Identification of 40S ribosomal protein S8 as a novel biomarker for alcohol‑associated hepatocellular carcinoma using weighted gene co‑expression network analysis

Bi, Ningrui; Sun, Yihong; Lei, Shan; Zeng, Zhirui; Zhang, Yan; Sun, Chengyi; Yu, Chao

doi:10.3892/or.2020.7634

Cited by 19 publications

(10 citation statements)

References 31 publications

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“…AURKB is considered to be an abnormally expressed gene in many cancer and tumor cell lines. [24][25][26][27][28] AURKB overexpression is an independent molecular marker predicting tumor invasiveness and poor prognosis of HCC. 29 AURKB has several functions during mitosis, including spindle assembly, chromosome segregation, and cytokinesis.…”

Section: Figurementioning

confidence: 99%

AURKB, CHEK1 and NEK2 as the Potential Target Proteins of Scutellaria barbata on Hepatocellular Carcinoma: An Integrated Bioinformatics Analysis

Huang¹,

Luo²,

Huang³

et al. 2021

IJGM

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Objective: We aim to explore the potential anti-HCC mechanism of Scutellaria barbata through integrated bioinformatics analysis. Methods: We searched active ingredients and related targets of Scutellaria barbata via TCMSP database, PubChem and SwissTargetPrediction database. Then, we identified HCC disease targets from GEO dataset by WGCNA. Next, the intersected targets of disease targets and drug targets were input into STRING database to construct PPI networking in order to obtain potential therapeutic targets of Scutellaria barbata. Cytoscape software was used to carry out network topology analysis of potential targets. We used the R package for GO analysis and KEGG analysis. Finally, we used AutoDock vina and PyMOL software for molecular docking. Results: Sixteen active components from Scutellaria barbata were lastly selected for further investigation. A total of 442 component targets were identified from 16 active ingredients of Scutellaria barbata after the removal of duplicate targets. GSE45436 was selected for construction of WGCNA and screening of differentially expressed genes. A total of 354 genes were up-regulated in HCC samples and 100 were down-regulated in HCC patients. Twenty-one common genes were obtained by intersection and 10 critical targets were filtered for further investigation. The enrichment analysis showed that cell cycle, DNA replication, p53 signaling pathway were mainly involved. The molecular docking results showed that 4 potential combinations were with the best binding energy and molecular interactions. Conclusion: AURKB, CHEK1 and NEK2 could be the potential target proteins of Scutellaria barbata in treating HCC. Cell cycle, DNA replication, p53 signaling pathway consist of the fundamental regulation cores in this mechanism.

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Section: Figurementioning

confidence: 99%

AURKB, CHEK1 and NEK2 as the Potential Target Proteins of Scutellaria barbata on Hepatocellular Carcinoma: An Integrated Bioinformatics Analysis

Huang¹,

Luo²,

Huang³

et al. 2021

IJGM

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“…A fragments per kilobase of transcript per million mapped reads (FPKM) value of <0.5 was used as the threshold for removing the genes with low expression. This was necessary as a gene must be expressed at a minimal level before it is likely to be translated into a protein or be considered biologically important ( 13 ). Consequently, 15,703 genes expressed in the 54 HPV-negative HNSCC tissues, along with the corresponding clinical characteristics data, were used in the WGCNA.…”

Section: Methodsmentioning

confidence: 99%

PSMC2, ORC5 and KRTDAP are specific biomarkers for HPV‑negative head and neck squamous cell carcinoma

Zeng

Rong

et al. 2021

Oncol Lett

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The prognosis of patients with human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC) is poorer than those with HPV-positive HNSCC. The present study aimed to identify novel and specific biomarkers of HPV-negative HNSCC using bioinformatics analysis and associated experiments. The gene expression profiles of HPV-negative HNSCC tissues and corresponding clinical data were downloaded from The Cancer Genome Atlas database and used in a weighted gene co-expression network analysis. Genes in clinically significant co-expression modules were used to construct a protein-protein interaction (PPI) network. The genes demonstrating a high degree score in the PPI network and a high correlation with tumor grade were considered hub genes. The diagnostic value of the hub genes associated with HPV-negative and HPV-positive HNSCC was analyzed using differential expression gene (DEG) analysis, immunohistochemical (IHC) staining and a receiver operating characteristic (ROC) curve analysis. Seven genes [Serrate RNA effector molecule (SRRT), checkpoint kinase 2 (CHEK2), small nuclear ribonucleoprotein polypeptide E (SNRPE), proteasome 26S subunit ATPase 2 (PSMC2), origin recognition complex subunit 5 (ORC5), S100 calcium binding protein A7 and keratinocyte differentiation associated protein (KRTDAP)] were demonstrated to be hub genes in clinically significant co-expression modules. DEG, IHC and ROC curve analyses revealed that SRRT, CHEK2 and SNRPE were significantly upregulated in HPV-negative and HPV-positive HNSCC tissues compared with in adjacent tissues, and these genes demonstrated a high diagnostic value for distinguishing HNSCC tissues. However, PSMC2, ORC5 and KRTDAP were the only differentially expressed genes identified in HPV-negative HNSCC tissues, and these genes demonstrated a high diagnostic value for HPV-negative HNSCC. PSMC2, ORC5 and KRTDAP may therefore serve as novel and specific biomarkers for HPV-negative HNSCC, potentially improving the diagnosis and treatment of patients with HPV-negative HNSCC.

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“…RPL36 is found to be up-regulated in 75% of 60 HCC patients especially in early stages of carcinogenesis suggesting its potential role as a biomarker in liver cancer [ 78 ]. On the other hand, RPS8 is found to be up-regulated in alcohol-associated HCC and not in non-alcoholic-associated HCC which makes RPS8 a biomarker and a novel therapeutic target for HCC linked to alcohol [ 79 ].…”

Section: Rps In Liver Cancermentioning

confidence: 99%

Deregulation of ribosomal proteins in human cancers

Khoury

Nasr

2021

Bioscience Reports

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The ribosome, the site for protein synthesis, is composed of ribosomal RNAs (rRNAs) and ribosomal proteins (RPs). The latter have been shown to have many ribosomal and extra-ribosomal functions. RPs are implicated in a variety of pathological processes, especially tumorigenesis and cell transformation. In this review, we will focus on the recent advances that shed light on the effects of RPs deregulation in different types of cancer and their roles in regulating the tumor cell fate.

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Identification of 40S ribosomal protein S8 as a novel biomarker for alcohol‑associated hepatocellular carcinoma using weighted gene co‑expression network analysis

Cited by 19 publications

References 31 publications

AURKB, CHEK1 and NEK2 as the Potential Target Proteins of Scutellaria barbata on Hepatocellular Carcinoma: An Integrated Bioinformatics Analysis

AURKB, CHEK1 and NEK2 as the Potential Target Proteins of Scutellaria barbata on Hepatocellular Carcinoma: An Integrated Bioinformatics Analysis

PSMC2, ORC5 and KRTDAP are specific biomarkers for HPV‑negative head and neck squamous cell carcinoma

Deregulation of ribosomal proteins in human cancers

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