Tumor suppressor gene mutations correlate with prognosis and immunotherapy benefit in hepatocellular carcinoma

Liu, Long; Guo, Chunguang; Sun, Yu; Meng, Lingfang; Zhou, Xueliang; Han, Xinwei

doi:10.1016/j.intimp.2021.108340

Cited by 29 publications

(22 citation statements)

References 43 publications

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“…To estimate the stromal and immune cells in tumor tissues, the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm was adopted to calculate the stromal score, immune score, and tumor purity of each patient based on ssGSEA ( Yoshihara et al, 2013 ; Liu et al, 2021a ; Liu et al, 2021b ; Liu et al, 2021c ; Liu et al, 2022a ; Liu et al, 2022b ). To evaluate the proportion of 22 immune cells, the abundance of immune cell infiltration in the low-NOP2-expressing and high-NOP2-expressing groups was estimated using the cell type identification by estimating the relative subsets of RNA transcripts (CIBERSORT) algorithm ( Newman et al, 2015 ).…”

Section: Methodsmentioning

confidence: 99%

Molecular Characterization Clinical and Immunotherapeutic Characteristics of m5C Regulator NOP2 Across 33 Cancer Types

Liu

Zhang

Lin

et al. 2022

Front. Cell Dev. Biol.

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Background: Recent studies have identified that RNA 5-methylcytosine (m5C) is a wide-spread epigenetic modification in tumorigenesis. However, the clinical and immunotherapeutic values of m5C regulator NOP2 in 33 cancers remain unclear.Methods: The mRNA expression data and clinical data of 33 cancers were downloaded from The Cancer Genome Atlas (TCGA) database. The immunotherapy data including GSE67501, GSE78220, GSE35640, and IMvigor210 were downloaded from the Gene Expression Omnibus (GEO) database and the website based on the Creative Commons 3.0 license (http://research-pub.Gene.com/imvigor210corebiologies). The expression, survival, clinical parameters, tumor mutation burden (TMB), microsatellite instability (MSI), and tumor microenvironment (TME) were evaluated. Finally, the relationship between NOP2 and immunotherapy response was further explored.Results: NOP2 was significantly upregulated in most cancers, and high NOP2 expression was associated with poor prognosis. TMB, MSI, and NOP2 activities were involved in the dysregulation of NOP2. NOP2 was closely associated with immune cell infiltration, immune modulators, and immunotherapeutic inactivation.Conclusions: We comprehensively explored the clinical and immunotherapeutic values of NOP2 in cancers, providing evidence regarding the function of NOP2 and its role in clinical treatment.

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Section: Methodsmentioning

confidence: 99%

Molecular Characterization Clinical and Immunotherapeutic Characteristics of m5C Regulator NOP2 Across 33 Cancer Types

Liu

Zhang

Lin

et al. 2022

Front. Cell Dev. Biol.

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“…The association between the expression of CD93 and other clinical characteristics (age, gender, and TNM stage) was also investigated. Meanwhile, the CD93 expression activity between normal and tumor tissues was analyzed via the R package (version 4.0.3) of GSEABase and gene set variation analysis (GSVA) ( Liu et al, 2021a ; Liu et al, 2021d ).…”

Section: Methodsmentioning

confidence: 99%

Pan-Cancer Analysis Identified CD93 as a Valuable Biomarker for Predicting Patient Prognosis and Immunotherapy Response

Tong

Wang

Zhu

et al. 2022

Front. Mol. Biosci.

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Background: The rapid development of immunotherapy has significantly improved patient outcomes in recent years. CD93, a novel biomarker expressed on vascular endothelial cells, is essential for tumor angiogenesis. Recent studies have shown that CD93 is closely related to immune cell infiltration and immunotherapy. However, its role in pan-cancer has not been reported.Methods: The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA), cbioportal, Gene Expression Omnibus (GEO), Tumor Immune Estimation Resource (TIMER2.0), and the Tumor–Immune System Interactions and Drug Bank (TISIDB) databases were used to analyze CD93 in pan-cancers. R software was used for statistical analysis and mapping.Results: There were significant differences in the expression of CD93 between tumor tissues and adjacent normal tissues in pan-cancer. The high expression of CD93 was associated with poor prognosis and high TNM stage in multiple tumor types. However, a high expression of CD93 was a protective factor in kidney renal clear cell carcinoma (KIRC). In addition, CD93 was closely related to immune cell infiltration in tumor tissues. Moreover, CD93 presented a robust correlation with immune modulators and immunotherapeutic markers [e.g., tumor mutation burden (TMB) and microsatellite instability (MSI)]. The results of gene set enrichment analysis (GSEA) showed that CD93 was correlated with tumor angiogenesis. Importantly, patients with a low expression of CD93 were more sensitive to immunotherapy in urothelial cancer.Conclusion: CD93, which is involved in various immune responses, controls immune cell infiltration and impacts on the malignant properties of various cancer types. Therefore, CD93 has potential value to be biomarker for determining the prognosis and immune infiltration in multiple cancers.

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“…symbols.gmt). After that, the CIBERSORT ( Newman et al, 2015 ; Liu et al, 2022b ), MCP-counter ( Shi et al, 2020 ; Liu et al, 2021b ) and single-sample gene set enrichment analysis (ssGSEA) ( Yi et al, 2020 ; Liu et al, 2022c ) algorithms were used to explore the infiltration abundance of different immune cells between the high- and low-risk groups. Heatmaps and boxplots were used to uncover the degree of difference in the responses of various immune cell subsets between the two groups under different algorithms.…”

Section: Methodsmentioning

confidence: 99%

Development and Validation of Ischemic Events Related Signature After Carotid Endarterectomy

Guo

Cao

Zheng

et al. 2022

Front. Cell Dev. Biol.

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Background: Ischemic events after carotid endarterectomy (CEA) in carotid artery stenosis patients are unforeseeable and alarming. Therefore, we aimed to establish a novel model to prevent recurrent ischemic events after CEA.Methods: Ninety-eight peripheral blood mononuclear cell samples were collected from carotid artery stenosis patients. Based on weighted gene co-expression network analysis, we performed whole transcriptome correlation analysis and extracted the key module related to ischemic events. The biological functions of the 292 genes in the key module were annotated via GO and KEGG enrichment analysis, and the protein-protein interaction (PPI) network was constructed via the STRING database and Cytoscape software. The enrolled samples were divided into train (n = 66), validation (n = 28), and total sets (n = 94). In the train set, the random forest algorithm was used to identify critical genes for predicting ischemic events after CEA, and further dimension reduction was performed by LASSO logistic regression. A diagnosis model was established in the train set and verified in the validation and total sets. Furthermore, fifty peripheral venous blood samples from patients with carotid stenosis in our hospital were used as an independent cohort to validation the model by RT-qPCR. Meanwhile, GSEA, ssGSEA, CIBERSORT, and MCP-counter were used to enrichment analysis in high- and low-risk groups, which were divided by the median risk score.Results: We established an eight-gene model consisting of PLSCR1, ECRP, CASP5, SPTSSA, MSRB1, BCL6, FBP1, and LST1. The ROC-AUCs and PR-AUCs of the train, validation, total, and independent cohort were 0.891 and 0.725, 0.826 and 0.364, 0.869 and 0.654, 0.792 and 0.372, respectively. GSEA, ssGSEA, CIBERSORT, and MCP-counter analyses further revealed that high-risk patients presented enhanced immune signatures, which indicated that immunotherapy may improve clinical outcomes in these patients.Conclusion: An eight-gene model with high accuracy for predicting ischemic events after CEA was constructed. This model might be a promising tool to facilitate the clinical management and postoperative surveillance of carotid artery stenosis patients.

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Tumor suppressor gene mutations correlate with prognosis and immunotherapy benefit in hepatocellular carcinoma

Cited by 29 publications

References 43 publications

Molecular Characterization Clinical and Immunotherapeutic Characteristics of m5C Regulator NOP2 Across 33 Cancer Types

Molecular Characterization Clinical and Immunotherapeutic Characteristics of m5C Regulator NOP2 Across 33 Cancer Types

Pan-Cancer Analysis Identified CD93 as a Valuable Biomarker for Predicting Patient Prognosis and Immunotherapy Response

Development and Validation of Ischemic Events Related Signature After Carotid Endarterectomy

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