA
Project description:We determined if up- and/or down-regulated genes in pancreatic tumor cells cultured under low-glutamine conditions were accompanied by alterations in genome-wide chromatin accessibility and then performed ATAC-seq of KPC1199 cells treated with low glutamine concentrations versus normal-media-treated controls. The ATAC-seq was performed according to the TruePrep Tagment Enzyme for ATACseq kit (TD501, Vazyme). DNA libraries were constructed following the manufacturer’s instructions of the Trueprep index kit v2 (TD202, Vazyme) and thereafter sequenced to an average of 20 million reads per sample.
2024-04-30 | GSE229051 | GEO