Transfer RNA-derived small RNAs (tsRNAs) sequencing revealed a differential expression landscape of tsRNAs between glioblastoma and low-grade glioma

Tu, Ming; Zuo, Ziyi; Chen, Cuie; Zhang, Xixi; Wang, Shi; Chen, Changwei; Sun, Yuanyuan

doi:10.1016/j.gene.2022.147114

Cited by 5 publications

(2 citation statements)

References 48 publications

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“…They propose tRF-1-32-chrM.Lys-TTT, tiRNA-1-33-Gly-GCC-1, and tiRNA-1-33-Gly-CCC-1 asso-ciated with nucleotide excision repair, Hippo signaling, and cancer-related pathways, tRF-1-31-His-GTG-1, tiRNA-1-33-Gly-GCC-2-M3, and tiRNA-1-34-Lys-CTT-1-M2 may be responsible for the higher malignant grade of GBM. 91 tRNA Leu CAA derived tRFdb-3012-a/b is linked to IDH mutation status in the glioma, 92 which is one of the important markers for LG and GBM and is associated with well survival outcome. 93 Additionally, ts-26 may regulate glioma by binding to the 3′UTR of HOXA13, which is significantly associated with poor survival outcome of glioma patients.…”

Section: Gliomamentioning

confidence: 99%

“…A recent study using sequencing analysis of tumor tissues revealed differentially expressed tsRNAs between GBM and low‐grade glioma (LG). They propose tRF‐1‐32‐chrM.Lys‐TTT, tiRNA‐1‐33‐Gly‐GCC‐1, and tiRNA‐1‐33‐Gly‐CCC‐1 associated with nucleotide excision repair, Hippo signaling, and cancer‐related pathways, tRF‐1‐31‐His‐GTG‐1, tiRNA‐1‐33‐Gly‐GCC‐2‐M3, and tiRNA‐1‐34‐Lys‐CTT‐1‐M2 may be responsible for the higher malignant grade of GBM 91 . tRNA Leu CAA derived tRFdb‐3012‐a/b is linked to IDH mutation status in the glioma, 92 which is one of the important markers for LG and GBM and is associated with well survival outcome 93 .…”

Section: Roles Of Tsrnas In the Occurrence And Development Of Central...mentioning

confidence: 99%

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Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

Yang

Sun

Zhao

et al. 2023

Clinical and Translational Dis

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Transfer RNA‐derived small RNAs (tsRNAs) are fragments that originate from mature or precursor tRNAs and are a subclass of sRNAs. With the development of high‐throughput sequencing techniques, the real feature of tsRNAs has gradually been revealed. tsRNAs are functional fragments of distinct lengths produced by the cleavage of mature or precursor tRNAs by different ribonuclease enzymes. tsRNAs exert extensive functions, including gene silencing, translational regulation, and reverse transcriptional regulation, affecting cell viability and differentiation and participating in pathological processes of various diseases, including central nervous system (CNS) diseases. Emerging sequencing evidence indicates that tsRNAs are expressed differently in various CNS diseases, preliminary suggesting that tsRNAs are involved in the occurrence and progression of neurodegenerative diseases, stroke, glioma, epilepsy, and other CNS diseases. In addition, significant differences expression of extracellular tsRNAs in circulating or cerebrospinal fluid between patients and normal individuals have demonstrated the diagnostic and prognostic value of tsRNAs as biomarkers for liquid biopsy. In this review, we provide a detailed summary of the biogenesis, function, and chemical modification of tsRNAs, focusing on the current status and prospects of research on tsRNAs in neurodegenerative diseases, stroke, glioma, epilepsy, and others.

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Section: Gliomamentioning

confidence: 99%

Section: Roles Of Tsrnas In the Occurrence And Development Of Central...mentioning

confidence: 99%

Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

Yang

Sun

Zhao

et al. 2023

Clinical and Translational Dis

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tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis

Shi,

Xu,

et al. 2023

Genome Res.

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A class of noncoding RNAs, referred to as tsRNAs, is emerging with a potential to exert a new layer in gene regulation. These RNAs are breakdown products of tRNAs, either through active processing or passive cleavage or both. Since tRNAs are part of the general machinery for translation, their expression levels and activities are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize thatDrosophilapupation, being a special developmental stage during which there is a global limitation of nutrients, represents a system in which such a link may readily reveal itself. We show that specific tsRNAs indeed exhibit a dynamic accumulation upon entering the pupal stage. We describe experiments to characterize the mode of tsRNA action and, through the use of such gained knowledge, conduct a genome-wide analysis to assess the functions of dynamically expressed tsRNAs. Our results show that the predicted target genes are highly enriched in biological processes specific to this stage of development including metamorphosis. We further show that tsRNA action is required for successful pupation, providing direct support to the hypothesis that tsRNAs accumulated during this stage are critical to the gene expression program at this stage of development.

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Dysregulated transfer RNA-derived small RNAs as potential gastric cancer biomarkers

Yuan,

Gu,

et al. 2024

Exp. Biol. Med.

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Gastric cancer (GC) is the kind of carcinoma that has the highest rates of morbidity and death worldwide. In the early stages of GC, there is currently an absence of sensitive and specific biomarkers. The newly-discovered class of non-coding RNAs (ncRNAs) known as transfer RNA-derived small RNAs (tsRNAs) is highly expressed in bodily fluids and neoplastic cells. High-throughput sequencing was initially employed to identify differentially expressed tsRNAs in early GC patients, followed by validation in patient serum, GC tissues, and cell lines by quantitative real-time polymerase chain reaction (qRT-PCR). We identified dysregulated tsRNAs (the up-regulated tsRNAs included tRF-31-PNR8YP9LON4VD, tRF-30-MIF91SS2P4FI, and tRF-30-IK9NJ4S2I7L7, whereas the down-regulated tsRNAs included tRF-38-W6RM7KYUPRENRHD2, tRF-37-LBRY73W0K5KKOV2, tRF-36-JB59V3WD8YQ84VD, tRF-25-MBQ4NKKQBR, and tRF-36-0KFMNKYUHRF867D) in GC, and we verified that the serum of patients, GC cells and tissues both consistently expressed these tsRNAs. Additionally, GC patients’ serum had considerably greater expression levels of the three up-regulated tsRNAs than did healthy controls. Receiver operating characteristic (ROC) curve analysis demonstrated that the sensitivity and specificity of the three up-regulated tsRNAs were superior to those of CEA, CA199, and CA724 in the process of diagnosing GC, particularly in its early stages. This suggests that tsRNAs have great diagnostic efficacy and potential as new “liquid biopsy” biomarkers for the diagnosis of GC. Using bioinformatics software, we predicted that dysregulation of tsRNAs may be a potential regulatory mechanism for the development of GC.

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Transfer RNA-derived small RNAs (tsRNAs) sequencing revealed a differential expression landscape of tsRNAs between glioblastoma and low-grade glioma

Cited by 5 publications

References 48 publications

Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

tRNA-derived small RNAs are embedded in the gene regulatory network instructingDrosophilametamorphosis

Dysregulated transfer RNA-derived small RNAs as potential gastric cancer biomarkers

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