Identifying hub genes of papillary thyroid carcinoma in the TCGA and GEO database using bioinformatics analysis

Wang, Ying; Zhang, Xiaolian; Leng, Huilin; Wang, Yin; Zeng, Weizhong; Zhang, Congling

doi:10.7717/peerj.9120

Cited by 23 publications

(24 citation statements)

References 28 publications

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“…Second, to verify the results of bioinformatics analysis, the effect of RAB5A knockdown on exosome secretion was assessed experimentally. Due to the pervasive usage of combined scores of the STRING database as a cut‐off value in advance bioinformatics analyses, 54,55 we decided to validate its PPI interactions with different combined scores experimentally as our last objective.…”

Section: Discussionmentioning

confidence: 99%

RAB5A is associated with genes involved in exosome secretion: Integration of bioinformatics analysis and experimental validation

Gorji-Bahri

Moghimi

Hashemi

2020

J of Cellular Biochemistry

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Exosomes, as cell–cell communicators with an endosomal origin, are involved in the progression of various diseases. RAB5A, a member of the small Rab GTPases family, which is well known as a key regulator of cellular endocytosis, is expected to be involved in exosome secretion. Here, we found the impact of RAB5A on exosome secretion from human hepatocellular carcinoma cell line using a rapid yet reliable bioinformatics approach followed by experimental analysis. Initially, RAB5A and exosome secretion‐related genes were gathered from bioinformatics tools, namely, CTD, COREMINE, and GeneMANIA; and published papers. Protein–protein interaction (PPI) was then constructed by the Search Tool for Retrieval of Interacting Genes (STRING) database. Among them, several genes with different combined scores were validated by the real‐time quantitative polymerase chain reaction (RT‐qPCR) in stable RAB5A knockdown cells. Thereafter, to validate the bioinformatics results functionally, the impact of RAB5A knockdown on exosome secretion was evaluated. Bioinformatics analysis showed that RAB5A interacts with 37 genes involved in exosome secretion regulatory pathways. Validation by RT‐qPCR confirmed the association of RAB5A with candidate interacted genes and interestingly showed that even medium to low combined scores of the STRING database could be experimentally valid. Moreover, the functional analysis demonstrated that the stable silencing of RAB5A could experimentally decrease exosome secretion. In conclusion, we suggest RAB5A as a regulator of exosome secretion based on our bioinformatics approach and experimental analysis. Also, we propose the usage of PPI‐derived from the STRING database regardless of their combined scores in advanced bioinformatics analysis.

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Section: Discussionmentioning

confidence: 99%

RAB5A is associated with genes involved in exosome secretion: Integration of bioinformatics analysis and experimental validation

Gorji-Bahri

Moghimi

Hashemi

2020

J of Cellular Biochemistry

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“…With the growing popularity of chip and sequencing technology, comprehensive bioinformatic analysis has become a promising method for exploring disease-related biomarkers and their molecular mechanisms ( Sakharkar et al, 2019 ; Wan et al, 2020 ). For example, Zhang et al found that the adipose tissues of insulin-resistant and non-insulin-resistant patients with obesity had differential expression of a number of genes, including matrix metallopeptidase 9, interleukin (IL ) 6 , C-X-C motif chemokine ligand ( CXCL ) 8 , C-C motif chemokine ligand 4, and CXCL10 , which are enriched for several functions, including cytokine-cytokine receptor interactions, tumor necrosis factor (TNF) signaling, and pathways in cancer ( Zhang et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People

Meng

Sun

et al. 2021

Front. Genet.

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As the prevalence of obesity increases, so does the occurrence of obesity-related complications, such as cardiovascular and cerebrovascular diseases, diabetes, and some cancers. Increased adipose tissue is the main cause of harm in obesity. To better understand obesity and its related complications, we analyzed the mRNA expression profiles of adipose tissues from 126 patients with obesity and 275 non-obese controls. Using an integrated bioinformatics method, we explored the functions of 113 differentially expressed genes (DEGs) between them. Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses revealed that upregulated DEGs were enriched in immune cell chemotaxis, complement-related cascade activation, and various inflammatory signaling pathways, while downregulated DEGs enriched in nutrient metabolism. The CIBERSORT algorithm indicated that an increase in macrophages may be the main cause of adipose tissue inflammation, while decreased γδ T cells reduce sympathetic action, leading to dysregulation of adipocyte thermogenesis. A protein-protein interaction network was constructed using the STRING database, and the top 10 hub genes were identified using the cytoHubba plug-in in Cytoscape. All were confirmed to be obesity-related using a separate dataset. In addition, we identified chemicals related to these hub genes that may contribute to obesity. In conclusion, we have successfully identified several hub genes in the development of obesity, which provide insights into the possible mechanisms controlling obesity and its related complications, as well as potential biomarkers and therapeutic targets for further research.

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“…Furthermore, MSC-AS1 facilitates the progression of LUAD by sponging miR-33b-5p to up-regulate GPAM 60 . Previous studies also showed that BCL2 Apoptosis Regulator (BCL2) 61 and Cadherin 2 (CDH2) 62 play an important role in the pathogenesis of thyroid cancer. Therefore, the present study further combined these mRNAs with tumor-related lncRNAs and miRNAs in thyroid cancer, providing a basis for studying the common mechanisms of multiple genes in thyroid cancer.…”

Section: Discussionmentioning

confidence: 97%

Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma

et al. 2021

Sci Rep

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Thyroid Carcinoma (THCA) is the most common endocrine tumor that is mainly treated using surgery and radiotherapy. In addition, immunotherapy is a recently developed treatment option that has played an essential role in the management of several types of tumors. However, few reports exist on the use of immunotherapy to treat THCA. The study downloaded the miRNA, mRNA and lncRNA data for THCA patients from the TCGA database (https://portal.gdc.cancer.gov/). Thereafter, the tumor samples were divided into cold and hot tumors, based on the immune score of the tumor microenvironment. Moreover, the differentially expressed lncRNAs and miRNAs were obtained. Finally, the study jointly constructed a ceRNA network through differential analysis of the mRNA data for cold and hot tumors. The study first assessed the level of immune infiltration in the THCA tumor microenvironment then divided the samples into cold and hot tumors, based on the immune score. Additionally, a total of 568 up-regulated and 412 down-regulated DEGs were screened by analyzing the differences between hot and cold tumors. Thereafter, the study examined the differentially expressed genes for lncRNA and miRNA. The results revealed 629 differentially expressed genes related to lncRNA and 114 associated with miRNA. Finally, a ceRNA network of the differentially expressed genes was constructed. The results showed a five-miRNA hubnet, i.e., hsa-mir-204, hsa-mir-128, hsa-mir-214, hsa-mir-150 and hsa-mir-338. The present study identified the immune-related mRNA, lncRNA and miRNA in THCA then constructed a ceRNA network. These results are therefore important as they provide more insights on the immune mechanisms in THCA. The findings also provides additional information for possible THCA immunotherapy.

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Identifying hub genes of papillary thyroid carcinoma in the TCGA and GEO database using bioinformatics analysis

Cited by 23 publications

References 28 publications

RAB5A is associated with genes involved in exosome secretion: Integration of bioinformatics analysis and experimental validation

RAB5A is associated with genes involved in exosome secretion: Integration of bioinformatics analysis and experimental validation

Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People

Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma

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