Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Non-canonical small noncoding RNAs in the Plasma extracellular vesicles as novel biomarkers in gastric cancer

ABSTRACT: Identifying robust diagnostic biomarkers for gastric cancer (GC) remains a significant challenge. Emerging studies highlight extracellular vesicle (EV)-derived RNAs in cancer biology, but the diagnostic potential of circulating EV-derived small non-coding RNAs (sncRNAs) in GC is poorly understood. Using panoramic RNA display by overcoming RNA modification aborted sequencing (PANDORA-seq), we mapped non-canonical sncRNAs—specifically ribosomal RNA-derived small RNAs (rsRNAs) and transfer RNA-derived small RNAs (tsRNAs)—in plasma EVs. We identified a three-rs/tsRNA signature that discriminates GC patients from healthy individuals with high sensitivity (80.42%) and specificity (87.43%) (143 GC vs 167 controls). For early_x0002_stage GC (stage I), sensitivity and specificity were 81.97% and 81.44%, respectively. Furthermore, the three_x0002_rs/tsRNA signature was evaluated in two independent cohorts, resulting in AUC values of 0.97 and 0.91 for distinguishing GC from healthy controls. Functional analyses revealed that these rs/tsRNAs regulate the ErbB/Hippo pathways, suggesting them in the underlying pathogenesis andtherapeutic potential. This study establishes a novel EV-derived sncRNA signature for early GC detection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE291630 | GEO | 2025/04/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

PANDORA-seq uncovers sensitive mitochondrial small RNA alterations associated with increased lysosome activity in an Alzheimer’s Disease Mouse Model

Project description:Emerging small noncoding RNAs (sncRNAs), including tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), are critical in diverse biological processes, such as neurological diseases. Traditional sncRNA-seq protocols often miss these sncRNAs due to their modifications. We have recently developed PANDORA-seq, a method enabling more comprehensive detection of modified sncRNAs by overcoming the RNA modifications. Using PANDORA-seq, we have revealed an updated sncRNA profile enriched by tsRNAs/rsRNAs in the mouse cortex and found a particularly significant downregulation of mitochondrial tsRNAs and rsRNAs in an Alzheimer's disease (AD) mouse model, compared to genomic tsRNAs and rsRNAs. Moreover, our integrated analysis of cortex gene expression and sncRNA profiles reveals that those downregulated mitochondrial sncRNAs are negatively correlated with enhanced lysosomal activity, suggesting a crucial interplay between mitochondrial RNA dynamics and lysosomal function in AD. Given the versatile tsRNA/tsRNA molecular actions in cellular regulation, our data provides insights for future mechanistic study of AD with potential therapeutic strategies.

2024-12-17 | GSE277483 | GEO

Identification of RNA helicases that mediate processing of tRNAs into distinct tRNA fragments by LC-MS/MS.

Project description:Specific environmental insults cause the limited fragmentation of transfer RNAs (tRNAs) into tRNA-derived small RNAs (tsRNAs), which have been implicated in a wide range of biological processes. tRNA fragmentation results from endonucleolytic activities targeting single-stranded tRNA regions. However, how a tRNA with a single hydrolyzed phosphodiester bond in the anticodon loop (‘nicked’ tRNA) gives rise to distinct tsRNAs remains poorly understood. By utilizing biochemical fractionation of tsRNA-containing ribonucleoprotein complexes (RNPs) coupled with LC-MS/MS, we identified several RNA helicase enzymes that represent putative tRNA/tsRNA processing enzymes. Furthermore, a combination of biochemical and computational approaches revealed that specific RNA helicases indeed bind specific tRNAs with high affinity, as well as process nicked tRNAs into individual tsRNAs. In summary, these findings reveal that tRNA-derived duplexes can be substrates of well-known RNA helicases, thereby expanding their potential for cellular function to the creation of individual tsRNAs during the cellular stress response.

2023-01-09 | PXD029869 | Pride

Clinical utility and biological function of Transfer RNA-derived small RNAs in Patients with Acute Coronary Syndrome [RNA-seq]

Project description:Acute coronary syndrome (ACS) is one of the leading causes of death worldwide. Aberrant expression of Transfer RNA-derived small RNAs (tsRNA) contributed to various human disease. However, the clincal utility and biological function of tsRNA in ACS are largely unknown. High throughput sequencing revealed a landscape of novel sncRNAs in the human PBMCs. tsRNAs represented a characteristic expression pattern in responding to acute coronary syndrome; tRF-Gly-GCC-06 and tRF-Lys-CTT-02 were significantly up-regulated in patients with unstable angina(UA) and acute myocardial infarction(AMI). Both of the two tRFs demonstrated reasonable diagnostic accuracy for ACS detection. tRF-Gly-GCC-06 and tRF-Lys-CTT-02 upregulation were independent predictors of an increased risk of ACS. Both of the two tRFs expression levels show a significantly positive correlation with Gensini score.Our study identified novel tsRNA alterations associated with ACS and provided potential clinical biomarkers and therapeutic targets.

2025-04-30 | GSE279975 | GEO

Clinical utility and biological function of Transfer RNA-derived small RNAs in Patients with Acute Coronary Syndrome [ncRNA-seq]

2025-04-30 | GSE279974 | GEO

Early cleavage of preimplantation embryos is regulated by tRNAGln-TTG-derived small RNAs present in mature spermatozoa

Project description:Sperm-derived tsRNAs could act as acquired epigenetic factors and contribute to offspring phenotypes. However, the roles of specific tsRNAs in early embryo development remain to be elucidated. Here, by using pigs as a research model, we probed the tsRNA dynamics during spermatogenesis and sperm maturation, and demonstrated the delivery of tsRNAs from semen-derived exosomes to spermatozoa. By microinjection of the antisense sequence into in vitro fertilized oocytes and subsequent single-cell RNA-sequencing of embryos, we identified a specific functional tsRNA group (Gln-TTGs) that participate in the early cleavage of porcine preimplantation embryos, probably by regulating cell cycle-associated genes. Thus, specific tsRNAs present in mature spermatozoa play significant roles during preimplantation embryo development.

2020-07-13 | PXD019054 | Pride

Transcriptome and Translatome in Drosophila S2 cells treated by tsRNA transfection, serum deprivation, ago2 knockdown and rapamycin

Project description:Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of small RNAs, yet their regulatory roles have not been well understood. Here we studied the molecular mechanisms and consequences of tsRNA-mediated regulation in Drosophila. By carrying out mRNA sequencing and ribosome profiling of S2 cells transfected with single-stranded tsRNA mimics and mocks, we show that tsRNAs recognize target mRNAs through conserved complementary sequence matching and suppress target genes by translational inhibition. Serum starvation experiments confirm tsRNAs participate in cellular starvation responses by preferential targeting the ribosomal proteins and translational initiation or elongation factors. Knock-down of AGO2 in S2 cells under normal and starved conditions reveals a dependence of the tsRNA-mediated regulation on AGO2. Our study suggests the tsRNA-mediated regulation might be crucial for the energy homeostasis and the metabolic adaptation in the cellular systems.

2018-03-02 | GSE106697 | GEO

A 5’ tRNA-Ala derived small RNA regulates anti-fungal defense in plants

Project description:Apart from their primordial role in protein synthesis, tRNAs can be cleaved to produce tRNA-derived small RNAs (tsRNAs). The biological functions of tsRNAs in plants remain largely unknown. In this study, we developed RtcB-based RNA sequencing, a method that captures and distinguishes between 2’,3’-cyclic-phosphate (cP)-terminated RNAs and 3’-OH-terminated RNAs, and profiled 5’ tsRNAs and 5’ tRNA halves in Arabidopsis thaliana. We found that Arabidopsis 5’ tsRNAs and 5’ tRNA halves predominantly contain a cP at the 3’ end and require S-like RNase 1 (RNS1) and RNS3 for their production. One of the most abundant 5’ tsRNA, 5’ tsR-Ala, likely by associating with AGO1, negatively regulates Cytochrome P450 71A13 (CYP71A13) expression and camalexin biosynthesis to repress anti-fungal defense. 5’ tsR-Ala is downregulated upon fungal infection. Our study provides a global view of 5’ tsRNAs and 5’ tRNA halves in Arabidopsis and unravels an important role of a 5’ tsRNA in regulating anti-fungal defense.

2022-02-16 | GSE183560 | GEO

Identification of tRNA-derived Small RNAs and Their Potential Roles in Myocardial Infarction

Project description:tRNA-derived small RNAs (tsRNAs), as a novel type of non-coding RNAs are significantly involved in multiple cellular processes and biological functions in many diseases. Microarray analysis was used to evaluated the tsRNA expression profiles of myocardial tissue in myocardial infarction (MI) (n = 3) and sham in mice (n = 3). Bioinformatics analysis and functional experiment indicated that tsRNAs potential biological functions involved in MI.

2025-04-30 | GSE249120 | GEO

Small RNA sequencing on affinity capture-purified tRNA-derived small RNAs (tsRNAs)

Project description:During stress conditions, particular tRNAs are cleaved by stress-induced endonucleases resulting in distinct tRNA-derived small RNAs (tsRNAs). These small RNAs have been implicated in a wide array of mostly stress-related biological processes, however how exactly they exert their functions mechanistically is still largely unknown. Since parental tRNAs carry post-transcriptional modifications, stress-induced tsRNAs are likely modified, too. In order to use endogenously modified tsRNAs, we developed a biochemical pipeline for the production and purification of specific tsRNAs using a human cell culture system. Ectopic expression of Angiogenin combined with chromatography of small RNAs resulted in the production of endogenously modified 5’ tsRNAs on a preparative scale. Small RNA sequencing on purified tsRNAs was used to determine the identity and purity of the 5’ tsRNA preparations.

2020-03-01 | GSE139124 | GEO

PANDORA-seq: expanding the small RNA repertoire by overcoming RNA modifications

Project description:Small non-coding RNAs (sncRNAs) are key molecules regulating gene expression. High-throughput RNA-seq greatly advanced sncRNA discovery; however, traditional cDNA library construction protocols generate biased sequencing results, in part due to RNA modifications that interfere with adapter ligation and reverse transcription processes, preventing the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (Panoramic RNA Display by Overcoming RNA modification Aborted Sequencing), employing a combination of enzymatic treatments to remove key RNA modifications that block adapter ligation and reverse transcription during cDNA library construction. PANDORA-Seq enables the discovery of thousands of modified sncRNAs previously undetected, mostly tRNA-derived small RNAs (tsRNAs) and rRNA-derived small RNAs (rsRNAs), which are tissue/cell-specifically detected across mouse brain, liver, spleen, sperm, mouse and human embryonic stem cells, and HeLa cells. Moreover, PANDORA-Seq reveals dynamic changes of tsRNAs and rsRNAs during reprogramming of induced pluripotent stem cells (iPSCs), pointing to future investigations on their potential regulatory functions.

2021-02-16 | GSE144666 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data