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Serum exosomes lncRNAs: TCONS_I2_00013502 and ENST00000363624 are new diagnostic markers for rheumatoid arthritis

ABSTRACT: Serum exosomes lncRNAs: TCONS_I2_00013502 and ENST00000363624 are new diagnostic markers for rheumatoid arthritis

PROVIDER: PRJNA1130372 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29660677_1.fastq.gz	Fastqsanger.gz
	SRR29660677_2.fastq.gz	Fastqsanger.gz
	SRR29660678_1.fastq.gz	Fastqsanger.gz
	SRR29660678_2.fastq.gz	Fastqsanger.gz
	SRR29660679_1.fastq.gz	Fastqsanger.gz

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Serum exosomes lncRNAs: TCONS_I2_00013502 and ENST00000363624 are new diagnostic markers for rheumatoid arthritis

Project description:The lack of diagnostic markers limits the window of effectiveness for rheumatoid arthritis (RA) therapies. Here, we isolated exosomes of serum samples from four distinct groups RA patients, according to disease activity and with/without medication. Then, total RNA of exosomes was extracted for whole-transcriptome sequencing. Focusing on lncRNA sequencing, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were performed. We found that the number of upregulated lncRNAs were significantly higher than that of downregulated lncRNAs in each four RA groups. And most importantly, we identified two specific lncRNAs from differentially expressed lncRNAs, TCONS_I2_00013502 (up-regulated) and ENST00000363624 (down-regulated) in RA. Receiver Operating Characteristic (ROC) curve analysis showed that the two lncRNAs were promising biomarkers for RA diagnosis. These findings highlight lncRNAs of the serum exosome are important biomarkers and provide application potential for diagnosis of RA.

2024-07-04 | GSE271161 | GEO

Identify the expression of lncRNAs in peripheral blood mononuclear cells from rheumatoid arthritis

Project description:The expression profiles of lncRNAs in peripheral blood mononuclear cells (PBMCs) from rheumatoid arthritis (RA) patients have not been well researched. Therefore, we identified the lncRNA expression profiles in PBMCs from female patients with RA and explored the possible role of the abundantly expressed lncRNAs in RA.

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Proteome Profiling Identifies Serum Biomarkers in Rheumatoid Arthritis

Project description:Rheumatoid arthritis (RA) causes serious disability and productivity loss, and there is an urgent need for appropriate biomarkers for diagnosis, treatment assessment, and prognosis evaluation. To identify serum markers of RA, we performed mass spectrometry (MS)-based proteomics, and we obtained 24 important markers in normal and RA patient samples using a random forest machine learning model and 11 protein-protein interaction (PPI) network topological analysis methods. Re-analyze markers using additional proteomics datasets, immune infiltration status, tissue specificity, subcellular localization, correlation analysis with disease activity-based diagnostic indications, diagnostic receiver-operating characteristic analysis We discovered that ORM1 in serum is significantly differentially expressed in normal and RA patient samples, which is positively correlated with disease activity, and is closely related to CD56dim natural killer cell, effector memory CD8+ T cell and natural killer cell in the pathological mechanism, which can be better utilized for diagnosis, monitoring disease progression and efficacy assessment. This study supplies a comprehensive strategy for discovering potential serum biomarkers of RA, and provides a different perspective for comprehending the pathological mechanism of RA, identifying potential therapeutic targets, and disease management.

2022-04-19 | PXD032912 | Pride

Comparison of Rheumatoid Arthritis Patient and Control Sample Serum Proteomes

Project description:Rheumatoid arthritis is an autoimmune inflammatory joint condition which primarily affects the synovium of joints, characterised by synovial inflammation as well as articular cartilage and underlying bone destruction. Within this study, the proteomes of serum obtained from rheumatoid arthritis patients, and appropriate human controls, were analysed using liquid chromatography-tandem mass spectrometry. ProteoMiner™ equalisation columns were used to deplete high abundant proteins and reduce the protein concentration dynamic range.

2022-04-04 | PXD020235 | Pride

Rheumatoid arthritis

Project description:Rheumatoid arthritis (RA) is a chronic, inflammatory joint disease of unknown etiology and pronounced inter-patient heterogeneity. To characterize RA at the molecular level and to uncover key pathomechanisms, we performed whole-genome gene expression analyses. Synovial tissues from rheumatoid arthritis patients were compared to those from osteoarthritis patients and to normal donors. Keywords: disease state analysis

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Project description:This study presented serum antigen profiling of RA. Among them, three panels of antigens were identified to classify RA, ACPA-positive and ACPA-negative RA patients as diagnostic biomarkers.

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Project description:Fibroblast-like synoviocytes (FLSs) are critical for synovial aggressiveness and joint destruction in rheumatoid arthritis (RA).The role and expression patterns of long noncoding RNAs (lncRNAs) in RA are largely unknown. We performed lncRNA and mRNA microarrays to identify differentially expressed lncRNAs and mRNAs in fibroblast-like synoviocytes from rheumatoid arthritis patients compared with fibroblast-like synoviocytes from trauma patients.

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Project description:Background:To understand the roles of serum exosomes in rheumatoid arthritis (RA), we comprehensively investigated the protein profiles of serum exosomes in patients with RA. Methods:Exosomes were isolated from serum samples obtained from 33 patients (12 with active RA [aRA], 11 with inactive RA [iRA], 10 with osteoarthritis [OA]) and 10 healthy donors (HLs). Proteins extracted from the exosomes were separated by two-dimensional differential gel electrophoresis (2D-DIGE) and identified by mass spectrometry. Results:In total, 204 protein spots were detected by 2D-DIGE. In the aRA, iRA, and OA groups, 24, 5, and 7 spots showed approximately ≥ ±1.3-fold intensity differences compared with the HL group, respectively. We were able to identify proteins in six protein spots. Among them, the protein spot identified as Toll-like receptor 3 (TLR3) showed approximately 6-fold higher intensity in the aRA group than in the other groups. Conclusions:Patients with active RA possessed considerably different protein profiles of serum exosomes from patients with iRA, patients with OA, and healthy donors. The unique protein profile of serum exosomes, such as the possession of abundant TLR3 fragments, may reflect the pathophysiology of active RA.

| S-EPMC6390805 | biostudies-other

Long noncoding RNAs expression profile in patients with rheumatoid arthritis

Project description:Long noncoding RNAs (lncRNAs) belong to a new class of noncoding RNAs. Emerging evidence has shown that lncRNAs play a crucial role in the regulation of autoimmunity. During the past few years, the modifying effects of lncRNAs in rheumatoid arthritis (RA) have drawn much attention. However, the underlying molecular mechanisms involved in RA pathogenesis remain largely unknown. Herein, we aim to investigate the expression profile of lncRNAs in patients with RA and identify promising targets for RA diagnosis and treatment.Microarray screening and real-time PCR of lncRNAs were performed in the serum from 3 RA patients and 3 healthy controls. Significantly differentially expressed lncRNAs were selectively verified in 43 RA patients and 40 healthy controls by real-time PCR. LncRNA-mRNA co-expression and gene-pathway networks were assured in the bioinformatics analysis.After microarray analysis, there were a total of 73 up-regulated and 61 down-regulated lncRNAs as well as 128 up-regulated and 37 down-regulated mRNAs in the serum of RA patients. After validated by real-time PCR, 5 of these lncRNAs were found to be significantly up-regulated in the serum of RA patients including RNA143598, RNA143596, HIX0032090, IGHCgamma1, and XLOC_002730. Significant association was observed between these lncRNAs and the disease course, erythrocyte sedimentation rate (ESR), rheumatoid factor (RF) as well as anti-cyclic citrullinated peptide (anti-CCP) antibody. Computational analysis revealed that 55 of the differentially expressed mRNAs were associated with 41 lncRNAs involved in signaling pathways of toll like receptors (TLRs), nuclear factor-kappa B (NF-κB), and cytokine, especially the IRF3/IRF7 mediated signaling transduction.

2019-12-31 | GSE94519 | GEO

RNA expression profiles in fibroblast-like synoviocytes from rheumatoid arthritis patients and trauma patients

Project description:LncRNA and mRNA microarrays were performed to identify differentially expressed lncRNAs and mRNAs in fibroblast-like synoviocytes from rheumatoid arthritis patients compared with fibroblast-like synoviocytes from trauma patients. Fibroblast-like synoviocytes were isolated from synovial tissues. LncRNA and mRNA microarrays were performed using fibroblast-like synoviocytes at passage 3.

2016-06-10 | E-GEOD-83147 | biostudies-arrayexpress

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