Key circular RNAs identified in male osteoporosis patients by whole transcriptome sequencing
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ABSTRACT:
PROVIDER: PRJNA667727 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12781535.fastq.gz | Fastqsanger.gz | |||
| SRR12781536.fastq.gz | Fastqsanger.gz | |||
| SRR12781537.fastq.gz | Fastqsanger.gz | |||
| SRR12781538.fastq.gz | Fastqsanger.gz | |||
| SRR12781539.fastq.gz | Fastqsanger.gz |
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Project description:Background: Osteoporosis (OP) is a systemic disease with bone loss and microstructural deterioration. Numerous noncoding RNAs have been proved to participate in various diseases, especially for circular RNAs (circRNAs). However, the expression profile and hidden mechanisms of circRNAs in male osteoporosis have not been explored yet. Methods: Here we investigated the whole transcriptome expression profile and differences of mRNAs, circRNAs and miRNAs in peripheral blood samples of patients with osteoporosis and healthy controls of male with age larger than 60 years old. Results: A total of 398 circRNAs, 51 miRNAs and 642 mRNAs were identified that were significant differentially expressed in osteoporosis compared with healthy controls. GO and KEGG enrichment analysis showed the host genes of significantly differentially expressed circRNAs were mainly enriched in regulation of cell cycle process BP, organelle part CC, protein binding MF and Toll-like receptor signaling pathway, TNF signaling pathway and Thyroid hormone signaling pathway. circRNA-miRNA-mRNA regulatory network was constructed using the differentialy expressed RNAs. Moreover, key circRNAs in osteoporosis were discovered further and validated by qPCR, such as hsa_circ_0042409. Those key cicrRNAs may play an important role in the pathogenesis of osteoporosis and could be used as potential biomarkers or targets in the diagnosis and treatment of osteoporosis.
2020-10-07 | GSE159121 | GEO
Project description:BackgroundOsteoporosis (OP) is a systemic disease with bone loss and microstructural deterioration. Numerous noncoding RNAs (ncRNAs) have been proved to participate in various diseases, especially circular RNAs (circRNAs). However, the expression profile and mechanisms underlying circRNAs in male osteoporosis have not yet been explored.MethodsThe whole transcriptome expression profile and differences in mRNAs, circRNAs, and microRNAs (miRNAs) were investigated in peripheral blood samples of patients with osteoporosis and healthy controls consisting of males ≥ 60-years-old.ResultsA total of 398 circRNAs, 51 miRNAs, and 642 mRNAs were significantly and differentially expressed in osteoporosis compared to healthy controls. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the host genes of significantly differentially expressed circRNAs were mainly enriched in the regulation of cell cycle process: biological process (BP), organelle part cellular components (CC), protein binding molecular function (MF), Toll-like receptor signaling pathway, tumor necrosis factor (TNF) signaling pathway, and thyroid hormone signaling pathway. circRNA-miRNA-mRNA regulatory network was constructed using the differentially expressed RNAs. Moreover, key circRNAs (hsa_circ_0042409) in osteoporosis were discovered and validated by qPCR.ConclusionsThe key cicrRNAs plays a major role in the pathogenesis of osteoporosis and could be used as potential biomarkers or targets in the diagnosis and treatment of osteoporosis.
| S-EPMC8164409 | biostudies-literature
Project description:Circular RNA is implicated in numerous diseases and conditions, including traumatic injury to the central nervoussystem. However, we know little regarding their role in completely transected spinal cord injury (SCI). Our studyused high-throughput sequencing to analyze circular RNA expression in rats after experimental completetransection of spinal cord. We found differential expression in 400 circular RNAs after SCI, with 249 significantlyup-regulated and 151 significantly down-regulated. We then selected five circular RNAs for qRT-PCR validation,and the results were in agreement with RNA sequencing. Additionally, we predicted the function of circular RNAin SCI through GO and KEGG analyses, as well as the construction of circRNA/microRNA interaction networks.Furthermore, we identified circular RNA chr9:1829226-1834212 and mRNA Hdac11 as key molecules after SCI.In conclusion, this study is the first to characterize circular RNA function in rats after completely transected SCI,through identifying their differential expression. Our results provide insight into the mechanism and therapeutictargets of SCI.
2020-08-28 | GSE156999 | GEO
Project description:A comprehensive analysis identified the key differentially expressed circular RNAs and methylation-related function in pheochromocytomas and paragangliomas
| PRJNA580024 | ENA
Project description:Background: Osteoporosis is one of the most common chronic diseases around the world, especially in postmenopausal women. Circular RNAs (circRNAs) are emerging as important regulators in human disease. The aim of the present study was to analyze circRNA expression profiles in osteoporosis and to explore the clinical significance. Methods: The serum samples were collected from osteoporosis patients and healthy people. The circRNA array was performed to screen for differentially expressed circRNAs. The mRNA expression levels of target genes were analyzed by quantitative real-time PCR (qRT-PCR). Results: Hsa_circ_0006859 was identified as one of the most upregulated circRNAs in the microarray analysis. Hsa_circ_0006859 in exosome was upregulated in osteoporosis patients compared with healthy controls. Hsa_circ_0006859 could differentiate osteopenia or osteoporosis patients from healthy controls with high sensitivity and specificity. Conclusion: Exosomal hsa_circ_0006859 is a potential biomarker for postmenopausal osteoporosis.
2020-11-13 | GSE161361 | GEO
Project description:Osteoporosis is caused by imbalanced bone remodelling homeostasis and is highly prevalent in post-menopausal women. The impact of osteoporosis on mesenchymal stromal cells (MSCs) is a key area of research as they are the progenitors of osteoblasts and are therefore critical to bone homeostasis. TBioinformatic analysis of transcriptional profiling data revealed specific misregulation of genes involved in the processing and trafficking of cellular components, as well as downregulation of Neo1 which has an important role in controlling cell fate choice. These data indicate that the therapeutic targeting of bone marrow MSCs to increase their numbers, to support the appropriate processing of cellular contents, or to redirect cell fate choice may provide new methods for the treatment of osteoporosis, thereby reducing fracture-associated morbidity and improving quality of life for the 200 million people living with osteoporosis globally.
2024-04-09 | GSE189524 | GEO
Project description:Aim: To investigate the differentially expressed circular RNAs (circRNAs) and their potential functions in pheochromocytomas and paragangliomas (PCC/PGLs). Materials & Methods: We analyzed the expression levels of circRNAs through RNA sequencing in tumor and adjacent normal tissues from 7 PCC/PGL patients. Real-time qPCR was conducted to verify the key candidates identified in the sequencing data. GO and KEGG Pathway analyses were performed to predict the functions of these circRNAs. The circRNA-miRNA-mRNA coding-noncoding gene co-expression (CNC) networks were mapped to show the potential binding relationship between circRNAs and their targets in PCC/PGLs. Results: A total of 367 circRNAs were shown to have differential expression between tumor and normal samples. The top 3 histone methylation-related circRNAs (hsa_circ_0000567, hsa_circ_0002897, hsa_circ_0004473) and their target miRNAs were identified and validated. The top 5 mRNAs, 88 miRNAs, and 132 circRNAs related to the pathogenesis were utilized to map the CNC network, and we observed that the interactions of these candidates with their target miRNAs regulated the procedure of histone-methylation, and further controlled the pathogenesis of PCC/PGLs. Conclusions: Our study is the first to provide the whole profile of differentially expressed circRNAs in PCC/PGLs, and our data indicates that the altered circRNAs may control the pathogenesis of PCC/PGLs by regulating the histone-methylation processes and act as biomarkers.
2019-10-29 | GSE139518 | GEO
Project description:Circular RNA expression profiling and selection of key circular RNAs in the hypothalamus of heat-acclimated rats
| PRJNA542381 | ENA
Project description:Purpose: We are using the illumina sequencing to compare the false positive and true positive circular RNA findings to confine the method to detect the true circular RNAs Methods: The testis whole transcriptome profiling was generated from 4-week mouse testis using illumina Nextseq, duplicated. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: our data suggest that circular RNAs identified based on junction sequences in the RNA-seq reads, especially those from Illumina Hiseq sequencing, mostly result from template-switching events during reverse transcription by MMLV-derived reverse transcriptases. It is critical to employ reverse transcriptases lacking terminal transferase activity (e.g., MonsterScript) to construct sequencing library or perform RT-PCR for identification and quantification of true circular RNAs. Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. The wild type mouse testis RNAs were constructed NGS library by two different enzyme, then parallel sequenced in illumina Nextseq
2016-07-05 | E-GEOD-83992 | biostudies-arrayexpress
Project description:Osteoporosis is a metabolic bone disease characterized by a decrease in bone mass and degradation of the bone microstructure, which increases bone fragility and risk of fracture. However, the molecular mechanisms of osteoporosis remain unclear. The current study attempts to elucidate the role of exosomal long noncoding RNA in the pathology of osteoporosis. Peripheral blood was collected from persons with (OP) or without (NC) osteoporosis, and the serum exosomes were extracted using ultra centrifugation process. Total RNA of exosomes was isolated, and the lncRNAs profiling was done using RNA-Seq experiments. In silico analysis resulted in identification of 393 differentially expressed (DE) lncRNAs in OP vs NC, with 296 that were up-regulated and 97 were down-regulated. Bioinformatics analysis of potential target mRNAs of lncRNAs with cis-acting mechanism showed that mRNAs co-located with DE lncRNAs were highly enriched in osteoporosis-related pathways, including regulation of insulin secretion, activation of MAPK activity, cellular response to metal ions, fucosylation and proteolysis. Together these results suggest that lncRNAs of serum exosomes could play a significant role in development of osteoporosis and such information may be helpful in developing diagnostic markers and therapeutic modules for osteoporosis.
2020-10-03 | GSE152293 | GEO