Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas

Gao, Xueren; Wang, Jianguo; Zhang, Shulong

doi:10.1155/2019/9651380

Cited by 18 publications

(15 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Genes with an adjusted P<0.05 identified by DESeq2 ( 25 , 26 ) were classified as differentially expressed. Subsequently, the clusterProfiler R package ( 27 ) was used for Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis ( 27 , 28 ). Differentially expressed genes were analyzed using the edgeR program (version 3.11) ( 29 ).…”

Section: Methodsmentioning

confidence: 99%

Structure identification, antitumor activity and mechanisms of a novel polysaccharide from Ramaria flaccida (Fr.) Quél

2020

View full text Add to dashboard Cite

It is an important aspect of current cancer research to search for effective and low-toxicity anticancer drugs and adjuvants. Polysaccharides, as immunomodulators, can improve the immune function of the body, kill tumor cells directly and prevent tumor development by increasing the resistance of the body to carcinogenic factors. The aim of the present study was to identify natural polysaccharide compounds with novel structure and antitumor activity via the separation and analysis of polysaccharide components from Ramaria flaccida (Fr.) Quél. (RF-1). In the present study, high-performance gel permeation chromatography, gas chromatography-mass spectrometry and nuclear magnetic resonance were used to identify the structure of polysaccharides from RF-1. Subsequently, the antitumor activity and mechanism of RF-1 were studied by establishing an in vivo S180 tumor model, and by using Illumina sequencing technology and enzyme-linked immunosorbent assay (ELISA). The present results revealed that the average molecular weight of RF-1 was 17,093 Da and that RF-1 was composed of the monosaccharides glucose and galactose, with a 2:1 ratio. The main chain of RF-1 consisted of (1→6, 2)-α-D-galactopyranose and (1→6, 4)- α-D-glucopyranose. One of the branched chains was linked to 4-O of the main glucose chain by (1→6)-α-D-glucopyranose and next linked by one (→4)-β-D-glucopyranose. The other two branched chains were both linked to 2-O of the main glucose chain by one (→4)-β-D-glucopyranose. In addition, RF-1 inhibited the growth of S180 tumors in vivo . When the concentration of RF-1 was 20 mg/kg, the inhibition rate of S180 tumors in mice was 48.4%. Compared with the blank control group, 1,971 differentially expressed genes were identified, of which 818 were upregulated and 1,153 were downregulated in the RF-1 group. A Gene Ontology enrichment analysis generated 47,091 assignments to biological processes, 5,250 assignments to cellular components, and 6,466 assignments to molecular functions. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that the Wnt and MAPK signaling pathways were significantly enriched. The number of differentially annotated genes in these two pathways was 19 and 33, respectively. Additionally, ELISA results revealed that the protein levels of interleukin (IL)-1β, IL-6, vascular endothelial growth factor (VEGF) and VEGF receptor in the RF-1 group were significantly downregulated compared with the S180 blank control group (P<0.01).

show abstract

Section: Methodsmentioning

confidence: 99%

Structure identification, antitumor activity and mechanisms of a novel polysaccharide from Ramaria flaccida (Fr.) Quél

2020

View full text Add to dashboard Cite

show abstract

“…Meanwhile, a large number of cancer-related data are stored in publicly available databases, such as The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A reanalysis of these data could facilitate the discovery of a vast range of valuable biological information (Gao et al, 2018(Gao et al, , 2019Liu et al, 2019;Zhou et al, 2019). For instance, several novel genes associated with poor prognosis of patients with pancreatic ductal adenocarcinoma (PDAC) were identified by analyzing the array data from GEO.…”

Section: Introductionmentioning

confidence: 99%

Identification of Genes Related to Clinicopathological Characteristics and Prognosis of Patients with Colorectal Cancer

Gao

Yang

2020

DNA and Cell Biology

Self Cite

View full text Add to dashboard Cite

The aim of this study was to identify genes with clinical significance in colorectal cancer (CRC). Gene expression profiles of 585 CRC tissues and 61 normal colorectal tissues from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to identify differentially expressed genes (DEGs) between CRC and normal colorectal tissues. DAVID and KOBAS tools were used to explore Gene Ontology (GO) and KEGG pathways enriched by DEGs, respectively. In addition, TCGA data sets were also used to identify prognostic factors and develop a prognostic prediction model for CRC. A total of 353 DEGs including 117 upregulated and 236 downregulated genes in CRC were identified based on GSE32323 data set. These DEGs were significantly enriched in the biological process related to the regulation of cell proliferation and 50 signaling pathways, such as ''TGF-beta signaling pathway,'' ''Wnt signaling pathway,'' and ''Jak-STAT signaling pathway.'' GCG, ADH1B, SLC4A4, ZG16, and CLCA4 were the top five downregulated in CRC. FOXQ1, LGR5, CLDN1, KRT23, and DPEP1 were the top five upregulated in CRC. KRT23 expression could affect tumor stage and regional lymph node metastasis in CRC patients. FOXQ1 expression could affect tumor distant metastasis in CRC patients. Survival analysis indicated that SLC4A4 expression was associated with the prognosis of CRC patients. Prognostic prediction model developed based on age, tumor stage, and SLC4A4 expression exhibited an efficient performance in predicting 1-, 3-, and 5-year overall survival of CRC patients. In conclusion, the current study identified several genes and pathways related to CRC, which provided new insight in understanding molecular mechanism of tumorigenesis and development of CRC.

show abstract

“…1 receptor-associated kinase-1 (IRAK1) and tumor necrosis factor receptor-associated factor-6 (TRAF6), thereby reducing NF-κB activity and preventing the occurrence of hyperimmune inflammatory response [24,25], and some research and analysis show that FEN1 is significantly enriched in the NF-κB pathway, that is, its expression level is elevated, which fully indicates that miR-146a elevate the expression of FEN1 after inhibiting downstream target genes, and then regulating HBV replication. [26] In addition, other studies have shown that Ago2 can act as a carrier to play a role in miR-18a interaction [16], which is different from the traditional function that is Ago protein family (Ago1-4) and microRNAs can form immune complexes to promote the processing and maturation of microRNAs [17,18]. Therefore, we hypothesize that Ago2 also plays a very important auxiliary role in the regulation of miR-146a.…”

Section: Discussionmentioning

confidence: 85%

The cooperative complex of Argonaute-2/MicroRNA-146a regulates Hepatitis B Virus replication through FEN1

Mei

Jing

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: The regulatory of HBV replication is still unclear. FEN1 can repair HBV rcDNA to HBV cccDNA and promote HBV DNA replication. However, its specific regulatory detail remains unclear. MicroRNA regulates gene expression at post-transcriptional level. Especially, miR-146a, it plays an important role that is closely related to regulation of HBV replication. Based on above, we hypothesize that miR-146a may be regulate HBV cccDNA formation through FEN1. So, we will investigate the effect of miR-146a on the replication of hepatitis B virus and its molecular mechanism. Results: We found that level of miR-146a was significantly up-regulated in HepG2.2.15 cells (11.755±0.069) than that in HepG2 (1.000±0.038) (P<0.05). Furthermore, HBV-DNA copies and FEN1 were significantly increased and decreased, respectively, in HepG2.2.15 cells transfected with miR-146a mimic and inhibitor for 48h,[(3.215±0.001); (2.623±0.083)] compared with the control group (2.813±0.015) (P<0.05),. After transfection FEN1 plasmid, HBV-DNA Copies (5.712±0.371) is significantly higher than the control group（2.661±0.009）(P<0.05), and the level of miR-146a（3.431±0.004）is significantly higher than the control group (1.023±0.224） (P<0.05). The expression level of IRAK1/TRAF6 are significantly lower and higher [(0.114±0.013); (0.390±0.014); (1.222±0.073); (2.145±0.271)] than the control group [(1.000±0.038); (1.007±0.119)] (P<0.05) after transfection miR-146a mimic and inhibitor into HepG2.2.15. After Ago2 siRNA, the level of miR-146a (0.105±0.002) is significantly decreased than the control group (1.000±0.041) (P<0.05) from Ago2 protein RIP. After transfection Ago2 siRNA then added into exogenous miR-146a into HepG2.2.15, The expression level of FEN1 is significantly reduced (0.485±0.100) than the control group (1.000±0.023) (P<0.05), and the HBV-DNA copies is significantly lower (3.230±0.047) than the control group (3.789±0.041) (P<0.05). Conclusion: Ago2 cooperates with miR-146a to regulate the transcription the expression level of FEN1 protein through the downstream target gene IRAK1/TRAF6, then promoting HBV replication.

show abstract

Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas

Cited by 18 publications

References 48 publications

Structure identification, antitumor activity and mechanisms of a novel polysaccharide from Ramaria flaccida (Fr.) Quél

Structure identification, antitumor activity and mechanisms of a novel polysaccharide from Ramaria flaccida (Fr.) Quél

Identification of Genes Related to Clinicopathological Characteristics and Prognosis of Patients with Colorectal Cancer

The cooperative complex of Argonaute-2/MicroRNA-146a regulates Hepatitis B Virus replication through FEN1

Contact Info

Product

Resources

About