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Comprehensive analysis of bioinformatics and system biology reveals the association between Girdin and hepatocellular carcinoma

ABSTRACT: Comprehensive analysis of bioinformatics and system biology reveals the association between Girdin and hepatocellular carcinoma

PROVIDER: PRJNA1055890 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27325803_1.fastq.gz	Fastqsanger.gz
	SRR27325803_2.fastq.gz	Fastqsanger.gz
	SRR27325804_1.fastq.gz	Fastqsanger.gz
	SRR27325804_2.fastq.gz	Fastqsanger.gz
	SRR27325805_1.fastq.gz	Fastqsanger.gz

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Comprehensive analysis of bioinformatics and system biology reveals the association between Girdin and hepatocellular carcinoma

Project description:Introduction: Hepatocellular carcinoma stands as the most common cause of global cancer-related mortality. The actin-binding protein Girdin exhibits elevated expression in diverse tumors, fostering tumorigenesis and progression. Nevertheless, the precise mechanism by which Girdin regulates liver cancer remains elusive. Methods: This study comprehensively analyzed the expression level of Girdin in liver cancer and adjacent tissue, along with the correlation between Girdin expression and the clinical characteristics and prognosis of liver cancer. The analysis involved the integration of data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), Clinical Proteomic Tumor Analysis Consortium (CPTAC) database, and immunohistochemistry. Subsequently, the expression level of Girdin was knocked down to elucidate its role in the progression of liver cancer. Transcriptome sequencing was employed to investigate the mechanistic underpinnings of Girdin's regulatory impact on liver cancer. Additionally, the Comparative Toxicogenomics Database (CTD) was utilized to identify potential drugs or molecules for liver cancer treatment. Results: The findings revealed elevated Girdin expression in liver cancer tissues, and heightened Girdin expression correlated with adverse clinical features and prognosis. Silencing of Girdin markedly impeded the proliferation and migration of hepatocellular carcinoma cells. Moreover, transcriptome sequencing demonstrated that silencing Girdin led to differential expression of 176 genes and inhibition of the PI3K/Akt signaling pathway. Ultimately, we propose that Imatinib Mesylate, Orantinib, Resveratrol, Sorafenib, and Curcumin mayinteract with Girdin, potentially contributing to the treatment of liver cancer. Conclusion: This study reveals the association between Girdin and hepatocellular carcinoma, providing novel clues for future research and treatment of hepatocellular carcinoma.

2023-12-25 | GSE251899 | GEO

Platelet microRNA bioinformatics analysis in patients with hepatocellular carcinoma

Project description:Platelet microRNA bioinformatics analysis in patients with hepatocellular carcinoma

| PRJNA665508 | ENA

Comprehensive analysis of bioinformatics and system biology reveals the association between Girdin and hepatocellular carcinoma.

Project description:IntroductionHepatocellular carcinoma is one of the leading causes of cancer-related mortality worldwide. The actin-binding protein Girdin is overexpressed in various tumors, promoting tumorigenesis and progression. However, the exact mechanisms by which Girdin regulates liver cancer remain poorly understood.MethodsThis study comprehensively analyzed the expression level of Girdin in liver cancer and adjacent tissue, along with the correlation between Girdin expression and the clinical characteristics and prognosis of liver cancer. The analysis integrated data from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Clinical Proteomic Tumor Analysis Consortium (CPTAC) database. Subsequently, Girdin expression was knocked down to elucidate its role in the progression of liver cancer. Transcriptome sequencing was employed to investigate the mechanistic underpinnings of Girdin's regulatory impact on liver cancer. Additionally, the Comparative Toxicogenomics Database (CTD) was utilized to identify potential drugs or molecules for liver cancer treatment.ResultsThe findings revealed elevated Girdin expression in liver cancer tissues, and heightened Girdin expression correlating with adverse clinical features and prognosis. Silencing of Girdin markedly impeded the proliferation and migration of hepatocellular carcinoma cells. Moreover, transcriptome sequencing demonstrated that silencing Girdin led to differential expression of 176 genes and inhibition of the PI3K/Akt signaling pathway, as well as its upstream pathways-Cytokine-cytokine receptor interaction and Chemokine signaling pathway. Ultimately, we propose that Imatinib Mesylate, Orantinib, Resveratrol, Sorafenib, and Curcumin may interact with Girdin, potentially contributing to the treatment of liver cancer.ConclusionThis study reveals the association between Girdin and hepatocellular carcinoma, providing novel clues for future research and treatment of hepatocellular carcinoma.

| S-EPMC11642971 | biostudies-literature

Platelet microRNA bioinformatics analysis in patients with hepatocellular carcinoma

Project description:Purpose:To reveal platelet microRNAs（miRNAs） expression status and its potential clinical significance in patients with hepatocellular carcinoma(HCC) by bioinformatics analysis. Method: 5 patients (4 male, 1 female) with hepatocellular carcinoma, and 5 healthy individuals(3 male，2 female) as control from June 2019 to November 2019 were taken part in this cohort. The leukocyte—depleted platelets were prepared from the anticoagulated whole blood samples. The platelet RNA were extracted to construct miRNA libraries by using conventional gradient centrifugation, MACS and instructions of miRNeasy Mini Kit, performed data analysis and bioinformatics analysis after sequencing. Results: The DESeq2 package of R software was used to compare the gene expression level difference between the HCC group and the normal group. The cut-off criteria of differentially expressed miRNAs was |log2FC| >1 and p<0.05. Total 250 differentially expressed miRNAs were screened out, of which 111 miRNAs were down-regulated and 139 miRNAs were up-regulated. Gene Ontology(GO) analysis found that the differential miRNAs are involved in Positional Regulatory of Catabolic process, positional regulatory of cell catabolic process, negative regulation of phosphorylation, Wnt signaling pathway. Kyoto Encyclopedia of Genes and Genomes (KEGG)pathway analysis showed that platelet miRNAs are involved in a number of signal pathways, including FoxO signaling pathway, ubiquitin mediated proteolysis, axon guidance, autophagy-animal, TGF-beta signaling pathway. Conclusion:MiRNAs in platelets of patients with hepatocellular carcinoma were differentially expressed. Platelet miRNAs should be involved in the biological process of hepatocellular carcinoma, while more samples and molecular biological experiments are needed.

2021-09-21 | GSE158523 | GEO

Comprehensive analysis of Transcriptome Profiles in Hepatocellular Carcinoma patients

Project description:Comprehensive analysis of Transcriptome Profiles in Hepatocellular Carcinoma patients

| PRJNA414787 | ENA

CIDR: Genome-Wide Association Study (GWAS) in Hepatocellular Carcinoma (HCC)

Project description:CIDR: Genome-Wide Association Study (GWAS) in Hepatocellular Carcinoma (HCC)

| PRJNA505573 | ENA

CIDR: Genome-Wide Association Study (GWAS) in Hepatocellular Carcinoma (HCC)

Project description:CIDR: Genome-Wide Association Study (GWAS) in Hepatocellular Carcinoma (HCC)

| PRJNA505574 | ENA

Association between HMGA1 and immunosuppression in hepatocellular carcinoma: A comprehensive bioinformatics analysis.

Project description:The high mobility group A1 (HMGA1) gene is overexpressed in malignant tumors, and its expression level correlates with the progression and metastasis of tumors. However, the specific role of HMGA1 in hepatocellular carcinoma (HCC) and relevant influencing approaches in tumor immunity remain unclear. In this study, the expression and clinical significance of HMGA1 in HCC immunity were analyzed. The expression levels of HMGA1 mRNA and protein in HCC tissue and normal liver tissue were analyzed based on the cancer genome atlas, the gene expression omnibus and the Human Protein Atlas databases. The correlation between HMGA1 and clinicopathological factors was analyzed, and survival was estimated based on the expression of HMGA1. Gene set cancer analysis and the TISIDB database were used to identify tumor-infiltrating immune cells and immune inhibitors. Gene set enrichment analysis was performed to determine the involved signaling pathway. The HMGA1 genetic alterations were identified with the cBioPortal for Cancer Genomics. The expression of HMGA1 mRNA and protein was significantly higher in HCC tissue and negatively correlated with survival. Neutrophils, Th17 cells, several immune inhibitors, and signaling pathways were positively correlated with the expression of HMGA1. Amplification was the main type of genetic alteration in HMGA1. These findings demonstrate that HMGA1 can be a therapeutic target and a potential biomarker to predict the prognosis of patients with HCC. HMGA1 may affect the progression of HCC by suppressing the immune function of these patients.

| S-EPMC9876027 | biostudies-literature

Comprehensive analysis of the miRNA profile between HBV-related Hepatocellular carcinoma (HBCC) and no HBV-related Hepatocellular carcinoma (HNCC)

Project description:Comprehensive analysis of the miRNA profile between HBV-related Hepatocellular carcinoma (HBCC) and no HBV-related Hepatocellular carcinoma (HNCC)

| PRJNA635823 | ENA

Comprehensive analysis of the miRNA profile between HBV-related Hepatocellular carcinoma (HBCC) and no HBV-related Hepatocellular carcinoma (HNCC)

Project description:To explore the miRNA expression profiles between HBV-related Hepatocellular carcinoma and no HBV-related Hepatocellular carcinoma To performe microarray analysis to detect the miRNA expression profiles between HBV-related Hepatocellular carcinoma and no HBV-related Hepatocellular carcinoma

2021-05-29 | GSE151441 | GEO

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