scholarly journals Rheumatoid Arthritis with Deficiency Pattern in Traditional Chinese Medicine Shows Correlation with Cold and Hot Patterns in Gene Expression Profiles

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Minzhi Wang ◽  
Gao Chen ◽  
Cheng Lu ◽  
Cheng Xiao ◽  
Li Li ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Immune Response ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Gene Transcription ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Nucleotide Metabolism ◽  
Toll Like Receptor

In our precious study, the correlation between cold and hot patterns in traditional Chinese medicine (TCM) and gene expression profiles in rheumatoid arthritis (RA) has been explored. Based on TCM theory, deficiency pattern is another key pattern diagnosis among RA patients, which leads to a specific treatment principle in clinical management. Therefore, a further analysis was performed aiming at exploring the characteristic gene expression profile of deficiency pattern and its correlation with cold and hot patterns in RA patients by bioinformatics analysis approach based on gene expression profiles data detected with microarray technology. The TCM deficiency pattern-related genes network comprises 7 significantly, highly connected regions which are mainly involved in protein transcription processes, protein ubiquitination, toll-like receptor activated NF-κB regulated gene transcription and apoptosis, RNA clipping, NF-κB signal, nucleotide metabolism-related apoptosis, and immune response processes. Toll-like receptor activated NF-κB regulated gene transcription and apoptosis pathways are potential specific pathways related to TCM deficiency patterns in RA patients; TCM deficiency pattern is probably related to immune response. Network analysis can be used as a powerful tool for detecting the characteristic mechanism related to specific TCM pattern and the correlations between different patterns.

scholarly journals GEPSI: A Gene Expression Profile Similarity-Based Identification Method of Bioactive Components in Traditional Chinese Medicine Formula

2018 ◽  
Vol 2018 ◽  
pp. 1-9
Author(s):  
Baixia Zhang ◽  
Shuaibing He ◽  
Chenyang Lv ◽  
Yanling Zhang ◽  
Yun Wang
Keyword(s):  
Gene Expression ◽  
Molecular Docking ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Small Molecule ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Bioactive Components ◽  
Target Proteins ◽  
Small Molecule Drugs

The identification of bioactive components in traditional Chinese medicine (TCM) is an important part of the TCM material foundation research. Recently, molecular docking technology has been extensively used for the identification of TCM bioactive components. However, target proteins that are used in molecular docking may not be the actual TCM target. For this reason, the bioactive components would likely be omitted or incorrect. To address this problem, this study proposed the GEPSI method that identified the target proteins of TCM based on the similarity of gene expression profiles. The similarity of the gene expression profiles affected by TCM and small molecular drugs was calculated. The pharmacological action of TCM may be similar to that of small molecule drugs that have a high similarity score. Indeed, the target proteins of the small molecule drugs could be considered TCM targets. Thus, we identified the bioactive components of a TCM by molecular docking and verified the reliability of this method by a literature investigation. Using the target proteins that TCM actually affected as targets, the identification of the bioactive components was more accurate. This study provides a fast and effective method for the identification of TCM bioactive components.

scholarly journals The Classification ofSiniDecoction Pattern in Traditional Chinese Medicine by Gene Expression Profiling

2016 ◽  
Vol 2016 ◽  
pp. 1-13
Author(s):  
Hung-Tsu Cheng ◽  
Chaang-Ray Chen ◽  
Chia-Yang Li ◽  
Chao-Ying Huang ◽  
Wun-Yi Shu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Clustering Algorithm ◽  
Mononuclear Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
City Hospital ◽  
Test Results ◽  
Peripheral Blood Mononuclear

We investigated the syndromes of theSinidecoction pattern (SDP), a common ZHENG in traditional Chinese medicine (TCM). The syndromes of SDP were correlated with various severeYang deficiencyrelated symptoms. To obtain a common profile for SDP, we distributed questionnaires to 300 senior clinical TCM practitioners. According to the survey, we concluded 2 sets of symptoms for SDP: (1) pulse feels deep or faint and (2) reversal cold of the extremities. Twenty-four individuals from Taipei City Hospital, Linsen Chinese Medicine Branch, Taiwan, were recruited. We extracted the total mRNA of peripheral blood mononuclear cells from the 24 individuals for microarray experiments. Twelve individuals (including 6 SDP patients and 6 non-SDP individuals) were used as the training set to identify biomarkers for distinguishing the SDP and non-SDP groups. The remaining 12 individuals were used as the test set. The test results indicated that the gene expression profiles of the identified biomarkers could effectively distinguish the 2 groups by adopting a hierarchical clustering algorithm. Our results suggest the feasibility of using the identified biomarkers in facilitating the diagnosis of TCM ZHENGs. Furthermore, the gene expression profiles of biomarker genes could provide a molecular explanation corresponding to the ZHENG of TCM.

scholarly journals Modulation of the Immune Response by Deferasirox in Myelodysplastic Syndrome Patients

2021 ◽  
Vol 14 (1) ◽  
pp. 41
Author(s):  
Hana Votavova ◽  
Zuzana Urbanova ◽  
David Kundrat ◽  
Michaela Dostalova Merkerova ◽  
Martin Vostry ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Blood Cell ◽  
Myelodysplastic Syndrome ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Adaptive Immune Response ◽  
Gene Expression Profiles ◽  
Iron Chelator ◽  
Multiple Cancer

Deferasirox (DFX) is an oral iron chelator used to reduce iron overload (IO) caused by frequent blood cell transfusions in anemic myelodysplastic syndrome (MDS) patients. To study the molecular mechanisms by which DFX improves outcome in MDS, we analyzed the global gene expression in untreated MDS patients and those who were given DFX treatment. The gene expression profiles of bone marrow CD34+ cells were assessed by whole-genome microarrays. Initially, differentially expressed genes (DEGs) were determined between patients with normal ferritin levels and those with IO to address the effect of excessive iron on cellular pathways. These DEGs were annotated to Gene Ontology terms associated with cell cycle, apoptosis, adaptive immune response and protein folding and were enriched in cancer-related pathways. The deregulation of multiple cancer pathways in iron-overloaded patients suggests that IO is a cofactor favoring the progression of MDS. The DEGs between patients with IO and those treated with DFX were involved predominantly in biological processes related to the immune response and inflammation. These data indicate DFX modulates the immune response mainly via neutrophil-related genes. Suppression of negative regulators of blood cell differentiation essential for cell maturation and upregulation of heme metabolism observed in DFX-treated patients may contribute to the hematopoietic improvement.

Differential Gene Expression Profiles May Differentiate Responder and Nonresponder Patients with Rheumatoid Arthritis for Methotrexate (MTX) Monotherapy and MTX plus Tumor Necrosis Factor Inhibitor Combined Therapy

2012 ◽  
Vol 39 (8) ◽  
pp. 1524-1532 ◽  
Author(s):  
RENÊ DONIZETI RIBEIRO OLIVEIRA ◽  
VANESSA FONTANA ◽  
CRISTINA MORAES JUNTA ◽  
MÁRCIA MARIA CHIQUITELLI MARQUES ◽  
CLÁUDIA MACEDO ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Tumor Necrosis Factor ◽  
Differential Gene Expression ◽  
Tumor Necrosis ◽  
Expression Profiles ◽  
Combined Therapy ◽  
Gene Expression Profiles ◽  
Differential Gene ◽  
Necrosis Factor

Objective.We aimed to evaluate whether the differential gene expression profiles of patients with rheumatoid arthritis (RA) could distinguish responders from nonresponders to methotrexate (MTX) and, in the case of MTX nonresponders, responsiveness to MTX plus anti-tumor necrosis factor-α (anti-TNF) combined therapy.Methods.We evaluated 25 patients with RA taking MTX 15–20 mg/week as a monotherapy (8 responders and 17 nonresponders). All MTX nonresponders received infliximab and were reassessed after 20 weeks to evaluate their anti-TNF responsiveness using the European League Against Rheumatism response criteria. A differential gene expression analysis from peripheral blood mononuclear cells was performed in terms of hierarchical gene clustering, and an evaluation of differentially expressed genes was performed using the significance analysis of microarrays program.Results.Hierarchical gene expression clustering discriminated MTX responders from nonresponders, and MTX plus anti-TNF responders from nonresponders. The evaluation of only highly modulated genes (fold change > 1.3 or < 0.7) yielded 5 induced (4 antiapoptotic and CCL4) and 4 repressed (4 proapoptotic) genes in MTX nonresponders compared to responders. In MTX plus anti-TNF non-responders, the CCL4, CD83, and BCL2A1 genes were induced in relation to responders.Conclusion.Study of the gene expression profiles of RA peripheral blood cells permitted differentiation of responders from nonresponders to MTX and anti-TNF. Several candidate genes in MTX non-responders (CCL4, HTRA2, PRKCD, BCL2A1, CAV1, TNIP1, CASP8AP2, MXD1, and BTG2) and 3 genes in MTX plus anti-TNF nonresponders (CCL4, CD83, and BCL2A1) were identified for further study.

scholarly journals Network-Based Gene Expression Biomarkers for Cold and Heat Patterns of Rheumatoid Arthritis in Traditional Chinese Medicine

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Cheng Lu ◽  
Xuyan Niu ◽  
Cheng Xiao ◽  
Gao Chen ◽  
Qinglin Zha ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Cell Proliferation ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Protein Interactions ◽  
Acid Metabolism ◽  
Protein Protein Interactions ◽  
Significant Gene ◽  
Heat Pattern

In Traditional Chinese Medicine (TCM), patients with Rheumatoid Arthritis (RA) can be classified into two main patterns: cold-pattern and heat-pattern. This paper identified the network-based gene expression biomarkers for both cold- and heat-patterns of RA. Gene expression profilings of CD4+ T cells from cold-pattern RA patients, heat-pattern RA patients, and healthy volunteers were obtained using microarray. The differentially expressed genes and related networks were explored using DAVID, GeneSpring software, and the protein-protein interactions (PPI) method. EIF4A2, CCNT1, and IL7R, which were related to the up-regulation of cell proliferation and the Jak-STAT cascade, were significant gene biomarkers of the TCM cold pattern of RA. PRKAA1, HSPA8, and LSM6, which were related to fatty acid metabolism and the I-κB kinase/NF-κB cascade, were significant biomarkers of the TCM heat-pattern of RA. The network-based gene expression biomarkers for the TCM cold- and heat-patterns may be helpful for the further stratification of RA patients when deciding on interventions or clinical trials.

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