Transcriptomic Analysis of CAD Cell Differentiation
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE291553 | GEO | 2025/03/12
REPOSITORIES: GEO
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Project description:p53, a critical tumor suppressor, regulates the cell cycle in response to DNA damage and metabolic changes. While p53 stability and activity are predominantly governed by post-translational modifications, the role of deamidation in modulating p53 function remains unclear. This study demonstrates that 6-diazo-5-oxo-L-norleucine (DON) inhibits CAD, a glutamine amidotransferase, to block p53 deamidation, thereby activating the p53 signaling pathway and suppressing tumor cell proliferation. Metabolomic analyses confirmed that DON inhibits CAD-mediated pyrimidine biosynthesis, but this metabolic disruption is not the primary driver of p53 activation. CAD deamidates p53 at N235 and N239, impairing its transcriptional activity and promoting tumor growth. DON restores p53 function by inhibiting CAD’s deamidase activity. Clinical data revealed elevated CAD expression in tumors with wild-type TP53, correlating with poor patient survival. Our findings uncover a novel mechanism by which CAD suppresses p53 activity via deamidation and propose that DON treatment may benefit cancer patients with wild-type TP53 and high CAD expression.
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Project description:Purpose: We applied the next-generation sequencing to explore the differential gene expression in CAD cells differentiated with dexamethasone (Dex), compared to the undifferentiated cells using Illumna -based RNA-sequencing. Methods: Total RNAs were extracted from undifferentiated CAD cells and Dex-differentiated cells (5 days). Three independent samples were collected from both experimental groups. Samples then underwent to the sequencing step performed on NextSeq with a 75 base-pair end read length. Quality filtered reads were mapped to the mouse reference genome (GRCm38.p6). Feature Counts software was implemented to obtain raw counts for all mouse genes. The gene counts were used for differential expression analysis with the DESeq2 package to identify differentially expressed genes (DEGs) in the Dex-differentiated CAD cells, as compared to the undifferentiated CAD cells. Results: The sequence reads (expression level) per sample was obtained in a range of 9.8-11.2 million. The high quality of sequence reads was mapped to the mouse reference transcriptome (GRCm38.p6). The gene counts were used for differential expression analysis. The sample-to-sample distance demonstrated that the clustering of the undifferentiated groups was completely separated from the clustering of Dex-differentiated groups. A PCA plot showed that there was a huge variation (PC 1 =99%) between the Dex-differentiated group and the undifferentiated group but less variation was observed within the same group (PC2 = 0%). These statistic profiles indicate that the transcriptomic profile between Dex-differentiated CAD cells and undifferentiated CAD cells had the different pattern. A total of 1,183 differentially expressed genes (DEGs) were identified in the Dex-differentiated CAD cells compared to the undifferentiated CAD cells (false discovery rate < 0.01 and |log2 [fold change] | > 2). Of these, 803 and 380 genes were significantly upregulated and downregulated in the Dex-differentiated group, respectively. Conclusion: Dexamethasone causes extensive changes in gene expression of CAD cells.
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Project description:affy_rnai_cadpoplar - affy_rnai_cadpoplars - This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl Alcohol Dehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesis pathway. Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expected phenotype (red xylem, reduced CAD activity).Biological question (15 lines max):This experiment aims to characterize global gene expression in young xylem of transgenic RNAi-CAD poplars in comparison to WT poplars. Cinnamyl AlcoholDehydrogenase (CAD) is the final enzyme involved in the monolignol biosynthesispathway.Transgenic poplars were produced using RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003) and exhibited the expectedphenotype (red xylem, reduced CAD activity). -RNAi-CAD transgenic poplars were produced using hairpin RNAi strategy (pHellsgate 8 vector, Helliwell and Waterhouse, 2003). For this transcriptome anaylsis, 2 independent transgenic lines (named pHG8-CAD2 and pHG8-CAD19) from the same transformation procedure were used as biological repeats. Four-month-old poplar plants were inclined at 30° in the greenhouse and sampled after 26 days. Young differentiating xylem originating from the lower side of stems - opposite wood - (ODX) was sampled on each individual tree by scrapping slightly the debarked stem with a scalpel. Samples were immediately flash frozen in liquid nitrogen, ground with mortar and pestle, and total RNAs were extracted from fine ground powder using the QIAGEN miRNeasy kit according to the manufacturer. One Affymetrix slide corresponds to a pool of RNA samples from 2-4 individual trees (WT, RNAi-CAD transgenic lines 2 and 19). Total number of slides = 2 genotypes (WT/RNAi line) x 1 tissue x 2 biological replicates = 4 slides were done.
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Project description:Transcriptomic Analysis of CAD Cell Differentiation
| PRJNA1234137 | ENA