A Systems Biology Approach for miRNA-mRNA Expression Patterns Analysis in Rheumatoid Arthritis.

2020 ◽  
Vol 23 ◽  
Author(s):  
Fataneh Tavasolian ◽  
Ahmad Zavaran Hosseini ◽  
Sara Soudi ◽  
Mahmood Naderi ◽  
Amirhossein Sahebkar
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Vitamin D ◽  
Systems Biology ◽  
Vitamin D Receptor ◽  
Expression Patterns ◽  
Gene Expression Omnibus ◽  
Ncbi Gene Expression Omnibus ◽  
Comprehensive Knowledge ◽  
Microarray Datasets

Objective: Considering the molecular complexity and heterogeneity of rheumatoid arthritis (RA), the identification of novel molecular contributors involved in RA initiation and progression using systems biology approaches will open up potential therapeutic strategies. The bioinformatics method allows the detection of associated miRNA-mRNA as both therapeutic and prognostic targets for RA. Method: This research used a system biology approach based on a systematic re-analysis of the RA-related microarray datasets in the NCBI Gene Expression Omnibus (GEO) database to find out deregulated miRNAs. We then studied the deregulated miRNA-mRNA using Enrichr and MolecularSignatures Database (MSigDB) to identify novel RA-related markers followed by an overview of miRNA-mRNA interaction networks and RA-related pathways. Results: This research mainly focused on mRNA and miRNA interactions in all tissues and blood/serum associated with RA to obtain a comprehensive knowledge on RA. Recent systems biology approach analyzed seven independent studies and presented important RA-related deregulated miRNAs (miR-145-5p, miR-146a-5p, miR-155-5p, miR-15a-5p, miR-29c-3p, miR103a-3p, miR-125a-5p, miR-125b-5p, miR-218); upregulation of miR-125b is shown in the study (GSE71600). While the findings of the Enrichr showed cytokine and vitamin D receptor pathways and inflammatory pathways. Further analysis revealed a negative correlation between the vitamin D receptor (VDR) and miR-125b in RA-associated gene expression. Conclusion: Since vitamin D is capable of regulating the immune homeostasis and decreasing the autoimmune process through its receptor (VDR), it is regarded as a potential target for RA. According to the results obtained, a comparative correlation between negative expression of the vitamin D receptor (VDR) and miR-125b was suggested in RA. The increasing miR-125b expression would reduce the VitD uptake through its receptor.

scholarly journals Immunological analysis of vitamin D receptor gene expression in Egyptian patients with rheumatoid arthritis: relation to disease activity and functional disability

2020 ◽  
Vol 47 (1) ◽  
Author(s):  
Nevine Mohannad ◽  
Eman Saad Nassar ◽  
Mai Moaaz ◽  
Rehab Elnemr ◽  
Eman Anwar Sultan
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Vitamin D ◽  
Disease Activity ◽  
Vitamin D Receptor ◽  
Functional Disability ◽  
Receptor Gene ◽  
Roc Curve Analysis ◽  
Vdr Gene ◽  
Egyptian Patients

Abstract Background Vitamin D (vit D) deficiency has recently been associated with risk of development of rheumatoid arthritis (RA). The aim of this research was to assess vitamin D receptor (VDR) gene expression in Egyptian patients with RA and its relation with the inflammatory state, disease activity, and functional disability. Results RA patients had significantly lower vit D level and VDR gene expression compared to controls (mean ± 17.0 ± 6.65, 20.73 ± 8.42 ng/ml, p < 0.05 and 3.29 ± 5.47, 14.22 ± 12.60, p < 0.001 respectively). Receiver operating characteristic (ROC) curve analysis for VDR gene expression in RA patients revealed (area under the curve 0.826, cutoff value for low VDR expression 1.05 ng/ml). Patients with low VDR expression had significantly higher ESR, CRP, double positive RF+ anti-CCP+, DAS28, and MHAQ (p < 0.001, p = 0.001, p < 0.05, p < 0.001, p < 0.001) respectively. Conclusion Vitamin D and VDR expression are significantly lower in RA patients than controls. Patients with low VDR gene expression had significantly higher disease activity and disability. This may suggest that apart from low vit D levels, low VDR expression is associated with inflammatory process and it has a potential role in RA pathogenesis and prognosis. Further multicenter studies are needed to confirm these findings.

Association of vitamin D receptor genotypes with early onset rheumatoid arthritis

2001 ◽  
Vol 28 (1) ◽  
pp. 89-93 ◽  
Author(s):  
J. R. Garcia-Lozano ◽  
M. F. Gonzalez-Escribano ◽  
A. Valenzuela ◽  
A. Garcia ◽  
A. Nunez-Roldan
Keyword(s):  
Rheumatoid Arthritis ◽  
Vitamin D ◽  
Vitamin D Receptor ◽  
Early Onset

Decoding Psoriasis: Integrated Bioinformatics Approach to Understand Hub Genes and Involved Pathways

2020 ◽  
Vol 26 (29) ◽  
pp. 3619-3630
Author(s):  
Saumya Choudhary ◽  
Dibyabhaba Pradhan ◽  
Noor S. Khan ◽  
Harpreet Singh ◽  
George Thomas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Gene ◽  
Therapeutic Targets ◽  
Interaction Network ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Keratinocyte Differentiation ◽  
Hub Genes ◽  
Lesional Skin ◽  
Ncbi Gene Expression Omnibus

Background: Psoriasis is a chronic immune mediated skin disorder with global prevalence of 0.2- 11.4%. Despite rare mortality, the severity of the disease could be understood by the accompanying comorbidities, that has even led to psychological problems among several patients. The cause and the disease mechanism still remain elusive. Objective: To identify potential therapeutic targets and affecting pathways for better insight of the disease pathogenesis. Method: The gene expression profile GSE13355 and GSE14905 were retrieved from NCBI, Gene Expression Omnibus database. The GEO profiles were integrated and the DEGs of lesional and non-lesional psoriasis skin were identified using the affy package in R software. The Kyoto Encyclopaedia of Genes and Genomes pathways of the DEGs were analyzed using clusterProfiler. Cytoscape, V3.7.1 was utilized to construct protein interaction network and analyze the interactome map of candidate proteins encoded in DEGs. Functionally relevant clusters were detected through Cytohubba and MCODE. Results: A total of 1013 genes were differentially expressed in lesional skin of which 557 were upregulated and 456 were downregulated. Seven dysregulated genes were extracted in non-lesional skin. The disease gene network of these DEGs revealed 75 newly identified differentially expressed gene that might have a role in development and progression of the disease. GO analysis revealed keratinocyte differentiation and positive regulation of cytokine production to be the most enriched biological process and molecular function. Cytokines -cytokine receptor was the most enriched pathways. Among 1013 identified DEGs in lesional group, 36 DEGs were found to have altered genetic signature including IL1B and STAT3 which are also reported as hub genes. CCNB1, CCNA2, CDK1, IL1B, CXCL8, MKI 67, ESR1, UBE2C, STAT1 and STAT3 were top 10 hub gene. Conclusion: The hub genes, genomic altered DEGs and other newly identified differentially dysregulated genes would improve our understanding of psoriasis pathogenesis, moreover, the hub genes could be explored as potential therapeutic targets for psoriasis.

scholarly journals A Positive GATA Element and a Negative Vitamin D Receptor-Like Element Control Atrial Chamber-Specific Expression of a Slow Myosin Heavy-Chain Gene during Cardiac Morphogenesis

1998 ◽  
Vol 18 (10) ◽  
pp. 6023-6034 ◽  
Author(s):  
Gang Feng Wang ◽  
William Nikovits ◽  
Mark Schleinitz ◽  
Frank E. Stockdale
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Vitamin D Receptor ◽  
Heavy Chain ◽  
Inhibitory Activity ◽  
Binding Motif ◽  
Specific Expression ◽  
Ventricular Cardiomyocytes ◽  
Slow Myosin Heavy Chain ◽  
Slow Myhc

ABSTRACT We have used the slow myosin heavy chain (MyHC) 3 gene to study the molecular mechanisms that control atrial chamber-specific gene expression. Initially, slow MyHC 3 is uniformly expressed throughout the tubular heart of the quail embryo. As cardiac development proceeds, an anterior-posterior gradient of slow MyHC 3 expression develops, culminating in atrial chamber-restricted expression of this gene following chamberization. Two cis elements within the slow MyHC 3 gene promoter, a GATA-binding motif and a vitamin D receptor (VDR)-like binding motif, control chamber-specific expression. The GATA element of the slow MyHC 3 is sufficient for expression of a heterologous reporter gene in both atrial and ventricular cardiomyocytes, and expression of GATA-4, but not Nkx2-5 or myocyte enhancer factor 2C, activates reporter gene expression in fibroblasts. Equivalent levels of GATA-binding activity were found in extracts of atrial and ventricular cardiomyocytes from embryonic chamberized hearts. These observations suggest that GATA factors positively regulate slow MyHC 3 gene expression throughout the tubular heart and subsequently in the atria. In contrast, an inhibitory activity, operating through the VDR-like element, increased in ventricular cardiomyocytes during the transition of the heart from a tubular to a chambered structure. Overexpression of the VDR, acting via the VDR-like element, duplicates the inhibitory activity in ventricular but not in atrial cardiomyocytes. These data suggest that atrial chamber-specific expression of the slow MyHC 3 gene is achieved through the VDR-like inhibitory element in ventricular cardiomyocytes at the time distinct atrial and ventricular chambers form.

scholarly journals Presence of gene expression of vitamin D receptor and 24-hydroxylase in OK cells

FEBS Letters ◽  
1994 ◽  
Vol 337 (1) ◽  
pp. 48-51 ◽  
Author(s):  
Eiji Ishimura ◽  
Shigeichi Shoji ◽  
Hidenori Koyama ◽  
Masaaki Inaba ◽  
Yoshiki Nishizawa ◽  
...  
Keyword(s):  
Gene Expression ◽  
Vitamin D ◽  
Vitamin D Receptor ◽  
Ok Cells

scholarly journals Systems Approaches to Treatment Response to Imatinib in Severe Asthma: A Pilot Study

2021 ◽  
Vol 11 (4) ◽  
pp. 240
Author(s):  
Seung Han Baek ◽  
Dinah Foer ◽  
Katherine N. Cahill ◽  
Elliot Israel ◽  
Enrico Maiorino ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Trial ◽  
Systems Biology ◽  
Pilot Study ◽  
Severe Asthma ◽  
Treated Patient ◽  
Expression Patterns ◽  
Airflow Limitation ◽  
Response To Treatment ◽  
Imatinib Treatment

There is an acute need for advances in pharmacologic therapies and a better understanding of novel drug targets for severe asthma. Imatinib, a tyrosine kinase inhibitor, has been shown to improve forced expiratory volume in 1 s (FEV1) in a clinical trial of patients with severe asthma. In a pilot study, we applied systems biology approaches to epithelium gene expression from these clinical trial patients treated with imatinib to better understand lung function response with imatinib treatment. Bronchial brushings from ten imatinib-treated patient samples and 14 placebo-treated patient samples were analyzed. We used personalized perturbation profiles (PEEPs) to characterize gene expression patterns at the individual patient level. We found that strong responders—patients with greater than 20% increase in FEV1—uniquely shared multiple downregulated mitochondrial-related pathways. In comparison, weak responders (5–10% FEV1 increase), and non-responders to imatinib shared none of these pathways. The use of PEEP highlights its potential for application as a systems biology tool to develop individual-level approaches to predicting disease phenotypes and response to treatment in populations needing innovative therapies. These results support a role for mitochondrial pathways in airflow limitation in severe asthma and as potential therapeutic targets in larger clinical trials.

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