LncRNA and mRNA expression profiles associated with response to Tripterygium wilfordii Hook F in the treatment of rheumatoid arthritis
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE106893 | GEO | 2017/11/15
SECONDARY ACCESSION(S): PRJNA418333
REPOSITORIES: GEO
Similar Datasets
Project description:miRNA expression profile in peripheral blood mononuclear cells obtained from a discovery cohort The discovery cohort includes12 RA patients (6 responders and 6 non-responders) treated with TwHF was detected by Affymetrix miRNA 4.0 arrays.
2017-11-15 | GSE106894 | GEO
Project description:Objective: Glucocorticoids (GC) have been a cornerstone of Rheumatoid arthritis (RA)-therapy for the last decades. However, about a third of RA-patients do not respond adequately. As monocytes and T-cells play an important role in RA-pathogenesis, the differential gene expression of these cells before pulse therapy with methylprednisolone was evaluated in order to find predictors for clinical response to GC. Methods: CD14-positive and CD4-positive cells were isolated by MACS sorting from five GC-Responders meeting the European League against Rheumatism (EULAR) response criteria and five Non-Responders. The clinical response was measured by disease activity score (DAS28) at the end of pulse therapy (3x 1000mg Methylprednisolone) at day 5. Cellular RNA was hybridized to Agilent 4x44K microarray chips and differentially expressed genes were calculated by MAANOVA. False discovery rate (FDR) was used as multiple testing correction. Selected genes were verified by quantitative real-time PCR (qPCR). Results: Eight genes were differentially regulated in CD14-cells and 4 genes in CD4-T-cells of GC-Responders compared to Non-Responders. Up-regulation of ERAP2 in monocytes and CD4-cells and LST1 and FAM26F in CD4-Tcells of GC-Responders was verified by qPCR and correlated with DAS28 at day 5 and (for LST1 and FAM26F) with smoking. Conclusion: As ERAP2 and LST1 are implicated in autoimmune disease, their increased expression in GC-Responders before GC-therapy may constitute not only a new tool for prediction of the clinical response to GC in RA, but also warrants further investigation to elucidate their role in the inflammatory process of RA.
2017-11-11 | GSE48823 | GEO
Project description:Comparative gene expression profiling of mononuclear cells from synovial fluid samples of rheumatoid arthritis (RA) and spondyloarthropathy (SpA) cases was performed. A total of 72 transcripts were found to be differentially expressed in RA compared to SpA, with p-value threshold of 0.05 and using the Benjamini-Hochberg False Discovery rate multiple comparison corrections. From the list, 57 transcripts were found to be upregulated in RA as compared to SpA and 15 downregulated by a fold change cut-off of 1.5-fold.
2013-07-15 | GSE30023 | GEO
Project description:Despite the increasing of available drugs in RA, the overall rate of non response is 30 to 40% of treated patients. To optimize the drug prescription and better elaborate the therapeutic strategies, gene profiling in PBMCs was used to predict the responsiveness to anakinra. Thirty two patients treated by anakinra (100mg/day s.c.) and méthotrexate, were categorized as responders whenever a change of Disease Activity Score 28 > 1.2 was obtained at 3 months. Blood from treated patients was collected at baseline. In 7 responders and 7 non responders, 51 mRNAs identified by microarray were expressed as a function of the response to treatment and an unsupervised hierarchical clustering perfectly separated responders from non responders. Keywords: anakinra effect PBMC then RNA were extracted from blood samples of 7 anakinra responders, 7 anakinra non responders and 1 pool of healthy subjects used as control. Each sample was hybridized twice in different nylon membrane. The control sample was hybridized twice in each nylon membrane.
2010-06-26 | E-GEOD-11827 | biostudies-arrayexpress
Project description:Despite the increasing of available drugs in RA, the overall rate of non response is 30 to 40% of treated patients. To optimize the drug prescription and better elaborate the therapeutic strategies, gene profiling in PBMCs was used to predict the responsiveness to anakinra. Thirty two patients treated by anakinra (100mg/day s.c.) and méthotrexate, were categorized as responders whenever a change of Disease Activity Score 28 > 1.2 was obtained at 3 months. Blood from treated patients was collected at baseline. In 7 responders and 7 non responders, 51 mRNAs identified by microarray were expressed as a function of the response to treatment and an unsupervised hierarchical clustering perfectly separated responders from non responders. Keywords: anakinra effect
2008-06-19 | GSE11827 | GEO
Project description:The objective of this study was to identify specific gene expression profiles able to predict the response of rheumatoid arthritis patients treated with methotrexate /abatacept (Aba). Thirty six RA patients were received Abatacept. The drug efficacy was evaluated with the DAS28 score after 6 months of treatment according to the EULAR response criteria. Among 36 Aba RA patients, 17 were responders and 19 were classified as no-responders. A blood sample was carried out in patients just before the first injection of treatment in PaxGene tubes. Two color experiments : patient(Cy5)/Control pool (Cy3).
2017-05-17 | E-GEOD-68215 | biostudies-arrayexpress
Project description:Genome wide microRNA profiling in peripheral blood mononuclear cells from rheumatoid arthritis (RA) patients and healthy controls. The Affymetrix miRNA 4.0 chip was used to obtain RNA profiles in 28 RA patients and 18 healthy controls.
2020-03-17 | GSE124373 | GEO
Project description:The objective of this study was to identify specific gene expression profiles able to predict the response of rheumatoid arthritis patients treated with methotrexate /abatacept (Aba). Thirty six RA patients were received Abatacept. The drug efficacy was evaluated with the DAS28 score after 6 months of treatment according to the EULAR response criteria. Among 36 Aba RA patients, 17 were responders and 19 were classified as no-responders. A blood sample was carried out in patients just before the first injection of treatment in PaxGene tubes.
2017-05-17 | GSE68215 | GEO
Project description:Background: Pathogenesis of Rheumatoid arthritis (RA) is driven by monocytes and T-cells, which are heavily influenced by Glucocorticoids (GC). Although a cornerstone of RA-therapy, one third of RA-patients do not respond adequately to GC and the mechanisms of resistance have not yet been clarified. Objective: To find differences in GC-working mechanism in RA-patients responding versus GC-resistant patients by gene expression profiling. Methods: Patients were treated with 3x 1000mg Methylprednisolone. Before start (T0) and 24 hours (T24) after first treatment, CD14+ and CD4+cells were MACS-isolated At day 5, response was determined using the DAS28. Labeled cRNA from 5 GC-Responders and 5 Non-Responders was hybridized to Agilent 4x44K microarray chips. Differentially expressed genes between T0 and T24 were identified using MAANOVA, FWER (family wise error rate) correction and a >1.5 ratio cut-off. Gene Ontology was used for pathway analysis; Transcription-factors were identified via TRANSFAC. Selected genes were validated by qPCR. Results: After 24 hours, 48 genes were exclusively changed in GC-Responders’ monocytes (CD4+cells: 19), 253 exclusively in Non-Responders (CD4+cells: 104) and 104 genes in both (CD4+: 18). In both cell-types a more pronounced down-regulation of interferon related genes was seen in Non-Responders, which was validated by qPCR in CD4+cells. At T24 higher expression of ERAP2 and FAM26F was seen in GC-Responders compared to Non-Responders. Several relevant transcription-factors were identified, among which LEF1in both cell types. Conclusion: GC treatment resulted in stronger suppression of the interferon signature in Non-Responders. This might be disease-specific, but should prompt further investigation of GC-mechanism in several auto-immune diseases known for an interferon signature.
2020-01-30 | GSE53221 | GEO
Project description:Large-scale gene expression profiling of peripheral blood mononuclear cells from Rheumatoid Arthritis (RA) patients could provide a molecular description that reflects the contribution of diverse cellular responses associated with this disease. The aim of our study is to identify peripheral blood gene expression profiles for RA patients, using Illumina technology, to gain insights into RA molecular mechanisms. The Illumina Human-6v2 Expression BeadChips were used for a complete genome-wide transcript profiling of peripheral blood mononuclear cells from 18 RA patients and 15 Controls. Differential analysis per gene was performed with one-way analysis of variance (ANOVA) and P values were adjusted to control the False Discovery Rate (FDR<5%). Genes differentially expressed at significant level between patients and controls were analyzed using Gene Ontology (GO) in the PANTHER database to identify biological processes. A differentially expression of 339 Reference Sequence genes (238 down-regulated and 101 up-regulated) between the two groups was observed. We identified a remarkably elevated expression of a spectrum of genes involved in Immunity and Defense in peripheral blood mononuclear cells of RA patients compared to Controls. This result is confirmed by GO analysis, suggesting that these genes could be activated systemically in RA. No significant down-regulated ontology groups were found. Microarrays data were validated by real time PCR in a set of nine genes showing a high degree of correlation. Our study highlighted several new genes that could contribute in the identification of innovative clinical biomarkers for diagnostic procedures and therapeutic intervention. Further studies on larger scale groups of patients should be performed with the same technology to replicate these results and to allow clinical stratification. 33 samples analyzed corresponding to 18 Rheumatoid Arthritis Patients and 15 Controls
2010-05-08 | E-GEOD-15573 | biostudies-arrayexpress