Network analysis and transcriptome profiling in peripheral blood mononuclear cells of patients with rheumatoid arthritis

Long, Yan; Liu, Jian; Jiang, Hui; Xin, Ling; Wan, Lei; Sun, Yue; Zhang, Pingheng; Wen, Jianting; Huang, Dan; Sun, Yanqiu; Zhang, Ying; Bao, Bingxi; Sun, Guanghan

doi:10.3892/etm.2020.9601

Cited by 6 publications

(3 citation statements)

References 33 publications

(33 reference statements)

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“…There is increasing evidence that suggests that the alteration of lncRNAs in PBMCs could be used as a biomarker for diagnosis and disease monitoring in many chronic disorders [ 18 , 19 , 20 ]. Moreover, the transcriptomic analyses in PBMCs have revealed differential expression patterns between cancerous and non-cancerous samples in several types of malignant tumors, including HCC [ 21 , 22 , 23 ].…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analyses Reveal Long Non-Coding RNA in Peripheral Blood Mononuclear Cells as a Novel Biomarker for Diagnosis and Prognosis of Hepatocellular Carcinoma

Kunadirek

Pinjaroen

Nookaew

et al. 2022

IJMS

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Novel biomarkers are highly required for the diagnosis and predicting prognosis of hepatocellular carcinoma (HCC). In this study, we investigated the profiles of long non-coding RNAs (lncRNAs) obtained from the peripheral blood mononuclear cells (PBMCs) of patients with HCC and PBMCs from a co-culture model using transcriptomic analysis. The differentially expressed lncRNAs (DElncRNAs) were then characterized and integrated as cancer-induced lncRNAs. Among them, three up-regulating DElncRNAs including MIR4435-2HG, SNHG9 and lnc-LCP2-1 and one down-regulating, lnc-POLD3-2, were identified. The functional analysis showed that these enriched lncRNAs were mainly associated with carcinogenesis and immune responses. Following further validation in PBMCs samples (100 HBV-related HCC, 100 chronic hepatitis B and 100 healthy controls), MIR4435-2HG, lnc-POLD3-2 and their combination were revealed to be sensitive biomarkers in discriminating HCC from non-HCC (AUROC = 0.78, 0.80, and 0.87, respectively), particularly among individuals with normal serum alpha-fetoprotein levels. Additionally, high circulating SNHG9 expression was shown to be an independent prognostic factor of overall survival in patients with HCC. These results indicate that determining these lncRNAs in PBMCs could serve as novel diagnostic and prognostic biomarkers for HBV-related HCC.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic Analyses Reveal Long Non-Coding RNA in Peripheral Blood Mononuclear Cells as a Novel Biomarker for Diagnosis and Prognosis of Hepatocellular Carcinoma

Kunadirek

Pinjaroen

Nookaew

et al. 2022

IJMS

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“…[ 4 , 5 , 6 ] In recent years, an increasing number of studies have found that lncRNA plays an important role in regulating autoimmunity and maintaining immune homeostasis. [ 11 ] Moreover, multiple lines of evidence link dysregulation of lncRNA to diverse human autoimmune diseases, such as SSc, [ 22 ] RA, [ 23 ] SLE, [ 24 ] and SS. [ 25 ] Previous studies have found that lncRNA is involved in the pathogenesis of SSc-ILD and RA-ILD, [ 26 , 27 ] however, the commonalities and differences amongst CTD-ILD mechanisms are poorly understood.…”

Section: Discussionmentioning

confidence: 99%

Identification and functional prediction of long non-coding RNA and mRNA related to connective tissue disease-associated interstitial lung diseases

Dai,

He,

Lei

et al. 2023

Rheumatology and Immunology Research

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Objective Recently, the role of long non-coding RNA (lncRNA) in rheumatic immune diseases has attracted widespread attention. However, knowledge of lncRNA in connective tissue disease-associated interstitial lung disease (CTD-ILD) is limited. This study explored the expression profile and possible mechanisms of lncRNA and mRNA in peripheral blood mononuclear cells (PBMCs) of CTD-ILD patients, especially systemic sclerosis (SSc)-ILD and rheumatoid arthritis (RA)-ILD. Methods LncRNA microarray analysis identified 240 diferentially expressed lncRNAs and 218 diferentially expressed mRNA in the CTD-ILD group and the connective tissue disease without associated interstitial lung disease (CTD-NILD) group. The bioinformatics analysis of diferential genes has identified several important biological processes and signal pathways, including nuclear factor kappa B (NF-kappa B) signaling pathway, interleukin 17 (IL-17) signaling pathway, B cell receptor signaling pathway. Relative expression levels of five diferentially expressed lncRNAs and one mRNA in 120 SSc and RA patients with or without ILD were detected by quantitative reverse-transcription (PCR). Results The ENST00000604692 expression level was significantly higher in the ILD than the without interstitial lung disease (NILD) group; T311354 and arginase-1 were significantly higher in SSc than RA group. Conclusion These data suggest that the specific profile of lncRNA in PBMCs of CTD-ILD patients and the potential signal pathways related to the pathogenesis of CTD-ILD, which may provide newfound insights for the diagnosis and treatment of CTD-ILD patients.

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“…Through transcriptome sequencing (RNA-seq), Long et al. found 341 differentially expressed lncRNAs in peripheral blood mononuclear cells (PBMCs) in three RA patients and normal people [ 87 ]. Zhang et al.…”

Section: Lncrnas and Circrnas As Latent Diagnostic And Prognostic Bio...mentioning

confidence: 99%

Long noncoding RNA/circular RNA regulates competitive endogenous RNA networks in rheumatoid arthritis: molecular mechanisms and traditional Chinese medicine therapeutic significances

et al. 2023

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Rheumatoid arthritis (RA) is a systemic and autoimmune disease that is mainly featured abnormal fibroblast-like synoviocyte (FLS) proliferation and inflammatory cell infiltration. Abnormal expression or function of long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) are closely related to human diseases, including RA. There has been increasing evidence showing that in the competitive endogenous RNA (ceRNA) networks, both lncRNA and circRNA are vital in the biological functions of cells. Nevertheless, the exact mechanism of ceRNA in RA remains to be investigated. Herein, we summarized the molecular potencies of lncRNA/circRNA-mediated ceRNA networks in RA, with emphasis on the phenotypic regulation of ceRNA in the progression of RA, including regulation of proliferation, invasion, inflammation and apoptosis, as well as the role of ceRNA in traditional Chinese medicine (TCM) in the treatment of RA. In addition, we also discussed the future direction and potential clinical value of ceRNA in the treatment of RA, which may provide potential reference value for clinical trials of TCM therapy for the treatment of RA. Key messages Long noncoding RNA/circular RNA can work as the competitive endogenous RNA sponge and participate in the pathogenesis of rheumatoid arthritis. Traditional Chinese medicine and its agents have shown potential roles in the prevention and treatment of rheumatoid arthritis via competitive endogenous RNA.

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Network analysis and transcriptome profiling in peripheral blood mononuclear cells of patients with rheumatoid arthritis

Cited by 6 publications

References 33 publications

Transcriptomic Analyses Reveal Long Non-Coding RNA in Peripheral Blood Mononuclear Cells as a Novel Biomarker for Diagnosis and Prognosis of Hepatocellular Carcinoma

Transcriptomic Analyses Reveal Long Non-Coding RNA in Peripheral Blood Mononuclear Cells as a Novel Biomarker for Diagnosis and Prognosis of Hepatocellular Carcinoma

Identification and functional prediction of long non-coding RNA and mRNA related to connective tissue disease-associated interstitial lung diseases

Long noncoding RNA/circular RNA regulates competitive endogenous RNA networks in rheumatoid arthritis: molecular mechanisms and traditional Chinese medicine therapeutic significances

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