High-throughput transcriptome sequencing reveals extremely high doses of ionizing radiation-response genes in Caenorhabditis elegans
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ABSTRACT:
PROVIDER: PRJNA507178 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8247842.fastq.gz | Fastqsanger.gz | |||
| SRR8247843.fastq.gz | Fastqsanger.gz | |||
| SRR8247844.fastq.gz | Fastqsanger.gz | |||
| SRR8247845.fastq.gz | Fastqsanger.gz | |||
| SRR8247846.fastq.gz | Fastqsanger.gz |
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Project description:Objectives: Exposure to ionizing radiation has been linked to cardiovascular diseases. However, the impact of moderate doses of radiation on abdominal aortic aneurysm (AAA) remains unknown. Approaches : Angiotensin II-infused Apoe-/- mice were irradiated (acute, 1 Gray) either 3 days before (Day-3) or 1 day after (Day+1) pomp implantation. Primary aortic smooth muscle cells (SMCs) isolated were irradiated (acutely 1 Gray) for mechanistic studies and functional tested in vitro. Results: Day-3 and Day+1 irradiation resulted in a significant reduction in aorta dilation (Control: 1.39+/-0.12; Day-3: 1.12+/-0.11; Day+1: 1.15+/-0.08 mm, P<0.001) and AAA incidence (Control: 81.0%; Day-3: 33.3%, Day+1: 53.3%) compared to the non_x0002_irradiated group. Day-3 and Day+1 irradiation led to an increase in collagen content in the adventitia (Thickness control: 23.64+/-2.9; Day-3: 54.39+/-15.5; Day+1 37.55+/- 10.8 mm, P=0.006). However, the underlying protective mechanisms were different between Day-3 and Day+1 groups. Irradiation before Angiotensin II (AngII) infusion mainly modulated vascular smooth muscle cells (VSMCs) phenotype with a decrease in contractile profile and enhanced proliferative and migratory activity. Irradiation after AngII infusion led to an increase in macrophage content with a local anti-inflammatory phenotype characterized by the upregulation of M2-like gene and IL-10 expression. Conclusion: Moderate doses of ionizing radiation mitigates AAA either through VSCM phenotype or inflammation modulation according to the time of irradiation.
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Project description:The aim of the present study is to analyze by microarray techniques how gene expression is modulated after exposure to low and very low doses of ionizing radiation, to evaluate if the pattern of gene expression shows dose dependence, and to search for putative regulatory mechanisms behind the observed gene-expression modifications.For this, whole blood samples from five healthy donors diluted in IMDM (1:10) were exposed at six doses between 5 and 500 mGy. Total RNA extraction from CD4+ lymphocytes was done at four different post-irradiation times (150, 300, 450 and 600 min). After mRNA amplification, aRNAs were hybridized on 4x44k DNA microarrays. The results indicated that up-regulation were twice than down-regulation. Surprisingly, the number of modulated genes doesn’t seem to change drastically with dose, even at the lowest dose of 5 mGy. Clustering analysis revealed seven gene expression clusters with different dose dependence profiles. The functional analysis showed that the genes which increased their expression with the dose were related to p53 pathway and DNA damage response. This could be observed from 25 mGy, but becomes very clear at doses equal or greater than 100 mGy. On the other hand, genes with a constant modulation of their expression in all the tested doses were related to cellular respiration, ATP metabolic process and chromatin organization. These latter molecular mechanisms seem to be triggered at very low doses (5-25 mGy). In-silico promoter analysis seems to confirm the implication of transcription factors related to the pathways mentioned above.
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Project description:This study sought novel ionizing radiation-response (IR-response) genes in Caenorhabditis elegans (C. elegans). C. elegans was divided into three groups and exposed to different high doses of IR: 0 gray (Gy), 200 Gy, and 400 Gy. Total RNA was extracted from each group and sequenced. When the transcriptomes were compared among these groups, many genes were shown to be differentially expressed, and these genes were significantly enriched in IR-related biological processes and pathways, including gene ontology (GO) terms related to cellular behaviours, cellular growth and purine metabolism and kyoto encyclopedia of genes and genomes (KEGG) pathways related to ATP binding, GTPase regulator activity, and RNA degradation. Quantitative reverse-transcription PCR (qRT-PCR) confirmed that these genes displayed differential expression across the treatments. Further gene network analysis showed a cluster of novel gene families, such as the guanylate cyclase (GCY), Sm-like protein (LSM), diacylglycerol kinase (DGK), skp1-related protein (SKR), and glutathione S-transferase (GST) gene families which were upregulated. Thus, these genes likely play important roles in IR response. Meanwhile, some important genes that are well known to be involved in key signalling pathways, such as phosphoinositide-specific phospholipase C-3 (PLC-3), phosphatidylinositol 3-kinase age-1 (AGE-1), Raf homolog serine/threonine-protein kinase (LIN-45) and protein cbp-1 (CBP-1), also showed differential expression during IR response, suggesting that IR response might perturb these key signalling pathways. Our study revealed a series of novel IR-response genes in Caenorhabditis elegans that might act as regulators of IR response and represent promising markers of IR exposure.
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Project description:The aim of the present study is to analyze by microarray techniques how gene expression is modulated after exposure to low and very low doses of ionizing radiation, to evaluate if the pattern of gene expression shows dose dependence, and to search for putative regulatory mechanisms behind the observed gene-expression modifications.For this, whole blood samples from five healthy donors diluted in IMDM (1:10) were exposed at six doses between 5 and 500 mGy. Total RNA extraction from CD4+ lymphocytes was done at four different post-irradiation times (150, 300, 450 and 600 min). After mRNA amplification, aRNAs were hybridized on 4x44k DNA microarrays. The results indicated that up-regulation were twice than down-regulation. Surprisingly, the number of modulated genes doesnM-bM-^@M-^Yt seem to change drastically with dose, even at the lowest dose of 5 mGy. Clustering analysis revealed seven gene expression clusters with different dose dependence profiles. The functional analysis showed that the genes which increased their expression with the dose were related to p53 pathway and DNA damage response. This could be observed from 25 mGy, but becomes very clear at doses equal or greater than 100 mGy. On the other hand, genes with a constant modulation of their expression in all the tested doses were related to cellular respiration, ATP metabolic process and chromatin organization. These latter molecular mechanisms seem to be triggered at very low doses (5-25 mGy). In-silico promoter analysis seems to confirm the implication of transcription factors related to the pathways mentioned above. Human whole blood samples from 5 healthy donors were diluted in IMDM medium (1:10) and exposed to 500,100,50,25,10 and 5 mGy of Cobalt 60 gamma-rays. Gene expression alterations were measured 150, 300, 450 and 600 min post exposure after negative cell sorting of lymphocytes TCD4+ cells.
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