Identification of Differentially Expressed Genes Associated with the Prognosis and Diagnosis of Hepatocellular Carcinoma by Integrated Bioinformatics Analysis

Kakar, Mohib Ullah; Mehboob, Muhammad Zubair; Akram, Muhammad; Shah, Muddaser; Shakir, Yasmeen; Ijaz, Hafza Wajeeha; Aziz, Ubair; Ullah, Zahid; Ahmad, Sajjad; Ali, Sikandar; Yin, Yongxiang

doi:10.1155/2022/4237633

Cited by 6 publications

(5 citation statements)

References 68 publications

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“…The study emphasizes techniques including surgical resection, biannual ultrasonography surveillance, and liver transplantation for cirrhotic patients, acknowledging the therapeutic importance of these findings within the larger framework of liver cancer research. The necessity for continuous research to improve clinical procedures and the management of HCC is highlighted by common methods such as image-guided ablation, chemoembolization, and systemic therapy [ 15 , 16 ].…”

Section: Discussionmentioning

confidence: 99%

Influence of Pterostilbene on Gene Expression in Liver Cancer: An In Silico Analysis

Prasad,

Tamil Selvan,

Shanmugam

2024

Cureus

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Background Liver cancer, in particular, is a serious threat to global health and has few viable treatments. One natural molecule that shows potential in cancer therapy is pterostilbene, especially for hepatocellular carcinoma (HCC). The molecular details of pterostilbene’s interactions with liver cancer are uncovered in this study using an in silico method. Methodology This study determines the differentially expressed genes (DEGs) in HCC and the way pterostilbene affects them using data from Gene Expression Omnibus (GEO) datasets. To identify the intricate linkages and possible treatment targets, network pharmacology, protein-protein interaction (PPI) analysis, and pathway enrichment investigations were performed. Results The study revealed complex relationships between pterostilbene and liver cancer, identified important DEGs in HCC, and showed enriched pathways. Pterostilbene shows promise as a target for therapeutic approaches in HCC due to its modulation of important signaling pathways. Conclusions This work offers an extensive knowledge of pterostilbene’s potential in liver cancer, despite intrinsic computational limitations. In addition to the importance of experimental validation, the pathways and DEGs that have been found provide insightful information for future investigation, highlighting the ongoing research that is necessary to create targeted therapeutics for HCC.

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Section: Discussionmentioning

confidence: 99%

Influence of Pterostilbene on Gene Expression in Liver Cancer: An In Silico Analysis

Prasad,

Tamil Selvan,

Shanmugam

2024

Cureus

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“…These findings provide insights into the potential roles of these key genes in immune invasion in liver cancer. (45)(46)(47). Nucleolar and spindle-associated protein 1 (NUSAP1) is a member of the NUSP1 family of nucleolar-spindle-associated proteins and is involved in spindle microtubule organization (48).…”

Section: Discussionmentioning

confidence: 99%

Anti-tumor target screening of sea cucumber saponin Frondoside A: a bioinformatics and molecular docking analysis

Liu,

Zhang,

Lin

et al. 2023

Front. Oncol.

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Cancer remains the leading cause of death worldwide. In spite of significant advances in targeted and immunotherapeutic approaches, clinical outcomes for cancer remain poor. The aim of the present study was to investigate the potential mechanisms and therapeutic targets of Frondoside A for the treatment of liver, pancreatic, and bladder cancers. The data presented in our study demonstrated that Frondoside A reduced the viability and migration of HepG2, Panc02, and UM-UC-3 cancer cell in vitro. Moreover, we utilized the GEO database to screen and identify for differentially expressed genes (DEGs) in liver, pancreatic, and bladder cancers, which resulted in the identification of 714, 357, and 101 DEGs, respectively. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation were performed using the Metascape database for DEGs that were significantly associated with cancer development. The protein-protein interaction (PPI) networks of the identified DEGs in liver, pancreatic, and bladder cancers were analyzed using Cytoscape 3.9.0 software, and subsequently identified potential key genes that were associated with these networks. Subsequently, their prognostic values were assessed by gene expression level analysis and Kaplan-Meier survival analysis (GEPIA). Furthermore, we utilized TIMER 2.0 to investigate the correlation between the expression of the identified key gene and cancer immune infiltration. Finally, molecular docking simulations were performed to assess the affinity of Frondoside A and key genes. Our results showed a significant correlation between these DEGs and cancer progression. Combined, these analyses revealed that Frondoside A involves in the regulation of multiple pathways, such as drug metabolism, cell cycle in liver cancer by inhibiting the expression of CDK1, TOP2A, CDC20, and KIF20A, and regulates protein digestion and absorption, receptor interaction in pancreatic cancer by down-regulation of ASPM, TOP2A, DLGAP5, TPX2, KIF23, MELK, LAMA3, and ANLN. While in bladder cancer, Frondoside A regulates muscle contraction, complement and coagulation cascade by increase FLNC expression. In conclusion, the present study offers valuable insights into the molecular mechanism underlying the anticancer effects of Frondoside A, and suggests that Frondoside A can be used as a functional food supplement or further developed as a natural anti-cancer drug.

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“…To further confirm and evaluate potential therapeutic values from the novel identified up-regulated DEGs with the impacts of decreased survival in the current study, we chose to validate genes that were the top ten up-regulated DEGs with decreased survival and not shown to be associated with tumorigenesis. Among them, studies have proved that CCNB1, RACGAP1 and NUSAP1 promote the progression of multiple cancers (Aljohani et al 2022;Gu et al 2022;Guo et al 2020), and NCAPG and CCNB2 have been found to be associated with a poor prognosis of ES (Kakar et al 2022;Zhao et al 2022), while ASPM, CENPF, CKS2, and DTL have not been studied in ES to the best of our knowledge. Interestingly, these four genes were also found in the GO analysis and GSEA results (Fig.…”

Section: In Vitro Verification Of Four Up-regulated Degs With Decreas...mentioning

confidence: 98%

Integrative analyses of bulk microarray data to discover genes, pathways, and immune infiltration characteristics associated with targeting of Ewing sarcoma

Cao

Sun

Fan

et al. 2023

J Cancer Res Clin Oncol

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Purpose To explore transcriptome and immunological features of patients with Ewing sarcoma (ES) using all publicly available microarray data. Methods Data of 479 ES tissues were integrated and normalized. Gene expression, immune infiltration, and cancer-specific pathways were analyzed. Genes of interest were knocked down, followed by cell proliferation and colony formation assays. Results Consistent with the previous reports of differential expressed genes (DEGs) in ES, our analysis identified CCND1, HMCN1, and NKX2-2 were among the most highly expressed, while TWNC1, MYBPC1, and CKM were among the lowest expressed genes. GO, KEGG, and GSEA enrichment analysis identified that the DEGs related to bone and muscle functioning, those that contributed to crucial cellular, and metabolism pathways such as actin binding, apoptosis, TCA cycle, and cell cycle were also significantly enriched. Immune infiltration analysis discovered that many T cell subsets including CD4T, CD8 T, and Gamma delta T cells were highly infiltrated, while monocytes and B cells were less infiltrated in tumors. A total of 138 genes were both significantly up-regulated in tumors and associated with decreased survival, while 38 significantly down-regulated genes were associated with increased survival, many of which were previously reported as oncogenes and tumor suppressors in ES and other cancers. Silencing of four newly identified top ranked up-regulated genes with decreased survivals in ES inhibited proliferation and colony formation of ES cells. Conclusion This study may provide a clear representative transcriptome profile of ES, providing diagnostic biomarkers, pathways, and immune infiltrative characteristics targets for ES.

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Identification of Differentially Expressed Genes Associated with the Prognosis and Diagnosis of Hepatocellular Carcinoma by Integrated Bioinformatics Analysis

Cited by 6 publications

References 68 publications

Influence of Pterostilbene on Gene Expression in Liver Cancer: An In Silico Analysis

Influence of Pterostilbene on Gene Expression in Liver Cancer: An In Silico Analysis

Anti-tumor target screening of sea cucumber saponin Frondoside A: a bioinformatics and molecular docking analysis

Integrative analyses of bulk microarray data to discover genes, pathways, and immune infiltration characteristics associated with targeting of Ewing sarcoma

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