Comprehensive Analysis of tsRNA Expression in Endometriosis using PANDORA-seq technology
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE283910 | GEO | 2025/07/16
REPOSITORIES: GEO
Similar Datasets
Project description:Comprehensive Analysis of tsRNA Expression in Endometriosis using PANDORA-seq technology
| PRJNA1196187 | ENA
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
Project description:Endometriosis is a benign gynecological disease characterized by the presence of endometrial-like cells outside the uterus. The prevalence of this disease reaches 10-15% in women of reproductive age which accounts for approximately 200 mln of women worldwide. The existing therapeutic approaches include medications and surgical options, but the risk of post-treatment recurrence of endometriosis remains high. There are currently no effective biomarkers of endometriosis in clinical practice and laparoscopy remains the gold standard for its diagnosis. However, laparoscopy is highly invasive procedure that frequently leads to complications and cannot be used as a routine screening test. In this study we profiled by RNA sequencing 52 endometrial pathological samples and 12 corresponding normal human tissues. We performed two-step differential gene expression analysis of endometrial samples and lesions of patients with endometriosis in comparison with normal reproductive tissues. Based on this analysis we generated a characteristic signature of five genes downregulated in endometriosis with respect to healthy endometrium. The 5-gene expression signature identified had significant predictive power (AUC>0.85) thus suggesting that the marker gene set identified can be used for a low invasive molecular diagnostic of endometriosis. Our data also suggest that the statistical method of five-fold cross validation of differential gene expression analysis procedure can be used for the ability to generate robust gene signatures using real-world clinical data.
2019-10-01 | GSE135485 | GEO
Project description:Objective Lung cancer has the highest incidence and mortality rates globally, with the majority of cases classified as non-small cell lung cancer (NSCLC). Due to the absence of specific tumor biomarkers, most lung cancer cases are diagnosed at an advanced stage. Therefore, the identification of novel molecular biomarkers with high sensitivity and specificity for early diagnosis is deemed crucial for enhancing the treatment of NSCLC. Transfer RNA-derived small RNA (tsRNA) is closely associated with malignant tumors and holds promise as a potential biomarker for tumor diagnosis. This study aimed to investigate whether serum tsRNA could serve as a biomarker for NSCLC. Methods Differentially expressed tsRNAs were identified through high-throughput sequencing of serum samples obtained from patients with NSCLC and healthy individuals. Additional serum samples were collected for validation using Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR). The diagnostic performance of these tsRNAs was assessed through Receiver Operating Characteristic (ROC) Curve Analysis. Furthermore, preliminary functional exploration was undertaken through cell experiments. Results tsRNA-49-73-Glu-CTC is highly expressed in the serum of patients with NSCLC and demonstrates superior diagnostic value compared to commonly used tumor markers in clinical practice, such as Carcinoembryonic Antigen (CEA), Neuron-Specific Enolase (NSE), and Cytokeratin 19 Fragment (CYFRA). A combined diagnostic approach enhances the accuracy of NSCLC detection. Additionally, tsRNA-49-73-Glu-CTC is highly expressed in A549 cells, and transfection with a tsRNA-49-73-Glu-CTC inhibitor significantly reduces both proliferation and migration capabilities. Conclusions tsRNA-49-73-Glu-CTC has the potential to serve as a novel molecular diagnostic biomarker for NSCLC and plays a significant role in the biological processes associated with NSCLC proliferation and migration.
2025-02-18 | GSE278659 | GEO
Project description:Age is an independent risk factor for atrial fibrillation (AF), and curcumin can delay aging related disease through reducing oxidative stress and inflammation. However, its target in aging-related AF remains unclear. Transfer RNA-derived small RNA (tsRNA) is a novel short non-coding RNA (sncRNA), and exerts a potential regulatory function in aging. This study was to explore the therapeutic targets of curcumin in atrium of aged mice by PANDORA-seq. Aged mice (18 month) were treated with curcumin (100mg/kg). Rapid transjugular atrial pacing was performed to observe AF inducibility. SA-β-gal staining, ROS detection and qRT-PCR were used to assess the degree of aging and oxidative stress/inflammation levels. PANDORA-seq was performed to reveal the differentially expressed sncRNAs in the atrium of mice. The results showed that curcumin reduced the susceptibility AF of aged mice by improving aging-related atrial fibrosis. Compared to young mice (5 month) group, aged mice yielded 473 significantly altered tsRNA sequences, while 947 tsRNA sequences were significantly altered after treated with curcumin. Enrichment analysis revealed that the target genes were mainly related to DNA damage and protein modification. Compared with the 5mo group, the expression levels of mature-mt_tRNA-Val-TAC_CCA_end, mature-mt_tRNA-Glu-TTC_CCA_end, and mature-tRNA-Asp-GTC_CCA_end were up-regulated in the 18mo group, while the expression of mature-mt_tRNA-Thr-TGT_5_end was down-regulated. This trend was reversed in the 18mo+curcumin group. Increased cellular ROS levels, inflammation expression and senescence in aged mice atrium were improved by the down-regulation of mature-mt_tRNA-Val-TAC_CCA_end. In conclusion, our findings identified mature-mt_tRNA-Val-TAC_CCA_end participated in the mechanism of aging-related atrial fibrosis, providing new intervention target of aging-related AF.
2024-05-30 | GSE217761 | GEO
Project description:Symbion pandora Transcriptome or Gene expression
| PRJNA308778 | ENA
Project description:Endometriosis is a chronic, estrogen-dependent gynecological condition that affects approximately 10% of women of reproductive age. The most widely accepted theory of the etiology of endometriosis includes the process of retrograde menstruation, where menstrual effluent travels up the Fallopian tubes, accesses the peritoneal cavity, and in some people is able to establish endometriotic lesions. Recent reports suggest the uterus is not devoid of bacteria, as was once believed. Thus, the refluxed menstrual effluent may also carry bacteria along with it, and this bacteria has been suggested to contribute to inflammation, and establishment and growth of endometriotic lesions. Here, we sought to compare and contrast the uterine bacteria (endometrial microbiota) in women with surgically confirmed presence or absence of endometriosis using next-generation 16S rRNA gene sequencing. We obtained an average of more than 9000 sequence reads per endometrial biopsy, and found that the endometrial microbiota of women with endometriosis was more diverse (greater Shannon Diversity Index and greater proportion of ‘Other’ taxa) than that of symptomatic controls (women with pelvic pain, but with surgically confirmed absence of endometriosis; diagnosed with other benign gynecological conditions at surgery). The difference in endometrial microbiotas was supported in unsupervised cluster analyses where some clustering of endometrial microbiota by disease status (endometriosis vs. controls) was observed. The bacterial taxa enriched in the endometrial microbiota of women with endometriosis belonged to the Actinobacteria phylum, Oxalobacteraceae and Streptococcaceae families, and Tepidimonas genus, while those enriched in the symptomatic controls (without endometriosis) belonged to the Burkholderiaceae family, and Ralstonia genus. Taken together, our findings suggest the endometrial microbiota is perturbed in people with endometriosis.
2021-04-16 | GSE172172 | GEO
Project description:Endometriosis is a debilitating gynecological disorder affecting approximately 10% of the female population. Despite its prevalence, robust methods to classify and treat endometriosis remain elusive. Changes throughout the menstrual cycle in tissue size, architecture, cellular composition, and individual cell phenotypes make it extraordinarily challenging to identify markers or cell types associated with uterine pathologies since disease-state alterations in gene and protein expression are convoluted with cycle phase variations. Here, we developed an integrated workflow to generate both proteomic and single-cell RNA-sequencing (scRNA-seq) data sets using tissues and cells isolated from the uteri of control and endometriotic donors. Using a linear mixed effect model (LMM), we identified proteins associated with cycle stage and disease, revealing a set of genes that drive separation across these two biological variables. Further, we analyzed our scRNA-seq data to identify cell types expressing cycle and disease- associated genes identified in our proteomic data. A module scoring approach was used to identify cell types driving the enrichment of certain biological pathways, revealing several pathways of interest across different cell subpopulations. Finally, we identified ligand-receptor pairs including Axl/Tyro3 – Gas6, that may modulate interactions between endometrial macrophages and/or endometrial stromal/epithelial cells. Analysis of these signaling pathways in an independent cohort of endometrial biopsies revealed a significant decrease in Tyro3 expression in patients with endometriosis compared to controls, both transcriptionally and through histological staining. This measured decrease in Tryo3 in patients with disease could serve as a novel diagnostic biomarker or treatment avenue for patients with endometriosis. Taken together, this integrated approach provides a framework for integrating LMMs, proteomic and RNA-seq data to deconvolve the complexities of complex uterine diseases and identify novel genes and pathways underlying endometriosis.
2023-09-05 | PXD045115 | Pride