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Expression profiles of tRNA-derived small RNAs and their potential roles in primary nasopharyngeal carcinoma

ABSTRACT: Expression profiles of tRNA-derived small RNAs and their potential roles in primary nasopharyngeal carcinoma

PROVIDER: PRJNA670406 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12857075.fastq.gz	Fastqsanger.gz
	SRR12857076.fastq.gz	Fastqsanger.gz
	SRR12857077.fastq.gz	Fastqsanger.gz
	SRR12857078.fastq.gz	Fastqsanger.gz
	SRR12857079.fastq.gz	Fastqsanger.gz

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Expression profiles of tRNA-derived small RNAs and their potential roles in primary nasopharyngeal carcinoma

Project description:Transfer-RNA-Derived Small RNA (tsRNA) is a novel class of short non-coding RNA including stress-induced tRNA fragments (tiRNA) and tRNA-derived fragments (tRF). Using RNA sequencing, we evaluated the tsRNA expression profiles in the fresh nasopharyngeal carcinoma tissue specimens (n = 4) and mucosal tissue specimens (n = 4) in patients’ primary nasopharyngeal carcinoma (P-NPC) and nasopharyngitis. Bioinformatics analyses indicated that tsRNAs were the important regulators and potential new biomarkers of P-NPC.

2022-01-11 | GSE159746 | GEO

Expression Profiles of tRNA-Derived Small RNAs and Their Potential Roles in Primary Nasopharyngeal Carcinoma.

Project description:Introduction: tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs, are divided into two categories: tRNA-related fragments (tRFs) and tRNA halves (tiRNAs). Abnormal expression of tsRNAs has been found in diverse cancers, which indicates that further understanding of the function of tsRNAs will help identify new biomarkers and potential therapeutic targets. Until now, the underlying roles of tsRNAs in primary nasopharyngeal carcinoma (NPC) are still unknown. Methods: tRF and tiRNA sequencing was performed on four pairs of NPC tissues and healthy controls. Thirty pairs of NPC samples were used for quantitative real-time polymerase chain reaction (qRT-PCR) verification, and the ROC analysis was used to evaluate the diagnostic efficiency initially. Target prediction and bioinformatics analysis of validated tRFs and tiRNAs were conducted to explore the mechanisms of tsRNAs in NPC's pathogenesis. Results: A total of 158 differentially expressed tRFs and tiRNAs were identified, of which 88 are upregulated and 70 are downregulated in NPC. Three validated tRFs in the results of qRT-PCR were consistent with the sequencing data: two upregulations (tRF-1:28-Val-CAC-2 and tRF-1:24-Ser-CGA-1-M3) and one downregulation (tRF-55:76-Arg-ACG-1-M2). The GO and KEGG pathway enrichment analysis showed that the potential target genes of validated tRFs are widely enriched in cancer pathways. The related modules may play an essential role in the pathogenesis of NPC. Conclusions: The tsRNAs may become a novel class of biological diagnostic indicators and possible targets for NPC.

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Circular RNAs in nasopharyngeal carcinoma cell lines with different metastasis potential

Project description:Increasing evidence has demonstrated a significant role for circular RNAs (circRNAs) in tumorigenesis. However, their functions in nasopharyngeal carcinoma (NPC) metastasis remain largely unknown. In this study, a model compared high and low metastatic NPC cell lines (S18 vs. S26) was constructed to determine the expression profile of circRNAs using the RNA sequencing analysis.

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Deep Sequencing of Human Nuclear and Cytoplasmic Small RNAs Reveals an Unexpectedly Complex Subcellular Distribution of miRNAs and tRNA 3' Trailers

Project description:Background: MicroRNAs (miRNAs) are 22-nt small non-coding regulatory RNAs that have generally been considered to regulate gene expression at the post-transcriptional level in the cytoplasm. However, recent studies have reported that some miRNAs localize to and function in the nucleus. Methodology/Principal Findings: To determine the number of miRNAs localized to the nucleus, we systematically investigated the subcellular distribution of small RNAs (sRNAs) by independent deep sequencing the nuclear and cytoplasmic pools of 18- to 30-nucleotide sRNAs from human cells. We identified 339 nuclear and 324 cytoplasmic known miRNAs, 300 of which overlap, suggesting that the majority of miRNAs are imported into the nucleus. With the exception of a few miRNAs evidently enriched in the nuclear pool, such as the mir-29b, the ratio of miRNA abundances in the nuclear fraction versus in the cytoplasmic fraction vary to some extent. Moreover, our results revealed that a large number of tRNA 3' trailers are exported from the nucleus and accumulate in the cytoplasm. These tRNA 3' trailers accumulate in a variety of cell types, implying that the biogenesis of tRNA 3' trailers is conserved and that they have a potential functional role in vertebrate cells. Conclusion/Significance: Our results provide the first comprehensive view of the subcellular distribution of diverse sRNAs and new insights into the roles of miRNAs and tRNA 3' trailers in the cell Discovery and characterization of small RNA species through deep sequencing of nuclear and cytoplasmic small RNA fractions from 5-8F cells, a nasopharyngeal carcinoma cell line.

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Expression profiles and their potential roles of tRNA-derived small RNAs in hippocampus of nicotine dependence rat

Project description:Expression profiles and their potential roles of tRNA-derived small RNAs in hippocampus of nicotine dependence rat

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Project description:Long non-coding RNAs (lncRNAs) play important roles in the tumorigenesis and progression of cancers. However, the clinical significance of lncRNAs and their regulatory mechanisms in nasopharyngeal carcinogenesis (NPC) are largely unknown. In this study, we used the microarray analysis to study the different expression profiles of lncRNAs and mRNAs in human nasopharyngeal carcinoma tissues. We performed genome-wide lncRNAs expression in 3 pairs of NPC and normal nasopharynx tissues and identified 384 dysregulated lncRNAs (fold change ≥2 and P <0.05).

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Lack of TRMT2A, a tRNA methyltransferase, induces the generation of tRNA-derived small RNAs due to m5U54 tRNA hypomodification [Seq]

Project description:Transfer RNA (tRNA) molecules contain a variety of post-transcriptional modifications which are crucial for tRNA stability, translation efficiency, and fidelity. Besides their canonical roles in translation, tRNAs also originate tRNA-derived small RNAs (tsRNAs), a class of small non-coding RNAs with regulatory functions ranging from translation regulation, to gene expression control and cellular stress response. Recent evidence show that tsRNAs are also modified, however the impact of tRNA epitranscriptome deregulation on tsRNAs generation is only now beginning to be uncovered. The 5-methyluridine (m5U) modification at position 54 of cytosolic tRNAs is one of the most common and conserved tRNA modifications among species. This modification is catalyzed by the tRNA methyltransferase TRMT2A, but its biological role remains largely unexplored. Here, we show that TRMT2A knockdown in human cells induces m5U54 tRNA hypomodification, resulting in angiogenin (ANG) dependent tsRNA formation. More specifically, m5U54 hypomodification is followed by ANG overexpression and tRNA cleavage near the anticodon, resulting in accumulation of 5’tRNA-derived stress-induced RNAs (5’tiRNAs), in particular 5’tiRNA-GlyGCC and 5’tiRNA-GluCTC. Additionally, transcriptomic analysis confirms that down-regulation of TRMT2A and consequently m5U54 hypomodification impacts the cellular stress response and RNA stability, which is often correlated with tsRNA generation. Accordingly, exposure to oxidative stress conditions induces TRMT2A down-regulation and tsRNA formation in mammalian cells. These results establish a link between tRNA demethylation and tsRNAs formation and unravel m5U54 as a tRNA cleavage protective mark.

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Lack of TRMT2A, a tRNA methyltransferase, induces the generation of tRNA-derived small RNAs due to m5U54 tRNA hypomodification [Array]

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N7-methylguanosine tRNA modification promotes tumorigenesis and chemoresistance through WNT/β-Catenin pathway in nasopharyngeal carcinoma

Project description:Treatment selections are very limited for patients with advanced nasopharyngeal carcinoma (NPC) experiencing disease progression. Uncovering the potential mechanism underlying NPC progression is crucial for identify novel treatments. Here we show that N7-methylguanosine (m7G) tRNA modification enzyme METTL1 and its partner WDR4 are significantly elevated in NPC and associated with poor prognosis. Loss-of-function and gain-of-function assays demonstrated that METTL1/WDR4 mediated m7G tRNA modification promotes NPC growth and metastasis in vitro and in vivo. Mechanistically, m7G tRNA modification selectively regulates the translation of transcripts with higher percentage of m7G tRNA decoded codons. Moreover, further analysis revealed that METTL1-mediated m7G tRNA modification activates WNT/β-Catenin signaling pathway to promote NPC cell epithelial-mesenchymal transition (EMT) and chemoresistance to cisplatin and docetaxel in vitro and in vivo. Our work uncovers a novel layer of mRNA translation regulation mechanism at codon recognition step mediated by tRNA modification and reveals the critical function of tRNA modification in cancer progression.

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