scholarly journals Identification of Drug Targets and Potential Molecular Mechanisms of Wantong Jingu Tablet in Treatment of Rats with Collagen-Induced Arthritis based on 16S rDNA High-Throughput Sequencing and Metabolomic Analysis

2020 ◽  
Author(s):  
Zhaodong Li ◽  
Fangyuan Qi ◽  
Fan Li
Keyword(s):  
16S Rdna ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Caspase 3 ◽  
Collagen Induced Arthritis ◽  
Apoptosis Pathway ◽  
Bacterial Phyla ◽  
Joint Pathology

Abstract Background: Wantong Jingu Tablet (WJT), a mixture of traditional Chinese medicine, can reduce the symptoms of rheumatoid arthritis (RA), but its pharmacological mechanism is unclear. The aims of this study were to investigate the therapeutic mechanisms of WJT for RA in vivo.Methods: The effects of WJT on the joint pathology, and the levels of Bax, Bcl-2,caspase-3, cleaved-caspase-3, ERK1/2, pERK1/2, TNF-α, IL-1β, and IL-6 were demonstrated based on several experiments in the model of collagen-induced arthritis (CIA) in rats. 16S rDNA high-throughput sequencing was used to investigate the effect of WJT on the overall structure and composition of gut microbiota. Meanwhile, metabolite changes in faeces were analyzed by metabolomics techniques. Results: The results showed that WJT restored the joint pathology in CIA rats, upregulated Bax and cleaved-caspase-3, downregulated Bcl-2, caspase-3, and pERK1/2, and reduced the levels of pro-inflammatory cytokines. The overall gut microbial structure in CIA rats was altered after WJT treatment. Three bacterial phyla were prominently restored: Bacteroidetes,Tenericutes and Deferribacteres, and three bacterial genera were significantly reversed: Vibrio, Macrococcus and Vagococcus. Furthermore, five specific metabolites associated with these specific bacterial genera were identified by correlation analysis. In addition, WJT supplement trended to down-regulate the other five metabolites according to metabolomic analyses. Conclusions: These results revealed that WJT restored the pathological changes of RA might through activating the mitochondrial apoptosis pathway, inhibited MEK/ERK signaling, and modulating the special bacteria and the special metabolites.

scholarly journals Identification of drug targets and potential molecular mechanisms of Wantong Jingu Tablet in treatment of rats with collagen-induced arthritis based on 16S rDNA high-throughput sequencing and metabolomic analysis

2020 ◽  
Author(s):  
Zhaodong Li ◽  
Fangyuan Qi ◽  
Fan Li
Keyword(s):  
Rheumatoid Arthritis ◽  
16S Rdna ◽  
High Throughput ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Caspase 3 ◽  
Collagen Induced Arthritis ◽  
Apoptosis Pathway ◽  
Joint Pathology

Abstract Background: Wantong Jingu Tablet (WJT), a mixture of traditional Chinese medicine, can reduce the symptoms of rheumatoid arthritis (RA), but its pharmacological mechanism is unclear. The aims of this study were to investigate the therapeutic mechanisms of WJT for RA in vivo.Methods: The effects of WJT on the joint pathology, and the levels of Bax, Bcl-2,caspase-3, cleaved-caspase-3, ERK1/2, pERK1/2, TNF-α, IL-1β, and IL-6 were demonstrated based on several experiments in the model of collagen-induced arthritis (CIA) in rats. 16S rDNA high-throughput sequencing was used to investigate the effect of WJT on the overall structure and composition of gut microbiota. Meanwhile, metabolite changes in faeces were analyzed by metabolomics techniques.Results: The results showed that WJT restored the joint pathology in CIA rats, upregulated Bax and cleaved-caspase-3, downregulated Bcl-2, caspase-3, and pERK1/2, and reduced the levels of pro-inflammatory cytokines. The overall gut microbial structure in CIA rats was altered after WJT treatment. Three bacterial phyla were prominently restored: Bacteroidetes,Tenericutes and Deferribacteres, and three bacterial genera were significantly reversed: Vibrio, Macrococcus and Vagococcus. Furthermore, five specific metabolites associated with these specific bacterial genera were identified by correlation analysis. In addition, WJT supplement trended to down-regulate the other five metabolites according to metabolomic analyses.Conclusions: These results revealed that WJT restored the pathological changes of RA might through activating the mitochondrial apoptosis pathway, inhibited MEK/ERK signaling, and modulating the special bacteria and the special metabolites.Keywords: Rheumatoid arthritis; 16S rDNA high-throughput sequencing; metabolomics; drug targets; Wantong Jingu Tablet

scholarly journals CircRNA_0000392 Promotes Colorectal Cancer Progression by Sponging miR-193a-5p

2020 ◽  
Author(s):  
Hanchen Xu ◽  
Yujing Liu ◽  
Peiqiu Cheng ◽  
Chunyan Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Expression Profile ◽  
High Throughput ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Malignant Progression ◽  
Luciferase Assay ◽  
Circular Rnas

Abstract Background: Circular RNAs (circRNAs), an important member of the non-coding RNA family, have been revealed the role in the pathogenic progression of diseases in recent years, particularly in the malignant progression of cancer. With the application of high-throughput sequencing technology, a large number of circRNAs have been found in tumor tissues, and some circRNAs have demonstrated the role as oncogenic genes. In this study, we analyzed the circRNA expression profile in colorectal cancer (CRC) tissues and normal adjacent tissues by high-throughput sequencing, focusing on the circRNA_0000392, a circRNA with significantly increased expression in colorectal cancer tissues, and further investigating its function in the progression of colorectal cancer.Methods: The expression profile of circRNAs in 6 pairs of CRC tissues and normal adjacent tissues was analyzed by RNA-sequencing. We verified the differential circRNAs with expanded samples by qRT-PCR, focused on circRNA_0000392, and evaluated its associations with clinicopathological features. Then we knocked down circRNA_0000392 in CRC cells and evaluated the effect in vitro and in vivo by functional experiments. The dual luciferase assay and RNA pull-down were performed to further explore the downstream potential molecular mechanisms.Results: CircRNA_0000392 was significantly up-regulated in CRC compared with normal adjacent tissues and cell line. The expression level of circRNA_0000392 was positively correlated with the malignant progression of CRC. Functional studies revealed that reducing the expression of circRNA_0000392 could inhibit the proliferation and invasion of CRC both in vitro and in vivo. Mechanistically, circRNA­_0000392 could act as a sponge of miR-193a-5p and regulate the expression of PIK3R3, then affect the activation of the AKT-mTOR pathway in CRC cells.Conclusions: The circRNA_0000392 has the function as an oncogene through miR-193a-5p/PIK3R3-Akt axis in CRC cells, implying that circRNA_0000392 is a potential therapeutic target for the treatment of colorectal cancer and a predictive marker for CRC patients.

scholarly journals CircRNA_0000392 promotes colorectal cancer progression through the miR-193a-5p/PIK3R3/AKT axis

2020 ◽  
Author(s):  
Hanchen Xu ◽  
Yujing Liu ◽  
Peiqiu Cheng ◽  
Chunyan Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Expression Profile ◽  
High Throughput ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Malignant Progression ◽  
Circular Rnas

Abstract Background: Circular RNAs (circRNAs), important members of the noncoding RNA family, have been recently revealed to play a role in the pathogenic progression of diseases, particularly in the malignant progression of cancer. With the application of high-throughput sequencing technology, a large number of circRNAs have been identified in tumor tissues, and some circRNAs have been demonstrated to act as oncogenes. In this study, we analyzed the circRNA expression profile in colorectal cancer (CRC) tissues and normal adjacent tissues by high-throughput sequencing. We focused on circRNA_0000392, a circRNA with significantly increased expression in CRCtissues, and further investigated its function in the progression of colorectal cancer.Methods: The expression profile of circRNAs in 6 pairs of CRC tissues and normal adjacent tissues was analyzed by RNA sequencing. We verified the identified differentially expressed circRNAs in additional samples by qRT-PCR and selected circRNA_0000392 to evaluate its associations with clinicopathological features. Then, we knocked down circRNA_0000392 in CRC cells and investigated the in vitro and in vivo effects using functional experiments. Dual luciferase and RNA pull-down assays were performed to further explore the downstream potential molecular mechanisms.Results: CircRNA_0000392 was significantly upregulated in CRC compared with normal adjacent tissues and cell lines. The expression level of circRNA_0000392 was positively correlated with the malignant progression of CRC. Functional studies revealed that reducing the expression of circRNA_0000392 could inhibit the proliferation and invasion of CRC both in vitro and in vivo. Mechanistically, circRNA­_0000392 could act as a sponge of miR-193a-5p and regulate the expression of PIK3R3, affecting the activation of the AKT-mTOR pathway in CRC cells.Conclusions: CircRNA_0000392 functions as an oncogene through the miR-193a-5p/PIK3R3/Akt axis in CRC cells, suggesting that circRNA_0000392 is a potential therapeutic target for the treatment of colorectal cancer and a predictive marker for CRC patients.

scholarly journals CircRNA_0000392 promotes colorectal cancer progression through the miR-193a-5p/PIK3R3/AKT axis

2020 ◽  
Vol 39 (1) ◽  
Author(s):  
Hanchen Xu ◽  
Yujing Liu ◽  
Peiqiu Cheng ◽  
Chunyan Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Expression Profile ◽  
High Throughput ◽  
Noncoding Rna ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Malignant Progression ◽  
Circular Rnas

Abstract Background Circular RNAs (circRNAs), important members of the noncoding RNA family, have been recently revealed to play a role in the pathogenic progression of diseases, particularly in the malignant progression of cancer. With the application of high-throughput sequencing technology, a large number of circRNAs have been identified in tumor tissues, and some circRNAs have been demonstrated to act as oncogenes. In this study, we analyzed the circRNA expression profile in colorectal cancer (CRC) tissues and normal adjacent tissues by high-throughput sequencing. We focused on circRNA_0000392, a circRNA with significantly increased expression in CRCtissues, and further investigated its function in the progression of colorectal cancer. Methods The expression profile of circRNAs in 6 pairs of CRC tissues and normal adjacent tissues was analyzed by RNA sequencing. We verified the identified differentially expressed circRNAs in additional samples by qRT-PCR and selected circRNA_0000392 to evaluate its associations with clinicopathological features. Then, we knocked down circRNA_0000392 in CRC cells and investigated the in vitro and in vivo effects using functional experiments. Dual luciferase and RNA pull-down assays were performed to further explore the downstream potential molecular mechanisms. Results CircRNA_0000392 was significantly upregulated in CRC compared with normal adjacent tissues and cell lines. The expression level of circRNA_0000392 was positively correlated with the malignant progression of CRC. Functional studies revealed that reducing the expression of circRNA_0000392 could inhibit the proliferation and invasion of CRC both in vitro and in vivo. Mechanistically, circRNA_0000392 could act as a sponge of miR-193a-5p and regulate the expression of PIK3R3, affecting the activation of the AKT-mTOR pathway in CRC cells. Conclusions CircRNA_0000392 functions as an oncogene through the miR-193a-5p/PIK3R3/Akt axis in CRC cells, suggesting that circRNA_0000392 is a potential therapeutic target for the treatment of colorectal cancer and a predictive marker for CRC patients.

scholarly journals Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons

2011 ◽  
Vol 11 (1) ◽  
pp. 244 ◽  
Author(s):  
Huma Siddiqui ◽  
Alexander J Nederbragt ◽  
Karin Lagesen ◽  
Stig L Jeansson ◽  
Kjetill S Jakobsen
Keyword(s):  
16S Rdna ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Female Urine

scholarly journals CDK10 Regulates Gastric Cancer Metastasis By Inhibiting lncRNA-C5ORF42-5 Via Phosphorylation Level of AKT/ERK

2021 ◽  
Author(s):  
Zi-Jian Deng ◽  
Dong-Wen Chen ◽  
Xi-Jie Chen ◽  
Jia-Ming Fang ◽  
Liang Xv ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cancer Cells ◽  
Cell Line ◽  
High Throughput ◽  
Cancer Metastasis ◽  
High Throughput Sequencing ◽  
Gastric Cancer Cells ◽  
Related Proteins

Abstract Background: Gastric cancer is the fourth most common malignant disease. Both CDK10 and long noncoding RNAs (lncRNAs) have been found to exert biological functions in multiple cancers. However, it is still unclear whether CDK10 represses tumor progression in gastric cancer by reducing potential targeting lncRNAs.Methods: The functions of CDK10 and lncRNA-C5ORF42-5 in proliferation, invasion and migration were assessed by MTS assays, colony formation assays, cell cycle and apoptosis assays, Transwell assays, wound healing assays and animal experiments. We used high-throughput sequencing to confirm the existence of lncRNA-C5ORF42-5 and quantitative real-time PCR was used to evaluate lncRNA expression. Then, with RNA-seq sequencing as well as GO function and KEGG enrichment analysis, we identified the signaling pathways in which lncRNA-C5ORF42-5 was involved in gastric cancer. Finally, western blotting was used to identify the genes regulated by lncRNA-C5ORF42-5.Results: Our results showed that CDK10 is expressed at relatively low levels in gastric cancer cell lines and inhibits the progression of gastric cancer cells both in vitro and in vivo. Next, based on high-throughput sequencing, we identified a novel lncRNA, lncRNA-C5ORF42-5, in the stable CDK10-overexpressing cell line compared with the CDK-knockdown cell line and their controls. Additionally, we confirmed that lncRNA-C5ORF42-5 acts as an oncogene to promote metastasis in gastric cancer in vitro and in vivo. We then ascertained that lncRNA-C5ORF42-5 is a major contributor to the function of CDK10 in gastric cancer metastasis by upregulating lncRNA-C5ORF42-5 to reverse the effects of CDK10 overexpression. Finally, we explored the mechanism by which lncRNA-C5ORF42-5 overexpression affects gastric cancer cells to elucidate whether lncRNA-C5ORF42-5 may increase the activity of the SMAD pathway of BMP signaling and promote the expression of EMT-related proteins, such as E-cadherin. Additionally, overexpression of lncRNA-C5ORF42-5 affected the phosphorylation levels of AKT and ERK.Conclusion: Our findings suggest that CDK10 overexpression represses gastric cancer tumor progression by reducing lncRNA-C5ORF42-5 and hindering activation of the related proteins in metastatic signaling pathways, which provides new insight into developing effective therapeutic strategies in the treatment of metastatic gastric cancer.

scholarly journals The Transcriptional landscape of Streptococcus pneumoniae reveals a complex operon architecture and abundant riboregulation critical for growth and virulence

2018 ◽  
Author(s):  
Indu Warrier ◽  
Nikhil Ram-Mohan ◽  
Zeyu Zhu ◽  
Ariana Hazery ◽  
Michelle M Meyer ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
High Throughput ◽  
Transcription Initiation ◽  
High Throughput Sequencing ◽  
Regulatory Element ◽  
Fine Tuning ◽  
Transcriptional Units ◽  
Rna Elements ◽  
Transcriptional Landscape

AbstractEfficient and highly organized transcription initiation and termination is fundamental to an organism’s ability to survive, proliferate, and quickly respond to its environment. Over the last decade, our simplistic outlook of bacterial transcriptional regulation and architecture has evolved to include stimulus-responsive regulation by untranslated RNA and the formation of alternate transcriptional units. In this study, we map the transcriptional landscape of the bacterial pathogen Streptococcus pneumoniae by applying a combination of high-throughput RNA-sequencing techniques. Our study reveals a complex transcriptome wherein environment-respondent alternate transcriptional units are observed within operons stemming from internal transcription start sites (TSS) and transcription terminators (TTS) suggesting that more fine-tuning of regulation occurs than previously thought. Additionally, we identify many putative cis-regulatory RNA elements and riboswitches within 5’-untranslated regions (5’-UTR) of genes. By integrating TSSs and TTSs with independently collected RNA-Seq datasets from a variety of conditions, we establish the response of these regulators to changes in growth conditions and validate several of them. Furthermore, to determine the importance of ribo-regulation by 5’-UTR elements for in vivo virulence, we show that the pyrR regulatory element is essential for survival, successful colonization and infection in mice suggesting that such RNA elements are potential drug targets. Importantly, we show that our approach of combining high-throughput sequencing with in vivo experiments can reconstruct a global understanding of regulation, but also pave the way for discovery of compounds that target (ribo-) regulators to mitigate virulence and antibiotic resistance.

scholarly journals Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
S. Le Guillou ◽  
A. Leduc ◽  
J. Laubier ◽  
S. Barbey ◽  
M.-N. Rossignol ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Milk Production ◽  
High Throughput ◽  
Genetic Background ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Whole Milk ◽  
Mammary Morphogenesis ◽  
Regulatory Properties

AbstractThe concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

Specific microbes of saliva and vaginal fluid of Guangdong Han females based on 16S rDNA high-throughput sequencing

2019 ◽  
Vol 133 (3) ◽  
pp. 699-710 ◽  
Author(s):  
Hongyan Huang ◽  
Ting Yao ◽  
Weibin Wu ◽  
Chuangyan Zhai ◽  
Tianshan Guan ◽  
...  
Keyword(s):  
16S Rdna ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Vaginal Fluid
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