Gene signature to predict prognostic survival of hepatocellular carcinoma

Li, Li; Cao, Yundi; Fan, Yingrui; Li, Rong

doi:10.1515/med-2021-0405

Cited by 8 publications

(3 citation statements)

References 43 publications

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“…Previous studies have found that both protein and mRNA expression of DKC1 was higher in HCC than in non-cancerous liver tissues and was associated with advanced clinical stage and poor prognosis ( Liu et al, 2012 ; Ko et al, 2018 ; Zhang et al, 2021b ; Li et al, 2022a ). As for RNA-independent PUSs, their roles in HCC have rarely been explored.…”

Section: Discussionmentioning

confidence: 96%

Integrative multiomics evaluation reveals the importance of pseudouridine synthases in hepatocellular carcinoma

et al. 2022

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Background: The pseudouridine synthases (PUSs) have been reported to be associated with cancers. However, their involvement in hepatocellular carcinoma (HCC) has not been well documented. Here, we assess the roles of PUSs in HCC.Methods: RNA sequencing data of TCGA-LIHC and LIRI-JP were downloaded from the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC), respectively. GSE36376 gene expression microarray was downloaded from the Gene Expression Omnibus (GEO). Proteomics data for an HBV-related HCC cohort was obtained from the CPTAC Data Portal. The RT-qPCR assay was performed to measure the relative mRNA expression of genes in clinical tissues and cell lines. Diagnostic efficiency was evaluated by the ROC curve. Prognostic value was assessed using the Kaplan-Meier curve, Cox regression model, and time-dependent ROC curve. Copy number variation (CNV) was analyzed using the GSCA database. Functional analysis was carried out with GSEA, GSVA, and clusterProfiler package. The tumor microenvironment (TME) related analysis was performed using ssGSEA and the ESTIMATE algorithm.Results: We identified 7 PUSs that were significantly upregulated in HCC, and 5 of them (DKC1, PUS1, PUS7, PUSL1, and RPUSD3) were independent risk factors for patients’ OS. Meanwhile, the protein expression of DKC1, PUS1, and PUS7 was also upregulated and related to poor survival. Both mRNA and protein of these PUSs were highly diagnostic of HCC. Moreover, the CNV of PUS1, PUS7, PUS7L, and RPUSD2 was also associated with prognosis. Further functional analysis revealed that PUSs were mainly involved in pathways such as genetic information processing, substance metabolism, cell cycle, and immune regulation.Conclusion: PUSs may play crucial roles in HCC and could be used as potential biomarkers for the diagnosis and prognosis of patients.

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Section: Discussionmentioning

confidence: 96%

Integrative multiomics evaluation reveals the importance of pseudouridine synthases in hepatocellular carcinoma

et al. 2022

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“… 20 A prognostic gene model consisting of four genes, including SAPCD2, was constructed to predict the OS of HCC patients. 21 SAPCD2 exhibited increased expression in late stage HCC, which added to the evidence that SAPCD2 performs a critical function in HCC.…”

Section: Discussionmentioning

confidence: 75%

Prognostic Analysis and Biomarkers Identification of Immune Infiltration in Early and Late Stage Hepatocellular Carcinoma Based on TCGA Data

Jiang¹,

Wang²,

Yu³

et al. 2023

IJGM

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Background Hepatocellular carcinoma (HCC) is a major cause of cancer death in the world. The aim of this study was to establish a new model to predict the prognosis of HCC. Materials and Methods The mRNA, miRNA and lncRNA expression profiles of early (stage I–II) and late (stage III–IV) stage HCC patients were acquired from The Cancer Genome Atlas (TCGA) database. The differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs) and lncRNAs (DElncRNAs) were identified between early and late stage HCC. Key molecules associated with the prognosis, and important immune cell types in HCC were identified. The nomogram based on incorporating age, gender, stage, and all important factors was constructed to predict the survival of HCC. Results A total of 1516 DEmRNAs, 97 DEmiRNAs and 87 DElncRNAs were identified. A DElncRNA-DEmiRNA-DEmRNA regulatory network including 78 mRNAs, 50 miRNAs and 1 lncRNA was established. Among the regulatory network, 11 molecules were significantly correlated with the prognosis of HCC based on Lasso regression analysis. Then, Preadipocytes and 3 survival-associated DEmRNAs were identified as crucial biomarkers. Subsequently, a nomogram with a differentiation degree of 0.758, including 1 immune cell, 11 mRNAs and 3 miRNAs, was generated. Conclusion Our study constructed a model by incorporating clinical information, significant biomarkers and immune cells to predict the survival of HCC, which achieved a good performance.

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“…Hepatocellular carcinoma (HCC) is a malignant tumor generating from liver cells, which is very common in Asia including China, accounting for approximately 80% of all liver cancer types [1,2]. At present, a growing number of studies have suggested that the occurrence and progression of HCC were associated with the abnormal expression of many oncogenes and the inactivation of cancer suppressor genes, which were increasingly used in the early diagnosis and treatment of HCC [3,4].…”

Section: Introductionmentioning

confidence: 99%

Loss of WNK1 Suppressed the Malignant Behaviors of Hepatocellular Carcinoma Cells by Promoting Autophagy and Activating AMPK Pathway

et al. 2022

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Background. WNK lysine deficient protein kinase 1 (WNK1) has been shown to be highly expressed in hepatocellular carcinoma (HCC) samples and related to poor prognosis of HCC patients based on bioinformatics analysis. However, the specific function of WNK1 in HCC has not been analyzed. This study is aimed at exploring the function of WNK1 in HCC progression as well as its related molecular mechanism. Methods. After knockdown of WNK1 by small interference RNA, cell counting kit-8, colony formation, western blot, Transwell, and wound healing assays were employed to evaluate the biological behaviors of HCC cells. Immunofluorescent staining was applied to detect the effect of WNK1 on LC3 II. GSK690693 or si-AMPK was applied to block AMPK pathway. The expression of autophagy and AMPK pathway related molecules was examined by western blot assay. Results. WNK1 was highly expressed in HCC cell lines and loss of WNK1 inhibited HCC cell proliferation, cell cycle, migration, and invasion. Additionally, we demonstrated that loss of WNK1 promoted the autophagy and activated AMPK pathway in HCC cells. While, GSK690693 treatment or si-AMPK transfection suppressed the autophagy and promoted HCC cells proliferation. However, WNK1 knockdown counteracted the effect of GSK690693 or si-AMPK in regulating HCC cell proliferation. Finally, we demonstrated that WNK1 regulated the malignant behaviors of HCC cells by modulating autophagy and AMPK pathway. Conclusions. The above results indicated that WNK1 may be a worthwhile target to be considered for therapy of HCC.

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Gene signature to predict prognostic survival of hepatocellular carcinoma

Cited by 8 publications

References 43 publications

Integrative multiomics evaluation reveals the importance of pseudouridine synthases in hepatocellular carcinoma

Integrative multiomics evaluation reveals the importance of pseudouridine synthases in hepatocellular carcinoma

Prognostic Analysis and Biomarkers Identification of Immune Infiltration in Early and Late Stage Hepatocellular Carcinoma Based on TCGA Data

Loss of WNK1 Suppressed the Malignant Behaviors of Hepatocellular Carcinoma Cells by Promoting Autophagy and Activating AMPK Pathway

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