scholarly journals Characterization of Rheumatoid Arthritis Risk-Associated SNPs and Identification of Novel Therapeutic Sites Using an In-Silico Approach

Biology ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 501
Author(s):  
Mehran Akhtar ◽  
Yasir Ali ◽  
Zia-ul Islam ◽  
Maria Arshad ◽  
Mamoona Rauf ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Target Genes ◽  
Interaction Network ◽  
Underlying Mechanism ◽  
Nucleotide Polymorphisms ◽  
Gene Interaction Network ◽  
Rheumatoid Arthritis Risk ◽  
Novel Therapeutic

Single-nucleotide polymorphisms (SNPs) are reported to be associated with many diseases, including autoimmune diseases. In rheumatoid arthritis (RA), about 152 SNPs are reported to account for ~15% of its heritability. These SNPs may result in the alteration of gene expression and may also affect the stability of mRNA, resulting in diseased protein. Therefore, in order to predict the underlying mechanism of these SNPs and identify novel therapeutic sites for the treatment of RA, several bioinformatics tools were used. The damaging effect of 23 non-synonymous SNPs on proteins using different tools suggested four SNPs, including rs2476601 in PTPN22, rs5029941 and rs2230926 in TNFAIP3, and rs34536443 in TYK2, to be the most damaging. In total, 42 of 76 RA-associated intronic SNPs were predicted to create or abolish potential splice sites. Moreover, the analysis of 11 RA-associated UTR SNPs indicated that only one SNP, rs1128334, located in 3′UTR of ETS1, caused functional pattern changes in BRD-BOX. For the identification of novel therapeutics sites to treat RA, extensive gene–gene interaction network interactive pathways were established, with the identification of 13 potential target sites for the development of RA drugs, including three novel target genes. The anticipated effect of these findings on RA pathogenesis may be further validated in both in vivo and in vitro studies.

scholarly journals PTEN Methylation Promotes Inflammation and Activation of Fibroblast-Like Synoviocytes in Rheumatoid Arthritis

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao-Feng Li ◽  
Sha Wu ◽  
Qi Yan ◽  
Yuan-Yuan Wu ◽  
He Chen ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Articular Cartilage ◽  
Dna Methyltransferase ◽  
Underlying Mechanism ◽  
Cartilage Destruction ◽  
Specific Pcr ◽  
Methylation Inhibitor ◽  
Fibroblast Like Synoviocytes

Rheumatoid arthritis (RA) is characterized by a tumor-like expansion of the synovium and subsequent destruction of adjacent articular cartilage and bone. In our previous work we showed that phosphatase and tension homolog deleted on chromosome 10 (PTEN) contributes to the activation of fibroblast-like synoviocytes (FLS) in adjuvant-induced arthritis (AIA), but the underlying mechanism is not unknown. In this study, we show that PTEN is downregulated while DNA methyltransferase (DNMT)1 is upregulated in FLS from RA patients and a rat model of AIA. DNA methylation of PTEN was increased by administration of tumor necrosis factor (TNF)-α in FLS of RA patients, as determined by chromatin immunoprecipitation and methylation-specific PCR. Treatment with the methylation inhibitor 5-azacytidine suppressed cytokine and chemokine release and FLS activation in vitro and alleviated paw swelling in vivo. PTEN overexpression reduced inflammation and activation of FLS via protein kinase B (AKT) signaling in RA, and intra-articular injection of PTEN-expressing adenovirus into the knee of AIA rats markedly reduced inflammation and paw swelling. Thus, PTEN methylation promotes the inflammation and activation of FLS in the pathogenesis of RA. These findings provide insight into the molecular basis of articular cartilage destruction in RA, and indicate that therapeutic strategies that prevent PTEN methylation may an effective treatment.

scholarly journals Drug Repurposing Using Modularity Clustering in Drug-Drug Similarity Networks Based on Drug–Gene Interactions

Pharmaceutics ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2117
Author(s):  
Vlad Groza ◽  
Mihai Udrescu ◽  
Alexandru Bozdog ◽  
Lucreţia Udrescu
Keyword(s):  
Interaction Network ◽  
Drug Repurposing ◽  
Gene Interaction ◽  
New Drugs ◽  
Interaction Data ◽  
Gene Interaction Network ◽  
Drug Databases ◽  
Drug Similarity

Drug repurposing is a valuable alternative to traditional drug design based on the assumption that medicines have multiple functions. Computer-based techniques use ever-growing drug databases to uncover new drug repurposing hints, which require further validation with in vitro and in vivo experiments. Indeed, such a scientific undertaking can be particularly effective in the case of rare diseases (resources for developing new drugs are scarce) and new diseases such as COVID-19 (designing new drugs require too much time). This paper introduces a new, completely automated computational drug repurposing pipeline based on drug–gene interaction data. We obtained drug–gene interaction data from an earlier version of DrugBank, built a drug–gene interaction network, and projected it as a drug–drug similarity network (DDSN). We then clustered DDSN by optimizing modularity resolution, used the ATC codes distribution within each cluster to identify potential drug repurposing candidates, and verified repurposing hints with the latest DrugBank ATC codes. Finally, using the best modularity resolution found with our method, we applied our pipeline to the latest DrugBank drug–gene interaction data to generate a comprehensive drug repurposing hint list.

scholarly journals Targeted delivery of antisense oligonucleotides to pancreatic β-cells

2018 ◽  
Vol 4 (10) ◽  
pp. eaat3386 ◽  
Author(s):  
C. Ämmälä ◽  
W. J. Drury ◽  
L. Knerr ◽  
I. Ahlstedt ◽  
P. Stillemark-Billton ◽  
...  
Keyword(s):  
Targeted Delivery ◽  
Target Genes ◽  
Cell Types ◽  
Cell Type Specificity ◽  
Β Cells ◽  
Pancreatic Β Cells ◽  
Glucagon Like Peptide 1 ◽  
Novel Therapeutic

Antisense oligonucleotide (ASO) silencing of the expression of disease-associated genes is an attractive novel therapeutic approach, but treatments are limited by the ability to deliver ASOs to cells and tissues. Following systemic administration, ASOs preferentially accumulate in liver and kidney. Among the cell types refractory to ASO uptake is the pancreatic insulin-secreting β-cell. Here, we show that conjugation of ASOs to a ligand of the glucagon-like peptide-1 receptor (GLP1R) can productively deliver ASO cargo to pancreatic β-cells both in vitro and in vivo. Ligand-conjugated ASOs silenced target genes in pancreatic islets at doses that did not affect target gene expression in liver or other tissues, indicating enhanced tissue and cell type specificity. This finding has potential to broaden the use of ASO technology, opening up novel therapeutic opportunities, and presents an innovative approach for targeted delivery of ASOs to additional cell types.

scholarly journals Dietary Fiber: An Opportunity for a Global Control of Hyperlipidemia

2021 ◽  
Vol 2021 ◽  
pp. 1-20
Author(s):  
Ying Nie ◽  
Feijun Luo
Keyword(s):  
Dietary Fiber ◽  
Target Genes ◽  
Binding Capacity ◽  
Protective Action ◽  
Underlying Mechanism ◽  
Mapk Signaling ◽  
Lipid Lowering ◽  
Dietary Fibers

Dietary fiber has a long history in the intervention study of hyperlipidemia. In this review, current understandings of structures, sources, and natures of various kinds of dietary fibers (DFs) were analyzed first. Available evidences for the use of different varieties of DFs in the lipid-lowering action both in vitro and in vivo were subsequently classified, including both soluble ones, such as glucans, pectins, and gums, and insoluble ones, including arabinooxylans and chitosans, in order to draw a primary conclusion of their dose and molecular weight relationship with lipid-lowering effect. Their potential mechanisms, especially the related molecular mechanism of protective action in the treatment and prevention of hyperlipidemia, were summarized at last. Five major mechanisms are believed to be responsible for the antihyperlipidemic benefits of DFs, including low levels of energy, bulking effect, viscosity, binding capacity, and fermentation thus ameliorating the symptoms of hyperlipidemia. From the molecular level, DFs could possibly affect the activities of HMG-CoA reductase, LDL receptors, CYP7A1, and MAPK signaling pathway as well as other lipid metabolism-related target genes. In summary, dietary fibers could be used as alternative supplements to exert certain lipid-lowering effects on humans. However, more clinical evidence is needed to strengthen this proposal and its fully underlying mechanism still requires more investigation.

scholarly journals Hypoxia-mediated carbohydrate metabolism and transport promote early-stage murine follicle growth and survival

2014 ◽  
Vol 306 (8) ◽  
pp. E893-E903 ◽  
Author(s):  
Yogeshwar Makanji ◽  
David Tagler ◽  
Jennifer Pahnke ◽  
Lonnie D. Shea ◽  
Teresa K. Woodruff
Keyword(s):  
Target Genes ◽  
Early Stage ◽  
Fold Increase ◽  
Underlying Mechanism ◽  
Culture Conditions ◽  
Follicle Growth ◽  
Growth And Survival ◽  
Lactate Levels

Oxygen tension is critical for follicle growth and metabolism, especially for early-stage follicles, where vascularity is limited. Its role and underlying mechanism in the in vitro activation and maturation of immature to ovulatory follicles is largely unknown. In this study, early secondary (110 μm) murine follicles were isolated and encapsulated in alginate hydrogels to replicate the in vivo environment of the growing/maturing follicle. Encapsulated follicles were cultured for 8 days at either 2.5 or 20% O2. Survival (2.6-fold) and growth (1.2-fold) were significantly higher for follicles cultured at 2.5% compared with 20% O2. Using a mouse hypoxia-signaling pathway qRT-PCR array and GeneGo Metacore analysis, we found that direct target genes of the hypoxia-activated HIF1-complex were significantly upregulated in follicles cultured for 8 days at 2.5% compared with 20% O2, including the carbohydrate transport and metabolism genes Slc2a3, Vegfa, Slc2a1, Edn1, Pgk1, Ldha, and Hmox1. Other upregulated genes included carbohydrate transporters ( Slc2a1, Slc2a3, and Slc16a3) and enzymes essential for glycolysis ( Pgk1, Hmox1, Hk2, Gpi1, Pfkl, Pfkp, Aldoa, Gapdh, Pgam1, Eno1, Pkm2, and Ldha). For follicles cultured at 2.5% O2, a 7.2-fold upregulation of Vegfa correlated to an 18-fold increase in VEGFA levels, and a 3.2-fold upregulation of Ldha correlated to a 4.8-fold increase in lactate levels. Both VEGFA and lactate levels were significantly higher in follicles cultured at 2.5% compared with 20% O2. Therefore, enhanced hypoxia-mediated glycolysis is essential for growth and survival of early secondary follicles and provides vital insights into improving in vitro culture conditions.

scholarly journals Sonic Hedgehog Signaling Drives Proliferation of Synoviocytes in Rheumatoid Arthritis: A Possible Novel Therapeutic Target

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Mingxia Wang ◽  
Shangling Zhu ◽  
Weixiang Peng ◽  
Qiuxia Li ◽  
Zhaoxia Li ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Sonic Hedgehog ◽  
Therapeutic Target ◽  
Hedgehog Signaling ◽  
Specific Inhibitor ◽  
Sonic Hedgehog Signaling ◽  
Shh Signaling ◽  
Novel Therapeutic

Sonic hedgehog (Shh) signaling controls many aspects of human development, regulates cell growth and differentiation in adult tissues, and is activated in a number of malignancies. Rheumatoid arthritis (RA) is characterized by chronic synovitis and pannus formation associated with activation of fibroblast-like synoviocytes (FLS). We investigated whether Shh signaling plays a role in the proliferation of FLS in RA. Expression of Shh signaling related components (Shh, Ptch1, Smo, and Gli1) in RA synovial tissues was examined by immunohistochemistry (IHC) and in FLS by IHC, immunofluorescence (IF), quantitative RT-PCR, and western blotting. Expression of Shh, Smo, and Gli1 in RA synovial tissue was higher than that in control tissue (P<0.05). Cyclopamine (a specific inhibitor of Shh signaling) decreased mRNA expression of Shh, Ptch1, Smo, and Gli1 in cultured RA FLS, Shh, and Smo protein expression, and significantly decreased FLS proliferation. Flow cytometry analysis suggested that cyclopamine treatment resulted in cell cycle arrest of FLS in G1phase. Our data show that Shh signaling is activated in synovium of RA patientsin vivoand in cultured FLS form RA patientsin vitro, suggesting a role in the proliferation of FLS in RA. It may therefore be a novel therapeutic target in RA.

scholarly journals Uncovering pharmacological mechanisms of Wu-tou decoction acting on rheumatoid arthritis through systems approaches: drug-target prediction, network analysis and experimental validation

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Yanqiong Zhang ◽  
Ming Bai ◽  
Bo Zhang ◽  
Chunfang Liu ◽  
Qiuyan Guo ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Experimental Validation ◽  
Joint Destruction ◽  
Target Prediction ◽  
Interaction Network ◽  
Convincing Evidence ◽  
Topological Features ◽  
Regulatory Effects

Abstract Wu-tou decoction (WTD) has been extensively used for the treatment of rheumatoid arthritis (RA). Due to lack of appropriate methods, pharmacological mechanisms of WTD acting on RA have not been fully elucidated. In this study, a list of putative targets for compositive compounds containing in WTD were predicted by drugCIPHER-CS. Then, the interaction network of the putative targets of WTD and known RA-related targets was constructed and hub nodes were identified. After constructing the interaction network of hubs, four topological features of each hub, including degree, node betweenness, closeness and k-coreness, were calculated and 79 major hubs were identified as candidate targets of WTD, which were implicated into the imbalance of the nervous, endocrine and immune (NEI) systems, leading to the main pathological changes during the RA progression. Further experimental validation also demonstrated the preventive effects of WTD on inflammation and joint destruction in collagen-induced arthritis (CIA) rats and its regulatory effects on candidate targets both in vitro and in vivo systems. In conclusion, we performed an integrative analysis to offer the convincing evidence that WTD may attenuate RA partially by restoring the balance of NEI system and subsequently reversing the pathological events during RA progression.

scholarly journals Estrogen Receptor 1 Inhibition of Wnt/β-Catenin Signaling Contributes to Sex Differences in Hepatocarcinogenesis

2021 ◽  
Vol 11 ◽  
Author(s):  
Mamatha Bhat ◽  
Elisa Pasini ◽  
Chiara Pastrello ◽  
Marc Angeli ◽  
Cristina Baciu ◽  
...  
Keyword(s):  
Estrogen Receptor ◽  
Sex Differences ◽  
Mouse Model ◽  
Cell Lines ◽  
Target Genes ◽  
Interaction Network ◽  
Protein Product ◽  
Tumor Burden

BackgroundHepatocellular Carcinoma (HCC) is a sexually dimorphic cancer, with female sex being independently protective against HCC incidence and progression. The aim of our study was to understand the mechanism of estrogen receptor signaling in driving sex differences in hepatocarcinogenesis.MethodsWe integrated 1,268 HCC patient sample profiles from publicly available gene expression data to identify the most differentially expressed genes (DEGs). We mapped DEGs into a physical protein interaction network and performed network topology analysis to identify the most important proteins. Experimental validation was performed in vitro on HCC cell lines, in and in vivo, using HCC mouse model.ResultsWe showed that the most central protein, ESR1, is HCC prognostic, as increased ESR1 expression was protective for overall survival, with HR=0.45 (95%CI 0.32-0.64, p=4.4E-06), and was more pronounced in women. Transfection of HCC cell lines with ESR1 and exposure to estradiol affected expression of genes involved in the Wnt/β-catenin signaling pathway. ER-α (protein product of ESR1) agonist treatment in a mouse model of HCC resulted in significantly longer survival and decreased tumor burden (p&lt;0.0001), with inhibition of Wnt/β-Catenin signaling. In vitro experiments confirmed colocalization of β-catenin with ER-α, leading to inhibition of β-catenin-mediated transcription of target genes c-Myc and Cyclin D1.ConclusionCombined, the centrality of ESR1 and its inhibition of the Wnt/β-catenin signaling axis provide a biological rationale for protection against HCC incidence and progression in women.

scholarly journals Anti-inflammatory and Pro-apoptotic Effects of 18beta-Glycyrrhetinic Acid In Vitro and In Vivo Models of Rheumatoid Arthritis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yunhui Feng ◽  
Liyan Mei ◽  
Maojie Wang ◽  
Qingchun Huang ◽  
Runyue Huang
Keyword(s):  
Rheumatoid Arthritis ◽  
Cell Cycle ◽  
Cell Apoptosis ◽  
Underlying Mechanism ◽  
Mrna Levels ◽  
Pathological Changes ◽  
Collagen Induced Arthritis ◽  
Tnf Α

18β-Glycyrrhetinic acid (18β-GA), an active component from Glycyrrhiza glabra L. root (licorice), has been demonstrated to be able to protect against inflammatory response and reduce methotrexate (MTX)-derived toxicity. This study was therefore designed to test the therapeutic possibility of 18β-GA on rheumatoid arthritis (RA) and to explore the underlying mechanism. LPS or TNF-α-induced inflammatory cell models and collagen-induced arthritis (CIA) animal models were applied in this study. Real-time quantitative PCR (RT-qPCR) was used to measure the mRNA levels of various cytokines and FOXO family members. The protein levels of molecules in the MAPK/NF-κB signaling pathway were analyzed using western blot. The cell proliferation assay and colony-forming assay were used to test the influence of 18β-GA on cell viability. The cell apoptosis assay and cell cycle assay were performed to detect the effect of 18β-GA on cell proliferative capacity by using flow cytometry. Hematoxylin and eosin (H&amp;E) staining was performed to evaluate pathological changes after drug administration. The enzyme-linked immunosorbent assay (ELISA) was carried out for the detection of cytokines in serum. In vitro, we found that 18β-GA decreased the mRNA levels of IL-1β, IL-6, and COX-2 by inhibiting the MAPK/NF-κB signaling pathway in MH7A and RAW264.7 cell lines. Moreover, 18β-GA was able to suppress cell viability, trigger cell apoptosis, and G1 phase cell cycle arrest in our in vitro studies. 18β-GA dramatically enhanced the mRNA level of FOXO3 in both TNF-α- and LPS-induced inflammation models in vitro. Interestingly, after analyzing GEO datasets, we found that the FOXO3 gene was significantly decreased in the RA synovial tissue as compared to healthy donors in multiple microarray studies. In vivo, 18β-GA exhibited a promising therapeutic effect in a collagen-induced arthritis mouse model by alleviating joint pathological changes and declining serum levels of TNF-α, IL-1β, and IL-6. Finally, we observed that 18β-GA administration could mitigate liver damage caused by collagen or MTX. Collectively, the current study demonstrates for the first time that 18β-GA can inhibit inflammation and proliferation of synovial cells, and the underlying mechanism may be associated with its inhibition of MAPK/NF-κB signaling and promotion of FOXO3 signaling. Therefore, 18β-GA is expected to be a new drug candidate for RA therapy.

scholarly journals A Functional Polymorphism-Mediated Disruption of EGR1/ADAM10 Pathway Confers the Risk of Sepsis Progression

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Feng Chen ◽  
Yan Wang ◽  
Wenying Zhang ◽  
Yujie Cai ◽  
Tian Zhao ◽  
...  
Keyword(s):  
Sample Size ◽  
Tissue Injury ◽  
Underlying Mechanism ◽  
Large Sample Size ◽  
Nucleotide Polymorphisms ◽  
Clinical Genetic ◽  
Mobility Shift ◽  
Large Sample

ABSTRACT Increasing evidence has indicated that single nucleotide polymorphisms (SNPs) are related to the susceptibility of sepsis and might provide potential evidence for the mechanisms of sepsis. Our recent preliminary study showed that the ADAM10 genetic polymorphism was clinically associated with the development of sepsis, and little is known about the underlying mechanism. The aim of this study was to confirm the association between the ADAM10 promoter rs653765 G→A polymorphism and the progression of sepsis and to discover the underlying mechanism. Clinical data showed that the rs653765 G→A polymorphism was positively correlated with the development of sepsis, as evidenced by a multiple-center case-control association study with a large sample size, and showed that EGR1 and ADAM10 levels were associated well with the different subtypes of sepsis patients. In vitro results demonstrated that the rs653765 G→A variants could functionally modulate ADAM10 promoter activity by altering the binding of the EGR1 transcription factor (TF) to the ADAM10 promoter, affecting the transcription and translation of the ADAM10 gene. Electrophoretic mobility shift assay (EMSA) followed by chromatin immunoprecipitation (ChIP) assay indicated the direct interaction. Functional studies further identified that the EGR1/ADAM10 pathway is important for the inflammatory response. EGR1 intervention in vivo decreased host proinflammatory cytokine secretion and rescued the survival and tissue injury of the mouse endotoxemia model. IMPORTANCE Sepsis is characterized as life-threatening organ dysfunction, with unacceptably high mortality. Evidence has indicated that functional SNPs within inflammatory genes are associated with susceptibility, progression, and prognosis of sepsis. These mechanisms on which these susceptible sites depended often suggest the key pathogenesis and potential targets in sepsis. In the present study, we confirmed that a functional variant acts as an important genetic factor that confers the progression of sepsis in a large sample size and in multiple centers and revealed that the variants modulate the EGR1/ADAM10 pathway and influence the severity of sepsis. We believe that we provide an important insight into this new pathway involving the regulation of inflammatory process of sepsis based on the clinical genetic evidence, which will enhance the understanding of nosogenesis of sepsis and provide the potential target for inflammation-related diseases.

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