Putative functional variants of lncRNA identified by RegulomeDB were associated with knee osteoarthritis susceptibility

Wang, Kejie; Chu, Minjie; Ding, Wenge; Jiang, Qing

doi:10.1186/s12891-018-2197-1

Cited by 16 publications

(16 citation statements)

References 38 publications

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“…There are only several studies uncovering the diagnostic values of lncRNAs for KOA. For instance, a study reveals that the putative functional variants of lncRNA are correlated with risk of KOA, including H19 rs2067051 T allele and MEG3 rs4378559 T allele (the former associates with lower KOA risk while the latter correlates with higher KOA risk) 19 . Another study reports that lnc‐MFI 2 ‐AS 1 level is elevated in cartilage tissue of KOA patients compared to normal cartilage tissue (obtained from undamaged areas of KOA patients) 20 .…”

Section: Discussionmentioning

confidence: 99%

Retracted: A landscape of circulating long non‐coding RNA (lncRNA) expression profile and the predictive value of candidate lncRNAs for disease risk of knee osteoarthritis

Liu

Zhang

et al. 2020

Clinical Laboratory Analysis

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Background This study aimed to investigate the plasma long non‐coding RNA (lncRNA) expression profile in knee osteoarthritis (KOA) patients and the value of candidate lncRNAs for predicting KOA risk. Methods Plasma was obtained for RNA sequencing (RNA‐seq) in eight KOA patients and eight healthy controls (Ctrls). Ten candidate lncRNAs were then selected from the differentially expressed (DE) lncRNAs according to the rank of absolute value of Log2 (fold change). Afterward, RT‐qPCR was used to examine 10 candidate lncRNAs expressions in plasma of 100 KOA patients and 100 Ctrls. Results In eight KOA patients and eight Ctrls, principal component analysis and heatmap plots disclosed that lncRNA and mRNA expression profile could distinguish KOA patients from Ctrls. Then Volcano plot identified 418 upregulated lncRNAs, 347 downregulated lncRNAs, 521 upregulated mRNAs, and 333 downregulated mRNAs in KOA patients compared to Ctrls. Next, enrichment analyses revealed that DE lncRNAs were mainly enriched in biological processes, molecular functions, and signaling pathways related to inflammation and bone formation. In 100 KOA patients and 100 Ctrls, eight candidate lncRNAs were dysregulated in KOA patients compared to Ctrls, including lncRNA ABCF2P2, lncRNA RP13‐16H11.7, lncRNA CTC‐340A15.2, lncRNA RP4‐735C1.6, lncRNA RP11‐293G6‐B.8, lncRNA RP11‐1246C19.1, lncRNA RP11‐303E16.6, and lncRNA RP5‐882C2.2. Receiver operating characteristic curve analysis revealed that these eight candidate lncRNAs presented with values for predicting KOA risk. Furthermore, multivariate logistic regression elucidated that six candidate lncRNAs could independently predict KOA risk. Conclusion We disclosed a landscape of circulating lncRNA expression profile in KOA patients, and discovered several specific lncRNAs which could assist in KOA management.

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Section: Discussionmentioning

confidence: 99%

Retracted: A landscape of circulating long non‐coding RNA (lncRNA) expression profile and the predictive value of candidate lncRNAs for disease risk of knee osteoarthritis

Liu

Zhang

et al. 2020

Clinical Laboratory Analysis

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“…All SNPs had minor allele frequencies >5% in the global population from the 1,000 Genome Projects (http://www.internationalgenome.org/). Then, we used Regulome DB (Wang, Chu, Ding, & Jiang, ; http://www.regulomedb.org/) and HaploReg V4.1 (Ward & Kellis, ; https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php) to predict SNP function. Genomic DNA was extracted from 5 ml whole‐blood samples using the Whole Blood Genomic DNA Extraction Kit (GoldMag Co. Ltd) following the manufacturer's protocol.…”

Section: Methodsmentioning

confidence: 99%

TIMP3 gene polymorphisms and relation to Ankylosing spondylitis susceptibility in Chinese Han population

Xiong

Sun

et al. 2019

Int J Immunogenetics

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Background Ankylosing spondylitis (AS) is a type of chronic progressive inflammatory disease, which often causes significant damage to the patients on the physical function, labour ability and quality of life. The study found that the enzyme system tissue inhibitor of matrix metalloproteinases (TIMPs) was important for the development of AS. The aim of this study was to investigate the association of polymorphisms of TIMP3 gene with AS in Chinese Han population. Methods To evaluate the correlation of TIMP3 polymorphisms with AS risk, Agena MassARRAY was used to determine the genotypes of 268 AS patients and 654 controls. The correlation between TIMP3 variants and AS risk was examined by unconditional logistic regression analysis. Haplotype construction and analysis in TIMP3 were also applied to detect the potential association. Results We identified that rs11547635 in the TIMP3 gene (odds ratio[OR] = 0.79, 95% confidence intervals [CI]: 0.63–0.98, p = .029) was significantly associated with a decreased risk of AS in the alleles model. Rs715572 AG genotype (OR = 1.57, 95% CI: 1.05–2.34, p = .041) was potentially associated with an increased risk of AS, and also rs715572 in the dominant model (OR = 1.61, 95% CI: 1.10–2.36, p = .013) and log‐additive model (OR = 1.41, 95% CI: 1.07–1.86, p = .016) adjusted by age and gender were significantly correlated with an increased AS risk. Conclusion These findings suggested that polymorphisms of the TIMP3 gene may be associated with susceptibility to AS.

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“…LncRNAs play important regulatory roles in oncogenic pathways [4][5][6][7][8] . The biological function of lncRNAs has been reported to be associated with knee OA progression 9 . As a member of lncRNA, maternally expressed 3 (MEG3) has been proved to participate in the development of tumors 10 .…”

Section: Introductionmentioning

confidence: 99%

MEG3 promotes proliferation and inhibits apoptosis in osteoarthritis chondrocytes by miR-361-5p/FOXO1 axis

Wang

Zhang

et al. 2019

Preprint

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Background: This study aimed to investigate the role of long non-coding RNA (lncRNA) maternally expressed 3 (MEG3) and related molecular mechanisms in osteoarthritis (OA). Methods: Patients with OA and patients undergoing thigh amputation were involved in OA group and normal group, respectively. Cartilage tissues of all patients were isolated and cultured. Based on different transfection, MEG3 cells were grouped into Blank, pcDNA3.1-NC, pcDNA3.1-MEG3, si-NC, si-MEG3, pcDNA3.1-NC + mimics NC, pcDNA3.1-MEG3 + mimics NC, pcDNA3.1-NC + miR-361-5p mimics and pcDNA3.1-MEG3 + miR-361-5p mimics group. The RT-qPCR was used to detect the expression of MEG3, miR-361-5p and FOXO1. Moreover, western blot, luciferase reporter assay, RIP, CCK-8 and flow cytometry analysis were performed to reveal the morphology, proliferation and apoptosis in cartilage cells. Finally, the histological analysis and immunostaining were performed on OA rat model. Results: The expression of MEG3 and FOXO1 in OA was significantly decreased while miR-361-5p was increased compared with the normal group. MEG3 might serve as a ceRNA of miR-361-5p in OA chondrocytes. Moreover, the western blot and CCK-8 assay showed that MEG3, targeted miR-361-5p/FOXO1, might elevate cell proliferation and impair cell apoptosis. Finally, rat model analysis showed that MEG3 suppressed the cartilage matrix degradation. Conclusion: Taken together, MEG3 can contribute to cell proliferation, inhibit cell apoptosis and extracellular matrix (ECM) degradation via miR-361-5p/FOXO1 axis in OA chondrocytes.

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Putative functional variants of lncRNA identified by RegulomeDB were associated with knee osteoarthritis susceptibility

Cited by 16 publications

References 38 publications

Retracted: A landscape of circulating long non‐coding RNA (lncRNA) expression profile and the predictive value of candidate lncRNAs for disease risk of knee osteoarthritis

Retracted: A landscape of circulating long non‐coding RNA (lncRNA) expression profile and the predictive value of candidate lncRNAs for disease risk of knee osteoarthritis

TIMP3 gene polymorphisms and relation to Ankylosing spondylitis susceptibility in Chinese Han population

MEG3 promotes proliferation and inhibits apoptosis in osteoarthritis chondrocytes by miR-361-5p/FOXO1 axis

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