Uncovering small non-coding RNAs involved in carcinogenesis of Glioma
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA810721 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18150858_1.fastq.gz | Fastqsanger.gz | |||
| SRR18150858_2.fastq.gz | Fastqsanger.gz | |||
| SRR18150859.fastq.gz | Fastqsanger.gz |
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Project description:Glioblastoma (GBM) is a lethal brain tumor without effective treatment options. Data about proteomics in glioma is sparse and it has not yet been integrated into the routine diagnostic work-up or exploited to find potential actionable targets to prevent GBM-induced immune evasion mechanisms and recurrence. We performed proteomic analysis of diffuse glioma samples classified into six subgroups defined by DNA methylation and patient-paired primary and recurrent samples in order to i) provide an inventory of proteins commonly or individually overexpressed in each of the four HGG subgroups compared to the LGG and deduce relevant pathways for each subgroup and ii) identify specific proteins involved in tumor recurrence after surgical removal.
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Project description:Aim: Small non-coding RNAs (sncRNAs) such as microRNAs (miRNAs) have important functions in the regulation of numerous biological processes. High-throughput RNA sequencing (RNA-seq) method has advanced sncRNA discovery, but RNA modifications have been known to interfere with the cDNA library construction process, leading to the biased sequencing results. To overcome this obstacle, we previously developed an advanced PANDORA-seq method to overcome RNA modification-elicited sequence interferences. PANDORA-seq is able to detect the highly modified sncRNAs including transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs) that are otherwise undetectable by traditional RNA-seq protocol. Macrophages are the major immune cells involved in the initiation and progression of atherosclerosis. This study aims to identify novel macrophage sncRNAs associated with atherosclerosis development by using PANDORA-seq. Methods: To identify atherosclerosis-associated macrophage sncRNAs, LDLR-/- mice were fed a low-cholesterol diet (LCD; 0.02% cholesterol) or high-cholesterol diet (HCD; 0.5% cholesterol) for 9 weeks. Total RNAs were isolated from peritoneal macrophages and subjected to both traditional RNA-seq and PANDORA-seq analyses. Results: By overcoming RNA modification-elicited limitations, PANDORA-seq revealed a rsRNA- and tsRNA-enriched sncRNA landscape in the peritoneal macrophages of LDLR-/- mice which was strikingly different from that detected by traditional RNA-seq. Traditional RNA-seq still identified miRNAs as the predominant sncRNA species in macrophages. Strikingly, PANDORA-seq results demonstrated that rsRNAs and tsRNAs were the major macrophage sncRNA types and miRNAs only accounted for ~ 0.2% of total detected sncRNAs. In addition, PANDORA-seq also detected over 286 differentially expressed macrophage sncRNAs induced by HCD feeding. Intriguingly, several HCD-stimulated rsRNAs/tsRNAs promoted pro-atherogenic gene expression in macrophages in vitro, indicating potentially important roles of those “hidden” sncRNAs in atherogenesis. Conclusion: Our findings revealed a comprehensive macrophage sncRNA landscape by uncovering the highly modified rsRNAs/tsRNAs. These abundant rsRNAs/tsRNAs may have important functions in atherosclerosis and warrant future investigations.
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Project description:<p><strong>INTRODUCTION:</strong> Neuronal activity regulated by synaptic communication exerts an important role in tumorigenesis and progression in brain tumors. Genes for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) annotated with the function ‘vesicle’ about synaptic connectivity were identified and one of these proteins, synaptosomal-associated protein 25 (SNAP25), was found to have discrepant expression levels in neuropathies. However, the specific mechanism and prognostic value of SNAP25 during glioma progression remain unclear. </p><p><strong>METHODS:</strong> Using RNA sequencing data from The Cancer Genome Atlas (TCGA) database, the differential synaptosis-related genes between LGG and GBM were identified as highly correlated. Cox proportional hazards regression analysis and survival analysis indicated that the candidate gene SNAP25 could differentiate the outcome of low- and high-risk patients, and the Chinese Glioma Genome Atlas (CGGA) cohort was used for validation of the data set. RT-qPCR, western blot, and immunohistochemistry assays were performed to examine the expression level of SNAP25 in glioma cells and samples. Functional assays were performed to identify the effects of SNAP25 knockdown and overexpression on cell viability, migration, and invasion. Then, an immunofluorescence assay of the xenograft tissue was applied to evaluate the expression of the neuronal dendron formation marker-MAP2. Liquid chromatography-high re solution mass spectrometry (LC-MS)-based metabolomics approach was presented for identifying crucial metabolic disturbances in glioma cells. In situ mouse xenograft model was used to investigate the role of SNAP25 in vivo.</p><p><strong>RESULTS:</strong> SNAP25 was down expressed in glioma tissues and cell lines and low-level SNAP25 indicated an unfavorable prognosis of glioma patients. SNAP25 inhibited cell proliferation, migration, invasion and fostered glutamate metabolism of glioma cells, exerting a tumor suppressor role. SNAP25 overexpression expressed lower expression of MAP2, indicating poor neuronal plasticity and connectivity. SNAP25 could interact with glutaminase（GLS）and GLS knockdown could rescue the anti-tumor effect of SNAP25 in glioma cells. Moreover, upregulation of SNAP25 also decreased tumor volume and prolonged the overall survival (OS) of the xenograft mouse.</p><p><strong>CONCLUSION:</strong> SNAP25 inhibited carcinogenesis of glioma via sponging glutamate metabolism by regulating GLS expression, as well as inhibiting dendritic formation, which could be considered as a molecular target for glioma diagnosis and therapy.</p>
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